Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 70 of 186
Found at i:22359673 original size:54 final size:52
Alignment explanation
Indices: 22359594--22359797 Score: 158
Period size: 54 Copynumber: 3.8 Consensus size: 52
22359584 ATCTCAAACT
*** * *
22359594 CTTTTATTTT-CCCCAAAAAAATTACTTTTCCTCAAACCCTTAAAAATTTTTC
1 CTTTTATTTTCCCCCAAAACTTTTACTTCT-CTCAAACCCTAAAAAATTTTTC
* * **
22359646 CTTTTATTTTCCCTCCAAAATTTTTACTTCTCTAAAAACCCTCAAAACTTTTTTC
1 CTTTTATTTTCCC-CCAAAACTTTTACTTCTCT-CAAACCCT-AAAAAATTTTTC
* * * * **
22359701 CTTTTAATTTCCTTCTAAAACTTTTACTTCTCTCAAACCTCCAAAAAAAATTTC
1 CTTTTATTTTCC-CCCAAAACTTTTACTTCTCTCAAACC-CTAAAAAATTTTTC
** * * *
22359755 CTTTTGCTTTCCCCCAAAACTTTTAGTTTCTATGAAACCCTAA
1 CTTTTATTTTCCCCCAAAACTTTTA-CTTCTCTCAAACCCTAA
22359798 TTTTTTTGAA
Statistics
Matches: 119, Mismatches: 26, Indels: 13
0.75 0.16 0.08
Matches are distributed among these distances:
52 10 0.08
53 18 0.15
54 53 0.45
55 38 0.32
ACGTcount: A:0.30, C:0.26, G:0.01, T:0.42
Consensus pattern (52 bp):
CTTTTATTTTCCCCCAAAACTTTTACTTCTCTCAAACCCTAAAAAATTTTTC
Found at i:22359726 original size:55 final size:54
Alignment explanation
Indices: 22359627--22359779 Score: 159
Period size: 55 Copynumber: 2.8 Consensus size: 54
22359617 ACTTTTCCTC
* * *
22359627 AAACCCTTAAAAATTTTTCCTTTTATTTTCCCTCCAAAATTTTTACTTCTCTAA
1 AAACCCTCAAAAATTTTTCCTTTTAATTTCCCTCCAAAACTTTTACTTCTCTAA
* * * *
22359681 AAACCCTCAAAACTTTTTTCCTTTTAATTTCCTTCTAAAACTTTTACTTCTCT-C
1 AAACCCTCAAAA-ATTTTTCCTTTTAATTTCCCTCCAAAACTTTTACTTCTCTAA
** **
22359735 AAA-CCTCCAAAAAAAATTTCCTTTTGCTTTCCC-CCAAAACTTTTA
1 AAACCCT-C-AAAAATTTTTCCTTTTAATTTCCCTCCAAAACTTTTA
22359780 GTTTCTATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
53 14 0.17
54 29 0.35
55 39 0.48
ACGTcount: A:0.30, C:0.27, G:0.01, T:0.42
Consensus pattern (54 bp):
AAACCCTCAAAAATTTTTCCTTTTAATTTCCCTCCAAAACTTTTACTTCTCTAA
Found at i:22360049 original size:20 final size:20
Alignment explanation
Indices: 22360010--22360049 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22360000 AAAAATCACA
*
22360010 TTTTTTTATATTTAATATAT
1 TTTTTTTATATTTAAAATAT
22360030 TTTTTTTA-ATTTCAAAATAT
1 TTTTTTTATATTT-AAAATAT
22360050 ATGGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTATATTTAAAATAT
Found at i:22365649 original size:26 final size:26
Alignment explanation
Indices: 22365620--22365673 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
22365610 TGAACCCCGG
22365620 TTTGCAACTT-ACTTGGCGAACACTAA
1 TTTGCAACTTAAC-TGGCGAACACTAA
* *
22365646 TTTGCAACTTAACTGGTGAACCCTAA
1 TTTGCAACTTAACTGGCGAACACTAA
22365672 TT
1 TT
22365674 CGCCAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (26 bp):
TTTGCAACTTAACTGGCGAACACTAA
Found at i:22367606 original size:13 final size:13
Alignment explanation
Indices: 22367569--22367619 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
22367559 GCAAAGTGCA
*
22367569 TAAAAACACAATT
1 TAAAAACATAATT
22367582 TATAAAACCATAATT
1 TA-AAAA-CATAATT
22367597 TAAAAACAT-ATCT
1 TAAAAACATAAT-T
22367610 T-AAAACATAA
1 TAAAAACATAA
22367620 ACTTGCATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 9 0.27
13 8 0.24
14 8 0.24
15 8 0.24
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAAACATAATT
Found at i:22367654 original size:12 final size:12
Alignment explanation
Indices: 22367639--22367694 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
22367629 GGAGTATGCA
*
22367639 TAAAACTTATTT
1 TAAAACATATTT
22367651 TAAAACATAGCTTT
1 TAAAACATA--TTT
* *
22367665 AAAAACTTATTT
1 TAAAACATATTT
22367677 TGAAAACATATTT
1 T-AAAACATATTT
22367690 TAAAA
1 TAAAA
22367695 ACAGAGTGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 15 0.42
13 11 0.31
14 10 0.28
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (12 bp):
TAAAACATATTT
Found at i:22367671 original size:26 final size:26
Alignment explanation
Indices: 22367640--22367696 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
22367630 GAGTATGCAT
22367640 AAAACTTATTTT-AAAACATAGCTTTA
1 AAAACTTATTTTGAAAACATA-CTTTA
*
22367666 AAAACTTATTTTGAAAACATATTTTA
1 AAAACTTATTTTGAAAACATACTTTA
22367692 AAAAC
1 AAAAC
22367697 AGAGTGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAACTTATTTTGAAAACATACTTTA
Found at i:22367682 original size:13 final size:13
Alignment explanation
Indices: 22367640--22367697 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
22367630 GAGTATGCAT
*
22367640 AAAACTTATTTT-
1 AAAACATATTTTA
*
22367652 AAAACATAGCTTTA
1 AAAACATA-TTTTA
* *
22367666 AAAACTTATTTTG
1 AAAACATATTTTA
22367679 AAAACATATTTTA
1 AAAACATATTTTA
22367692 AAAACA
1 AAAACA
22367698 GAGTGTCAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 7 0.19
13 23 0.62
14 7 0.19
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.36
Consensus pattern (13 bp):
AAAACATATTTTA
Found at i:22368269 original size:26 final size:26
Alignment explanation
Indices: 22368213--22368271 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
22368203 TTGGAGAACT
22368213 CCTAGTTTGCAACTTACCTGGTGTAC
1 CCTAGTTTGCAACTTACCTGGTGTAC
*
22368239 ACTAGTTTGCAACTTTA-CTGGT-TAAC
1 CCTAGTTTGCAAC-TTACCTGGTGT-AC
22368265 CCTAGTT
1 CCTAGTT
22368272 CGCCAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 25 0.86
27 3 0.10
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (26 bp):
CCTAGTTTGCAACTTACCTGGTGTAC
Found at i:22368686 original size:118 final size:118
Alignment explanation
Indices: 22368530--22368891 Score: 457
Period size: 118 Copynumber: 3.0 Consensus size: 118
22368520 CACACCATGT
*
22368530 AACATCTATTTAACATGCAATGAACGTATATGAAAATACTTACACACTTGTACAACAATATGTAG
1 AACATCTATTTAACATGCAATGAACGTACATGAAAATACTTACACACTTGTACAACAATATGTAG
* * *
22368595 CACGTTCAGTCACAATTTTTACACATAACATTGGACTTATATAACCCAGAATAC
66 CACGTTCAGTCACCATTTTTACACA-AACATTGGACTCATATGACCCAGAATAC
* * *
22368649 AACATCT-TTTAACATGCAATGAACATACATGCAAATACTCACACACTTGTACAACAATA--T-G
1 AACATCTATTTAACATGCAATGAACGTACATGAAAATACTTACACACTTGTACAACAATATGTAG
* * *
22368710 CATGTTCAGTCACCATTTTTACAC-AATATTGGAATCATATGACCCAGAATAC
66 CACGTTCAGTCACCATTTTTACACAAACATTGGACTCATATGACCCAGAATAC
* * * *
22368762 AACATTTATTTAACATGCAATGAACGTACATGTAAATA-TTCACTCACTTGTACAATAATATGTA
1 AACATCTATTTAACATGCAATGAACGTACATGAAAATACTT-ACACACTTGTACAACAATATGTA
* *
22368826 TTTGCAGCATGTTCAGTCACCATTTTTACACACAACATTGGACTCATATGACCCAAAATAA
65 ---GCA-C--GTTCAGTCACCATTTTTACACA-AACATTGGACTCATATGACCCAGAATAC
22368887 AACAT
1 AACAT
22368892 AAATCATTTA
Statistics
Matches: 209, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
113 31 0.15
114 45 0.22
115 23 0.11
116 2 0.01
118 48 0.23
119 7 0.03
120 3 0.01
123 21 0.10
125 29 0.14
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (118 bp):
AACATCTATTTAACATGCAATGAACGTACATGAAAATACTTACACACTTGTACAACAATATGTAG
CACGTTCAGTCACCATTTTTACACAAACATTGGACTCATATGACCCAGAATAC
Found at i:22370559 original size:18 final size:18
Alignment explanation
Indices: 22370521--22370559 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22370511 TTTGGTTTGG
* *
22370521 TTATTTTACTTAGTATTT
1 TTATTTAACTTAGTATAT
*
22370539 TTATTTAACTTAGTGTAT
1 TTATTTAACTTAGTATAT
22370557 TTA
1 TTA
22370560 CTTTTTACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (18 bp):
TTATTTAACTTAGTATAT
Found at i:22372166 original size:14 final size:15
Alignment explanation
Indices: 22372140--22372168 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22372130 AAATCAGATC
22372140 ATGTCACCAACAAAA
1 ATGTCACCAACAAAA
22372155 ATGTCA-CAACAAAA
1 ATGTCACCAACAAAA
22372169 CAATATCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (15 bp):
ATGTCACCAACAAAA
Found at i:22372873 original size:19 final size:19
Alignment explanation
Indices: 22372849--22372886 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
22372839 GATAATGAAG
22372849 AATGTCACACCATTGGCTT
1 AATGTCACACCATTGGCTT
22372868 AATGTCACACCATTGGCTT
1 AATGTCACACCATTGGCTT
22372887 GATAGAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
AATGTCACACCATTGGCTT
Found at i:22380574 original size:43 final size:43
Alignment explanation
Indices: 22380513--22380613 Score: 175
Period size: 43 Copynumber: 2.3 Consensus size: 43
22380503 TTGTGAATTC
*
22380513 TCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGA
1 TCCACAGCTCGTGTGAGCAGCATCATGTAGCCTAACATCTCGA
22380556 TCCACAGCTCGTGTGAGCAGCATCATGTAGCCTAACATCTCGA
1 TCCACAGCTCGTGTGAGCAGCATCATGTAGCCTAACATCTCGA
* *
22380599 CCCACAGCTTGTGTG
1 TCCACAGCTCGTGTG
22380614 GCCAGGCCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.24
Consensus pattern (43 bp):
TCCACAGCTCGTGTGAGCAGCATCATGTAGCCTAACATCTCGA
Found at i:22382182 original size:42 final size:44
Alignment explanation
Indices: 22382136--22382231 Score: 160
Period size: 44 Copynumber: 2.2 Consensus size: 44
22382126 TCCTAGACTG
*
22382136 GGTCTTACACG-AAATCA-AATACGATGCCAATGTCCCAGACGT
1 GGTCTTACACGTAAATCATAATACGATGCCAACGTCCCAGACGT
*
22382178 GGTCTTACACGTAAATCATAATTCGATGCCAACGTCCCAGACGT
1 GGTCTTACACGTAAATCATAATACGATGCCAACGTCCCAGACGT
22382222 GGTCTTACAC
1 GGTCTTACAC
22382232 AAAAACACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 11 0.22
43 6 0.12
44 33 0.66
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
GGTCTTACACGTAAATCATAATACGATGCCAACGTCCCAGACGT
Found at i:22385222 original size:43 final size:43
Alignment explanation
Indices: 22385163--22385247 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
22385153 TGAGGTATGT
*
22385163 AGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCA
1 AGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCA
*
22385206 AGCATCTGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGC
1 AGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGC
22385248 GATTCATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (43 bp):
AGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCA
Found at i:22392283 original size:47 final size:47
Alignment explanation
Indices: 22392217--22392359 Score: 141
Period size: 47 Copynumber: 3.0 Consensus size: 47
22392207 GATAATTGAA
* *
22392217 TCTATTTTAATATTCTACCATCTCGGATAGGCTGACAACGATGGTTT
1 TCTATTTCAATATACTACCATCTCGGATAGGCTGACAACGATGGTTT
* * *
22392264 TCT-TTTCCAATATGCTACCATCT-GGA-ATGGCCTGACAACGATAGCTT
1 TCTATTT-CAATATACTACCATCTCGGATA-GG-CTGACAACGATGGTTT
* * * *
22392311 TCTATTTTAATATACTGCCATCTCGGAT-GGCTCGAGAATGATGGTTT
1 TCTATTTCAATATACTACCATCTCGGATAGGCT-GACAACGATGGTTT
22392358 TC
1 TC
22392360 ACAATTTACT
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
45 1 0.01
46 10 0.13
47 61 0.78
48 6 0.08
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (47 bp):
TCTATTTCAATATACTACCATCTCGGATAGGCTGACAACGATGGTTT
Found at i:22394588 original size:11 final size:11
Alignment explanation
Indices: 22394569--22394627 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
22394559 AAACACAACA
22394569 AAAAGCAGCAGC
1 AAAA-CAGCAGC
22394581 AAAACAGCA-C
1 AAAACAGCAGC
22394591 TAAAACAGCAGC
1 -AAAACAGCAGC
*
22394603 AAAACAGCATC
1 AAAACAGCAGC
*
22394614 AAAACAGCACC
1 AAAACAGCAGC
22394625 AAA
1 AAA
22394628 TAGCAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 1 0.02
11 37 0.86
12 5 0.12
ACGTcount: A:0.56, C:0.27, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAACAGCAGC
Found at i:22394638 original size:21 final size:21
Alignment explanation
Indices: 22394556--22394648 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 21
22394546 CAAAAAAATA
*
22394556 ACAAAACA-CAACAAAAAGCAGC
1 ACAAAACAGCAA-TAAAA-CAGC
*
22394578 AGCAAAACAGCACTAAAACAGC
1 A-CAAAACAGCAATAAAACAGC
22394600 AGCAAAACAGC-ATCAAAACAGC
1 A-CAAAACAGCAAT-AAAACAGC
* * *
22394622 ACCAAATAGCAATAAAATAGC
1 ACAAAACAGCAATAAAACAGC
22394643 ACAAAA
1 ACAAAA
22394649 AACAGCATCG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
21 20 0.33
22 27 0.45
23 11 0.18
24 2 0.03
ACGTcount: A:0.59, C:0.25, G:0.11, T:0.05
Consensus pattern (21 bp):
ACAAAACAGCAATAAAACAGC
Found at i:22398247 original size:18 final size:18
Alignment explanation
Indices: 22398224--22398258 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
22398214 TGGACGGTGG
22398224 AGGTGGTGGTGAGCTAGA
1 AGGTGGTGGTGAGCTAGA
22398242 AGGTGGTGGTGAGCTAG
1 AGGTGGTGGTGAGCTAG
22398259 GGATTTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.51, T:0.23
Consensus pattern (18 bp):
AGGTGGTGGTGAGCTAGA
Found at i:22398378 original size:11 final size:10
Alignment explanation
Indices: 22398344--22398375 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
22398334 GTTACTTTAA
22398344 AATTAAAAAT
1 AATTAAAAAT
22398354 AA--AAAAAT
1 AATTAAAAAT
22398362 AATTAAAAAT
1 AATTAAAAAT
22398372 AATT
1 AATT
22398376 TAATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATTAAAAAT
Found at i:22398380 original size:18 final size:18
Alignment explanation
Indices: 22398339--22398386 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
22398329 GTAAAGTTAC
22398339 TTTAA-AATTAAAAATAA
1 TTTAATAATTAAAAATAA
***
22398356 AAAAATAATTAAAAATAA
1 TTTAATAATTAAAAATAA
22398374 TTTAAT-ATTAAAA
1 TTTAATAATTAAAA
22398387 TCAGGTTGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAATAATTAAAAATAA
Found at i:22398891 original size:16 final size:17
Alignment explanation
Indices: 22398867--22398898 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
22398857 TATTTTACTT
22398867 ATTCTTAATTTTAAATC
1 ATTCTTAATTTTAAATC
22398884 ATTC-TAATTTTAAAT
1 ATTCTTAATTTTAAAT
22398899 TTAAACCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTCTTAATTTTAAATC
Found at i:22407879 original size:7 final size:7
Alignment explanation
Indices: 22407869--22407893 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22407859 TAAACTTAGG
22407869 GGTTTAA
1 GGTTTAA
22407876 GGTTTAA
1 GGTTTAA
22407883 GGTTTAA
1 GGTTTAA
22407890 GGTT
1 GGTT
22407894 CAAGTTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (7 bp):
GGTTTAA
Found at i:22419441 original size:32 final size:32
Alignment explanation
Indices: 22419405--22419468 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
22419395 ACCAAGTCCA
22419405 TAAGGGCTAAGGCAAAAGAAGTAATGGAGCCC
1 TAAGGGCTAAGGCAAAAGAAGTAATGGAGCCC
22419437 TAAGGGCTAAGGCAAAAGAAGTAATGGAGCCC
1 TAAGGGCTAAGGCAAAAGAAGTAATGGAGCCC
22419469 ATACATGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (32 bp):
TAAGGGCTAAGGCAAAAGAAGTAATGGAGCCC
Found at i:22422460 original size:5 final size:5
Alignment explanation
Indices: 22422450--22422512 Score: 56
Period size: 5 Copynumber: 11.8 Consensus size: 5
22422440 ATTAAAAATA
*
22422450 ATTAT ATTAT ATTAT ATTAT ATTTAT ATTAAAT ATTA- ATATAT ATTCAA
1 ATTAT ATTAT ATTAT ATTAT A-TTAT ATT--AT ATTAT AT-TAT ATT-AT
*
22422499 ATTAT GTTAT ATTA
1 ATTAT ATTAT ATTA
22422513 AATAAGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 30 0.62
6 11 0.23
7 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (5 bp):
ATTAT
Found at i:22422502 original size:23 final size:23
Alignment explanation
Indices: 22422458--22422502 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
22422448 TAATTATATT
* *
22422458 ATATTATATTATATTTATATTAA
1 ATATTATATTATATTCAAATTAA
22422481 ATATTA-ATATATATTCAAATTA
1 ATATTATAT-TATATTCAAATTA
22422503 TGTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTATATTATATTCAAATTAA
Found at i:22422882 original size:26 final size:26
Alignment explanation
Indices: 22422846--22422905 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
22422836 GCGATAAGAG
22422846 TATTATATTATAA-ATGAAAAATATTA
1 TATTATATTATAACAT-AAAAATATTA
*
22422872 TATTATATTATAAGCATAAAATTATTA
1 TATTATATTATAA-CATAAAAATATTA
22422899 TATTATA
1 TATTATA
22422906 ATAAATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 13 0.42
27 16 0.52
28 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
TATTATATTATAACATAAAAATATTA
Found at i:22423434 original size:274 final size:275
Alignment explanation
Indices: 22422903--22423452 Score: 1030
Period size: 274 Copynumber: 2.0 Consensus size: 275
22422893 TTATTATATT
22422903 ATAATAAATTAGAACAATCAACTCACTATTTAATAGTAATAAAAATTTTAGTCTATATTAATTAT
1 ATAATAAATTAGAACAATCAACTCACTATTTAATAGTAATAAAAATTTTAGTCTATATTAATTAT
22422968 CCTAACTCGTTTCACCTAACTTTAGTTGCATCGACTAAATTATATATTAATACTAATACTATATA
66 CCTAACTCGTTTCACCTAACTTTAGTTGCATCGACTAAATTATATATTAATACTAATACTATATA
*
22423033 AAAAGTATAAAATTAATAATTTCTTCTATTATAATAACAAATAATAAAACTTTATCTGTTAAATG
131 AAAAGTATAAAATTAATAATTTCTTCTATTATAATAACAAATAATAAAACTTTATCAGTTAAATG
*
22423098 TGCCCGTTTTAAACTTTAAAATAGAAAATTAAAAAATTAAAAAGAATCATTTATATAACAAACAA
196 TGCCCGTTTTAAACTTTAAAATAGAAAATTAAAAAATTAAAAAGAATCATTGATATAACAAACAA
22423163 ATGGAAAAGAGAGAG
261 ATGGAAAAGAGAGAG
*
22423178 ATAATAAATTAGAACAATCAACTCACTATTTAATAGTAATAAAAATTTTAGTCTATATTGATTAT
1 ATAATAAATTAGAACAATCAACTCACTATTTAATAGTAATAAAAATTTTAGTCTATATTAATTAT
* *
22423243 CCTAACTCGTTTCACCTAACTTTAGTTGCATCGACTAAATTGTATATTGATACTAATACTATAT-
66 CCTAACTCGTTTCACCTAACTTTAGTTGCATCGACTAAATTATATATTAATACTAATACTATATA
*
22423307 AAAAGTATAAAATTAATAATTTCTTCTGTTATAATAACAAATAATAAAACTTTATCAGTTAAATG
131 AAAAGTATAAAATTAATAATTTCTTCTATTATAATAACAAATAATAAAACTTTATCAGTTAAATG
*
22423372 TGCCCGTTTTAAACTTTAAAATAGAAGATTAAAAAATTAAAAAGAATCATTGATATAACAAACAA
196 TGCCCGTTTTAAACTTTAAAATAGAAAATTAAAAAATTAAAAAGAATCATTGATATAACAAACAA
22423437 ATGGAAAAGAGAGAG
261 ATGGAAAAGAGAGAG
22423452 A
1 A
22423453 GAAAGACAAA
Statistics
Matches: 268, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
274 142 0.53
275 126 0.47
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.34
Consensus pattern (275 bp):
ATAATAAATTAGAACAATCAACTCACTATTTAATAGTAATAAAAATTTTAGTCTATATTAATTAT
CCTAACTCGTTTCACCTAACTTTAGTTGCATCGACTAAATTATATATTAATACTAATACTATATA
AAAAGTATAAAATTAATAATTTCTTCTATTATAATAACAAATAATAAAACTTTATCAGTTAAATG
TGCCCGTTTTAAACTTTAAAATAGAAAATTAAAAAATTAAAAAGAATCATTGATATAACAAACAA
ATGGAAAAGAGAGAG
Found at i:22423637 original size:12 final size:13
Alignment explanation
Indices: 22423612--22423643 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
22423602 AGATGATTTT
22423612 TTTATTTTTAGAG
1 TTTATTTTTAGAG
22423625 TTTATTTTT-GAG
1 TTTATTTTTAGAG
22423637 TTT-TTTT
1 TTTATTTT
22423644 ATAATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 6 0.32
13 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
TTTATTTTTAGAG
Found at i:22424238 original size:10 final size:10
Alignment explanation
Indices: 22424206--22424265 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 10
22424196 AAATTCAAAT
22424206 AATTATAAAAA
1 AATT-TAAAAA
*
22424217 ACTATTTTAAAA
1 A--ATTTAAAAA
22424229 AATTT-AAAA
1 AATTTAAAAA
22424238 AATTT-AAAA
1 AATTTAAAAA
22424247 AATTTAAAAA
1 AATTTAAAAA
22424257 AA-TTAAAAA
1 AATTTAAAAA
22424266 TATATAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 25 0.56
10 10 0.22
11 1 0.02
12 6 0.13
13 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:22424273 original size:10 final size:9
Alignment explanation
Indices: 22424222--22424303 Score: 83
Period size: 9 Copynumber: 8.9 Consensus size: 9
22424212 AAAAAACTAT
22424222 TTTAAAAAA
1 TTTAAAAAA
22424231 TTTAAAAAA
1 TTTAAAAAA
22424240 TTTAAAAAA
1 TTTAAAAAA
22424249 TTTAAAAAA
1 TTTAAAAAA
*
22424258 ATTAAAAATA
1 TTTAAAAA-A
* * *
22424268 TATAAATAT
1 TTTAAAAAA
*
22424277 TTGTAAAATA
1 TT-TAAAAAA
**
22424287 TTTTTAAAA
1 TTTAAAAAA
22424296 TTTAAAAA
1 TTTAAAAA
22424304 GAATAATTAA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
9 45 0.79
10 12 0.21
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:22435934 original size:22 final size:22
Alignment explanation
Indices: 22435909--22435951 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22435899 ATCTAATTTC
22435909 ATTAAAATGTTATATGT-TTAGA
1 ATTAAAA-GTTATATGTGTTAGA
*
22435931 ATTATAAGTTATATGTGTTAG
1 ATTAAAAGTTATATGTGTTAG
22435952 GTATTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (22 bp):
ATTAAAAGTTATATGTGTTAGA
Found at i:22438406 original size:24 final size:24
Alignment explanation
Indices: 22438375--22438422 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
22438365 AGAAAGTTCT
22438375 CTTTTTCCCCTATAAAGTCTATTA
1 CTTTTTCCCCTATAAAGTCTATTA
*
22438399 CTTTTTCCCCTGTAAAGTCTATTA
1 CTTTTTCCCCTATAAAGTCTATTA
22438423 GAACTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.06, T:0.46
Consensus pattern (24 bp):
CTTTTTCCCCTATAAAGTCTATTA
Found at i:22441370 original size:49 final size:47
Alignment explanation
Indices: 22441312--22441664 Score: 589
Period size: 47 Copynumber: 7.4 Consensus size: 47
22441302 ATTGATGTAC
* * * * *
22441312 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
22441359 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
22441408 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
22441457 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
22441504 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
22441551 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* * *
22441598 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
22441645 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
22441665 TCCCGAAGGG
Statistics
Matches: 295, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 203 0.69
49 92 0.31
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
Found at i:22445107 original size:50 final size:51
Alignment explanation
Indices: 22444976--22445115 Score: 174
Period size: 50 Copynumber: 2.8 Consensus size: 51
22444966 TGATCTATTG
* * * * *
22444976 TGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAAC
1 TGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAAAAC
* * ** **
22445027 TGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAG-ATGC
1 TGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAAAAC
22445077 TGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGT
1 TGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGT
22445116 CACGTGTGTA
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
50 39 0.51
51 37 0.49
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (51 bp):
TGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAAAAC
Found at i:22445118 original size:33 final size:33
Alignment explanation
Indices: 22445081--22445148 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
22445071 AGATGCTGAG
*
22445081 GTCACGTGTGTAGTACTAAGTGCAGGCTACTAC
1 GTCACGTGTGTAGTACTAAGTGCAGGCCACTAC
22445114 GTCACGTGTGTAGTACTAAGTGCAGGCCACTAC
1 GTCACGTGTGTAGTACTAAGTGCAGGCCACTAC
22445147 GT
1 GT
22445149 GTACCAGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (33 bp):
GTCACGTGTGTAGTACTAAGTGCAGGCCACTAC
Found at i:22448088 original size:46 final size:46
Alignment explanation
Indices: 22448036--22448401 Score: 473
Period size: 46 Copynumber: 8.0 Consensus size: 46
22448026 GCTCTTTGAA
* * *
22448036 ATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
22448082 ATGAAATGTTTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
22448128 ATGAAATGAATAAGACCATGGTTGAAAGATACCATCGCAACATTAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
22448174 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
22448220 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
22448266 GGGAAATGAATAAGACCATGGTTGAAGGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
22448312 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
22448358 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
22448402 TCAAAGATAA
Statistics
Matches: 286, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 285 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:22448245 original size:21 final size:21
Alignment explanation
Indices: 22448177--22448246 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 21
22448167 ACATTATATA
22448177 AAATGTGTAAGACCATGGTTG
1 AAATGTGTAAGACCATGGTTG
* *
22448198 AAA-G-ATACCATGACAACATGATATG
1 AAATGTGTA--A-GAC--CATGGT-TG
22448223 AAATGTGTAAGACCATGGTTG
1 AAATGTGTAAGACCATGGTTG
22448244 AAA
1 AAA
22448247 GATACTATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 9 0.24
22 8 0.22
24 8 0.22
25 6 0.16
26 1 0.03
27 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.24
Consensus pattern (21 bp):
AAATGTGTAAGACCATGGTTG
Found at i:22448287 original size:138 final size:138
Alignment explanation
Indices: 22448039--22448401 Score: 521
Period size: 138 Copynumber: 2.6 Consensus size: 138
22448029 CTTTGAAATG
* *
22448039 AAATGTGTAAGACCATGATTGAAAGATACCATGGCAACATGATATGAAATGTTTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGT
* * *
22448104 TGAAAGATACCATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATCGCAAC
66 TGAAAGATACTATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATCGCAAC
* * *
22448169 ATTATATA
131 ATGACAGA
*
22448177 AAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGATATGAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGT
* * *
22448242 TGAAAGATACTATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAGGATACCATGGCAAC
66 TGAAAGATACTATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATCGCAAC
* *
22448307 ATGACGGG
131 ATGACAGA
** * * *
22448315 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG-AAATGTGTAAGACCATGG
* *
22448379 TTGAAAGACACTATGGCATCATG
65 TTGAAAGATACTATGGCAACATG
22448402 TCAAAGATAA
Statistics
Matches: 202, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
137 1 0.00
138 201 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (138 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGT
TGAAAGATACTATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATCGCAAC
ATGACAGA
Found at i:22451652 original size:40 final size:40
Alignment explanation
Indices: 22451590--22451845 Score: 419
Period size: 40 Copynumber: 6.4 Consensus size: 40
22451580 AAACCAAGTA
* * *
22451590 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
22451629 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
22451669 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
22451709 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
22451749 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
22451789 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
22451829 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
22451846 CGTTATCATC
Statistics
Matches: 207, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
39 14 0.07
40 193 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:22460859 original size:48 final size:46
Alignment explanation
Indices: 22460801--22461021 Score: 181
Period size: 46 Copynumber: 4.7 Consensus size: 46
22460791 TATATCGAGG
* * *
22460801 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCCCAAGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTAGC-TCT-CATCCCAAGGC
* * * * *
22460850 CGATGCATGTCCTAGACATGTCTTACATTAGCTCTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCCCAAGGC
* * * ** *
22460896 CGATGCATGTCCCATACATGTCTTACACTGGATCTCATAACATGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCCCAAGGC
* * * ** ** *
22460942 TGATTCATGTCCCAGACATGTCTTACACTGGCTCTCATAACGTGAC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCCCAAGGC
* * * *
22460988 TGATGCATGTTCTAGACATGTCTTACACTGGCTC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTC
22461022 ATATACCACC
Statistics
Matches: 145, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
46 114 0.79
47 2 0.01
48 24 0.17
49 5 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCCCAAGGC
Found at i:22461019 original size:46 final size:45
Alignment explanation
Indices: 22460851--22461021 Score: 198
Period size: 46 Copynumber: 3.7 Consensus size: 45
22460841 TCCCAAGGCC
* * * * ** *
22460851 GATGCATGTCCTAGACATGTCTTACATTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAAC-ATGCT
* *
22460897 GATGCATGTCCCATACATGTCTTACACTGGATCTCATAACATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAACAT-GCT
* *
22460943 GATTCATGTCCCAGACATGTCTTACACTGGCTCTCATAACGTGACT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAACATG-CT
* *
22460989 GATGCATGTTCTAGACATGTCTTACACTGGCTC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTC
22461022 ATATACCACC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 3 0.03
46 104 0.97
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAACATGCT
Found at i:22461524 original size:20 final size:19
Alignment explanation
Indices: 22461483--22461525 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
22461473 TATAGTGACC
* *
22461483 CAAAATTCCTATTATTTCA
1 CAAAATTACTATCATTTCA
*
22461502 CAAAATTACTATCCATTTTA
1 CAAAATTACTAT-CATTTCA
22461522 CAAA
1 CAAA
22461526 CTTTACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAATTACTATCATTTCA
Found at i:22468794 original size:26 final size:26
Alignment explanation
Indices: 22468765--22468926 Score: 121
Period size: 26 Copynumber: 6.2 Consensus size: 26
22468755 ATGCTAAAAA
22468765 AGCAGGCCTTGAGCTAGTGGTTATTT
1 AGCAGGCCTTGAGCTAGTGGTTATTT
** *
22468791 AGCAGGCCTCAAGCTAATGGTTATTT
1 AGCAGGCCTTGAGCTAGTGGTTATTT
* * * * * *
22468817 AGCAGACATCGAGAT-GACGCTTATTT
1 AGCAGGCCTTGAGCTAG-TGGTTATTT
* * *
22468843 AGCAGGCCTTGAGCAAGTGTTTGTTT
1 AGCAGGCCTTGAGCTAGTGGTTATTT
* * *
22468869 AGCAGACCTTGAGTTGGTGGTTATTT
1 AGCAGGCCTTGAGCTAGTGGTTATTT
* * *
22468895 AACAGGCTTTGAGCCAGT-GTATATTT
1 AGCAGGCCTTGAGCTAGTGGT-TATTT
*
22468921 ATCAGG
1 AGCAGG
22468927 TACTATGTAT
Statistics
Matches: 102, Mismatches: 31, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
25 2 0.02
26 99 0.97
27 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (26 bp):
AGCAGGCCTTGAGCTAGTGGTTATTT
Found at i:22468893 original size:52 final size:52
Alignment explanation
Indices: 22468765--22468921 Score: 145
Period size: 52 Copynumber: 3.0 Consensus size: 52
22468755 ATGCTAAAAA
* * * ** *
22468765 AGCAGGCCTTGAGCTAGTGGTTATTTAGCAGGCCTCAAGCTAA-TGGTTATTT
1 AGCAGACCTTGAGATGGTGGTTATTTAGCAGGCCTTGAGC-AAGTGTTTATTT
* * ** * *
22468817 AGCAGACATCGAGATGACGCTTATTTAGCAGGCCTTGAGCAAGTGTTTGTTT
1 AGCAGACCTTGAGATGGTGGTTATTTAGCAGGCCTTGAGCAAGTGTTTATTT
* * * * *
22468869 AGCAGACCTTGAGTTGGTGGTTATTTAACAGGCTTTGAGCCAGTGTATATTT
1 AGCAGACCTTGAGATGGTGGTTATTTAGCAGGCCTTGAGCAAGTGTTTATTT
22468921 A
1 A
22468922 TCAGGTACTA
Statistics
Matches: 81, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (52 bp):
AGCAGACCTTGAGATGGTGGTTATTTAGCAGGCCTTGAGCAAGTGTTTATTT
Found at i:22470170 original size:21 final size:21
Alignment explanation
Indices: 22470139--22470189 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
22470129 ACGGTCTGAG
* *
22470139 CACACGAGCGTGTGGGGTAGT
1 CACACGGGCGTGTGGGGTAGC
*
22470160 CGCACGGGCGTGTGGGGTAGC
1 CACACGGGCGTGTGGGGTAGC
22470181 CACACGGGC
1 CACACGGGC
22470190 TAGCCTCTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.45, T:0.14
Consensus pattern (21 bp):
CACACGGGCGTGTGGGGTAGC
Found at i:22471844 original size:13 final size:13
Alignment explanation
Indices: 22471826--22471860 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
22471816 GGCTCGGCCC
22471826 ATATTAATTTTTT
1 ATATTAATTTTTT
22471839 ATATT-A-TTTTT
1 ATATTAATTTTTT
22471850 ATATTAATTTT
1 ATATTAATTTT
22471861 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.50
12 2 0.10
13 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:22472446 original size:17 final size:17
Alignment explanation
Indices: 22472426--22472472 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
22472416 ATATGCTTTT
22472426 TTCA-TTTGAGATTTAAG
1 TTCATTTTGAG-TTTAAG
22472443 TTCATTTTGAGTTTAA-
1 TTCATTTTGAGTTTAAG
*
22472459 TT-ATTTTAAGTTTA
1 TTCATTTTGAGTTTA
22472473 GATGTTTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 9 0.32
18 6 0.21
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (17 bp):
TTCATTTTGAGTTTAAG
Found at i:22478075 original size:17 final size:17
Alignment explanation
Indices: 22478053--22478085 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22478043 CTCTTAAAGA
22478053 CCATCC-TACTACTTGGG
1 CCATCCTTAC-ACTTGGG
22478070 CCATCCTTACACTTGG
1 CCATCCTTACACTTGG
22478086 TGGTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.36, G:0.15, T:0.30
Consensus pattern (17 bp):
CCATCCTTACACTTGGG
Found at i:22483446 original size:28 final size:28
Alignment explanation
Indices: 22483406--22483470 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
22483396 ATGTACTAGA
*
22483406 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
22483434 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
22483462 ATACCCCTA
1 ATACCCCTA
22483471 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:22483617 original size:28 final size:27
Alignment explanation
Indices: 22483576--22483665 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
22483566 AGGAAGCGTC
22483576 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
22483604 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
22483631 CTAGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
22483660 CTGGTG
1 CTGGTG
22483666 ATTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 25 0.47
29 6 0.11
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:22483637 original size:27 final size:27
Alignment explanation
Indices: 22483586--22483657 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
22483576 CTGGTGGCTA
* *
22483586 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAA-TATCTGTTCTAGTGGCAC
*
22483614 TGCCACATATATCTGTTCTAGTGGCAC
1 TGCCACAAATATCTGTTCTAGTGGCAC
22483641 TGCCACAAAATATCTGT
1 TGCCAC-AAATATCTGT
22483658 ATCTGGTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTAGTGGCAC
Found at i:22495846 original size:22 final size:21
Alignment explanation
Indices: 22495816--22495859 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
22495806 CTCACTCCAT
*
22495816 AAAAGCCTACCTTTACAATTA
1 AAAAGCCTACCTTCACAATTA
22495837 AAAACGCCTACCTTCACAATTA
1 AAAA-GCCTACCTTCACAATTA
22495859 A
1 A
22495860 CCCTTAGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAGCCTACCTTCACAATTA
Found at i:22499511 original size:16 final size:16
Alignment explanation
Indices: 22499490--22499529 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
22499480 AGTTAAATGG
22499490 ATTAAAAG-AATTTGAA
1 ATTAAAAGAAATTT-AA
22499506 ATTAAAAGAAATTTAA
1 ATTAAAAGAAATTTAA
*
22499522 ATAAAAAG
1 ATTAAAAG
22499530 TCCTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (16 bp):
ATTAAAAGAAATTTAA
Found at i:22500906 original size:15 final size:16
Alignment explanation
Indices: 22500885--22500926 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
22500875 TAACCTAAAT
22500885 TAATAAAATAAAATAA
1 TAATAAAATAAAATAA
22500901 -AATAAAA-ATAAATAA
1 TAATAAAATA-AAATAA
*
22500916 TAAAAAAATAA
1 TAATAAAATAA
22500927 TATCTTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
16 7 0.32
17 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TAATAAAATAAAATAA
Found at i:22510387 original size:20 final size:23
Alignment explanation
Indices: 22510364--22510406 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
22510354 CAAATACTTG
22510364 CAAACA-TAT-ACC-AGCCAATT
1 CAAACATTATAACCAAGCCAATT
22510384 CAAACATTATAACCAAGCCAATT
1 CAAACATTATAACCAAGCCAATT
22510407 TTAACATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 3 0.15
22 3 0.15
23 8 0.40
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.21
Consensus pattern (23 bp):
CAAACATTATAACCAAGCCAATT
Found at i:22516308 original size:23 final size:23
Alignment explanation
Indices: 22516292--22516417 Score: 127
Period size: 23 Copynumber: 5.6 Consensus size: 23
22516282 CAGCTTGTAT
*
22516292 GAGCTTACCGTTTCAGCTCTTAT
1 GAGCTTACCGTTTCAGCTCTTAG
*
22516315 GAGCTTACCG-TTCAGCTCTTCG
1 GAGCTTACCGTTTCAGCTCTTAG
* *
22516337 GAGCTTATCGTTTCAGTTCTTAG
1 GAGCTTACCGTTTCAGCTCTTAG
* *
22516360 GGGCTTACCGTTTCAACTC-TACG
1 GAGCTTACCGTTTCAGCTCTTA-G
*
22516383 GAGCTTACTG-TTCAGCTCAATT--
1 GAGCTTACCGTTTCAGCTC--TTAG
22516405 GAGCTTACCGTTT
1 GAGCTTACCGTTT
22516418 ATCGGCTCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
22 37 0.44
23 46 0.55
25 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCTTAG
Found at i:22516349 original size:45 final size:44
Alignment explanation
Indices: 22516292--22516416 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 44
22516282 CAGCTTGTAT
* *
22516292 GAGCTTACCGTTTCAGCTCTTATGAGCTTACCGTTCAGCTCTTCG
1 GAGCTTA-CGTTTCAGCTCTTATGAGCTTACCGTTCAACTCTACG
* * *
22516337 GAGCTTATCGTTTCAGTTCTTAGGGGCTTACCGTTTCAACTCTACG
1 GAGCTTA-CGTTTCAGCTCTTATGAGCTTACCG-TTCAACTCTACG
*
22516383 GAGCTTAC-TGTTCAGCTC-AATTGAGCTTACCGTT
1 GAGCTTACGT-TTCAGCTCTTA-TGAGCTTACCGTT
22516417 TATCGGCTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 4 0.06
45 46 0.69
46 17 0.25
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.36
Consensus pattern (44 bp):
GAGCTTACGTTTCAGCTCTTATGAGCTTACCGTTCAACTCTACG
Found at i:22520429 original size:15 final size:15
Alignment explanation
Indices: 22520405--22520452 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
22520395 AGGAAACTGA
22520405 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
22520420 ATAGAGAAATCCAAA
1 ATAAAGAAATCCAAG
*
22520435 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
22520450 ATA
1 ATA
22520453 CGATACTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:22527075 original size:16 final size:17
Alignment explanation
Indices: 22527046--22527089 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
22527036 ACCGATAAAA
* *
22527046 TATTTTTTTATTTTTTG
1 TATTTTCTTATTTTCTG
22527063 TATTTTCTT-TTTTCTG
1 TATTTTCTTATTTTCTG
*
22527079 TATTTTTTTAT
1 TATTTTCTTAT
22527090 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.80
Consensus pattern (17 bp):
TATTTTCTTATTTTCTG
Found at i:22542240 original size:20 final size:20
Alignment explanation
Indices: 22542215--22542254 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22542205 TGATTAAGTA
22542215 AAACCATGACTAAGTTATTC
1 AAACCATGACTAAGTTATTC
22542235 AAACCATGACTAAGTTATTC
1 AAACCATGACTAAGTTATTC
22542255 TTGCATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
AAACCATGACTAAGTTATTC
Found at i:22547423 original size:42 final size:41
Alignment explanation
Indices: 22547367--22547468 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 41
22547357 TGCCGATAGC
* *
22547367 CCAGATATGGTCTTACACGAAATTTCATAACGGTGCCACAT
1 CCAGATATGGTCTTACACGAAATCTCATAACGATGCCACAT
* * * *
22547408 CTTAGATGTGGTCTTACACGAAATCTCATATCGATGCCATAT
1 C-CAGATATGGTCTTACACGAAATCTCATAACGATGCCACAT
22547450 CCAGATATGGTCTTACACG
1 CCAGATATGGTCTTACACG
22547469 TAGACTTAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.33
42 35 0.67
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (41 bp):
CCAGATATGGTCTTACACGAAATCTCATAACGATGCCACAT
Found at i:22548688 original size:21 final size:19
Alignment explanation
Indices: 22548662--22548700 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
22548652 ATGACCCCTA
*
22548662 TTTAGTGAAAAGTTTTCTAAG
1 TTTAGT-AAAA-TTTCCTAAG
22548683 TTTAGTAAAATTTCCTAA
1 TTTAGTAAAATTTCCTAA
22548701 AGATTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (19 bp):
TTTAGTAAAATTTCCTAAG
Found at i:22556258 original size:48 final size:47
Alignment explanation
Indices: 22556196--22556468 Score: 173
Period size: 48 Copynumber: 5.7 Consensus size: 47
22556186 AAAATGGTAA
* *
22556196 AATGTCGATGCCATGTCCAAGACATGGTCTTACATTGATACATATAAC
1 AATGCCGATGCCATGTCCAA-ACATGGTCTTACATTGCTACATATAAC
* * * **
22556244 AATGCTGATGCCATGTTCCAAACAAGGTCTTACACTGGCT-C-TCATATT
1 AATGCCGATGCCATG-TCCAAACATGGTCTTACA-TTGCTACAT-ATAAC
* * * * * **
22556292 GAGGCCGATGCCATGTCCCAGA-ATGGCCTTACACTGGCT-CGCATAAC
1 AATGCCGATGCCATGT-CCAAACATGGTCTTACA-TTGCTACATATAAC
* * *
22556339 AATGCCAATGCCATGTTCGAAACATGGTCTTACATTGGCTCACATATACC
1 AATGCCGATGCCATG-TCCAAACATGGTCTTACATT-GCT-ACATATAAC
** * *
22556389 GGTGCCGATGCCATGTCCCAAACATGGTCTTACA---CTAACACATATC
1 AATGCCGATGCCATGT-CCAAACATGGTCTTACATTGCT-ACATATAAC
** *
22556435 AGGGCCGATGCCATGTCCTAGACATGGTCTTACA
1 AATGCCGATGCCATGTCC-AAACATGGTCTTACA
22556469 CTGGCTCTCT
Statistics
Matches: 177, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
45 2 0.01
46 37 0.21
47 37 0.21
48 59 0.33
49 9 0.05
50 33 0.19
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCAAACATGGTCTTACATTGCTACATATAAC
Found at i:22556368 original size:95 final size:95
Alignment explanation
Indices: 22556201--22556477 Score: 276
Period size: 95 Copynumber: 2.9 Consensus size: 95
22556191 GGTAAAATGT
* * * *
22556201 CGATGCCATGT-CCAAGACATGGTCTTACATTGATACATATAACAATGCTGATGCCATGTTCCAA
1 CGATGCCATGTCCCAA-ACATGGCCTTACACT-A-ACACATAACAATGCCGATGCCATGTTCCAA
* *
22556265 ACAAGGTCTTACACTGGCTCTCATAT-TGAG-GC
63 ACATGGTCTTACACTGGCTCTCATATACG-GTGC
* ** * * *
22556297 CGATGCCATGTCCCAGA-ATGGCCTTACACTGGCTCGCATAACAATGCCAATGCCATGTTCGAAA
1 CGATGCCATGTCCCAAACATGGCCTTACACT--AACACATAACAATGCCGATGCCATGTTCCAAA
* *
22556361 CATGGTCTTACATTGGCTCACATATACCGGTGC
64 CATGGTCTTACACTGGCTCTCATATA-CGGTGC
* * ** *
22556394 CGATGCCATGTCCCAAACATGGTCTTACACTAACACATATCAGGGCCGATGCCATG-TCCTAGAC
1 CGATGCCATGTCCCAAACATGGCCTTACACTAACACATAACAATGCCGATGCCATGTTCC-AAAC
22556458 ATGGTCTTACACTGGCTCTC
65 ATGGTCTTACACTGGCTCTC
22556478 TTATCGCCAT
Statistics
Matches: 147, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
95 60 0.41
96 53 0.36
97 22 0.15
98 12 0.08
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (95 bp):
CGATGCCATGTCCCAAACATGGCCTTACACTAACACATAACAATGCCGATGCCATGTTCCAAACA
TGGTCTTACACTGGCTCTCATATACGGTGC
Found at i:22562858 original size:48 final size:48
Alignment explanation
Indices: 22562784--22563050 Score: 198
Period size: 48 Copynumber: 5.6 Consensus size: 48
22562774 AACATCGGTA
*
22562784 TCGATGCCATGTCCCAGACATCGTCTTACACTGACACATATAACAATG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATG
* * * ** *** *
22562832 TCGATGCCATATTCCCA-ACATGGTCTTGCACTGACTCGCATATTGAGG
1 TCGATGCCAT-GTCCCAGACATGGTCTTACACTGACACATATAACAATG
* * * * * * **
22562880 ACAATGCCATGTCCTAGAAATGGTCTTACACTGGCTCGCATAACAATG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATG
* * * * * **
22562928 TCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCGCATATACCGGTG
1 TCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATATAACAATG
* * *
22562978 TCGATGCCATGTCCCAGACATGGTTTTACACTAACACATAT--CAAGG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATG
* * **
22563024 CCAATTTCATGTCCCAGACATGGTCTT
1 TCGATGCCATGTCCCAGACATGGTCTT
22563051 TTCCGTTAAT
Statistics
Matches: 167, Mismatches: 48, Indels: 10
0.74 0.21 0.04
Matches are distributed among these distances:
46 24 0.14
47 4 0.02
48 96 0.57
49 6 0.04
50 37 0.22
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (48 bp):
TCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATG
Found at i:22563035 original size:96 final size:95
Alignment explanation
Indices: 22562736--22563050 Score: 278
Period size: 96 Copynumber: 3.3 Consensus size: 95
22562726 GTAAAATGCT
* * * * * *
22562736 GATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCAAACATCGGTATCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCGCATATA-CGGTGTCGATGCCATGTCCCAG
* *
22562801 ACATCGTCTTACACTGACACATATAACAATGTC
65 ACATGGTCTTACACTAACACATAT--CAATGTC
* * * * * *
22562834 GATGCCATATTCCC-AACATGGTCTTGCACT-GACTCGCATAT-TGAG-GACAATGCCATGTCCT
1 GATGCCAT-GTCCCAAACATGGTCTTACACTAG-CTCGCATATACG-GTGTCGATGCCATGTCCC
* ** * *
22562895 AGAAATGGTCTTACACTGGCTCGCATAACAATGTC
63 AGACATGGTCTTACACT--AACACATATCAATGTC
*
22562930 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCGCATATACCGGTGTCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCGCATATA-CGGTGTCGATGCCATGTCCCAG
* * *
22562995 ACATGGTTTTACACTAACACATATCAAGGCC
65 ACATGGTCTTACACTAACACATATCAATGTC
* ** *
22563026 AATTTCATGTCCCAGACATGGTCTT
1 GATGCCATGTCCCAAACATGGTCTT
22563051 TTCCGTTAAT
Statistics
Matches: 169, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
95 3 0.02
96 97 0.57
97 4 0.02
98 61 0.36
99 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (95 bp):
GATGCCATGTCCCAAACATGGTCTTACACTAGCTCGCATATACGGTGTCGATGCCATGTCCCAGA
CATGGTCTTACACTAACACATATCAATGTC
Found at i:22567984 original size:30 final size:30
Alignment explanation
Indices: 22567943--22568003 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
22567933 AAAAAATGCA
22567943 TGAATAGTAAATCATCTATCTACGGCATAC
1 TGAATAGTAAATCATCTATCTACGGCATAC
* *
22567973 TGAATATTAAATCATCTATCTACGGCGTAC
1 TGAATAGTAAATCATCTATCTACGGCATAC
22568003 T
1 T
22568004 ATATTTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (30 bp):
TGAATAGTAAATCATCTATCTACGGCATAC
Found at i:22572346 original size:48 final size:43
Alignment explanation
Indices: 22572264--22572422 Score: 156
Period size: 44 Copynumber: 3.5 Consensus size: 43
22572254 ATGTGTGCTG
* * *
22572264 GTGTAAGACATGTCTAGGACATGCATCAGTCTCGAGATATGCAAGCCA
1 GTGTAAGACCTGTCTAGGACATGCATC-GGCTC--GACATG--AGCCA
* *
22572312 GTGTAAGACCTGTCTAGGACATCGCATCGGCTCGACATGTGTCA
1 GTGTAAGACCTGTCTAGGACAT-GCATCGGCTCGACATGAGCCA
* * * *
22572356 GTGTAAGACCTGTCTGGGACATGACATCGGCTTGACATGTGTCA
1 GTGTAAGACCTGTCTAGGACATG-CATCGGCTCGACATGAGCCA
* *
22572400 ATGTAAGACCTGTCTGGGACATG
1 GTGTAAGACCTGTCTAGGACATG
22572423 GTATTGACAC
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
43 1 0.01
44 65 0.64
46 5 0.05
48 25 0.25
49 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (43 bp):
GTGTAAGACCTGTCTAGGACATGCATCGGCTCGACATGAGCCA
Found at i:22572370 original size:44 final size:44
Alignment explanation
Indices: 22572310--22572422 Score: 183
Period size: 44 Copynumber: 2.6 Consensus size: 44
22572300 ATATGCAAGC
*
22572310 CAGTGTAAGACCTGTCTAGGACATCG-CATCGGCTCGACATGTGT
1 CAGTGTAAGACCTGTCTGGGACAT-GACATCGGCTCGACATGTGT
*
22572354 CAGTGTAAGACCTGTCTGGGACATGACATCGGCTTGACATGTGT
1 CAGTGTAAGACCTGTCTGGGACATGACATCGGCTCGACATGTGT
*
22572398 CAATGTAAGACCTGTCTGGGACATG
1 CAGTGTAAGACCTGTCTGGGACATG
22572423 GTATTGACAC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.02
44 64 0.98
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (44 bp):
CAGTGTAAGACCTGTCTGGGACATGACATCGGCTCGACATGTGT
Found at i:22577147 original size:28 final size:28
Alignment explanation
Indices: 22577100--22577164 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
22577090 AAATTAACCC
*
22577100 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
22577128 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
22577156 TAGGGGTAT
1 TAGGGGTAT
22577165 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:22587095 original size:19 final size:19
Alignment explanation
Indices: 22587059--22587097 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
22587049 TTTTCATCAT
* *
22587059 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
22587078 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
22587097 A
1 A
22587098 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:22591921 original size:47 final size:49
Alignment explanation
Indices: 22591695--22592217 Score: 868
Period size: 49 Copynumber: 10.9 Consensus size: 49
22591685 NNNNNNNNNN
*
22591695 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
22591744 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
22591793 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
22591842 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
* * * * * * *
22591891 -T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
22591936 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
22591985 ATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
22592034 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
22592081 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
22592128 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
22592175 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
22592218 CTATCATTTC
Statistics
Matches: 453, Mismatches: 17, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 212 0.47
48 1 0.00
49 239 0.53
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (49 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:22592027 original size:192 final size:192
Alignment explanation
Indices: 22591695--22592217 Score: 906
Period size: 192 Copynumber: 2.7 Consensus size: 192
22591685 NNNNNNNNNN
22591695 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC--ATATATACACTTTCAC
* *
22591760 ATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACGTCGGCC
64 ATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCC
22591825 ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
129 ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * * * * *
22591889 ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
22591954 TCATCACATCGGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
66 TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
*
22592019 TGGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
131 TAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
22592081 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
22592146 TCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCAT
66 TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
22592209 TAGGCCTTA
131 TAGGCCTTA
22592218 CTATCATTTC
Statistics
Matches: 308, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
190 42 0.14
192 226 0.73
194 40 0.13
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (192 bp):
ATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
TAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:22603924 original size:13 final size:13
Alignment explanation
Indices: 22603906--22603935 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22603896 GAACACAGGT
22603906 GTGTGCCATGGGC
1 GTGTGCCATGGGC
*
22603919 GTGTGCCATGGGG
1 GTGTGCCATGGGC
22603932 GTGT
1 GTGT
22603936 CCCTGCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.50, T:0.27
Consensus pattern (13 bp):
GTGTGCCATGGGC
Found at i:22611312 original size:26 final size:26
Alignment explanation
Indices: 22611276--22611332 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
22611266 CATCAAAGTA
*
22611276 CAAATCTGATCTCACTTCGATCTCCT
1 CAAATCCGATCTCACTTCGATCTCCT
22611302 CAAATCCGATCTCACTTCGATCTCCT
1 CAAATCCGATCTCACTTCGATCTCCT
22611328 CAAAT
1 CAAAT
22611333 GGAACGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.35, G:0.07, T:0.32
Consensus pattern (26 bp):
CAAATCCGATCTCACTTCGATCTCCT
Found at i:22634670 original size:40 final size:40
Alignment explanation
Indices: 22634625--22634945 Score: 446
Period size: 40 Copynumber: 8.1 Consensus size: 40
22634615 CGAATACACG
* * * *
22634625 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * ** * *
22634665 ACACCAGCATGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
22634705 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
22634745 TCACTAGCATGAATGCTCTTCGGGACTTAGTCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
22634785 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * *
22634825 TCACTAGCACGAATGCTCTTCGGAACTCAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
22634865 TCACTAGCATGAATGCTCTTTGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
22634905 TCACTAGCACGAATGCTCTTCGGGACTTAGCCTGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
22634944 TC
1 TC
22634946 GTCGAGACCT
Statistics
Matches: 251, Mismatches: 30, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
39 4 0.02
40 247 0.98
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:22637102 original size:43 final size:44
Alignment explanation
Indices: 22637041--22637137 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
22637031 TCCTAATTGG
*
22637041 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
22637084 GAAAATAGTTTCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
22637128 -AAAATA-TTTC
1 GAAAATAGTTTC
22637138 TAGAATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.90
44 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (44 bp):
GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:22638730 original size:57 final size:56
Alignment explanation
Indices: 22638641--22638765 Score: 207
Period size: 57 Copynumber: 2.2 Consensus size: 56
22638631 ACTATTTTTT
*
22638641 TCCCTACAGGTAATTCCATTGTTTCCCATGTACCTGTTTTTTCAAGAGCACGCATC
1 TCCCTACAAGTAATTCCATTGTTTCCCATGTACCTGTTTTTTCAAGAGCACGCATC
*
22638697 TNCCCTACAAGTAATTCCATTGTTTCTCATGTACCTGTTTTTTCAAGAGCACGCATC
1 T-CCCTACAAGTAATTCCATTGTTTCCCATGTACCTGTTTTTTCAAGAGCACGCATC
22638754 TCCTCTA-AAGTA
1 TCC-CTACAAGTA
22638766 GCCTCCTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
56 8 0.12
57 57 0.88
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.36
Consensus pattern (56 bp):
TCCCTACAAGTAATTCCATTGTTTCCCATGTACCTGTTTTTTCAAGAGCACGCATC
Found at i:22651753 original size:43 final size:43
Alignment explanation
Indices: 22651579--22651751 Score: 185
Period size: 43 Copynumber: 4.0 Consensus size: 43
22651569 ACATAGTATT
* *
22651579 TCGATATGTG-TTATCGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATTTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
*
22651622 TCGACT-TATGATTTACGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGA-TATTTGA-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * * *
22651666 TCG-TATTTGATTTCGTATAAGACC-CTATCTGGGACAG-TGACA
1 TCGATATTTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
22651708 TTGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
22651751 T
1 T
22651752 TGTACGAGCT
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 28 0.26
43 43 0.40
44 33 0.31
45 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TCGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:22652595 original size:57 final size:57
Alignment explanation
Indices: 22652533--22652647 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
22652523 TTAAGCTTGA
22652533 AATTGGTTGATAATGTTATGCCTTATTTGGTATATGTATTGGTTGTAAAATGGTTGT
1 AATTGGTTGATAATGTTATGCCTTATTTGGTATATGTATTGGTTGTAAAATGGTTGT
* *
22652590 AATTGGTTGATAATGTTATGGCTTATTTGGTGTATGTATTGGTTGTAAAATGGTTGT
1 AATTGGTTGATAATGTTATGCCTTATTTGGTATATGTATTGGTTGTAAAATGGTTGT
22652647 A
1 A
22652648 CATTTGGTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (57 bp):
AATTGGTTGATAATGTTATGCCTTATTTGGTATATGTATTGGTTGTAAAATGGTTGT
Found at i:22661736 original size:17 final size:18
Alignment explanation
Indices: 22661714--22661748 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
22661704 TACTTAACAT
*
22661714 TTTTTTAATATAT-TTAA
1 TTTTTTAAAATATATTAA
22661731 TTTTTTAAAATATATTAA
1 TTTTTTAAAATATATTAA
22661749 ATATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTAAAATATATTAA
Found at i:22661742 original size:19 final size:19
Alignment explanation
Indices: 22661720--22661760 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
22661710 ACATTTTTTT
* * *
22661720 AATATATTTAATTTTTTAA
1 AATATATTAAATATATTAA
22661739 AATATATTAAATATATTAA
1 AATATATTAAATATATTAA
22661758 AAT
1 AAT
22661761 TTTAAAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATATTAAATATATTAA
Found at i:22661752 original size:71 final size:71
Alignment explanation
Indices: 22661666--22661955 Score: 245
Period size: 71 Copynumber: 4.1 Consensus size: 71
22661656 ATATTTTTAA
*
22661666 AAAATATATTGAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTTAATATATTTAA
1 AAAATAT-TTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTTAATATATTTAA
22661731 -TTTTTT
65 GTTTTTT
* *
22661737 AAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTATTATATTTAATT
1 AAAATAT-TTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTT-TTA-A--T-ATA
*
22661802 TTTAAATTTTTTT
60 TTT-AAGTTTTTT
* ** * * * ***
22661815 AAAA-ATTTAAATATATTAAAA----AAATCTTTTTTAT-CTTTACCTGTTAAAAATATATATTA
1 AAAATATTTAAATATATTAAAATTTTAAA-ATTAGTTATACTTAACATTTTTTTAATATAT-TTA
* *
22661874 AGTATATT
64 AGTTTTTT
* * * * *
22661882 AAAAT-TTCAAATATATTAAACTTTTAAAATTAATTATACTTAACATTTTCTTAATATATTTAAA
1 AAAATATTTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTTAATATATTTAAG
*
22661946 TTTTTA
66 TTTTTT
22661952 AAAA
1 AAAA
22661956 ACTTTTAAAA
Statistics
Matches: 173, Mismatches: 31, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
67 27 0.16
68 3 0.02
70 18 0.10
71 69 0.40
72 14 0.08
73 7 0.04
75 1 0.01
76 20 0.12
77 4 0.02
78 10 0.06
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (71 bp):
AAAATATTTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTTAATATATTTAAG
TTTTTT
Found at i:22661944 original size:20 final size:20
Alignment explanation
Indices: 22661911--22661949 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22661901 ACTTTTAAAA
22661911 TTAATTATACTTAACATTTTC
1 TTAATTATACTTAA-ATTTTC
*
22661932 TTAA-TATATTTAAATTTT
1 TTAATTATACTTAAATTTT
22661950 TAAAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAATTTTC
Found at i:22662726 original size:20 final size:20
Alignment explanation
Indices: 22662698--22662742 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
22662688 TGACCAGTTA
22662698 TAATATATATTTTTAATTTT
1 TAATATATATTTTTAATTTT
* *
22662718 TAATTTATATTTTTACTTTT
1 TAATATATATTTTTAATTTT
22662738 TAATA
1 TAATA
22662743 AATGTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TAATATATATTTTTAATTTT
Found at i:22662750 original size:20 final size:20
Alignment explanation
Indices: 22662698--22662751 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
22662688 TGACCAGTTA
*
22662698 TAATATATATTTTTAATTTT
1 TAATAAATATTTTTAATTTT
** *
22662718 TAATTTATATTTTTACTTTT
1 TAATAAATATTTTTAATTTT
*
22662738 TAATAAATGTTTTT
1 TAATAAATATTTTT
22662752 TAAATAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TAATAAATATTTTTAATTTT
Found at i:22662915 original size:14 final size:15
Alignment explanation
Indices: 22662896--22662928 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
22662886 ATTTTTAAAA
22662896 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
22662910 ATAATTTAAAATATT
1 ATAATTTAAAATATT
22662925 ATAA
1 ATAA
22662929 ATCAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:22662941 original size:21 final size:20
Alignment explanation
Indices: 22662912--22662950 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22662902 TAAAAATTAT
* *
22662912 AATTTAAAATATTATAAATCA
1 AATTAAAAAAATTA-AAATCA
22662933 AATTAAAAAAATTAAAAT
1 AATTAAAAAAATTAAAAT
22662951 TTCCAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTAAAAAAATTAAAATCA
Found at i:22663073 original size:7 final size:6
Alignment explanation
Indices: 22663063--22663105 Score: 50
Period size: 7 Copynumber: 6.5 Consensus size: 6
22663053 CAAAACTTAA
22663063 AAAAAG TAAAAAG AAAAAAG AAAGAAG AAAAAG AAAGAAG AAA
1 AAAAAG -AAAAAG -AAAAAG AAA-AAG AAAAAG AAA-AAG AAA
22663106 GTAATAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 9 0.27
7 24 0.73
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:22663081 original size:14 final size:14
Alignment explanation
Indices: 22663062--22663105 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
22663052 ACAAAACTTA
22663062 AAAAAAGTAAA-AAG
1 AAAAAAG-AAAGAAG
22663076 AAAAAAGAAAGAAG
1 AAAAAAGAAAGAAG
22663090 -AAAAAGAAAGAAG
1 AAAAAAGAAAGAAG
22663103 AAA
1 AAA
22663106 GTAATAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAGAAG
Found at i:22663106 original size:7 final size:7
Alignment explanation
Indices: 22663073--22663106 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
22663063 AAAAAGTAAA
*
22663073 AAGAAAA
1 AAGAAAG
22663080 AAGAAAG
1 AAGAAAG
22663087 AAGAAA-
1 AAGAAAG
22663093 AAGAAAG
1 AAGAAAG
22663100 AAGAAAG
1 AAGAAAG
22663107 TAATAGGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:22663292 original size:29 final size:28
Alignment explanation
Indices: 22663244--22663298 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
22663234 CTAGAGATTT
* *
22663244 TAGGTCATTTACGTATTTAATTGAAAAAA
1 TAGGTAATTTACGTAATTAATT-AAAAAA
*
22663273 TAGGTAATTTATGTAATTAATTAAAA
1 TAGGTAATTTACGTAATTAATTAAAA
22663299 TTTTTAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (28 bp):
TAGGTAATTTACGTAATTAATTAAAAAA
Found at i:22665606 original size:52 final size:52
Alignment explanation
Indices: 22665528--22665632 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
22665518 TAGCACGGAC
22665528 AGTTAATATTTGTTTTCCACTTATTTTTATATGTTAAAATGATATTAAATAA
1 AGTTAATATTTGTTTTCCACTTATTTTTATATGTTAAAATGATATTAAATAA
22665580 AGTTAATATTTGTTTTCCACTTATTTTTATATGTTAAAATGATATTAAATAA
1 AGTTAATATTTGTTTTCCACTTATTTTTATATGTTAAAATGATATTAAATAA
22665632 A
1 A
22665633 TGATATGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (52 bp):
AGTTAATATTTGTTTTCCACTTATTTTTATATGTTAAAATGATATTAAATAA
Found at i:22670879 original size:43 final size:43
Alignment explanation
Indices: 22670809--22670956 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 43
22670799 CGGAAAGCTC
* * *
22670809 ATACAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAACTGTCCCAGACATGGTCTTACATGTAACCAA
*
22670851 ATATCGATGCC-ACTGTCCCAGACATGGTCTTACATGAAACCAA
1 ATA-CGATGCCAACTGTCCCAGACATGGTCTTACATGTAACCAA
* * *
22670894 ATACGATGCCGA-TGTCCCAGACATGATCTTACACGTAAATCTCAA
1 ATACGATGCCAACTGTCCCAGACATGGTCTTACATGT-AA-C-CAA
*
22670939 AT-CAATGCCAAC-GTCCCA
1 ATACGATGCCAACTGTCCCA
22670957 AATGTTGTCT
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
42 33 0.37
43 38 0.42
44 14 0.16
45 5 0.06
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
ATACGATGCCAACTGTCCCAGACATGGTCTTACATGTAACCAA
Found at i:22695801 original size:23 final size:23
Alignment explanation
Indices: 22695775--22695831 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
22695765 CATTTACCAT
* *
22695775 TATTACCAGCTTTGTTGCG-TTAC
1 TATTAGCAGCTTTGCTG-GATTAC
22695798 TATTAGCAGCTTTGCTGGATTAC
1 TATTAGCAGCTTTGCTGGATTAC
22695821 TATTAGCAGCT
1 TATTAGCAGCT
22695832 ACGCTGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (23 bp):
TATTAGCAGCTTTGCTGGATTAC
Found at i:22695837 original size:23 final size:23
Alignment explanation
Indices: 22695794--22695837 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
22695784 CTTTGTTGCG
**
22695794 TTACTATTAGCAGCTTTGCTGGA
1 TTACTATTAGCAGCTACGCTGGA
22695817 TTACTATTAGCAGCTACGCTG
1 TTACTATTAGCAGCTACGCTG
22695838 CGATATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
TTACTATTAGCAGCTACGCTGGA
Found at i:22705656 original size:8 final size:8
Alignment explanation
Indices: 22705643--22705677 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
22705633 TAACGCCCCA
22705643 AAAATCCC
1 AAAATCCC
*
22705651 AAAATCCT
1 AAAATCCC
*
22705659 AAAATCCT
1 AAAATCCC
22705667 AAAATCCC
1 AAAATCCC
22705675 AAA
1 AAA
22705678 CTTTCTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATCCC
Found at i:22706769 original size:29 final size:29
Alignment explanation
Indices: 22706727--22706814 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
22706717 GAACTACCCT
22706727 CATATAAATGTGATTTGGGCCTAATGGGC
1 CATATAAATGTGATTTGGGCCTAATGGGC
*
22706756 CATATACAA-GTGATTTGGGCCTAATGTGC
1 CATATA-AATGTGATTTGGGCCTAATGGGC
* * * *
22706785 CATATGAATATGA-TTAGGCTTAATGGGC
1 CATATAAATGTGATTTGGGCCTAATGGGC
22706813 CA
1 CA
22706815 GATACAGGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 16 0.31
29 33 0.65
30 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (29 bp):
CATATAAATGTGATTTGGGCCTAATGGGC
Found at i:22714899 original size:28 final size:28
Alignment explanation
Indices: 22714867--22714928 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
22714857 TACTAGAATG
*
22714867 CCCCTATGTATGCAAAATTACCAGTATA
1 CCCCTATGTATGCAAAATGACCAGTATA
* **
22714895 CCCCTATGTGTGCAAAATGACCTTTATA
1 CCCCTATGTATGCAAAATGACCAGTATA
22714923 CCCCTA
1 CCCCTA
22714929 GGGTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (28 bp):
CCCCTATGTATGCAAAATGACCAGTATA
Found at i:22715075 original size:28 final size:29
Alignment explanation
Indices: 22715034--22715096 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
22715024 AGGAAGCGTC
*
22715034 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
22715062 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
22715091 CTGGTG
1 CTGGTG
22715097 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:22715107 original size:29 final size:28
Alignment explanation
Indices: 22715044--22715107 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
22715034 CTGGTGGCTA
* *
22715044 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
22715072 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
22715101 TGTCACA
1 TGCCACA
22715108 TTTTCTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:22715589 original size:18 final size:18
Alignment explanation
Indices: 22715550--22715590 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
22715540 TAATAAGGCC
* *
22715550 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
22715568 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
22715586 TTTTA
1 TTTTA
22715591 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:22721613 original size:12 final size:13
Alignment explanation
Indices: 22721585--22721617 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22721575 TTATTTCTTT
22721585 TTCTCCATCTACC
1 TTCTCCATCTACC
*
22721598 TTCTCC-TCTTCC
1 TTCTCCATCTACC
22721610 TTCTCCAT
1 TTCTCCAT
22721618 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:22722718 original size:28 final size:28
Alignment explanation
Indices: 22722686--22722750 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
22722676 ATTTACTAGA
*
22722686 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
22722714 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
22722742 ATACCCCTA
1 ATACCCCTA
22722751 GGGTTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:22722897 original size:28 final size:27
Alignment explanation
Indices: 22722856--22722945 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
22722846 AAGAAGCGTC
22722856 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* ** *
22722884 CTGGTGGCCCTGCCACGTATATTTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
22722911 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
22722940 CTGGTG
1 CTGGTG
22722946 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:22722956 original size:29 final size:28
Alignment explanation
Indices: 22722866--22722956 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
22722856 CTGGTGGCTA
* * *
22722866 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** * *
22722894 TGCCAC-GTATATTTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
22722921 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
22722950 TGTCACA
1 TGCCACA
22722957 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 22 0.44
28 13 0.26
29 15 0.30
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:22723438 original size:18 final size:18
Alignment explanation
Indices: 22723399--22723439 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
22723389 TAATAAGGCC
* *
22723399 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
22723417 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
22723435 TTTTA
1 TTTTA
22723440 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:22737113 original size:42 final size:43
Alignment explanation
Indices: 22737005--22737161 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
22736995 ATTTCGTACA
* *
22737005 ATGCCAA-CGTCCCAAATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATC-TCCCAAACGTGGTCTTACATGAAATCAAATATCG
* * * * **
22737048 ATGCCACTGTCCTAGACAAGGTCTTACATGAAATCAAATA-CG
1 ATGCCAATCTCCCAAACGTGGTCTTACATGAAATCAAATATCG
* *
22737090 ATGCTAATCTCCCAAACGTGGTCTTACACAT-AAATCAAA-AGTCA
1 ATGCCAATCTCCCAAACGTGGTCTT--ACATGAAATCAAATA-TCG
*
22737134 ATGCCAA-CGTCCCAGACGTGGTCTTACA
1 ATGCCAATC-TCCCAAACGTGGTCTTACA
22737162 CGATAACACA
Statistics
Matches: 90, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
42 24 0.27
43 40 0.44
44 26 0.29
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCCAATCTCCCAAACGTGGTCTTACATGAAATCAAATATCG
Found at i:22737576 original size:29 final size:31
Alignment explanation
Indices: 22737535--22737598 Score: 114
Period size: 29 Copynumber: 2.1 Consensus size: 31
22737525 TACAAAATAA
22737535 CCCTCACATTTTCATATTTTGACAATTTAG-
1 CCCTCACATTTTCATATTTTGACAATTTAGT
22737565 CCCTCACA-TTTCATATTTTGACAATTTAGT
1 CCCTCACATTTTCATATTTTGACAATTTAGT
22737595 CCCT
1 CCCT
22737599 AATCACAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (31 bp):
CCCTCACATTTTCATATTTTGACAATTTAGT
Found at i:22747566 original size:42 final size:42
Alignment explanation
Indices: 22747458--22747617 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 42
22747448 ATCTCGTACA
** * * *
22747458 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCA
1 ATGCCAATGTCCCAGATGTGGTCTTACACGAAATCAAATA-CG
* * *
22747501 ATGCCACTGTCCTAGACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGA-TGTGGTCTTACACGAAATCAAATACG
*
22747543 ATGCCAATGTCTCAGATGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGATGTGGTCTTACACG-AAATCA-AA-TACG
* *
22747587 ATGCCAACGTCCCAAATGTGGTCTTACACGA
1 ATGCCAATGTCCCAGATGTGGTCTTACACGA
22747618 TAACACATAT
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 25 0.26
43 40 0.41
44 31 0.32
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGATGTGGTCTTACACGAAATCAAATACG
Found at i:22747606 original size:44 final size:42
Alignment explanation
Indices: 22747520--22747617 Score: 135
Period size: 44 Copynumber: 2.3 Consensus size: 42
22747510 TCCTAGACAG
* * *
22747520 GGTCTTACACGAAATCAAATACGATGCCAATGTCTCAGATGT
1 GGTCTTACACGAAATCAAATACGATGCCAACGTCCCAAATGT
22747562 GGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCAAATGT
1 GGTCTTACACG-AAATCA-AA-TACGATGCCAACGTCCCAAATGT
22747606 GGTCTTACACGA
1 GGTCTTACACGA
22747618 TAACACATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 11 0.22
43 7 0.14
44 31 0.62
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAACGTCCCAAATGT
Found at i:22751671 original size:49 final size:48
Alignment explanation
Indices: 22751458--22751731 Score: 163
Period size: 49 Copynumber: 5.8 Consensus size: 48
22751448 TTGGGACGAG
* * * *
22751458 AGCCAGCGTAAGACATGTCTAGGACAT-GCATCAGCCTCGAGATATGGA
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATAT-GA
* * ** * * *
22751506 AGCCAGTGTAAGACCTGTTTGGAACAACGCATC-GGCTTG--ACATG-
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGA
* * * * *
22751550 TGTCAGTATAAGACCTGTCTAGGACATGGCATTCA-CAC-CGATAGATGA
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCA-TCAGC-CTCGATATATGA
* * *
22751598 GAGCCAGTGTAAGAACTATTTGGGACATGGCATCAGCCTCGATATATGGA
1 -AGCCAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATAT-GA
* * * * * *
22751648 AGTCAGTGTAAGACCTGTCTGGGATATAGG-ATC-GACTTAGATGTGTG-
1 AGCCAGTGTAAGACCTGTCTGGGACAT-GGCATCAG-CCTCGATATATGA
* *
22751695 AGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGC
1 AGCCAGTGTAAGACC-TGTCTGGGACATGGCATCAGC
22751732 ATCGTACCCT
Statistics
Matches: 169, Mismatches: 41, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
44 23 0.14
45 4 0.02
46 4 0.02
47 20 0.12
48 44 0.26
49 70 0.41
50 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
AGCCAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGA
Found at i:22758228 original size:92 final size:92
Alignment explanation
Indices: 22758037--22758285 Score: 240
Period size: 92 Copynumber: 2.7 Consensus size: 92
22758027 TATGTGTGCT
* * * * *
22758037 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCCAGTGTAAGACATATCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAATATGAGAGCCAGTGTAAGACCTATCTAG
* *
22758101 GACATGCATCGATATTAAGACGAGAGCC
66 AACACGCATCGATATT-AGACGAGAGCC
* *
22758129 AGCGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATATGCA-AGCCAGTGTAAGACCTATCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-ATATG-AGAGCCAGTGTAAGACCTATCT
* * *
22758193 AGAACAACGCATCGA-CTT-GAC-ATATGTC
64 AGAAC-ACGCATCGATATTAGACGAGA-GCC
* * * *
22758221 AGTGTAAGACCTGTCTGGGACATGGCATCGACACT-GATAGATGAGAGCCAGTGTAAGAACTATC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTCGA-ATATGAGAGCCAGTGTAAGACCTATC
22758285 T
63 T
22758286 GGGACATGGC
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
91 2 0.02
92 56 0.43
93 33 0.25
94 30 0.23
95 9 0.07
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAATATGAGAGCCAGTGTAAGACCTATCTAG
AACACGCATCGATATTAGACGAGAGCC
Found at i:22758276 original size:49 final size:47
Alignment explanation
Indices: 22758037--22758376 Score: 200
Period size: 49 Copynumber: 7.2 Consensus size: 47
22758027 TATGTGTGCT
* * ** *
22758037 AGTGTAAGACATGTCTGGGACATGCATC-AGCCACAT-TATGAGAGCC
1 AGTGTAAGACCTATCTGGGACATGCATCGA-CCTGATAGATGAGAGCC
* ** * *
22758083 AGTGTAAGACATATCTGGGACATGCATCGATATTA-AGACGAGAGCC
1 AGTGTAAGACCTATCTGGGACATGCATCGACCTGATAGATGAGAGCC
* * * * * * *
22758129 AGCGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATATGCA-AGCC
1 AGTGTAAGACCTATCTGGGACATGCATCGACCT-GATAGATG-AGAGCC
* * * * * * *
22758177 AGTGTAAGACCTATCTAGAACAACGCATCGACTTG--ACAT-A-TGTC
1 AGTGTAAGACCTATCTGGGAC-ATGCATCGACCTGATAGATGAGAGCC
*
22758221 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAGATGAGAGCC
1 AGTGTAAGACCTATCTGGGACAT-GCATCGAC-CTGATAGATGAGAGCC
* * * *
22758270 AGTGTAAGAACTATCTGGGACATGGCAT-TAGCCTCGATATAT-AGAAGTC
1 AGTGTAAGACCTATCTGGGACAT-GCATCGA-CCT-GATAGATGAG-AGCC
* * *
22758319 AGTGTAAGACCTATCTGGGACATAGCATTGACTTAGAT-G-TGTGAGCC
1 AGTGTAAGACCTATCTGGGACAT-GCATCGACCT-GATAGATGAGAGCC
22758366 AGTGTAAGACC
1 AGTGTAAGACC
22758377 ATGTTTGGAA
Statistics
Matches: 228, Mismatches: 49, Indels: 33
0.74 0.16 0.11
Matches are distributed among these distances:
43 1 0.00
44 29 0.13
45 2 0.01
46 66 0.29
47 20 0.09
48 30 0.13
49 79 0.35
50 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCTATCTGGGACATGCATCGACCTGATAGATGAGAGCC
Found at i:22758352 original size:142 final size:138
Alignment explanation
Indices: 22758082--22758334 Score: 330
Period size: 142 Copynumber: 1.8 Consensus size: 138
22758072 TTATGAGAGC
* * * *
22758082 CAGTGTAAGACATATCTGGGACATGCATCGATATTAAGACGAGAGCCAGCGTAAGACATGTTTGG
1 CAGTGTAAGACATATCTGGGACATGCATCGACATGAAGACGAGAGCCAGCGTAAGACATATCTGG
*
22758147 GACATGCATCGGCCTCGAGATATGCAAGCCAGTGTAAGACCTATCTAGAACAACGCATCGACTTG
66 GACATGCATCAGCCTCGAGATATGCAAGCCAGTGTAAGACCTATCTAGAACAACGCATCGACTTG
22758212 ACATATGT
131 ACATATGT
* * * *
22758220 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAGATGAGAGCCAGTGTAAGA-ACTAT
1 CAGTGTAAGACATATCTGGGACAT-GCATCGACA-TGA-AGACGAGAGCCAGCGTAAGACA-TAT
* * *
22758284 CTGGGACATGGCATTAGCCTCGATATATAG-AAGTCAGTGTAAGACCTATCT
62 CTGGGACAT-GCATCAGCCTCGAGATAT-GCAAGCCAGTGTAAGACCTATCT
22758335 GGGACATAGC
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
138 22 0.23
139 8 0.08
140 3 0.03
141 28 0.29
142 35 0.36
143 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (138 bp):
CAGTGTAAGACATATCTGGGACATGCATCGACATGAAGACGAGAGCCAGCGTAAGACATATCTGG
GACATGCATCAGCCTCGAGATATGCAAGCCAGTGTAAGACCTATCTAGAACAACGCATCGACTTG
ACATATGT
Found at i:22760359 original size:22 final size:22
Alignment explanation
Indices: 22760324--22760380 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
22760314 GTATCGAAGG
* *
22760324 CACACAGGCATGTCCCTGTGTC
1 CACACAGGCGTGTCCCTGTATC
*
22760346 CACACGGGCGTGTCCCTGTATC
1 CACACAGGCGTGTCCCTGTATC
22760368 CACACAGGCGTGT
1 CACACAGGCGTGT
22760381 GGCCTTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (22 bp):
CACACAGGCGTGTCCCTGTATC
Found at i:22761129 original size:25 final size:25
Alignment explanation
Indices: 22761100--22761147 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
22761090 GGAGGTAAGT
22761100 TCGACTTTACAGACACATTTGGTAA
1 TCGACTTTACAGACACATTTGGTAA
*
22761125 TCGACTTTACGGACACATTTGGT
1 TCGACTTTACAGACACATTTGGT
22761148 GATGTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (25 bp):
TCGACTTTACAGACACATTTGGTAA
Found at i:22761887 original size:4 final size:4
Alignment explanation
Indices: 22761878--22761962 Score: 71
Period size: 4 Copynumber: 20.8 Consensus size: 4
22761868 GAATAAGTTA
* *** ** *
22761878 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT CCAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
22761928 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
22761963 TAGAATAGGG
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
4 59 0.94
5 3 0.05
6 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Done.