Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 111 of 276
Found at i:35221167 original size:51 final size:51
Alignment explanation
Indices: 35221107--35221218 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
35221097 AGTTATCCGA
*
35221107 ATGAAATATGAAGCTCTTGTTGAAGCTAGA-AGACCAAAGTAATAATTCCAG
1 ATGAAATATGAAGCTCTTGTTGAAGCTAGAGA-AACAAAGTAATAATTCCAG
* *
35221158 ATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTTCGG
1 ATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTCCAG
*
35221209 ATGAAGTATG
1 ATGAAATATG
35221219 CAGTAAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (51 bp):
ATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTCCAG
Found at i:35222875 original size:31 final size:31
Alignment explanation
Indices: 35222803--35222946 Score: 213
Period size: 31 Copynumber: 4.7 Consensus size: 31
35222793 TTAGTCTTGA
* * *
35222803 CATAT-ACTGGGCCGAAGCCTTTCCTTTAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
**
35222833 GGT-T-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
35222862 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
35222893 CATATCACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
35222924 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
35222947 ACTGTAAACG
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
29 24 0.23
30 2 0.02
31 77 0.75
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:35223017 original size:42 final size:42
Alignment explanation
Indices: 35222970--35223103 Score: 259
Period size: 42 Copynumber: 3.2 Consensus size: 42
35222960 TGGCCCTTAG
*
35222970 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
35223012 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
35223054 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
35223096 GCCCATTT
1 GCCCATTT
35223104 GGGGAGACTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:35225494 original size:46 final size:46
Alignment explanation
Indices: 35225427--35225678 Score: 335
Period size: 46 Copynumber: 5.5 Consensus size: 46
35225417 GGGTGCTACA
35225427 GAAAGATACCATGGCAACATGATATGAAAT-ATGTAAGACCATGGTT
1 GAAAGATACCATGGCAACATGATATGAAATGA-GTAAGACCATGGTT
* *
35225473 GAAAGATACCATGGCAACATGATATGAAGTGTGTAAGACCATGGTT
1 GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTT
*
35225519 GAAATATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTT
1 GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTT
* *** *
35225565 GAAAGACACCATGGCAACATGACGGGGAAATGAATAAGACCATGGTT
1 GAAAGATACCATGGCAACATGA-TATGAAATGAGTAAGACCATGGTT
* ** *
35225612 GAAAGATACCATGGCAACATGACAAAAAATGAGTAAGACCATAGTT
1 GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTT
* * * *
35225658 AAAAGACACTATGGCATCATG
1 GAAAGATACCATGGCAACATG
35225679 TCGAAGATAA
Statistics
Matches: 182, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
46 141 0.77
47 41 0.23
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTT
Found at i:35225642 original size:93 final size:92
Alignment explanation
Indices: 35225427--35225678 Score: 344
Period size: 93 Copynumber: 2.7 Consensus size: 92
35225417 GGGTGCTACA
*
35225427 GAAAGATACCATGGCAACATGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 GAAAGATACCATGGCAACATGATATGAAATGA-GTAAGACCATGGTTGAAAGACACCATGGCAAC
* * * **
35225491 ATGATATGAAGTGTGTAAGACCATGGTT
65 ATGAGAGGAAATGAATAAGACCATGGTT
*
35225519 GAAATATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGACACCATGGCAACA
1 GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGACACCATGGCAACA
*
35225584 TGACGGGGAAATGAATAAGACCATGGTT
66 TGA-GAGGAAATGAATAAGACCATGGTT
* ** * * * *
35225612 GAAAGATACCATGGCAACATGACAAAAAATGAGTAAGACCATAGTTAAAAGACACTATGGCATCA
1 GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGACACCATGGCAACA
35225677 TG
66 TG
35225679 TCGAAGATAA
Statistics
Matches: 142, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
92 64 0.45
93 78 0.55
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (92 bp):
GAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGACACCATGGCAACA
TGAGAGGAAATGAATAAGACCATGGTT
Found at i:35225791 original size:26 final size:24
Alignment explanation
Indices: 35225761--35225830 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 24
35225751 ACTAGATGAC
*
35225761 AAATGGTTATATGAATTGGTTATACA
1 AAATGGTTATATGAAAT-GTT-TACA
* *
35225787 AAATGGTTGTGTGAAATGTTTACA
1 AAATGGTTATATGAAATGTTTACA
35225811 AGAATTGGTTATATAGAAAT
1 A-AA-TGGTTATAT-GAAAT
35225831 ATATATGTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 5 0.14
25 5 0.14
26 21 0.58
27 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (24 bp):
AAATGGTTATATGAAATGTTTACA
Found at i:35226863 original size:23 final size:22
Alignment explanation
Indices: 35226837--35226881 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
35226827 ATTAAATTGT
35226837 AAAGCATGTAAAAGT-ATTATGCG
1 AAAGCA-GTAAAAGTGA-TATGCG
*
35226860 AAAGGAGTAAAAGTGATATGCG
1 AAAGCAGTAAAAGTGATATGCG
35226882 TGCATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (22 bp):
AAAGCAGTAAAAGTGATATGCG
Found at i:35228572 original size:14 final size:14
Alignment explanation
Indices: 35228553--35228579 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35228543 TAATGAGATA
35228553 TTTTATTATTTTAT
1 TTTTATTATTTTAT
35228567 TTTTATTATTTTA
1 TTTTATTATTTTA
35228580 ATATAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTATTTTAT
Found at i:35229851 original size:51 final size:51
Alignment explanation
Indices: 35229775--35229890 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
35229765 AAGTTATCCA
*
35229775 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCCG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTCCG
*
35229826 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTTCG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTCCG
* *
35229877 AATGAAGTATGAAG
1 GATGAAATATGAAG
35229891 TAAGTTTGAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (51 bp):
GATGAAATATGAAGCTCTTGTTGAAGCTAGAGAAACAAAGTAATAATTCCG
Found at i:35230789 original size:46 final size:46
Alignment explanation
Indices: 35230722--35231061 Score: 457
Period size: 46 Copynumber: 7.4 Consensus size: 46
35230712 GCTTTCTAAA
* * *
35230722 ATGAAATGTGTAAGACAATTGTTGAAAGATACCATGGTAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
35230768 ATGAAATATTTAAGACCATTGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
35230814 ATGAAATGTGTAAGACCATGGTTGAAATATGCCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
35230860 ATGAAATGTGTAAGACCATGGTTGAAATATACCATGGCAACGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
**
35230906 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
35230952 ATGAAATGTGTAAGACCATGGTTGAAATATACCATGGCAACGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
35230998 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGAAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
35231044 A-GAAAATGAGTAAGACCA
1 ATG-AAATGTGTAAGACCA
35231062 CATGTCGAAG
Statistics
Matches: 261, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 260 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:35230839 original size:21 final size:21
Alignment explanation
Indices: 35230815--35230887 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
35230805 CAACATGATA
35230815 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* * * * *
35230836 TGAAATATGCCATGGCAACATGAT
1 TGAAATGTG-TA-AG-ACCATGGT
35230860 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
35230882 TGAAAT
1 TGAAAT
35230888 ATACCATGGC
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
21 14 0.37
22 7 0.18
23 2 0.05
24 7 0.18
25 8 0.21
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:35230865 original size:25 final size:25
Alignment explanation
Indices: 35230790--35230866 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
35230780 AGACCATTGT
* *
35230790 TGAAAGATACCATGGCAACATGATA
1 TGAAATATGCCATGGCAACATGATA
* * * * *
35230815 TGAAATGTG-TA-AG-ACCATGGT-
1 TGAAATATGCCATGGCAACATGATA
35230836 TGAAATATGCCATGGCAACATGATA
1 TGAAATATGCCATGGCAACATGATA
35230861 TGAAAT
1 TGAAAT
35230867 GTGTAAGACC
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
21 8 0.22
22 7 0.19
23 2 0.06
24 7 0.19
25 12 0.33
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (25 bp):
TGAAATATGCCATGGCAACATGATA
Found at i:35231178 original size:26 final size:24
Alignment explanation
Indices: 35231148--35231217 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 24
35231138 ACCAGATGAC
*
35231148 AAATGGTTATATGAATTGGTTATACA
1 AAATGGTTATATGAAAT-GTT-TACA
* *
35231174 AAATGGTTGTGTGAAATGTTTACA
1 AAATGGTTATATGAAATGTTTACA
35231198 AGAATTGGTTATATAGAAAT
1 A-AA-TGGTTATAT-GAAAT
35231218 ATATATGTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 5 0.14
25 5 0.14
26 21 0.58
27 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (24 bp):
AAATGGTTATATGAAATGTTTACA
Found at i:35233620 original size:24 final size:24
Alignment explanation
Indices: 35233582--35233642 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
35233572 TAGATTATAT
**
35233582 ATATTAATTATTATTATTTTTATTG
1 ATATT-ATTATTATTATTTAAATTG
*
35233607 CTATTATTATTATTATTTAAATTG
1 ATATTATTATTATTATTTAAATTG
35233631 ATATTA-TATTAT
1 ATATTATTATTAT
35233643 AAAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 6 0.19
24 22 0.69
25 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (24 bp):
ATATTATTATTATTATTTAAATTG
Found at i:35233770 original size:19 final size:20
Alignment explanation
Indices: 35233748--35233790 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
35233738 AAATAGATAT
35233748 TTATTTA-AATAATAAATTA
1 TTATTTATAATAATAAATTA
* *
35233767 TTA-TTATAATTATTAATTA
1 TTATTTATAATAATAAATTA
35233786 TTATT
1 TTATT
35233791 AATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.15
19 16 0.80
20 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTATAATAATAAATTA
Found at i:35233775 original size:16 final size:18
Alignment explanation
Indices: 35233762--35233803 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
35233752 TTAAATAATA
35233762 AATTATTATTATAATTATT
1 AATTATTATTATAATTA-T
35233781 AATTATTATTA-ATATTAT
1 AATTATTATTATA-ATTAT
35233799 -ATTAT
1 AATTAT
35233804 GAAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTATTATAATTAT
Found at i:35234187 original size:9 final size:9
Alignment explanation
Indices: 35234173--35234198 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35234163 AAATAGATTT
35234173 TTATTATAG
1 TTATTATAG
35234182 TTATTATAG
1 TTATTATAG
35234191 TTATTATA
1 TTATTATA
35234199 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
TTATTATAG
Found at i:35235038 original size:2 final size:2
Alignment explanation
Indices: 35235033--35235062 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35235023 TATATATATA
35235033 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35235063 AATGAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35235318 original size:9 final size:9
Alignment explanation
Indices: 35235304--35235329 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35235294 AAATAGATTT
35235304 TTATTATAG
1 TTATTATAG
35235313 TTATTATAG
1 TTATTATAG
35235322 TTATTATA
1 TTATTATA
35235330 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
TTATTATAG
Found at i:35236169 original size:2 final size:2
Alignment explanation
Indices: 35236164--35236193 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35236154 TATATATATA
35236164 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35236194 AATGAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35236692 original size:6 final size:6
Alignment explanation
Indices: 35236672--35236705 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
35236662 ATGTGTCGAA
*
35236672 TACTGT TACTGGT TACTGT TACTGT TACTAT TAC
1 TACTGT TACT-GT TACTGT TACTGT TACTGT TAC
35236706 CGATTCGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.47
Consensus pattern (6 bp):
TACTGT
Found at i:35236754 original size:6 final size:6
Alignment explanation
Indices: 35236733--35236778 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
35236723 TGCCGGATAT
*
35236733 TGTTAC TATTAC -GTTAC TGTTAC TG-TAC TG-TAC TGTTAC TGTTAC
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC
35236778 T
1 T
35236779 ATTGTTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 14 0.39
6 22 0.61
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (6 bp):
TGTTAC
Found at i:35236925 original size:19 final size:19
Alignment explanation
Indices: 35236903--35236953 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
35236893 AAAGATCGAC
35236903 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
35236922 TGTTACTGTAT-ATCTAAT
1 TGTTACTGAATAATTTAAT
35236940 T-TTACTGAATAATT
1 TGTTACTGAATAATT
35236954 GACTGTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.30
18 9 0.33
19 10 0.37
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:35236964 original size:18 final size:18
Alignment explanation
Indices: 35236900--35236969 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
35236890 TGGAAAGATC
35236900 GACTGTTACTGAATAATTT
1 GACTGTTACTGAATAA-TT
* * *
35236919 AATTGTTACTGTAT-ATCT
1 GACTGTTACTGAATAAT-T
* *
35236937 -AATTTTACTGAATAATT
1 GACTGTTACTGAATAATT
*
35236954 GACTGTTACTGGATAA
1 GACTGTTACTGAATAA
35236970 CCGATCAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.31
18 16 0.41
19 11 0.28
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (18 bp):
GACTGTTACTGAATAATT
Found at i:35236999 original size:18 final size:19
Alignment explanation
Indices: 35236976--35237024 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
35236966 ATAACCGATC
35236976 AATTGATTGA-TACTGAAT
1 AATTGATTGATTACTGAAT
*
35236994 AATTGATT-ATTATTGAAT
1 AATTGATTGATTACTGAAT
35237012 AATTGATTG-TTAC
1 AATTGATTGATTAC
35237025 CGACTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (19 bp):
AATTGATTGATTACTGAAT
Found at i:35238593 original size:6 final size:6
Alignment explanation
Indices: 35238573--35238606 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
35238563 ATGTGTCGAA
*
35238573 TACTGT TACTGGT TACTGT TACTGT TACTAT TAC
1 TACTGT TACT-GT TACTGT TACTGT TACTGT TAC
35238607 CGATTCGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.47
Consensus pattern (6 bp):
TACTGT
Found at i:35238655 original size:6 final size:6
Alignment explanation
Indices: 35238634--35238679 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
35238624 TGCCGGATAT
*
35238634 TGTTAC TATTAC -GTTAC TGTTAC TG-TAC TG-TAC TGTTAC TGTTAC
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC
35238679 T
1 T
35238680 ATTGTTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 14 0.39
6 22 0.61
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (6 bp):
TGTTAC
Found at i:35238826 original size:19 final size:19
Alignment explanation
Indices: 35238804--35238854 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
35238794 AAAGATCGAC
35238804 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
35238823 TGTTACTGTAT-ATCTAAT
1 TGTTACTGAATAATTTAAT
35238841 T-TTACTGAATAATT
1 TGTTACTGAATAATT
35238855 GACTGTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.30
18 9 0.33
19 10 0.37
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:35238865 original size:18 final size:18
Alignment explanation
Indices: 35238801--35238870 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
35238791 TGGAAAGATC
35238801 GACTGTTACTGAATAATTT
1 GACTGTTACTGAATAA-TT
* * *
35238820 AATTGTTACTGTAT-ATCT
1 GACTGTTACTGAATAAT-T
* *
35238838 -AATTTTACTGAATAATT
1 GACTGTTACTGAATAATT
*
35238855 GACTGTTACTGGATAA
1 GACTGTTACTGAATAA
35238871 CCGATCAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.31
18 16 0.41
19 11 0.28
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (18 bp):
GACTGTTACTGAATAATT
Found at i:35238900 original size:18 final size:19
Alignment explanation
Indices: 35238877--35238925 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
35238867 ATAACCGATC
35238877 AATTGATTGA-TACTGAAT
1 AATTGATTGATTACTGAAT
*
35238895 AATTGATT-ATTATTGAAT
1 AATTGATTGATTACTGAAT
35238913 AATTGATTG-TTAC
1 AATTGATTGATTAC
35238926 CGACTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (19 bp):
AATTGATTGATTACTGAAT
Found at i:35240961 original size:17 final size:17
Alignment explanation
Indices: 35240941--35240974 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35240931 ATTAGTCCCT
35240941 ATTTCAAAATTGAAAAC
1 ATTTCAAAATTGAAAAC
**
35240958 ATTTTTAAATTGAAAAC
1 ATTTCAAAATTGAAAAC
35240975 CTTTTTAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (17 bp):
ATTTCAAAATTGAAAAC
Found at i:35240979 original size:17 final size:17
Alignment explanation
Indices: 35240947--35240982 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35240937 CCCTATTTCA
35240947 AAATTGAAAACATTTTT
1 AAATTGAAAACATTTTT
*
35240964 AAATTGAAAACCTTTTT
1 AAATTGAAAACATTTTT
35240981 AA
1 AA
35240983 CATTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATTGAAAACATTTTT
Found at i:35241425 original size:18 final size:21
Alignment explanation
Indices: 35241385--35241430 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
35241375 TTTTGGTTGG
*
35241385 TTATTATTACTATCATTATTT
1 TTATTATTACTATAATTATTT
35241406 TTATTATT-CT-TAATTA-TT
1 TTATTATTACTATAATTATTT
35241424 TTATTAT
1 TTATTAT
35241431 GGATTTGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 2 0.08
21 8 0.33
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTACTATAATTATTT
Found at i:35242149 original size:13 final size:13
Alignment explanation
Indices: 35242130--35242160 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35242120 TTAAAAGTTC
35242130 AAAATTCAAAATT
1 AAAATTCAAAATT
*
35242143 CAAATTCAAAATT
1 AAAATTCAAAATT
35242156 AAAAT
1 AAAAT
35242161 AATAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTCAAAATT
Found at i:35242159 original size:6 final size:7
Alignment explanation
Indices: 35242122--35242160 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
35242112 ATTGATTCTT
35242122 AAAAGTTC
1 AAAA-TTC
35242130 AAAATTC
1 AAAATTC
35242137 AAAATTC
1 AAAATTC
35242144 -AAATTC
1 AAAATTC
35242150 AAAATT-
1 AAAATTC
35242156 AAAAT
1 AAAAT
35242161 AATAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 11 0.37
7 15 0.50
8 4 0.13
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (7 bp):
AAAATTC
Found at i:35243346 original size:17 final size:18
Alignment explanation
Indices: 35243326--35243361 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
35243316 TTAATTTAAA
35243326 TTTAAAATT-TTTTATTT
1 TTTAAAATTATTTTATTT
35243343 TTTAAAATTATTTTATTT
1 TTTAAAATTATTTTATTT
35243361 T
1 T
35243362 GTTGATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAAAATTATTTTATTT
Found at i:35243991 original size:26 final size:26
Alignment explanation
Indices: 35243954--35244115 Score: 297
Period size: 26 Copynumber: 6.2 Consensus size: 26
35243944 TGATACAAAT
*
35243954 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
35243980 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35244006 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35244032 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35244058 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
35244084 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35244110 TGATAA
1 TGATAA
35244116 GAATTTCATG
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 132 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:35257502 original size:27 final size:25
Alignment explanation
Indices: 35257446--35257521 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 25
35257436 ACAAATTTTC
* * **
35257446 TCAAAATTTTATTGAGGGTAAAATTT
1 TCAAAACTTTACTG-GGGTAAAATCA
35257472 TCAAAACTTTACTGGATGGTAAAATCA
1 TCAAAACTTTACTGG--GGTAAAATCA
* *
35257499 TCAAAATTTTATTGGGGTAAAAT
1 TCAAAACTTTACTGGGGTAAAAT
35257522 TGGGATGAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
25 9 0.21
26 12 0.29
27 21 0.50
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (25 bp):
TCAAAACTTTACTGGGGTAAAATCA
Found at i:35259822 original size:42 final size:42
Alignment explanation
Indices: 35259776--35259880 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
35259766 CCGCATGGGA
* * * *
35259776 AGCTTCACTGATAAACAGTTTAACATTTAAGCTTACGTAGAG
1 AGCTTCGCTGATAAACAGCTTAACACTTAAGCTAACGTAGAG
* * * *
35259818 AGCTTTGCTAATACAA-AGCTTATCACTTAAGCTAACGTAGGG
1 AGCTTCGCTGATA-AACAGCTTAACACTTAAGCTAACGTAGAG
*
35259860 AGCTTCGCTGATACACAGCTT
1 AGCTTCGCTGATAAACAGCTT
35259881 GTAAAATCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.02
42 47 0.94
43 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
AGCTTCGCTGATAAACAGCTTAACACTTAAGCTAACGTAGAG
Found at i:35268162 original size:49 final size:49
Alignment explanation
Indices: 35268101--35268414 Score: 208
Period size: 49 Copynumber: 6.6 Consensus size: 49
35268091 ACATCAAAGT
35268101 CGATGCCATGTCCCAGACAAGTCTTACACTGACTTTTATATATCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTGACTTTTATATATCGAGGC
* * * * * * * * *
35268150 CAATGCCGTGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGT
1 CGATGCCATGTCCCAGACAAGTCTTACACTGACTTTTATATATCGAG-GC
* * *
35268199 CGATGCCATGTCCCAGACAGGTCTTACACTGAC----ACATATC-AAGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTGACTTTTATATATCGAGGC
* * *
35268243 TGATGCCATGTCCCAGA-AAGGTCTTACACT-AGCTTGTATATCTCGAGGC
1 CGATGCCATGTCCCAGACAA-GTCTTACACTGA-CTTTTATATATCGAGGC
* * ** ** *
35268292 CGATG-CATGTCCCAGACATGTCTTACACT-AGCTCTCGT-T-TAAATGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTGA-CTTTTATATATCGAGGC
* * * * * * *
35268338 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATA-AT-GTGGT
1 CGATGCCATGTCCCAGACA-AGTCTTACACTGACTTTTATATATCGAGGC
*
35268386 CGATG-CATGTCCCAGACATGTCTTACACT
1 CGATGCCATGTCCCAGACAAGTCTTACACT
35268415 AGCACACATA
Statistics
Matches: 209, Mismatches: 41, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
43 2 0.01
44 28 0.13
45 5 0.02
46 18 0.09
47 27 0.13
48 53 0.25
49 76 0.36
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAAGTCTTACACTGACTTTTATATATCGAGGC
Found at i:35268395 original size:142 final size:142
Alignment explanation
Indices: 35268059--35268417 Score: 356
Period size: 142 Copynumber: 2.5 Consensus size: 142
35268049 ATGTCGACGT
* * * * *
35268059 CATGTCCTAGACATGGTCTTATACTGGCTAGCACATCAAAGTCGATGCCATGTCCCAGACAAGTC
1 CATGTCCCAGACA-GGTCTTACACTGAC-A-CATATCAAGGTCGATGCCATGTCCCAGA-AAGTC
* * * *
35268124 TTACACT-GACTTTTATATATCGAGGCCAATGCCGTGTCCTAGACAGGTCTTACACTGGCTCTCA
62 TTACACTAG-CTTGTATATATCGAGGCCAATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCA
*** *
35268188 TCTATCGGTGTCGATGC
126 TCTATAAATGCCGATGC
*
35268205 CATGTCCCAGACAGGTCTTACACTGACACATATCAAGCT-GATGCCATGTCCCAGAAAGGTCTTA
1 CATGTCCCAGACAGGTCTTACACTGACACATATCAAGGTCGATGCCATGTCCCAGAAA-GTCTTA
* * * *
35268269 CACTAGCTTGTATATCTCGAGGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCGT-T-
65 CACTAGCTTGTATATATCGAGGCCAATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTA
35268331 TAAATGCCGATGC
130 TAAATGCCGATGC
* * * *
35268344 CATGTCCCAGACATGGTCTTACATTGGCTC-TCAT-AATGTGGTCGATG-CATGTCCCAGACATG
1 CATGTCCCAGACA-GGTCTTACACTGACACAT-ATCAA---GGTCGATGCCATGTCCCAGA-AAG
35268406 TCTTACACTAGC
60 TCTTACACTAGC
35268418 ACACATATCA
Statistics
Matches: 181, Mismatches: 23, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
139 25 0.14
140 16 0.09
141 30 0.17
142 71 0.39
143 14 0.08
144 1 0.01
145 12 0.07
146 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (142 bp):
CATGTCCCAGACAGGTCTTACACTGACACATATCAAGGTCGATGCCATGTCCCAGAAAGTCTTAC
ACTAGCTTGTATATATCGAGGCCAATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTAT
AAATGCCGATGC
Found at i:35268401 original size:94 final size:92
Alignment explanation
Indices: 35268152--35268425 Score: 295
Period size: 94 Copynumber: 2.9 Consensus size: 92
35268142 ATCGAGGCCA
* * *
35268152 ATGCCGTGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCGGTGTCGATGCCATGTCCCAGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAT-AATCGG-GTCGATG-CATGTCCCAGAC
* * *
35268217 AGGTCTTACACT-G-ACACATATCAAGCTG
63 ATGTCTTACACTAGCACACATATAAAGCCG
* * * * *
35268245 ATGCCATGTCCCAGAAAGGTCTTACACTAGCT-TGTATATCTCGAGGCCGATGCATGTCCCAGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATA-ATCG-GGTCGATGCATGTCCCAGAC
* * * *
35268309 ATGTCTTACACTAGCTCTCGTTTAAATGCCG
63 ATGTCTTACACTAGCACACATATAAA-GCCG
*
35268340 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAT-GTGGTCGATGCATGTCCCAGACA
1 ATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATAATCG-GGTCGATGCATGTCCCAGACA
35268404 TGTCTTACACTAGCACACATAT
64 TGTCTTACACTAGCACACATAT
35268426 CACCTAAATG
Statistics
Matches: 147, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
92 24 0.16
93 40 0.27
94 46 0.31
95 20 0.14
96 16 0.11
97 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (92 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATAATCGGGTCGATGCATGTCCCAGACATG
TCTTACACTAGCACACATATAAAGCCG
Found at i:35281782 original size:30 final size:30
Alignment explanation
Indices: 35281746--35281808 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
35281736 GTATTTTTAG
35281746 AGTTTAATTTTGGCCTTCTAGAAGGATGGA
1 AGTTTAATTTTGGCCTTCTAGAAGGATGGA
35281776 AGTTTAATTTTGGCCTTCTAGAAGGATGGA
1 AGTTTAATTTTGGCCTTCTAGAAGGATGGA
35281806 AGT
1 AGT
35281809 GGTGTGAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (30 bp):
AGTTTAATTTTGGCCTTCTAGAAGGATGGA
Found at i:35284954 original size:24 final size:24
Alignment explanation
Indices: 35284926--35284976 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
35284916 ATGTGTCGGC
35284926 AAAAGCCAAAATGCCGAAAAGTCG
1 AAAAGCCAAAATGCCGAAAAGTCG
35284950 AAAAGCCAAAATGCCGAAAAGTCG
1 AAAAGCCAAAATGCCGAAAAGTCG
35284974 AAA
1 AAA
35284977 GTTTGGCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.08
Consensus pattern (24 bp):
AAAAGCCAAAATGCCGAAAAGTCG
Found at i:35285268 original size:28 final size:28
Alignment explanation
Indices: 35285187--35285272 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
35285177 GTGAGCATTA
* * *
35285187 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCTTAATGGGCC
*
35285215 ATATAAATGTGATTTGGGCTTAATGGGCC
1 ATATGAATGTGA-TTGGGCTTAATGGGCC
*
35285244 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCTTAATGGGCC
35285272 A
1 A
35285273 GATACATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 28 0.55
29 23 0.45
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCTTAATGGGCC
Found at i:35286143 original size:18 final size:18
Alignment explanation
Indices: 35286120--35286154 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35286110 TTTCATTATG
35286120 TTATTATTATTTGCATTA
1 TTATTATTATTTGCATTA
*
35286138 TTATTATTATTTTCATT
1 TTATTATTATTTGCATT
35286155 GTAAACGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TTATTATTATTTGCATTA
Found at i:35289585 original size:28 final size:28
Alignment explanation
Indices: 35289504--35289589 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
35289494 GTGAGCATTA
* *
35289504 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
* *
35289532 ATATAAATGTGATTTGGGCCTAATGGGCT
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* *
35289561 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
35289589 A
1 A
35289590 GATATAGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 26 0.53
29 23 0.47
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:35304163 original size:5 final size:5
Alignment explanation
Indices: 35304155--35304189 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
35304145 ATTATTAAGT
35304155 TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA
35304190 AAACATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:35304197 original size:15 final size:15
Alignment explanation
Indices: 35304164--35304197 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35304154 TTAATATAAT
* *
35304164 ATAATATAATATAAT
1 ATAATATAATAAAAC
35304179 ATAATATAATAAAAC
1 ATAATATAATAAAAC
35304194 ATAA
1 ATAA
35304198 ATTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATATAATAAAAC
Found at i:35304484 original size:21 final size:20
Alignment explanation
Indices: 35304452--35304526 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 20
35304442 ATGTTGAAAT
35304452 AATTAAAGAATTAGGGGTTA
1 AATTAAAGAATTAGGGGTTA
****
35304472 AATTAACAGAATTTCAAGTTA
1 AATTAA-AGAATTAGGGGTTA
35304493 GAATTAAAGAATTAGGGGTTA
1 -AATTAAAGAATTAGGGGTTA
35304514 AATTAACAGAATT
1 AATTAA-AGAATT
35304527 TCAAGTTAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 12 0.27
21 26 0.59
22 6 0.14
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.31
Consensus pattern (20 bp):
AATTAAAGAATTAGGGGTTA
Found at i:35304511 original size:42 final size:42
Alignment explanation
Indices: 35304452--35304541 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
35304442 ATGTTGAAAT
35304452 AATTAAAGAATTAGGGGTTAAATTAACAGAATTTCAAGTTAG
1 AATTAAAGAATTAGGGGTTAAATTAACAGAATTTCAAGTTAG
35304494 AATTAAAGAATTAGGGGTTAAATTAACAGAATTTCAAGTTAG
1 AATTAAAGAATTAGGGGTTAAATTAACAGAATTTCAAGTTAG
35304536 AATTAA
1 AATTAA
35304542 GAAAAGGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (42 bp):
AATTAAAGAATTAGGGGTTAAATTAACAGAATTTCAAGTTAG
Found at i:35304534 original size:21 final size:22
Alignment explanation
Indices: 35304468--35304541 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
35304458 AGAATTAGGG
35304468 GTTA-AATTAACAGAATTTCAA
1 GTTAGAATTAACAGAATTTCAA
****
35304489 GTTAGAATTAA-AGAATTAGGG
1 GTTAGAATTAACAGAATTTCAA
35304510 GTTA-AATTAACAGAATTTCAA
1 GTTAGAATTAACAGAATTTCAA
35304531 GTTAGAATTAA
1 GTTAGAATTAA
35304542 GAAAAGGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.14
21 24 0.57
22 12 0.29
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (22 bp):
GTTAGAATTAACAGAATTTCAA
Found at i:35306773 original size:42 final size:42
Alignment explanation
Indices: 35306704--35306859 Score: 134
Period size: 42 Copynumber: 3.7 Consensus size: 42
35306694 GTATGTGTTA
* ** * *
35306704 TCATGTAAGATCATATCTGGGATATGGCGTTGATATGAGATT
1 TCATGTAAGACCACGTCTGGGACATGGCGTCGATATGAGATT
* * *
35306746 TCGTGTAAGACCACGTCTGAGACATGGCAG-CGAAATGAGATT
1 TCATGTAAGACCACGTCTGGGACATGGC-GTCGATATGAGATT
* ** * ** * *
35306788 TCATATAAGACCATATCTGGGATATGGCAACGATGTGAGATC
1 TCATGTAAGACCACGTCTGGGACATGGCGTCGATATGAGATT
* *
35306830 CCATGTAAGACCACGTTTGGGACATGGCGT
1 TCATGTAAGACCACGTCTGGGACATGGCGT
35306860 TGACATCTTA
Statistics
Matches: 86, Mismatches: 26, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
42 85 0.99
43 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (42 bp):
TCATGTAAGACCACGTCTGGGACATGGCGTCGATATGAGATT
Found at i:35306814 original size:84 final size:84
Alignment explanation
Indices: 35306704--35306857 Score: 209
Period size: 84 Copynumber: 1.8 Consensus size: 84
35306694 GTATGTGTTA
* * *** ** *
35306704 TCATGTAAGATCATATCTGGGATATGGCGTTGATATGAGATTTCGTGTAAGACCACGTCTGAGAC
1 TCATATAAGACCATATCTGGGATATGGCAACGATATGAGATCCCATGTAAGACCACGTCTGAGAC
35306769 ATGGCAGCGAAATGAGATT
66 ATGGCAGCGAAATGAGATT
* * *
35306788 TCATATAAGACCATATCTGGGATATGGCAACGATGTGAGATCCCATGTAAGACCACGTTTGGGAC
1 TCATATAAGACCATATCTGGGATATGGCAACGATATGAGATCCCATGTAAGACCACGTCTGAGAC
35306853 ATGGC
66 ATGGC
35306858 GTTGACATCT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 59 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (84 bp):
TCATATAAGACCATATCTGGGATATGGCAACGATATGAGATCCCATGTAAGACCACGTCTGAGAC
ATGGCAGCGAAATGAGATT
Found at i:35314323 original size:42 final size:42
Alignment explanation
Indices: 35314144--35314324 Score: 148
Period size: 42 Copynumber: 4.2 Consensus size: 42
35314134 ATTTGAGTTG
**
35314144 ATGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCAT
1 ATGAGATTTCGTATAAGACCATATCTGGGATATGGCATC-G-AT
* * * * *
35314188 -TGGTATGTGTTATCATGTAAGACCATATCTGGGATATGGCGTTGAT
1 AT-G-A-G-ATT-TCGTATAAGACCATATCTGGGATATGGCATCGAT
* * ** * *
35314234 ATGAGATTTCGTGTAAGACAACGTCTGGGACATGGCATCGAA
1 ATGAGATTTCGTATAAGACCATATCTGGGATATGGCATCGAT
* *
35314276 ATGAGATTTCGTATAATACCATATCTGGGATATGGCAACGAT
1 ATGAGATTTCGTATAAGACCATATCTGGGATATGGCATCGAT
*
35314318 GTGAGAT
1 ATGAGAT
35314325 CCCATGTAAG
Statistics
Matches: 106, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
42 66 0.62
43 3 0.03
44 2 0.02
45 2 0.02
46 4 0.04
47 3 0.03
48 26 0.25
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
ATGAGATTTCGTATAAGACCATATCTGGGATATGGCATCGAT
Found at i:35331825 original size:17 final size:19
Alignment explanation
Indices: 35331792--35331827 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35331782 TTAAATTACA
35331792 AATATATATGTATAATAAT
1 AATATATATGTATAATAAT
35331811 AATATATAT-TA-AATAAT
1 AATATATATGTATAATAAT
35331828 TTAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATATATGTATAATAAT
Found at i:35339642 original size:31 final size:31
Alignment explanation
Indices: 35339607--35339668 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
35339597 ATTAAAGATG
35339607 ATAATTTGAATATGTGATTTAAATAAATAGT
1 ATAATTTGAATATGTGATTTAAATAAATAGT
35339638 ATAATTTGAATATGTGATTTAAATAAATAGT
1 ATAATTTGAATATGTGATTTAAATAAATAGT
35339669 TTATTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (31 bp):
ATAATTTGAATATGTGATTTAAATAAATAGT
Found at i:35344473 original size:24 final size:24
Alignment explanation
Indices: 35344441--35344495 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
35344431 TCTTCTATTT
35344441 AAACTCTGTTTATTTGTTTCAATC
1 AAACTCTGTTTATTTGTTTCAATC
*
35344465 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
35344489 AAACTCT
1 AAACTCT
35344496 ACTTAGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:35349438 original size:18 final size:18
Alignment explanation
Indices: 35349420--35349454 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35349410 TTAGATATAT
*
35349420 TTATAA-AATTTTTATTA
1 TTATAATAATTATTATTA
35349437 TTATAATAATTATTATTA
1 TTATAATAATTATTATTA
35349455 GATAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAATAATTATTATTA
Found at i:35351321 original size:19 final size:19
Alignment explanation
Indices: 35351297--35351340 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
35351287 TAAGGCTTAA
35351297 TGGGCCGAAAACGGGTTAG
1 TGGGCCGAAAACGGGTTAG
35351316 TGGGCCGAAAACGGGTTAG
1 TGGGCCGAAAACGGGTTAG
35351335 TGGGCC
1 TGGGCC
35351341 AACGGGCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.43, T:0.16
Consensus pattern (19 bp):
TGGGCCGAAAACGGGTTAG
Found at i:35351834 original size:20 final size:20
Alignment explanation
Indices: 35351804--35351848 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35351794 CTGTTTTGTT
*
35351804 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTATATTAAA
* *
35351823 ATGGGCCCAACTATGTTAAT
1 ATGGGCCCAACTATATTAAA
35351843 ATGGGC
1 ATGGGC
35351849 AAGGCCCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTATATTAAA
Found at i:35351917 original size:60 final size:59
Alignment explanation
Indices: 35351841--35351979 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 59
35351831 AACTATGTTA
* *
35351841 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * *
35351901 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
35351961 ATATGGGCTAAGGCCCAAT
1 ATATGGGCT-AGGCCCAAT
35351980 TAACACTGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 1 0.01
60 52 0.74
61 17 0.24
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:35351989 original size:27 final size:28
Alignment explanation
Indices: 35351877--35351989 Score: 72
Period size: 28 Copynumber: 3.9 Consensus size: 28
35351867 ACTTGTAATA
* * *
35351877 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTAAGGCCCAGATTAACACTGATAT
*
35351905 GGGCT-AGGCCCA-A-TATACTCTGATACTGT
1 GGGCTAAGGCCCAGATTA-ACACTGATA---T
* * *
35351934 AAGGGGCTATGGCCCAGATTAATATTGATAT
1 ---GGGCTAAGGCCCAGATTAACACTGATAT
35351965 GGGCTAAGGCCCA-ATTAACACTGAT
1 GGGCTAAGGCCCAGATTAACACTGAT
35351990 TTCTGAATAG
Statistics
Matches: 64, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
25 1 0.02
26 8 0.12
27 16 0.25
28 17 0.27
29 1 0.02
31 1 0.02
32 5 0.08
33 6 0.09
34 7 0.11
35 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAACACTGATAT
Found at i:35355769 original size:2 final size:2
Alignment explanation
Indices: 35355764--35355943 Score: 360
Period size: 2 Copynumber: 90.0 Consensus size: 2
35355754 CAATGTCTCT
35355764 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35355806 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35355848 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35355890 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35355932 CA CA CA CA CA CA
1 CA CA CA CA CA CA
35355944 TATATATATA
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 178 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:35359111 original size:16 final size:16
Alignment explanation
Indices: 35359090--35359120 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35359080 TACTATCCTG
*
35359090 ATTCAATAATTATTTC
1 ATTCAATAACTATTTC
35359106 ATTCAATAACTATTT
1 ATTCAATAACTATTT
35359121 ATCTTACAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTCAATAACTATTTC
Found at i:35366920 original size:82 final size:82
Alignment explanation
Indices: 35366781--35366943 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 82
35366771 ATCACTATTG
*
35366781 GTTAGATCTTAGGTGCAGTCTACTAGTGGTACTCGACTTCAGCTTTGGATTGTGGTTCTACTTTT
1 GTTAGATCTTAGGTGCAGTCTACTAGTGGTACTCGACTTCAGCTTTGGATTGGGGTTCTACTTTT
35366846 TTCAAAAAACCCTTTTT
66 TTCAAAAAACCCTTTTT
35366863 GTTAGATCTTAGGTGCAGTCTACTAGTGGTACTCGACTTCAGCTTTGGATTGGGGTTCTACTTTT
1 GTTAGATCTTAGGTGCAGTCTACTAGTGGTACTCGACTTCAGCTTTGGATTGGGGTTCTACTTTT
35366928 TTCAAAAAACCCTTTT
66 TTCAAAAAACCCTTTT
35366944 CGTCTTTCTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (82 bp):
GTTAGATCTTAGGTGCAGTCTACTAGTGGTACTCGACTTCAGCTTTGGATTGGGGTTCTACTTTT
TTCAAAAAACCCTTTTT
Found at i:35368000 original size:28 final size:28
Alignment explanation
Indices: 35367947--35368000 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
35367937 TTTTTATATC
* *
35367947 ATTATTTACTGAAATGGCTGACTTTTTG
1 ATTATTTACGGAAATGGCTCACTTTTTG
35367975 ATTATTTACCGGAAATGGC-CA-TTTTT
1 ATTATTTA-CGGAAATGGCTCACTTTTT
35368001 CGCAAAAGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 9 0.39
29 9 0.39
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (28 bp):
ATTATTTACGGAAATGGCTCACTTTTTG
Found at i:35368126 original size:11 final size:10
Alignment explanation
Indices: 35368078--35368127 Score: 64
Period size: 11 Copynumber: 4.6 Consensus size: 10
35368068 CACAATAGTC
35368078 CTCTCACAATT
1 CTCTCA-AATT
35368089 CTCTCTAAATT
1 CTCTC-AAATT
35368100 CTCTCCAAATT
1 CTCT-CAAATT
35368111 CTCTCAAATTT
1 CTCTCAAA-TT
35368122 CTCTCA
1 CTCTCA
35368128 GTTTTTGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.11
11 30 0.83
12 2 0.06
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (10 bp):
CTCTCAAATT
Found at i:35368145 original size:21 final size:21
Alignment explanation
Indices: 35368121--35368160 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35368111 CTCTCAAATT
*
35368121 TCTCTC-AGTTTTTGTCAAAGC
1 TCTCTCTAATTTTTG-CAAAGC
35368142 TCTCTCTAATTTTTGCAAA
1 TCTCTCTAATTTTTGCAAA
35368161 AAAACTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (21 bp):
TCTCTCTAATTTTTGCAAAGC
Found at i:35369855 original size:18 final size:18
Alignment explanation
Indices: 35369832--35369875 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35369822 ATGCCATGTG
*
35369832 TGTATCCTAGCCCTTATA
1 TGTATCCTAACCCTTATA
*
35369850 TGTATCCTAACCCTTTTA
1 TGTATCCTAACCCTTATA
*
35369868 TGTTTCCT
1 TGTATCCT
35369876 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:35370404 original size:39 final size:39
Alignment explanation
Indices: 35370352--35370436 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
35370342 CTTTTTTTAA
* * *
35370352 TTTTAATACAATAAATATTCTTTTAAATTA-GCCAATAAT
1 TTTTAATAAAATAAATATTATTTTAAA-TACGACAATAAT
* * *
35370391 TTTTATTAAAATAAATGTTATTTTGAATACGACAATAA-
1 TTTTAATAAAATAAATATTATTTTAAATACGACAATAAT
35370429 TTTTAATA
1 TTTTAATA
35370437 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
38 9 0.24
39 29 0.76
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (39 bp):
TTTTAATAAAATAAATATTATTTTAAATACGACAATAAT
Found at i:35373855 original size:6 final size:7
Alignment explanation
Indices: 35373803--35373835 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
35373793 TAAAACCTAA
35373803 AAACCCT
1 AAACCCT
35373810 AAACCACT
1 AAACC-CT
35373818 AAACCCT
1 AAACCCT
35373825 -AACCCT
1 AAACCCT
35373831 AAACC
1 AAACC
35373836 AATCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:35374498 original size:44 final size:45
Alignment explanation
Indices: 35374441--35374537 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 45
35374431 CTATTATAAC
* *
35374441 ATTT-ATTCTATTCAACCAAATATAA-GAA-TA-TTATTACAGTTCT
1 ATTTCATTCTATTCAA-CAAA-ATAATGAATTACTAATTACAATTCT
35374484 ATTTCATTCTATTCAACAAAATAATTGAATTACTAATTACAATTCT
1 ATTTCATTCTATTCAACAAAATAA-TGAATTACTAATTACAATTCT
35374530 ATTTCATT
1 ATTTCATT
35374538 ATAGTCTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
42 4 0.09
43 8 0.17
44 14 0.30
45 2 0.04
46 19 0.40
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.43
Consensus pattern (45 bp):
ATTTCATTCTATTCAACAAAATAATGAATTACTAATTACAATTCT
Found at i:35379244 original size:31 final size:29
Alignment explanation
Indices: 35379175--35379248 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
35379165 ACAAAATAAT
**
35379175 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
*
35379204 AACATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
*
35379235 AACAAAAGTGACTA
1 AACATAAGTGACTA
35379249 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:35379996 original size:27 final size:28
Alignment explanation
Indices: 35379966--35380025 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
35379956 TGTTCGAGTT
* *
35379966 AATTTTT-TAAAAAATGATTTTCTTTAA
1 AATTTTTCAAAAAAATAATTTTCTTTAA
35379993 AATTTTTCAAAAAAATAATTTTCTTTAA
1 AATTTTTCAAAAAAATAATTTTCTTTAA
35380021 AATTT
1 AATTT
35380026 CTAAACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (28 bp):
AATTTTTCAAAAAAATAATTTTCTTTAA
Found at i:35382839 original size:24 final size:25
Alignment explanation
Indices: 35382812--35382870 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
35382802 AGTTTTAGCA
* ** *
35382812 TTTATTTATAATTAA-TTATTTAAT
1 TTTATTTATAATAAAGTTATCAAAA
35382836 TTTATTTA-AATAAAGTTATCAAAA
1 TTTATTTATAATAAAGTTATCAAAA
35382860 TTTATTTATAA
1 TTTATTTATAA
35382871 GTCTTCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 22 0.76
25 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTATTTATAATAAAGTTATCAAAA
Found at i:35382962 original size:16 final size:16
Alignment explanation
Indices: 35382941--35382972 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35382931 TTTATATCCC
35382941 GAGAATATATTAAATA
1 GAGAATATATTAAATA
35382957 GAGAATATATTAAATA
1 GAGAATATATTAAATA
35382973 TTCTCTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
GAGAATATATTAAATA
Found at i:35383519 original size:17 final size:17
Alignment explanation
Indices: 35383497--35383547 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
35383487 CAAGTTGGAA
35383497 TTAAGAATTTATAATAT
1 TTAAGAATTTATAATAT
* *
35383514 TTAAGATTTTTCTAAT-T
1 TTAAGA-ATTTATAATAT
*
35383531 CTAA-AATTTATAATAT
1 TTAAGAATTTATAATAT
35383547 T
1 T
35383548 CAAGTTATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.27
16 2 0.08
17 10 0.38
18 7 0.27
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (17 bp):
TTAAGAATTTATAATAT
Found at i:35383829 original size:3 final size:3
Alignment explanation
Indices: 35383823--35383856 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35383813 TTTTGATGAT
35383823 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
35383857 GAGTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35384560 original size:3 final size:3
Alignment explanation
Indices: 35384546--35384585 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
35384536 TTTTCACAAT
*
35384546 ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
35384586 CTGAATCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:35394403 original size:87 final size:87
Alignment explanation
Indices: 35394295--35394548 Score: 267
Period size: 87 Copynumber: 2.9 Consensus size: 87
35394285 TACATGCATA
* *
35394295 AGGTTGAG-TTCTTACTCTTAATGAATTCATATCACAGGGTTTGGATGGTCCTATTGACACGGAC
1 AGGTTGAGTTTCTTACTCTTAATGAGTTCATATCACAGAGTTTGGATGGTCCTATTGACACGGAC
* ** ** **
35394359 ATGATGAATTCATGATTATGTG
66 ATGATGAATTAACCAACACATG
* * * *
35394381 AGGTTGAGTTTCTTACTCTTAATGAGTTTATATCCCAGAGTTTGGCTGGTCCTATTGAGACGGAC
1 AGGTTGAGTTTCTTACTCTTAATGAGTTCATATCACAGAGTTTGGATGGTCCTATTGACACGGAC
*
35394446 TTGATGAATTAACCAACACATG
66 ATGATGAATTAACCAACACATG
** * * * * * * **
35394468 AGGTTGAGTTTCTTACTCCAAATGAGTTCATATCCCAAAGTTTGGGTGATCTTATTGAGATAGAC
1 AGGTTGAGTTTCTTACTCTTAATGAGTTCATATCACAGAGTTTGGATGGTCCTATTGACACGGAC
* *
35394533 TTGATGAATTCACCAA
66 ATGATGAATTAACCAA
35394549 ACTTAAATTT
Statistics
Matches: 143, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 8 0.06
87 135 0.94
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (87 bp):
AGGTTGAGTTTCTTACTCTTAATGAGTTCATATCACAGAGTTTGGATGGTCCTATTGACACGGAC
ATGATGAATTAACCAACACATG
Found at i:35402012 original size:20 final size:20
Alignment explanation
Indices: 35401948--35402014 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
35401938 ATTTTGATAA
*
35401948 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* * *
35401968 GCATAACATGTATGATATGC
1 ACATGATATGTATGATATGC
35401988 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
35402008 ACATGAT
1 ACATGAT
35402015 GTAATCATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:35402091 original size:24 final size:24
Alignment explanation
Indices: 35402064--35402135 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
35402054 GAGGAAGTGA
35402064 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
35402088 AAAAGGCCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
35402112 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
35402136 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 31 0.76
25 10 0.24
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:35402364 original size:31 final size:31
Alignment explanation
Indices: 35402329--35402392 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
35402319 CGTTTACAGT
35402329 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
35402360 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
35402391 AA
1 AA
35402393 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:35410025 original size:20 final size:20
Alignment explanation
Indices: 35410002--35410040 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35409992 TAAACATGGT
35410002 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
35410022 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
35410041 TGTAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:35410117 original size:24 final size:23
Alignment explanation
Indices: 35410092--35410208 Score: 137
Period size: 23 Copynumber: 5.0 Consensus size: 23
35410082 AGGAAGTGTA
35410092 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
35410115 AAAGGACTTATTCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
35410138 AAAGAGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
35410161 AAAAGGGCTTTTGCCCTAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
35410185 CAAAGTGGC-TAGGCCTCCAGTTAT
1 -AAAG-GGCTTATGCC-CCAGTTAT
35410209 ATGATAAAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 41 0.52
24 28 0.35
25 10 0.13
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:35413844 original size:36 final size:36
Alignment explanation
Indices: 35413767--35413852 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 36
35413757 CACCACTTCG
* * *
35413767 TCCACCTTGCACACCACATTAGGGCTATAGTAGGCCCA
1 TCCACCTT--ACACCACATTAGGACCATAGTAAGCCCA
35413805 TCCATCCTGTACACCACA-TAGGACCATA-TAAGCCCA
1 TCCA-CCT-TACACCACATTAGGACCATAGTAAGCCCA
35413841 TCCACCTTACAC
1 TCCACCTTACAC
35413853 ACCACAAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
34 5 0.12
35 3 0.07
36 11 0.26
37 8 0.19
38 12 0.28
39 3 0.07
40 1 0.02
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.21
Consensus pattern (36 bp):
TCCACCTTACACCACATTAGGACCATAGTAAGCCCA
Found at i:35413855 original size:36 final size:37
Alignment explanation
Indices: 35413767--35413858 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 37
35413757 CACCACTTCG
* * *
35413767 TCCACCTTGCACACCACATTAGGGCTATAGTAGGCCCA
1 TCCACCTT-CACACCACATTAGGACCATAGTAAGCCCA
35413805 TCCATCCTGT-ACACCACA-TAGGACCATA-TAAGCCCA
1 TCCA-CCT-TCACACCACATTAGGACCATAGTAAGCCCA
35413841 TCCACCTTACACACCACA
1 TCCACCTT-CACACCACA
35413859 AATGTGGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 1 0.02
35 3 0.06
36 19 0.40
37 8 0.17
38 12 0.26
39 3 0.06
40 1 0.02
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.20
Consensus pattern (37 bp):
TCCACCTTCACACCACATTAGGACCATAGTAAGCCCA
Found at i:35417241 original size:47 final size:47
Alignment explanation
Indices: 35417132--35417242 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
35417122 CCGGGATAAG
* *
35417132 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
35417179 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
35417226 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
35417243 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:35418022 original size:4 final size:4
Alignment explanation
Indices: 35418005--35418085 Score: 63
Period size: 4 Copynumber: 19.8 Consensus size: 4
35417995 CCCTTTTCTA
* ** * * * **
35418005 TTTC TTTT TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTA ACTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC TTTC
*
35418055 TTTC TATC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
35418086 TTTAACTTAC
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
4 55 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.05, C:0.25, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:35418149 original size:19 final size:17
Alignment explanation
Indices: 35418112--35418160 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
35418102 ATCTATATTC
35418112 AATATAATAATATTAAT
1 AATATAATAATATTAAT
* *
35418129 AATATAATATTATT-CT
1 AATATAATAATATTAAT
*
35418145 AATAAAATAAT-TTAAT
1 AATATAATAATATTAAT
35418161 CTATAAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.08
16 11 0.42
17 13 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAATAATATTAAT
Found at i:35418662 original size:20 final size:20
Alignment explanation
Indices: 35418614--35418677 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
35418604 AACCTGTTTG
35418614 AAAATCATTTTGA--TGTGTT
1 AAAATCATTTTGACTTG-GTT
*
35418633 AAAATGATTTT-ATCTTGGTT
1 AAAATCATTTTGA-CTTGGTT
*
35418653 GAAATCATTTTGACTTGGTT
1 AAAATCATTTTGACTTGGTT
35418673 AAAAT
1 AAAAT
35418678 TTGAAGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.03
19 10 0.27
20 23 0.62
21 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (20 bp):
AAAATCATTTTGACTTGGTT
Found at i:35419343 original size:58 final size:60
Alignment explanation
Indices: 35419278--35419394 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 60
35419268 TAATCACTAA
* *
35419278 TATTAAATTAATATAATAATTA-T-CAAGATAAATATTCAATTCAATTTAATATTAAAAC
1 TATTAAATTAATAGAATAATTACTACAAGATAAATATTAAATTCAATTTAATATTAAAAC
* *
35419336 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTTAATTTAATATTAAA
1 TATTAAATTAATAGAATAATTA-CTACAAGATAAATATTAAATTCAATTTAATATTAAA
35419395 TTAACAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.38
60 1 0.02
61 31 0.60
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (60 bp):
TATTAAATTAATAGAATAATTACTACAAGATAAATATTAAATTCAATTTAATATTAAAAC
Found at i:35419433 original size:48 final size:51
Alignment explanation
Indices: 35419336--35419443 Score: 141
Period size: 48 Copynumber: 2.2 Consensus size: 51
35419326 ATATTAAAAC
* * * *
35419336 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTTAATTTAA
1 TATTAAATTAACAAAATACTTA-CTACAAGATAAATATCAAATTAAATTTAA
*
35419388 TATTAAATTAACAAAATAC-TA-TA-AAGATAAGTATCAAATTAAATTTAA
1 TATTAAATTAACAAAATACTTACTACAAGATAAATATCAAATTAAATTTAA
35419436 TATTAAAT
1 TATTAAAT
35419444 CTATTAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 30 0.59
49 2 0.04
51 2 0.04
52 17 0.33
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (51 bp):
TATTAAATTAACAAAATACTTACTACAAGATAAATATCAAATTAAATTTAA
Found at i:35419740 original size:18 final size:19
Alignment explanation
Indices: 35419717--35419752 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35419707 CTTCGCATAC
35419717 TAGAC-TAGTTTTGGGTTT
1 TAGACTTAGTTTTGGGTTT
35419735 TAGACTTAGTTTTGGGTT
1 TAGACTTAGTTTTGGGTT
35419753 CTCGGACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (19 bp):
TAGACTTAGTTTTGGGTTT
Found at i:35419909 original size:14 final size:13
Alignment explanation
Indices: 35419890--35419928 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
35419880 TACTTTATCA
35419890 AAATTAATTTTCCC
1 AAATTAATTTT-CC
*
35419904 AAATTAGATTTTCT
1 AAATTA-ATTTTCC
35419918 AAATTAATTTT
1 AAATTAATTTT
35419929 TCAAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (13 bp):
AAATTAATTTTCC
Found at i:35420721 original size:23 final size:23
Alignment explanation
Indices: 35420691--35420748 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
35420681 CGTCACAAGT
35420691 GAATTAATTCATAAATGGATTCA
1 GAATTAATTCATAAATGGATTCA
35420714 GAATTAATTCATAAATGGATTCA
1 GAATTAATTCATAAATGGATTCA
35420737 GAATTAATTCAT
1 GAATTAATTCAT
35420749 CTTGGGTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (23 bp):
GAATTAATTCATAAATGGATTCA
Found at i:35427784 original size:19 final size:19
Alignment explanation
Indices: 35427760--35427796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35427750 ATCTAAAAAT
35427760 ATAAAAAAATAAAAATAAC
1 ATAAAAAAATAAAAATAAC
* *
35427779 ATAAAATAATGAAAATAA
1 ATAAAAAAATAAAAATAA
35427797 AAATAATTAA
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:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
ATAAAAAAATAAAAATAAC
Found at i:35436695 original size:27 final size:27
Alignment explanation
Indices: 35436641--35436691 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
35436631 CATCCCATTA
*
35436641 AAAAATAATTTTATATCAATATTAAAT
1 AAAAATAATTGTATATCAATATTAAAT
35436668 AAAAATAATTGTAT-T-AATATTAAA
1 AAAAATAATTGTATATCAATATTAAA
35436692 AATATCCCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
27 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AAAAATAATTGTATATCAATATTAAAT
Found at i:35441557 original size:38 final size:38
Alignment explanation
Indices: 35441506--35441583 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
35441496 TTTGGGGATG
35441506 AAATTCTTTTAAGGGGGAGAGAGTTGTAACATTCAAAA
1 AAATTCTTTTAAGGGGGAGAGAGTTGTAACATTCAAAA
35441544 AAATTCTTTTAAGGGGGAGAGAGTTGTAACATTCAAAA
1 AAATTCTTTTAAGGGGGAGAGAGTTGTAACATTCAAAA
35441582 AA
1 AA
35441584 TCGAGTTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (38 bp):
AAATTCTTTTAAGGGGGAGAGAGTTGTAACATTCAAAA
Found at i:35442935 original size:168 final size:168
Alignment explanation
Indices: 35442657--35442994 Score: 667
Period size: 168 Copynumber: 2.0 Consensus size: 168
35442647 AACATATCTC
35442657 AATTTATCTAGATTATACATGCCATACTTTAACATTTACACTTTCAAAAGGTACCAAAGATAAGT
1 AATTTATCTAGATTATACATGCCATACTTTAACATTTACACTTTCAAAAGGTACCAAAGATAAGT
35442722 TTGATAGTGTGGTGATGATCCTTGATGATCCCCAAGCTCTCGGTAGCTTCGATATCTATAAAACA
66 TTGATAGTGTGGTGATGATCCTTGATGATCCCCAAGCTCTCGGTAGCTTCGATATCTATAAAACA
35442787 GATGAAAAACACACAAAGTAAGCTTTCAAAAGCTTAGT
131 GATGAAAAACACACAAAGTAAGCTTTCAAAAGCTTAGT
35442825 AATTTATCTAGATTATACATGCCATACTTTAACATTTACACTTTCAAAAGGTACCAAAGATAAGT
1 AATTTATCTAGATTATACATGCCATACTTTAACATTTACACTTTCAAAAGGTACCAAAGATAAGT
*
35442890 TTGATAGTGTGGTGATGATCCTTGATGATCCCCAAGCTCTCGGTAGCTTCGATATCTATCAAACA
66 TTGATAGTGTGGTGATGATCCTTGATGATCCCCAAGCTCTCGGTAGCTTCGATATCTATAAAACA
35442955 GATGAAAAACACACAAAGTAAGCTTTCAAAAGCTTAGT
131 GATGAAAAACACACAAAGTAAGCTTTCAAAAGCTTAGT
35442993 AA
1 AA
35442995 GCCATATACA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (168 bp):
AATTTATCTAGATTATACATGCCATACTTTAACATTTACACTTTCAAAAGGTACCAAAGATAAGT
TTGATAGTGTGGTGATGATCCTTGATGATCCCCAAGCTCTCGGTAGCTTCGATATCTATAAAACA
GATGAAAAACACACAAAGTAAGCTTTCAAAAGCTTAGT
Found at i:35448159 original size:2 final size:2
Alignment explanation
Indices: 35448152--35448187 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35448142 AAAACAAGCA
35448152 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35448188 GAAAAGCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35455270 original size:9 final size:9
Alignment explanation
Indices: 35455256--35455314 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
35455246 ATAAGTATAA
35455256 AATTAACCG
1 AATTAACCG
*
35455265 AATTAACCA
1 AATTAACCG
*
35455274 AATTAATCG
1 AATTAACCG
**
35455283 AATTGCCCG
1 AATTAACCG
*
35455292 AATTACCCG
1 AATTAACCG
35455301 AATTAACCG
1 AATTAACCG
35455310 AATTA
1 AATTA
35455315 TTTGTATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:35455348 original size:5 final size:6
Alignment explanation
Indices: 35455333--35455373 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
35455323 AAATTATATG
*
35455333 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
35455374 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:35456496 original size:48 final size:48
Alignment explanation
Indices: 35456417--35456741 Score: 392
Period size: 48 Copynumber: 6.8 Consensus size: 48
35456407 GAGGGTAAAT
* * *
35456417 TGCCGATTCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
*
35456465 TGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGT-ACATATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC-TCACATATCAA
*
35456513 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* * * * * *
35456561 CGTCGATTCCATGTCCTAGACATGGTCTTACACTAGCGCACCTATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* *
35456609 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCT--CTTAT-AA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* * * *
35456654 TGTGGCCGATGCCATGTCCCAGAGATGGTCTTACACTGGCTCTCATA--ATG
1 --T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCA-A
*
35456704 TGGCCGATGCCATGTCCCAGACATGGTCTTATACTAGC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
35456742 GTATATATCA
Statistics
Matches: 243, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
45 2 0.01
46 4 0.02
47 1 0.00
48 231 0.95
49 2 0.01
50 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
Found at i:35458745 original size:48 final size:48
Alignment explanation
Indices: 35458666--35458990 Score: 392
Period size: 48 Copynumber: 6.8 Consensus size: 48
35458656 GAGGGTAAAT
* * *
35458666 TGCCGATTCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
*
35458714 TGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCGT-ACATATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC-TCACATATCAA
*
35458762 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* * * * * *
35458810 CGTCGATTCCATGTCCTAGACATGGTCTTACACTAGCGCACCTATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* *
35458858 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCT--CTTAT-AA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
* * * *
35458903 TGTGGCCGATGCCATGTCCCAGAGATGGTCTTACACTGGCTCTCATA--ATG
1 --T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCA-A
*
35458953 TGGCCGATGCCATGTCCCAGACATGGTCTTATACTAGC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
35458991 GTATATATCA
Statistics
Matches: 243, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
45 2 0.01
46 4 0.02
47 1 0.00
48 231 0.95
49 2 0.01
50 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
Found at i:35473823 original size:16 final size:17
Alignment explanation
Indices: 35473802--35473835 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
35473792 ATTATTTGGA
35473802 ATTAGGTT-ATTCAATT
1 ATTAGGTTGATTCAATT
35473818 ATTAGGTTGGATTCAATT
1 ATTAGGTT-GATTCAATT
35473836 TAAATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
ATTAGGTTGATTCAATT
Found at i:35475596 original size:96 final size:94
Alignment explanation
Indices: 35475448--35475776 Score: 356
Period size: 96 Copynumber: 3.4 Consensus size: 94
35475438 GACCATGGCG
* * * * * *
35475448 ATATGAGAGCC-GTGTAAGACCATGTCTGGGACATGGCATCGGTCTCGGTATGTGTCAATGTAAT
1 ATATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGTATTGTTATGTGTCAGTGTAAG
*
35475512 ACCATGTCTAGGACATGGCATCATCACCGGT
66 ACCATGTCTAGGACATGGCATC--CACCGAT
* * *
35475543 ATATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTATTGTTATGTGAGCCAGTGTA
1 ATATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGTATTGTTATGT--GTCAGTGTA
* * *
35475608 AGACCATGTCTGGGACATGGCATCGACCTCA-
64 AGACCATGTCTAGGACATGGCATCCACC-GAT
* * * * *
35475639 ATATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGAATTGTTAGATGTGTCGGTGTA
1 ATATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGTATTGTT--ATGTGTCAGTGTA
*
35475704 AGAACATGTCTAGGACATGGCATCGGCACCGAT
64 AGACCATGTCTAGGACATGGCATC--CACCGAT
* * * *
35475737 GTATGAGAGCTAGTGTAAGACCAGGTCTGGGACATGGCAT
1 ATATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCAT
35475777 TGGCATTTTA
Statistics
Matches: 198, Mismatches: 27, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
95 10 0.05
96 117 0.59
97 1 0.01
98 70 0.35
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (94 bp):
ATATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGTATTGTTATGTGTCAGTGTAAG
ACCATGTCTAGGACATGGCATCCACCGAT
Found at i:35475613 original size:48 final size:48
Alignment explanation
Indices: 35475449--35475776 Score: 234
Period size: 48 Copynumber: 6.8 Consensus size: 48
35475439 ACCATGGCGA
* * * *
35475449 TATGAGAGCC-GTGTAAGACCATGTCTGGGACATGGCATCGGTCTCGG
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCGT
* * * * * * *
35475496 TATGT--GTCAATGTAATACCATGTCTAGGACATGGCATC-ATCACCGGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGT-ATC-GT
* * *
35475543 ATATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTATTGT
1 -TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCGT
* *** **
35475592 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCGT
* * * * *
35475640 TATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGAATTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCGT
* * * * * * * *
35475688 TA-GATGTGTCGGTGTAAGAACATGTCTAGGACATGGCATCGGCACCGAT
1 TATG-TGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCG-T
* * * *
35475737 GTATGAGAGCTAGTGTAAGACCAGGTCTGGGACATGGCAT
1 -TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCAT
35475777 TGGCATTTTA
Statistics
Matches: 212, Mismatches: 58, Indels: 19
0.73 0.20 0.07
Matches are distributed among these distances:
45 3 0.01
46 27 0.13
47 6 0.03
48 114 0.54
49 3 0.01
50 57 0.27
51 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATCGT
Found at i:35477761 original size:25 final size:25
Alignment explanation
Indices: 35477728--35477776 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
35477718 TATAGCTCGG
35477728 TTTTACATAGTTGTGTACATTTAAT
1 TTTTACATAGTTGTGTACATTTAAT
35477753 TTTTACATAGTTGTGTACATTTAA
1 TTTTACATAGTTGTGTACATTTAA
35477777 GTCTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (25 bp):
TTTTACATAGTTGTGTACATTTAAT
Found at i:35477951 original size:21 final size:21
Alignment explanation
Indices: 35477927--35477966 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35477917 ATTGTTATCG
35477927 TGTTCACCATTACTGACCCGT
1 TGTTCACCATTACTGACCCGT
**
35477948 TGTTTGCCATTACTGACCC
1 TGTTCACCATTACTGACCC
35477967 ATTACCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (21 bp):
TGTTCACCATTACTGACCCGT
Found at i:35484026 original size:61 final size:61
Alignment explanation
Indices: 35483961--35484075 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
35483951 ATTAATTAAT
* *
35483961 ACTAAAATGTAACACGCGAAAAAGAACAGGAGACGAATAGGAAAATATTCCCAAATAAAGG
1 ACTAAAATATAACACACGAAAAAGAACAGGAGACGAATAGGAAAATATTCCCAAATAAAGG
* * ** * * *
35484022 ACTAAAATATAACGCATGAAAAAGAGTAGGGGGCGAATGGGAAAATATTCCCAA
1 ACTAAAATATAACACACGAAAAAGAACAGGAGACGAATAGGAAAATATTCCCAA
35484076 CCTTAGGACA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.50, C:0.14, G:0.22, T:0.15
Consensus pattern (61 bp):
ACTAAAATATAACACACGAAAAAGAACAGGAGACGAATAGGAAAATATTCCCAAATAAAGG
Found at i:35485244 original size:17 final size:16
Alignment explanation
Indices: 35485219--35485271 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 16
35485209 GTAAGTAGAC
35485219 TTGGATTTTTTTATTTT
1 TTGG-TTTTTTTATTTT
35485236 TTGGTTTTTTTA--TT
1 TTGGTTTTTTTATTTT
*
35485250 TT-GTTTATTTA-TTT
1 TTGGTTTTTTTATTTT
35485264 TTGGTTTT
1 TTGGTTTT
35485272 GGGCTAGACG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 4 0.12
16 8 0.25
17 4 0.12
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.77
Consensus pattern (16 bp):
TTGGTTTTTTTATTTT
Found at i:35485498 original size:44 final size:44
Alignment explanation
Indices: 35485444--35485807 Score: 293
Period size: 44 Copynumber: 8.0 Consensus size: 44
35485434 AACTTCAGGG
* * * * *
35485444 GTAGTTTCAATCTACTCCGCTATAACTTCAGGGAGATGAGATTC
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTT
* * * * *
35485488 GTAGCTTCAATTTGCTCTACTACAACTTCAAGGAAATAAGATTT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTT
* * * * *
35485532 GTAGCTTTAATCTACTCCATTGCAACTTCAGAGAGATGAGACTCGCTAT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGA-T---T-T
* * * *
35485581 GGTAGATTTAATCTGAC-CCACTGCAACTTCAGAGG-TATAAGATTT
1 -GTAGCTTCAATCT-ACTCCACTACAACTTCAG-GGAGATAAGATTT
* *
35485626 GTCA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
1 GT-AGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTT
* * ** *
35485670 ATAGCTTCAATCTGCTCCACTGTAACTTCAAGGAGATAAAGATTTGTTGTT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGAT-AAGA-----T-TT
* *
35485721 GTAGCTTCAATCTACTCCACTAAAACTTTAGGGAGATAAGATTT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTT
* *
35485765 GTAGCTTTAATCTACTCCACTACAACTTTAGGGAGATAAGATT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATT
35485808 CGCTATGGTC
Statistics
Matches: 261, Mismatches: 40, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
43 4 0.02
44 173 0.66
45 8 0.03
46 1 0.00
48 1 0.00
49 2 0.01
50 36 0.14
51 36 0.14
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTT
Found at i:35485748 original size:95 final size:94
Alignment explanation
Indices: 35485444--35485807 Score: 252
Period size: 95 Copynumber: 3.9 Consensus size: 94
35485434 AACTTCAGGG
* * * * ** * * *
35485444 GTAGTTTCAATCTACTCCGCTATAACTTCAGGGAGATGAGATTCGTAGCTTCAATTTGCTCTACT
1 GTAGCTTCAATCTACTCCACTAAAACTTCAGGGAGATAAGATTTATAGCTTCAATCTACTCCACT
*
35485509 ACAACTTCAAGGAAATAAGA-----T-TT
66 ACAACTTCAAGGAGATAAGATTTGTTGTT
* * ** * * * * *
35485532 GTAGCTTTAATCTACTCCATTGCAACTTCAGAGAGATGAGACTCGCTATGGTAGATTTAATCTGA
1 GTAGCTTCAATCTACTCCACTAAAACTTCAGGGAGATAAGA-T---T-T-ATAGCTTCAATCT-A
* *
35485597 C-CCACTGCAACTTCAGAGG-TATAAGA--T-TTG-T
59 CTCCACTACAACTTCA-AGGAGATAAGATTTGTTGTT
* * ** *
35485628 -CA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTCAATCTGCTCCACT
1 GTAGCTTCAATCTACTCCACTAAAACTTCAGGGAGATAAGATTTATAGCTTCAATCTACTCCACT
**
35485691 GTAACTTCAAGGAGATAAAGATTTGTTGTT
66 ACAACTTCAAGGAGAT-AAGATTTGTTGTT
* * *
35485721 GTAGCTTCAATCTACTCCACTAAAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTACTCCACT
1 GTAGCTTCAATCTACTCCACTAAAACTTCAGGGAGATAAGATTTATAGCTTCAATCTACTCCACT
* *
35485786 ACAACTTTAGGGAGATAAGATT
66 ACAACTTCAAGGAGATAAGATT
35485808 CGCTATGGTC
Statistics
Matches: 217, Mismatches: 39, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
87 4 0.02
88 59 0.27
89 6 0.03
90 1 0.00
91 1 0.00
92 4 0.02
93 2 0.01
94 67 0.31
95 71 0.33
96 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (94 bp):
GTAGCTTCAATCTACTCCACTAAAACTTCAGGGAGATAAGATTTATAGCTTCAATCTACTCCACT
ACAACTTCAAGGAGATAAGATTTGTTGTT
Found at i:35491872 original size:47 final size:49
Alignment explanation
Indices: 35491801--35492060 Score: 236
Period size: 49 Copynumber: 5.5 Consensus size: 49
35491791 AGGGTATAAC
*
35491801 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-CATC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACATCGAA
* * *
35491848 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-ATCGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-ACATCGAA
* * * * * *
35491897 GCCGACGCCATGTCTCAAACATGGTCTTACACTAGCTC-TCACATATCCAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAC--ATCGAA
* * * * *
35491947 GACGATGCCATGTACCAGACATGGTCTTACACTGACACAT--C-TCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACATCGAA
* ** *
35491993 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTA-CATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACATCGAA
*
35492039 GCCGATG-CATGTCCCAGTCATG
1 GCCGATGCCATGTCCCAGACATG
35492061 TCACTAGCTC
Statistics
Matches: 170, Mismatches: 32, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
44 13 0.08
45 13 0.08
46 34 0.20
47 35 0.21
48 4 0.02
49 36 0.21
50 34 0.20
51 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCACATCGAA
Found at i:35491980 original size:99 final size:96
Alignment explanation
Indices: 35491801--35491980 Score: 263
Period size: 96 Copynumber: 1.8 Consensus size: 96
35491791 AGGGTATAAC
* * * *
35491801 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCCAG
1 GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGACGATGCCATGTACCAG
35491866 ACATGGTCTTACACTGGCTATCGAAATCGAG
66 ACATGGTCTTACACTGGCTATCGAAATCGAG
* *
35491897 GCCGACGCCATGTCTCAAACATGGTCTTACACTAGCTC-TCACATATCCATGACGATGCCATGTA
1 GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATC-C--AT-CAAGACGATGCCATGTA
35491961 CCAGACATGGTCTTACACTG
62 CCAGACATGGTCTTACACTG
35491981 ACACATCTCG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
95 2 0.03
96 36 0.49
98 2 0.03
99 34 0.46
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (96 bp):
GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGACGATGCCATGTACCAG
ACATGGTCTTACACTGGCTATCGAAATCGAG
Found at i:35491997 original size:96 final size:96
Alignment explanation
Indices: 35491801--35492023 Score: 262
Period size: 96 Copynumber: 2.3 Consensus size: 96
35491791 AGGGTATAAC
* * *
35491801 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCCAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGACGATGCCATGTACCAG
*
35491866 ACATGGTCTTACACTGGCTATCGAAATCGAG
66 ACATGGTCTTACACTGACTATCGAAATCGAG
* * *
35491897 GCCGACGCCATGTCTCAAACATGGTCTTACACTAGCTC-TCACATATCCATGACGATGCCATGTA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATC-C--AT-CAAGACGATGCCATGTA
**
35491961 CCAGACATGGTCTTACACTGAC-A-C-ATCTCGTA-
62 CCAGACATGGTCTTACACTGACTATCGAAATCG-AG
*
35491993 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT
35492024 GGCTTACATG
Statistics
Matches: 110, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
94 10 0.09
95 14 0.13
96 46 0.42
97 2 0.02
98 3 0.03
99 35 0.32
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGACGATGCCATGTACCAG
ACATGGTCTTACACTGACTATCGAAATCGAG
Found at i:35492062 original size:46 final size:47
Alignment explanation
Indices: 35491801--35492060 Score: 246
Period size: 46 Copynumber: 5.5 Consensus size: 47
35491791 AGGGTATAAC
* *
35491801 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCT-CATCCATC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACAT--ATCGAG
* *
35491848 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA-C-ATATCGAG
* * * * * *
35491897 GCCGACGCCATGTCTCAAACATGGTCTTACACTAGCTCTCACATATCCAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-GCT-ACATATCGAG
* * * *
35491947 GACGATGCCATGTACCAGACATGGTCTTACACTGAC-ACATCTCGTA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATATCG-AG
*
35491993 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TACATATCGAG
*
35492039 GCCGATG-CATGTCCCAGTCATG
1 GCCGATGCCATGTCCCAGACATG
35492061 TCACTAGCTC
Statistics
Matches: 176, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
44 12 0.07
45 14 0.08
46 39 0.22
47 36 0.20
48 4 0.02
49 32 0.18
50 35 0.20
51 3 0.02
52 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATATCGAG
Found at i:35492113 original size:38 final size:38
Alignment explanation
Indices: 35492068--35492183 Score: 214
Period size: 38 Copynumber: 3.1 Consensus size: 38
35492058 ATGTCACTAG
35492068 CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
1 CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
35492106 CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
1 CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
* *
35492144 CTTTCGTCTCAATGCCGATGCCATGTCCCAGACATGGC
1 CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
35492182 CT
1 CT
35492184 TACACTGGCT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (38 bp):
CTCTCGTCTCAATGCCGATGCCATGTCCCAAACATGGC
Done.