Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008030.1 Hibiscus syriacus cultivar Beakdansim tig00110506_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: 64952
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1918 original size:14 final size:16
Alignment explanation
Indices: 1881--1933 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 16
1871 TGCAATCACC
*
1881 CATATCACACATATAT
1 CATATCATACATATAT
*
1897 CATGTCATACA-AT-T
1 CATATCATACATATAT
1911 CATATCATACATCATAT
1 CATATCATACAT-ATAT
1928 ACATAT
1 -CATAT
1934 ATTACATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.37
15 2 0.07
16 11 0.37
17 1 0.03
18 5 0.17
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (16 bp):
CATATCATACATATAT
Found at i:6630 original size:23 final size:23
Alignment explanation
Indices: 6596--6661 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
6586 CACCACAACT
*
6596 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
6619 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
6642 CGTAGAAATGTACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
6662 TTATATAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:6944 original size:7 final size:7
Alignment explanation
Indices: 6932--6960 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6922 GGTCATATAA
6932 ATCACAT
1 ATCACAT
6939 ATCACAT
1 ATCACAT
6946 ATCACAT
1 ATCACAT
6953 AT-ACAT
1 ATCACAT
6959 AT
1 AT
6961 AACCACATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCACAT
Found at i:7710 original size:2 final size:2
Alignment explanation
Indices: 7703--7756 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
7693 ATCTTATGTT
7703 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
7745 CA CA CA CA CA CA
1 CA CA CA CA CA CA
7757 TATATATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:7761 original size:2 final size:2
Alignment explanation
Indices: 7756--7785 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7746 ACACACACAC
7756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7786 CAATGATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11970 original size:15 final size:15
Alignment explanation
Indices: 11913--11970 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
11903 GGTTCAATAC
11913 ATTTTAATATTTTGAT
1 ATTTTAATATTTTG-T
*
11929 ATTTAAACTA-TTTGT
1 ATTTTAA-TATTTTGT
* * *
11944 ACTTGAACATTTTGT
1 ATTTTAATATTTTGT
11959 ATTTTAATATTT
1 ATTTTAATATTT
11971 GATATGTGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 10 0.30
17 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTTTAATATTTTGT
Found at i:20388 original size:81 final size:81
Alignment explanation
Indices: 20281--20951 Score: 1094
Period size: 81 Copynumber: 8.3 Consensus size: 81
20271 TGCCAAAAAA
*
20281 CACAGTTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
20346 ACATTTCTGTCAAATG
66 ACATTTCTGTCAAATG
*
20362 CACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20427 ACATTTCTGTAAAATG
66 ACATTTCTGTCAAATG
20443 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20508 ACATTTATGTCAAATG
66 ACATTTCTGTCAAATG
* * *
20524 CACAGCTAGGCAATTAATCTTTTACTCAAATGTATTTAACCTTTCATTTAACTGGCATGATCGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20589 ACCTTTCTGTCAAATG
66 ACATTTCTGTCAAATG
20605 CACAGCTAGGCAATTAATC-TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20669 ACATATT-TGTTAAATG
66 ACAT-TTCTGTCAAATG
* * *
20685 CACAGCTAGGCAATTAATATGTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
* * *
20750 ACATTTTTATTAAATG
66 ACATTTCTGTCAAATG
* *
20766 CACAACTAGGCAATTAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20831 ACCTTTCTGTCAAATG
66 ACATTTCTGTCAAATG
* * * * *
20847 CACAACTAGACAATTAATCTTTTACTCAAAGATATTTAACCTTCCATCTAACTAGCATGATTGAC
1 CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
*
20912 ACCTTTCTGTCAAATG
66 ACATTTCTGTCAAATG
*
20928 CACAGCTAGACAATTAATCTTTTA
1 CACAGCTAGGCAATTAATCTTTTA
20952 TTTTAAAACA
Statistics
Matches: 554, Mismatches: 33, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
80 73 0.13
81 481 0.87
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (81 bp):
CACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAC
ACATTTCTGTCAAATG
Found at i:20889 original size:323 final size:323
Alignment explanation
Indices: 20261--20949 Score: 1121
Period size: 323 Copynumber: 2.1 Consensus size: 323
20251 TTCCATTAAT
* ** *
20261 GACACCTTTCTGCCAAAAAACACAGTTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTC
1 GACACCTTTCTGTC-AAATGCACAGCTAGGCAATTAATC-TTTACTCAAAGGTATTTAACCTTTC
* *
20326 ATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAA
64 ATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCAATTAATATGTTACTCAA
* * *
20391 AGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTAAAATGCACAGCTAGGCAA
129 AGGTATTTAACATTTCATCTAACTGGCATGATTGACACATTTCTATAAAATGCACAACTAGGCAA
*
20456 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTCAA
194 TTAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTCAA
* * * * *
20521 ATGCACAGCTAGGCAATTAATCTTTTACTCAAATGTATTTAACCTTTCATTTAACTGGCATGATC
259 ATGCACAACTAGACAATTAATCTTTTACTCAAATGTATTTAACCTTCCATCTAACTAGCATGATC
20586 GACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTACTCAAAGGTATTTAACCTTTCAT
1 GACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTACTCAAAGGTATTTAACCTTTCAT
* *
20651 CTAACTGGCATGATTGACACATATT-TGTTAAATGCACAGCTAGGCAATTAATATGTTACTCAAA
66 CTAACTGGCATGATTGACACAT-TTCTGTCAAATGCACAACTAGGCAATTAATATGTTACTCAAA
* *
20715 GGTATTTAACATTTCATCTAACTGGCATGATTGACACATTTTTATTAAATGCACAACTAGGCAAT
130 GGTATTTAACATTTCATCTAACTGGCATGATTGACACATTTCTATAAAATGCACAACTAGGCAAT
* *
20780 TAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAA
195 TAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTCAAA
*
20845 TGCACAACTAGACAATTAATCTTTTACTCAAA-GATATTTAACCTTCCATCTAACTAGCATGATT
260 TGCACAACTAGACAATTAATCTTTTACTCAAATG-TATTTAACCTTCCATCTAACTAGCATGATC
*
20909 GACACCTTTCTGTCAAATGCACAGCTAGACAATTAATCTTT
1 GACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTT
20950 TATTTTAAAA
Statistics
Matches: 339, Mismatches: 23, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
322 1 0.00
323 302 0.89
324 23 0.07
325 13 0.04
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (323 bp):
GACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTACTCAAAGGTATTTAACCTTTCAT
CTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCAATTAATATGTTACTCAAAG
GTATTTAACATTTCATCTAACTGGCATGATTGACACATTTCTATAAAATGCACAACTAGGCAATT
AATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTCAAAT
GCACAACTAGACAATTAATCTTTTACTCAAATGTATTTAACCTTCCATCTAACTAGCATGATC
Found at i:21916 original size:2 final size:2
Alignment explanation
Indices: 21911--21972 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
21901 CCAAAAAAGT
21911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21953 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
21973 ACATCATTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24900 original size:23 final size:23
Alignment explanation
Indices: 24838--24907 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
24828 GAGTCGAGGG
* * *
24838 TTCTACACGGTCCTTCAGAACAA
1 TTCTACGCGGTCCTTCGGGACAA
* *
24861 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
24884 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
24907 T
1 T
24908 ACAATATGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.30
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:24907 original size:46 final size:46
Alignment explanation
Indices: 24838--24931 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
24828 GAGTCGAGGG
* * *
24838 TTCTACACGGTCCTTCAGAACAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACACGGTCCTTCAGAACAATACAACATGGTCCTTCGGGACAT
* * * * *
24884 TTCTACGCGGTCCTTCGGGACAATACAATATGGTCTTTCGGGACAT
1 TTCTACACGGTCCTTCAGAACAATACAACATGGTCCTTCGGGACAT
24930 TT
1 TT
24932 TTATGTTGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (46 bp):
TTCTACACGGTCCTTCAGAACAATACAACATGGTCCTTCGGGACAT
Found at i:25182 original size:2 final size:2
Alignment explanation
Indices: 25143--25167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25133 GACGATGATG
25143 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 A
25168 CATGTGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27806 original size:16 final size:16
Alignment explanation
Indices: 27764--27824 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
27754 TTACCCGACT
* *
27764 TGTTTTCAACCTGACA
1 TGTTTTTAACCTGGCA
* *
27780 TGTTATGAACCTGGCA
1 TGTTTTTAACCTGGCA
*
27796 TGTTTTTAACCTGGCC
1 TGTTTTTAACCTGGCA
*
27812 TATTTTTAACCTG
1 TGTTTTTAACCTG
27825 ACCTGTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (16 bp):
TGTTTTTAACCTGGCA
Found at i:28135 original size:23 final size:24
Alignment explanation
Indices: 28097--28146 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
28087 ATGCAAAAGA
28097 AAATTAATATAATTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
*
28121 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
28144 AAA
1 AAA
28147 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTAATATAATTTAATTTATAT
Found at i:31492 original size:3 final size:3
Alignment explanation
Indices: 31479--31550 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
31469 TTACCCATTT
* *
31479 TTA TT- TTA TTA TTA TAA TTA TTA TTA TTA TAA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
31524 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
31551 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 59 0.94
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:32916 original size:26 final size:25
Alignment explanation
Indices: 32887--32936 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
32877 TATATATATA
32887 ATAAATAATATTTATATATTT-TTTAC
1 ATAAATAAT-TTTA-ATATTTATTTAC
*
32913 ATAAATTATTTTAATATTTATTTA
1 ATAAATAATTTTAATATTTATTTA
32937 TTTATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
26 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAAATAATTTTAATATTTATTTAC
Found at i:37007 original size:15 final size:15
Alignment explanation
Indices: 36987--37015 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36977 GGATCAATAC
36987 CTTTTTGCATACATA
1 CTTTTTGCATACATA
37002 CTTTTTGCATACAT
1 CTTTTTGCATACAT
37016 TCATTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (15 bp):
CTTTTTGCATACATA
Found at i:44359 original size:10 final size:10
Alignment explanation
Indices: 44344--44378 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
44334 ATGCTTGAAG
44344 AAAAGAAAAA
1 AAAAGAAAAA
44354 AAAAGAAAAA
1 AAAAGAAAAA
44364 AAAAGAAAAA
1 AAAAGAAAAA
44374 GAAAA
1 -AAAA
44379 AAGGGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:44379 original size:15 final size:14
Alignment explanation
Indices: 44341--44380 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
44331 ATTATGCTTG
44341 AAGAAAAGAAAAAAA
1 AAGAAAA-AAAAAAA
44356 AAGAAAAAAAAAGAAA
1 AAG-AAAAAAAA-AAA
44372 AAGAAAAAA
1 AAGAAAAAA
44381 GGGGGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:45724 original size:93 final size:93
Alignment explanation
Indices: 45565--45762 Score: 362
Period size: 93 Copynumber: 2.1 Consensus size: 93
45555 AACAAGTGCC
45565 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGATATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGATATGAACCCCA
45630 AAAACCAATCATTGGATTTGAAAGATGA
66 AAAACCAATCATTGGATTTGAAAGATGA
*
45658 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA-ATGAACCCC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTT-GATATGAACCCC
45722 AAAAACCAATCATTGGATTTGAAAGATGA
65 AAAAACCAATCATTGGATTTGAAAGATGA
*
45751 ATGTGATCATAG
1 ATGTGCTCATAG
45763 TAGAAATAAG
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
93 100 0.98
94 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGATATGAACCCCA
AAAACCAATCATTGGATTTGAAAGATGA
Found at i:46843 original size:114 final size:114
Alignment explanation
Indices: 46550--47174 Score: 1157
Period size: 114 Copynumber: 5.5 Consensus size: 114
46540 TAGCAAAGAT
* *
46550 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
*
46615 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
46663 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
46728 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
46777 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
46842 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
46891 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
46956 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
47005 TCAAATCCATCATTTAATGGATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
47069 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
47118 TTAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAAC
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAAC
47175 ATTGTTCAAC
Statistics
Matches: 500, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
113 237 0.47
114 263 0.53
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:47047 original size:227 final size:228
Alignment explanation
Indices: 46550--47174 Score: 1166
Period size: 227 Copynumber: 2.8 Consensus size: 228
46540 TAGCAAAGAT
*
46550 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
*
46615 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGGTCAAATCCATCATTTA
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTA
46679 ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
131 ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
46744 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
46777 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
46842 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTA
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTA
46907 ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
131 ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
46972 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
47005 TCAAATCCATCATTTAATGGATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
* *
47069 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTA
47134 ATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAAC
131 ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAAC
47175 ATTGTTCAAC
Statistics
Matches: 390, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
226 23 0.06
227 216 0.55
228 151 0.39
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (228 bp):
TCAAATCCATCATTTAATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTA
ATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:47205 original size:74 final size:73
Alignment explanation
Indices: 47077--47215 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 73
47067 TGAAGAAGGA
* **
47077 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATCA
47142 GCTTTTCC
66 GCTTTTCC
* * *
47150 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AGAAGAAA-TTCATAATGAGAAGAA-ATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGAT
47214 CA
64 CA
47216 ACATTACCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 3 0.05
73 20 0.34
74 35 0.60
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (73 bp):
AGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATCA
GCTTTTCC
Found at i:47205 original size:187 final size:187
Alignment explanation
Indices: 46964--47361 Score: 557
Period size: 187 Copynumber: 2.1 Consensus size: 187
46954 TGAAGAAGGA
* *
46964 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGAT
1 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
* * *
47027 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
65 CAACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
* * *
47092 TGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAGCTTTTCC
130 TGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
* ** *
47150 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
**** *
47215 AACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
66 AACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* * * *
47280 GAGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGGATTAACATTGCC
131 GAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
** *
47337 AGGTAGAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAAC
47362 TCGTCATCTG
Statistics
Matches: 186, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
185 3 0.02
186 20 0.11
187 163 0.88
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (187 bp):
AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
AACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
GAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGATCAACATTGCC
Found at i:47234 original size:74 final size:74
Alignment explanation
Indices: 47077--47248 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 74
47067 TGAAGAAGGA
* **
47077 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTTAAATCCATCATTTGATGGAT
1 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGAT
* * *
47140 CAGCTTTTCC
65 CAACATTACC
* * *
47150 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATC
47215 AACATTACC
66 AACATTACC
**** *
47224 AGTTCGAGTTCATAATAAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAAC
47249 TCATCTGAAG
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 3 0.04
73 20 0.24
74 60 0.72
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (74 bp):
AGAAAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTTAAATCCATCATTCAATGGATC
AACATTACC
Found at i:47287 original size:300 final size:301
Alignment explanation
Indices: 46850--47473 Score: 902
Period size: 300 Copynumber: 2.1 Consensus size: 301
46840 TGAAGAAGGA
* *
46850 AGAAGAAA-TTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGAT
1 AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
* * * *
46913 CAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
66 CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* *
46978 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATCAACTTTTCCAGAG-A
131 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATCAACATTGCCAG-GTA
47042 AAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
195 AAGTTCATAATGAGAAGAACTCATCAT-AAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
* *
47106 TCAACCTTTTGCTTAAATCCATCATTTGATGGATCAGCTTTTCC
258 TCAACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
* ** *
47150 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
**** *
47214 CAACATTACCAG-TTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
66 CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* * * * * * *
47278 ATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGGATTAACATTGCCAGGTAG
131 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATCAACATTGCCAGGTAA
* ** *
47343 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATACTGAGAAGAATTTGTTCA
196 AGTTCATAATGAGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
47408 ACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
261 ACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
47449 A-AAGAAAGTTCATAATGAGAAGAAC
1 AGAAGAAAGTTCATAATGAGAAGAAC
47474 TCATCTGAAG
Statistics
Matches: 289, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
298 2 0.01
299 98 0.34
300 146 0.51
301 43 0.15
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (301 bp):
AGAAGAAAGTTCATAATGAGAAGAACATTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGAT
CAACATTACCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTAATGGATCAACATTGCCAGGTAA
AGTTCATAATGAGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTAAAATCCATCACTTGATGGATCAGCTTTTCC
Found at i:47434 original size:112 final size:109
Alignment explanation
Indices: 47150--47523 Score: 414
Period size: 112 Copynumber: 3.4 Consensus size: 109
47140 CAGCTTTTCC
* * * *
47150 AGAA-AAAGTTCATAATGAGAAGAACATTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AGAAGAAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTTAAATTCATCATT-GATGGAT
* * *
47214 CAACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGA
64 CAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
47260 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCGTCATTTGATGG
1 A-GAAG-A-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGG
* *
47325 ATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
62 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * *
47376 AGAAGAAA-TTCATACTGAGAAGAATTTGTTCAACCTTTTGCTAAAATCCATCACTTGATGGATC
1 AGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATC
* * * * *
47440 AGCTTTTCCAAAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
65 AACATTACC-AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* ** *
47485 AGAAG-AAGTTCACAATGAGAAGAGCTTGTTCAACATTTT
1 AGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
47524 ACATAATTTT
Statistics
Matches: 226, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
108 2 0.01
109 42 0.19
110 2 0.01
111 3 0.01
112 74 0.33
113 64 0.28
114 22 0.10
115 5 0.02
116 12 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (109 bp):
AGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCA
ACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:47762 original size:3 final size:3
Alignment explanation
Indices: 47754--47807 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
47744 CCCATTTTAT
*
47754 TTA TTA TTA TAA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
47799 TTA TTA TTA
1 TTA TTA TTA
47808 AAAAAATAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:50165 original size:16 final size:16
Alignment explanation
Indices: 50144--50177 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50134 TTTATAATTA
50144 ATATTAAAATAAATAT
1 ATATTAAAATAAATAT
* *
50160 ATATTATAATTAATAT
1 ATATTAAAATAAATAT
50176 AT
1 AT
50178 TAATTAATAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTAAAATAAATAT
Found at i:50175 original size:12 final size:12
Alignment explanation
Indices: 50135--50237 Score: 52
Period size: 12 Copynumber: 8.2 Consensus size: 12
50125 AATAAAGTAT
50135 TTATAATTAATA
1 TTATAATTAATA
*
50147 TTAAAATAAATATATA
1 TT---ATAATTA-ATA
50163 TTATAATTAATA
1 TTATAATTAATA
50175 -TATTAATTAATA
1 TTA-TAATTAATA
*
50187 TTA-ATATTAA-C
1 TTATA-ATTAATA
50198 TTAT-ATTAATA
1 TTATAATTAATA
* * *
50209 ATATAGTTTATAA
1 TTATAATTAAT-A
*
50222 TTTGTAATTAATA
1 -TTATAATTAATA
50235 TTA
1 TTA
50238 ATATAAAATA
Statistics
Matches: 67, Mismatches: 12, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
10 5 0.07
11 9 0.13
12 25 0.37
13 10 0.15
14 7 0.10
15 6 0.09
16 5 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (12 bp):
TTATAATTAATA
Found at i:50266 original size:30 final size:30
Alignment explanation
Indices: 50230--50288 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
50220 AATTTGTAAT
50230 TAATATTAATATAAAATATA-GTCTATAAAA
1 TAATATTAATATAAAATATATGT-TATAAAA
*
50260 TAATATTAATATAAACTATATGTTATAAA
1 TAATATTAATATAAAATATATGTTATAAA
50289 TTATATAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
TAATATTAATATAAAATATATGTTATAAAA
Found at i:50333 original size:15 final size:14
Alignment explanation
Indices: 50304--50446 Score: 65
Period size: 15 Copynumber: 9.4 Consensus size: 14
50294 TAGTATAGTT
*
50304 TATAACTATAGTTAA
1 TATAATTATA-TTAA
50319 TATAATTAATATTAA
1 TATAATT-ATATTAA
* *
50334 TAT-AGTATAGTTTA
1 TATAATTATA-TTAA
*
50348 TA-AACTATAGTTAA
1 TATAATTATA-TTAA
50362 TATAATTAATATTAA
1 TATAATT-ATATTAA
* *
50377 TATAGTATAGTTTATAAA
1 TATA--AT--TATATTAA
*
50395 CTATATACTATATTAA
1 -TATA-ATTATATTAA
50411 TATAAATTATAGTTAA
1 TAT-AATTATA-TTAA
* *
50427 GATAATTAACATTAA
1 TATAATT-ATATTAA
50442 TATAA
1 TATAA
50447 AATATATAGT
Statistics
Matches: 100, Mismatches: 15, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
13 3 0.03
14 18 0.18
15 44 0.44
16 21 0.21
17 2 0.02
18 7 0.07
19 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (14 bp):
TATAATTATATTAA
Found at i:50367 original size:43 final size:43
Alignment explanation
Indices: 50291--50423 Score: 211
Period size: 43 Copynumber: 3.2 Consensus size: 43
50281 GTTATAAATT
50291 ATATAGTATAGTTTAT-AACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
50333 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
* *
50376 ATATAGTATAGTTTATAAACTATA--TACTAT-ATTAATATAA
1 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
50416 ATTATAGT
1 A-TATAGT
50424 TAAGATAATT
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
40 10 0.11
41 11 0.13
42 16 0.18
43 50 0.57
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (43 bp):
ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
Found at i:50497 original size:17 final size:18
Alignment explanation
Indices: 50471--50505 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
50461 TAATATAAAC
*
50471 TATAGTTTATAAA-TATA
1 TATAGGTTATAAAGTATA
50488 TATAGGTTATAAAGTATA
1 TATAGGTTATAAAGTATA
50506 AACTATATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
TATAGGTTATAAAGTATA
Found at i:50604 original size:57 final size:55
Alignment explanation
Indices: 50543--50678 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 55
50533 TTGTTTATAA
* *
50543 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATAC-TATAAATAG-TT-TATACATACATAT
* * * * *
50600 ACTATATGTTATATATATAGTTTATATATACTATACATAGTTTATACATAGATGT
1 ACTATAAGTTACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
50655 ACTATAAGTTACATATATAGTTTA
1 ACTATAAGTTACATATATAGTTTA
50679 CATTTATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
55 32 0.46
56 2 0.03
57 34 0.49
58 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
Found at i:50616 original size:55 final size:56
Alignment explanation
Indices: 50555--50678 Score: 146
Period size: 55 Copynumber: 2.2 Consensus size: 56
50545 TATAGGTTAC
* *
50555 ATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATATACTATATGTTAT-
1 ATATATAGTTTATATATAC-TATAAATAG-TT-TATACATACATATACTATAAGTTATA
* * * *
50612 ATATATAGTTTATATATACTATACATAGTTTATACATAGATGTACTATAAGTTA-C
1 ATATATAGTTTATATATACTATAAATAGTTTATACATACATATACTATAAGTTATA
50667 ATATATAGTTTA
1 ATATATAGTTTA
50679 CATTTATATA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
55 32 0.53
56 2 0.03
57 24 0.40
58 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (56 bp):
ATATATAGTTTATATATACTATAAATAGTTTATACATACATATACTATAAGTTATA
Found at i:50625 original size:20 final size:20
Alignment explanation
Indices: 50559--50645 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
50549 GGTTACATAT
*
50559 ATAGTTTATATA-ACATATAA
1 ATAGTTTATATATAC-TATAC
50579 ATAGATTGTATATATACATATAC
1 ATAG-TT-TATATATAC-TATAC
* *
50602 -TA---TATGT-TA-TATAT
1 ATAGTTTATATATACTATAC
50616 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTATAC
50636 ATAGTTTATA
1 ATAGTTTATA
50646 CATAGATGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
14 4 0.08
15 2 0.04
16 2 0.04
17 4 0.08
18 4 0.08
19 2 0.04
20 18 0.34
21 2 0.04
22 8 0.15
23 7 0.13
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:50748 original size:7 final size:7
Alignment explanation
Indices: 50736--50789 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
50726 TATGCATAGT
50736 GTTTAGG
1 GTTTAGG
50743 GTTTA-G
1 GTTTAGG
*
50749 GTTTATG
1 GTTTAGG
50756 GTTTAGG
1 GTTTAGG
*
50763 GTATAGG
1 GTTTAGG
* *
50770 TTTTATG
1 GTTTAGG
*
50777 ATTTAGG
1 GTTTAGG
50784 GTTTAG
1 GTTTAG
50790 AATTTATGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:50783 original size:14 final size:14
Alignment explanation
Indices: 50737--50823 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
50727 ATGCATAGTG
*
50737 TTTAGGGTTTA-GG
1 TTTAGGGTTTATGA
* * *
50750 TTTATGGTTTAGGG
1 TTTAGGGTTTATGA
* *
50764 TATAGGTTTTATGA
1 TTTAGGGTTTATGA
50778 TTTAGGGTTTA-GAA
1 TTTAGGGTTTATG-A
* * *
50792 TTTATGATTTAAGA
1 TTTAGGGTTTATGA
50806 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
50820 TTTA
1 TTTA
50824 TAATTTTGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
13 11 0.19
14 46 0.79
15 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:50795 original size:21 final size:21
Alignment explanation
Indices: 50737--50823 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
50727 ATGCATAGTG
*
50737 TTTAGGGTTTA-GGTTTATGG
1 TTTAGGGTTTAGGGTTTATGA
* *
50757 TTTAGGGTATAGGTTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
**
50778 TTTAGGGTTTAGAATTTATGA
1 TTTAGGGTTTAGGGTTTATGA
* *
50799 TTTAAGATTTAGGGTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
50820 TTTA
1 TTTA
50824 TAATTTTGGT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 10 0.18
21 46 0.82
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATGA
Found at i:50801 original size:7 final size:7
Alignment explanation
Indices: 50771--50838 Score: 50
Period size: 7 Copynumber: 9.9 Consensus size: 7
50761 GGGTATAGGT
50771 TTTATGA
1 TTTATGA
* *
50778 TTTAGGG
1 TTTATGA
50785 TTTA-GAA
1 TTTATG-A
50792 TTTATGA
1 TTTATGA
*
50799 TTTAAGA
1 TTTATGA
* *
50806 TTTAGGG
1 TTTATGA
50813 TTTATGA
1 TTTATGA
*
50820 TTTATAA
1 TTTATGA
*
50827 TTT-TGG
1 TTTATGA
50833 TTTATG
1 TTTATG
50839 CATAGTGTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
6 5 0.11
7 41 0.87
8 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (7 bp):
TTTATGA
Found at i:50822 original size:28 final size:28
Alignment explanation
Indices: 50771--50829 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
50761 GGGTATAGGT
* *
50771 TTTATGATTTAGGGTTTAGAATTTATGA
1 TTTAAGATTTAGGGTTTAGAATTTATAA
50799 TTTAAGATTTAGGGTTTATG-ATTTATAA
1 TTTAAGATTTAGGGTTTA-GAATTTATAA
50827 TTT
1 TTT
50830 TGGTTTATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.53
Consensus pattern (28 bp):
TTTAAGATTTAGGGTTTAGAATTTATAA
Found at i:50829 original size:21 final size:20
Alignment explanation
Indices: 50792--50838 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
50782 GGGTTTAGAA
50792 TTTATGATTTAAGATTTAGGG
1 TTTATGATTTAAGATTT-GGG
*
50813 TTTATGATTTATA-ATTTTGG
1 TTTATGATTTA-AGATTTGGG
50833 TTTATG
1 TTTATG
50839 CATAGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (20 bp):
TTTATGATTTAAGATTTGGG
Found at i:50974 original size:19 final size:20
Alignment explanation
Indices: 50941--51002 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
50931 ATAAGTAATT
* *
50941 TACTTTATATGGTTTATATA
1 TACTATATATAGTTTATATA
50961 TA-TATATATAGTTTATATA
1 TACTATATATAGTTTATATA
* *
50980 TACTATACATAGTTTATACA
1 TACTATATATAGTTTATATA
51000 TAC
1 TAC
51003 ATGTACTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (20 bp):
TACTATATATAGTTTATATA
Found at i:51029 original size:35 final size:36
Alignment explanation
Indices: 50988--51061 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
50978 TATACTATAC
*
50988 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
51023 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
51060 AT
1 AT
51062 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:51254 original size:100 final size:99
Alignment explanation
Indices: 51150--51403 Score: 284
Period size: 100 Copynumber: 2.5 Consensus size: 99
51140 CTGTCTATAC
51150 ATATATAATATATAGATTACTTATATTAGTATACATATATATATAT-TA-ATATAAATTATA-AT
1 ATATAT-ATATATAGA-TA--TATA-TA-TATACATATATATATATATATATATAAATTATAGAT
51212 TATAAAC-TATA-TTTATATAGTTTATACATATATAATTT
60 TATAAACATATACTTTATATAGTTTATACATATATAATTT
* * *
51250 ATATATATATATATATATATATATATATATATATATATATATATATATAAATTATAGTTTATAAA
1 ATATATATATATAGATATATATATATACATATATATATATATATATATAAATTATAGATTATAAA
* *
51315 CTATATACTTTTTATAGTTTATACATATATAGTTT
66 C-ATATACTTTATATAGTTTATACATATATAATTT
* * * *
51350 ATATACATAGTTTATATATAGTTCATATAAACATAATATATATATATATATATA
1 ATATATATA-TATAGATATA--T-ATATATACAT-ATATATATATATATATATA
51404 TATCTTATAA
Statistics
Matches: 134, Mismatches: 9, Indels: 17
0.84 0.06 0.11
Matches are distributed among these distances:
94 16 0.12
95 4 0.03
96 16 0.12
97 8 0.06
98 2 0.01
99 12 0.09
100 39 0.29
101 9 0.07
103 1 0.01
104 8 0.06
105 19 0.14
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (99 bp):
ATATATATATATAGATATATATATATACATATATATATATATATATATAAATTATAGATTATAAA
CATATACTTTATATAGTTTATACATATATAATTT
Found at i:51359 original size:13 final size:13
Alignment explanation
Indices: 51328--51367 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
51318 TATACTTTTT
*
51328 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
51343 ATAGTTTATATAC
1 ATAGTTTATATAC
51356 ATAGTTTATATA
1 ATAGTTTATATA
51368 TAGTTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:51367 original size:15 final size:15
Alignment explanation
Indices: 51328--51369 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
51318 TATACTTTTT
* *
51328 ATAGTTTATACATAT
1 ATAGTTTATATATAC
51343 ATAG-TT-TATATAC
1 ATAGTTTATATATAC
51356 ATAGTTTATATATA
1 ATAGTTTATATATA
51370 GTTCATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (15 bp):
ATAGTTTATATATAC
Found at i:51473 original size:2 final size:2
Alignment explanation
Indices: 51145--51457 Score: 158
Period size: 2 Copynumber: 158.5 Consensus size: 2
51135 ATTAACTGTC
* * *
51145 TA TA CA TA TA TA -A TA TA TA GA T- TA CT- TA TA T- TA GTA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* *
51185 TA TA TA TA TA T- TA -A TA TA AA T- TA TA -A T- TA 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 TA
* * * *
51223 TT TA TA TA GTT TA TA CA TA TA TA -A TT TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
51265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
51306 GTT TA TA AA CTA TA TA CTT TT TA TA GTT TA TA CA TA TA TA GTT TA
1 -TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
51351 TA TA CA TA GTT TA TA TA TA GT- TCA TA TA AA CA TA -A TA TA TA
1 TA TA TA TA -TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* *
51392 TA TA TA TA TA TA TA TC T- TA TA -A TA -A TA TA TA GTT TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
51431 TA TA -A TA TA GTT TA TA TA TA TA TA TA T
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA T
51458 TAAAACTTAT
Statistics
Matches: 235, Mismatches: 44, Indels: 64
0.69 0.13 0.19
Matches are distributed among these distances:
1 18 0.08
2 202 0.86
3 15 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:54854 original size:23 final size:22
Alignment explanation
Indices: 54828--54877 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
54818 AAACGTGTCA
*
54828 AAAGCAAGAGGAAAATACGTTAT
1 AAAGCAA-AGGAAAACACGTTAT
* *
54851 AAAGGTAAAGGAAAACATGTTAT
1 AAA-GCAAAGGAAAACACGTTAT
54874 AAAG
1 AAAG
54878 GAATAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 19 0.83
24 3 0.13
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (22 bp):
AAAGCAAAGGAAAACACGTTAT
Found at i:63907 original size:15 final size:16
Alignment explanation
Indices: 63889--64037 Score: 58
Period size: 15 Copynumber: 9.2 Consensus size: 16
63879 CTTCTCCTTC
63889 TCCTTCT-CTTCTTTT
1 TCCTTCTCCTTCTTTT
* * *
63904 TCCTTCTTC-TCCTTC
1 TCCTTCTCCTTCTTTT
63919 TCCTTCTCCTTCTTCTT
1 TCCTTCTCCTTCTT-TT
* *
63936 CTCCTTCTGCTTCTGCTTC
1 -TCCTTCTCCTTCT--TTT
* * *
63955 TGCTTCTTCTTC-TTC
1 TCCTTCTCCTTCTTTT
* * *
63970 TCATTCTCCTTGTCCTTC
1 TCCTTCTCC-T-TCTTTT
**
63988 TCCTTCTCCTTC-TCC
1 TCCTTCTCCTTCTTTT
*
64003 TCCTTCTCCTTCTCCTT
1 TCCTTCTCCTTCT-TTT
*
64020 T--TTCTCCTTCTTCT
1 TCCTTCTCCTTCTTTT
64034 TCCT
1 TCCT
64038 ATTCTTCTTC
Statistics
Matches: 102, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
14 2 0.02
15 52 0.51
16 8 0.08
17 5 0.05
18 33 0.32
19 1 0.01
20 1 0.01
ACGTcount: A:0.01, C:0.42, G:0.03, T:0.55
Consensus pattern (16 bp):
TCCTTCTCCTTCTTTT
Found at i:64048 original size:6 final size:6
Alignment explanation
Indices: 63876--64101 Score: 152
Period size: 6 Copynumber: 37.7 Consensus size: 6
63866 AAAAAAATCA
* * * * *
63876 CTTCTT CTCCTT CTCCTT C-TCTT CTTTTT CCTTCTT CTCCTT CTCCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT -CTTCTT CTTCTT CTTCTT
* * * * *
63924 CTCCTT CTTCTT CTCCTT CTGCTT CTGCTT CTGCTT CTTCTT CTTC-T
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * * * * *
63971 CATTCTC CTTGTC CTTCTC CTTCTC CTTCTC CTCCTT CTCCTT CTCCTT
1 C-TTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * *
64020 TTTCTC CTTCTT CTTCCT ATTCTT CTTCTT CATCAT CTTCTT CTT-TCT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCT-T
* * *
64068 CCTCTT CCTCCT CTTCTT CTTCTT CTTCTT CTTC
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTC
64102 AAAACAAAAC
Statistics
Matches: 183, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
5 7 0.04
6 169 0.92
7 7 0.04
ACGTcount: A:0.02, C:0.41, G:0.02, T:0.56
Consensus pattern (6 bp):
CTTCTT
Done.