Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000887.1 Hibiscus syriacus cultivar Beakdansim tig00001732_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: 662576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:603592 original size:22 final size:22
Alignment explanation
Indices: 603564--603607 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
603554 CACTCTCTCA
603564 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
603586 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
603608 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:603896 original size:20 final size:20
Alignment explanation
Indices: 603871--603908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
603861 CGATTCTCTC
603871 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
603891 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
603909 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:605249 original size:18 final size:18
Alignment explanation
Indices: 605228--605272 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
605218 TCCACTTCGG
* *
605228 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
605246 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
605264 GAGCCATCA
1 GAGCCATCA
605273 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:605792 original size:19 final size:19
Alignment explanation
Indices: 605742--605804 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
605732 TTTACTTTCA
*
605742 CAACACGAAATGACTATCG
1 CAACGCGAAATGACTATCG
* *
605761 TAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCG
* **
605781 CAATGCGAAATGAAAATCG
1 CAACGCGAAATGACTATCG
605800 CAACG
1 CAACG
605805 ACAAAATCGC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
CAACGCGAAATGACTATCG
Found at i:605822 original size:33 final size:33
Alignment explanation
Indices: 605777--605867 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
605767 GGAAATGGCT
*
605777 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
605810 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
605842 ATCGCAACGCGAAATTAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
605868 TACGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:605861 original size:19 final size:18
Alignment explanation
Indices: 605777--605867 Score: 72
Period size: 14 Copynumber: 5.4 Consensus size: 18
605767 GGAAATGGCT
*
605777 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAAT-AAA
*
605796 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAATAAA
*
605810 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAATAAA
*
605828 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAATAAA
605842 ATCGCAACGCGAAATTAAA
1 ATCGCAACGCGAAA-TAAA
605861 ATCGCAA
1 ATCGCAA
605868 TACGATTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
14 20 0.35
15 1 0.02
16 6 0.11
17 2 0.04
18 11 0.19
19 17 0.30
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (18 bp):
ATCGCAACGCGAAATAAA
Found at i:605903 original size:14 final size:14
Alignment explanation
Indices: 605884--605941 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
605874 TTGTGTTTCG
605884 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
605898 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
605914 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
605930 CGTTGCGATTTT
1 CGTTGCGATTTT
605942 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:605916 original size:32 final size:33
Alignment explanation
Indices: 605879--605957 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
605869 ACGATTTGTG
605879 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
605911 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
605944 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
605958 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:605956 original size:19 final size:19
Alignment explanation
Indices: 605898--606015 Score: 88
Period size: 20 Copynumber: 6.4 Consensus size: 19
605888 GCGATTTTGT
605898 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
605916 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
605930 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
605949 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
*
605969 CGTTGCGATAGTT-ATTTCG
1 CGTTGCGAT-TTTCATTTCG
*
605988 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
606008 TGTTGCGA
1 CGTTGCGA
606016 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 13 0.16
19 25 0.32
20 26 0.33
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:605976 original size:20 final size:19
Alignment explanation
Indices: 605942--605996 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
605932 TTGCGATTTT
*
605942 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
605961 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
605981 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
605997 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:606093 original size:27 final size:26
Alignment explanation
Indices: 606031--606095 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
606021 AACTATTCTT
*
606031 CTTCTGGAATGTTTATATATGCTGTC
1 CTTCTGGAATGTTTATATATGCTGTA
**
606057 CTT-TTAAATGTTTATATAAGTGCT-TA
1 CTTCTGGAATGTTTATAT-A-TGCTGTA
606083 CTTCTGGAATGTT
1 CTTCTGGAATGTT
606096 ATCTGAGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 12 0.39
26 8 0.26
27 11 0.35
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (26 bp):
CTTCTGGAATGTTTATATATGCTGTA
Found at i:608012 original size:19 final size:19
Alignment explanation
Indices: 607988--608103 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
607978 AAAACAGACT
* *
607988 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
608007 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
608026 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
608045 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
608059 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
608078 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
608092 ATCGCAATGCGA
1 ATCGCAATGCGA
608104 TTTTCATTTC
Statistics
Matches: 87, Mismatches: 2, Indels: 18
0.81 0.02 0.17
Matches are distributed among these distances:
14 22 0.25
15 2 0.02
16 4 0.05
17 4 0.05
18 1 0.01
19 54 0.62
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:608058 original size:14 final size:14
Alignment explanation
Indices: 608041--608098 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
608031 AATGCGAAAT
608041 GAAAATCGCAACGA
1 GAAAATCGCAACGA
608055 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
608073 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
608088 GAAAATCGCAA
1 GAAAATCGCAA
608099 TGCGATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.28
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:608116 original size:33 final size:33
Alignment explanation
Indices: 607988--608103 Score: 169
Period size: 33 Copynumber: 3.4 Consensus size: 33
607978 AAAACAGACT
* *
607988 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
608026 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
608059 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
608092 ATCGCAATGCGA
1 ATCGCAATGCGA
608104 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
33 49 0.64
34 1 0.01
36 2 0.03
38 24 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:608147 original size:20 final size:20
Alignment explanation
Indices: 608122--608178 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
608112 TCGCATTGCG
*
608122 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
608142 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACC
*
608162 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
608179 GTCAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:609255 original size:24 final size:24
Alignment explanation
Indices: 609228--609281 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
609218 GTATTCGAAA
* *
609228 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
609252 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
609276 TTTGAT
1 TTTGAT
609282 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:611711 original size:19 final size:19
Alignment explanation
Indices: 611689--611818 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
611679 GAAATTACTT
611689 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
611708 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
611722 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
* **
611741 TCGCAA--CG--CT-AATT
1 TCGCAATGCGAAATGAAAA
611755 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
**
611774 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGAAAA
611788 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
611807 TCGCAACGCGAA
1 TCGCAATGCGAA
611819 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:611731 original size:33 final size:33
Alignment explanation
Indices: 611689--611814 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
611679 GAAATTACTT
611689 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
** *
611722 TCGCAATGCGAAATGAAAATCGCAACGCTA-ATT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
*
611755 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
611788 TCGCAATGCGAAATGAAAATCGCAACG
1 TCGCAATGCGAAATGAAAATCGCAACG
611815 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:611793 original size:66 final size:66
Alignment explanation
Indices: 611687--611821 Score: 252
Period size: 66 Copynumber: 2.0 Consensus size: 66
611677 CGGAAATTAC
*
611687 TTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTA
1 TTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGA
611752 A
66 A
*
611753 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGA
1 TTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGA
611818 A
66 A
611819 TTT
1 TTT
611822 AATTTCGCGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (66 bp):
TTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGA
A
Found at i:611836 original size:19 final size:20
Alignment explanation
Indices: 611814--611856 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
611804 AAATCGCAAC
611814 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
611833 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
611853 GCGA
1 GCGA
611857 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:611841 original size:14 final size:14
Alignment explanation
Indices: 611842--611875 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
611832 TGCGATTTTC
611842 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
611856 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
611870 ATTTTC
1 ATTTTC
611876 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:612016 original size:14 final size:14
Alignment explanation
Indices: 611997--612033 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
611987 CATCAATTAA
611997 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
612011 ACAAATCACCTTTT
1 ACAAATCAACTTTT
612025 ACAAATCAA
1 ACAAATCAA
612034 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:613456 original size:21 final size:21
Alignment explanation
Indices: 613390--613456 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
613380 GTGAATCGGG
*
613390 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
613410 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
613432 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
613453 CTCT
1 CTCT
613457 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:613475 original size:42 final size:41
Alignment explanation
Indices: 613390--613512 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
613380 GTGAATCGGG
* * * *
613390 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
613432 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
613474 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
613513 CGAGTCAGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:615542 original size:20 final size:19
Alignment explanation
Indices: 615511--615571 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
615501 TCTTTTGGTT
615511 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
615530 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
615551 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
615570 GA
1 GA
615572 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:615594 original size:33 final size:33
Alignment explanation
Indices: 615536--615623 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
615526 ACGAGATAAT
*
615536 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
615570 GAGAATCGCAACGCAAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
615603 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
615624 AAATCACAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:615628 original size:19 final size:19
Alignment explanation
Indices: 615606--615657 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
615596 GCGACCAGAC
*
615606 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
*
615625 AATCACAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
*
615645 AATCGCAATGCGA
1 AATCGCAACGCGA
615658 TTTTGGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:615679 original size:19 final size:19
Alignment explanation
Indices: 615657--615693 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
615647 TCGCAATGCG
*
615657 ATTTTGGTTTCGCGTTGCA
1 ATTTTGATTTCGCGTTGCA
*
615676 ATTTTTATTTCGCGTTGC
1 ATTTTGATTTCGCGTTGC
615694 GATTATCTCG
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:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (19 bp):
ATTTTGATTTCGCGTTGCA
Found at i:616300 original size:20 final size:20
Alignment explanation
Indices: 616252--616344 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
616242 CGCTATGTAA
*
616252 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
*
616272 ATCGAGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
* *** * *
616292 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-AAGTAAGT
* *
616313 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
616333 ATCGCATTGCGA
1 ATCGCGTTGCGA
616345 TTTTCCCAAT
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.77
21 13 0.23
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:616363 original size:21 final size:21
Alignment explanation
Indices: 616334--616426 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
616324 ATAGTAAGTA
616334 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
616355 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
616375 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
616396 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
616416 TCGCATTGCGA
1 TCGCATTGCGA
616427 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:616364 original size:41 final size:41
Alignment explanation
Indices: 616277--616407 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
616267 TCAGTATCGA
* * * ** *
616277 GTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATTATCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT-TCGC
*
616318 ATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
* **
616359 GTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAATTCGC
1 GTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTCGC
616400 GTTGCGAT
1 GTTGCGAT
616408 TTACTTATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 71 0.92
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
Found at i:616408 original size:41 final size:41
Alignment explanation
Indices: 616334--616426 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
616324 ATAGTAAGTA
616334 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
616375 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
616416 TCGCATTGCGA
1 TCGCATTGCGA
616427 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:617921 original size:19 final size:19
Alignment explanation
Indices: 617897--617933 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
617887 ATGACCAACA
*
617897 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
617916 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
617934 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:618021 original size:20 final size:20
Alignment explanation
Indices: 617962--618022 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
617952 TCCAGATTCA
*
617962 CAACGCGATTTTGACTATCG
1 CAACGCGATTATGACTATCG
* * *
617982 CAATGCGAATATGTA-AATCG
1 CAACGCGATTATG-ACTATCG
618002 CAACGCGATTATGACTATCG
1 CAACGCGATTATGACTATCG
618022 C
1 C
618023 GTTGCGATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
CAACGCGATTATGACTATCG
Found at i:618226 original size:22 final size:22
Alignment explanation
Indices: 618201--618243 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
618191 GGCGACATCC
618201 GTCCCAATCTCCGACGAAATCT
1 GTCCCAATCTCCGACGAAATCT
* *
618223 GTCCCTATCTCCGGCGAAATC
1 GTCCCAATCTCCGACGAAATC
618244 CATCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.23
Consensus pattern (22 bp):
GTCCCAATCTCCGACGAAATCT
Found at i:618664 original size:20 final size:20
Alignment explanation
Indices: 618639--618691 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
618629 CTATTTTAGT
618639 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
618659 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
618679 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
618692 TTTCATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:618697 original size:20 final size:20
Alignment explanation
Indices: 618659--618714 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
618649 GATAGTCAAA
* **
618659 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
618679 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
618699 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
618715 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:618721 original size:20 final size:20
Alignment explanation
Indices: 618678--618721 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
618668 CGATAGTCAT
* *
618678 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
618698 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
618718 TTTC
1 TTTC
618722 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:620346 original size:21 final size:21
Alignment explanation
Indices: 620303--620358 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
620293 TGGTGTATGG
* *
620303 CGTGATGAGGTATCCACTTTA
1 CGTGATGAGGTAGCCACTCTA
**
620324 CGTGATGAGGTAGCGGCTCTA
1 CGTGATGAGGTAGCCACTCTA
620345 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
620359 ATCGTTGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (21 bp):
CGTGATGAGGTAGCCACTCTA
Found at i:620651 original size:20 final size:20
Alignment explanation
Indices: 620628--620696 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
620618 GAAACTTAAA
620628 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
620648 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
620668 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
620688 ATCGCAACG
1 ATCGCAACG
620697 GGATAATCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:620725 original size:33 final size:34
Alignment explanation
Indices: 620688--620762 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
620678 GAATTTGACT
* *
620688 ATCGCAACGGGATAATCGTAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* * *
620721 ATCGCAACGTGAAAATTGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
*
620755 ATCACAAC
1 ATCGCAAC
620763 ACAAATTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 21 0.60
34 14 0.40
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:620805 original size:19 final size:20
Alignment explanation
Indices: 620768--620806 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
620758 ACAACACAAA
* *
620768 TTTAGTTTCGCGTTGTGATT
1 TTTAGTTTCGCATTATGATT
620788 TTTA-TTTCGCATTATGATT
1 TTTAGTTTCGCATTATGATT
620807 ATCTTGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (20 bp):
TTTAGTTTCGCATTATGATT
Found at i:620840 original size:20 final size:20
Alignment explanation
Indices: 620815--620859 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
620805 TTATCTTGTT
620815 GCGATAGTCATTTCCGCGTC
1 GCGATAGTCATTTCCGCGTC
* *
620835 GCGATAGTCATTTTCGCGTT
1 GCGATAGTCATTTCCGCGTC
620855 GCGAT
1 GCGAT
620860 TTTAAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
GCGATAGTCATTTCCGCGTC
Found at i:621432 original size:42 final size:42
Alignment explanation
Indices: 621373--621466 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
621363 CACTTGTCAT
621373 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAC
** *
621415 CGTTCAAGAGGCCCCTATCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
*
621457 CATTCAAGAG
1 CGTTCAAGAG
621467 CCTGATTCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:621439 original size:21 final size:21
Alignment explanation
Indices: 621369--621451 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
621359 GACTCACTTG
621369 TCATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
621390 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
621411 CCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
621432 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
621452 CCCACCATTC
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:621465 original size:21 final size:21
Alignment explanation
Indices: 621397--621466 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
621387 CTATCATCCC
621397 TCAAGA-GTCCCCTCCCACCGT
1 TCAAGAGGT-CCCTCCCACCGT
* ** *
621418 TCAAGAGGCCCCTATCATCGT
1 TCAAGAGGTCCCTCCCACCGT
* *
621439 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCACCGT
621460 TCAAGAG
1 TCAAGAG
621467 CCTGATTCAC
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAAGAGGTCCCTCCCACCGT
Found at i:622697 original size:20 final size:19
Alignment explanation
Indices: 622674--622719 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
622664 GGAAACTAAT
*
622674 TTGCGATACTGGAGATCGCA
1 TTGCGAT-CTAGAGATCGCA
*
622694 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
622713 TTGCGAT
1 TTGCGAT
622720 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:622709 original size:19 final size:19
Alignment explanation
Indices: 622685--622721 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
622675 TGCGATACTG
622685 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
622704 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
622722 TGTTGGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:624923 original size:20 final size:20
Alignment explanation
Indices: 624898--624937 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
624888 GTTTCAACAC
*
624898 TCGACTACTAATACTCTGAA
1 TCGACTACCAATACTCTGAA
*
624918 TCGACTACCAATCCTCTGAA
1 TCGACTACCAATACTCTGAA
624938 AAGTGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (20 bp):
TCGACTACCAATACTCTGAA
Found at i:637237 original size:19 final size:20
Alignment explanation
Indices: 637204--637247 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
637194 AATGAGTATT
637204 AATGAGTTCAAGTATGA-GTA
1 AATGAGTTCAAGTAT-ATGTA
637224 AATGAGTT-AAGTATATGTA
1 AATGAGTTCAAGTATATGTA
637243 AATGA
1 AATGA
637248 ATGAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (20 bp):
AATGAGTTCAAGTATATGTA
Found at i:637471 original size:20 final size:20
Alignment explanation
Indices: 637446--637500 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
637436 AGAATGTTAT
* *
637446 CAGGGTATCTATACTATAGG
1 CAGGGTATCTATACCATAGA
637466 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
*
637486 CAAGGTATCTATACC
1 CAGGGTATCTATACC
637501 TCAGTTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:638062 original size:22 final size:22
Alignment explanation
Indices: 638034--638081 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
638024 AAGGTTACAG
*
638034 TGGTCCTTCGGGATATATCCAA
1 TGGTCCTTCGGGACATATCCAA
*
638056 TGGTCCTTCGGGACATATCCAG
1 TGGTCCTTCGGGACATATCCAA
638078 TGGT
1 TGGT
638082 TATTTGGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (22 bp):
TGGTCCTTCGGGACATATCCAA
Found at i:639591 original size:11 final size:12
Alignment explanation
Indices: 639567--639602 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
639557 ATCGTGCTAA
639567 AGCTTTGAAAAG
1 AGCTTTGAAAAG
639579 AGCTTTGAAAGAG
1 AGCTTTGAAA-AG
*
639592 AGATTTGAAAA
1 AGCTTTGAAAA
639603 TTCAAGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (12 bp):
AGCTTTGAAAAG
Found at i:644295 original size:66 final size:67
Alignment explanation
Indices: 644151--644305 Score: 158
Period size: 66 Copynumber: 2.3 Consensus size: 67
644141 ATAATTTTTG
* **
644151 GTCA-TAGGGTATCGATATCATATGAAGGGGTATCGATACCTCCTTTTGAATGAAAAATTACAGA
1 GTCAGTAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCCTGAATGAAAAATTACAGA
644215 AT
66 AT
* * * * *
644217 GTCAGTATGGTATCGATACCCTAT-AGGGGGTATCGATACC-CC-CCTGAAGATGAAAATTTTCA
1 GTCAGTAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCCTG-A-ATGAAAAATTACA
644279 GAAT
64 GAAT
* *
644283 GTTA-TCAGGGTATCTATACCATA
1 GTCAGT-AGGGTATCGATACCATA
644306 GACAAGGTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
64 2 0.03
65 4 0.05
66 51 0.70
67 16 0.22
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (67 bp):
GTCAGTAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCCTGAATGAAAAATTACAGA
AT
Found at i:644316 original size:20 final size:20
Alignment explanation
Indices: 644291--644342 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
644281 ATGTTATCAG
644291 GGTATCTATACCATAGACAA
1 GGTATCTATACCATAGACAA
644311 GGTATCTATACCATAGACAA
1 GGTATCTATACCATAGACAA
*
644331 GGTATTTATACC
1 GGTATCTATACC
644343 TCAGTTAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (20 bp):
GGTATCTATACCATAGACAA
Found at i:644693 original size:18 final size:18
Alignment explanation
Indices: 644670--644713 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
644660 ATACATAATT
644670 TATTATGTTTTAATATGA
1 TATTATGTTTTAATATGA
644688 TATTATGTTTTAATATGA
1 TATTATGTTTTAATATGA
644706 TATTATGT
1 TATTATGT
644714 GAACGAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TATTATGTTTTAATATGA
Found at i:644922 original size:22 final size:22
Alignment explanation
Indices: 644894--644950 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
644884 AGGGTTACAG
644894 TGGTCCTTCGGGACATATCCAA
1 TGGTCCTTCGGGACATATCCAA
644916 TGGTCCTT-GAGGACATATCCAA
1 TGGTCCTTCG-GGACATATCCAA
*
644938 TGGTCATTCGGGA
1 TGGTCCTTCGGGA
644951 AAAATATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (22 bp):
TGGTCCTTCGGGACATATCCAA
Found at i:646196 original size:21 final size:23
Alignment explanation
Indices: 646158--646206 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
646148 AAAAACAATA
*
646158 TTTTTTATTTTGT-TAAAACTGT
1 TTTTTTATTTTGTAAAAAACTGT
*
646180 TTTTTTCTTTT-TAAAAAACTGT
1 TTTTTTATTTTGTAAAAAACTGT
*
646202 ATTTT
1 TTTTT
646207 ACGTGATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (23 bp):
TTTTTTATTTTGTAAAAAACTGT
Found at i:646758 original size:34 final size:34
Alignment explanation
Indices: 646715--646832 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
646705 TTCGTCATAC
646715 TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
* *
646749 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAAGATAGAA-TTT
*
646784 GCTAGGATTC-AA-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
* *
646814 TATGATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
646833 GATAGGATCC
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
28 6 0.09
29 2 0.03
30 3 0.04
31 13 0.19
34 32 0.46
35 3 0.04
36 2 0.03
37 8 0.12
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
Found at i:647379 original size:16 final size:18
Alignment explanation
Indices: 647358--647392 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
647348 TTTACTCATT
647358 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
647374 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
647392 T
1 T
647393 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:649528 original size:18 final size:18
Alignment explanation
Indices: 649505--649544 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
649495 TTCCTTCAAG
649505 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
649523 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
649541 TCTG
1 TCTG
649545 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:650065 original size:8 final size:8
Alignment explanation
Indices: 650052--650090 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
650042 GAACATTTCG
*
650052 TGCATTCT
1 TGCATTTT
650060 TGCA-TTT
1 TGCATTTT
650067 TGCATTTT
1 TGCATTTT
*
650075 TGCCTTTT
1 TGCATTTT
650083 TGCATTTT
1 TGCATTTT
650091 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:651279 original size:16 final size:16
Alignment explanation
Indices: 651240--651313 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
651230 AGATCCAATC
*
651240 AAGAACAAAAAAAAA-G
1 AAGAA-AAAAAAAAACA
*
651256 AAGTAAAAAAAAAACA
1 AAGAAAAAAAAAAACA
* *
651272 AAGAAAAAGAGAAAC-
1 AAGAAAAAAAAAAACA
*
651287 AAGAACAAAAAGAAAAAA
1 AAGAA-AAAAA-AAAACA
*
651305 AAGCAAAAA
1 AAGAAAAAA
651314 TCAAAAAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 14 0.31
16 20 0.44
17 7 0.16
18 4 0.09
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (16 bp):
AAGAAAAAAAAAAACA
Found at i:651303 original size:7 final size:7
Alignment explanation
Indices: 651240--651333 Score: 53
Period size: 7 Copynumber: 12.1 Consensus size: 7
651230 AGATCCAATC
651240 AAGAACAA
1 AAGAA-AA
*
651248 AAAAAAA
1 AAGAAAA
651255 GAAGTAAAA
1 -AAG-AAAA
*
651264 AAAAAACA
1 AAGAAA-A
651272 AAGAAAA
1 AAGAAAA
*
651279 AGAGAAAC
1 A-AGAAAA
651287 AAGAACAAA
1 AAG-A-AAA
651296 AAGAAAAAA
1 AAG--AAAA
*
651305 AAGCAAA
1 AAGAAAA
**
651312 AATCAAA
1 AAGAAAA
651319 AAGAAAA
1 AAGAAAA
651326 AAGAAAA
1 AAGAAAA
651333 A
1 A
651334 GGGACAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
7 31 0.45
8 21 0.30
9 15 0.22
10 2 0.03
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:652007 original size:21 final size:20
Alignment explanation
Indices: 651965--652007 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
651955 CATCAATCTT
*
651965 TTGAGCATCCAATGTCAACC
1 TTGAGCATCCAATGCCAACC
651985 TTGAGCAT-CAAGTGCCAAACC
1 TTGAGCATCCAA-TGCC-AACC
652006 TT
1 TT
652008 TGACCAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (20 bp):
TTGAGCATCCAATGCCAACC
Found at i:652965 original size:36 final size:36
Alignment explanation
Indices: 652922--653069 Score: 237
Period size: 36 Copynumber: 4.1 Consensus size: 36
652912 ACTAGAAGAG
652922 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
652958 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
652994 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
653030 --TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
653064 TATTTG
1 T-TTTG
653070 AATATGTTTA
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
34 31 0.31
36 67 0.66
37 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:653141 original size:36 final size:36
Alignment explanation
Indices: 653081--653196 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
653071 ATATGTTTAT
* * *
653081 TTGAAACAA-TTCCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAGTTTCGTCTCTCTTGAGACAGTTTCTC
*
653116 TTGGAACTAAGTTT-GTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAGTTTCGTCTCTCTTGAGACAGTTTCTC
* * *
653152 TTGAAACAATTTTCGTCTATCTTGAGACAGTTTCCC
1 TTGAAACAAGTTTCGTCTCTCTTGAGACAGTTTCTC
653188 TTGAAACAA
1 TTGAAACAA
653197 AACCTTGAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 11 0.16
36 57 0.81
37 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGAAACAAGTTTCGTCTCTCTTGAGACAGTTTCTC
Found at i:653155 original size:98 final size:97
Alignment explanation
Indices: 652984--653160 Score: 257
Period size: 98 Copynumber: 1.8 Consensus size: 97
652974 ACAGTTTCTC
* *
652984 TTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTGTCTCTCTTGAGACAGT
1 TTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTGTCTCTCTTGAGACAGT
653049 TTCCCTTGAAACAAATATTTGAATATGTTTAT
66 TTCCCTTGAAACAAATATTTGAATATGTTTAT
* ** * *
653081 TTGAAAC-AATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTGTCTCTCTTGAGACA
1 TTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATAA-ATTGTCTCTCTTGAGACA
*
653145 GTTTCTCTTGAAACAA
64 GTTTCCCTTGAAACAA
653161 TTTTCGTCTA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
96 25 0.36
97 13 0.19
98 32 0.46
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (97 bp):
TTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTGTCTCTCTTGAGACAGT
TTCCCTTGAAACAAATATTTGAATATGTTTAT
Found at i:653240 original size:64 final size:66
Alignment explanation
Indices: 653167--653327 Score: 191
Period size: 67 Copynumber: 2.5 Consensus size: 66
653157 ACAATTTTCG
* * *
653167 TCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTT-GAATTTATTTCCCCTAAAACA-AATTTT
1 TCTACCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTT
653230 A
66 A
* * * *
653231 TCTACCTTGAGACAGTTACTCTTGAAACCCAAATCTTCAAATTTATTTCCCTTAAAACATAATTT
1 TCTACCTTGAGACAGTTTCTCTTGAAA-CAAAACCTTCAAATTTATTTCCCCTAAAACATAATTT
*
653296 TG
65 TA
* * * *
653298 TTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TCTACCTTGAGACAGTTTCTCTTGAAACAA
653328 CAGATATCTT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 24 0.30
65 7 0.09
66 21 0.26
67 28 0.35
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (66 bp):
TCTACCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTT
A
Found at i:654266 original size:97 final size:101
Alignment explanation
Indices: 653931--654356 Score: 458
Period size: 102 Copynumber: 4.2 Consensus size: 101
653921 TTTCAACTCC
* *
653931 ACGAAGGATATCGTGGCACTCGAGGCAACACAA-TTC-ACTTCACAACGAA-GGACGCTGGTTGT
1 ACGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGCTGCTTGT
*
653993 CAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
63 CAA-CAACAACTTCTC-A-TTCAGAGCCAATTTCAACTT-ACA
* *
654036 ACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACGCTGCTTGTCA
1 ACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGCTGCTTGTCA
* *
654100 ACAACAACTTCCCAATCAGAGCCAATTTCAACTTCACA
65 ACAACAACTTCTCATTCAGAGCCAATTTCAACTT-ACA
* * * *
654138 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGCTTGTCA
1 ACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGCTGCTTGTCA
**
654203 ACAA-AA-TT-TCATTCAGATTCAATTTC-ACTT-CA
65 ACAACAACTTCTCATTCAGAGCCAATTTCAACTTACA
* *
654235 ACGAAGGATATTGGACTCGAGACAACACAAGTTAAACTTCACAACGAAGGGACTGCTGGTTGTCA
1 ACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC-GCTGCTTGTCA
* * * *
654300 ACAAACAA-TTCCCGGTTCCAGAACCAATTTCAACTTCACG
65 AC-AACAACTTCTC-ATT-CAGAGCCAATTTCAACTT-ACA
* *
654340 ATGGAGGATATTGGACT
1 ACGAAGGATATTGGACT
654357 TGGACAATGC
Statistics
Matches: 281, Mismatches: 25, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
96 1 0.00
97 61 0.22
98 2 0.01
99 8 0.03
100 15 0.05
101 6 0.02
102 95 0.34
103 29 0.10
104 22 0.08
105 42 0.15
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (101 bp):
ACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGCTGCTTGTCAA
CAACAACTTCTCATTCAGAGCCAATTTCAACTTACA
Found at i:654933 original size:33 final size:33
Alignment explanation
Indices: 654891--654957 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
654881 TTCGTCCTAC
654891 TAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
654924 TAGGATTCAAACTCCTAAAGATATGATAGAATT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATT
654957 T
1 T
654958 TGCTAGGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (33 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:655509 original size:17 final size:17
Alignment explanation
Indices: 655452--655510 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
655442 ACTTTTTTTT
655452 TTTAT-TATTTTACTTA
1 TTTATATATTTTACTTA
*
655468 TATATATATATGCTTTACTTT
1 T-T-TATATAT--TTTACTTA
*
655489 TTTATATATTTTACTCA
1 TTTATATATTTTACTTA
655506 TTTAT
1 TTTAT
655511 TATCTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 3 0.09
19 10 0.29
20 1 0.03
21 8 0.23
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTATATATTTTACTTA
Done.