Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 65 of 75
Found at i:20915686 original size:10 final size:10
Alignment explanation
Indices: 20915671--20915709 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
20915661 GTTTCGGGTA
20915671 AATTTTATAT
1 AATTTTATAT
20915681 AATTTTATAT
1 AATTTTATAT
* *
20915691 AATTGTATTT
1 AATTTTATAT
20915701 AATTTTATA
1 AATTTTATA
20915710 ATTATTCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
AATTTTATAT
Found at i:20916752 original size:16 final size:16
Alignment explanation
Indices: 20916731--20916928 Score: 69
Period size: 16 Copynumber: 12.0 Consensus size: 16
20916721 ACACTTATTA
20916731 AACTTACATAATACAT
1 AACTTACATAATACAT
*
20916747 AACTTACAT-GT---T
1 AACTTACATAATACAT
20916759 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
20916775 GACTTATATAAACTTTTTATAT
1 AACTTACAT-AA-----TACAT
20916797 AAACTTACATAATACAT
1 -AACTTACATAATACAT
* *
20916814 TACTTACATATTAACTTATAT
1 AACTTAC--A-TAA--TACAT
20916835 AAACTTACATAATACAT
1 -AACTTACATAATACAT
*
20916852 TACTTACATAGCATACAT
1 AACTTACATA--ATACAT
20916870 AACTTAC-----AC--
1 AACTTACATAATACAT
*
20916879 AACTTAAATAATACA-
1 AACTTACATAATACAT
20916894 AAGCTTACATAACTTACAT
1 AA-CTTACATAA--TACAT
*
20916913 AACCTACATAATACAT
1 AACTTACATAATACAT
20916929 TATAACTTAC
Statistics
Matches: 136, Mismatches: 17, Indels: 58
0.64 0.08 0.27
Matches are distributed among these distances:
9 6 0.04
11 2 0.01
12 10 0.07
13 1 0.01
14 2 0.01
15 3 0.02
16 45 0.33
17 10 0.07
18 25 0.18
19 8 0.06
20 1 0.01
21 4 0.03
22 12 0.09
23 7 0.05
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:20916754 original size:9 final size:9
Alignment explanation
Indices: 20916731--20916956 Score: 95
Period size: 9 Copynumber: 25.0 Consensus size: 9
20916721 ACACTTATTA
20916731 AACTTACAT
1 AACTTACAT
20916740 AA--TACAT
1 AACTTACAT
20916747 AACTTACATGTT
1 AACTTACA---T
20916759 AACTTACAT
1 AACTTACAT
20916768 AA--TACAT
1 AACTTACAT
* *
20916775 GACTTATAT
1 AACTTACAT
*
20916784 AAACTTTTTATAT
1 -AAC---TTACAT
20916797 AAACTTACAT
1 -AACTTACAT
20916807 AA--TACAT
1 AACTTACAT
*
20916814 TACTTACATATT
1 AACTTAC--A-T
*
20916826 AACTTATAT
1 AACTTACAT
20916835 AAACTTACAT
1 -AACTTACAT
20916845 AA--TACAT
1 AACTTACAT
*
20916852 TACTTACAT
1 AACTTACAT
* *
20916861 AGCATACAT
1 AACTTACAT
*
20916870 AACTTACAC
1 AACTTACAT
*
20916879 AACTTAAAT
1 AACTTACAT
20916888 AA--TACA-
1 AACTTACAT
20916894 AAGCTTACAT
1 AA-CTTACAT
20916904 AACTTACAT
1 AACTTACAT
*
20916913 AACCTACAT
1 AACTTACAT
20916922 AA--TACATTAT
1 AACTTAC---AT
20916932 AACTTAC--
1 AACTTACAT
20916939 AACTTACAT
1 AACTTACAT
*
20916948 AACATACAT
1 AACTTACAT
20916957 TACTNNNNNN
Statistics
Matches: 167, Mismatches: 20, Indels: 60
0.68 0.08 0.24
Matches are distributed among these distances:
6 2 0.01
7 38 0.23
9 76 0.46
10 22 0.13
11 1 0.01
12 18 0.11
13 10 0.06
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:20916796 original size:13 final size:13
Alignment explanation
Indices: 20916778--20916802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20916768 AATACATGAC
20916778 TTATATAAACTTT
1 TTATATAAACTTT
20916791 TTATATAAACTT
1 TTATATAAACTT
20916803 ACATAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATATAAACTTT
Found at i:20916858 original size:38 final size:39
Alignment explanation
Indices: 20916759--20916861 Score: 149
Period size: 38 Copynumber: 2.7 Consensus size: 39
20916749 CTTACATGTT
*
20916759 AACTTACATAATACATGACTT--ATATAAACTTTTTATATA
1 AACTTACATAATACATTACTTACATATAAAC--TTTATATA
*
20916798 AACTTACATAATACATTACTTACATATTAAC-TTATATA
1 AACTTACATAATACATTACTTACATATAAACTTTATATA
20916836 AACTTACATAATACATTACTTACATA
1 AACTTACATAATACATTACTTACATA
20916862 GCATACATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 33 0.55
39 20 0.33
41 7 0.12
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.39
Consensus pattern (39 bp):
AACTTACATAATACATTACTTACATATAAACTTTATATA
Found at i:20916890 original size:43 final size:43
Alignment explanation
Indices: 20916836--20916920 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
20916826 AACTTATATA
* * * *
20916836 AACTTACATAATACATTA-CTTACATAGCATACATAACTTACAC
1 AACTTAAATAATACA-AAGCTTACATAACATACATAACCTACAC
*
20916879 AACTTAAATAATACAAAGCTTACATAACTTACATAACCTACA
1 AACTTAAATAATACAAAGCTTACATAACATACATAACCTACA
20916921 TAATACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.28
Consensus pattern (43 bp):
AACTTAAATAATACAAAGCTTACATAACATACATAACCTACAC
Found at i:20916892 original size:25 final size:26
Alignment explanation
Indices: 20916864--20916923 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
20916854 CTTACATAGC
20916864 ATACATAA-CTTACACAACTTAAATA
1 ATACATAAGCTTACACAACTTAAATA
* *
20916889 ATACA-AAGCTTACATAACTTACATA
1 ATACATAAGCTTACACAACTTAAATA
20916914 ACCTACATAA
1 A--TACATAA
20916924 TACATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 21 0.72
27 4 0.14
28 2 0.07
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.27
Consensus pattern (26 bp):
ATACATAAGCTTACACAACTTAAATA
Found at i:20916903 original size:34 final size:34
Alignment explanation
Indices: 20916856--20916927 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
20916846 ATACATTACT
* *
20916856 TACATAGCATACATAACTTACACAACTTAAATAA
1 TACAAAGCATACATAACTTACACAACCTAAATAA
* * *
20916890 TACAAAGCTTACATAACTTACATAACCTACATAA
1 TACAAAGCATACATAACTTACACAACCTAAATAA
20916924 TACA
1 TACA
20916928 TTATAACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (34 bp):
TACAAAGCATACATAACTTACACAACCTAAATAA
Found at i:20916954 original size:28 final size:27
Alignment explanation
Indices: 20916902--20916958 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
20916892 CAAAGCTTAC
20916902 ATAACTTACATAACCTACATAATACATT
1 ATAACTTACA-AACCTACATAATACATT
*
20916930 ATAACTTAC-AACTTACATAACATACATT
1 ATAACTTACAAACCTACAT-A-ATACATT
20916958 A
1 A
20916959 CTNNNNNNNN
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 8 0.31
27 1 0.04
28 17 0.65
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAACTTACAAACCTACATAATACATT
Found at i:20926220 original size:21 final size:21
Alignment explanation
Indices: 20926194--20926264 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
20926184 CTACAACTTA
*
20926194 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
* ** *
20926215 AAGCAGCGGCTACAGCAAGGG
1 AAGCAGAGGCCGCAGCGAGGG
* *
20926236 AAGCGGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGGG
20926257 AAGCAGAG
1 AAGCAGAG
20926265 CAGAGCAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.45, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGGG
Found at i:20926631 original size:42 final size:42
Alignment explanation
Indices: 20926585--20926694 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 42
20926575 TTTTGTATAA
* *
20926585 AAACGCCGCTAAAGACCATGTTCTTTAGCA-GTACTTA-AGAAT
1 AAACGCCGCTAAAGAACATGTTCTTTAG-AGGCACTTATA-AAT
*
20926627 AAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTATAAAT
1 AAACGCCGCTAAAGAACATGTTCTTTAGAGGCACTTATAAAT
*
20926669 AAACGCCGCTAAAGAACATGATCTTT
1 AAACGCCGCTAAAGAACATGTTCTTT
20926695 CGCGGCGTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
41 1 0.02
42 60 0.97
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGAGGCACTTATAAAT
Found at i:20926830 original size:83 final size:84
Alignment explanation
Indices: 20926673--20926831 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 84
20926663 ATAAATAAAC
* * *
20926673 GCCGCTAAAGAACATGATCTTTCGCGGCGTTTTTTTCTAAGTGCCGCTAAACAACATGGTCTTTA
1 GCCGCTAAAGAACACGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAACAACATGGTCTTTA
*
20926738 GCGGCGTTTTTTTTAAAGT
66 GCAGCGTTTTTTTTAAAGT
* * * *
20926757 GCCGCTAAAGAACACGGTCTTTAGGGGC-TTTTTTT-TAAAGCGCTGCTAAAGAACATGGTCTTT
1 GCCGCTAAAGAACACGATCTTTAGCGGCGTTTTTTTCT-AAGCGCCGCTAAACAACATGGTCTTT
* *
20926820 ATCAGTGTTTTT
65 AGCAGCGTTTTT
20926832 GTTTGTAAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 1 0.02
83 39 0.61
84 24 0.38
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (84 bp):
GCCGCTAAAGAACACGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAACAACATGGTCTTTA
GCAGCGTTTTTTTTAAAGT
Found at i:20926831 original size:42 final size:42
Alignment explanation
Indices: 20926626--20926820 Score: 218
Period size: 42 Copynumber: 4.7 Consensus size: 42
20926616 TACTTAAGAA
* * * ***
20926626 TAAA-CGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTATAAA
1 TAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTT
* *
20926668 TAAA-CGCCGCTAAAGAACATGATCTTTCGCGGCGTTTTTTT
1 TAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
* *
20926709 CT-AAGTGCCGCTAAACAACATGGTCTTTAGCGGCGTTTTTTT
1 -TAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
* * *
20926751 TAAAGTGCCGCTAAAGAACACGGTCTTTAGGGGC-TTTTTTT
1 TAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
*
20926792 TAAAGCGCTGCTAAAGAACATGGTCTTTA
1 TAAAGCGCCGCTAAAGAACATGGTCTTTA
20926821 TCAGTGTTTT
Statistics
Matches: 133, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
41 39 0.29
42 94 0.71
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
Found at i:20929565 original size:5 final size:5
Alignment explanation
Indices: 20929549--20929594 Score: 83
Period size: 5 Copynumber: 9.0 Consensus size: 5
20929539 GAAAGGACCA
20929549 TATAT ATATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
20929595 ATTATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:20930340 original size:43 final size:44
Alignment explanation
Indices: 20930292--20930379 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
20930282 CTAGAAATCA
20930292 TTTTACGGAAAATATTTTACTGGCAAACAAAC-GACCCTAAACT
1 TTTTACGGAAAATATTTTACTGGCAAACAAACGGACCCTAAACT
20930335 TTTTACGGAAAATATTTTACTGGCAAACAAACGGACCCTAAACT
1 TTTTACGGAAAATATTTTACTGGCAAACAAACGGACCCTAAACT
20930379 T
1 T
20930380 CTGCCAAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 32 0.73
44 12 0.27
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (44 bp):
TTTTACGGAAAATATTTTACTGGCAAACAAACGGACCCTAAACT
Found at i:20936322 original size:31 final size:31
Alignment explanation
Indices: 20936284--20936343 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
20936274 TTGATCACTG
*
20936284 ACCTATTCAAAA-GTTTTCATTTAAGTCACCA
1 ACCTATTCAAAACGCTTT-ATTTAAGTCACCA
20936315 ACCTATTCAAAACGCTTTATTTAAGTCAC
1 ACCTATTCAAAACGCTTTATTTAAGTCAC
20936344 TAAACTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (31 bp):
ACCTATTCAAAACGCTTTATTTAAGTCACCA
Found at i:20937785 original size:20 final size:20
Alignment explanation
Indices: 20937724--20937785 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
20937714 AATATTAGAT
20937724 TAAATTTAATATTAAATTAA
1 TAAATTTAATATTAAATTAA
20937744 TTAAATTTAATATTAAGA-TAA
1 -TAAATTTAATATTAA-ATTAA
* *
20937765 TCACTTTAATATTAAATTAA
1 TAAATTTAATATTAAATTAA
20937785 T
1 T
20937786 TTAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.46
21 18 0.49
22 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAATTTAATATTAAATTAA
Found at i:20937796 original size:16 final size:16
Alignment explanation
Indices: 20937679--20937797 Score: 67
Period size: 16 Copynumber: 7.8 Consensus size: 16
20937669 ACTTAATCAT
20937679 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
* *
20937695 TATAATACTT--ATCAA
1 TTTAATA-TTAAATTAA
* * *
20937710 GATAAATATTAGATTAAA
1 -TTTAATATTAAATT-AA
20937728 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
*
20937744 -TTAA-ATTTAA-T-A
1 TTTAATATTAAATTAA
* * *
20937756 -TTAAGA-T-AATCAC
1 TTTAATATTAAATTAA
20937769 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
20937785 TTTAATATTAAAT
1 TTTAATATTAAAT
20937798 CTATTAAAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
11 2 0.03
12 6 0.08
13 2 0.03
14 10 0.13
15 11 0.14
16 29 0.38
17 15 0.19
18 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAATATTAAATTAA
Found at i:20954221 original size:7 final size:7
Alignment explanation
Indices: 20954185--20954252 Score: 75
Period size: 7 Copynumber: 9.9 Consensus size: 7
20954175 TTGAGTTCAA
*
20954185 GGTTTAT
1 GGTTTAG
*
20954192 GGTGTA-
1 GGTTTAG
20954198 GGTTTAG
1 GGTTTAG
*
20954205 GGCTTAG
1 GGTTTAG
*
20954212 GGTTTGG
1 GGTTTAG
*
20954219 GGTTTAA
1 GGTTTAG
*
20954226 GGTTTAA
1 GGTTTAG
20954233 GGTTTAG
1 GGTTTAG
20954240 GGTTTAG
1 GGTTTAG
20954247 GGTTTA
1 GGTTTA
20954253 TGTTTTAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
6 5 0.10
7 47 0.90
ACGTcount: A:0.16, C:0.01, G:0.40, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:20954348 original size:21 final size:21
Alignment explanation
Indices: 20954324--20954364 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20954314 TAGGGCTTGA
* * *
20954324 TGTTTATGGTTTACGGTTTAG
1 TGTTAATGATTTAAGGTTTAG
20954345 TGTTAATGATTTAAGGTTTA
1 TGTTAATGATTTAAGGTTTA
20954365 CAATGCATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (21 bp):
TGTTAATGATTTAAGGTTTAG
Found at i:20954399 original size:7 final size:7
Alignment explanation
Indices: 20954379--20954428 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
20954369 GCATGGTGTT
*
20954379 GGGTTTT
1 GGGTTTA
*
20954386 GGATTTA
1 GGGTTTA
20954393 GGGTTTA
1 GGGTTTA
20954400 GGGTTTA
1 GGGTTTA
* *
20954407 AGATTTA
1 GGGTTTA
*
20954414 AGGTTTA
1 GGGTTTA
20954421 GGGTTTA
1 GGGTTTA
20954428 G
1 G
20954429 TATTTAGTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:20954403 original size:21 final size:21
Alignment explanation
Indices: 20954379--20954435 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
20954369 GCATGGTGTT
*
20954379 GGGTTTTGGATTTAGGGTTTA
1 GGGTTTAGGATTTAGGGTTTA
* *
20954400 GGGTTTAAGATTTAAGGTTTA
1 GGGTTTAGGATTTAGGGTTTA
*
20954421 GGGTTTAGTATTTAG
1 GGGTTTAGGATTTAG
20954436 TGTTACAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (21 bp):
GGGTTTAGGATTTAGGGTTTA
Found at i:20958731 original size:148 final size:149
Alignment explanation
Indices: 20958571--20958869 Score: 591
Period size: 148 Copynumber: 2.0 Consensus size: 149
20958561 TAATATATAA
20958571 TATAAATATTTTTTATTTTTAATATTTTAAGGAATAGTTATTTAGATTAATTTATTAAATTTAAG
1 TATAAATATTTTTTATTTTTAATATTTTAAGGAATAGTTATTTAGATTAATTTATTAAATTTAAG
20958636 TCACGATTTGGCTGAGACCTTGAACATGTCTATAAACAAAACAATAGAGCTAAGTTTAATTTTCC
66 TCACGATTTGGCTGAGACCTTGAACATGTCTATAAACAAAACAATAGAGCTAAGTTTAATTTTCC
20958701 AAG-AAAAAGGCTTCTTAT
131 AAGAAAAAAGGCTTCTTAT
20958719 TATAAATATTTTTTATTTTTAATATTTTAAGGAATAGTTATTTAGATTAATTTATTAAATTTAAG
1 TATAAATATTTTTTATTTTTAATATTTTAAGGAATAGTTATTTAGATTAATTTATTAAATTTAAG
20958784 TCACGATTTGGCTGAGACCTTGAACATGTCTATAAACAAAACAATAGAGCTAAGTTTAATTTTCC
66 TCACGATTTGGCTGAGACCTTGAACATGTCTATAAACAAAACAATAGAGCTAAGTTTAATTTTCC
20958849 AAGAAAAAAGGCTTCTTAT
131 AAGAAAAAAGGCTTCTTAT
20958868 TA
1 TA
20958870 AGAGAGTGTA
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 133 0.89
149 17 0.11
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (149 bp):
TATAAATATTTTTTATTTTTAATATTTTAAGGAATAGTTATTTAGATTAATTTATTAAATTTAAG
TCACGATTTGGCTGAGACCTTGAACATGTCTATAAACAAAACAATAGAGCTAAGTTTAATTTTCC
AAGAAAAAAGGCTTCTTAT
Found at i:20959082 original size:41 final size:39
Alignment explanation
Indices: 20959037--20959133 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
20959027 AGCGGTATTT
*
20959037 TTAGCGGCGTTCAGATAAAAAATGCCGCTAAAAATCGAGCA
1 TTAGCGGCGTT--GATAAAAAATGCCGCTAAAAATAGAGCA
** *
20959078 TTAGCGGCGCTTTTTGAAAAATGCCGCTAAAAATAGAGCA
1 TTAGCGGCG-TTGATAAAAAATGCCGCTAAAAATAGAGCA
* *
20959118 TTAACGGCGTTTATAA
1 TTAGCGGCGTTGATAA
20959134 GGAAGCGCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 5 0.10
40 32 0.67
41 9 0.19
42 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (39 bp):
TTAGCGGCGTTGATAAAAAATGCCGCTAAAAATAGAGCA
Found at i:20959317 original size:82 final size:79
Alignment explanation
Indices: 20959181--20959430 Score: 261
Period size: 82 Copynumber: 3.1 Consensus size: 79
20959171 CTGAGGCTTT
* ** *
20959181 GGGGACTTTAGCTGCGTTTTTGAAGAAGCGTCGCTAATGT-TGGGGGATTTAGCGGCGTTTTTGA
1 GGGGA-TTTAGC-GCGTTTTTG-AGAAACGTCGCTAAT-TCTCTGGGCTTTAGCGGCGTTTTT--
* *
20959245 AGAAA-CGTCGCTAATGCTG
60 AGAAAGCGCCGCTAATGCTC
20959264 GGGGATTTAGCGGCGTTTTTGAGGAAACGTCGCTAATTCTCTGGGCTTTAGCGGCGTTTTCTAGA
1 GGGGATTTAGC-GCGTTTTTGA-GAAACGTCGCTAATTCTCTGGGCTTTAGCGGCGTTTT-TAGA
* *
20959329 AAGCGCCGCTATTGCTT
63 AAGCGCCGCTAATGCTC
* * * * * *
20959346 TGGGTTTTAGCGCGTTTTTTTAGAAAGCGCCGCTAATTCTCTAGGCTTTAGCGGCATTTTTAGAA
1 GGGGATTTAGCGCG-TTTTTGAGAAA-CGTCGCTAATTCTCTGGGCTTTAGCGGCGTTTTTAGAA
20959411 AGCGCCGCTAATGCTC
64 AGCGCCGCTAATGCTC
20959427 GGGG
1 GGGG
20959431 CTTTTAGGGT
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
81 36 0.25
82 102 0.71
83 6 0.04
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (79 bp):
GGGGATTTAGCGCGTTTTTGAGAAACGTCGCTAATTCTCTGGGCTTTAGCGGCGTTTTTAGAAAG
CGCCGCTAATGCTC
Found at i:20959437 original size:41 final size:40
Alignment explanation
Indices: 20959181--20959434 Score: 219
Period size: 41 Copynumber: 6.2 Consensus size: 40
20959171 CTGAGGCTTT
* * * *
20959181 GGGGACTTTAGCTGCGTTTTT-GAAGAAGCGTCGCTAATGTTG
1 GGGG-CTTTAGCGGCGTTTTTAG-A-AAGCGCCGCTAATGCTC
* * *
20959223 GGGGATTTAGCGGCGTTTTTGAAGAAA-CGTCGCTAATGCTG
1 GGGGCTTTAGCGGCGTTTTT--AGAAAGCGCCGCTAATGCTC
* * *
20959264 GGGGATTTAGCGGCGTTTTTGAGGAAA-CGTCGCTAATTCTC
1 GGGGCTTTAGCGGCGTTTTT-A-GAAAGCGCCGCTAATGCTC
* * *
20959305 TGGGCTTTAGCGGCGTTTTCTAGAAAGCGCCGCTATTGCTT
1 GGGGCTTTAGCGGCGTTTT-TAGAAAGCGCCGCTAATGCTC
* * *
20959346 TGGGTTTTAGC-GCGTTTTTTTAGAAAGCGCCGCTAATTCTC
1 GGGGCTTTAGCGGCG--TTTTTAGAAAGCGCCGCTAATGCTC
** *
20959387 TAGGCTTTAGCGGCATTTTTAGAAAGCGCCGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTC
20959427 GGGGCTTT
1 GGGGCTTT
20959435 TAGGGTTAAC
Statistics
Matches: 181, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
40 38 0.21
41 128 0.71
42 13 0.07
43 1 0.01
44 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (40 bp):
GGGGCTTTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTC
Found at i:20959697 original size:21 final size:21
Alignment explanation
Indices: 20959648--20959713 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20959638 TATAAGATAT
* *
20959648 TTTAGTGTTT-TGTTTTAGGG
1 TTTAGTGTTTATGATTTAAGG
* * *
20959668 CTT-GATGTTTATGGTTTACGG
1 TTTAG-TGTTTATGATTTAAGG
*
20959689 TTTAGTGTTAATGATTTAAGG
1 TTTAGTGTTTATGATTTAAGG
20959710 TTTA
1 TTTA
20959714 CAATGCATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
21 27 0.75
22 1 0.03
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (21 bp):
TTTAGTGTTTATGATTTAAGG
Found at i:20960086 original size:156 final size:156
Alignment explanation
Indices: 20959803--20960116 Score: 585
Period size: 156 Copynumber: 2.0 Consensus size: 156
20959793 GGTTAATTAC
20959803 TTTTGTGATACCAAATTCAAAAAAATTACAAATACTTTTTGTTTTTTACTTCTTATTATGTTATT
1 TTTTGTGATACCAAATTCAAAAAAATTACAAATACTTTTTGTTTTTTACTTCTTATTATGTTATT
20959868 AGGGTTCTAAGTGACACGAATGCTTAGTTTATTGACTCGTCGTGGCATATATGTTATAATGAAAC
66 AGGGTTCTAAGTGACACGAATGCTTAGTTTATTGACTCGTCGTGGCATATATGTTATAATGAAAC
20959933 AAATTAATTGTGTTATTTG-ATTCGT
131 AAATTAATTGTGTTATTTGCATTCGT
*
20959958 TTTTGTGATATCAAATTCAAAAAAATTACAAATACTTTTTGTTTTTTTACTTCTTATTATGTTAT
1 TTTTGTGATACCAAATTCAAAAAAATTACAAATACTTTTTG-TTTTTTACTTCTTATTATGTTAT
* *
20960023 TAGGGTTCTAAGTGACACGAATGCTTAGTTTATTGACTCGTGGTGGCATATATGTTATGATGAAA
65 TAGGGTTCTAAGTGACACGAATGCTTAGTTTATTGACTCGTCGTGGCATATATGTTATAATGAAA
20960088 CAAATTAATTGTGTTATTTGCATTCGT
130 CAAATTAATTGTGTTATTTGCATTCGT
20960115 TT
1 TT
20960117 ATTAACTTAA
Statistics
Matches: 154, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
155 40 0.26
156 106 0.69
157 8 0.05
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (156 bp):
TTTTGTGATACCAAATTCAAAAAAATTACAAATACTTTTTGTTTTTTACTTCTTATTATGTTATT
AGGGTTCTAAGTGACACGAATGCTTAGTTTATTGACTCGTCGTGGCATATATGTTATAATGAAAC
AAATTAATTGTGTTATTTGCATTCGT
Found at i:20960662 original size:83 final size:83
Alignment explanation
Indices: 20960386--20960648 Score: 436
Period size: 83 Copynumber: 3.2 Consensus size: 83
20960376 AAAGTGAATA
* * *
20960386 ATTAGTGGCGTTTTGTCAATAAACGCCGTAAAGAAAATAATAAAAATTGAACAAAACGGCGCCGT
1 ATTAGTGGCATTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
*
20960451 TTCATTGATGAATTAAAT
66 TTCATTGACGAATTAAAT
* * * *
20960469 ATTAGTGGCGTTTTGTCAATAAACGCCGCAAATAATATAATTAAAATTGAACAAAACGACGCCGT
1 ATTAGTGGCATTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
20960534 TTCATTGACGAATTAAAT
66 TTCATTGACGAATTAAAT
* *
20960552 ATTAGTGGCATTTTGTCAATAAACGCCGCGAAGAATATAATAAAAATTGAACAAAACGGCGTCGT
1 ATTAGTGGCATTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
20960617 TTCATTGACGAATTAAAT
66 TTCATTGACGAATTAAAT
20960635 ATTAGTGGCATTTT
1 ATTAGTGGCATTTT
20960649 ATCTCCAAAC
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 168 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (83 bp):
ATTAGTGGCATTTTGTCAATAAACGCCGCAAAGAATATAATAAAAATTGAACAAAACGGCGCCGT
TTCATTGACGAATTAAAT
Found at i:20961624 original size:31 final size:31
Alignment explanation
Indices: 20961550--20961629 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
20961540 TTGGATTTTA
*
20961550 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
20961581 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
* *
20961612 ATTGATTTTTGCTACTAA
1 ATTGGTTTTTGCTGCTAA
20961630 ATCAACCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
Found at i:20962475 original size:12 final size:12
Alignment explanation
Indices: 20962458--20962485 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20962448 GCTAGCCATG
20962458 ATGTTACTATTA
1 ATGTTACTATTA
20962470 ATGTTACTATTA
1 ATGTTACTATTA
20962482 ATGT
1 ATGT
20962486 CCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:20967089 original size:45 final size:45
Alignment explanation
Indices: 20966995--20967117 Score: 149
Period size: 45 Copynumber: 2.7 Consensus size: 45
20966985 CTGCAAACTT
* * * * *
20966995 TTTATCTGAAAATAATGATGGTTTACCCACAATTTTTACTGGTAG
1 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
20967040 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
1 TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
* * * *
20967085 TTTATC-ACAAATTATTGGTGATTTATCCACAAT
1 TTTATCTA-AAAATAATGGTGGTTTACCCACAAT
20967118 GCGGTGTGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 67 0.99
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (45 bp):
TTTATCTAAAAATAATGGTGGTTTACCCACAATTTTTACGGGCAA
Found at i:20974767 original size:2 final size:2
Alignment explanation
Indices: 20974760--20974786 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20974750 TAAACTCATG
20974760 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20974787 CGGTGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20980904 original size:27 final size:27
Alignment explanation
Indices: 20980866--20980933 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
20980856 ATGTTTATAT
20980866 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
** * *
20980893 ACAGTCATTTTACCACGTGGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
20980920 ACAGTCATTTTATA
1 ACAGTCATTTTATA
20980934 TCAGTTTGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGCATA
Found at i:20981175 original size:17 final size:18
Alignment explanation
Indices: 20981153--20981187 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20981143 TACCCATGTG
20981153 AGGCCCAC-AGGCCCATT
1 AGGCCCACAAGGCCCATT
20981170 AGGCCCACAAGGCCCATT
1 AGGCCCACAAGGCCCATT
20981188 TTGGCCCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (18 bp):
AGGCCCACAAGGCCCATT
Found at i:20982116 original size:46 final size:46
Alignment explanation
Indices: 20982049--20982140 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
20982039 GCTACCTTAG
20982049 AAGAATAAACATGCACTAATTAAGTATTGTGTCGACTAATTACAAT
1 AAGAATAAACATGCACTAATTAAGTATTGTGTCGACTAATTACAAT
20982095 AAGAATAAACATGCACTAATTAAGTATTGTGTCGACTAATTACAAT
1 AAGAATAAACATGCACTAATTAAGTATTGTGTCGACTAATTACAAT
20982141 TTCAATACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (46 bp):
AAGAATAAACATGCACTAATTAAGTATTGTGTCGACTAATTACAAT
Found at i:20987122 original size:18 final size:18
Alignment explanation
Indices: 20987101--20987156 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
20987091 TTTTAGAAAA
*
20987101 TTTATAAATTTTTAGT-TT
1 TTTATAAATTTATA-TATT
*
20987119 TTTATATATTTATATATT
1 TTTATAAATTTATATATT
* *
20987137 TTCATAAATTTATAAATT
1 TTTATAAATTTATATATT
20987155 TT
1 TT
20987157 AACTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATAAATTTATATATT
Found at i:20987129 original size:46 final size:45
Alignment explanation
Indices: 20987061--20987184 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 45
20987051 TATATATGAG
* *
20987061 ATTTTTAATTCTTTTATATATTTATATTTTTTTTAGAAAATTTATAA
1 ATTTTTAATT-TTTTATATATTTATATTATTTTCA-AAAATTTATAA
* *
20987108 ATTTTTAGTTTTTTATATATTTATA-TATTTTCATAAATTTATAA
1 ATTTTTAATTTTTTATATATTTATATTATTTTCAAAAATTTATAA
20987152 A-TTTTAACTTTTTATTTATATATTATATATTAT
1 ATTTTTAA---TTT-TTTATATATT-TATATTAT
20987185 ANNNNNNNNN
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
43 5 0.08
44 11 0.17
45 6 0.09
46 18 0.27
47 19 0.29
48 4 0.06
49 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (45 bp):
ATTTTTAATTTTTTATATATTTATATTATTTTCAAAAATTTATAA
Found at i:20987148 original size:44 final size:45
Alignment explanation
Indices: 20987061--20987182 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 45
20987051 TATATATGAG
* *
20987061 ATTTTTAATTCTTTTATATATTTATATTTTTTTTAGAAAATTTATAA
1 ATTTTTAATT-TTTTATATATTTATA-TATTTTCAGAAAATTTATAA
* *
20987108 ATTTTTAGTTTTTTATATATTTATATATTTTCA-TAAATTTATAA
1 ATTTTTAATTTTTTATATATTTATATATTTTCAGAAAATTTATAA
*
20987152 A-TTTTAACTTTTTATTTATATATTATATATT
1 ATTTTTAA-TTTTT-TATATAT-TTATATATT
20987183 ATANNNNNNN
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
43 5 0.08
44 16 0.24
45 12 0.18
46 24 0.36
47 9 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (45 bp):
ATTTTTAATTTTTTATATATTTATATATTTTCAGAAAATTTATAA
Found at i:20994223 original size:5 final size:5
Alignment explanation
Indices: 20994213--20994253 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
20994203 TTAAGTTTAA
20994213 ATATT ATATT ATATT ATATT ATATT ATATT ATATT A-ATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
20994254 TATAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:20994801 original size:31 final size:31
Alignment explanation
Indices: 20994766--20994831 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
20994756 ATTTTCGTTA
* * *
20994766 AATTCAACT-TTTTATAAAATGTTGATGGTCG
1 AATTCAACTCCTTT-TAAAATGTTAAGGGTCG
*
20994797 AATTCCACTCCTTTTAAAATGTTAAGGGTCG
1 AATTCAACTCCTTTTAAAATGTTAAGGGTCG
20994828 AATT
1 AATT
20994832 TAGTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (31 bp):
AATTCAACTCCTTTTAAAATGTTAAGGGTCG
Found at i:20994913 original size:3 final size:3
Alignment explanation
Indices: 20994905--20995056 Score: 78
Period size: 3 Copynumber: 49.0 Consensus size: 3
20994895 TGTGAGTTAA
* * *
20994905 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT GAT GAAGT TAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT AAT
* * * * * * **
20994951 AAC ACCA- AAT AAT AAT AAC GAT AAT CAT ATT AACT ACT -AT TCT AAT
1 AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* *
20994997 ATT AAA AAT AAT AA- AAGT GAATT GAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T -AA-T -AAT AAT AAT AAT AAT AAT AAT AAT
20995045 AAT AAT AAT AAT
1 AAT AAT AAT AAT
20995057 GAAAAGAAAT
Statistics
Matches: 115, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
2 6 0.05
3 95 0.83
4 6 0.05
5 8 0.07
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20995145 original size:23 final size:24
Alignment explanation
Indices: 20995114--20995162 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
20995104 AAATATCTCC
* *
20995114 AAATCAAAATATTTAA-AATTAAA
1 AAATCAAAATAATGAACAATTAAA
*
20995137 AAATGAAAATAATGAACAATTAAA
1 AAATCAAAATAATGAACAATTAAA
20995161 AA
1 AA
20995163 TAAAAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (24 bp):
AAATCAAAATAATGAACAATTAAA
Found at i:21003377 original size:44 final size:44
Alignment explanation
Indices: 21003327--21003645 Score: 250
Period size: 44 Copynumber: 7.0 Consensus size: 44
21003317 AAGTGTTGGA
*
21003327 GAGCAGATTAAAGCTACAAATCTTATCTCTTTGAAGTTGCAGTG
1 GAGCAGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTG
*
21003371 GAGCAGATTGAAGCTACAAATCTTATCT-TCCTGAAGTTGCAGTG
1 GAGCAGATTAAAGCTACAAATCTTATCTCT-CTGAAGTTGCAGTG
* * *
21003415 GAGCAGATTAAAGCTACAAATCTTATCTCACTAAAGTTGTAGTG
1 GAGCAGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTG
* * * *
21003459 GAGCAGATTGAAG-TGACAAATCCTATAC-CTCTTAAGTTGTAGTG
1 GAGCAGATTAAAGCT-ACAAATCTTAT-CTCTCTGAAGTTGCAGTG
* * * * * *
21003503 G-GTCGGATTAAATCTACCATAGCGAGTCTTATTTCCCTGAAGTTGTAGTA
1 GAG-CAGATTAAAGCTA-CA-A---A-TCTTATCTCTCTGAAGTTGCAGTG
* * * *
21003553 GAACAAATTAAAGCTACAAGCTACAAATCTTATCTCCCTGAAGTTGTAGTG
1 GAGCAGA-T-----TA-AAGCTACAAATCTTATCTCTCTGAAGTTGCAGTG
* * * *
21003604 GAGCAGATTGAAGCTACGAATCTCATCTCCCTGAAGTTGCAG
1 GAGCAGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAG
21003646 CGGGGTAGAT
Statistics
Matches: 224, Mismatches: 30, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
43 3 0.01
44 153 0.68
45 5 0.02
46 1 0.00
49 1 0.00
50 22 0.10
51 28 0.12
52 1 0.00
55 1 0.00
56 4 0.02
57 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
GAGCAGATTAAAGCTACAAATCTTATCTCTCTGAAGTTGCAGTG
Found at i:21003656 original size:44 final size:44
Alignment explanation
Indices: 21003570--21003659 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
21003560 TTAAAGCTAC
* * *
21003570 AAGCTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTG
1 AAGCTACAAATCTCATCTCCCTGAAGTTGCAGCGGAGCAGATTG
* * *
21003614 AAGCTACGAATCTCATCTCCCTGAAGTTGCAGCGGGGTAGATTG
1 AAGCTACAAATCTCATCTCCCTGAAGTTGCAGCGGAGCAGATTG
21003658 AA
1 AA
21003660 ATTACAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
AAGCTACAAATCTCATCTCCCTGAAGTTGCAGCGGAGCAGATTG
Found at i:21007160 original size:24 final size:24
Alignment explanation
Indices: 21007108--21007177 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
21007098 CTTTCATCTA
*
21007108 TTCATCGCTGGTTCTTTGTT-C-C
1 TTCATCACTGGTTCTTTGTTCCTC
21007130 -TC-T-ACTGGTTCTTTGTTCCTC
1 TTCATCACTGGTTCTTTGTTCCTC
21007151 TTCATCACTGGTTCTTTGTTCCTC
1 TTCATCACTGGTTCTTTGTTCCTC
21007175 TTC
1 TTC
21007178 TCCATTGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 13 0.31
20 2 0.05
21 3 0.07
22 2 0.05
23 1 0.02
24 21 0.50
ACGTcount: A:0.06, C:0.29, G:0.14, T:0.51
Consensus pattern (24 bp):
TTCATCACTGGTTCTTTGTTCCTC
Found at i:21007558 original size:14 final size:14
Alignment explanation
Indices: 21007520--21007552 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21007510 GCCGAACAAT
*
21007520 TTCTGGCATTTTAG
1 TTCTAGCATTTTAG
21007534 TTCTAGCATTTTAG
1 TTCTAGCATTTTAG
21007548 TTCTA
1 TTCTA
21007553 CAATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
TTCTAGCATTTTAG
Found at i:21015480 original size:24 final size:24
Alignment explanation
Indices: 21015328--21015470 Score: 223
Period size: 24 Copynumber: 6.0 Consensus size: 24
21015318 AGTAGTTGGT
21015328 GGACTGCCACCTCCATATGATGGG
1 GGACTGCCACCTCCATATGATGGG
21015352 GGACTGCCACCTCCATATGATGGG
1 GGACTGCCACCTCCATATGATGGG
*
21015376 GGACTGCCACCTCCGTATGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
21015400 GGACTGCCTCCTCCATACGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
21015424 GGACTGCCTCCTCCATACGATGGG
1 GGACTGCCACCTCCATATGATGGG
* *
21015448 GGACTACCACCTCCAGATGATGG
1 GGACTGCCACCTCCATATGATGG
21015471 TGGAGTACCA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 111 1.00
ACGTcount: A:0.20, C:0.31, G:0.29, T:0.20
Consensus pattern (24 bp):
GGACTGCCACCTCCATATGATGGG
Found at i:21023782 original size:2 final size:2
Alignment explanation
Indices: 21023775--21023804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21023765 CTGCCTAAAC
21023775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21023805 TTGCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21032169 original size:46 final size:46
Alignment explanation
Indices: 21032116--21032254 Score: 251
Period size: 46 Copynumber: 3.0 Consensus size: 46
21032106 ACATTGCTAT
*
21032116 AACTCAGTATGGTTTTCTTCATTGAAACACCATACTTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
21032162 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
**
21032208 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
21032254 A
1 A
21032255 CTTTACCATG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 90 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:21043972 original size:18 final size:18
Alignment explanation
Indices: 21043949--21043988 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21043939 ACCCAATCCA
*
21043949 AACCCAAGTATCCAACCT
1 AACCCAAGTATCCAACCC
* *
21043967 AACCCAATTATCGAACCC
1 AACCCAAGTATCCAACCC
21043985 AACC
1 AACC
21043989 TAATCATAAA
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:0.40, C:0.40, G:0.05, T:0.15
Consensus pattern (18 bp):
AACCCAAGTATCCAACCC
Found at i:21044156 original size:9 final size:9
Alignment explanation
Indices: 21044138--21044213 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
21044128 GTAGTGATTC
21044138 AATTCGGGT
1 AATTCGGGT
*
21044147 AATTCAGGT
1 AATTCGGGT
21044156 AATTCGGGT
1 AATTCGGGT
* *
21044165 AATTTGGCT
1 AATTCGGGT
* *
21044174 AATTCAGTT
1 AATTCGGGT
21044183 AATTCGGGT
1 AATTCGGGT
*
21044192 AATTCGGTT
1 AATTCGGGT
*
21044201 AATTCGGTT
1 AATTCGGGT
21044210 AATT
1 AATT
21044214 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:21044176 original size:27 final size:27
Alignment explanation
Indices: 21044138--21044213 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
21044128 GTAGTGATTC
*
21044138 AATTCGGGTAATTCAGGTAATTCGGGT
1 AATTCGGCTAATTCAGGTAATTCGGGT
* *
21044165 AATTTGGCTAATTCAGTTAATTCGGGT
1 AATTCGGCTAATTCAGGTAATTCGGGT
*
21044192 AATTCGGTTAATTC-GGTTAATT
1 AATTCGGCTAATTCAGG-TAATT
21044214 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (27 bp):
AATTCGGCTAATTCAGGTAATTCGGGT
Found at i:21049295 original size:21 final size:21
Alignment explanation
Indices: 21049247--21049295 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
21049237 CTCTACTATT
* * *
21049247 TCCGCATTGGTTTTGTCCAAC
1 TCCGCCTTGGTTCTGGCCAAC
* *
21049268 TCAGCCTTGGTTCTGGCCACC
1 TCCGCCTTGGTTCTGGCCAAC
21049289 TCCGCCT
1 TCCGCCT
21049296 GGAGTGCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.10, C:0.37, G:0.20, T:0.33
Consensus pattern (21 bp):
TCCGCCTTGGTTCTGGCCAAC
Found at i:21056795 original size:3 final size:3
Alignment explanation
Indices: 21056787--21056825 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
21056777 ATACACTCTG
* *
21056787 CTT CTT CTT CTT CTT CTT CTC CTT CTT CTT CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
21056826 TTACAACAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:21056804 original size:12 final size:12
Alignment explanation
Indices: 21056787--21056825 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
21056777 ATACACTCTG
*
21056787 CTTCTTCTTCTT
1 CTTCTTCTCCTT
21056799 CTTCTTCTCCTT
1 CTTCTTCTCCTT
21056811 CTTCTTCTCCTT
1 CTTCTTCTCCTT
21056823 CTT
1 CTT
21056826 TTACAACAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTCTTCTCCTT
Found at i:21060106 original size:421 final size:419
Alignment explanation
Indices: 21059220--21060260 Score: 1635
Period size: 421 Copynumber: 2.5 Consensus size: 419
21059210 GTAAACACCT
*
21059220 ACATTTTAGAGGATTTTCATTTTTTTACACAAATCACCAATTTGTATATTC-AGAGGATTACTAA
1 ACATTTTAGAGGTTTTTCA-TTTTTTACACAAATCACCAATTTGTATATTCGA-AGGATTACTAA
* * *
21059284 TTGAACCATAAAAACTAGAG-AGATTTTTAGTTGGGCCTTCGAAAAATTACAAGGTTCTAGTTAA
64 TTGAGCCATAAAAACTAGAGAAG-TTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAA
* * * *
21059348 GCTACAAAAATTATGAAATGGTTCTACCTTAACCCAAGTAAATAATAGATAGTTGTGAATG-T-T
128 GCTACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTAT
** * *
21059411 ACCTTGTCCTTGAAAGATGCCAATTAGTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAA
193 ACCTTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAA
21059476 CTTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAA
258 CTTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAA
* *
21059541 TTACACTTTCCAACTCTTCGGTGAGGGTGAGAATTGGAGTAATTACGCAAGTAATTACACCAAAA
323 TTACACTTTCCAACTCTTAGGCGAGGGTGAGAATTGGAGTAATTACGCAAGTAATTACACCAAAA
* *
21059606 TCCAATTACTATATGGCTTTCCAAACACTCAT
388 TCCAATTACTATATGACTTTCCAAACACTCAA
*
21059638 ACATTTTAGAGGTTTTTCATTTTCTTACACATATCACCAATTTGTATATTCGAAGGATTACTAAT
1 ACATTTTAGAGGTTTTTCATTTT-TTACACAAATCACCAATTTGTATATTCGAAGGATTACTAAT
21059703 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
65 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
*
21059768 TACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAAAGAGTTGTGAAAGTTATAC
130 TACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATAC
* *
21059833 CTTGTTATTGAAAGATACCAATTACTGAACTGGGAAAACCTTTTGGCTATGTTTGGAAAA-CAAC
195 CTTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTT-GAAAAGCAAC
* * * *
21059897 TTAGTAATTGAATTTGGGTGTAATTGGTGGATCCCATTAAATTGTGTATAATTGAAGCACCCCAA
259 TTAGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCA-CCCAA
21059962 TTACACTTTCCAACTCTTAGGCGAGGGTGAGAATTGGAGTAATTACGCAAGTAATTACACCAAAA
323 TTACACTTTCCAACTCTTAGGCGAGGGTGAGAATTGGAGTAATTACGCAAGTAATTACACCAAAA
*
21060027 TCCAATTACTATATGACTTTGCAAACACTCAA
388 TCCAATTACTATATGACTTTCCAAACACTCAA
* * *
21060059 ACATTTTTGAGGTTTTTCATTTGTTTATACAAATCACCAATTTGTATATTCGGAGGATTACTAAT
1 ACATTTTAGAGGTTTTTCATTT-TTTACACAAATCACCAATTTGTATATTCGAAGGATTACTAAT
* ** * *
21060124 TGAGCCATAAAAACTAGATAAGTTTTTAGTTAAGCCTTCGAAAAGTTAGAAGGTTTTAGTTAGGC
65 TGAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGC
* * * *
21060189 TACAAAACCTATGAAATGGTTCTATCTTAGCCCCAAGTAAATAATAGAGTGTTGTGAAGGTTATA
130 TACAAAAACTATGAAATGGTTCTATCTTA-ACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATA
21060254 CC-TGTTA
194 CCTTGTTA
21060261 GAATTGTAAA
Statistics
Matches: 575, Mismatches: 39, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
417 4 0.01
418 169 0.29
419 4 0.01
420 110 0.19
421 254 0.44
422 34 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (419 bp):
ACATTTTAGAGGTTTTTCATTTTTTACACAAATCACCAATTTGTATATTCGAAGGATTACTAATT
GAGCCATAAAAACTAGAGAAGTTTTTAGTTGGGCCTTCGAAAAGTTAGAAGGTTCTAGTTAAGCT
ACAAAAACTATGAAATGGTTCTATCTTAACCCAAGTAAATAATAGAGAGTTGTGAAAGTTATACC
TTGTTATTGAAAGATACCAATTACTGAACTGAGAAAACCTTTAGGCTATGTTTGAAAAGCAACTT
AGTAATTGAATTTGGGTGTAACTGGTGGATCACATTAAAATGGGTATAATTGAAGCACCCAATTA
CACTTTCCAACTCTTAGGCGAGGGTGAGAATTGGAGTAATTACGCAAGTAATTACACCAAAATCC
AATTACTATATGACTTTCCAAACACTCAA
Found at i:21071987 original size:25 final size:27
Alignment explanation
Indices: 21071930--21071988 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
21071920 TACTCATACC
*
21071930 TTATTTCACTATCTCAATTCCATTAGA
1 TTATTTCACTATCTCAATTCCAATAGA
21071957 TT-TTTCAC-ATCTC-ATTCCAATAG-
1 TTATTTCACTATCTCAATTCCAATAGA
21071980 TTCATTTCA
1 TT-ATTTCA
21071989 ATTCATATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 9 0.31
25 10 0.34
26 6 0.21
27 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (27 bp):
TTATTTCACTATCTCAATTCCAATAGA
Found at i:21076929 original size:2 final size:2
Alignment explanation
Indices: 21076922--21076954 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21076912 CCTAATTCGC
*
21076922 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21076955 CCTAATCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21077231 original size:44 final size:43
Alignment explanation
Indices: 21077167--21077307 Score: 174
Period size: 44 Copynumber: 3.2 Consensus size: 43
21077157 ACCATTTAAA
* * *
21077167 TTCTTACCTAAACAATCAACCAAGACAATTATATTACATGTCCAT
1 TTCTTACC-AAACAATCAACCAA-ACAATTATAATGCATGTTCAT
* * *
21077212 TTCTTGCCAAACAATCAACCAAACATTTATAATGCGTGTTCAT
1 TTCTTACCAAACAATCAACCAAACAATTATAATGCATGTTCAT
* * *
21077255 TTATTACCAAGACAACCAATCAAACAATTATAATGCATGTTCAT
1 TTCTTACCAA-ACAATCAACCAAACAATTATAATGCATGTTCAT
21077299 TTCTTACCA
1 TTCTTACCA
21077308 TTTAACAACT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 24 0.29
44 51 0.62
45 7 0.09
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (43 bp):
TTCTTACCAAACAATCAACCAAACAATTATAATGCATGTTCAT
Found at i:21081530 original size:22 final size:22
Alignment explanation
Indices: 21081502--21081545 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
21081492 ATTAGATAAA
21081502 ATTGCATATGATGTTTATTCTT
1 ATTGCATATGATGTTTATTCTT
21081524 ATTGCATATGATGTTTATTCTT
1 ATTGCATATGATGTTTATTCTT
21081546 CTTCTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (22 bp):
ATTGCATATGATGTTTATTCTT
Found at i:21084915 original size:19 final size:21
Alignment explanation
Indices: 21084889--21084929 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21084879 CCAAATAGCA
21084889 TATATATTTTA-TCATAAAATT
1 TATAT-TTTTAGTCATAAAATT
21084910 TATATTTTTAGTCATAAAAT
1 TATATTTTTAGTCATAAAAT
21084930 ATGAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATTTTTAGTCATAAAATT
Found at i:21086361 original size:23 final size:21
Alignment explanation
Indices: 21086322--21086365 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
21086312 TTTTTTCAAC
21086322 TTTAACTTTTATTCAAAACAT
1 TTTAACTTTTATTCAAAACAT
*
21086343 TTTAATTTGTTATATCAAAACAT
1 TTTAACTT-TTAT-TCAAAACAT
21086366 ATTATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAACTTTTATTCAAAACAT
Found at i:21098501 original size:30 final size:31
Alignment explanation
Indices: 21098467--21098525 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
21098457 AACAAATAAT
*
21098467 TCAAAATTT-ATAAAAATATAAATAACTAAA
1 TCAAAATTTAATAAAAATATAAAAAACTAAA
*
21098497 TCAAAATTTAAATTAAAATATAAAAAACT
1 TCAAAATTT-AATAAAAATATAAAAAACT
21098526 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
32 16 0.64
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (31 bp):
TCAAAATTTAATAAAAATATAAAAAACTAAA
Found at i:21099113 original size:131 final size:132
Alignment explanation
Indices: 21098879--21099144 Score: 525
Period size: 131 Copynumber: 2.0 Consensus size: 132
21098869 AAACTTTGAT
21098879 ATTTTAAGCCTAACTTTTTAAATTTTTTATCTTAAACCATTTTAATTTTTTATAATTACATTTAA
1 ATTTTAAGCCTAACTTTTTAAATTTTTTATCTTAAACCATTTTAATTTTTTATAATTACATTTAA
21098944 AATTAATAATTATTACATTAAATTATCGAACATAACTAATAATTTTAACACTTATTTTT-TATAT
66 AATTAATAATTATTACATTAAATTATCGAACATAACTAATAATTTTAACACTTATTTTTGTATAT
21099008 AA
131 AA
21099010 ATTTTAAGCCTAACTTTTTAAATTTTTTATCTTAAACCATTTTAATTTTTTATAATTACATTTAA
1 ATTTTAAGCCTAACTTTTTAAATTTTTTATCTTAAACCATTTTAATTTTTTATAATTACATTTAA
21099075 AATTAATAATTATTACATTAAATTATCGAACATAACTAATAATTTTAACACTTATTTTTGTATAT
66 AATTAATAATTATTACATTAAATTATCGAACATAACTAATAATTTTAACACTTATTTTTGTATAT
21099140 AA
131 AA
21099142 ATT
1 ATT
21099145 GAGATATATT
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 124 0.93
132 10 0.07
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (132 bp):
ATTTTAAGCCTAACTTTTTAAATTTTTTATCTTAAACCATTTTAATTTTTTATAATTACATTTAA
AATTAATAATTATTACATTAAATTATCGAACATAACTAATAATTTTAACACTTATTTTTGTATAT
AA
Found at i:21103164 original size:6 final size:6
Alignment explanation
Indices: 21103135--21103191 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
21103125 GAGAACTTTG
* * *
21103135 TTTTT- TTTTTCC TCTTTC TCTTTC ATTTTC ATTTTT- TTTTTC TTTTTC
1 TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
21103183 TTTTTC TTT
1 TTTTTC TTT
21103192 CCCTCCAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
5 10 0.23
6 26 0.59
7 8 0.18
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:21113034 original size:34 final size:34
Alignment explanation
Indices: 21112991--21113062 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
21112981 ATTTGTAAAC
21112991 ATTGGAAGTTTAAAGACAGAAAAATAAAGTCACT
1 ATTGGAAGTTTAAAGACAGAAAAATAAAGTCACT
21113025 ATTGGAAGTTTAAAGACAGAAAAATAAAGTCACT
1 ATTGGAAGTTTAAAGACAGAAAAATAAAGTCACT
21113059 ATTG
1 ATTG
21113063 AAATGCCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (34 bp):
ATTGGAAGTTTAAAGACAGAAAAATAAAGTCACT
Found at i:21113884 original size:5 final size:5
Alignment explanation
Indices: 21113874--21113904 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
21113864 AAAAAATGCA
21113874 AAAAG AAAAG AAAAG -AAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
21113905 TCAAAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:21113892 original size:14 final size:14
Alignment explanation
Indices: 21113875--21113919 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
21113865 AAAAATGCAA
21113875 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
21113889 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
** *
21113903 AATCAAAAGAACAG
1 AAAGAAAAGAAAAG
21113917 AAA
1 AAA
21113920 CATGAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:21119535 original size:25 final size:25
Alignment explanation
Indices: 21119479--21119536 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
21119469 AGCACTCTCT
* * *
21119479 CGAGCCATATAATAGGAAGCTCATG
1 CGAGCTATGTAATAGGAAGCTCATC
* *
21119504 TGAGCTATGTAATAGGAAGCTTATC
1 CGAGCTATGTAATAGGAAGCTCATC
*
21119529 CGGGCTAT
1 CGAGCTAT
21119537 AACATGAAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (25 bp):
CGAGCTATGTAATAGGAAGCTCATC
Found at i:21119620 original size:24 final size:24
Alignment explanation
Indices: 21119592--21119639 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21119582 TAACGGGTAA
*
21119592 CTCCGAAGAGCTATTATTAGGAAG
1 CTCCGAAGAGCCATTATTAGGAAG
* *
21119616 CTCCGGATAGCCATTATTAGGAAG
1 CTCCGAAGAGCCATTATTAGGAAG
21119640 TTCAAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (24 bp):
CTCCGAAGAGCCATTATTAGGAAG
Found at i:21119684 original size:26 final size:25
Alignment explanation
Indices: 21119651--21119699 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
21119641 TCAAGCGAGC
21119651 TATATCGGGAAGCTCATGAAGAGCCA
1 TATATCGGGAAGCTCAT-AAGAGCCA
*
21119677 TATATCGGGACGCTCATAAGAGC
1 TATATCGGGAAGCTCATAAGAGC
21119700 TGTGGTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (25 bp):
TATATCGGGAAGCTCATAAGAGCCA
Found at i:21124520 original size:24 final size:23
Alignment explanation
Indices: 21124493--21124573 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 23
21124483 ACATATAAAA
*
21124493 GTTCGCATACCTATGTACATAAGT
1 GTTCGCATACATAT-TACATAAGT
* * *
21124517 GTTCACATGCATATTTACTTTAAGT
1 GTTCGCATACATA-TTAC-ATAAGT
*
21124542 -TTCGCATACTTATTCACATAAG-
1 GTTCGCATACATATT-ACATAAGT
21124564 GTTTCGCATA
1 G-TTCGCATA
21124574 TTAGTTCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
23 6 0.14
24 32 0.73
25 6 0.14
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (23 bp):
GTTCGCATACATATTACATAAGT
Found at i:21126661 original size:8 final size:8
Alignment explanation
Indices: 21126648--21126675 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
21126638 TCTTATACAC
21126648 AATTTTAT
1 AATTTTAT
21126656 AATTTTAT
1 AATTTTAT
21126664 AATTTTAT
1 AATTTTAT
21126672 AATT
1 AATT
21126676 AAAATTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:21128557 original size:24 final size:24
Alignment explanation
Indices: 21128530--21128581 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
21128520 AAACAAAAAC
* *
21128530 TAAAT-AAAAATAAATTATTAGAAT
1 TAAATCAAAAATAAA-AAATAGAAT
*
21128554 TAAATCTAAAATAAAAAATAGAAT
1 TAAATCAAAAATAAAAAATAGAAT
21128578 TAAA
1 TAAA
21128582 ACTAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
TAAATCAAAAATAAAAAATAGAAT
Found at i:21128806 original size:15 final size:17
Alignment explanation
Indices: 21128788--21128824 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
21128778 AGAAATTATA
21128788 TAAATAA-TATATAA-G
1 TAAATAATTATATAAGG
*
21128803 TAAATAATTATTTAAGG
1 TAAATAATTATATAAGG
21128820 TAAAT
1 TAAAT
21128825 TAAGAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
TAAATAATTATATAAGG
Found at i:21129376 original size:17 final size:17
Alignment explanation
Indices: 21129325--21129378 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
21129315 CACGTGTTTT
*
21129325 ATAAAATTATT-ATTTAA
1 ATAAAATTATTGA-TAAA
*
21129342 ATAACAA-TA-TGGTAAA
1 ATAA-AATTATTGATAAA
21129358 ATAAAATTATTGATAAA
1 ATAAAATTATTGATAAA
21129375 ATAA
1 ATAA
21129379 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 16 0.53
18 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAAAATTATTGATAAA
Found at i:21129411 original size:20 final size:20
Alignment explanation
Indices: 21129374--21129410 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
21129364 TTATTGATAA
21129374 AATAATATTTAAAATATATG
1 AATAATATTTAAAATATATG
21129394 AATAAT-TTTAAAA-ATAT
1 AATAATATTTAAAATATAT
21129411 ACTTAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AATAATATTTAAAATATATG
Found at i:21129618 original size:21 final size:21
Alignment explanation
Indices: 21129576--21129618 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
21129566 ATATATATTT
**
21129576 AATACTTTTTTTAATTTTAGA
1 AATACTTTTTTTAATTCCAGA
21129597 AATACATTTTTTTAA-TCCAGA
1 AATAC-TTTTTTTAATTCCAGA
21129618 A
1 A
21129619 GTAAAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (21 bp):
AATACTTTTTTTAATTCCAGA
Found at i:21130316 original size:27 final size:28
Alignment explanation
Indices: 21130286--21130352 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
21130276 TATGAGATTT
* * *
21130286 ATAACTTTAAGTT-AAATATTGAAATTA
1 ATAAATTTAAATTCAAATATTAAAATTA
*
21130313 ATAAATTTAAATTCAAATTTTAAAATTA
1 ATAAATTTAAATTCAAATATTAAAATTA
*
21130341 A-AAATTAAAATT
1 ATAAATTTAAATT
21130353 GTGTTATGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (28 bp):
ATAAATTTAAATTCAAATATTAAAATTA
Found at i:21135851 original size:35 final size:35
Alignment explanation
Indices: 21135805--21135875 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
21135795 TATCATAATT
21135805 TTTGGATTACTACAATTGCCTATAGGGATACTCTG
1 TTTGGATTACTACAATTGCCTATAGGGATACTCTG
21135840 TTTGGATTACTACAATTGCCTATAGGGATACTCTG
1 TTTGGATTACTACAATTGCCTATAGGGATACTCTG
21135875 T
1 T
21135876 CCTTAACATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (35 bp):
TTTGGATTACTACAATTGCCTATAGGGATACTCTG
Found at i:21137988 original size:20 final size:20
Alignment explanation
Indices: 21137949--21137989 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21137939 ATTTAATATA
**
21137949 AACATATATAATTATTATTT
1 AACATATATAATTAAAATTT
*
21137969 AACATTTATAATTAAAATTT
1 AACATATATAATTAAAATTT
21137989 A
1 A
21137990 TAATATAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AACATATATAATTAAAATTT
Found at i:21146528 original size:13 final size:14
Alignment explanation
Indices: 21146504--21146532 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21146494 GTAATGTGAT
21146504 TTTTGTTTTATTTA
1 TTTTGTTTTATTTA
21146518 TTTTG-TTTATTTA
1 TTTTGTTTTATTTA
21146531 TT
1 TT
21146533 ATTAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTGTTTTATTTA
Found at i:21151096 original size:28 final size:28
Alignment explanation
Indices: 21151022--21151212 Score: 107
Period size: 28 Copynumber: 6.8 Consensus size: 28
21151012 ATTACTGTAA
* * *
21151022 ATGTGGAAGTTCGTTAGGACTATTTTAT
1 ATGTGGAAGTCCGTTAAGACTATCTTAT
* * ** *
21151050 ATGTTGAAATTTGTCAAGACTATCTTAT
1 ATGTGGAAGTCCGTTAAGACTATCTTAT
*
21151078 ATGTGGAAGTCCGTTAAGACTATCTTAA
1 ATGTGGAAGTCCGTTAAGACTATCTTAT
** * * *
21151106 ATACGAAAGTTCGTT-AGAACTATATTAT
1 ATGTGGAAGTCCGTTAAG-ACTATCTTAT
* * * * *
21151134 AAGTGGAAATCCATCAGGACTATCTTAT
1 ATGTGGAAGTCCGTTAAGACTATCTTAT
* * * *
21151162 ATATGGAAGTCTG-TCAGAACTATATTAT
1 ATGTGGAAGTCCGTTAAG-ACTATCTTAT
* * * *
21151190 AAGTGGAAATCCGTCAAGGCTAT
1 ATGTGGAAGTCCGTTAAGACTAT
21151213 TTTACAAATA
Statistics
Matches: 115, Mismatches: 44, Indels: 8
0.69 0.26 0.05
Matches are distributed among these distances:
27 3 0.03
28 109 0.95
29 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (28 bp):
ATGTGGAAGTCCGTTAAGACTATCTTAT
Found at i:21151128 original size:56 final size:56
Alignment explanation
Indices: 21151068--21151212 Score: 175
Period size: 56 Copynumber: 2.6 Consensus size: 56
21151058 ATTTGTCAAG
* * * * *
21151068 ACTATCTTATATGTGGAAGTCCGTTAAGACTATCTTAAATACGAAAGT-TCGTTAGA
1 ACTATATTATAAGTGGAAATCCGTCAAGACTATCTTAAATACGAAAGTCT-GTCAGA
* * * * *
21151124 ACTATATTATAAGTGGAAATCCATCAGGACTATCTTATATATGGAAGTCTGTCAGA
1 ACTATATTATAAGTGGAAATCCGTCAAGACTATCTTAAATACGAAAGTCTGTCAGA
*
21151180 ACTATATTATAAGTGGAAATCCGTCAAGGCTAT
1 ACTATATTATAAGTGGAAATCCGTCAAGACTAT
21151213 TTTACAAATA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
56 74 0.99
57 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (56 bp):
ACTATATTATAAGTGGAAATCCGTCAAGACTATCTTAAATACGAAAGTCTGTCAGA
Found at i:21176403 original size:13 final size:13
Alignment explanation
Indices: 21176385--21176412 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21176375 ACAAAATTGG
21176385 AAAGATGATAAAT
1 AAAGATGATAAAT
21176398 AAAGATGATAAAT
1 AAAGATGATAAAT
21176411 AA
1 AA
21176413 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:21177157 original size:28 final size:30
Alignment explanation
Indices: 21177098--21177154 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
21177088 AACTAAATTG
* *
21177098 TGTATATTTATATGTTTAAATTTAATGTTA
1 TGTATATGTATATGTATAAATTTAATGTTA
21177128 TGTATATGTAT-TGTAT-AATTTACATGT
1 TGTATATGTATATGTATAAATTTA-ATGT
21177155 ATGAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 8 0.33
30 10 0.42
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTATATGTATATGTATAAATTTAATGTTA
Found at i:21177463 original size:26 final size:26
Alignment explanation
Indices: 21177434--21177491 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
21177424 CCTGTTATAT
21177434 GGCT-TTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTT-GTGAGCTTCCCGATTAAA
* *
21177460 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTTGTGAGCTTCCCGATTAAA
21177486 GGCTCT
1 GGCTCT
21177492 CCAGAGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCCGATTAAA
Found at i:21181082 original size:71 final size:69
Alignment explanation
Indices: 21180966--21181108 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 69
21180956 CTTAAATCAT
* *
21180966 TAAGGTATATAATGTTCACATGTAGATAAAATGATAAGTTTTAATGCATTATAGCAAATAGGTAA
1 TAAGGTATATAATGCTCACATGTAGATAAAATGATAAGTTTTAATGCATCATAGC--ATAGGTAA
21181031 GATTGG
64 GATTGG
*
21181037 TAAGGTATATAATGCTCACATGTATATAAAATGATAAGTTTTAATGCATCATAGCATAGGTAAGA
1 TAAGGTATATAATGCTCACATGTAGATAAAATGATAAGTTTTAATGCATCATAGCATAGGTAAGA
21181102 TTGG
66 TTGG
21181106 TAA
1 TAA
21181109 TTGAAGAGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 17 0.25
71 52 0.75
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (69 bp):
TAAGGTATATAATGCTCACATGTAGATAAAATGATAAGTTTTAATGCATCATAGCATAGGTAAGA
TTGG
Found at i:21198135 original size:2 final size:2
Alignment explanation
Indices: 21198128--21198153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21198118 TCAAACTTTA
21198128 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
21198154 TTAACTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21208639 original size:20 final size:21
Alignment explanation
Indices: 21208616--21208669 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
21208606 ATATGGGTGG
21208616 TTATTTTT-AAATATATATTT
1 TTATTTTTGAAATATATATTT
**
21208636 TTATTATTTGTTATATATATTT
1 TTATT-TTTGAAATATATATTT
*
21208658 TTAATTTTGAAA
1 TTATTTTTGAAA
21208670 ACCATCTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATTTTTGAAATATATATTT
Found at i:21209875 original size:30 final size:30
Alignment explanation
Indices: 21209841--21209898 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21209831 ATTTTCATCA
*
21209841 TTTTTGAAGGGATTAAACGTAATTTTACTT
1 TTTTTGAAGGGATAAAACGTAATTTTACTT
* * *
21209871 TTTTTGGAGGGCTAAAATGTAATTTTAC
1 TTTTTGAAGGGATAAAACGTAATTTTAC
21209899 CATAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (30 bp):
TTTTTGAAGGGATAAAACGTAATTTTACTT
Found at i:21213880 original size:2 final size:2
Alignment explanation
Indices: 21213873--21213902 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21213863 NTCTAGTGAG
21213873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21213903 TACAATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21238721 original size:24 final size:24
Alignment explanation
Indices: 21238693--21238747 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
21238683 GCCCTTTAAG
* *
21238693 GGACGTTTGAGATCCCCTTATGTA
1 GGACGTATGAGAGCCCCTTATGTA
*
21238717 GGACGTATGAGAGCCCTTTATG--
1 GGACGTATGAGAGCCCCTTATGTA
21238739 GGACGTATG
1 GGACGTATG
21238748 GAAGACCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.32
24 19 0.68
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (24 bp):
GGACGTATGAGAGCCCCTTATGTA
Found at i:21238745 original size:22 final size:22
Alignment explanation
Indices: 21238680--21238747 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
21238670 ACCAGTATAT
* *
21238680 AGAGCCCTTTAAGGGACGTTTG
1 AGAGCCCTTTATGGGACGTATG
* *
21238702 AGATCCCCTTATGTAGGACGTATG
1 AGAGCCCTTTATG--GGACGTATG
21238726 AGAGCCCTTTATGGGACGTATG
1 AGAGCCCTTTATGGGACGTATG
21238748 GAAGACCATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 19 0.50
24 19 0.50
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (22 bp):
AGAGCCCTTTATGGGACGTATG
Found at i:21238860 original size:28 final size:29
Alignment explanation
Indices: 21238829--21238899 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
21238819 CAAGACTGTC
* *
21238829 TAAATGTAAGAAGTCCT-CAAGACGATCT
1 TAAATGTAGGAAGTCCTCCAAGACAATCT
*
21238857 TAAATGT-GGAAGTCGTCCAAGACAATCT
1 TAAATGTAGGAAGTCCTCCAAGACAATCT
21238885 TAAATG-AGGAAGTCC
1 TAAATGTAGGAAGTCC
21238900 GTCTGGATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.19
28 30 0.81
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (29 bp):
TAAATGTAGGAAGTCCTCCAAGACAATCT
Found at i:21240707 original size:97 final size:96
Alignment explanation
Indices: 21240541--21240738 Score: 369
Period size: 97 Copynumber: 2.1 Consensus size: 96
21240531 ATCTGAGTGG
*
21240541 AGGTTTATTTGTGATTGAGACCATGTTTCATGATAATAATAAAGCCACCACTTCTACTTATATTG
1 AGGTTTATTTGTGATTGAGACCATGTTTAATGATAATAATAAAGCCACCACTTCTACTTATATTG
21240606 CTGAATCCATTGACATGTGGCATGCTAGATT
66 CTGAATCCATTGACATGTGGCATGCTAGATT
*
21240637 AAGGTTTATTTGTGATTGAGACCATGTTTAATGATAATAATACAGCCACCACTTCTACTTATATT
1 -AGGTTTATTTGTGATTGAGACCATGTTTAATGATAATAATAAAGCCACCACTTCTACTTATATT
21240702 GCTGAATCCATTGACATGTGGCATGCTAGATT
65 GCTGAATCCATTGACATGTGGCATGCTAGATT
21240734 AGGTT
1 AGGTT
21240739 ATGTGAATAT
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 5 0.05
97 94 0.95
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (96 bp):
AGGTTTATTTGTGATTGAGACCATGTTTAATGATAATAATAAAGCCACCACTTCTACTTATATTG
CTGAATCCATTGACATGTGGCATGCTAGATT
Found at i:21260231 original size:4 final size:4
Alignment explanation
Indices: 21260222--21260268 Score: 58
Period size: 4 Copynumber: 10.8 Consensus size: 4
21260212 AATCTAATTC
21260222 TTTA TTTA TTTA TTTA TTTA TTTA TTTCA TTTTA TGTTGA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A -TTTA T-TT-A TTTA TTT
21260269 TGAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 28 0.72
5 6 0.15
6 5 0.13
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:21267214 original size:5 final size:5
Alignment explanation
Indices: 21267204--21267230 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21267194 TAGATTTTGC
21267204 TCTTT TCTTT TCTTT TCTTT TCTTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TC
21267231 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:21270262 original size:361 final size:362
Alignment explanation
Indices: 21269598--21270320 Score: 1439
Period size: 361 Copynumber: 2.0 Consensus size: 362
21269588 GTATTAAAGC
21269598 GTATTATCCTCCTATTTATGGGTTGTGGAGAGACTATGGGTAATGGTAAGTATTACATCAAAACC
1 GTATTATCCTCCTATTTATGGGTTGTGGAGAGACTATGGGTAATGGTAAGTATTACATCAAAACC
21269663 TGTGATAAATTTGTTGAAAAAAAAATAAACTCTATAAAAAGTATTCGAAAGCTCAAAATGTTATT
66 TGTGATAAATTTGTTGAAAAAAAAATAAACTCTATAAAAAGTATTCGAAAGCTCAAAATGTTATT
21269728 AAATTTATATTAAAAAATAAAATTTTCATAAACACAATTACAAAGAATACAAGTGTTTAATTTAT
131 AAATTTATATTAAAAAATAAAATTTTCATAAACACAATTACAAAGAATACAAGTGTTTAATTTAT
21269793 TTAATTTTTAGATTTTTAATTATGCTTAAAATATATAATTAGGTTGTCTTAATTAAAGGAGTAAA
196 TTAATTTTTAGATTTTTAATTATGCTTAAAATATATAATTAGGTTGTCTTAATTAAAGGAGTAAA
21269858 TACTTTGCCAATGGACATTTTTCTATCAATTTATTTTGATGTACTGCTTCAAATTTATCATTATT
261 TACTTTGCCAATGGACATTTTTCTATCAATTTATTTTGATGTACTGCTTCAAATTTATCATTATT
21269923 TTTTAAAAAAAATTGATATATATAT-ATAAATATTTA
326 TTTTAAAAAAAATTGATATATATATAATAAATATTTA
21269959 GTATTATCCTCCTATTTATGGGTTGTGGAGAGACTATGGGTAATGGTAAGTATTACATCAAAACC
1 GTATTATCCTCCTATTTATGGGTTGTGGAGAGACTATGGGTAATGGTAAGTATTACATCAAAACC
21270024 TGTGATAAATTTGTTGAAAAAAAAATAAACTCTATAAAAAGTATTCGAAAGCTCAAAATGTTATT
66 TGTGATAAATTTGTTGAAAAAAAAATAAACTCTATAAAAAGTATTCGAAAGCTCAAAATGTTATT
21270089 AAATTTATATTAAAAAATAAAATTTTCATAAACACAATTACAAAGAATACAAGTGTTTAATTTAT
131 AAATTTATATTAAAAAATAAAATTTTCATAAACACAATTACAAAGAATACAAGTGTTTAATTTAT
21270154 TTAATTTTTAGATTTTTAATTATGCTTAAAATATATAATTAGGTTGTCTTAATTAAAGGAGTAAA
196 TTAATTTTTAGATTTTTAATTATGCTTAAAATATATAATTAGGTTGTCTTAATTAAAGGAGTAAA
21270219 TACTTTGCCAATGGACATTTTTCTATCAATTTATTTTGATGTACTGCTTCAAATTTATCATTATT
261 TACTTTGCCAATGGACATTTTTCTATCAATTTATTTTGATGTACTGCTTCAAATTTATCATTATT
21270284 TTTTAAAAAAAATTGATATATATATAATAAATATTTA
326 TTTTAAAAAAAATTGATATATATATAATAAATATTTA
21270321 CAATTATTTC
Statistics
Matches: 361, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
361 350 0.97
362 11 0.03
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (362 bp):
GTATTATCCTCCTATTTATGGGTTGTGGAGAGACTATGGGTAATGGTAAGTATTACATCAAAACC
TGTGATAAATTTGTTGAAAAAAAAATAAACTCTATAAAAAGTATTCGAAAGCTCAAAATGTTATT
AAATTTATATTAAAAAATAAAATTTTCATAAACACAATTACAAAGAATACAAGTGTTTAATTTAT
TTAATTTTTAGATTTTTAATTATGCTTAAAATATATAATTAGGTTGTCTTAATTAAAGGAGTAAA
TACTTTGCCAATGGACATTTTTCTATCAATTTATTTTGATGTACTGCTTCAAATTTATCATTATT
TTTTAAAAAAAATTGATATATATATAATAAATATTTA
Found at i:21278340 original size:13 final size:13
Alignment explanation
Indices: 21278322--21278346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21278312 ATTATAAAAA
21278322 AAATTTCTTTTTG
1 AAATTTCTTTTTG
21278335 AAATTTCTTTTT
1 AAATTTCTTTTT
21278347 CTTCTTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
AAATTTCTTTTTG
Found at i:21280750 original size:60 final size:60
Alignment explanation
Indices: 21280670--21280822 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 60
21280660 TTCATCTTCA
* * *
21280670 GATGAAGTGTTTTCTTCATCAGAATTATAACTAGTGACTTTTATGTCTTCATCCTGATCT
1 GATGAAGTTTTTTCTTCATCAGAATTATAACTAGTAACATTTATGTCTTCATCCTGATCT
* * * * *
21280730 GTTGAAGTTTTTTCTTCATCAG-ATTGATTACTAGTAACATTTATGTCTTCTTTCTGGTCT
1 GATGAAGTTTTTTCTTCATCAGAATT-ATAACTAGTAACATTTATGTCTTCATCCTGATCT
* *
21280790 GATGAAGTTTTTTCTTCATCAGATTTAAAACTA
1 GATGAAGTTTTTTCTTCATCAGAATTATAACTA
21280823 CTACTATCTG
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 3 0.04
60 74 0.94
61 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (60 bp):
GATGAAGTTTTTTCTTCATCAGAATTATAACTAGTAACATTTATGTCTTCATCCTGATCT
Found at i:21308917 original size:3 final size:3
Alignment explanation
Indices: 21308909--21308954 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
21308899 CAACCAATAA
21308909 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
21308955 ACTAAACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:21309767 original size:27 final size:27
Alignment explanation
Indices: 21309726--21309796 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
21309716 AAAACGGGTC
*
21309726 GAGCCTGTCAAATAGGCGCGACTAATT
1 GAGCCTGCCAAATAGGCGCGACTAATT
* * * *
21309753 GAGCCTGCCAGATAGGTGCTACTAATC
1 GAGCCTGCCAAATAGGCGCGACTAATT
* * *
21309780 GCGCCTGACAAGTAGGC
1 GAGCCTGCCAAATAGGC
21309797 ATGAATGGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (27 bp):
GAGCCTGCCAAATAGGCGCGACTAATT
Found at i:21315114 original size:20 final size:20
Alignment explanation
Indices: 21315089--21315126 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21315079 ACTATATCTG
*
21315089 TTAAAAAATTTTCGAAATTC
1 TTAAAAAAGTTTCGAAATTC
*
21315109 TTAAAACAGTTTCGAAAT
1 TTAAAAAAGTTTCGAAAT
21315127 GCAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (20 bp):
TTAAAAAAGTTTCGAAATTC
Found at i:21315470 original size:27 final size:27
Alignment explanation
Indices: 21315426--21315505 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
21315416 GCCCCACCAT
* * *
21315426 TCACGCCTCTGAGTTAGGCACAATTAG
1 TCACGCCTCTCAGATAGGCACAACTAG
** * *
21315453 TTGCGCCTGTCAGATAGGCTCAACTAG
1 TCACGCCTCTCAGATAGGCACAACTAG
* *
21315480 TCACGCCTCTGAGATAGGCTCAACTA
1 TCACGCCTCTCAGATAGGCACAACTA
21315506 ATCGCGTCTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (27 bp):
TCACGCCTCTCAGATAGGCACAACTAG
Found at i:21315523 original size:27 final size:27
Alignment explanation
Indices: 21315456--21315523 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
21315446 CAATTAGTTG
* * *
21315456 CGCCTGTCAGATAGGCTCAACTAGTCA
1 CGCCTATCAAATAGGCTCAACTAATCA
* * * *
21315483 CGCCTCTGAGATAGGCTCAACTAATCG
1 CGCCTATCAAATAGGCTCAACTAATCA
*
21315510 CGTCTATCAAATAG
1 CGCCTATCAAATAG
21315524 CCGCAACCTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (27 bp):
CGCCTATCAAATAGGCTCAACTAATCA
Found at i:21317334 original size:97 final size:97
Alignment explanation
Indices: 21317168--21317359 Score: 357
Period size: 97 Copynumber: 2.0 Consensus size: 97
21317158 AAAACTATCG
*
21317168 ATACTTTTTGGCTTGGAGCTATACTGACTTGTTTTAAAAACAGTTTGACTAGTTGAAAGAATTAT
1 ATACTTTTTGGCCTGGAGCTATACTGACTTGTTTTAAAAACAGTTTGACTAGTTGAAAGAATTAT
21317233 TACTTGATTAAAATCATTTTAACTTGATTTCA
66 TACTTGATTAAAATCATTTTAACTTGATTTCA
*
21317265 ATACTTTTTGGCCTGGAGCTATACTGACTTGTTTTAAAAACAGTTTGACTAGTTGAAATAATTAT
1 ATACTTTTTGGCCTGGAGCTATACTGACTTGTTTTAAAAACAGTTTGACTAGTTGAAAGAATTAT
*
21317330 TACTTGATTAAAATCATTTTAACTTTATTT
66 TACTTGATTAAAATCATTTTAACTTGATTT
21317360 TAAAGTTGAT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (97 bp):
ATACTTTTTGGCCTGGAGCTATACTGACTTGTTTTAAAAACAGTTTGACTAGTTGAAAGAATTAT
TACTTGATTAAAATCATTTTAACTTGATTTCA
Found at i:21317473 original size:22 final size:24
Alignment explanation
Indices: 21317448--21317491 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
21317438 ATTTTGTTTA
21317448 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
21317470 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
21317492 TATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:21318422 original size:11 final size:13
Alignment explanation
Indices: 21318406--21318439 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
21318396 AATTTTGAGG
21318406 AAAAATTTCG-T-
1 AAAAATTTCGTTC
21318417 AAAAATTTCGTTC
1 AAAAATTTCGTTC
21318430 AAAAATTTCG
1 AAAAATTTCG
21318440 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:21339550 original size:62 final size:62
Alignment explanation
Indices: 21339479--21339610 Score: 255
Period size: 62 Copynumber: 2.1 Consensus size: 62
21339469 TAATGCATAT
21339479 TAGCCTATTATCGTCAAATTGTTATGATGATATATTTTGATTAATTAATTGGACACAATAAA
1 TAGCCTATTATCGTCAAATTGTTATGATGATATATTTTGATTAATTAATTGGACACAATAAA
21339541 TAGCCTATTATCGTCAAATTGTTATGATGATATATTTTGATTAATTAATTGGACACAATAAA
1 TAGCCTATTATCGTCAAATTGTTATGATGATATATTTTGATTAATTAATTGGACACAATAAA
*
21339603 TAGTCTAT
1 TAGCCTAT
21339611 CTTCTTTCTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 69 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (62 bp):
TAGCCTATTATCGTCAAATTGTTATGATGATATATTTTGATTAATTAATTGGACACAATAAA
Found at i:21347139 original size:3 final size:3
Alignment explanation
Indices: 21347133--21347161 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21347123 AGATGAAAAA
21347133 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
21347162 AATTGCTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21355624 original size:53 final size:53
Alignment explanation
Indices: 21355566--21355735 Score: 166
Period size: 53 Copynumber: 3.2 Consensus size: 53
21355556 AAATTAAATG
21355566 ATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTT
1 ATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTT
** * ** * * * ** * * *
21355619 ATAATTTTTAAAAGATTAAATCA-AATTTTTA-TTTTTTAA-AGAAGAAATTAAATG
1 ATAATTTTTATGATAAAAAAT-ATAA-TTTCACTATTCTAATAGACTATATT--TTT
21355673 ATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTT
1 ATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTT
21355726 ATAATTTTTA
1 ATAATTTTTA
21355736 AAAGATTAAA
Statistics
Matches: 84, Mismatches: 26, Indels: 14
0.68 0.21 0.11
Matches are distributed among these distances:
52 7 0.08
53 40 0.48
54 30 0.36
55 7 0.08
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (53 bp):
ATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTT
Found at i:21355696 original size:107 final size:108
Alignment explanation
Indices: 21355555--21355770 Score: 425
Period size: 107 Copynumber: 2.0 Consensus size: 108
21355545 TACAAAAATT
21355555 GAAATTAAATGATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTTA
1 GAAATTAAATGATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTTA
21355620 TAATTTTTAAAAGATTAAATCAAATTTTTAT-TTTTTAAAGAA
66 TAATTTTTAAAAGATTAAATCAAATTTTTATATTTTTAAAGAA
21355662 GAAATTAAATGATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTTA
1 GAAATTAAATGATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTTA
21355727 TAATTTTTAAAAGATTAAATCAAATTTTTATATTTTTAAAGAA
66 TAATTTTTAAAAGATTAAATCAAATTTTTATATTTTTAAAGAA
21355770 G
1 G
21355771 TTAAAATATA
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 96 0.89
108 12 0.11
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (108 bp):
GAAATTAAATGATAATTTTTATGATAAAAAATATAATTTCACTATTCTAATAGACTATATTTTTA
TAATTTTTAAAAGATTAAATCAAATTTTTATATTTTTAAAGAA
Found at i:21355753 original size:53 final size:53
Alignment explanation
Indices: 21355589--21355753 Score: 156
Period size: 53 Copynumber: 3.1 Consensus size: 53
21355579 TAAAAAATAT
21355589 AATTTCACTATTCTAATAGACTATATTTTTATAATTTTTAAAAGATTAAATCA
1 AATTTCACTATTCTAATAGACTATATTTTTATAATTTTTAAAAGATTAAATCA
* * * ** * * * ** * **
21355642 AATTTTTA-TTTTTTAA-AGAAGAAATTAAATGATAATTTTTATGATAAAAAAT-A
1 AA-TTTCACTATTCTAATAGACTATATT--TTTATAATTTTTAAAAGATTAAATCA
21355695 TAATTTCACTATTCTAATAGACTATATTTTTATAATTTTTAAAAGATTAAATCA
1 -AATTTCACTATTCTAATAGACTATATTTTTATAATTTTTAAAAGATTAAATCA
21355749 AATTT
1 AATTT
21355754 TTATATTTTT
Statistics
Matches: 79, Mismatches: 26, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
52 7 0.09
53 35 0.44
54 30 0.38
55 7 0.09
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (53 bp):
AATTTCACTATTCTAATAGACTATATTTTTATAATTTTTAAAAGATTAAATCA
Found at i:21373285 original size:7 final size:7
Alignment explanation
Indices: 21373270--21373299 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
21373260 GAAAATGAAA
*
21373270 TGTGAAT
1 TGTGGAT
21373277 TGTGGAT
1 TGTGGAT
21373284 TGTGGAT
1 TGTGGAT
21373291 TGTGGAT
1 TGTGGAT
21373298 TG
1 TG
21373300 AATTGGGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (7 bp):
TGTGGAT
Found at i:21374147 original size:30 final size:30
Alignment explanation
Indices: 21374111--21374182 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
21374101 TAACAGTAGA
*
21374111 GTGACTAAATTGGACAACTTATCTAACGA-G
1 GTGACTAAATT-GACAACTTATCTAACAAGG
*
21374141 GTGACTAAAATTGACAACTTATCTAATAAGG
1 GTGACT-AAATTGACAACTTATCTAACAAGG
21374172 GTGACTAAATT
1 GTGACTAAATT
21374183 ATATTCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (30 bp):
GTGACTAAATTGACAACTTATCTAACAAGG
Found at i:21375453 original size:44 final size:44
Alignment explanation
Indices: 21375390--21375587 Score: 254
Period size: 44 Copynumber: 4.3 Consensus size: 44
21375380 TTATCACTTG
* *
21375390 TCACTTGTCCCAGATCAGATAAGTGTAGCTAAAGCTACCACTCA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
*
21375434 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTCATCA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCA--C-TCA
* *
21375481 CTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCT-CTCACTTA
1 ----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC-CACTCA
* *
21375529 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
21375573 TCACTTGTCACTGAT
1 TCACTTGTCACTGAT
21375588 TAGAAGTACT
Statistics
Matches: 137, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
44 92 0.67
45 1 0.01
46 1 0.01
47 3 0.02
48 2 0.01
49 1 0.01
50 1 0.01
51 36 0.26
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
Found at i:21375545 original size:95 final size:95
Alignment explanation
Indices: 21375382--21375584 Score: 327
Period size: 95 Copynumber: 2.1 Consensus size: 95
21375372 GATCACATTT
*
21375382 ATCACTTGTCACTTGTCCCAGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTG
1 ATCACTTGTCACTTGTCACAGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTG
* *
21375447 ATCAGATAAGTGTAGCTAAAGTTACCACTC
66 ATCAAATAAGTGTAGCTAAAGCTACCACTC
* * *
21375477 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCT-CTCACTTATCACTTGTCACT
1 ATCACTTGTCACTTGTCACAGATCAGATAAGTGTAGCTAAAGCTAC-CACTCATCACTTGTCACT
*
21375541 GATCAAATAAGTGTAGCTAAAGCTACCACTT
65 GATCAAATAAGTGTAGCTAAAGCTACCACTC
21375572 ATCACTTGTCACT
1 ATCACTTGTCACT
21375585 GATTAGAAGT
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 1 0.01
95 99 0.99
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (95 bp):
ATCACTTGTCACTTGTCACAGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTG
ATCAAATAAGTGTAGCTAAAGCTACCACTC
Found at i:21390470 original size:9 final size:9
Alignment explanation
Indices: 21390450--21390533 Score: 62
Period size: 9 Copynumber: 9.3 Consensus size: 9
21390440 GGCATTGTTT
*
21390450 ATGATGAAG
1 ATGATGATG
*
21390459 ATGAAGATG
1 ATGATGATG
**
21390468 ATGATGGGG
1 ATGATGATG
* *
21390477 CTGATGGTG
1 ATGATGATG
*
21390486 ATGGTGATG
1 ATGATGATG
21390495 ATGATGATG
1 ATGATGATG
*
21390504 ATGATGGAAG
1 ATGAT-GATG
21390514 -TGATGATG
1 ATGATGATG
* *
21390522 GTGATGGTG
1 ATGATGATG
21390531 ATG
1 ATG
21390534 CATGCAACAC
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
8 3 0.05
9 52 0.90
10 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.42, T:0.29
Consensus pattern (9 bp):
ATGATGATG
Done.