Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 69 of 320
Found at i:21157671 original size:27 final size:27
Alignment explanation
Indices: 21157641--21157869 Score: 173
Period size: 27 Copynumber: 8.7 Consensus size: 27
21157631 CTACCCTACA
**
21157641 AGGGTATTTCAATAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTATAAATCG
* * **
21157668 AGGGTATTTCAGTAATTTTA-CAATTA
1 AGGGTATTTCGGTAATTTTATAAATCG
* **
21157694 ACGGTATTTCGGTAATTTTGCAAATCG
1 AGGGTATTTCGGTAATTTTATAAATCG
* * *
21157721 AGGATATTTGGGCAATTTTATAAA-CG
1 AGGGTATTTCGGTAATTTTATAAATCG
* * * * *
21157747 GGGGTACTTGGGTAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTATAAATCG
** * *
21157774 AGGGTATTTTAGTCATTTTA-CAATCG
1 AGGGTATTTCGGTAATTTTATAAATCG
*
21157800 ACGGTATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTATAAATCG
* * *
21157827 GGGGTACTTT-GGTAATTTTACAACT-G
1 AGGGTA-TTTCGGTAATTTTATAAATCG
*
21157853 -GGGTATTTCAGTAATTT
1 AGGGTATTTCGGTAATTT
21157870 GGTAGACTAA
Statistics
Matches: 158, Mismatches: 39, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
24 3 0.02
25 12 0.08
26 61 0.39
27 79 0.50
28 3 0.02
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTATAAATCG
Found at i:21157719 original size:53 final size:53
Alignment explanation
Indices: 21157614--21157849 Score: 204
Period size: 53 Copynumber: 4.4 Consensus size: 53
21157604 CTACCCTACA
* ** * ** *
21157614 AGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAATAATTTTATAAATCG
1 AGGGTATTTCAGTAATTTTACAAT-CAACGGTATTTCGGTAATTTTACAAATCG
* *
21157668 AGGGTATTTCAGTAATTTTACAATTAACGGTATTTCGGTAATTTTGCAAATCG
1 AGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGGTAATTTTACAAATCG
* ** * * * *** * * *
21157721 AGGATATTTGGGCAATTTTATAAACGGGGGTACTTGGGTAATTTTACAAGTCG
1 AGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGGTAATTTTACAAATCG
* * * *
21157774 AGGGTATTTTAGTCATTTTACAATCGACGGTATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGGTAATTTTACAAATCG
* *
21157827 GGGGTACTTT-GGTAATTTTACAA
1 AGGGTA-TTTCAGTAATTTTACAA
21157850 CTGGGGTATT
Statistics
Matches: 142, Mismatches: 39, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 118 0.83
54 24 0.17
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (53 bp):
AGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGGTAATTTTACAAATCG
Found at i:21159812 original size:18 final size:17
Alignment explanation
Indices: 21159784--21159817 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21159774 GGCTTTAACC
21159784 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
21159801 CATTATCAGAATCAGAA
1 CATTA-CAGAATAAGAA
21159818 TCAATCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:21159814 original size:6 final size:6
Alignment explanation
Indices: 21159805--21159894 Score: 59
Period size: 6 Copynumber: 15.8 Consensus size: 6
21159795 AAGAAACATT
* * *
21159805 ATCAGA ATCAGA ATC--A ATCAGA ATTAGA ATTA-A GTCACAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
21159852 AT-AGA ATCAGT ATCAG- -TAAGA ATCA-A ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
21159895 GTAACAGAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 7 0.10
5 12 0.18
6 45 0.67
7 1 0.01
8 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (6 bp):
ATCAGA
Found at i:21159826 original size:16 final size:16
Alignment explanation
Indices: 21159805--21159887 Score: 62
Period size: 16 Copynumber: 5.0 Consensus size: 16
21159795 AAGAAACATT
21159805 ATCAGAATCAGAATCA
1 ATCAGAATCAGAATCA
* *
21159821 ATCAGAATTAGAATTA
1 ATCAGAATCAGAATCA
*
21159837 AGTCACAGAATCAGAATAGA
1 A-T--CAGAATCAGAAT-CA
* *
21159857 ATCAGTATCAGTAA-GA
1 ATCAGAATCAG-AATCA
21159873 ATCA-AATCAGAATCA
1 ATCAGAATCAGAATCA
21159888 GTATCAGGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.04
15 6 0.11
16 21 0.39
17 9 0.17
18 2 0.04
19 12 0.22
20 2 0.04
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (16 bp):
ATCAGAATCAGAATCA
Found at i:21159884 original size:27 final size:29
Alignment explanation
Indices: 21159841--21159914 Score: 100
Period size: 27 Copynumber: 2.6 Consensus size: 29
21159831 GAATTAAGTC
21159841 ACAGAATCAGAATAGAATCAGTATCA-GT-
1 ACAGAATCA-AATAGAATCAGTATCAGGTA
21159869 A-AGAATCAAATCAGAATCAGTATCAGGTA
1 ACAGAATCAAAT-AGAATCAGTATCAGGTA
21159898 ACAGAATCAAAATAGAA
1 ACAGAATC-AAATAGAA
21159915 AAAAAAAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.07
27 20 0.49
28 3 0.07
29 1 0.02
30 10 0.24
31 4 0.10
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (29 bp):
ACAGAATCAAATAGAATCAGTATCAGGTA
Found at i:21174708 original size:40 final size:40
Alignment explanation
Indices: 21174598--21174714 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 40
21174588 CAGTTATTTG
* * *
21174598 TGGCACTTAGTGTGCGATAC-AATATAGCTTCGACTATATA
1 TGGCACTTAGTGTGCGAT-CTAACATAGCTTTGGCTATATA
* * * *
21174638 TGACATTTAGTGTGCGAT-TCGACATTGCTTTGGCTATATA
1 TGGCACTTAGTGTGCGATCT-AACATAGCTTTGGCTATATA
* *
21174678 TGGCACTTAGTGTGCGATCTAAGATAGCTTTAGCTAT
1 TGGCACTTAGTGTGCGATCTAACATAGCTTTGGCTAT
21174715 GTATAGAACT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 60 0.98
41 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATCTAACATAGCTTTGGCTATATA
Found at i:21174809 original size:16 final size:16
Alignment explanation
Indices: 21174787--21174841 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
21174777 GTTTGGTTCA
*
21174787 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
* *
21174803 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
21174819 CTGTAATGGAATA-ATG
1 CTGTAATGGAATAGA-G
21174835 CTGTAAT
1 CTGTAAT
21174842 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:21175111 original size:17 final size:17
Alignment explanation
Indices: 21175089--21175121 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21175079 AATTATTATT
21175089 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
21175106 AAATATAATTTAATAA
1 AAATATAATTTAATAA
21175122 CATTCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:21181389 original size:48 final size:48
Alignment explanation
Indices: 21181330--21181425 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
21181320 ATGTCAGTGT
21181330 ATGCCTTGCACACTTTCATTTAATAGTAACATTGACATTCATACATGC
1 ATGCCTTGCACACTTTCATTTAATAGTAACATTGACATTCATACATGC
21181378 ATGCCTTGCACACTTTCATTTAATAGTAACATTGACATTCATACATGC
1 ATGCCTTGCACACTTTCATTTAATAGTAACATTGACATTCATACATGC
21181426 TTTTAGTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (48 bp):
ATGCCTTGCACACTTTCATTTAATAGTAACATTGACATTCATACATGC
Found at i:21181419 original size:23 final size:23
Alignment explanation
Indices: 21181344--21181419 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
21181334 CTTGCACACT
21181344 TTCATTTAATAGTAACATTGACA
1 TTCATTTAATAGTAACATTGACA
* * *
21181367 TTCA--TACAT-GCATGCCTTGCACA
1 TTCATTTA-ATAGTA-ACATTG-ACA
21181390 CTTTCATTTAATAGTAACATTGACA
1 --TTCATTTAATAGTAACATTGACA
21181415 TTCAT
1 TTCAT
21181420 ACATGCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 12 0.31
25 7 0.18
26 6 0.15
27 4 0.10
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (23 bp):
TTCATTTAATAGTAACATTGACA
Found at i:21185174 original size:21 final size:20
Alignment explanation
Indices: 21185146--21185184 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
21185136 ATTGAAACAG
21185146 GGGCACACACCCGTGTGGAA
1 GGGCACACACCCGTGTGGAA
**
21185166 GGGCTACACGTCCGTGTGG
1 GGGC-ACACACCCGTGTGG
21185185 CCTTCTTGAC
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:0.18, C:0.28, G:0.38, T:0.15
Consensus pattern (20 bp):
GGGCACACACCCGTGTGGAA
Found at i:21186532 original size:93 final size:93
Alignment explanation
Indices: 21186418--21186586 Score: 236
Period size: 93 Copynumber: 1.8 Consensus size: 93
21186408 CATCTAAGTA
* *
21186418 GATGCCATGTCCCAGATAGGTCTTACACTAGCTCTCGC-T-TATCTG-TGTCGATGCCATGTCCC
1 GATGCCATGTCCCAGATAGGTCTTACACTAGCT-T-GCATATAT-TGAGGCCGATGCCATGTCCC
* *
21186480 AGATAGTTCTTACATTGACACACCTCAAGCC
63 AGACAGGTCTTACATTGACACACCTCAAGCC
* *
21186511 GATGCCGTGTCTCAGATAGGTCTTACACTAGCTTGCATATATTGAGGCCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGATAGGTCTTACACTAGCTTGCATATATTGAGGCCGATGCCATGTCCCAGA
21186576 CAGGTCTTACA
66 CAGGTCTTACA
21186587 CTAGCACGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
91 2 0.03
92 4 0.06
93 61 0.91
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGATAGGTCTTACACTAGCTTGCATATATTGAGGCCGATGCCATGTCCCAGA
CAGGTCTTACATTGACACACCTCAAGCC
Found at i:21186758 original size:14 final size:14
Alignment explanation
Indices: 21186741--21186770 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21186731 TAAATACAAA
21186741 TAAATTACATTATT
1 TAAATTACATTATT
21186755 TAAATTACATTATT
1 TAAATTACATTATT
21186769 TA
1 TA
21186771 CGTACAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTACATTATT
Found at i:21200536 original size:24 final size:24
Alignment explanation
Indices: 21200491--21200536 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
21200481 TTTCTTATGT
*
21200491 GGAGAAATAAGGAAGATGAGAGAA
1 GGAGAAATAAGGAAAATGAGAGAA
21200515 GGAGAAATAAGGAGAAAT-AGAG
1 GGAGAAATAAGGA-AAATGAGAG
21200537 TGAAATAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (24 bp):
GGAGAAATAAGGAAAATGAGAGAA
Found at i:21202427 original size:46 final size:46
Alignment explanation
Indices: 21202375--21202545 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
21202365 TCATCTCATA
21202375 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCTTGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCTTGAG
* ** *
21202421 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TATCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTAT-GTCTTGAG
* * ** *
21202467 GCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCA--TAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-T-ATGTCTTGAG
*
21202515 GCCGATGCATGTCCCAGATATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
21202546 AGCTCACAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
45 3 0.03
46 54 0.52
47 25 0.24
48 19 0.18
50 1 0.01
51 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCTTGAG
Found at i:21202520 original size:94 final size:91
Alignment explanation
Indices: 21202378--21202549 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 91
21202368 TCTCATAGCC
**
21202378 GATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCTTGAGGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTA-GTAATGAGGCCGATGCATGTCCCAGACATG
21202443 TCTTACACTAGCTATCGTCTCAATGCT
65 TCTTACACTAGCTATCGTCTCAATGCT
* * *
21202470 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCA-TAATGTGGCCGATGCATGTCCCAGAT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-T-AGTAATGAGGCCGATGCATGTCCCAGAC
21202534 ATGTCTTACACTAGCT
62 ATGTCTTACACTAGCT
21202550 CACAAACAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 4 0.06
93 13 0.18
94 52 0.73
95 1 0.01
96 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (91 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTAGTAATGAGGCCGATGCATGTCCCAGACATGT
CTTACACTAGCTATCGTCTCAATGCT
Found at i:21202926 original size:30 final size:30
Alignment explanation
Indices: 21202881--21202938 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
21202871 AAATTCACAT
* * *
21202881 CTTTGGTAAATTGACCATTTTGCCCCTAAA
1 CTTTGGCAAAATGACCATTTTACCCCTAAA
21202911 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
21202939 TGCTCGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAAA
Found at i:21210302 original size:35 final size:35
Alignment explanation
Indices: 21210256--21210329 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
21210246 GGCTAGTTAC
21210256 AACCATTGGATTATCATGCCAACATTAGCCAAATT
1 AACCATTGGATTATCATGCCAACATTAGCCAAATT
*
21210291 AACCATTGGATTATCATGCCAACATTGGCCAAATT
1 AACCATTGGATTATCATGCCAACATTAGCCAAATT
21210326 AACC
1 AACC
21210330 TATACATGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (35 bp):
AACCATTGGATTATCATGCCAACATTAGCCAAATT
Found at i:21219636 original size:43 final size:43
Alignment explanation
Indices: 21219549--21219933 Score: 452
Period size: 43 Copynumber: 9.0 Consensus size: 43
21219539 ATTTTGTACA
* * * * *
21219549 ATGCCAATGTCCCTGACGTGGTCTTACATGTAATCTCATCTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
21219592 ATGTC-ACTGTCCCAGACAG-GGTCTTACTCTTAAACACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* **** *
21219635 ATGCCAACATTTTGGACGTGGTCTTACACGAAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
21219678 ATGCCAACGTCCCAGATGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
21219721 ATG-CAATGTCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
21219763 ATGCTAACGTCCTAGACGTGATCTTACACGTAATCACATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * *
21219806 ATGCCGACATCCCAGACGTGGTCTAACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
21219849 ATGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * * *
21219892 ATGCCAACATCCTAAATGTGGTCTTACAAGTAATCACATATC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATC
21219934 AATGTCTCAT
Statistics
Matches: 289, Mismatches: 48, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
42 42 0.15
43 244 0.84
44 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:21219843 original size:171 final size:172
Alignment explanation
Indices: 21219549--21219938 Score: 489
Period size: 171 Copynumber: 2.3 Consensus size: 172
21219539 ATTTTGTACA
* * * * * *
21219549 ATGCCAATGTCCCTGACGTGGTCTTACATGTAATCTCATCTCGATGTCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACGTGGTCTTACAAGTAATCACATATCGATGTAACTGTCCCAGACAGGAT
* * **** *
21219614 CTTACTCTTAAACACATATCGATGCCAACATTTTGGACGTGGTCTTACACGAAATCACATATCGA
66 CTTACACGTAAACACATATCGATGCCAACATCCCAGACGTGGTCTAACACGAAATCACATATCGA
* **
21219679 TGCCAACGTCCCAGATGTGGTCTTACACGTAATCACATATCG
131 TGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
* *
21219721 ATG-CAATGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCTAAC-GTCCTAGAC-GTG
1 ATGCCAATGTCCCAGACGTGGTCTTACAAGTAATCACATATCGATG-TAACTGTCCCAGACAG-G
* * * *
21219783 ATCTTACACGTAATCACATATTGATGCCGACATCCCAGACGTGGTCTAACACGTAATCACATATC
64 ATCTTACACGTAAACACATATCGATGCCAACATCCCAGACGTGGTCTAACACGAAATCACATATC
21219848 GATGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
129 GATGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
** * * * *
21219892 ATGCCAACATCCTAAATGTGGTCTTACAAGTAATCACATATCAATGT
1 ATGCCAATGTCCCAGACGTGGTCTTACAAGTAATCACATATCGATGT
21219939 CTCATATACA
Statistics
Matches: 187, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
170 1 0.01
171 145 0.78
172 41 0.22
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (172 bp):
ATGCCAATGTCCCAGACGTGGTCTTACAAGTAATCACATATCGATGTAACTGTCCCAGACAGGAT
CTTACACGTAAACACATATCGATGCCAACATCCCAGACGTGGTCTAACACGAAATCACATATCGA
TGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:21220709 original size:15 final size:15
Alignment explanation
Indices: 21220686--21220716 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21220676 TCAAAAATTC
21220686 CAATACAAAACATAT
1 CAATACAAAACATAT
*
21220701 CAATCCAAAACATAT
1 CAATACAAAACATAT
21220716 C
1 C
21220717 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:21222410 original size:13 final size:12
Alignment explanation
Indices: 21222383--21222429 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
21222373 TGGTTTCTAT
21222383 TTTCA-TTTCCAA
1 TTTCATTTTCC-A
21222395 TTTCATCTTTCCA
1 TTTCAT-TTTCCA
*
21222408 TTTTAATTTTCCA
1 -TTTCATTTTCCA
21222421 TTTCATTTT
1 TTTCATTTT
21222430 TCCTTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 13 0.43
13 7 0.23
14 10 0.33
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCATTTTCCA
Found at i:21222430 original size:13 final size:13
Alignment explanation
Indices: 21222388--21222432 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
21222378 TCTATTTTCA
*
21222388 TTTCCAATTTCATC
1 TTTCC-ATTTCATT
* *
21222402 TTTCCATTTTAAT
1 TTTCCATTTCATT
21222415 TTTCCATTTCATT
1 TTTCCATTTCATT
21222428 TTTCC
1 TTTCC
21222433 TTATTCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTCCATTTCATT
Found at i:21223789 original size:11 final size:11
Alignment explanation
Indices: 21223769--21223802 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
21223759 GAGTTACTTG
21223769 ATTATAATTTA
1 ATTATAATTTA
* *
21223780 CTTATGATTTA
1 ATTATAATTTA
21223791 ATTATAATTTA
1 ATTATAATTTA
21223802 A
1 A
21223803 CTTTTTAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
ATTATAATTTA
Found at i:21227080 original size:19 final size:19
Alignment explanation
Indices: 21227058--21227124 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
21227048 TGATCTGAAC
21227058 TCATTGAGTTGGTCTGAGT
1 TCATTGAGTTGGTCTGAGT
* *
21227077 TCA-TGATATATGTGACATCTGAGC
1 TCATTGA-GT-TG-G---TCTGAGT
21227101 TCATTGAGTTGGTCTGAGT
1 TCATTGAGTTGGTCTGAGT
21227120 TCATT
1 TCATT
21227125 ATGTTTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
18 3 0.08
19 15 0.41
20 2 0.05
21 1 0.03
22 1 0.03
23 2 0.05
24 10 0.27
25 3 0.08
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (19 bp):
TCATTGAGTTGGTCTGAGT
Found at i:21232625 original size:53 final size:54
Alignment explanation
Indices: 21232447--21232639 Score: 190
Period size: 55 Copynumber: 3.6 Consensus size: 54
21232437 GCACTAAGAT
*** * * *
21232447 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAG-ACACGACATTGATGAGTTCTATAAGGC
* * * *
21232502 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACACGACATTGATGAGTT-CTATAAGGC
* * * * * * * *
21232557 AAAGTTCCCATGTAAGAACATGCCAAGGCACGACATTGGTGCGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACACGACATTGATGAGTTCTATAAGGC
*
21232610 AAGGATACCACGTAAGACCATGTCAAGACA
1 AAGGATACCATGTAAGACCATGTCAAGACA
21232640 TGGAAATGGT
Statistics
Matches: 112, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
53 30 0.27
54 18 0.16
55 64 0.57
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACACGACATTGATGAGTTCTATAAGGC
Found at i:21235679 original size:26 final size:26
Alignment explanation
Indices: 21235650--21235757 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
21235640 TGGTACAAAT
21235650 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
21235676 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21235702 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
21235728 TAATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21235754 TGAT
1 TGAT
21235758 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:21237274 original size:26 final size:26
Alignment explanation
Indices: 21237245--21237297 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
21237235 TTTACAGTTT
21237245 TACCCCTAGTGGATAAATT-ACCGAAA
1 TACCCCTAG-GGATAAATTGACCGAAA
* * *
21237271 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
21237297 T
1 T
21237298 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:21242181 original size:54 final size:54
Alignment explanation
Indices: 21242117--21242324 Score: 201
Period size: 54 Copynumber: 3.9 Consensus size: 54
21242107 TTGGTAAGAT
* *
21242117 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGC
* * *
21242171 AAGGAAATCATGTAACACCATGTCAAGACATGGCATTGATGAGTTACTATAAGG-
1 AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGC
* * * *
21242225 AA--AAATTCCCATGTAAGACTATGCCAAGGCATGGCATT-AGTGAGTTC-ATAAGTC
1 AAGGAAA-T--CATGTAAGACCATGCCAAGACATGGCATTGA-TAAGTTCTATAAGGC
* * * * * *
21242279 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
21242325 AAAAAGGAAA
Statistics
Matches: 126, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
52 3 0.02
53 36 0.29
54 46 0.37
55 39 0.31
56 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (54 bp):
AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGC
Found at i:21242343 original size:108 final size:109
Alignment explanation
Indices: 21242125--21242335 Score: 284
Period size: 108 Copynumber: 2.0 Consensus size: 109
21242115 ATAAGGATAT
* *
21242125 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAACACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAACACC
* * * *
21242190 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGAAAAATTCC
66 ATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAAATTCC
* * * * *
21242234 CATGTAAGACTATGCCAAGGCATGGCATT-AGTGAGTTC-ATAAGTCAAGGATACCACGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCATTGA-TAAGTTCTATAAGGCAAGGAAACCACGTAACAC
*
21242297 CATGTCAAGACATGGCAATGGTAAGTT-CAAAAAGGAAAA
65 CATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAA
21242336 GGTTCCCAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 10 0.11
108 45 0.51
109 34 0.38
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAACACC
ATGTCAAGACATGGCAATGATAAGTTACAAAAAGGAAAAATTCC
Found at i:21243334 original size:8 final size:8
Alignment explanation
Indices: 21243321--21243345 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21243311 AGTTATAGTT
21243321 TATATTTC
1 TATATTTC
21243329 TATATTTC
1 TATATTTC
21243337 TATATTTC
1 TATATTTC
21243345 T
1 T
21243346 TAGTGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTTC
Found at i:21247436 original size:43 final size:43
Alignment explanation
Indices: 21247350--21247436 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
21247340 AATGTATATG
* *
21247350 ATCTGAACTCATTGAGTTGGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCATTGAGTTGATCTGAGTTCATGATATATATGAC
* * *
21247393 ATCTGAGCTCATTGAGTTGATCTGAGTTCATGATGTTTATGAC
1 ATCTGAACTCATTGAGTTGATCTGAGTTCATGATATATATGAC
21247436 A
1 A
21247437 CATGTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (43 bp):
ATCTGAACTCATTGAGTTGATCTGAGTTCATGATATATATGAC
Found at i:21256733 original size:13 final size:14
Alignment explanation
Indices: 21256715--21256743 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21256705 CGCTTTCATG
21256715 TGCTTCAT-CTTAT
1 TGCTTCATACTTAT
21256728 TGCTTCATACTTAT
1 TGCTTCATACTTAT
21256742 TG
1 TG
21256744 ACCTGAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52
Consensus pattern (14 bp):
TGCTTCATACTTAT
Found at i:21264596 original size:44 final size:43
Alignment explanation
Indices: 21264548--21264652 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 43
21264538 GCCAATATAC
*
21264548 ATATATATAGCCGAATCTTTCTCGATCTCGCACACTAAGTGCAA
1 ATATATATAGCCGAATCTTT-TCGATCTCGCACAATAAGTGCAA
* * * * * *
21264592 ATATATATAGCTGAAGCTATTTTGATTTCGTACAATAAGTGCAC
1 ATATATATAGCCGAATCT-TTTCGATCTCGCACAATAAGTGCAA
21264636 ATA-AT-TAGCCGAATCTT
1 ATATATATAGCCGAATCTT
21264653 CATCGAACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 9 0.18
43 2 0.04
44 37 0.73
45 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (43 bp):
ATATATATAGCCGAATCTTTTCGATCTCGCACAATAAGTGCAA
Found at i:21265166 original size:20 final size:21
Alignment explanation
Indices: 21265127--21265167 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21265117 ACTTTAATAA
21265127 CTATCATCAAACACTCAAAAT
1 CTATCATCAAACACTCAAAAT
*
21265148 CTATCATTAAACA-TCAAAAT
1 CTATCATCAAACACTCAAAAT
21265168 AATCTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (21 bp):
CTATCATCAAACACTCAAAAT
Found at i:21267449 original size:19 final size:19
Alignment explanation
Indices: 21267413--21267452 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
21267403 AAAAATTAAT
21267413 ATTAACTAAATGCAAATGA
1 ATTAACTAAATGCAAATGA
21267432 ATTAATCTAAATGC-AATGA
1 ATTAA-CTAAATGCAAATGA
21267451 AT
1 AT
21267453 GAGATGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (19 bp):
ATTAACTAAATGCAAATGA
Found at i:21273008 original size:13 final size:12
Alignment explanation
Indices: 21272994--21273043 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 12
21272984 TGGTTTCTAT
21272994 TTTCATTTTCCA
1 TTTCATTTTCCA
21273006 TTTCATGTTTCCA
1 TTTCAT-TTTCCA
*
21273019 TTTTATTTTTCCA
1 TTTCA-TTTTCCA
21273032 TTTCAATTTTCC
1 TTTC-ATTTTCC
21273044 TTATTAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 6 0.18
13 25 0.76
14 2 0.06
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTCATTTTCCA
Found at i:21273015 original size:26 final size:26
Alignment explanation
Indices: 21272986--21273036 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
21272976 CATAATTTTG
*
21272986 GTTTCTATTTTCA-TTTTCCATTTCAT
1 GTTTCCATTTT-ATTTTTCCATTTCAT
21273012 GTTTCCATTTTATTTTTCCATTTCA
1 GTTTCCATTTTATTTTTCCATTTCA
21273037 ATTTTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.16, C:0.20, G:0.04, T:0.61
Consensus pattern (26 bp):
GTTTCCATTTTATTTTTCCATTTCAT
Found at i:21276780 original size:47 final size:47
Alignment explanation
Indices: 21276712--21276973 Score: 197
Period size: 47 Copynumber: 5.6 Consensus size: 47
21276702 TTTGTGCACT
*
21276712 AGTGTAAGACATGTCTAGGACAT-GCATCGCCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGCCCACATTATGAGAGCC
* * *
21276758 AGTGTAAGACCATGTCTGGGACATGGCATCG---GCATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGCCCACATT---ATGAGAGCC
* * *
21276806 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTC-TTAATGTA-AGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGCCCACATT-ATG-AGAGCC
* * * * * * *
21276852 AGTGTAAGATATGTCTAGGACAT-GCATCGACTACATGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGCCCACATTATGAGAGCC
* ** *
21276896 AGTGTAAGACCATGTCTGGGACATGGCATCAACTTA-ACT-TGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACATGGCATC-GCCCACATTATGAGAGCC
21276943 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACATGGCATCG
21276974 GTATTATACC
Statistics
Matches: 174, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
44 10 0.06
45 17 0.10
46 58 0.33
47 64 0.37
48 24 0.14
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGCCCACATTATGAGAGCC
Found at i:21276852 original size:46 final size:46
Alignment explanation
Indices: 21276710--21276880 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
21276700 CTTTTGTGCA
* *
21276710 CTAGTGTAAGACATGTCTAGGACATGCATCGCCCACATT-ATGAGAG
1 CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTC-TTAATGAGAG
* * * * *
21276756 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGACGAGAG
1 CTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCTTA-ATGAGAG
*
21276804 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCTTAATGTA-AG
1 CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCTTAATG-AGAG
*
21276850 CTAGTGTAAGATATGTCTAGGACATGCATCG
1 CTAGTGTAAGACATGTCTAGGACATGCATCG
21276881 ACTACATGAT
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
46 53 0.50
47 30 0.28
48 23 0.22
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (46 bp):
CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCTTAATGAGAG
Found at i:21281120 original size:21 final size:20
Alignment explanation
Indices: 21281091--21281129 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
21281081 AACACATTGG
*
21281091 GAGAACGAATATTATCCTAAA
1 GAGAACGAAGA-TATCCTAAA
*
21281112 GAGATCGAAGATATCCTA
1 GAGAACGAAGATATCCTA
21281130 TGAGGGTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (20 bp):
GAGAACGAAGATATCCTAAA
Found at i:21282779 original size:22 final size:24
Alignment explanation
Indices: 21282743--21282786 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
21282733 TTGCTTTTGT
21282743 TTTTCTTAGGCTTTC-TATTTTTC
1 TTTTCTTAGGCTTTCATATTTTTC
*
21282766 TTTTC-TAGGGTTTCATATTTT
1 TTTTCTTAGGCTTTCATATTTT
21282787 CTATCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTTCTTAGGCTTTCATATTTTTC
Found at i:21284402 original size:177 final size:177
Alignment explanation
Indices: 21284106--21284462 Score: 583
Period size: 177 Copynumber: 2.0 Consensus size: 177
21284096 TGATAGTCTC
* *
21284106 ACTTCGGAATAGGATCTTTCGATGAAGCGAATATAAAATAAACTTAGTAAAAGCTGAAAACTAAT
1 ACTTCGGAATAGGATCTTTCAATGAAGCGAATATAAAATAAACATAGTAAAAGCTGAAAACTAAT
**
21284171 AAAAACCTAAAGAATAAGTTTCTTCTCCCTAAATTTGAGTGTTTAATGTGTTGTTCTAAGCTCTT
66 AAAAACCTAAAGAATAAGTTTCTTCTCCCTAAATTTGAGTGTTTAATGTGTTGTTCTAAAATCTT
* * *
21284236 ATTTATATATTACATGTATTATGGCCTAATTAGGTCAAGTAAATATG
131 ATTTATATATTACATGTATTATGACCTAAATAGGTCAAGTAAATAGG
*
21284283 ACTTCGGAATAGGATCTTTCAATTAAGCGAATATAAAATAAACATAGTAAAAGCTGAAAACTAAT
1 ACTTCGGAATAGGATCTTTCAATGAAGCGAATATAAAATAAACATAGTAAAAGCTGAAAACTAAT
* * *
21284348 AAAAACCTAAAGAAT-ATTTTTTGTCTCCCTAAATTT-ATGTGTTTAATGTGTTGTTTTAAAATC
66 AAAAACCTAAAGAATAAGTTTCT-TCTCCCTAAATTTGA-GTGTTTAATGTGTTGTTCTAAAATC
21284411 TTATTTATATATTACATGTATTATGACCTAAATAGGTCAAGTAAATAGG
129 TTATTTATATATTACATGTATTATGACCTAAATAGGTCAAGTAAATAGG
21284460 ACT
1 ACT
21284463 AAGCATGTTA
Statistics
Matches: 167, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
176 6 0.04
177 161 0.96
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (177 bp):
ACTTCGGAATAGGATCTTTCAATGAAGCGAATATAAAATAAACATAGTAAAAGCTGAAAACTAAT
AAAAACCTAAAGAATAAGTTTCTTCTCCCTAAATTTGAGTGTTTAATGTGTTGTTCTAAAATCTT
ATTTATATATTACATGTATTATGACCTAAATAGGTCAAGTAAATAGG
Found at i:21285291 original size:20 final size:20
Alignment explanation
Indices: 21285262--21285305 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
21285252 GTTGGTTTAA
21285262 TAAA-AGGGTTGATTATGTT
1 TAAATAGGGTTGATTATGTT
21285281 TAAATAGGGTTGATTATGTT
1 TAAATAGGGTTGATTATGTT
21285301 TAAAT
1 TAAAT
21285306 TGGTATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (20 bp):
TAAATAGGGTTGATTATGTT
Found at i:21289520 original size:22 final size:21
Alignment explanation
Indices: 21289495--21289535 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21289485 ATTAGATTAA
21289495 AATTAAAATTAATAATATTATG
1 AATTAAAATTAATAA-ATTATG
* *
21289517 AATTAATATTCATAAATTA
1 AATTAAAATTAATAAATTA
21289536 GACCATCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTAAAATTAATAAATTATG
Found at i:21296128 original size:5 final size:4
Alignment explanation
Indices: 21296071--21296128 Score: 66
Period size: 4 Copynumber: 14.0 Consensus size: 4
21296061 CAAAATTCAG
21296071 AATA AATA AATA AATA AATA AATA AAT- AATA AA-A TAATAA AATA TAATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA -AAT-A AATA -AATA
21296120 AATA CAATA
1 AATA -AATA
21296129 TTGGGATCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.08
4 32 0.67
5 11 0.23
6 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:21297877 original size:28 final size:28
Alignment explanation
Indices: 21297835--21297894 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
21297825 ACATATACTA
* *
21297835 GAAATTTTATTTCACGCGTATGCATGTG
1 GAAATTTTATCTCACACGTATGCATGTG
*
21297863 GAAATTTTATCTCACACTTATGCATGTG
1 GAAATTTTATCTCACACGTATGCATGTG
21297891 GAAA
1 GAAA
21297895 CTACGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (28 bp):
GAAATTTTATCTCACACGTATGCATGTG
Found at i:21301600 original size:26 final size:26
Alignment explanation
Indices: 21301557--21301621 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
21301547 ATGGACATTT
* **
21301557 TATTTCTTAAAAATACTTTTTAAAA-
1 TATTTTTTAAAAGCACTTTTTAAAAG
*
21301582 TCATTTTTTCAAAGCACTTTTTAAAAG
1 T-ATTTTTTAAAAGCACTTTTTAAAAG
21301609 TATTTTTTAAAAG
1 TATTTTTTAAAAG
21301622 TAATGTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.03
26 31 0.94
27 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (26 bp):
TATTTTTTAAAAGCACTTTTTAAAAG
Found at i:21301621 original size:13 final size:13
Alignment explanation
Indices: 21301557--21301623 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
21301547 ATGGACATTT
* *
21301557 TATTTCTTAAAAA
1 TATTTTTTAAAAG
*
21301570 TACTTTTTAAAA-
1 TATTTTTTAAAAG
*
21301582 TCATTTTTTCAAAG
1 T-ATTTTTTAAAAG
* *
21301596 CACTTTTTAAAAG
1 TATTTTTTAAAAG
21301609 TATTTTTTAAAAG
1 TATTTTTTAAAAG
21301622 TA
1 TA
21301624 ATGTTAAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 1 0.02
13 42 0.98
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (13 bp):
TATTTTTTAAAAG
Found at i:21302311 original size:21 final size:19
Alignment explanation
Indices: 21302276--21302315 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
21302266 AGAATATATA
21302276 AATTATATTTTAAATATTT
1 AATTATATTTTAAATATTT
21302295 AATTATAATTATTAAATATTT
1 AATTAT-ATT-TTAAATATTT
21302316 GTAATTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTATATTTTAAATATTT
Found at i:21302311 original size:33 final size:30
Alignment explanation
Indices: 21302238--21302315 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 30
21302228 TTTAAGCAAT
21302238 GAATATT-AATTATTTATAAAATTTAATTA
1 GAATATTAAATTATTTATAAAATTTAATTA
*
21302267 GAATATATAAATTATATTTTAAATATTTAATTA
1 GAATAT-TAAATTAT-TTATAAA-ATTTAATTA
*
21302300 TAATTATTAAA-TATTT
1 GAA-TATTAAATTATTT
21302316 GTAATTAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 6 0.14
30 1 0.02
31 8 0.19
32 9 0.21
33 15 0.36
34 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
GAATATTAAATTATTTATAAAATTTAATTA
Found at i:21304165 original size:30 final size:30
Alignment explanation
Indices: 21304129--21304196 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
21304119 TACCAACTAG
* *
21304129 GTTCTCCTTTTGGTTTCACCTAGGCATATA
1 GTTCTCCTTTCGATTTCACCTAGGCATATA
*
21304159 GTTCTCCTTTCGATTTCATCTAGGCATATA
1 GTTCTCCTTTCGATTTCACCTAGGCATATA
*
21304189 GATCTCCT
1 GTTCTCCT
21304197 CTTAGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (30 bp):
GTTCTCCTTTCGATTTCACCTAGGCATATA
Found at i:21305581 original size:51 final size:51
Alignment explanation
Indices: 21305521--21305689 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
21305511 ATTAAACATT
* *
21305521 TCTCACATGGTCTTACACCTTATATCATATATG-GAGATACCATGAAGCCTC
1 TCTCACATGGTCTTATACCTCATATCATATATGTG-GATACCATGAAGCCTC
* * * *
21305572 TCTCACATGGTTTTATACCTCATATCATATTTGTGGATGCCATGCAGCCTC
1 TCTCACATGGTCTTATACCTCATATCATATATGTGGATACCATGAAGCCTC
* ** * *
21305623 TCTCACATGGTCTTATACCTCATA-CGATATCTGTGGATGTCATGGAGCCTT
1 TCTCACATGGTCTTATACCTCATATC-ATATATGTGGATACCATGAAGCCTC
*
21305674 TCTTACATGGTCTTAT
1 TCTCACATGGTCTTAT
21305690 GCTTTATTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.01
51 102 0.98
52 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (51 bp):
TCTCACATGGTCTTATACCTCATATCATATATGTGGATACCATGAAGCCTC
Found at i:21306268 original size:20 final size:20
Alignment explanation
Indices: 21306243--21306283 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
21306233 AAGCAGTGCC
21306243 TTACACTCACGCCCTACTAT
1 TTACACTCACGCCCTACTAT
21306263 TTACACTCACGCCCTACTAT
1 TTACACTCACGCCCTACTAT
21306283 T
1 T
21306284 CTTACACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.05, T:0.32
Consensus pattern (20 bp):
TTACACTCACGCCCTACTAT
Found at i:21308549 original size:49 final size:49
Alignment explanation
Indices: 21308492--21308663 Score: 188
Period size: 49 Copynumber: 3.5 Consensus size: 49
21308482 GTTGTGTGTT
* *
21308492 AGTGTAAGACCTGTCTAGGACATGGCATCGACAC-CGATAGATAAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATAAAAGCC
* **
21308541 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATAAAATTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATAAAAGCC
* * * ** ** *
21308590 AGTGTAAGACCTGTCTGGGACACGGCATCAACTTTAAT-G-TACTAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATAAAAGCC
21308637 AGTGTAAGACCATGTCTGGGACATGGC
1 AGTGTAAGACC-TGTCTGGGACATGGC
21308664 GTCGGCATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
47 14 0.13
48 15 0.14
49 75 0.72
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATAAAAGCC
Found at i:21309727 original size:40 final size:41
Alignment explanation
Indices: 21309677--21309756 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
21309667 AAGGTTTTTA
21309677 GACAAGGGCCA-GGACACGGGC-ATGTCATGGCCGTGTGAGG
1 GACAAGGGCCATGGACACGGGCGATGTCA-GGCCGTGTGAGG
* *
21309717 GACATGGGCCATGGACACGGGCGTGTGTCAGGCCGTGTGA
1 GACAAGGGCCATGGACACGGGCG-ATGTCAGGCCGTGTGA
21309757 AAACCCCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 10 0.29
41 10 0.29
42 10 0.29
43 5 0.14
ACGTcount: A:0.20, C:0.23, G:0.42, T:0.15
Consensus pattern (41 bp):
GACAAGGGCCATGGACACGGGCGATGTCAGGCCGTGTGAGG
Found at i:21312029 original size:12 final size:12
Alignment explanation
Indices: 21312000--21312029 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
21311990 AATAGTCTAA
21312000 TATTTTAATATT
1 TATTTTAATATT
21312012 TA-TTTAATATT
1 TATTTTAATATT
21312023 TATTTTA
1 TATTTTA
21312030 TAGTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTAATATT
Found at i:21312131 original size:62 final size:59
Alignment explanation
Indices: 21312065--21312181 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 59
21312055 AGTAATTATC
* * *
21312065 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
21312127 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
21312182 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 1 0.02
62 28 0.54
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:21313225 original size:20 final size:22
Alignment explanation
Indices: 21313200--21313239 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21313190 ATGCCATGCA
*
21313200 TATATT-GG-AAGCATGCCATT
1 TATATTAGGTAAGAATGCCATT
21313220 TATATTAGGTAAGAATGCCA
1 TATATTAGGTAAGAATGCCA
21313240 CTAGGACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (22 bp):
TATATTAGGTAAGAATGCCATT
Found at i:21317644 original size:40 final size:40
Alignment explanation
Indices: 21317585--21317703 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
21317575 TACATAGTCG
*
21317585 AAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCCA
1 AAGCTATCTCGAATCGCACACTAAGTGCCATATATAGCCA
* * * **
21317625 AAGCTTTCTCGAATTGCACACTAAGTGCCATATGTAGCTG
1 AAGCTATCTCGAATCGCACACTAAGTGCCATATATAGCCA
* * * *
21317665 AAGCTATGTTGAATCGCACACTAAGTGCCACAAATAGCC
1 AAGCTATCTCGAATCGCACACTAAGTGCCATATATAGCC
21317704 GATTTGTAGT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
AAGCTATCTCGAATCGCACACTAAGTGCCATATATAGCCA
Found at i:21328776 original size:28 final size:28
Alignment explanation
Indices: 21328735--21328794 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
21328725 ATATCGTTGA
* *
21328735 ATACTCAATGTCTCACACACTAAGTGTT
1 ATACTCAATATCTCACACACTAAGTGTC
* *
21328763 ATACTCGATATCTCGCACACTAAGTGTC
1 ATACTCAATATCTCACACACTAAGTGTC
21328791 ATAC
1 ATAC
21328795 ATAGCCGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (28 bp):
ATACTCAATATCTCACACACTAAGTGTC
Found at i:21328879 original size:40 final size:40
Alignment explanation
Indices: 21328775--21328880 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
21328765 ACTCGATATC
* * *
21328775 TCGCACACTAAGTGTCATACATAGCCGAAGCTATCTCAAA
1 TCGCACACTAAGTGCCATAAATAGCCAAAGCTATCTCAAA
* * * * *
21328815 TCACACACTAGGT-CGCATATATAGCCAAAGCTTTCTCGAA
1 TCGCACACTAAGTGC-CATAAATAGCCAAAGCTATCTCAAA
*
21328855 TCGCACACTAAGTGCCACAAATAGCC
1 TCGCACACTAAGTGCCATAAATAGCC
21328881 GATTTGTCAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
40 52 0.98
41 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATAAATAGCCAAAGCTATCTCAAA
Found at i:21329392 original size:21 final size:20
Alignment explanation
Indices: 21329368--21329407 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21329358 ACTTGTTTAA
21329368 CTATCAACAACCATTCAAAAT
1 CTATCAACAACCA-TCAAAAT
* *
21329389 CTATCATCAATCATCAAAA
1 CTATCAACAACCATCAAAA
21329408 ATCATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (20 bp):
CTATCAACAACCATCAAAAT
Found at i:21331892 original size:15 final size:15
Alignment explanation
Indices: 21331872--21331903 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21331862 CATTTCACTA
*
21331872 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
21331887 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
21331902 TT
1 TT
21331904 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:21339992 original size:16 final size:16
Alignment explanation
Indices: 21339950--21339992 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
21339940 GTAGCCAACC
21339950 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* * *
21339966 TTTCGGGTTTTTGGCA
1 TTTCAGCTTTTCGGCA
*
21339982 TTTCATCTTTT
1 TTTCAGCTTTT
21339993 GTCGGTCTAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:21347997 original size:19 final size:19
Alignment explanation
Indices: 21347973--21348011 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21347963 TTATCTTAAC
*
21347973 AGTATTTTATTACTTTACT
1 AGTATTTTATTAATTTACT
21347992 AGTATTTTATTAATTTACT
1 AGTATTTTATTAATTTACT
21348011 A
1 A
21348012 TTAAAGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (19 bp):
AGTATTTTATTAATTTACT
Found at i:21351193 original size:24 final size:24
Alignment explanation
Indices: 21351138--21351194 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
21351128 TAAAACAACA
* *
21351138 AAAATAAAATCTATTCTAAAAAGG
1 AAAAGAAAATCTAATCTAAAAAGG
** * *
21351162 AAGGGAAAATCTAATCTTAAAATG
1 AAAAGAAAATCTAATCTAAAAAGG
21351186 AAAAGAAAA
1 AAAAGAAAA
21351195 GAGAAGGAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (24 bp):
AAAAGAAAATCTAATCTAAAAAGG
Found at i:21351220 original size:5 final size:5
Alignment explanation
Indices: 21351212--21351239 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
21351202 AAAAGAAACT
21351212 TAACC TAACC TAACC TAACC TAACC TAA
1 TAACC TAACC TAACC TAACC TAACC TAA
21351240 AACTATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (5 bp):
TAACC
Found at i:21352476 original size:12 final size:11
Alignment explanation
Indices: 21352451--21352484 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
21352441 TCATTTTGGT
*
21352451 AAAATGAAAAA
1 AAAAAGAAAAA
21352462 AAAAAGAAAAGA
1 AAAAAGAAAA-A
21352474 AAAAAGAAAAA
1 AAAAAGAAAAA
21352485 GAGCATGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:21358589 original size:83 final size:83
Alignment explanation
Indices: 21358450--21358616 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
21358440 GTCGTTGTTG
21358450 AGAGATGAAGCCTATCAGTGGTGGCTTACTGTGAAAGAGGGTACTCAGCCCGATCGATTAACTTG
1 AGAGATGAAGCCTATCAGTGGTGGCTTACTGTGAAAGAGGGTACTCAGCCCGATCGATTAACTTG
21358515 GGAGTTTTTTAAAAATGT
66 GGAGTTTTTTAAAAATGT
21358533 AGAGATGAAGCCTATCAGTGGTGGCTTACTGTGAAAGAGGGTACTCAGCCCGATCGATTAACTTG
1 AGAGATGAAGCCTATCAGTGGTGGCTTACTGTGAAAGAGGGTACTCAGCCCGATCGATTAACTTG
21358598 GGAGTTTTTTAAAAATGT
66 GGAGTTTTTTAAAAATGT
21358616 A
1 A
21358617 TTCCAAGGGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (83 bp):
AGAGATGAAGCCTATCAGTGGTGGCTTACTGTGAAAGAGGGTACTCAGCCCGATCGATTAACTTG
GGAGTTTTTTAAAAATGT
Found at i:21371874 original size:9 final size:10
Alignment explanation
Indices: 21371847--21371873 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21371837 ATATTGATTG
21371847 TTATTTTTAA
1 TTATTTTTAA
21371857 TTATTTTTAA
1 TTATTTTTAA
21371867 TTATTTT
1 TTATTTT
21371874 ATGGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTTTAA
Found at i:21372596 original size:48 final size:50
Alignment explanation
Indices: 21372531--21372649 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
21372521 GTAGATGGAA
* *
21372531 GACTAAGATGATAAAACAAGTATC-C-AAATGAGTTGATAGAAGCTTGAT
1 GACTGAGATGATAAAACAAGTATCTCTAAATGAGTTGATAGAAGCCTGAT
* * * * * *
21372579 GATTGAGATAATAAAACAAGTCTCTCTACATGATTTGATGGAAGCCTGAT
1 GACTGAGATGATAAAACAAGTATCTCTAAATGAGTTGATAGAAGCCTGAT
*
21372629 GACTGAAATGATAAAACAAGT
1 GACTGAGATGATAAAACAAGT
21372650 TTTGTTTGCA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 20 0.34
49 1 0.02
50 37 0.64
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (50 bp):
GACTGAGATGATAAAACAAGTATCTCTAAATGAGTTGATAGAAGCCTGAT
Found at i:21384430 original size:17 final size:18
Alignment explanation
Indices: 21384408--21384441 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21384398 ATACTAATCA
*
21384408 TACA-TTATTAATCATAT
1 TACATTTATGAATCATAT
21384425 TACATTTATGAATCATA
1 TACATTTATGAATCATA
21384442 CCTCAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (18 bp):
TACATTTATGAATCATAT
Found at i:21385724 original size:35 final size:35
Alignment explanation
Indices: 21385613--21385726 Score: 140
Period size: 35 Copynumber: 3.3 Consensus size: 35
21385603 CAAGGTAACT
* * *
21385613 TCACATATAACCGAATATACAAGTTTAATATAAGC
1 TCACATGTAACCAAATATACAAGTTCAATATAAGC
* * *
21385648 TCACATTTAATCAAATACT-CAAGTTCAATATAACC
1 TCACATGTAACCAAATA-TACAAGTTCAATATAAGC
*
21385683 TCACATGTAGCCAAATATACAAGTTCAATATAAGC
1 TCACATGTAACCAAATATACAAGTTCAATATAAGC
*
21385718 TTACATGTA
1 TCACATGTA
21385727 CTTACCTATG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.97
36 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (35 bp):
TCACATGTAACCAAATATACAAGTTCAATATAAGC
Found at i:21388304 original size:39 final size:40
Alignment explanation
Indices: 21388204--21388467 Score: 310
Period size: 40 Copynumber: 6.7 Consensus size: 40
21388194 TTGAATGATG
* * *
21388204 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
** *
21388243 ATCCGGATTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
21388284 TCCGGGCTAAG-CCCGAAGGCA-TTGCTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAAT
*
21388323 TCCGGGCTAAG-CCCGAAGGCA-TTGCTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAAT
* *
21388362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
21388402 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
21388441 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
21388468 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
38 3 0.01
39 71 0.35
40 114 0.57
41 13 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:21388486 original size:80 final size:77
Alignment explanation
Indices: 21388205--21388467 Score: 284
Period size: 79 Copynumber: 3.3 Consensus size: 77
21388195 TGAATGATGT
* * * * *
21388205 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGATTAAGAT-CCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATT-TGC-GAGTTACTATATCCGGGTTAAG-TCCCGAAGGCATTT
* *
21388269 GTGCGAGATACTAATT
63 GTGCGAGTTACTAA-A
*
21388285 CCGGGCTAAG-CCCGAAGGCATTGCTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCA-TT
1 CCGGGCTAAGTCCCGAAGGCATT--TGCGAGTTACTATA-TCCGGGTTAAGTCCCGAAGGCATTT
21388346 GCTGCGAGTTACTAAA
63 G-TGCGAGTTACTAAA
* *
21388362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCA-TT-TGCGAGTTACTATATCCGGGTTAAGTCCCGAAGGCATTT
21388427 GTGCGAGTTACTATAA
63 GTGCGAGTTACTA-AA
*
21388443 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
21388468 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
77 3 0.02
78 33 0.21
79 60 0.38
80 57 0.36
81 5 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGAGTTACTATATCCGGGTTAAGTCCCGAAGGCATTTGTG
CGAGTTACTAAA
Found at i:21390225 original size:43 final size:43
Alignment explanation
Indices: 21390177--21390262 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
21390167 GTCTTATGAG
21390177 TTAGTTCATAATTCCAGTAATTATTAATGGATTTTTTATGATC
1 TTAGTTCATAATTCCAGTAATTATTAATGGATTTTTTATGATC
21390220 TTAGTTCATAATTCCAGTAATTATTAATGGATTTTTTATGATC
1 TTAGTTCATAATTCCAGTAATTATTAATGGATTTTTTATGATC
21390263 AAGCAGTAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (43 bp):
TTAGTTCATAATTCCAGTAATTATTAATGGATTTTTTATGATC
Found at i:21390532 original size:27 final size:25
Alignment explanation
Indices: 21390502--21390567 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 25
21390492 AAAATCATCT
21390502 CTTTCAAAAACCAAGGTTTAGAAAAAA
1 CTTTCAAAAACCAA--TTTAGAAAAAA
** * *
21390529 CTTTTGAAAACTCAATTTTGAGAAAA
1 CTTTCAAAAAC-CAATTTAGAAAAAA
21390555 CTTTTCAAAAACC
1 C-TTTCAAAAACC
21390568 CATTCCACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 11 0.35
27 17 0.55
28 3 0.10
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (25 bp):
CTTTCAAAAACCAATTTAGAAAAAA
Found at i:21393270 original size:84 final size:84
Alignment explanation
Indices: 21393129--21393381 Score: 497
Period size: 84 Copynumber: 3.0 Consensus size: 84
21393119 CTTTTACCAA
21393129 GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
1 GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
21393194 ATCCTCTTGCTTACGGTGG
66 ATCCTCTTGCTTACGGTGG
21393213 GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
1 GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
21393278 ATCCTCTTGCTTACGGTGG
66 ATCCTCTTGCTTACGGTGG
*
21393297 GTCTACAACTACTCCATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
1 GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
21393362 ATCCTCTTGCTTACGGTGG
66 ATCCTCTTGCTTACGGTGG
21393381 G
1 G
21393382 ATTCGAACTT
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 168 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (84 bp):
GTCTACAACTACTCTATAGAGTTCGAATCCACCACAAAGACTTGCCACCCAAGTAGCAAAGTAAA
ATCCTCTTGCTTACGGTGG
Found at i:21399525 original size:14 final size:15
Alignment explanation
Indices: 21399494--21399531 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
21399484 TAAGTAAGCA
21399494 AATTAAATGTTGATG
1 AATTAAATGTTGATG
21399509 AATTAAATGTT-ATG
1 AATTAAATGTTGATG
21399523 AATTAAATG
1 AATTAAATG
21399532 GTAAGTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (15 bp):
AATTAAATGTTGATG
Found at i:21410956 original size:43 final size:43
Alignment explanation
Indices: 21410908--21410991 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
21410898 TGAGGTATGT
* *
21410908 AGCATCCGAGGTCATTGAGAGGTCCGATTTCATTATGGATGAG
1 AGCATCCGAGCTCATTGAGAGGTCCGATTTCATGATGGATGAG
** * * *
21410951 AGCATCTTAGCTCGTTGAGTGGTTCGATTTCATGATGGATG
1 AGCATCCGAGCTCATTGAGAGGTCCGATTTCATGATGGATG
21410992 TGATTCATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (43 bp):
AGCATCCGAGCTCATTGAGAGGTCCGATTTCATGATGGATGAG
Found at i:21417270 original size:43 final size:43
Alignment explanation
Indices: 21417216--21417300 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
21417206 TGAGGTATAT
*
21417216 AGCATCAGAGCTCGTTGAGAGGT-CAGAGTTCATTATGGATGCA
1 AGCATCAGAGCTCGTTGAGAGGTCCA-AGTTCATGATGGATGCA
* * *
21417259 AGCATCTGAGCTCGTTGAGTGGTCCATGTTCATGATGGATGC
1 AGCATCAGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGC
21417301 GATTCATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
AGCATCAGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCA
Found at i:21422056 original size:18 final size:18
Alignment explanation
Indices: 21422002--21422056 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
21421992 CTTGGCTCAT
* *
21422002 TGCAATAACAATAAATAG
1 TGCAGTAACAATAAACAG
*
21422020 TGCAGTAACAATAATCAG
1 TGCAGTAACAATAAACAG
* *
21422038 TGCAGTTACAGTAAACAG
1 TGCAGTAACAATAAACAG
21422056 T
1 T
21422057 ATGCAAATCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (18 bp):
TGCAGTAACAATAAACAG
Found at i:21422418 original size:27 final size:27
Alignment explanation
Indices: 21422356--21422632 Score: 217
Period size: 27 Copynumber: 10.3 Consensus size: 27
21422346 ACATACATCA
* * * *
21422356 CATAGGGGCAAAATTGTCGTTCTA-CT
1 CATAAGGGCAAAACTGTCATTTTACCT
*
21422382 CATAATGGCAAAACTGTCATTTTACCT
1 CATAAGGGCAAAACTGTCATTTTACCT
* *
21422409 CATAAGGGCAAAA-TCGTCATTTTATCA
1 CATAAGGGCAAAACT-GTCATTTTACCT
** * *
21422436 CATAAGGGCAAAACAATCATTTTGCCA
1 CATAAGGGCAAAACTGTCATTTTACCT
* * * *
21422463 CATAATGGTAAAACCGTCATTTTAGCT
1 CATAAGGGCAAAACTGTCATTTTACCT
* *
21422490 TATAAGGGCAAAA-TCGTCATTTTATCAT
1 CATAAGGGCAAAACT-GTCATTTTA-CCT
* *
21422518 -ATAAAGGCAAAA-TAGTCATTTTTCCAT
1 CATAAGGGCAAAACT-GTCATTTTACC-T
* *
21422545 -ATAAGGGCAAAACCGTCATTTTACTT
1 CATAAGGGCAAAACTGTCATTTTACCT
* * *
21422571 TATAAGGGCAAAA-TCGTCATTTTATCA
1 CATAAGGGCAAAACT-GTCATTTTACCT
* *
21422598 CATAAGGGCAAAACAGTCATTTTATCT
1 CATAAGGGCAAAACTGTCATTTTACCT
21422625 CATAAGGG
1 CATAAGGG
21422633 TTCAGGTAGG
Statistics
Matches: 201, Mismatches: 40, Indels: 19
0.77 0.15 0.07
Matches are distributed among these distances:
26 22 0.11
27 178 0.89
28 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (27 bp):
CATAAGGGCAAAACTGTCATTTTACCT
Found at i:21422446 original size:54 final size:54
Alignment explanation
Indices: 21422356--21422632 Score: 283
Period size: 54 Copynumber: 5.1 Consensus size: 54
21422346 ACATACATCA
* * * * * * *
21422356 CATAGGGGCAAAATTGTCGTTCTA-CTCATAATGGCAAAACTGTCATTTTACCT
1 CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAGTCATTTTACCT
* * *
21422409 CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAATCATTTTGCCA
1 CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAGTCATTTTACCT
* * * * ** *
21422463 CATAATGGTAAAACCGTCATTTTAGCTTATAAGGGCAAAATC-GTCATTTTATCAT
1 CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAA-CAGTCATTTTA-CCT
* * * * *
21422518 -ATAAAGGCAAAATAGTCATTTT-TCCATATAAGGGCAAAACCGTCATTTTACTT
1 CATAAGGGCAAAATCGTCATTTTAT-CACATAAGGGCAAAACAGTCATTTTACCT
* *
21422571 TATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAGTCATTTTATCT
1 CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAGTCATTTTACCT
21422625 CATAAGGG
1 CATAAGGG
21422633 TTCAGGTAGG
Statistics
Matches: 183, Mismatches: 34, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
53 23 0.13
54 157 0.86
55 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (54 bp):
CATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAAAACAGTCATTTTACCT
Found at i:21422476 original size:81 final size:81
Alignment explanation
Indices: 21422382--21422620 Score: 370
Period size: 81 Copynumber: 3.0 Consensus size: 81
21422372 TCGTTCTACT
* *
21422382 CATAATGGCAAAACTGTCATTTTACCTCATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
1 CATAATGGCAAAACCGTCATTTTACCTTATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
*
21422447 AACAATCATTTTGCCA
66 AACAGTCATTTTGCCA
* * * *
21422463 CATAATGGTAAAACCGTCATTTTAGCTTATAAGGGCAAAATCGTCATTTTATCATATAAAGGCAA
1 CATAATGGCAAAACCGTCATTTTACCTTATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
* *
21422528 AATAGTCATTTTTCCA
66 AACAGTCATTTTGCCA
* * *
21422544 TATAAGGGCAAAACCGTCATTTTACTTTATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
1 CATAATGGCAAAACCGTCATTTTACCTTATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
21422609 AACAGTCATTTT
66 AACAGTCATTTT
21422621 ATCTCATAAG
Statistics
Matches: 141, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 141 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (81 bp):
CATAATGGCAAAACCGTCATTTTACCTTATAAGGGCAAAATCGTCATTTTATCACATAAGGGCAA
AACAGTCATTTTGCCA
Found at i:21422630 original size:81 final size:80
Alignment explanation
Indices: 21422352--21422632 Score: 343
Period size: 81 Copynumber: 3.5 Consensus size: 80
21422342 ATACACATAC
* ** * * * * *
21422352 ATCACATAGGGGCAAAATTGTCGTTCTA-CTCATAATGGCAAAACTGTCATTTTACCTCATAAGG
1 ATCACATAAGGGCAAAACAGTCATTTTATCTCATAAGGGCAAAACCGTCATTTTA-CTTATAAGG
21422416 GCAAAATCGTCATTTT
65 GCAAAATCGTCATTTT
* ** * * *
21422432 ATCACATAAGGGCAAAACAATCATTTTGCCACATAATGGTAAAACCGTCATTTTAGCTTATAAGG
1 ATCACATAAGGGCAAAACAGTCATTTTATCTCATAAGGGCAAAACCGTCATTTTA-CTTATAAGG
21422497 GCAAAATCGTCATTTT
65 GCAAAATCGTCATTTT
* * *
21422513 ATCATATAAAGGCAAAATAGTCATTTT-TC-CATATAAGGGCAAAACCGTCATTTTACTTTATAA
1 ATCACATAAGGGCAAAACAGTCATTTTATCTC--ATAAGGGCAAAACCGTCATTTTAC-TTATAA
21422576 GGGCAAAATCGTCATTTT
63 GGGCAAAATCGTCATTTT
21422594 ATCACATAAGGGCAAAACAGTCATTTTATCTCATAAGGG
1 ATCACATAAGGGCAAAACAGTCATTTTATCTCATAAGGG
21422633 TTCAGGTAGG
Statistics
Matches: 173, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
79 1 0.01
80 23 0.13
81 146 0.84
82 2 0.01
83 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (80 bp):
ATCACATAAGGGCAAAACAGTCATTTTATCTCATAAGGGCAAAACCGTCATTTTACTTATAAGGG
CAAAATCGTCATTTT
Found at i:21427145 original size:18 final size:19
Alignment explanation
Indices: 21427115--21427165 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
21427105 CTTGGCCCAT
*
21427115 TGCAGTAATAGTAAAT-AG
1 TGCAGTAACAGTAAATCAG
*
21427133 TGTAGTAACAGT-AATCAG
1 TGCAGTAACAGTAAATCAG
*
21427151 TGCAATAACAGTAAA
1 TGCAGTAACAGTAAA
21427166 CAATATGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 22 0.81
19 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (19 bp):
TGCAGTAACAGTAAATCAG
Found at i:21427546 original size:27 final size:27
Alignment explanation
Indices: 21427494--21427742 Score: 160
Period size: 27 Copynumber: 9.4 Consensus size: 27
21427484 ATACACATAC
21427494 ACCACA-AAGGGGCAAAAT-AGTCATTTT
1 ACCACATAA-GGGCAAAATCA-TCATTTT
* *
21427521 ACCTCATAAGGGCAAAATCATAATTTT
1 ACCACATAAGGGCAAAATCATCATTTT
*
21427548 ATCACATAAGGGCAAAAT-AGTCATTTT
1 ACCACATAAGGGCAAAATCA-TCATTTT
* *
21427575 GCCACATAAGGGCAAAA-CTGTCATTTT
1 ACCACATAAGGGCAAAATC-ATCATTTT
* * * *
21427602 AGCTCATAA-AGCAAAATCGTCATTTT
1 ACCACATAAGGGCAAAATCATCATTTT
* * * *
21427628 ATCGCATAAGAG-AAAAACATCATTTT
1 ACCACATAAGGGCAAAATCATCATTTT
* * *
21427654 GCCACATAAGGGCAAAATCGTCATTTA
1 ACCACATAAGGGCAAAATCATCATTTT
* *
21427681 ATCACCTAAGGG-AAAA--A-CATTTT
1 ACCACATAAGGGCAAAATCATCATTTT
** * *
21427704 GTCACCTAAGGG-AAAAACAATCATTTT
1 ACCACATAAGGGCAAAATC-ATCATTTT
* *
21427731 ATCTCATAAGGG
1 ACCACATAAGGG
21427743 TTCAGGTACG
Statistics
Matches: 178, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
23 20 0.11
26 47 0.26
27 108 0.61
28 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
ACCACATAAGGGCAAAATCATCATTTT
Found at i:21427566 original size:54 final size:53
Alignment explanation
Indices: 21427494--21427742 Score: 202
Period size: 53 Copynumber: 4.7 Consensus size: 53
21427484 ATACACATAC
* *
21427494 ACCACA-AAGGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAATCATAATTTT
1 ACCACATAA-GGGCAAAATAGTCATTTTACCACATAAGGGCAAAA-CATCATTTT
* * *
21427548 ATCACATAAGGGCAAAATAGTCATTTTGCCACATAAGGGCAAAACTGTCATTTT
1 ACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAAC-ATCATTTT
* * * * * * * *
21427602 AGCTCATAA-AGCAAAATCGTCATTTTATCGCATAAGAGAAAAACATCATTTT
1 ACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACATCATTTT
* * * * *
21427654 GCCACATAAGGGCAAAATCGTCATTTAATCACCTAAGGG-AAAA-A-CATTTT
1 ACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACATCATTTT
** * * * * * *
21427704 GTCACCTAAGGGAAAAACAATCATTTTATCTCATAAGGG
1 ACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGG
21427743 TTCAGGTACG
Statistics
Matches: 160, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
50 36 0.22
51 1 0.01
52 17 0.11
53 53 0.33
54 51 0.32
55 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (53 bp):
ACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACATCATTTT
Found at i:21427623 original size:26 final size:27
Alignment explanation
Indices: 21427503--21427697 Score: 166
Period size: 27 Copynumber: 7.3 Consensus size: 27
21427493 CACCACAAAG
* * *
21427503 GGGCAAAATAGTCATTTTACCTCATAA
1 GGGCAAAATCGTCATTTTAGCACATAA
* * *
21427530 GGGCAAAATCATAATTTTATCACATAA
1 GGGCAAAATCGTCATTTTAGCACATAA
*
21427557 GGGCAAAATAGTCATTTT-GCCACATAA
1 GGGCAAAATCGTCATTTTAG-CACATAA
*
21427584 GGGCAAAA-CTGTCATTTTAGCTCATAA
1 GGGCAAAATC-GTCATTTTAGCACATAA
* * *
21427611 -AGCAAAATCGTCATTTTATCGCATAA
1 GGGCAAAATCGTCATTTTAGCACATAA
* * *
21427637 GAG-AAAAACATCATTTT-GCCACATAA
1 GGGCAAAATCGTCATTTTAG-CACATAA
* * *
21427663 GGGCAAAATCGTCATTTAATCACCTAA
1 GGGCAAAATCGTCATTTTAGCACATAA
*
21427690 GGGAAAAA
1 GGGCAAAA
21427698 CATTTTGTCA
Statistics
Matches: 135, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
26 41 0.30
27 93 0.69
28 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
GGGCAAAATCGTCATTTTAGCACATAA
Found at i:21427701 original size:23 final size:23
Alignment explanation
Indices: 21427675--21427722 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
21427665 GCAAAATCGT
21427675 CATTTAATCACCTAAGGGAAAAA
1 CATTTAATCACCTAAGGGAAAAA
**
21427698 CATTTTGTCACCTAAGGGAAAAA
1 CATTTAATCACCTAAGGGAAAAA
21427721 CA
1 CA
21427723 ATCATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (23 bp):
CATTTAATCACCTAAGGGAAAAA
Found at i:21441783 original size:15 final size:16
Alignment explanation
Indices: 21441748--21441785 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21441738 ATGATTACTG
21441748 ATTTTATGTTTAGAAT
1 ATTTTATGTTTAGAAT
* *
21441764 ATTTTAT-TTTGGACT
1 ATTTTATGTTTAGAAT
21441779 ATTTTAT
1 ATTTTAT
21441786 AGCCGCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.61
Consensus pattern (16 bp):
ATTTTATGTTTAGAAT
Found at i:21444569 original size:33 final size:33
Alignment explanation
Indices: 21444498--21444570 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
21444488 TCTATCGGGG
*
21444498 TAGTAAACACGGAATAAAGTAAGTCTTTCAAGA
1 TAGTAAACACGAAATAAAGTAAGTCTTTCAAGA
* * *
21444531 CAGTAAACACGAAATAGAGTAAGT-TTGTCAGGA
1 TAGTAAACACGAAATAAAGTAAGTCTT-TCAAGA
21444564 TAGTAAA
1 TAGTAAA
21444571 TTAGGAACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (33 bp):
TAGTAAACACGAAATAAAGTAAGTCTTTCAAGA
Found at i:21446480 original size:68 final size:68
Alignment explanation
Indices: 21446314--21446489 Score: 159
Period size: 68 Copynumber: 2.6 Consensus size: 68
21446304 TAGTACCACT
* * * *
21446314 CATGCGACCTAGC--CA-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
*
21446376 CACT
65 CACA
* * *
21446380 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGCGACCTAGCTACATATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
21446442 ATCACA
63 ATCACA
*
21446448 CATGTGACCTAGCTACAATATAGTATCTCGTAGC-CTTCTTGT
1 CATGCGACCTAGCTAC-ATATA-TATCTCGTAGCTC-TCTTGT
21446490 ACACATGATG
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
66 13 0.14
67 1 0.01
68 35 0.39
69 9 0.10
70 6 0.07
71 26 0.29
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (68 bp):
CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:21448417 original size:17 final size:18
Alignment explanation
Indices: 21448373--21448406 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21448363 TTTAATTGGA
21448373 AAATTAATTTATCTAATT
1 AAATTAATTTATCTAATT
21448391 AAATTAATTTAT-TAAT
1 AAATTAATTTATCTAAT
21448407 AATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTAATTTATCTAATT
Found at i:21463309 original size:10 final size:10
Alignment explanation
Indices: 21463291--21463342 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
21463281 ATTATTAACA
*
21463291 TAATGAATTT
1 TAATTAATTT
21463301 TAATTAATTTT
1 TAATTAA-TTT
21463312 ATAATTAATTT
1 -TAATTAATTT
*
21463323 TGATTAATTT
1 TAATTAATTT
*
21463333 TGATT-ATTT
1 TAATTAATTT
21463342 T
1 T
21463343 CCACAGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 5 0.13
10 20 0.53
11 6 0.16
12 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (10 bp):
TAATTAATTT
Found at i:21463315 original size:22 final size:22
Alignment explanation
Indices: 21463290--21463333 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21463280 AATTATTAAC
21463290 ATAATGAATTTTAATTAATTTT
1 ATAATGAATTTTAATTAATTTT
* *
21463312 ATAATTAATTTTGATTAATTTT
1 ATAATGAATTTTAATTAATTTT
21463334 GATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATAATGAATTTTAATTAATTTT
Found at i:21467460 original size:26 final size:26
Alignment explanation
Indices: 21467431--21467485 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
21467421 TTTACAGTTT
21467431 TACCCCAAGGAGATAAATT-ACCGAAA
1 TACCCCAAGG-GATAAATTGACCGAAA
* * *
21467457 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCAAGGGATAAATTGACCGAAA
21467483 TAC
1 TAC
21467486 ATGTTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (26 bp):
TACCCCAAGGGATAAATTGACCGAAA
Found at i:21467870 original size:33 final size:34
Alignment explanation
Indices: 21467793--21467873 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
21467783 TATGGGCCAT
*
21467793 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * ** *
21467827 AATGTAATCTGAA-AA-GGGCTCTGGCCTAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
21467860 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
21467874 GGGCTTAGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 12 0.32
33 14 0.38
34 11 0.30
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:21473620 original size:17 final size:16
Alignment explanation
Indices: 21473589--21473622 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
21473579 AAATATTATG
21473589 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
21473605 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
21473622 A
1 A
21473623 TGCCATCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:21477821 original size:46 final size:46
Alignment explanation
Indices: 21477768--21477943 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
21477758 TATTTGGGCA
21477768 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAGCG
* * * * *
21477814 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATG---CGA-GCG
* * * * *
21477861 TCCGAGCTTGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAGCG
* * *
21477907 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGG
21477944 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 63 0.60
47 30 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAGCG
Found at i:21477923 original size:93 final size:93
Alignment explanation
Indices: 21477764--21477936 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
21477754 GGAATATTTG
* * *
21477764 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTCAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
21477829 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCAAGTTCGTGAGATGTAACTA
* * * *
21477857 GGCATCCGAGCTTGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTCAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
21477922 TTGAGTCCAAGTTCG
66 TTGAGTCCAAGTTCG
21477937 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTCAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCAAGTTCGTGAGATGTAACTA
Found at i:21480836 original size:15 final size:15
Alignment explanation
Indices: 21480797--21480876 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
21480787 GTATCTTGGG
*
21480797 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
21480812 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
21480827 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
21480842 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
21480857 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
21480871 TTTCTT
1 TTTCTT
21480877 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:21480866 original size:30 final size:30
Alignment explanation
Indices: 21480788--21480875 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
21480778 CATAGTATCG
* * *
21480788 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
21480818 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
21480848 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
21480876 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:21488460 original size:42 final size:42
Alignment explanation
Indices: 21488383--21488462 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
21488373 GTGCAAGGTT
* *
21488383 CACACGGCCAAGACACACACCTATGTTTTAGGCCGTGTAGCA
1 CACACGGCCAAGACACACACCCATGTTCTAGGCCGTGTAGCA
** *
21488425 CACACGGCTGAGACATACACCCATGTCTCTA-GCCGTGT
1 CACACGGCCAAGACACACACCCATGT-TCTAGGCCGTGT
21488463 GCCTAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (42 bp):
CACACGGCCAAGACACACACCCATGTTCTAGGCCGTGTAGCA
Found at i:21489851 original size:43 final size:42
Alignment explanation
Indices: 21489804--21489916 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 42
21489794 GCGATTACGT
* *
21489804 GTAAGACCACGTCTAGGACGTTGGCATCGATATGTGTTTACAA
1 GTAAGACCACGTCT-GGACGTTGGCATCGATATGAGGTTACAA
* * *
21489847 GTAAGAACATGTCTGGTAC-TGTGGCATCGATATGAGGTTACAT
1 GTAAGACCACGTCTGG-ACGT-TGGCATCGATATGAGGTTACAA
* *
21489890 GTAATACCACATCTGGGACGTTGGCAT
1 GTAAGACCACGTCT-GGACGTTGGCAT
21489917 TGTATGATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
42 3 0.05
43 51 0.89
44 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (42 bp):
GTAAGACCACGTCTGGACGTTGGCATCGATATGAGGTTACAA
Found at i:21495100 original size:22 final size:22
Alignment explanation
Indices: 21495075--21495118 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21495065 AATTATTAAC
*
21495075 ATAATTAATT-TTAATTAATTTT
1 ATAATAAATTGTT-ATTAATTTT
21495097 ATAATAAATTGTTATTAATTTT
1 ATAATAAATTGTTATTAATTTT
21495119 GATTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATAATAAATTGTTATTAATTTT
Found at i:21500365 original size:46 final size:45
Alignment explanation
Indices: 21500297--21500467 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 45
21500287 GTAACCCGCC
21500297 CATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
* * *
21500342 CAATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 C-ATAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-C-A-TTCGCAT
* * * *
21500392 C-TCA-CGAACTCAGACTCCACTCAATGAGCTCGGACATTCGCAT
1 CATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
21500435 CCATAAGTGAACTC-GACTCAACTCAATGAGCTC
1 -CATAAGCGAACTCAGACTCAACTCAACGAGCTC
21500468 AGATGCCCAA
Statistics
Matches: 103, Mismatches: 13, Indels: 20
0.76 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 21 0.20
46 38 0.37
47 25 0.24
48 3 0.03
49 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.20
Consensus pattern (45 bp):
CATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:21505808 original size:16 final size:16
Alignment explanation
Indices: 21505787--21505817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21505777 AAACTCTCTT
*
21505787 TCATACTTGGTAACTG
1 TCATACTCGGTAACTG
21505803 TCATACTCGGTAACT
1 TCATACTCGGTAACT
21505818 CTTTACGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
TCATACTCGGTAACTG
Found at i:21507815 original size:38 final size:38
Alignment explanation
Indices: 21507772--21507847 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21507762 ACAGTTAATG
21507772 AAGATTACCGAAGTGAACTAATAACCTATAAGTAGATT
1 AAGATTACCGAAGTGAACTAATAACCTATAAGTAGATT
21507810 AAGATTACCGAAGTGAACTAATAACCTATAAGTAGATT
1 AAGATTACCGAAGTGAACTAATAACCTATAAGTAGATT
21507848 TAATTAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (38 bp):
AAGATTACCGAAGTGAACTAATAACCTATAAGTAGATT
Found at i:21533124 original size:25 final size:25
Alignment explanation
Indices: 21533086--21533167 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 25
21533076 TCGCCACATA
21533086 TACTGATACTGGCAGCTTTGCTGCGT
1 TACTG-TACTGGCAGCTTTGCTGCGT
* * *
21533112 TACTGTACTGGCAGCCTTGCTACAAAAT
1 TACTGTACTGGCAGCTTTGCTGC---GT
*
21533140 TA-T-TACTGGCAGCTTTGCTGCGA
1 TACTGTACTGGCAGCTTTGCTGCGT
21533163 TACTG
1 TACTG
21533168 GTGTGTTGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
23 2 0.05
24 1 0.02
25 16 0.36
26 21 0.48
27 1 0.02
28 3 0.07
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (25 bp):
TACTGTACTGGCAGCTTTGCTGCGT
Found at i:21551667 original size:18 final size:17
Alignment explanation
Indices: 21551644--21551678 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21551634 GTTGGGCTAA
*
21551644 AATGGGCTATGTGGGCTT
1 AATGGGCT-TATGGGCTT
21551662 AATGGGCTTATGGGCTT
1 AATGGGCTTATGGGCTT
21551679 CACACGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.11, G:0.37, T:0.34
Consensus pattern (17 bp):
AATGGGCTTATGGGCTT
Found at i:21553689 original size:41 final size:40
Alignment explanation
Indices: 21553563--21553694 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 40
21553553 TTATGTTTTT
** * * *
21553563 CACTTAGTGTGCATTTTGAGATAGCTTTGGCAATATAAAG
1 CACTTAGTGTGCAGATTGAGATAGCTTTGGCTATATGATG
*
21553603 CACTTAGTGTGCA-ATTTG-GAGTAGCTTCGGCTATATG-TGG
1 CACTTAGTGTGCAGA-TTGAGA-TAGCTTTGGCTATATGAT-G
*
21553643 CACTTAGTGTGCGAGATTGAGATAGCTTTGGCTATTTGATG
1 CACTTAGTGTGC-AGATTGAGATAGCTTTGGCTATATGATG
*
21553684 TACTTAGTGTG
1 CACTTAGTGTG
21553695 TGAGATTATA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.03
40 42 0.55
41 29 0.38
42 4 0.05
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.36
Consensus pattern (40 bp):
CACTTAGTGTGCAGATTGAGATAGCTTTGGCTATATGATG
Found at i:21571433 original size:40 final size:40
Alignment explanation
Indices: 21571361--21571491 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 40
21571351 ACTATGTTTT
* *
21571361 GCACTTAGTGCGCG-TTTGAGATAGCTTTGGCTATATAAA
1 GCACTTAGTGTGCGATTTGAGATAGCTTCGGCTATATAAA
***
21571400 GCACTTAGTGTGCGATTTG-GAGTAGCTTCGGCTATATGTG
1 GCACTTAGTGTGCGATTTGAGA-TAGCTTCGGCTATATAAA
** * * * * *
21571440 GCACTTAGTGTGCGAGACTGAAATAGCTTTGGCTATGTGAT
1 GCACTTAGTGTGCGA-TTTGAGATAGCTTCGGCTATATAAA
21571481 GCACTTAGTGT
1 GCACTTAGTGT
21571492 CCTAGGTTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 15 0.20
40 33 0.43
41 27 0.36
42 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTTGAGATAGCTTCGGCTATATAAA
Found at i:21571485 original size:41 final size:40
Alignment explanation
Indices: 21571381--21571491 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
21571371 CGCGTTTGAG
* * ** *
21571381 ATAGCTTTGGCTATATAAAGCACTTAGTGTGCGATTTGGA
1 ATAGCTTTGGCTATATGATGCACTTAGTGTGCGAACTGAA
* *
21571421 GTAGCTTCGGCTATATG-TGGCACTTAGTGTGCGAGACTGAA
1 ATAGCTTTGGCTATATGAT-GCACTTAGTGTGCGA-ACTGAA
*
21571462 ATAGCTTTGGCTATGTGATGCACTTAGTGT
1 ATAGCTTTGGCTATATGATGCACTTAGTGT
21571492 CCTAGGTTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 29 0.50
41 28 0.48
42 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (40 bp):
ATAGCTTTGGCTATATGATGCACTTAGTGTGCGAACTGAA
Found at i:21575161 original size:11 final size:11
Alignment explanation
Indices: 21575145--21575171 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21575135 TGAAATAGAA
21575145 ATGATTATTTG
1 ATGATTATTTG
21575156 ATGATTATTTG
1 ATGATTATTTG
21575167 ATGAT
1 ATGAT
21575172 CCATGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (11 bp):
ATGATTATTTG
Found at i:21576414 original size:21 final size:21
Alignment explanation
Indices: 21576385--21576459 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 21
21576375 CTATGTGACA
*
21576385 TGAACTCATTGAGTTGTGGTC
1 TGAATTCATTGAGTTGTGGTC
* *
21576406 TGATTTCA-TGATATATGTGGCATC
1 TGAATTCATTGA-GT-TGTGG--TC
* *
21576430 TGAACTCATTGAGTTATGGTC
1 TGAATTCATTGAGTTGTGGTC
*
21576451 TGAGTTCAT
1 TGAATTCAT
21576460 GATGTATATG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.08
21 16 0.40
22 5 0.12
23 4 0.10
24 9 0.22
25 3 0.08
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
TGAATTCATTGAGTTGTGGTC
Found at i:21579633 original size:11 final size:12
Alignment explanation
Indices: 21579617--21579646 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21579607 ATGTGCTAAT
21579617 TTGTTTGA-TGG
1 TTGTTTGATTGG
21579628 TTGTTTGATTGG
1 TTGTTTGATTGG
21579640 TTGTTTG
1 TTGTTTG
21579647 TTATACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.60
Consensus pattern (12 bp):
TTGTTTGATTGG
Done.