Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000361.1 Hibiscus syriacus cultivar Beakdansim tig00000657_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: 127243
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10386 original size:12 final size:11
Alignment explanation
Indices: 10369--10404 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
10359 GGTCTGTAAT
10369 TATTTATTTATA
1 TATTTATTTA-A
10381 TATTTATTTAA
1 TATTTATTTAA
*
10392 TATGTATTTAA
1 TATTTATTTAA
10403 TA
1 TA
10405 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:10408 original size:3 final size:3
Alignment explanation
Indices: 10400--10470 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
10390 AATATGTATT
10400 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10448 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
10471 TGGATAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11754 original size:41 final size:40
Alignment explanation
Indices: 11708--11812 Score: 174
Period size: 41 Copynumber: 2.6 Consensus size: 40
11698 AAGTTGAACA
* *
11708 AGTTCTTCTCATTATGAACTTCTTCTTCTTTATTCAGATG
1 AGTTCTTCTCATTATGAACTTCTCCTTCCTTATTCAGATG
*
11748 ATGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATG
1 A-GTTCTTCTCATTATGAACTTCTCCTTCCTTATTCAGATG
11789 AGTTCTTCTCATTATGAACTTCTC
1 AGTTCTTCTCATTATGAACTTCTC
11813 TGGAAAAGCT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 24 0.39
41 37 0.61
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTCCTTCCTTATTCAGATG
Found at i:11772 original size:113 final size:113
Alignment explanation
Indices: 10790--11769 Score: 1636
Period size: 113 Copynumber: 8.7 Consensus size: 113
10780 AGAATTATAC
* * * *
10790 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * * * *
10855 TATGAACTCTCCCTGGCAATGTTGATCTATCAAATGATGAATTCAAACC
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGA-T
** *
10904 AAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
10969 TATGAACTTTCTCTGGAAAAAATAATCCATCCAGTGATGAATTCAGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
11017 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
11082 TATGAACTTTCTCTGGAAAAAATAATCCATCCAGTGATGAATTCAGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
*
11130 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
11195 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
*
11243 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
11308 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
11356 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
11421 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
11469 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
11534 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
11582 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
11647 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAAAC
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
* * * *
11695 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTATTCAGATGATGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCA
11760 TTATGAACTT
65 TTATGAACTT
11770 CTCCTTCCTT
Statistics
Matches: 832, Mismatches: 33, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
113 714 0.86
114 118 0.14
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGAT
Found at i:12710 original size:83 final size:83
Alignment explanation
Indices: 12563--13146 Score: 1059
Period size: 83 Copynumber: 7.1 Consensus size: 83
12553 GTTCTGTAGT
* *
12563 TTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
*
12628 TCTAAACTCAATGATTGG
66 TCTAAATTCAATGATTGG
* *
12646 TTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATC
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATC
12710 TTCTAAATTCAATGATTGG
65 TTCTAAATTCAATGATTGG
*
12729 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGACAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
12794 TCTAAATTCAATGATTGG
66 TCTAAATTCAATGATTGG
12812 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
12877 TCTAAATTCAATGATT-G
66 TCTAAATTCAATGATTGG
*
12894 TTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGACAAATTCATC
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATC
12958 TTCTAAATTCAATGATTGG
65 TTCTAAATTCAATGATTGG
12977 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
13042 TCTAAATTCAATGATTGG
66 TCTAAATTCAATGATTGG
13060 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
13125 TCTAAATTCAATGATT-G
66 TCTAAATTCAATGATTGG
13142 TTCTG
1 TTCTG
13147 GGATATCATA
Statistics
Matches: 489, Mismatches: 7, Indels: 11
0.96 0.01 0.02
Matches are distributed among these distances:
82 88 0.18
83 399 0.82
84 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
TCTAAATTCAATGATTGG
Found at i:13007 original size:248 final size:248
Alignment explanation
Indices: 12563--13146 Score: 1114
Period size: 248 Copynumber: 2.4 Consensus size: 248
12553 GTTCTGTAGT
* *
12563 TTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
*
12628 TCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TCTAAATTCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
12693 CTATTGACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
130 CTATTGACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
12758 GAACACTTCTAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAATGATTGG
195 GAACACTTCTAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAATGATTGG
12812 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
*
12877 TCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGC
66 TCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
12942 TATTGACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAG
131 TATTGACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAG
*
13007 AACACTTCTAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGG
196 AACACTTCTAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAATGATTGG
13060 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
13125 TCTAAATTCAATGATTGTTCTG
66 TCTAAATTCAATGATTGTTCTG
13147 GGATATCATA
Statistics
Matches: 330, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
248 252 0.76
249 78 0.24
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (248 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCT
TCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
TATTGACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAG
AACACTTCTAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAATGATTGG
Found at i:13722 original size:19 final size:19
Alignment explanation
Indices: 13700--13736 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13690 AATTATGTTA
13700 ATTTATAAAAATAAATTGG
1 ATTTATAAAAATAAATTGG
* *
13719 ATTTCTACAAATAAATTG
1 ATTTATAAAAATAAATTG
13737 AATCTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
ATTTATAAAAATAAATTGG
Found at i:14094 original size:6 final size:6
Alignment explanation
Indices: 14083--14129 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
14073 CTTGACCCTC
*
14083 CTTTTT CTTTTT CTTTTCT CTTTTTT CCTTTT -TTTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTT-T C-TTTTT CTTTTT CTTTTT CTTTTT CTTT
14130 CTTTTCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 24 0.67
7 4 0.11
8 4 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:14109 original size:20 final size:19
Alignment explanation
Indices: 14084--14134 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
14074 TTGACCCTCC
14084 TTTTTCTTTTTCTTTTCTCT
1 TTTTTCTTTTT-TTTTCTCT
*
14104 TTTTTCCTTTTTTTTTCTTT
1 TTTTT-CTTTTTTTTTCTCT
14124 TTCTTTCTTTT
1 TT-TTTCTTTT
14135 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTCTCT
Found at i:26666 original size:26 final size:26
Alignment explanation
Indices: 26636--26695 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
26626 TTGGGACGTG
26636 GCAGCGGCGGAGGCGGCGAGATAGCA
1 GCAGCGGCGGAGGCGGCGAGATAGCA
26662 GCAGCGGCGGAGGCGGCGAGATAGCA
1 GCAGCGGCGGAGGCGGCGAGATAGCA
*
26688 GCGGCGGC
1 GCAGCGGC
26696 CGCGTGTCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.52, T:0.03
Consensus pattern (26 bp):
GCAGCGGCGGAGGCGGCGAGATAGCA
Found at i:26927 original size:12 final size:11
Alignment explanation
Indices: 26910--26945 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
26900 GGTCTGTAAT
26910 TATTTATTTATA
1 TATTTATTTA-A
26922 TATTTATTTAA
1 TATTTATTTAA
*
26933 TATGTATTTAA
1 TATTTATTTAA
26944 TA
1 TA
26946 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:26949 original size:3 final size:3
Alignment explanation
Indices: 26941--27046 Score: 196
Period size: 3 Copynumber: 35.7 Consensus size: 3
26931 AATATGTATT
*
26941 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26989 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27036 TAA TAA TAA TA
1 TAA TAA TAA TA
27047 TGGATAAAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 98 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34170 original size:242 final size:242
Alignment explanation
Indices: 33745--34228 Score: 968
Period size: 242 Copynumber: 2.0 Consensus size: 242
33735 CTTACTATGG
33745 ATGGGATGCCAGGATGTGTTAGTATGTAAGCATATCCCTGCATTATTTTATCAGATGGGAATGGC
1 ATGGGATGCCAGGATGTGTTAGTATGTAAGCATATCCCTGCATTATTTTATCAGATGGGAATGGC
33810 CAGTGATTTTGTGTTGATCCAGTGTCATGGTTGTCAATGAAAGTTACAGCATTTTGAGGTAGAAT
66 CAGTGATTTTGTGTTGATCCAGTGTCATGGTTGTCAATGAAAGTTACAGCATTTTGAGGTAGAAT
33875 TCCTATCAGTCCAGGCGGTTTCCCATTCGAGTCCTTCAATAGCCATAACTTCCCTTGCACCGCGT
131 TCCTATCAGTCCAGGCGGTTTCCCATTCGAGTCCTTCAATAGCCATAACTTCCCTTGCACCGCGT
33940 CGTTCAGAATCCCTTTCGTAGTGAAGTCGAATGCCGTCACGACGCCC
196 CGTTCAGAATCCCTTTCGTAGTGAAGTCGAATGCCGTCACGACGCCC
33987 ATGGGATGCCAGGATGTGTTAGTATGTAAGCATATCCCTGCATTATTTTATCAGATGGGAATGGC
1 ATGGGATGCCAGGATGTGTTAGTATGTAAGCATATCCCTGCATTATTTTATCAGATGGGAATGGC
34052 CAGTGATTTTGTGTTGATCCAGTGTCATGGTTGTCAATGAAAGTTACAGCATTTTGAGGTAGAAT
66 CAGTGATTTTGTGTTGATCCAGTGTCATGGTTGTCAATGAAAGTTACAGCATTTTGAGGTAGAAT
34117 TCCTATCAGTCCAGGCGGTTTCCCATTCGAGTCCTTCAATAGCCATAACTTCCCTTGCACCGCGT
131 TCCTATCAGTCCAGGCGGTTTCCCATTCGAGTCCTTCAATAGCCATAACTTCCCTTGCACCGCGT
34182 CGTTCAGAATCCCTTTCGTAGTGAAGTCGAATGCCGTCACGACGCCC
196 CGTTCAGAATCCCTTTCGTAGTGAAGTCGAATGCCGTCACGACGCCC
34229 CCGGCAGCTA
Statistics
Matches: 242, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 242 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (242 bp):
ATGGGATGCCAGGATGTGTTAGTATGTAAGCATATCCCTGCATTATTTTATCAGATGGGAATGGC
CAGTGATTTTGTGTTGATCCAGTGTCATGGTTGTCAATGAAAGTTACAGCATTTTGAGGTAGAAT
TCCTATCAGTCCAGGCGGTTTCCCATTCGAGTCCTTCAATAGCCATAACTTCCCTTGCACCGCGT
CGTTCAGAATCCCTTTCGTAGTGAAGTCGAATGCCGTCACGACGCCC
Found at i:36557 original size:21 final size:21
Alignment explanation
Indices: 36531--36580 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
36521 GGAGTGTGGG
36531 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
36552 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
36573 GGGAATCG
1 GGGAATCG
36581 ATTCCCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:37043 original size:13 final size:14
Alignment explanation
Indices: 37019--37048 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37009 TTTAGTAATT
37019 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
37033 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
37046 TTA
1 TTA
37049 CTCCCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:37053 original size:67 final size:67
Alignment explanation
Indices: 36982--37125 Score: 261
Period size: 67 Copynumber: 2.1 Consensus size: 67
36972 TTTCAACAAT
*
36982 CTCCCCCTTTTTGATTTAACAAAACATTTTAGTAATTTTAAGATTTTGAAATTAAGTTTTGAAAT
1 CTCCCCCTTATTGATTTAACAAAACATTTTAGTAATTTTAAGATTTTGAAATTAAGTTTTGAAAT
37047 TA
66 TA
*
37049 CTCCCTCTTATTGATTTAACAAAACATTTTAGTAATTTTAAGATTTTGAAATTAAGTTTTGAAAT
1 CTCCCCCTTATTGATTTAACAAAACATTTTAGTAATTTTAAGATTTTGAAATTAAGTTTTGAAAT
37114 TA
66 TA
*
37116 CTCCCTCTTA
1 CTCCCCCTTA
37126 CTCTAACACT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (67 bp):
CTCCCCCTTATTGATTTAACAAAACATTTTAGTAATTTTAAGATTTTGAAATTAAGTTTTGAAAT
TA
Found at i:37110 original size:13 final size:14
Alignment explanation
Indices: 37086--37115 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37076 TTTAGTAATT
37086 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
37100 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
37113 TTA
1 TTA
37116 CTCCCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:37709 original size:21 final size:20
Alignment explanation
Indices: 37681--37719 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
37671 TCATTGTGGA
* *
37681 TAAATGAGACTCTATGGAAG
1 TAAATGAGAATCCATGGAAG
37701 TAAAGTGAGAATCCATGGA
1 TAAA-TGAGAATCCATGGA
37720 TGCATACTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (20 bp):
TAAATGAGAATCCATGGAAG
Found at i:39415 original size:21 final size:21
Alignment explanation
Indices: 39391--39449 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
39381 AGGGTATCGA
39391 TTCCCATACAGGGGGAATCAG
1 TTCCCATACAGGGGGAATCAG
* * *
39412 TTCCCCTTCAAAGGGGGAATCGG
1 TT-CCCAT-ACAGGGGGAATCAG
* *
39435 TTCCCCTTCAGGGGG
1 TTCCCATACAGGGGG
39450 TATCGATTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 8 0.27
22 8 0.27
23 14 0.47
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (21 bp):
TTCCCATACAGGGGGAATCAG
Found at i:39427 original size:23 final size:23
Alignment explanation
Indices: 39400--39444 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
39390 ATTCCCATAC
39400 AGGGGGAATCAGTTCCCCTTCAA
1 AGGGGGAATCAGTTCCCCTTCAA
*
39423 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCAGTTCCCCTTCA
39445 GGGGGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCAGTTCCCCTTCAA
Found at i:39454 original size:21 final size:21
Alignment explanation
Indices: 39377--39460 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
39367 ACCAGAACCC
* * *
39377 TCAGAGGGTATCGATTCCCAT
1 TCAGGGGGAATCGATTCCCCT
*
39398 ACAGGGGGAATC-AGTTCCCCT
1 TCAGGGGGAATCGA-TTCCCCT
*
39419 TCAAAGGGGGAATCGGTTCCCCT
1 TC--AGGGGGAATCGATTCCCCT
*
39442 TCAGGGGGTATCGATTCCC
1 TCAGGGGGAATCGATTCCC
39461 TCTGCACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 31 0.61
23 19 0.37
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAGGGGGAATCGATTCCCCT
Found at i:43541 original size:65 final size:63
Alignment explanation
Indices: 43455--43613 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 63
43445 AATTAAATTG
* * *
43455 AACATC-AATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCAATGCACTCAGGATATTT-TG-
43518 A
63 A
* * * *
43519 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCAATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCAATGCACTCAGGATATTTTGA
* * *
43583 AACATTGAATACACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
43614 TCTTAGAGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 34 0.41
65 42 0.51
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCAATGCACTCAGGATATTTTGA
Found at i:51426 original size:21 final size:21
Alignment explanation
Indices: 51400--51451 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
51390 ACCCCAGGAG
*
51400 CTAGCTCTTCACGAGCTACTC
1 CTAGCTCTTCACGAGCTACTA
*
51421 CTAGCTCTTCACGAGCTGCTA
1 CTAGCTCTTCACGAGCTACTA
51442 CTAGCTCTTC
1 CTAGCTCTTC
51452 TCGTGCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.31
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTACTA
Found at i:52911 original size:11 final size:11
Alignment explanation
Indices: 52895--52930 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
52885 ACAAGAAACA
52895 AGAATCAAGAG
1 AGAATCAAGAG
52906 AGAATCAAGAG
1 AGAATCAAGAG
52917 AGAATCAA-AG
1 AGAATCAAGAG
52927 AGAA
1 AGAA
52931 AACATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.58, C:0.08, G:0.25, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:55164 original size:17 final size:17
Alignment explanation
Indices: 55142--55183 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
55132 TCTTTCTTGA
55142 TTCTTGTTGATTGTTGT
1 TTCTTGTTGATTGTTGT
55159 TTCTTGTTGATTGTTGT
1 TTCTTGTTGATTGTTGT
55176 TTCTTGTT
1 TTCTTGTT
55184 TTTTATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (17 bp):
TTCTTGTTGATTGTTGT
Found at i:56031 original size:22 final size:21
Alignment explanation
Indices: 55989--56033 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
55979 ATTTTATATT
*
55989 TTTATTTAATTATTACTATTA
1 TTTATTTAATTATTACCATTA
*
56010 TTTATTTATTTCATTACCATTA
1 TTTATTTAATT-ATTACCATTA
56032 TT
1 TT
56034 GAACCTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTTAATTATTACCATTA
Found at i:60394 original size:7 final size:7
Alignment explanation
Indices: 60382--60407 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
60372 GTTATATAAA
60382 ATTTTAT
1 ATTTTAT
60389 ATTTTAT
1 ATTTTAT
60396 ATTTTAT
1 ATTTTAT
60403 ATTTT
1 ATTTT
60408 TAAACAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTAT
Found at i:63071 original size:16 final size:19
Alignment explanation
Indices: 63029--63066 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
63019 TCGCCGAATT
63029 ATATAAAT-TTTAAATAAA
1 ATATAAATATTTAAATAAA
63047 ATATAAATATTTAAA-AAA
1 ATATAAATATTTAAATAAA
63065 AT
1 AT
63067 TAATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAAATATTTAAATAAA
Found at i:63072 original size:20 final size:20
Alignment explanation
Indices: 63025--63072 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
63015 CCTGTCGCCG
63025 AATTATATAAATTTTAAATAA
1 AATTA-ATAAATTTTAAATAA
63046 AA-T-ATAAATATTTAAA-AA
1 AATTAATAAAT-TTTAAATAA
63064 AATTAATAA
1 AATTAATAA
63073 TTAATGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 5 0.21
21 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAATAAATTTTAAATAA
Found at i:63901 original size:2 final size:2
Alignment explanation
Indices: 63894--63927 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
63884 GAAATGCTTT
63894 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
63928 CTAGGGACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66406 original size:25 final size:26
Alignment explanation
Indices: 66378--66458 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
66368 TATCGAGAGT
66378 TTATAATTTTTAAA-TTTTAATTTAA
1 TTATAATTTTTAAATTTTTAATTTAA
***
66403 TTATAATTGGGAATATTTTTTAATTTAA
1 TTATAATTTTTAA-A-TTTTTAATTTAA
* *
66431 ATATAA-TTTTAAACTTTTAATTTAA
1 TTATAATTTTTAAATTTTTAATTTAA
66456 TTA
1 TTA
66459 ATTTTATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
25 23 0.52
26 2 0.05
27 3 0.07
28 16 0.36
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATAATTTTTAAATTTTTAATTTAA
Found at i:66779 original size:3 final size:3
Alignment explanation
Indices: 66767--66802 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
66757 TGATATTAAA
66767 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
66803 ATGTTACATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:70080 original size:16 final size:17
Alignment explanation
Indices: 70054--70089 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
70044 TCTACTAAAG
70054 CATGATTGGGTAGACAC
1 CATGATTGGGTAGACAC
*
70071 CATG-TTGGGTAGATAC
1 CATGATTGGGTAGACAC
70087 CAT
1 CAT
70090 ATGAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (17 bp):
CATGATTGGGTAGACAC
Found at i:80077 original size:18 final size:17
Alignment explanation
Indices: 80047--80092 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
80037 TATTTTGCTT
*
80047 AAAAAA-AAGAAAGGAA
1 AAAAAAGAAAAAAGGAA
80063 AAAAAACGAAAAAAGGAA
1 AAAAAA-GAAAAAAGGAA
*
80081 GAAAAAGAAAAA
1 AAAAAAGAAAAA
80093 GGGAGGGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 6 0.23
17 6 0.23
18 14 0.54
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGGAA
Found at i:81277 original size:54 final size:54
Alignment explanation
Indices: 81195--81383 Score: 265
Period size: 54 Copynumber: 3.5 Consensus size: 54
81185 TAGTGAAGCA
81195 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
81249 GAAGAAGATGTCCGAGTTTTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * **
81303 GAAGAAGATATTCGAGTTCTATACTCTCT-GAAGAAAGAGGGAGCGAACCCATAA
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
81357 GAAGAAGATTGTTCGAG-TCTTATACTC
1 GAAGAAGA-TGTTCGAGTTC-TATACTC
81384 TCTGAAGGAA
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 105 0.88
55 14 0.12
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (54 bp):
GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:81399 original size:55 final size:54
Alignment explanation
Indices: 81194--81441 Score: 247
Period size: 54 Copynumber: 4.6 Consensus size: 54
81184 GTAGTGAAGC
* * *
81194 AGAAGAAGATGTTCGAGT-TCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTT
1 AGAAGAAGATGTTCGAGTCT-TATACTCTCTGA-AGAAAGAGGGAGCGAACCCATA
* * * * * * *
81248 TGAAGAAGATGTCCGAGTTTTATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTT
1 AGAAGAAGATGTTCGAGTCTTATACTCTCTGA-AGAAAGAGGGAGCGAACCCATA
* *
81302 TGAAGAAGATATTCGAGT-TCTATACTCTCTGAAGAAAGAGGGAGCGAACCCATA
1 AGAAGAAGATGTTCGAGTCT-TATACTCTCTGAAGAAAGAGGGAGCGAACCCATA
* * *
81356 AGAAGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGAT-
1 AGAAGAAGA-TGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCGA-AC-CCATA
81411 AGAAGAAGATTGTTCGAGTCTTATACTCTCT
1 AGAAGAAGA-TGTTCGAGTCTTATACTCTCT
81442 AAAGGAATAG
Statistics
Matches: 173, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
53 1 0.01
54 102 0.59
55 66 0.38
56 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCGAACCCATA
Found at i:81447 original size:55 final size:54
Alignment explanation
Indices: 81194--81564 Score: 261
Period size: 55 Copynumber: 6.8 Consensus size: 54
81184 GTAGTGAAGC
* * * *
81194 AGAAGAAGATGTTCGAGT-TCTATACTCCCTAGAGAAAGAGGGAGC-GAACCCGTT
1 AGAAGAAGATGTTCGAGTCT-TATACTCTCTAAAGAAAGAGGGAGCAG-ACACGAT
* * * * * * * *
81248 TGAAGAAGATGTCCGAGTTTTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTT
1 AGAAGAAGATGTTCGAGTCTTATACTCTCTAAAGAAAGAGGGAGCAGACACGAT
* * * *
81302 TGAAGAAGATATTCGAGT-TCTATACTCTCTGAAGAAAGAGGGAGC-GA-ACCCAT
1 AGAAGAAGATGTTCGAGTCT-TATACTCTCTAAAGAAAGAGGGAGCAGACA-CGAT
* * *
81355 AAGAAGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGAT
1 -AGAAGAAGA-TGTTCGAGTCTTATACTCTCTAAAGAAAGAGGGAGCAGACACGAT
* * * * *
81411 AGAAGAAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGTGAGAAGACATGAT
1 AGAAGAAGA-TGTTCGAGTCTTATACTCTCTAAAGAAAGAGGGAGCAGACACGAT
* ** * * * * * *
81466 TGTTGAAGATTGTTCAAGTCTTATATTCTCTGAAGGAATAGGGAACAGACACGAGT
1 AGAAGAAGA-TGTTCGAGTCTTATACTCTCTAAAGAAAGAGGGAGCAGACACGA-T
** * *
81522 -GTTGAAGATGTTTGAGT-TCTATACTCCCTGAAAGAAAGAGGGA
1 AGAAGAAGATGTTCGAGTCT-TATACTCTCT-AAAGAAAGAGGGA
81565 ATGAACCCAT
Statistics
Matches: 267, Mismatches: 38, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
53 5 0.02
54 109 0.41
55 145 0.54
56 7 0.03
57 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.25
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTCTTATACTCTCTAAAGAAAGAGGGAGCAGACACGAT
Found at i:81584 original size:110 final size:108
Alignment explanation
Indices: 81194--81590 Score: 324
Period size: 110 Copynumber: 3.6 Consensus size: 108
81184 GTAGTGAAGC
* * * * *
81194 AGAAGAAGATGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-
1 AGAAGAAGATGTTCGAGTTCTATACTCTCTGAAAGAAAGAGGGA-AGAACCC-ATTGTAGAAGAT
* * * * * * * * * *
81257 TGTCCGAGTTTTATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTT
64 TGTTCAAGTCTTATACTCTCTGA-AGGAATAGGGAACAGACACGAT
* * * * *
81302 TGAAGAAGATATTCGAGTTCTATACTCTCTG-AAGAAAGAGGGAGCGAACCCATAAGAAGAAGAT
1 AGAAGAAGATGTTCGAGTTCTATACTCTCTGAAAGAAAGAGGGA-AGAACCCAT-TGTAGAAGAT
* *
81366 TGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGAT
64 TGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGAT
* * ** *
81411 AGAAGAAGATTGTTCGAG-TCTTATACTCTCT-AAAGGAATAGTGAGAAG-ACATGATTGTTGAA
1 AGAAGAAGA-TGTTCGAGTTC-TATACTCTCTGAAA-GAA-AGAGGGAAGAAC-CCATTGTAGAA
*
81473 GATTGTTCAAGTCTTATATTCTCTGAAGGAATAGGGAACAGACACGAGT
61 GATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGA-T
** * * *
81522 -GTTGAAGATGTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAATGAACCCATTGGTAGAAGAC
1 AGAAGAAGATGTTCGAGTTCTATACTCTCTGAAAGAAAGAGGGAA-GAACCCATT-GTAGAAGAT
81586 TGTTC
64 TGTTC
81591 GAGTTTCATA
Statistics
Matches: 236, Mismatches: 37, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
107 1 0.00
108 60 0.25
109 68 0.29
110 95 0.40
111 7 0.03
112 5 0.02
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (108 bp):
AGAAGAAGATGTTCGAGTTCTATACTCTCTGAAAGAAAGAGGGAAGAACCCATTGTAGAAGATTG
TTCAAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGAT
Found at i:81869 original size:3 final size:3
Alignment explanation
Indices: 81857--81898 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
81847 TTATATTAAA
81857 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
81899 ATGTTACATC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:86456 original size:17 final size:17
Alignment explanation
Indices: 86436--86474 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
86426 TATTAAAATT
86436 TTTATTTAATTATATA-A
1 TTTATTT-ATTATATATA
86453 TTTA-TTATTATATATA
1 TTTATTTATTATATATA
86469 TTTATT
1 TTTATT
86475 AATATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTTATTATATATA
Found at i:86473 original size:16 final size:15
Alignment explanation
Indices: 86444--86480 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
86434 TTTTTATTTA
86444 ATTATATAATTTATT
1 ATTATATAATTTATT
86459 ATTATATATATTTATT
1 ATTATATA-ATTTATT
*
86475 AATATA
1 ATTATA
86481 ATACAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATAATTTATT
Found at i:86650 original size:55 final size:54
Alignment explanation
Indices: 86552--86656 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 54
86542 TCTTAAATTT
* * *
86552 TAAAAATATTTTTTTATTTTTATCTTAACTTATTAAATATTTTTTATTTTAATG
1 TAAAAATATTATTTTATCTTTATCTTAACTTATAAAATATTTTTTATTTTAATG
* *
86606 TAAAAATATATATTTTATCTTTATCTTCATTTA-AAAATATTTTTTTATTTT
1 TAAAAATAT-TATTTTATCTTTATCTTAACTTATAAAATA-TTTTTTATTTT
86657 TATCTTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
54 14 0.32
55 30 0.68
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (54 bp):
TAAAAATATTATTTTATCTTTATCTTAACTTATAAAATATTTTTTATTTTAATG
Found at i:86659 original size:30 final size:30
Alignment explanation
Indices: 86550--86676 Score: 115
Period size: 30 Copynumber: 4.3 Consensus size: 30
86540 ATTCTTAAAT
86550 TTTAAAAATATTTTTTTATTTTTATCTTAA
1 TTTAAAAATATTTTTTTATTTTTATCTTAA
* *
86580 CTTATTAAATA-TTTTTTA----T-T-TTAA
1 TTTA-AAAATATTTTTTTATTTTTATCTTAA
* * * *
86604 TGTAAAAATATATATTTTATCTTTATCTTCA
1 TTTAAAAATAT-TTTTTTATTTTTATCTTAA
86635 TTTAAAAATATTTTTTTATTTTTATCTTAA
1 TTTAAAAATATTTTTTTATTTTTATCTTAA
86665 TTTTTAAAAATA
1 --TTTAAAAATA
86677 ACTTAAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
23 5 0.07
24 6 0.08
25 7 0.09
26 1 0.01
29 1 0.01
30 27 0.36
31 18 0.24
32 10 0.13
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAAAAATATTTTTTTATTTTTATCTTAA
Found at i:86836 original size:18 final size:17
Alignment explanation
Indices: 86782--86837 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
86772 ATTATTCTAT
*
86782 TAAATCATAATTTATTATA
1 TAAAT-ATAA-TTATTAAA
* *
86801 TATATATAACTATT-AA
1 TAAATATAATTATTAAA
86817 TAAATATAATTAATTAAA
1 TAAATATAATT-ATTAAA
86835 TAA
1 TAA
86838 CAATTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 9 0.30
19 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATAATTATTAAA
Found at i:88832 original size:23 final size:23
Alignment explanation
Indices: 88805--88850 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
88795 TTAAAATCAT
88805 ATTATTTATTTGAAATAGTATTA
1 ATTATTTATTTGAAATAGTATTA
*
88828 ATTATTTATTTGAAATATTATTA
1 ATTATTTATTTGAAATAGTATTA
88851 CTTTTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTATTTATTTGAAATAGTATTA
Found at i:89016 original size:29 final size:30
Alignment explanation
Indices: 88984--89041 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
88974 ATATTATTTC
88984 AAATAAATATTTTTTGTAAT-TTAAAAATT
1 AAATAAATATTTTTTGTAATGTTAAAAATT
*
89013 AAATAAATATTTTTTGTAATGTTACAAAT
1 AAATAAATATTTTTTGTAATGTTAAAAAT
89042 ATAGCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (30 bp):
AAATAAATATTTTTTGTAATGTTAAAAATT
Found at i:93951 original size:15 final size:15
Alignment explanation
Indices: 93914--93951 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
93904 AATGATTTTA
*
93914 AAAATAATTTATTAT
1 AAAATAATTTATTAC
*
93929 AAAGTAATTTATTAC
1 AAAATAATTTATTAC
93944 AAAATAAT
1 AAAATAAT
93952 AATAAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATAATTTATTAC
Found at i:109188 original size:19 final size:19
Alignment explanation
Indices: 109164--109202 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
109154 CTGACTCTCC
109164 TATGATCCTTCTCCTTTTT
1 TATGATCCTTCTCCTTTTT
** *
109183 TATGATTTTTTTCCTTTTT
1 TATGATCCTTCTCCTTTTT
109202 T
1 T
109203 GTTTCCCTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.18, G:0.05, T:0.67
Consensus pattern (19 bp):
TATGATCCTTCTCCTTTTT
Found at i:117349 original size:20 final size:22
Alignment explanation
Indices: 117312--117351 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
117302 GAGCATAGCC
*
117312 GTTGAGCCGATTCATAAGCCAA
1 GTTGAGCCGATACATAAGCCAA
117334 GTTGAGCCGA-AC-TAAGCC
1 GTTGAGCCGATACATAAGCC
117352 GTTGAATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (22 bp):
GTTGAGCCGATACATAAGCCAA
Found at i:118636 original size:31 final size:31
Alignment explanation
Indices: 118601--118724 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
118591 ATCCTCGGCA
* *
118601 ACTGTCCATAGGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* **
118632 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* *
118663 ACTATCCATATATCCCGAA-AGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-AT
* * *
118695 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
118725 AACCCTCGAC
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 49 0.65
32 24 0.32
33 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:122411 original size:32 final size:32
Alignment explanation
Indices: 122351--122411 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
122341 GGTGACCCTT
** *
122351 GGGTAGGCTCTTAAGCCTTAAGGTACTCCATA
1 GGGTAGGCTCTTAAGCCACAAGGCACTCCATA
122383 GGGTAGGCTC-TAAGACCACAAGGCACTCC
1 GGGTAGGCTCTTAAG-CCACAAGGCACTCC
122412 CTTAGGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
GGGTAGGCTCTTAAGCCACAAGGCACTCCATA
Done.