Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007221.1 Hibiscus syriacus cultivar Beakdansim tig00019106_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: 131285
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4558 original size:20 final size:21
Alignment explanation
Indices: 4535--4576 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4525 TTTTTTGAAA
*
4535 TTTTGGCTTTTTTT-TTTTTT
1 TTTTGCCTTTTTTTGTTTTTT
4555 TTTTGCCTTTTTTTGTTTTTT
1 TTTTGCCTTTTTTTGTTTTTT
4576 T
1 T
4577 GTTTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (21 bp):
TTTTGCCTTTTTTTGTTTTTT
Found at i:6021 original size:20 final size:20
Alignment explanation
Indices: 5996--6141 Score: 139
Period size: 20 Copynumber: 6.7 Consensus size: 20
5986 TGACTGAAAT
*
5996 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
6016 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
6042 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
6062 ACATGAAAGAATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
6088 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
6108 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
6128 GCATGAAAGGATGC
1 GCATGAAAGGATGC
6142 CATAAATGAA
Statistics
Matches: 105, Mismatches: 9, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
20 61 0.58
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 28 0.27
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:6034 original size:90 final size:91
Alignment explanation
Indices: 5926--6121 Score: 304
Period size: 90 Copynumber: 2.2 Consensus size: 91
5916 TAACTAAAAT
* * * * *
5926 GCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGA-CCATGAC
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATAAAAGAAGCCATAAC
* *
5990 TGAAATGCATGAAATGATGCATTAAG
66 TAAAATGCATGAAAGGATGCATTAAG
*
6016 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATGAAAGAATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATAAAAGAA-GCCATAA
6081 CTAAAATGCATGAAAGGATGCATTAAG
65 CTAAAATGCATGAAAGGATGCATTAAG
6108 GCATGAAAGGATGC
1 GCATGAAAGGATGC
6122 ATTAAGGCAT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
90 52 0.54
92 44 0.46
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (91 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATAAAAGAAGCCATAAC
TAAAATGCATGAAAGGATGCATTAAG
Found at i:6059 original size:46 final size:46
Alignment explanation
Indices: 5926--6121 Score: 306
Period size: 46 Copynumber: 4.3 Consensus size: 46
5916 TAACTAAAAT
* *
5926 GCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* * * *
5972 GCATAAAAGGA--CCATGACTGAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
6016 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* *
6062 ACATGAAAGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
6108 GCATGAAAGGATGC
1 GCATGAAAGGATGC
6122 ATTAAGGCAT
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
44 40 0.29
46 96 0.71
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
Found at i:6101 original size:26 final size:25
Alignment explanation
Indices: 5898--6103 Score: 125
Period size: 26 Copynumber: 7.7 Consensus size: 25
5888 GCATGAAATG
*
5898 ATGCATTAAAGGATGGCATAACTAAA
1 ATGCATGAAAGGAT-GCATAACTAAA
5924 ATGCATGAAAGGATGTCATAACTAAA
1 ATGCATGAAAGGATG-CATAACTAAA
*
5950 ATGCATGAAATGATGCATTAAGGCATAAA
1 ATGCATGAAAGGATGCA-TAA--C-TAAA
* ** * *
5979 AGGACCATGACTGAAATGCATGAAATGATGCATTA
1 ATG--CATGAAAG-GATGCAT-AACT-A---A--A
*
6014 AGGCATGAAAGGATGCCATAACTAAA
1 ATGCATGAAAGGATG-CATAACTAAA
*
6040 ATGCATGAAAGGATGCAT---TAAG
1 ATGCATGAAAGGATGCATAACTAAA
*
6062 A--CATGAAAGAATGCCATAACTAAA
1 ATGCATGAAAGGATG-CATAACTAAA
6086 ATGCATGAAAGGATGCAT
1 ATGCATGAAAGGATGCAT
6104 TAAGGCATGA
Statistics
Matches: 141, Mismatches: 17, Indels: 45
0.69 0.08 0.22
Matches are distributed among these distances:
20 11 0.08
21 3 0.02
22 4 0.03
24 4 0.03
25 9 0.06
26 66 0.47
28 2 0.01
29 7 0.05
30 1 0.01
31 7 0.05
32 13 0.09
33 10 0.07
35 4 0.03
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (25 bp):
ATGCATGAAAGGATGCATAACTAAA
Found at i:12723 original size:46 final size:46
Alignment explanation
Indices: 12656--13069 Score: 702
Period size: 46 Copynumber: 9.0 Consensus size: 46
12646 AAAACGAATT
*
12656 CATAACTAAAATGCATGAAAGGATGCATTAAGCCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
12702 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
12748 CATTACTGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
12794 CATAACTGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
12840 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
12886 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
12932 CATAACTAAAATGTATGAAATGATGCATTAAGACATGAACGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
12978 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
13024 CATAACTAAAATGGATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
13070 ATTAAGGCAT
Statistics
Matches: 348, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 348 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.21
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:14312 original size:2 final size:2
Alignment explanation
Indices: 14301--14359 Score: 57
Period size: 2 Copynumber: 28.5 Consensus size: 2
14291 TTGAAATAAC
* * *
14301 TA TA -A TA TA TA TA TA TA TA TA TA TA TA AA CTT TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
14344 TA TA TA TA GTA TA TA T
1 TA TA TA TA -TA TA TA T
14360 GGTTTAGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14431 original size:11 final size:11
Alignment explanation
Indices: 14415--14531 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 11
14405 TAGATAATAG
14415 TATATAAACTA
1 TATATAAACTA
14426 TATATAAA-TA
1 TATATAAACTA
*
14436 -ATATATACTA
1 TATATAAACTA
14446 CT-TAT--ACTA
1 -TATATAAACTA
*
14455 TATGTAAACTA
1 TATATAAACTA
14466 TATAT--ACTA
1 TATATAAACTA
*
14475 TATAGT---TTA
1 TATA-TAAACTA
* *
14484 CATATGAACTA
1 TATATAAACTA
14495 TATGTATAAACTA
1 TA--TATAAACTA
14508 TATATAAAC--
1 TATATAAACTA
*
14517 TATGTAAACTA
1 TATATAAACTA
14528 TATA
1 TATA
14532 ATATAGTTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 28
0.68 0.08 0.23
Matches are distributed among these distances:
8 2 0.02
9 33 0.40
10 5 0.06
11 32 0.39
13 10 0.12
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.39
Consensus pattern (11 bp):
TATATAAACTA
Found at i:14675 original size:27 final size:28
Alignment explanation
Indices: 14592--14780 Score: 131
Period size: 27 Copynumber: 6.7 Consensus size: 28
14582 ATACTACATA
* * * *
14592 TATAAACTATATATATAAACTATA-ATT
1 TATATACTATATATATATAGTTTATATT
* *
14619 TATATACTATATA-CTATAGTTGATATT
1 TATATACTATATATATATAGTTTATATT
*
14646 TATATACTATATATATATAGTTTACA-T
1 TATATACTATATATATATAGTTTATATT
* *
14673 TAT-TACATATGAACTATATATA-TGGTATATAC
1 TATATAC-TAT--A-TATATATAGT-TTATAT-T
* * *
14705 TATATA-TAAACTATAATTTATATTTATATT
1 TATATACTATA-TAT-ATATA-GTTTATATT
*
14735 TATATACTATATAT-TATAGTTGATATT
1 TATATACTATATATATATAGTTTATATT
14762 TATATACTATATATATATA
1 TATATACTATATATATATA
14781 AACTATAGTT
Statistics
Matches: 127, Mismatches: 20, Indels: 29
0.72 0.11 0.16
Matches are distributed among these distances:
26 8 0.06
27 56 0.44
28 16 0.13
29 7 0.06
30 24 0.19
31 10 0.08
32 4 0.03
33 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (28 bp):
TATATACTATATATATATAGTTTATATT
Found at i:14798 original size:2 final size:2
Alignment explanation
Indices: 14578--14780 Score: 62
Period size: 2 Copynumber: 96.5 Consensus size: 2
14568 TATTTATAAA
* * * *
14578 AT AT AT ACT AC AT AT AT AA ACT AT AT AT AT AA ACT AT A- AT TT
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
*
14620 AT AT ACT AT AT ACT AT AGT -T GAT AT TT AT AT ACT AT AT AT AT AT
1 AT AT A-T AT AT A-T AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT
* * * *
14664 AGT TT AC AT -T AT -T AC AT AT GA- ACT AT AT AT AT GGT AT AT ACT
1 A-T AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT -AT AT AT A-T
* * * *
14706 AT AT AT AA ACT AT A- AT TT AT AT TT AT AT TT AT AT ACT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
14749 -T AT AGT -T GAT AT TT AT AT ACT AT AT AT AT AT A
1 AT AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT A
14781 AACTATAGTT
Statistics
Matches: 147, Mismatches: 28, Indels: 52
0.65 0.12 0.23
Matches are distributed among these distances:
1 8 0.05
2 114 0.78
3 25 0.17
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14811 original size:18 final size:18
Alignment explanation
Indices: 14773--14812 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14763 ATATACTATA
**
14773 TATATATAAACTATAGTT
1 TATATATAAACTATAAAT
*
14791 TATATATAAATTATAAAT
1 TATATATAAACTATAAAT
14809 TATA
1 TATA
14813 GTTGATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TATATATAAACTATAAAT
Found at i:14812 original size:25 final size:24
Alignment explanation
Indices: 14769--14820 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
14759 ATTTATATAC
* *
14769 TATATATATATAAACTATAGTTTA
1 TATATAAATATAAACTATAGTTGA
*
14793 TATATAAATTATAAATTATAGTTGA
1 TATATAAA-TATAAACTATAGTTGA
14818 TAT
1 TAT
14821 TTATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (24 bp):
TATATAAATATAAACTATAGTTGA
Found at i:14826 original size:60 final size:60
Alignment explanation
Indices: 14698--14843 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
14688 ATATATATGG
** * *
14698 TATATACTATATATAAACTATAATTTATATTTATATTTATATACTATATATTATAGTTGATATT
1 TATATACTATATAT--A-TATAAACTATATTTATA-TTATAAACTATAAATTATAGTTGATATT
*
14762 TATATACTATATATATATAAACTATAGTTTATA-TATAAATTATAAATTATAGTTGATATT
1 TATATACTATATATATATAAACTATA-TTTATATTATAAACTATAAATTATAGTTGATATT
* *
14822 TATATAATTTATACTATATAAA
1 TATATACTATATA-TATATAAA
14844 TTCTATATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
60 35 0.48
61 17 0.23
62 7 0.10
64 14 0.19
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (60 bp):
TATATACTATATATATATAAACTATATTTATATTATAAACTATAAATTATAGTTGATATT
Found at i:14871 original size:60 final size:60
Alignment explanation
Indices: 14742--14872 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
14732 ATTTATATAC
* * * *
14742 TATATATTATAGTTGATATTTATATACTATATATATATAAACTATAGTTTATATATAAAT
1 TATATATTATAGTTGATATTTATATAATATATATATATAAACTATAGTATAAATATAAAG
* * * *
14802 TATAAATTATAGTTGATATTTATATAATTTATACTATATAAATTCTA-TATAAAT-TCAAAG
1 TATATATTATAGTTGATATTTATATAATATATA-TATATAAACTATAGTATAAATAT-AAAG
14862 TATATATTATA
1 TATATATTATA
14873 TGTGTGAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 1 0.02
60 48 0.80
61 11 0.18
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (60 bp):
TATATATTATAGTTGATATTTATATAATATATATATATAAACTATAGTATAAATATAAAG
Found at i:14989 original size:13 final size:13
Alignment explanation
Indices: 14963--15016 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
14953 TATAGTTTAC
* *
14963 ATATGAACTATAT
1 ATATAAACTGTAT
*
14976 ATAAAAACTGTAT
1 ATATAAACTGTAT
*
14989 ATATATA-TGGTAT
1 ATATAAACT-GTAT
15002 ATATAAACTGTAT
1 ATATAAACTGTAT
15015 AT
1 AT
15017 TATATAGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 1 0.03
13 31 0.94
14 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (13 bp):
ATATAAACTGTAT
Found at i:15052 original size:18 final size:18
Alignment explanation
Indices: 14992--15069 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
14982 ACTGTATATA
*
14992 TATATGGTATATATAAAC
1 TATATAGTATATATAAAC
* **
15010 TGTATA-T-TATAT-AGT
1 TATATAGTATATATAAAC
15025 TCAT-TAGTATATATAAAC
1 T-ATATAGTATATATAAAC
15043 TATATAGTATATATAAA-
1 TATATAGTATATATAAAC
15060 TATATA-TATA
1 TATATAGTATA
15070 GTTCATTAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.08
16 11 0.23
17 14 0.29
18 19 0.40
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATAGTATATATAAAC
Found at i:15082 original size:26 final size:27
Alignment explanation
Indices: 15012--15084 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 27
15002 ATATAAACTG
* *
15012 TATATTATATAGTTCATTAG-TATATA
1 TATACTATATAGTTCATTAGATATAAA
*
15038 TAAACTATATAG-T-A-T--ATATAAA
1 TATACTATATAGTTCATTAGATATAAA
15060 TATA-TATATAGTTCATTAGATATAA
1 TATACTATATAGTTCATTAGATATAA
15085 CCTATATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
21 7 0.19
22 9 0.24
23 2 0.05
24 2 0.05
25 1 0.03
26 16 0.43
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TATACTATATAGTTCATTAGATATAAA
Found at i:15114 original size:24 final size:25
Alignment explanation
Indices: 15053--15119 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
15043 TATATAGTAT
* *
15053 ATATAAATATATATATAGTTCATTAG
1 ATATAAACATATAT-TAATTCATTAG
* *
15079 ATAT-AACCTATATTAATTTATTA-
1 ATATAAACATATATTAATTCATTAG
15102 ATATAAACATATATTAAT
1 ATATAAACATATATTAAT
15120 CGAAAGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.11
24 20 0.57
25 7 0.20
26 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (25 bp):
ATATAAACATATATTAATTCATTAG
Found at i:15231 original size:61 final size:61
Alignment explanation
Indices: 15148--15287 Score: 212
Period size: 61 Copynumber: 2.3 Consensus size: 61
15138 TATAAGGATC
*
15148 AAATT-AAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
1 AAATTGAAACAAA-TTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTAGACT
* * * *
15209 AAATTGAAAGAAATTTAGATATGAAGCTTAAATTAATACATTGCATCATTAAATTTAGACT
1 AAATTGAAACAAATTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTAGACT
15270 AAATTG-AACAAATTTAAA
1 AAATTGAAACAAATTTAAA
15288 ATTAGGAGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
60 10 0.14
61 55 0.77
62 6 0.08
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (61 bp):
AAATTGAAACAAATTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTAGACT
Found at i:15700 original size:101 final size:102
Alignment explanation
Indices: 15579--15786 Score: 330
Period size: 101 Copynumber: 2.0 Consensus size: 102
15569 ACACCAAAAA
* *
15579 TTCATCAATGTTCATCCCAAAAATCATCTTTTGATCTTCACAAACACCAAAACCCAAACCATTTC
1 TTCATCAATGTTCATCCCAAAAACCATCCTTTGATCTTCACAAACACCAAAACCCAAACCATTTC
* *
15644 GTGTTTTT-TATCAAACACCCAAAAATTCAACCCTTG
66 GTGTTTTTCGATCAAACACCCAAAAATTCAACCATTG
* *
15680 TTCATCCATGCTT-ATCCCAAAAACCCTCCTTTGATCTTCACAAACACCAAAACCCAAACCATTT
1 TTCATCAATG-TTCATCCCAAAAACCATCCTTTGATCTTCACAAACACCAAAACCCAAACCATTT
*
15744 CGTGTTTTTCGATCAAACACTCAAAAATTCAACCATTG
65 CGTGTTTTTCGATCAAACACCCAAAAATTCAACCATTG
15782 TTCAT
1 TTCAT
15787 TCGTGTTCAT
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 66 0.67
102 32 0.33
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (102 bp):
TTCATCAATGTTCATCCCAAAAACCATCCTTTGATCTTCACAAACACCAAAACCCAAACCATTTC
GTGTTTTTCGATCAAACACCCAAAAATTCAACCATTG
Found at i:15926 original size:112 final size:111
Alignment explanation
Indices: 15709--15919 Score: 248
Period size: 112 Copynumber: 1.9 Consensus size: 111
15699 AAAACCCTCC
*
15709 TTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTGTTTTTCGATCAAACACTCAAAAATTC
1 TTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTGTTTTTCGATCAAACACTCAAAAATTA
* *** *
15774 AACCATTGTTCATTCGTGTTCATCTCAGTTCTTCCCCAAACCATTA
66 AACCATTGTTCATTCGTGTTCATCCCAAACCTTCCACAAACCATTA
** * *
15820 TTTGATCTTCACAAACACCAAAACTTAAA-CTTATTCTTGTTTTTTCGATCAAACAAC-CAAAAA
1 TTTGATCTTCACAAACACCAAAACCCAAACCAT-TTCGTG-TTTTTCGATCAAAC-ACTCAAAAA
* *
15883 TTAAACCCTTGTTCA-TCTGTGTTCTTCCCCAAACCTT
63 TTAAACCATTGTTCATTC-GTGTTCAT-CCCAAACCTT
15920 TACAAACACC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
110 2 0.02
111 34 0.40
112 40 0.48
113 8 0.10
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (111 bp):
TTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTGTTTTTCGATCAAACACTCAAAAATTA
AACCATTGTTCATTCGTGTTCATCCCAAACCTTCCACAAACCATTA
Found at i:16123 original size:18 final size:18
Alignment explanation
Indices: 16096--16160 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
16086 CCCAAACCCT
16096 AACCAGAACCCAAACTCGA
1 AACCA-AACCCAAACTCGA
* *
16115 AACCAAACCCGAACCCGA
1 AACCAAACCCAAACTCGA
**
16133 TTCCAAACCCAAACTCGA
1 AACCAAACCCAAACTCGA
*
16151 ACCCAAACCC
1 AACCAAACCC
16161 GAATCTACAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 33 0.87
19 5 0.13
ACGTcount: A:0.43, C:0.43, G:0.08, T:0.06
Consensus pattern (18 bp):
AACCAAACCCAAACTCGA
Found at i:16130 original size:36 final size:36
Alignment explanation
Indices: 16084--16163 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
16074 CATCTTCTCT
* *
16084 AACCCAAACCCTA-ACCAGAACCCAAACTCGAAACCA
1 AACCCGAACCCGATACCA-AACCCAAACTCGAAACCA
* *
16120 AACCCGAACCCGATTCCAAACCCAAACTCGAACCCA
1 AACCCGAACCCGATACCAAACCCAAACTCGAAACCA
16156 AACCCGAA
1 AACCCGAA
16164 TCTACACTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 36 0.92
37 3 0.08
ACGTcount: A:0.44, C:0.42, G:0.07, T:0.06
Consensus pattern (36 bp):
AACCCGAACCCGATACCAAACCCAAACTCGAAACCA
Found at i:17277 original size:19 final size:19
Alignment explanation
Indices: 17253--17291 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17243 TTATAATATT
*
17253 AGAATTATAAATAATATAA
1 AGAATTAGAAATAATATAA
* *
17272 AGAATTGGAATTAATATAA
1 AGAATTAGAAATAATATAA
17291 A
1 A
17292 AAACCAAATT
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:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (19 bp):
AGAATTAGAAATAATATAA
Found at i:21218 original size:17 final size:17
Alignment explanation
Indices: 21196--21228 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21186 TAATTACGAA
21196 TAAATACATTTATAACG
1 TAAATACATTTATAACG
21213 TAAATACATTTATAAC
1 TAAATACATTTATAAC
21229 TAGTGTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATACATTTATAACG
Found at i:21562 original size:17 final size:17
Alignment explanation
Indices: 21529--21574 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
21519 TTTTGTCCAG
21529 ATTATTATTTAATATTATA
1 ATTATTA-TT-ATATTATA
*
21548 ATTATTATTATATTATT
1 ATTATTATTATATTATA
21565 ATTATTATTA
1 ATTATTATTA
21575 AATTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
18 2 0.08
19 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTATTATATTATA
Found at i:21582 original size:27 final size:30
Alignment explanation
Indices: 21529--21588 Score: 90
Period size: 27 Copynumber: 2.1 Consensus size: 30
21519 TTTTGTCCAG
21529 ATTATTATTTAATATTATAATTATTATTAT
1 ATTATTATTTAATATTATAATTATTATTAT
*
21559 ATTATTA-TTATTATTA-AATT-TTATTAT
1 ATTATTATTTAATATTATAATTATTATTAT
21586 ATT
1 ATT
21589 TGTAGGCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 10 0.34
28 4 0.14
29 8 0.28
30 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTATTATTTAATATTATAATTATTATTAT
Found at i:21585 original size:3 final size:3
Alignment explanation
Indices: 21529--21574 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
21519 TTTTGTCCAG
* *
21529 ATT ATT ATTT AAT ATT ATA ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21574 A
1 A
21575 AATTTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:23374 original size:15 final size:16
Alignment explanation
Indices: 23333--23374 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
23323 TCGAACAAAA
*
23333 TAATATATTTTATTTT
1 TAATATATTTTAGTTT
*
23349 TGAATAAATTTT-GTTT
1 T-AATATATTTTAGTTT
23365 TAATATATTT
1 TAATATATTT
23375 AATATATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TAATATATTTTAGTTT
Found at i:31433 original size:257 final size:257
Alignment explanation
Indices: 30871--32079 Score: 1503
Period size: 257 Copynumber: 4.7 Consensus size: 257
30861 AACTTGTTTT
* * * *
30871 AAAAATGAGAAATCGATTTCCAAAGTTTCTTATTTAATATTTTCAAAAAATGAAATTTTTGAAAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
*
30936 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAG-CCATTCG
66 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCC-TTCG
* * * * * *
31000 -GACCATTAGTAAGTTTTTTGAGCATGATG-TTAAATCCTTC-GAGTCT-TCTATAAGTCCTTCG
130 AG-CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGA-T-TATCTGTAACTCTTTCG
* * * **
31061 AGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCT-GGATGTTTTCACATGATTT
192 AGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-GGGTAGGATGTTTTCACATGAACT
*
31125 TG
256 CG
* *
31127 AAAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAAAGTTTCTCAGAAAATGAAATTTTTGAAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTT-TCAGAAAATGAAATTTTTGAAA
* * *
31192 AGTAAGAAAGCAATTTCTAAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTCCTTCG
65 AGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* * * *
31257 AGCTATCAGTAAGTCTTTCGAGAATGATGCTTAAATCCTTCGGATTATCTGTAACTCTTTTGAGC
130 AGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGATTATCTGTAACTCTTTCGAGC
* *
31322 AAGATGATAAGTCCTTCGGGCCATCCGTAAGAACTTCGGGTAGGATGTTTTCACATGAACTCG
195 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAACTCG
* ** * *
31385 AAAAATAAGAAAGCGATTTCCATTGTTTCTCATTTAATGTTTTCAGAAAATAAAATCTTTGAAAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* *
31450 GTAAGAAAGCGATTTCCAAAGTTTCATACCTAGTAAATTATTTCCAAAATTTGTAAGTCCTTC-A
66 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCGA
* * * * * * * * * * *
31514 GGCCATTAGTAAGTCTTTGGACCATGATGCTTGAATCCTTCGGGTCATCTATAAGTCTTTTGAAC
131 -GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGATTATCTGTAACTCTTTCGAGC
*
31579 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTACGATGTTTTCACATGAACTTCG
195 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAAC-TCG
* * * *
31643 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAAGTTCTCAAAAAATGAAATTTTAGAAAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* * *
31708 GTAAGAAATCGATTTCCAAAGTTTCTTA-CCAGTAAAATATTTCCAAAATTTGTAAGTCCTTCGG
66 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCGA
** * *
31772 GCCATCAACAAGTCTTTCGAGCATGATGATTAAATCCTTCGTG-TCATTTGTAAGC-CTTTCGAG
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG-GATTATCTGTAA-CTCTTTCGAG
** * * * * *
31835 TGAGATGATAAGTCCTTC-GGTCATCCGTAAGACCTTTGGGTATGG-TGTTTTCACATGAATTTT
194 CAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTA-GGATGTTTTCACATGAA-CTC
31898 G
257 G
* *
31899 AAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATCTTTAT-AGAAAACT-AAATTTTTGAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTT-TCAGAAAA-TGAAATTTTTGAA
* * * * *
31962 AAGTAAGAAAG-TAGTTTCCAAAGTGTCTTACCCAGTAAAATATTTTCAAAATTAGTAAGTCCTT
64 AAGTAAGAAAGCGA-TTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTT
* * *
32026 CGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGTTATCTGT
128 CGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGATTATCTGT
32080 CAGTCTCACT
Statistics
Matches: 831, Mismatches: 103, Indels: 37
0.86 0.11 0.04
Matches are distributed among these distances:
255 1 0.00
256 154 0.19
257 471 0.57
258 203 0.24
259 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (257 bp):
AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCGA
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGATTATCTGTAACTCTTTCGAGCA
AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAACTCG
Found at i:34193 original size:16 final size:16
Alignment explanation
Indices: 34154--34196 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
34144 TCGAACAAAA
34154 TAATATATTTTATTTT
1 TAATATATTTTATTTT
34170 TGAATATATTTT-TGTTT
1 T-AATATATTTTAT-TTT
34187 TAATATATTT
1 TAATATATTT
34197 AATATACGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (16 bp):
TAATATATTTTATTTT
Found at i:36840 original size:258 final size:255
Alignment explanation
Indices: 36381--37252 Score: 1135
Period size: 258 Copynumber: 3.4 Consensus size: 255
36371 GATATTTTTA
* *
36381 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCT
1 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTCAT
* *
36446 TTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
66 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
* * * * * *
36511 AGCAAGATGATAAGTCCTTCAGGCCATTCGTAAGATCTTCAGATAGGATGTTTTCACATGAACTT
131 AGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAACTT
*
36576 CGAAAAATGAGAAATCATTTTCCAATGTTTCTCATTTAGTGTTTTCATAAAATGAAATCTTTG
196 CGAAAAATGAGAAAGCA-TTTCCAATGTTTCTCATTTA-TGTTTTCA-AAAATGAAATCTTTG
* * * *
36639 AAAAGTAAGAAAGTGACTTCCGAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTAAT
1 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTCAT
* * *
36704 TTGGTCCATCAGGAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
66 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
* * *
36769 AGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGACGTTTTCACATGAACTC
131 AGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAACTT
*
36834 CGAAAAATAAGAAAGCGATTTCCAATGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTG
196 CGAAAAATGAGAAAGC-ATTTCCAATGTTTCTCATTT-ATGTTTTCA-AAAATGAAATCTTTG
* *
36897 AAAAGTAAGAAAGCGATTTCCAAAATTTATTACCC-ATAAAATTATTTCCAAAATTTGTAAGTCA
1 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAT-AAATTATTTCCAAAATTTGTAAGTCA
* * *
36961 TTCGGGCCATCAATAATTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATATGTAAGTCTTTC
65 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTC
* * * * *
37026 GATCAAGATGATAAGTTCTTTGGGCAATCTATAAGACCTTCGGGCTA-GATGTTTTCACATG-A-
130 GAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGG-TAGGATGTTTTCACATGAAC
** * * *
37088 TTTTAAAAATGAGAAAGCAATTTGCAAAGTTTCTC----A-G------AAAATGAAATTTTTG
194 TTCGAAAAATGAGAAAGC-ATTTCCAATGTTTCTCATTTATGTTTTCAAAAATGAAATCTTTG
* * * * ** *
37140 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAATTTTTTCCAAAATTAATAAGTCCT
1 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTCAT
* * *
37205 TCGGGCTATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGT
66 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
37253 TATATGTCAG
Statistics
Matches: 547, Mismatches: 62, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
243 111 0.20
244 1 0.00
250 1 0.00
251 1 0.00
256 28 0.05
257 3 0.01
258 398 0.73
259 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (255 bp):
AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAAGTCAT
TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
AGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAACTT
CGAAAAATGAGAAAGCATTTCCAATGTTTCTCATTTATGTTTTCAAAAATGAAATCTTTG
Found at i:43194 original size:3 final size:3
Alignment explanation
Indices: 43186--43236 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
43176 TTTGTCTGGG
*
43186 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTT TTA TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A
43232 TTA TT
1 TTA TT
43237 TTTGCAGGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:48760 original size:14 final size:14
Alignment explanation
Indices: 48741--48770 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48731 TTTAGATTTT
*
48741 TTAAAATTACATTA
1 TTAAAAATACATTA
48755 TTAAAAATACATTA
1 TTAAAAATACATTA
48769 TT
1 TT
48771 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:49646 original size:7 final size:7
Alignment explanation
Indices: 49631--49676 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
49621 AATTATGTGA
49631 TAGGGTT
1 TAGGGTT
*
49638 TATGGTT
1 TAGGGTT
*
49645 TAGGGAT
1 TAGGGTT
*
49652 TATGGTT
1 TAGGGTT
49659 TAGGGTT
1 TAGGGTT
*
49666 TGGGGTT
1 TAGGGTT
49673 TAGG
1 TAGG
49677 TTTTGAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
TAGGGTT
Found at i:49648 original size:14 final size:14
Alignment explanation
Indices: 49631--49676 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
49621 AATTATGTGA
49631 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
*
49645 TAGGGATTATGGTT
1 TAGGGTTTATGGTT
**
49659 TAGGGTTTGGGGTT
1 TAGGGTTTATGGTT
49673 TAGG
1 TAGG
49677 TTTTGAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.43
Consensus pattern (14 bp):
TAGGGTTTATGGTT
Found at i:51622 original size:22 final size:22
Alignment explanation
Indices: 51579--51622 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
51569 AAATTTACAT
*
51579 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
51601 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
51623 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:53694 original size:3 final size:3
Alignment explanation
Indices: 53686--53752 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
53676 CAAAAATTTG
* * **
53686 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53730 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
53753 CGAAAAGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:54052 original size:40 final size:41
Alignment explanation
Indices: 53904--54193 Score: 179
Period size: 40 Copynumber: 6.9 Consensus size: 41
53894 TTTTGTTGGT
* * ** *
53904 GGGGACGACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC-A
* * * *
53948 AGGG-TGACACGGCTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-A
53991 -GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
* *
54028 GGGGAATGATACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---A
* * * * * *
54075 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-A
54119 -GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
*
54156 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG
54194 CCATCTAAAG
Statistics
Matches: 198, Mismatches: 31, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
38 6 0.03
39 4 0.02
40 61 0.31
41 2 0.01
42 55 0.28
43 33 0.17
44 5 0.03
46 28 0.14
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (41 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
Found at i:54118 original size:46 final size:44
Alignment explanation
Indices: 53911--54245 Score: 161
Period size: 40 Copynumber: 7.8 Consensus size: 44
53901 GGTGGGGACG
* ** * *
53911 ACACTGCTCATACGCAATGAAGAG-GTCTGGTCATCTAAGG-G-TG
1 ACACGGCTCATACGTGATGAAGAGAG-CTGGTTATCT-AGGTGATA
* * *
53954 ACACGGCTCCTACGTGATGAGGACG-GCTGGTTATCTAGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGTGATA
* * *
53996 ACACGGCTCATACGTGATGAAGAGATCTGG---TC--GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGTG-ATA
* ** **
54036 ATACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGGTGATA
* * * *
54082 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGTGATA
* * *
54124 ACACGGCTCATACGTGATGAAGAGATCTGG---TC--GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGTG-ATA
** **
54164 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGGTGATA
* * *
54210 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCT
54246 CTAGGGATAA
Statistics
Matches: 233, Mismatches: 34, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
37 4 0.02
38 2 0.01
39 4 0.02
40 61 0.26
41 2 0.01
42 56 0.24
43 32 0.14
44 5 0.02
46 59 0.25
47 8 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (44 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGTGATA
Found at i:54141 original size:128 final size:128
Alignment explanation
Indices: 53910--54245 Score: 579
Period size: 128 Copynumber: 2.6 Consensus size: 128
53900 TGGTGGGGAC
* ** * * * *
53910 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
53972 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
*
54035 GATACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
54100 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
54163 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
54228 GAGGACGGCTGGTTATCT
66 GAGGACGGCTGGTTATCT
54246 CTAGGGATAA
Statistics
Matches: 199, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
125 31 0.16
126 4 0.02
127 1 0.01
128 163 0.82
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (128 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
Found at i:54394 original size:38 final size:37
Alignment explanation
Indices: 54351--54449 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 37
54341 GACAAAATTC
*
54351 GTTTCAAGAGAAAC-GATCTCAAAGATATTAGTTT-TTTT
1 GTTTCAAGGGAAACAGAT-TCAAAGATA-T-GTTTGTTTT
54389 GTTTCAAGGGAAACAGATTCAAAG--ATGTTTGTTTT
1 GTTTCAAGGGAAACAGATTCAAAGATATGTTTGTTTT
54424 GTTTCAAGGGAAACAGATTCAAAGAT
1 GTTTCAAGGGAAACAGATTCAAAGAT
54450 GGTAAATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
34 4 0.07
35 29 0.52
36 1 0.02
38 19 0.34
39 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (37 bp):
GTTTCAAGGGAAACAGATTCAAAGATATGTTTGTTTT
Found at i:54431 original size:35 final size:35
Alignment explanation
Indices: 54381--54485 Score: 133
Period size: 35 Copynumber: 3.0 Consensus size: 35
54371 AAAGATATTA
54381 GTTTTTTTGTTTCAAGGGAAACAGATTCAAAGAT-
1 GTTTTTTTGTTTCAAGGGAAACAGATTCAAAGATG
54415 GTTTGTTTTGTTTCAAGGGAAACAGATTCAAAGATG
1 GTTT-TTTTGTTTCAAGGGAAACAGATTCAAAGATG
** * *
54451 GTAAATTTTGTTTCCAA-AGAAACAGACTCAAAGAT
1 GT-TTTTTTGTTT-CAAGGGAAACAGATTCAAAGAT
54486 TTTTCTCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
34 4 0.06
35 30 0.48
36 26 0.41
37 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (35 bp):
GTTTTTTTGTTTCAAGGGAAACAGATTCAAAGATG
Found at i:54768 original size:15 final size:15
Alignment explanation
Indices: 54725--54768 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
54715 AAGATGTTCT
*
54725 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
54740 TGTTTCAAAAGAAAA
1 TGTTTCAAGAGAAAA
*
54755 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
54769 CGACTCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:55303 original size:37 final size:37
Alignment explanation
Indices: 55252--55372 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 37
55242 ATTCAAAGAT
55252 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
* ** * * *
55289 TTTTGTTTCCAAAGAAACAAAC-TCA-A-AG----AT
1 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
55319 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
*
55356 TTTTGTTTCCAAAGAAA
1 TTTTGTTTCAAAAGAAA
55373 CAAACTCAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
30 19 0.30
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 2 0.03
37 35 0.55
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (37 bp):
TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
Found at i:55305 original size:67 final size:67
Alignment explanation
Indices: 55234--55402 Score: 320
Period size: 67 Copynumber: 2.5 Consensus size: 67
55224 TCATTTTAAG
* *
55234 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
55299 AA
66 AA
55301 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
55366 AA
66 AA
55368 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
55403 CAATCTCAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 100 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:55323 original size:30 final size:30
Alignment explanation
Indices: 55289--55419 Score: 127
Period size: 30 Copynumber: 4.1 Consensus size: 30
55279 AGAGACAAAA
*
55289 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
** * * *
55319 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG----AT
*
55356 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
55386 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
55416 TTTT
1 TTTT
55420 TTCCGCAAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
30 51 0.64
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 19 0.24
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:55553 original size:28 final size:29
Alignment explanation
Indices: 55507--55801 Score: 249
Period size: 29 Copynumber: 10.0 Consensus size: 29
55497 CAAAACTTCG
* * *
55507 TTTCAAAATAAATAGACTCAAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
55536 TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
* * *
55564 ATTCAAAAGGAACAAACTCCAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
* *
55593 ATTCAAAAGGAACAAACTCAAAGA-TTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
* *
55621 TTTCAAGAGGAACAAACTCAAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
** *** * *
55650 CCTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAACAAACTC-A-A-AG-----ATTTTT
* * *
55687 TTTCAAAATAAATAGACTCAAAGA-TTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
*
55715 TTTCAAAAGAAAC-AACTCAAAGATATTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
* * *
55743 ATTCAAAAGGAACAAACTCCAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTT
*
55772 ATTCAAAATG-AACAAACTCAAAGATTTTT
1 TTTCAAAA-GAAACAAACTCAAAGATTTTT
55801 T
1 T
55802 CAAGAGAAAC
Statistics
Matches: 218, Mismatches: 35, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
27 9 0.04
28 79 0.36
29 104 0.48
30 2 0.01
31 1 0.00
32 2 0.01
34 2 0.01
35 1 0.00
36 1 0.00
37 17 0.08
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTTCAAAAGAAACAAACTCAAAGATTTTT
Found at i:55749 original size:56 final size:56
Alignment explanation
Indices: 55687--55811 Score: 148
Period size: 56 Copynumber: 2.2 Consensus size: 56
55677 CAAAACTTTG
* * *
55687 TTTCAAAATAAATAGACTCAAAGATTTTT-TTCAAAA-GAA-ACAACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAATGAACA-AACTCAAAGAT-TT
* *
55742 TATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAATGAACAAACTCAAAGATTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTT
*
55799 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
55812 TGTCTCAAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
55 1 0.02
56 33 0.56
57 10 0.17
58 14 0.24
59 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (56 bp):
TTTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTT
Found at i:55787 original size:179 final size:179
Alignment explanation
Indices: 55478--55807 Score: 608
Period size: 179 Copynumber: 1.8 Consensus size: 179
55468 GACTTTTCAC
*
55478 GAAATTGTCTCAAGAGAGACAAAACTTCGTTTCAAAATAAATAGACTCAAAGATTTTTTTTCAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTCGTTTCAAAATAAATAGACTCAAAGATTTTTTTTCAAA
*
55543 AGAAACAACTCAAAGATTTTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
66 AGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
55608 ACTCAAAGATTTTTTTCAAGAGGAACAAACTCAAAGATTTTTCCTCAAAA
131 ACTCAAAGA-TTTTTTCAAGAGGAACAAACTCAAAGATTTTTCCTCAAAA
*
55658 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGA-TTTTTTTCAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTCGTTTCAAAATAAATAGACTCAAAGATTTTTTTTCAAA
*
55722 AGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAATGAACAA
66 AGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
55787 ACTCAAAGATTTTTTCAAGAG
131 ACTCAAAGATTTTTTCAAGAG
55808 AAACTGTCTC
Statistics
Matches: 146, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
178 12 0.08
179 83 0.57
180 51 0.35
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (179 bp):
GAAACTGTCTCAAGAGAGACAAAACTTCGTTTCAAAATAAATAGACTCAAAGATTTTTTTTCAAA
AGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
ACTCAAAGATTTTTTCAAGAGGAACAAACTCAAAGATTTTTCCTCAAAA
Found at i:56137 original size:36 final size:36
Alignment explanation
Indices: 56053--56157 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 36
56043 GAGAAAATGA
* * *
56053 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
* **
56087 AGTCTCAAATGAGACAAAATTTGTTTTTAGAAAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
*
56123 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AGAAAA
56158 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 20 0.34
35 4 0.07
36 28 0.48
37 6 0.10
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
Found at i:56165 original size:36 final size:33
Alignment explanation
Indices: 56054--56172 Score: 112
Period size: 36 Copynumber: 3.4 Consensus size: 33
56044 AGAAAATGAT
* * *
56054 GTCTCAAGCGAGACAAAATTTGCTTTAAGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-AAA
**
56088 GTCTCAAATGAGACAAAATTTGTTTTTAGAAAAA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAG-AAAA
*
56122 TTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAA
1 --GTCTCAAGCGAGACAAAATTTGTTTTT-AGAAAA
*
56158 CGATCTCAAGTGAGA
1 -G-TCTCAAGCGAGA
56173 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
34 27 0.39
35 2 0.03
36 39 0.56
37 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (33 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAAAA
Found at i:56303 original size:105 final size:101
Alignment explanation
Indices: 56124--56356 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 101
56114 TAGAAAAATT
*
56124 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAAT
* *
56188 GTGAAACAAATTCGAAATTTAG-ATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTT-GTATCTCAAAGGAAAAAG
* *
56226 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AGAAA-AAG-ATCTCAA-GTGAGATCAACTTTGTTT
* * *
56290 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
*
56331 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
56357 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 8 0.07
104 6 0.05
105 77 0.68
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:58000 original size:13 final size:12
Alignment explanation
Indices: 57966--58001 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
57956 CACTTTCTCT
57966 TTTTTTCTTTGA
1 TTTTTTCTTTGA
*
57978 TTTTTGCTTTGA
1 TTTTTTCTTTGA
57990 TTTTTCTCTTTG
1 TTTTT-TCTTTG
58002 CTCTTTGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:58018 original size:25 final size:24
Alignment explanation
Indices: 57963--58023 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
57953 GTCCACTTTC
* *
57963 TCTTTTTTTCTTTGATTTTTGCTT
1 TCTTTTTCTCTTTGATCTTTGCTT
* *
57987 TGATTTTTCTCTTTGCTCTTTGCTCT
1 T-CTTTTTCTCTTTGATCTTTGCT-T
58013 TC-TTTTCTCTT
1 TCTTTTTCTCTT
58024 CGCTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 10 0.33
25 18 0.60
26 2 0.07
ACGTcount: A:0.03, C:0.20, G:0.08, T:0.69
Consensus pattern (24 bp):
TCTTTTTCTCTTTGATCTTTGCTT
Found at i:58701 original size:26 final size:26
Alignment explanation
Indices: 58624--58702 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
58614 TTTCAAGGTG
58624 GAAAGAA-ATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
58649 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
58670 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
58695 GATAGAAT
1 GAAAGAAT
58703 GTCAAAATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 13
0.67 0.12 0.22
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 7 0.17
26 14 0.35
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.23
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:58703 original size:46 final size:44
Alignment explanation
Indices: 58612--58704 Score: 141
Period size: 46 Copynumber: 2.1 Consensus size: 44
58602 ATAAATACAG
* *
58612 TGTTTCAAGGTGGAAAGAAATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAAATTTCAAGGTCTCAAAGAGAGAGAA
*
58656 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAA-ATTTCAAGGTCTCAAAGAGAGAGAA
58702 TGT
1 TGT
58705 CAAAATTGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 11 0.25
45 7 0.16
46 26 0.59
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (44 bp):
TGTTTCAAGGTGAAAAGAAATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:62537 original size:22 final size:22
Alignment explanation
Indices: 62494--62537 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
62484 AAATTTACAT
*
62494 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
62516 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
62538 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:64603 original size:3 final size:3
Alignment explanation
Indices: 64595--64658 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
64585 CAAAAATTTG
* * **
64595 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64639 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
64659 CGAAAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:65951 original size:23 final size:23
Alignment explanation
Indices: 65921--65975 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
65911 TTTTTATAGG
*
65921 ATCGAGCTCAAAAACGAGCTTGA
1 ATCGAGCTCAAAAACGAGCTTCA
65944 ATCGAGCTCAAAAACGAGCTTCA
1 ATCGAGCTCAAAAACGAGCTTCA
65967 ATCGAGCTC
1 ATCGAGCTC
65976 GAGTCTAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
ATCGAGCTCAAAAACGAGCTTCA
Found at i:82973 original size:15 final size:15
Alignment explanation
Indices: 82949--82978 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82939 ATGGGTAGAT
*
82949 CTGAGGAGGTTGGGC
1 CTGAGCAGGTTGGGC
82964 CTGAGCAGGTTGGGC
1 CTGAGCAGGTTGGGC
82979 ATGTTTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (15 bp):
CTGAGCAGGTTGGGC
Found at i:85426 original size:21 final size:21
Alignment explanation
Indices: 85384--85426 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
85374 TTTTTGGGTT
* * *
85384 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
85405 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
85426 A
1 A
85427 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:85477 original size:19 final size:19
Alignment explanation
Indices: 85453--85489 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
85443 GAATGCTAGA
*
85453 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
85472 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
85490 TGTATAAAAA
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:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:86158 original size:149 final size:150
Alignment explanation
Indices: 85969--86284 Score: 537
Period size: 150 Copynumber: 2.1 Consensus size: 150
85959 GGGTAGAGGG
* *
85969 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
86033 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATTCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTATGGACATCATT
86098 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
86118 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
** *
86183 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTATGGACATCATT
86248 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
86268 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
86285 TGCATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 52 0.33
150 105 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:86296 original size:23 final size:23
Alignment explanation
Indices: 86252--86296 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
86242 ATCATTATAT
*
86252 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
86275 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
86297 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:88122 original size:6 final size:6
Alignment explanation
Indices: 88105--88143 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
88095 CTTCCTCACA
* * *
88105 AAGAGG ACGAGG AAGAGG CAGAGG AAGAGG CAGAGG AAG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAG
88144 GAACCCGTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.49, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:88122 original size:12 final size:12
Alignment explanation
Indices: 88113--88143 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
88103 CAAAGAGGAC
88113 GAGGAAGAGGCA
1 GAGGAAGAGGCA
88125 GAGGAAGAGGCA
1 GAGGAAGAGGCA
88137 GAGGAAG
1 GAGGAAG
88144 GAACCCGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.52, T:0.00
Consensus pattern (12 bp):
GAGGAAGAGGCA
Found at i:93113 original size:149 final size:150
Alignment explanation
Indices: 92921--93228 Score: 528
Period size: 150 Copynumber: 2.1 Consensus size: 150
92911 GGGTAGAGGG
* * *
92921 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
92985 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
93050 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
93070 TCTACGCGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
**
93135 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
*
93200 ATATGGCACTACGGTGTAAT
131 ATATGGCACTACGGTGCAAT
93220 TCTACGCGG
1 TCTACGCGG
93229 CACTTCGGTG
Statistics
Matches: 149, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
149 50 0.34
150 99 0.66
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:93248 original size:23 final size:23
Alignment explanation
Indices: 93204--93248 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
93194 ATCATTATAT
* *
93204 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
93227 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
93249 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:100053 original size:14 final size:13
Alignment explanation
Indices: 100034--100064 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
100024 AAATTTTGGC
*
100034 TTTTTTTTGTCTT
1 TTTTTTTTGCCTT
100047 TTTTTTTTGCCTT
1 TTTTTTTTGCCTT
100060 TTTTT
1 TTTTT
100065 GTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGCCTT
Found at i:106717 original size:23 final size:24
Alignment explanation
Indices: 106690--106740 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
106680 ACTTTTGGGT
*
106690 TGAAATGAAATAACTA-TTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
** *
106713 TGAAAAGACTTAATTATTTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
106737 TGAA
1 TGAA
106741 TAATCATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (24 bp):
TGAAAAGAAATAACTATTTTTTCA
Found at i:111411 original size:16 final size:17
Alignment explanation
Indices: 111374--111415 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
111364 ACTGAAATAA
111374 TAAATATAATATGAAACG
1 TAAATAT-ATATGAAACG
*
111392 -AAATATATAT-TAACG
1 TAAATATATATGAAACG
111407 TAAATATAT
1 TAAATATAT
111416 TACCACGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (17 bp):
TAAATATATATGAAACG
Found at i:112016 original size:23 final size:23
Alignment explanation
Indices: 111990--112039 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
111980 GATTTTTGGG
*
111990 TGAAATGAAATAACTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
** *
112013 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
112036 TGAA
1 TGAA
112040 TAGTCGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAAAGAAATAACTATTTTTCA
Found at i:120358 original size:15 final size:15
Alignment explanation
Indices: 120331--120368 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
120321 AGAATTAAAT
120331 TTTATAAAATATA-TA
1 TTTA-AAAATATATTA
120346 TTTAAAAATTATATTA
1 TTTAAAAA-TATATTA
120362 TTTAAAA
1 TTTAAAA
120369 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAAATATATTA
Found at i:120369 original size:15 final size:15
Alignment explanation
Indices: 120313--120370 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
120303 TTTGACCATC
* *
120313 ATTATTTTAGAATTAA
1 ATTA-TTTAAAATTAT
120329 ATT-TTATAAAA-TAT
1 ATTATT-TAAAATTAT
120343 A-TATTTAAAAATTAT
1 ATTATTT-AAAATTAT
120358 ATTATTTAAAATT
1 ATTATTTAAAATT
120371 TTTAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 2 0.06
14 11 0.31
15 14 0.40
16 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTATTTAAAATTAT
Found at i:120381 original size:23 final size:24
Alignment explanation
Indices: 120350--120397 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
120340 TATATATTTA
120350 AAAATTATATTATTTAAAATTTTT
1 AAAATTATATTATTTAAAATTTTT
* * *
120374 AAAA-TATATTTTTTCATATTTTT
1 AAAATTATATTATTTAAAATTTTT
120397 A
1 A
120398 TTAATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAAATTATATTATTTAAAATTTTT
Found at i:125230 original size:3 final size:3
Alignment explanation
Indices: 125222--125281 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
125212 TTTGTAAATG
* *
125222 ATA ATA ATA TTT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
125270 ATA ATA ATA ATA
1 ATA ATA ATA ATA
125282 TAGTGGTAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:125841 original size:42 final size:41
Alignment explanation
Indices: 125746--125846 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
125736 TGGTCTTATG
* * * *
125746 GATGGTCCGAAGGACTTATCATCTTGCTCGAAAGATTTAAA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAAA
* * * **
125787 GATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTAAA
125829 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
125847 TTAATCAAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAAA
Found at i:125965 original size:56 final size:56
Alignment explanation
Indices: 125905--126191 Score: 191
Period size: 56 Copynumber: 5.3 Consensus size: 56
125895 ATTTACAGTT
125905 ATCATCAAGAAAGCCCT-AAAATTAGACTTAGTTTCTTTAAAAATTCTTTGGAAATA
1 ATCATCAAGAAA-CCCTAAAAATTAGACTTAGTTTCTTTAAAAATTCTTTGGAAATA
* * *
125961 ATCATCAAGAAACCCTAAAAATCA-AGCTTAGCTTCTTTAAAATTTCATCTTTGGAAATA
1 ATCATCAAGAAACCCTAAAAATTAGA-CTTAGTTTCTTTAAAA-AT--TCTTTGGAAATA
* * * * *
126020 ATCATCAAGAAACCCCTGAAAATTAGGCTTATTTTCTTTACAAA---TTT----ATC
1 ATCATCAAGAAA-CCCTAAAAATTAGACTTAGTTTCTTTAAAAATTCTTTGGAAATA
* * * *
126070 AT-GTCAAGAAACCTCTGAAAATCAGACTTAGTTTC--TAAAAACTCATTT-G-AA-A
1 ATCATCAAGAAACC-CTAAAAATTAGACTTAGTTTCTTTAAAAATTC-TTTGGAAATA
* * * *
126122 A-CATCAAGAAACCCCCAAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTT-G-AA-A
1 ATCATCAAGAAA--CCCTAAAAATTAGACTTAGTTTCTTTAAAAATTC-TTTGGAAATA
126177 A-CATCAAGAAACCCT
1 ATCATCAAGAAACCCT
126192 TGAAAATCAA
Statistics
Matches: 186, Mismatches: 26, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
47 5 0.03
48 2 0.01
49 26 0.14
50 4 0.02
51 3 0.02
52 9 0.05
53 20 0.11
54 5 0.03
55 31 0.17
56 33 0.18
57 1 0.01
59 24 0.13
60 23 0.12
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (56 bp):
ATCATCAAGAAACCCTAAAAATTAGACTTAGTTTCTTTAAAAATTCTTTGGAAATA
Found at i:126153 original size:53 final size:55
Alignment explanation
Indices: 126087--126190 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
126077 GAAACCTCTG
126087 AAAATCAGACTTAG-TT-TCTAAAAACTCATTTGAAAACATCAAGAAACCCCCAA
1 AAAATCAGACTTAGCTTCTCTAAAAACTCATTTGAAAACATCAAGAAACCCCCAA
* * * * *
126140 AAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCC
1 AAAATCAGACTTAGCTTCTCTAAAAACTCATTTGAAAACATCAAGAAACCC
126191 TTGAAAATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 12 0.27
54 2 0.05
55 30 0.68
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (55 bp):
AAAATCAGACTTAGCTTCTCTAAAAACTCATTTGAAAACATCAAGAAACCCCCAA
Found at i:126176 original size:55 final size:54
Alignment explanation
Indices: 126107--126223 Score: 164
Period size: 55 Copynumber: 2.2 Consensus size: 54
126097 TTAGTTTCTA
* * *
126107 AAAACTCATTTGAAAACATCAAGAAACCCCCAAAAAATTAGGCTTAGCTTCTTTC
1 AAAATTCATTTGAAAACATCAAGAAA-CCCCAAAAAATCAAGCTTAGCTTCTTTC
***
126162 AAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAAGCTTAGCTTCTTTC
1 AAAATTCATTTGAAAACATCAAGAAACCCCAAAAAATCAAGCTTAGCTTCTTTC
126216 -AAATTCAT
1 AAAATTCAT
126224 ATCGATTAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 8 0.14
54 23 0.41
55 25 0.45
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (54 bp):
AAAATTCATTTGAAAACATCAAGAAACCCCAAAAAATCAAGCTTAGCTTCTTTC
Done.