Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 159 of 310
Found at i:52141725 original size:6 final size:6
Alignment explanation
Indices: 52141605--52141712 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
52141595 TCTTTTTTCG
* * * **
52141605 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
52141656 CAATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
52141704 -GTTTT CTTT
1 CTTTTT CTTT
52141713 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:52155480 original size:14 final size:14
Alignment explanation
Indices: 52155461--52155503 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
52155451 AACCGACCGA
*
52155461 TTTGTTCATACCAT
1 TTTGTTCCTACCAT
*
52155475 TTTGTTCCTACCCT
1 TTTGTTCCTACCAT
*
52155489 TTCGTTCCTACCAT
1 TTTGTTCCTACCAT
52155503 T
1 T
52155504 CCATTCGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (14 bp):
TTTGTTCCTACCAT
Found at i:52155886 original size:11 final size:11
Alignment explanation
Indices: 52155870--52155908 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52155860 TATACAAGTT
52155870 AAAAAAAATAA
1 AAAAAAAATAA
**
52155881 AAAAAAAATTC
1 AAAAAAAATAA
*
52155892 GAAAAAAATAA
1 AAAAAAAATAA
52155903 AAAAAA
1 AAAAAA
52155909 TCGAAAAAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:52161145 original size:19 final size:19
Alignment explanation
Indices: 52161121--52161160 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52161111 AGCTCCCATG
52161121 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
52161140 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
52161159 TA
1 TA
52161161 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:52162418 original size:14 final size:14
Alignment explanation
Indices: 52162396--52162443 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
52162386 ACCTAAACCG
* *
52162396 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
52162410 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
52162424 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
52162438 ACCATT
1 ACCATT
52162444 CCATTCGTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:52162759 original size:20 final size:20
Alignment explanation
Indices: 52162736--52162789 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
52162726 AGTTTTTCCC
*
52162736 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
52162756 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
52162776 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
52162790 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:52162771 original size:30 final size:30
Alignment explanation
Indices: 52162736--52162809 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
52162726 AGTTTTTCCC
52162736 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
52162766 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
52162796 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
52162810 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:52162799 original size:20 final size:20
Alignment explanation
Indices: 52162736--52162800 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
52162726 AGTTTTTCCC
* * * *
52162736 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
52162756 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
52162775 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
52162796 AGCTC
1 AGCTC
52162801 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:52164831 original size:25 final size:26
Alignment explanation
Indices: 52164767--52164836 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
52164757 CTAAGGCCTG
52164767 ATAGAATATGTCACAAAGGCGAGATAC
1 ATAG-ATATGTCACAAAGGCGAGATAC
*
52164794 ATA-ATACGTCACAAAGGC-A-ATAC
1 ATAGATATGTCACAAAGGCGAGATAC
*
52164817 ATAGAGTATGCCACAAAGGC
1 ATAGA-TATGTCACAAAGGC
52164837 TAGCAGAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.18
24 2 0.05
25 26 0.68
27 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (26 bp):
ATAGATATGTCACAAAGGCGAGATAC
Found at i:52164852 original size:20 final size:20
Alignment explanation
Indices: 52164824--52164867 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
52164814 TACATAGAGT
*
52164824 ATGCCACAAAGGCTAGCAGA
1 ATGCCACAAAGGCTAACAGA
*
52164844 ATGCTACAAAGGCTAACAGA
1 ATGCCACAAAGGCTAACAGA
52164864 ATGC
1 ATGC
52164868 GCCACCAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATGCCACAAAGGCTAACAGA
Found at i:52171023 original size:38 final size:39
Alignment explanation
Indices: 52170967--52171298 Score: 251
Period size: 38 Copynumber: 8.0 Consensus size: 39
52170957 ATTGATTCAT
* *
52170967 TAACGTGGTGCTAAGTGGATATACCATGGTTGA-ACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
* * *
52171005 TAACCTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTT-CATACA-TG
* *
52171046 ATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGA-ACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
* * *
52171090 TAACCTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTT-CATACA-TG
* *
52171131 ATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGA-ACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
* * *
52171175 TAACCTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTT-CATACA-TG
* *
52171216 ATTCATTAACGTGGTGCTAAGTGGATATACCATGGTT-AAACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
*
52171260 TAACGTGGTGCTAAGTGGATATGCCACGGTT-ATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
52171298 T
1 T
52171299 TAATTTGAAA
Statistics
Matches: 234, Mismatches: 33, Indels: 54
0.73 0.10 0.17
Matches are distributed among these distances:
38 120 0.51
39 3 0.01
40 6 0.03
41 6 0.03
44 6 0.03
45 7 0.03
46 2 0.01
47 84 0.36
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (39 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTCATACATG
Found at i:52171080 original size:85 final size:85
Alignment explanation
Indices: 52170937--52171291 Score: 692
Period size: 85 Copynumber: 4.2 Consensus size: 85
52170927 GGTGTTACAT
52170937 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
1 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
52171002 ATGTAACCTGGTGCTAAGTG
66 ATGTAACCTGGTGCTAAGTG
52171022 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
1 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
52171087 ATGTAACCTGGTGCTAAGTG
66 ATGTAACCTGGTGCTAAGTG
52171107 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
1 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
52171172 ATGTAACCTGGTGCTAAGTG
66 ATGTAACCTGGTGCTAAGTG
*
52171192 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTAAAC
1 GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
*
52171257 ATGTAACGTGGTGCTAAGTG
66 ATGTAACCTGGTGCTAAGTG
52171277 GATATGCCACGGTTA
1 GATATGCCACGGTTA
52171292 TACATGTTAA
Statistics
Matches: 268, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 268 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (85 bp):
GATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTGAAC
ATGTAACCTGGTGCTAAGTG
Found at i:52171552 original size:13 final size:13
Alignment explanation
Indices: 52171534--52171558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52171524 TATTTAAAAA
52171534 TTATTTTATGTGT
1 TTATTTTATGTGT
52171547 TTATTTTATGTG
1 TTATTTTATGTG
52171559 AATTATTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TTATTTTATGTGT
Found at i:52175469 original size:31 final size:31
Alignment explanation
Indices: 52175431--52175491 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
52175421 TCTTTTAGAC
*
52175431 TTAGTTTCATAAGAAATATATTAGTCAGAGG
1 TTAGTTTCATAAGAAATATATCAGTCAGAGG
* *
52175462 TTAGTTTCGTTAGAAATATATCAGTCAGAG
1 TTAGTTTCATAAGAAATATATCAGTCAGAG
52175492 ATTTATGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (31 bp):
TTAGTTTCATAAGAAATATATCAGTCAGAGG
Found at i:52179711 original size:13 final size:13
Alignment explanation
Indices: 52179693--52179717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52179683 TAGTTAAAAA
52179693 TTATTTTATGTGT
1 TTATTTTATGTGT
52179706 TTATTTTATGTG
1 TTATTTTATGTG
52179718 AATTTATATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TTATTTTATGTGT
Found at i:52185464 original size:30 final size:30
Alignment explanation
Indices: 52185430--52185526 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
52185420 TAAACTAAAA
*
52185430 TGAGCTAAACTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
52185460 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
52185490 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
52185520 TGAGCTA
1 TGAGCTA
52185527 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.86
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:52187745 original size:20 final size:20
Alignment explanation
Indices: 52187720--52187774 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
52187710 ACGAGTTAAA
* *
52187720 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
52187740 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
52187760 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
52187775 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:52190570 original size:28 final size:28
Alignment explanation
Indices: 52190531--52190594 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
52190521 TTTAGAGAAG
52190531 AAAATTCT-CACAAGATTAAATTCAATAA
1 AAAATT-TGCACAAGATTAAATTCAATAA
52190559 AAAATTTGCACAAGATTAAATTCAATAA
1 AAAATTTGCACAAGATTAAATTCAATAA
*
52190587 AAATTTTG
1 AAAATTTG
52190595 GCAAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAATTTGCACAAGATTAAATTCAATAA
Found at i:52191653 original size:30 final size:30
Alignment explanation
Indices: 52191619--52191715 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
52191609 TAAACTAAAA
52191619 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
52191649 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
52191679 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
52191709 TGAGCTA
1 TGAGCTA
52191716 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:52195862 original size:46 final size:46
Alignment explanation
Indices: 52195718--52195843 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 46
52195708 AACCCGCCCC
* * * *
52195718 TAAGTGAACTCGAACTCAACTCAATGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
* * * *
52195764 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
52195810 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52195844 TGCTCAACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCA
Found at i:52197974 original size:47 final size:49
Alignment explanation
Indices: 52197906--52198041 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 49
52197896 CGGGTGTTCG
* *
52197906 CATCCATGAGTGAACTCGGACTCAAATCAACGAGTTCGGATGCCTAGTTA
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTA
* * *
52197956 CAT-C-TTA-TGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTT
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
52197999 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
52198042 TAAACCATCC
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
43 6 0.08
44 2 0.03
45 2 0.03
46 30 0.40
47 29 0.39
48 2 0.03
49 1 0.01
50 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (49 bp):
CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
Found at i:52198038 original size:46 final size:46
Alignment explanation
Indices: 52197863--52198038 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
52197853 TGTAACCCGC
* * * * *** **
52197863 CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACAT
* * *
52197909 CCATGAGTGAACTCGGACTCAAATCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACAT
* *
52197959 -C-TTA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTTTCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACAT
52198002 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52198039 TGCTAAACCA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACAT
Found at i:52198057 original size:46 final size:46
Alignment explanation
Indices: 52197871--52198057 Score: 163
Period size: 46 Copynumber: 4.0 Consensus size: 46
52197861 GCCCATAAGC
* * * * **
52197871 GAACTCAGACTCAACTCAACAAGCTCGGGTG-T-TCGCATCCATGAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTATTACATCC-T-AGT
* *
52197917 GAACTCGGACTCAAATCAACGAGTTCGGATGCCTAGTTACATCTTA-T
1 GAACTCGGACTCAACTCAACGAGTTCGGATG-CTA-TTACATCCTAGT
*
52197964 GAACTCGGACTCAACTCAACGAGTTCGGA--C-ATTTTCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTA-TTACATCC-T-AGT
*
52198010 GAACTCGGACTCAACTCAACGAGTTCGGATGCTA-AACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTATTA-CATCCTAGT
52198056 GA
1 GA
52198058 CATGTCACTT
Statistics
Matches: 116, Mismatches: 14, Indels: 22
0.76 0.09 0.14
Matches are distributed among these distances:
43 7 0.06
44 2 0.02
45 1 0.01
46 61 0.53
47 30 0.26
48 8 0.07
49 2 0.02
50 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTATTACATCCTAGT
Found at i:52200458 original size:15 final size:15
Alignment explanation
Indices: 52200429--52200478 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
52200419 CAAAGATAAC
*
52200429 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
52200443 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
52200458 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
52200473 AAGAAA
1 AAGAAA
52200479 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:52200487 original size:15 final size:15
Alignment explanation
Indices: 52200440--52200487 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
52200430 AGAAAACCGA
52200440 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
52200454 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
52200470 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52200485 ATA
1 ATA
52200488 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52203588 original size:46 final size:46
Alignment explanation
Indices: 52203417--52203592 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
52203407 TGTAACCCGC
* * * *
52203417 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
52203463 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
52203513 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
52203556 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
52203593 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:52203588 original size:93 final size:93
Alignment explanation
Indices: 52203424--52203595 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52203414 CGCCCATAAG
* * *
52203424 CGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52203489 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
52203517 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
52203582 ATGAGTTCGGATGC
66 ACGAGTTCGGATGC
52203596 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:52205408 original size:579 final size:579
Alignment explanation
Indices: 52204544--52206027 Score: 2597
Period size: 579 Copynumber: 2.6 Consensus size: 579
52204534 TTTTACCCCT
* * * *
52204544 AAATGACCAAAATGCCCTTAC-TACTAAACTTTC-CAAAA-ATTCCATCCATGTCC-AATTTTTG
1 AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAA-TTTTG
* * * * * *
52204605 TCCAT-AGACTTAGAAATTGGTAAAATTTCTATTTAAGACCTCCTAATTAATATTTCAAAACAAT
65 TCCATGA-ACTTA-AAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGT
* * * * * *
52204669 TTCATACTAGAAACTTCTAGAATGCAAGTTTTACAAATTATTCGATTTAGTCCCTAA-TTTCAAT
128 TTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTT-AAA
* * * * * * *
52204733 TTAAGCACTTTATG-CATAAAATTTCTTCATGAAATTTTCACACAATCATGCAATCATATCATAG
192 TTAAACTCGTTATGCCA-AAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAA
* *
52204797 ACCTCGAAATAATCATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCC
256 ACCTCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCC
52204862 GACTAGGCCCAAAATCAGGATATTACAGGTATTTTTCCAAATATGAACTCTAACTCAAAATATTA
321 GACTAGGCCCAAAATCAGGATATTACAGGTATTTTTCCAAATATGAACTCTAACTCAAAATATTA
52204927 CTATCATAAGCTATATCGAGTTACCGGGATTTCAAAAATGTAAAAATCATTAAAAACGGGACTTG
386 CTATCATAAGCTATATCGAGTTACCGGGATTTCAAAAATGTAAAAATCATTAAAAACGGGACTTG
52204992 GAATCACTTACTATGAAGCTTGAAAGTTGAAGAAACCCTAGCTATGGAGAGAGGGAGCATTCGGC
451 GAATCACTTACTATGAAGCTTGAAAGTTGAAGAAACCCTAGCTATGGAGAGAGGGAGCATTCGGC
52205057 AACAACAAAGGAAGATGATAACCAATTTTGTGTTATTTTTCACTTTTTATTTCATTTAATATCC
516 AACAACAAAGGAAGATGATAACCAATTTTGTGTTATTTTTCACTTTTTATTTCATTTAATATCC
52205121 AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAATTTTGT
1 AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAATTTTGT
52205186 CCATGAACTTAAAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGTTTC
66 CCATGAACTTAAAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGTTTC
52205251 ATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTTAAATTAA
131 ATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTTAAATTAA
52205316 ACTCGTTATGCCAAAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAAACCTC
196 ACTCGTTATGCCAAAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAAACCTC
52205381 AAAATAATTATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCCGACTA
261 AAAATAATTATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCCGACTA
52205446 GGCCCAAAATCAGGATATTACAGGTATTTTTCCAAATATGAACTCTAACTCAAAATATTACTATC
326 GGCCCAAAATCAGGATATTACAGGTATTTTTCCAAATATGAACTCTAACTCAAAATATTACTATC
52205511 ATAAGCTATATCGAGTTACCGGGATTTCAAAAATGTAAAAATCATTAAAAACGGGACTTGGAATC
391 ATAAGCTATATCGAGTTACCGGGATTTCAAAAATGTAAAAATCATTAAAAACGGGACTTGGAATC
* *
52205576 ACTTATTATGAAGCTTGAAAGTTGAAGAAACCCTAGCTATGGAGAGAGGGAGCATTCGGCAGCAA
456 ACTTACTATGAAGCTTGAAAGTTGAAGAAACCCTAGCTATGGAGAGAGGGAGCATTCGGCAACAA
52205641 CAAAGGAAGATGATAACCAATTTTGTGTTATTTTTCACTTTTTATTTCATTTAATATCC
521 CAAAGGAAGATGATAACCAATTTTGTGTTATTTTTCACTTTTTATTTCATTTAATATCC
52205700 AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAATTTTGT
1 AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAATTTTGT
52205765 CCATGAACTTAAAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGTTTC
66 CCATGAACTTAAAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGTTTC
52205830 ATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTTAAATTAA
131 ATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTTAAATTAA
52205895 ACTCGTTATGCCAAAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAAACCTC
196 ACTCGTTATGCCAAAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAAACCTC
* * *
52205960 AAAATAATTATAAAATAATTATTTCTATCTC-GAATTTGTGGTCATGAAACCACTATTCCGATTA
261 AAAATAATTATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCCGACTA
52206024 GGCC
326 GGCC
52206028 TTAATTCGGA
Statistics
Matches: 870, Mismatches: 30, Indels: 13
0.95 0.03 0.01
Matches are distributed among these distances:
577 19 0.02
578 46 0.05
579 768 0.88
580 34 0.04
581 3 0.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (579 bp):
AAATGACCAAAATGCCCCTCCTTACTAAACTTTCAAAAAAGATTCCTTCCATGTCCTAATTTTGT
CCATGAACTTAAAATTGGTCAAAGTACCATTTAAGACCTCCTAATTAATATTTCAAAGCAGTTTC
ATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTTGATTTCGTCCCTAACTTTAAATTAA
ACTCGTTATGCCAAAAATTTCTTCACGAAATTTTCACTCAATTATGCAATCATATCATAAACCTC
AAAATAATTATAAAATAATTATTTCTATCTCGGATTTTGTGGTCACGAAACCACTATTCCGACTA
GGCCCAAAATCAGGATATTACAGGTATTTTTCCAAATATGAACTCTAACTCAAAATATTACTATC
ATAAGCTATATCGAGTTACCGGGATTTCAAAAATGTAAAAATCATTAAAAACGGGACTTGGAATC
ACTTACTATGAAGCTTGAAAGTTGAAGAAACCCTAGCTATGGAGAGAGGGAGCATTCGGCAACAA
CAAAGGAAGATGATAACCAATTTTGTGTTATTTTTCACTTTTTATTTCATTTAATATCC
Found at i:52209822 original size:51 final size:51
Alignment explanation
Indices: 52209746--52209847 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
52209736 CTGAGATTTA
* *
52209746 GGACCAACATTTCGCTTCTTAAAATTTCTATATGATTGCCCAGCTGAAACT
1 GGACCAACATTTCGCTTCTTAAAATTCCCATATGATTGCCCAGCTGAAACT
* *
52209797 GGACCCACATTTTGCTTCTTAAAATTCCCATATGATTGCCCAGCTGAAACT
1 GGACCAACATTTCGCTTCTTAAAATTCCCATATGATTGCCCAGCTGAAACT
52209848 TGGGGACGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGACCAACATTTCGCTTCTTAAAATTCCCATATGATTGCCCAGCTGAAACT
Found at i:52212347 original size:46 final size:45
Alignment explanation
Indices: 52212187--52212357 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
52212177 AACCCGCCCC
* * *
52212187 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCA
* * * *
52212233 TAAGTGAACTCAGACTCAACTCAACGAGTTCG-GATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGC-A--TCCA
*** *
52212279 TCTCTCGAACTCGGACTTAACTCAACGAGTTCGAACATTCGCATCCA
1 TAAGT-GAACTCGGACTCAACTCAACGAGTTCG-ACATTCGCATCCA
52212326 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
52212358 GATGCTCAAC
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 60 0.60
47 30 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
Found at i:52212351 original size:93 final size:93
Alignment explanation
Indices: 52212192--52212362 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
52212182 GCCCCTAAGT
* *
52212192 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
52212257 CGAGTTCGGATGCCTAGTTACATCTCTC
66 CGAGTTCGGATGCCTAGTTACATCTCTC
* * *
52212285 GAACTCGGACTTAACTCAACGAGTTC-GAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAG-ACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
52212349 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
52212363 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:52212378 original size:46 final size:46
Alignment explanation
Indices: 52212189--52212378 Score: 119
Period size: 46 Copynumber: 4.1 Consensus size: 46
52212179 CCCGCCCCTA
* * * *
52212189 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGATGCTCAACCATCC-T
*
52212234 AAGTGAACTCAGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CT
* * * * * * *
52212284 --CGAACTCGGACTTAACTCAACGAGTTCGAACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCG--GATGCTCAACCATCCT
52212328 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
52212374 AGTGA
1 AGTGA
52212379 CATGTCACTT
Statistics
Matches: 110, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
44 9 0.08
45 3 0.03
46 59 0.54
47 28 0.25
49 4 0.04
50 6 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:52214686 original size:27 final size:27
Alignment explanation
Indices: 52214650--52214711 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
52214640 CCGAAATAGA
*
52214650 AAAAATGACCAAAATACCCCTGTAGGG
1 AAAAATGACCAAAATACCCCTATAGGG
* * * *
52214677 TAAAATGACCATAATGCCCCTATATGG
1 AAAAATGACCAAAATACCCCTATAGGG
52214704 AAAAATGA
1 AAAAATGA
52214712 TGATTATGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAAATGACCAAAATACCCCTATAGGG
Found at i:52214939 original size:27 final size:27
Alignment explanation
Indices: 52214856--52214948 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
52214846 AGTACTATAT
* * *
52214856 TGGTGACTATGTCACATTTACTATTAC
1 TGGTGGCTATGCCACATTTACTGTTAC
* ** *
52214883 TAGTGGCTATGCCACAAATACTGATAC
1 TGGTGGCTATGCCACATTTACTGTTAC
* *
52214910 TGGTGGCTTTGCCACATTTACTGTTCC
1 TGGTGGCTATGCCACATTTACTGTTAC
**
52214937 TGGCAGCTATGC
1 TGGTGGCTATGC
52214949 TGTGTTATTA
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (27 bp):
TGGTGGCTATGCCACATTTACTGTTAC
Found at i:52215923 original size:42 final size:42
Alignment explanation
Indices: 52215877--52216025 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 42
52215867 TGAGTTTACG
* *
52215877 TGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
* * * * * *
52215919 TGTAAGACCATGTATAGGACATGGCATCGGTATGAGA-ATCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
* * * **
52215960 TGCAAGACCATAGCTGGGCTATTGGCATCGATATGAGATCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATATCA
* *
52216003 TGTAACACCATTTCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
52216026 ACATTGCTAT
Statistics
Matches: 82, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
41 16 0.20
42 49 0.60
43 17 0.21
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
Found at i:52216037 original size:84 final size:83
Alignment explanation
Indices: 52215875--52216037 Score: 191
Period size: 84 Copynumber: 2.0 Consensus size: 83
52215865 AATGAGTTTA
* * * ** *
52215875 CGTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTCATGTAAGACCATGTATAGGACA
1 CGTGCAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATGTAACACCATGTATAGGACA
* *
52215940 TGGCATCGGTATGAGAAT
66 TGACATCGCTATGAGAAT
* * * * *
52215958 CGTGCAAGACCATAGCTGGGCTATTGGCATCGATATGAGATCCCATGTAACACCATTTCTGGGAT
1 CGTGCAAGACCATAGCTGGGATA-TGGCATCGATATGAGATCCCATGTAACACCATGTATAGGAC
*
52216023 ATGACATTGCTATGA
65 ATGACATCGCTATGA
52216038 TTCTATGTGT
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
83 20 0.31
84 45 0.69
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (83 bp):
CGTGCAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATGTAACACCATGTATAGGACA
TGACATCGCTATGAGAAT
Found at i:52223415 original size:12 final size:12
Alignment explanation
Indices: 52223402--52223521 Score: 81
Period size: 12 Copynumber: 10.0 Consensus size: 12
52223392 AGAAAGAGAT
*
52223402 TGAAAAAGAAAT
1 TGAAAAAGAAAA
52223414 TG--AAAGAAAA
1 TGAAAAAGAAAA
52223424 T-AAAAAGAAAA
1 TGAAAAAGAAAA
*
52223435 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
52223447 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
52223460 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
52223470 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
52223484 -GAAAAAGAAAA
1 TGAAAAAGAAAA
52223495 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
52223509 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
52223522 AGCGAAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
10 11 0.13
11 10 0.12
12 37 0.43
13 14 0.16
14 12 0.14
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:52223429 original size:6 final size:6
Alignment explanation
Indices: 52223416--52223523 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
52223406 AAAGAAATTG
* * ** *
52223416 AAAG-A AAATAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
52223463 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
52223514 AAAGAA AAAG
1 AAAGAA AAAG
52223524 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:52223446 original size:18 final size:18
Alignment explanation
Indices: 52223420--52223523 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
52223410 AAATTGAAAG
*
52223420 AAAATAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
52223438 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
52223456 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
52223474 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
52223492 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
52223513 AAAAGAAAAAG
1 AAAAGAAAAAG
52223524 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:52223505 original size:14 final size:13
Alignment explanation
Indices: 52223484--52223521 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
52223474 AAAAGTGAGA
52223484 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
52223496 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
52223511 GAAAAAGAAAA
1 GAAAAAGAAAA
52223522 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:52223535 original size:21 final size:21
Alignment explanation
Indices: 52223485--52223535 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
52223475 AAAGTGAGAG
*
52223485 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
52223506 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
52223527 AAAAAGAAA
1 AAAAAGAAA
52223536 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:52223575 original size:33 final size:33
Alignment explanation
Indices: 52223538--52223600 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
52223528 AAAAGAAATT
52223538 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
52223571 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
52223601 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:52228034 original size:216 final size:216
Alignment explanation
Indices: 52227655--52228090 Score: 836
Period size: 216 Copynumber: 2.0 Consensus size: 216
52227645 CAAGCTGATC
* *
52227655 CTAGCTCATTTCTAGCTCCTCGAGCACCGTCCAGCTCAACTCAGCTCATTTGAGCTTGTTTCAGC
1 CTAGATCATTTCTAGCTCCTCGAGCACCGTCCAGCTCAACTCAGCTCATTTGAGCTTATTTCAGC
52227720 TCGTTTGAGCTCAACCGAGCTTACTTTCAGCTCCTTCTTTCTTTCTTTCAATAAACTAAGTCTTA
66 TCGTTTGAGCTCAACCGAGCTTACTTTCAGCTCCTTCTTTCTTTCTTTCAATAAACTAAGTCTTA
*
52227785 ATTTAGTTTATAATTAAGTTTGCTATAGCTCATGCCGAAACCCCTAGCTCAATTTCAACTCATTA
131 ATTTAGTTTATAATTAAGTTTGCTACAGCTCATGCCGAAACCCCTAGCTCAATTTCAACTCATTA
52227850 AGTGTTTTGACTATTTTTGAG
196 AGTGTTTTGACTATTTTTGAG
52227871 CTAGATCATTTCTAGCTCCTCGAGCACCGTCCAGCTCAACTCAGCTCATTTGAGCTTATTTCAGC
1 CTAGATCATTTCTAGCTCCTCGAGCACCGTCCAGCTCAACTCAGCTCATTTGAGCTTATTTCAGC
*
52227936 TCGTTTGATCTCAACCGAGCTTACTTTCAGCTCCTTCTTTCTTTCTTTCAATAAACTAAGTCTTA
66 TCGTTTGAGCTCAACCGAGCTTACTTTCAGCTCCTTCTTTCTTTCTTTCAATAAACTAAGTCTTA
52228001 ATTTAGTTTATAATTAAGTTTGCTACAGCTCATGCCGAAACCCCTAGCTCAATTTCAACTCATTA
131 ATTTAGTTTATAATTAAGTTTGCTACAGCTCATGCCGAAACCCCTAGCTCAATTTCAACTCATTA
52228066 AGTGTTTTGACTATTTTTGAG
196 AGTGTTTTGACTATTTTTGAG
52228087 CTAG
1 CTAG
52228091 CTGAATTTAT
Statistics
Matches: 216, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
216 216 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (216 bp):
CTAGATCATTTCTAGCTCCTCGAGCACCGTCCAGCTCAACTCAGCTCATTTGAGCTTATTTCAGC
TCGTTTGAGCTCAACCGAGCTTACTTTCAGCTCCTTCTTTCTTTCTTTCAATAAACTAAGTCTTA
ATTTAGTTTATAATTAAGTTTGCTACAGCTCATGCCGAAACCCCTAGCTCAATTTCAACTCATTA
AGTGTTTTGACTATTTTTGAG
Found at i:52231879 original size:16 final size:16
Alignment explanation
Indices: 52231855--52231889 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52231845 GTAGATCAAC
52231855 AAATCCCGAAAAGCCA
1 AAATCCCGAAAAGCCA
* *
52231871 AAATGCCGAAAAGTCA
1 AAATCCCGAAAAGCCA
52231887 AAA
1 AAA
52231890 GTTTGGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.23, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATCCCGAAAAGCCA
Found at i:52237391 original size:46 final size:45
Alignment explanation
Indices: 52237324--52237498 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
52237314 TGTAACCCGC
*
52237324 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * *
52237370 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * **
52237416 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
52237463 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
52237499 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 69 0.66
47 33 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:52237443 original size:93 final size:93
Alignment explanation
Indices: 52237331--52237503 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
52237321 CGCCCATAAG
** *
52237331 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52237396 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
52237424 CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
52237489 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
52237504 CAAATATCCT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:52239960 original size:30 final size:30
Alignment explanation
Indices: 52239894--52239969 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
52239884 CAAGAAAATC
* *
52239894 GAATAAAGAAATCCAATATAGAGAAACCCG
1 GAATAAAGAAATCCAATATAAAGAAACCAG
*
52239924 GAATAAAGAAATCCAGA-ATAAAGATATCCAG
1 GAATAAAGAAATCCA-ATATAAAGA-AACCAG
*
52239955 G-ATAAAGAAACCCAA
1 GAATAAAGAAATCCAA
52239970 GATACGATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (30 bp):
GAATAAAGAAATCCAATATAAAGAAACCAG
Found at i:52239973 original size:15 final size:15
Alignment explanation
Indices: 52239896--52239973 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
52239886 AGAAAATCGA
*
52239896 ATAAAGAAATCCAAT
1 ATAAAGAAATCCAAG
* **
52239911 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
52239925 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
52239940 AATAAAGATATCCAGG
1 -ATAAAGAAATCCAAG
*
52239956 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52239971 ATA
1 ATA
52239974 CGATACTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
14 2 0.04
15 44 0.90
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.14
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52240883 original size:40 final size:40
Alignment explanation
Indices: 52240828--52241425 Score: 917
Period size: 40 Copynumber: 14.8 Consensus size: 40
52240818 GAGCATTTGA
* *
52240828 ATATATCCGGGCTAAGACCCGCAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
52240868 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
52240908 ATATATCCGGGCTAAGACCCGCAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
52240948 ATATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
52240990 ATATATCCGGGCTAAGACCCGCAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
52241030 ATATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
52241072 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
52241112 ATATATCCGGGCTAAGACCCGCAGGCCTTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* * * *
52241152 ATATATCCGGGCTAAGAGCTGCAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
52241192 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
52241232 ATATATCCGGGCTAAGACCCGCAGGCCTTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* * * *
52241272 ATATATCCGGGCTAAGAGCTGCAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
52241312 ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
52241352 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** * * *
52241392 CTATGCCCGGGTTAAGACCCAAAGGCAATTGTGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
52241426 TTGTGGTAAT
Statistics
Matches: 512, Mismatches: 42, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
40 436 0.85
42 76 0.15
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:52245726 original size:70 final size:70
Alignment explanation
Indices: 52245613--52245752 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
52245603 AGTTTGCACA
*
52245613 TAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAGCGAAGTCGGACTCAACTCA
1 TAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAGCGAACTCGGACTCAACTCA
52245678 ACGAG
66 ACGAG
52245683 TAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAGCGAACTCGGACTCAACTCA
1 TAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAGCGAACTCGGACTCAACTCA
52245748 ACGAG
66 ACGAG
52245753 CTCGGACGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (70 bp):
TAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAGCGAACTCGGACTCAACTCA
ACGAG
Found at i:52245789 original size:46 final size:46
Alignment explanation
Indices: 52245722--52245897 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
52245712 TGTAACCCGC
*
52245722 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * *
52245768 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-TTCGCAT
* *** * * * *
52245814 ACATCTCTCGAACTCGGACTTAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
52245861 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
52245898 TGCCCAAATA
Statistics
Matches: 102, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
46 70 0.69
47 32 0.31
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:52245888 original size:93 final size:93
Alignment explanation
Indices: 52245729--52245901 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
52245719 CGCCCATAAG
* *
52245729 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
52245794 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * *
52245822 CGAACTCGGACTTAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
52245887 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
52245902 CAAATATCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:52253067 original size:40 final size:40
Alignment explanation
Indices: 52252922--52253107 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
52252912 GCTACTCGTT
* *
52252922 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
52252962 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
52253002 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** *** * *
52253042 TAAATGCCTTC-GGATCTTAGTCCGGATACGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
52253083 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
52253108 CATCATTCGA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 111 0.87
41 14 0.11
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52254438 original size:198 final size:199
Alignment explanation
Indices: 52254100--52254497 Score: 771
Period size: 198 Copynumber: 2.0 Consensus size: 199
52254090 CAACCTCAAA
52254100 CATACCTTGATCTAGATACAAGTATGGCCAAACCTCCTCCTAATCCTCTTCCAAACCAAACATGA
1 CATACCTTGATCTAGATACAAGTATGGCCAAACCTCCTCCTAATCCTCTTCCAAACCAAACATGA
52254165 AGCAAGAACTCCTTCCTCCTTCCTCAGAATTTTCGGCCAAAAGAAGATGAAAAACAAAATTTTTC
66 AGCAAGAACTCCTTCCTCCTTCCTCAGAATTTTCGGCCAAAAGAAGATGAAAAACAAAATTTTTC
52254230 TTTTCTTTTCTTTAACTCACGGCAAT-GGGGGGGAAACAACCACACACTTTTTTTTTGTTTCCAT
131 TTTTCTTTTCTTTAACTCACGGCAATGGGGGGGGAAACAACCACACACTTTTTTTTTGTTTCCAT
52254294 TTCT
196 TTCT
52254298 CATACCTTGATCTAGATACAAGTATGGCCAAACCTCCTCCTAATCCTCTTCCAAACCAAACATGA
1 CATACCTTGATCTAGATACAAGTATGGCCAAACCTCCTCCTAATCCTCTTCCAAACCAAACATGA
52254363 AGCAAGAACTCCTTCCTCCTTCCTCAGAATTTTCGGCCAAAAGAAGATGAAAAACAAAATTTTTC
66 AGCAAGAACTCCTTCCTCCTTCCTCAGAATTTTCGGCCAAAAGAAGATGAAAAACAAAATTTTTC
*
52254428 TTTTCTTTTCTTTAACTCACGGCAATGGGGGGGGGACACAACCACACACTTTTTTTTTGTTTCCA
131 TTTTCTTTTCTTTAACTCACGGCAAT-GGGGGGGGAAACAACCACACACTTTTTTTTTGTTTCCA
52254493 TTTCT
195 TTTCT
52254498 TTATTACCCA
Statistics
Matches: 197, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
198 156 0.79
200 41 0.21
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (199 bp):
CATACCTTGATCTAGATACAAGTATGGCCAAACCTCCTCCTAATCCTCTTCCAAACCAAACATGA
AGCAAGAACTCCTTCCTCCTTCCTCAGAATTTTCGGCCAAAAGAAGATGAAAAACAAAATTTTTC
TTTTCTTTTCTTTAACTCACGGCAATGGGGGGGGAAACAACCACACACTTTTTTTTTGTTTCCAT
TTCT
Found at i:52256812 original size:43 final size:43
Alignment explanation
Indices: 52256752--52256838 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
52256742 TGAGGTATGT
* * *
52256752 AGCATCCGAGATCGTTGAGAGGTCTGAGTTTATTATGGATGCG
1 AGCATCCGAGATAGTTGAGAGGTCTGAGTTCATGATGGATGCG
* * *
52256795 AGCATCCGAGCTAGTTGAGTGGTTTGAGTTCATGATGGATGCG
1 AGCATCCGAGATAGTTGAGAGGTCTGAGTTCATGATGGATGCG
52256838 A
1 A
52256839 TTCATGTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (43 bp):
AGCATCCGAGATAGTTGAGAGGTCTGAGTTCATGATGGATGCG
Found at i:52258359 original size:23 final size:23
Alignment explanation
Indices: 52258332--52258403 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
52258322 TGTCCCAAAG
52258332 CACACGGGCGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
* * **
52258355 CACACGGGC--ATACAAAG----
1 CACACGGGCGTGTGCATTGCCTC
52258372 CACACGGGCGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
52258395 CACACGGGC
1 CACACGGGC
52258404 ATATGAGGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
17 9 0.26
19 4 0.11
21 4 0.11
23 18 0.51
ACGTcount: A:0.21, C:0.35, G:0.29, T:0.15
Consensus pattern (23 bp):
CACACGGGCGTGTGCATTGCCTC
Found at i:52258382 original size:40 final size:40
Alignment explanation
Indices: 52258327--52258406 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
52258317 GGACGTGTCC
52258327 CAAAGCACACGGGCGTGTGCATTGCCTCCACACGGGCATA
1 CAAAGCACACGGGCGTGTGCATTGCCTCCACACGGGCATA
52258367 CAAAGCACACGGGCGTGTGCATTGCCTCCACACGGGCATA
1 CAAAGCACACGGGCGTGTGCATTGCCTCCACACGGGCATA
52258407 TGAGGCTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (40 bp):
CAAAGCACACGGGCGTGTGCATTGCCTCCACACGGGCATA
Found at i:52261314 original size:39 final size:39
Alignment explanation
Indices: 52261230--52261467 Score: 320
Period size: 39 Copynumber: 6.1 Consensus size: 39
52261220 CAAATCCAAT
* * *
52261230 CACCACCAC-AAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGAC-TT-AGCCCGGATATAA
* *
52261270 TACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGAC-TTAGCCCGGATATAA
* *
52261309 CACCAGCACGAATGCCTTCGGGGCTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
*
52261348 CACCAGCAC-AAATGCCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAAA-GCCTTCGGGACTTAGCCCGGATATAA
*
52261387 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
* *
52261426 CACCAACACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
52261465 CAC
1 CAC
52261468 TATTATAAAG
Statistics
Matches: 182, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
38 2 0.01
39 144 0.79
40 36 0.20
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
Found at i:52261376 original size:78 final size:78
Alignment explanation
Indices: 52261247--52261467 Score: 354
Period size: 78 Copynumber: 2.8 Consensus size: 78
52261237 ACAAAGCATG
* *
52261247 CGGGACTTTAAGCCCGGATATAATACCAGCACAAA-GCCTGCGGGACTTTAGCCCGGATATAACA
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAAATGCCTTCGGGAC-TTAGCCCGGATATAACA
52261311 CCAGCACGAATGCCTT
63 CCAGCACGAATGCCTT
* *
52261327 CGGGGCTTAGCCCGGATATAACACCAGCACAAATGCCTTCGAGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA
52261392 GCACGAATGCCTT
66 GCACGAATGCCTT
* *
52261405 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTTCGGGACTTAGCCCGGATATAACAC
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAC
52261468 TATTATAAAG
Statistics
Matches: 132, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
78 116 0.88
79 11 0.08
80 5 0.04
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (78 bp):
CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCA
GCACGAATGCCTT
Found at i:52261437 original size:117 final size:117
Alignment explanation
Indices: 52261257--52261467 Score: 361
Period size: 117 Copynumber: 1.8 Consensus size: 117
52261247 CGGGACTTTA
* *
52261257 AGCCCGGATATAATACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAAT
1 AGCCCGGATATAACACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAACACGAAT
*
52261322 GCCTTCGGGGCTTAGCCCGGATATAACACCAGCACAAATGCCTTCGAGACTT
66 GCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGAGACTT
* *
52261374 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAACACGAA
1 AGCCCGGATATAACACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAACACGAA
52261438 TGCCTTCGGGACTTAGCCCGGATATAACAC
65 TGCCTTCGGGACTTAGCCCGGATATAACAC
52261468 TATTATAAAG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 76 0.86
118 12 0.14
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (117 bp):
AGCCCGGATATAACACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAACACGAAT
GCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGAGACTT
Found at i:52261575 original size:28 final size:28
Alignment explanation
Indices: 52261542--52261623 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
52261532 ATTTAATCAT
* *
52261542 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
52261570 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
52261598 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
52261624 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:52262907 original size:29 final size:29
Alignment explanation
Indices: 52262873--52262953 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
52262863 ATTCACATAT
52262873 ATGTATATGGCCAATTAGGCCCAAATCAC
1 ATGTATATGGCCAATTAGGCCCAAATCAC
* *
52262902 CTGTATATGGCCCATTAGGCCCAAATCAC
1 ATGTATATGGCCAATTAGGCCCAAATCAC
* **
52262931 ATTTATATGGCCTGTTAGGCCCA
1 ATGTATATGGCCAATTAGGCCCA
52262954 GTCACATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (29 bp):
ATGTATATGGCCAATTAGGCCCAAATCAC
Found at i:52265935 original size:29 final size:29
Alignment explanation
Indices: 52265872--52265979 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 29
52265862 TTCACATACC
* * *
52265872 TGTATCTAGCCCATTAAGCCC-AATCATA
1 TGTATATAGCCCATTAGGCCCAAATCACA
* *
52265900 T-TCATATGGCCCATTAGGCCCAAATCACC
1 TGT-ATATAGCCCATTAGGCCCAAATCACA
*
52265929 TGTATATAGCCCATTAGGCCCAAATCAAA
1 TGTATATAGCCCATTAGGCCCAAATCACA
* *
52265958 TTTATATGGCCCATTAGGCCCA
1 TGTATATAGCCCATTAGGCCCA
52265980 GTCATATTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 16 0.24
29 49 0.73
30 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (29 bp):
TGTATATAGCCCATTAGGCCCAAATCACA
Found at i:52265979 original size:58 final size:57
Alignment explanation
Indices: 52265869--52265979 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 57
52265859 AAATTCACAT
* *
52265869 ACCTGTATCTAGCCCATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATAGCCCATTAAGCCCAATCAAATTCATATGGCCCATTAGGCCCAAATC
* *
52265926 ACCTGTATATAGCCCATTAGGCCCAAATCAAATTTATATGGCCCATTAGGCCCA
1 ACCTGTATATAGCCCATTAAGCCC-AATCAAATTCATATGGCCCATTAGGCCCA
52265980 GTCATATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 22 0.45
58 27 0.55
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (57 bp):
ACCTGTATATAGCCCATTAAGCCCAATCAAATTCATATGGCCCATTAGGCCCAAATC
Found at i:52266215 original size:8 final size:8
Alignment explanation
Indices: 52266202--52266252 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
52266192 GTAGCCAAAC
*
52266202 TTTTGGCT
1 TTTTGGCA
52266210 TTTTGGCA
1 TTTTGGCA
** *
52266218 TTTCAGCT
1 TTTTGGCA
52266226 TTTTGGCA
1 TTTTGGCA
*
52266234 TTTCGGCA
1 TTTTGGCA
52266242 TTTTGGC-
1 TTTTGGCA
52266249 TTTT
1 TTTT
52266253 ACCGATTCAT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
7 4 0.12
8 30 0.88
ACGTcount: A:0.08, C:0.16, G:0.22, T:0.55
Consensus pattern (8 bp):
TTTTGGCA
Found at i:52266228 original size:16 final size:16
Alignment explanation
Indices: 52266207--52266248 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52266197 CAAACTTTTG
52266207 GCTTTTTGGCATTTCA
1 GCTTTTTGGCATTTCA
*
52266223 GCTTTTTGGCATTTCG
1 GCTTTTTGGCATTTCA
*
52266239 GCATTTTGGC
1 GCTTTTTGGC
52266249 TTTTACCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.48
Consensus pattern (16 bp):
GCTTTTTGGCATTTCA
Found at i:52281019 original size:25 final size:25
Alignment explanation
Indices: 52280985--52281038 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
52280975 TCCAAAAAGA
*
52280985 TTCTGACGTGAGTTTTCTTCCTCTT
1 TTCTGACGTGAGTTTTCTTCCCCTT
52281010 TTCTGACGTGAGTTTTCTTCCCCTT
1 TTCTGACGTGAGTTTTCTTCCCCTT
52281035 TTCT
1 TTCT
52281039 TCTCTTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.07, C:0.26, G:0.15, T:0.52
Consensus pattern (25 bp):
TTCTGACGTGAGTTTTCTTCCCCTT
Found at i:52283983 original size:20 final size:20
Alignment explanation
Indices: 52283955--52283994 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52283945 TTGGAAGATG
*
52283955 AGAAAAAAAGATGAGAGAAA
1 AGAAAAAAAGAGGAGAGAAA
* *
52283975 AGAATAAAAGGGGAGAGAAA
1 AGAAAAAAAGAGGAGAGAAA
52283995 CAAAATGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (20 bp):
AGAAAAAAAGAGGAGAGAAA
Found at i:52284085 original size:28 final size:27
Alignment explanation
Indices: 52284052--52284106 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
52284042 AGAGGATAGA
*
52284052 AAAAGGTAAG-GAGTGAAACAAGAGGGAG
1 AAAAGGAAAGAGAG-GAAACAAG-GGGAG
*
52284080 AAAAGGAAAGAGAGGGAACAAGGGGAG
1 AAAAGGAAAGAGAGGAAACAAGGGGAG
52284107 TGAAAGGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 16 0.67
29 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.42, T:0.04
Consensus pattern (27 bp):
AAAAGGAAAGAGAGGAAACAAGGGGAG
Found at i:52285412 original size:20 final size:18
Alignment explanation
Indices: 52285383--52285422 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
52285373 TGTTTAGTAA
52285383 TGCTTAAAAAAATCACTTTT
1 TGCTT-AAAAAA-CACTTTT
*
52285403 TGCTTGAAAAACACTTTT
1 TGCTTAAAAAACACTTTT
52285421 TG
1 TG
52285423 AAGAAAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 5 0.26
20 5 0.26
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (18 bp):
TGCTTAAAAAACACTTTT
Found at i:52286138 original size:13 final size:13
Alignment explanation
Indices: 52286120--52286172 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
52286110 CTTAAACTAA
52286120 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
52286133 ACTTTTCTATAGC
1 ACTTTTCAAAAGC
* * *
52286146 ATTTTTAAAAAAC
1 ACTTTTCAAAAGC
*
52286159 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
52286172 A
1 A
52286173 ATGCTAAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:52286580 original size:33 final size:33
Alignment explanation
Indices: 52286500--52286582 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
52286490 TTTCACTAAG
* *
52286500 TAAAGACAAAA-TTAAACTTGGTTACTAAAGGC
1 TAAAGACAAAAGTTAAACTTGATTACTAAAGAC
* * * *
52286532 TATAGACAAAGGTTAAACTTGATTCCTAAATAC
1 TAAAGACAAAAGTTAAACTTGATTACTAAAGAC
*
52286565 TAAAGATAAAAGTTAAAC
1 TAAAGACAAAAGTTAAAC
52286583 ATAGTACAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 9 0.22
33 32 0.78
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (33 bp):
TAAAGACAAAAGTTAAACTTGATTACTAAAGAC
Found at i:52287700 original size:29 final size:29
Alignment explanation
Indices: 52287663--52287720 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
52287653 AAAAACCTTG
52287663 TACGATAAAAACCTAATAAAGGAAAAAGA
1 TACGATAAAAACCTAATAAAGGAAAAAGA
*
52287692 TACGATAAAAACCTAATGAAGGAAAAAGA
1 TACGATAAAAACCTAATAAAGGAAAAAGA
52287721 GTATACAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.14
Consensus pattern (29 bp):
TACGATAAAAACCTAATAAAGGAAAAAGA
Found at i:52289623 original size:27 final size:25
Alignment explanation
Indices: 52289586--52289697 Score: 89
Period size: 27 Copynumber: 4.2 Consensus size: 25
52289576 AGCATGACTG
*
52289586 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTG-CAGAGCCA
* * *
52289612 CCAGATACAGATATTCGTTGTAGAACCA
1 CCAGA-ACAGATAAT-G-TGCAGAGCCA
*
52289640 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGT-GCAGAGCCA
* *
52289667 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGT-GCAGAGCCA
52289694 CCAG
1 CCAG
52289698 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 7 0.10
27 48 0.70
28 12 0.17
29 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (25 bp):
CCAGAACAGATAATGTGCAGAGCCA
Found at i:52289695 original size:54 final size:54
Alignment explanation
Indices: 52289586--52289697 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
52289576 AGCATGACTG
* * * *
52289586 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATATTCGTTGTAGAACCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATATTCGTGGCAGAACCA
* * *
52289640 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATT-GTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGAT-ATTCGTGGCAGAACCA
52289694 CCAG
1 CCAG
52289698 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
54 28 0.57
55 21 0.43
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATATTCGTGGCAGAACCA
Found at i:52291140 original size:24 final size:24
Alignment explanation
Indices: 52291125--52291183 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
52291115 CCTTATCTGA
* *
52291125 TCCTAAATCCTATCCCTCATCAAG
1 TCCTAAATCCTATCCCTTATCAAC
52291149 TCCTAAATCCTATCCCTTATCAAC
1 TCCTAAATCCTATCCCTTATCAAC
52291173 TCCTAAATCCT
1 TCCTAAATCCT
52291184 CTCCTGACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.37, G:0.02, T:0.32
Consensus pattern (24 bp):
TCCTAAATCCTATCCCTTATCAAC
Found at i:52297470 original size:27 final size:26
Alignment explanation
Indices: 52297435--52297546 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
52297425 AGCATGGCTG
* *
52297435 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
52297461 CCAGATACAGATAATTGTGGCAGAACCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
*
52297489 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
52297516 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
52297543 CCAG
1 CCAG
52297547 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.70
28 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:52297527 original size:54 final size:54
Alignment explanation
Indices: 52297435--52297546 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
52297425 AGCATGGCTG
* *
52297435 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATTGTGGCAGAACCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATTGTGGCAGAACCA
* * *
52297489 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATTGTGGCAGAACCA
52297543 CCAG
1 CCAG
52297547 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATTGTGGCAGAACCA
Found at i:52298981 original size:24 final size:24
Alignment explanation
Indices: 52298954--52299024 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
52298944 CTAGATTTCC
**
52298954 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
52298978 TCCCTCATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
52299002 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
52299025 CTCCTGACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.25, C:0.39, G:0.01, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:52300525 original size:40 final size:37
Alignment explanation
Indices: 52300443--52300538 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 37
52300433 ACCATCTCCG
* * *
52300443 TCCAACCCAACACACCATGTGGGGAAAAATTGACCCA
1 TCCATCCCAACACACCATATGGGGAAAAATCGACCCA
* *
52300480 CCCATCCCAACACACCGTATATGGGGATATAATCGACCCA
1 TCCATCCCAACACACC--ATATGGGGA-AAAATCGACCCA
*
52300520 TCCATCCCTACACACCATA
1 TCCATCCCAACACACCATA
52300539 CAGTACCACA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
37 14 0.29
38 3 0.06
39 8 0.16
40 24 0.49
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.17
Consensus pattern (37 bp):
TCCATCCCAACACACCATATGGGGAAAAATCGACCCA
Found at i:52306683 original size:22 final size:22
Alignment explanation
Indices: 52306644--52306685 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52306634 TGCTGACCAT
*
52306644 TCTCCTCTTCTTTCTTTTCTCC
1 TCTCCTCTTCATTCTTTTCTCC
52306666 TCTCCTCTTCAATT-TTTTCT
1 TCTCCTCTTC-ATTCTTTTCT
52306686 TTTTCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.60
Consensus pattern (22 bp):
TCTCCTCTTCATTCTTTTCTCC
Found at i:52307087 original size:23 final size:23
Alignment explanation
Indices: 52307061--52307109 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
52307051 AAATTGAGTA
*
52307061 GAAATTAATTGGGATCATTGGCC
1 GAAATTAATTGGGATCATTAGCC
52307084 GAAATTAATTGGGATCATTAGCC
1 GAAATTAATTGGGATCATTAGCC
52307107 GAA
1 GAA
52307110 GGAACCGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (23 bp):
GAAATTAATTGGGATCATTAGCC
Found at i:52307606 original size:26 final size:26
Alignment explanation
Indices: 52307577--52307633 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
52307567 TTACAATTTT
52307577 ACCCCTAGGAGATAAATTACCAAAAA
1 ACCCCTAGGAGATAAATTACCAAAAA
* *
52307603 A-CCCTAGGAGATAAATTACCGAAAT
1 ACCCCTAGGAGATAAATTACCAAAAA
52307628 ACCCCT
1 ACCCCT
52307634 CGGGTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (26 bp):
ACCCCTAGGAGATAAATTACCAAAAA
Found at i:52321676 original size:12 final size:14
Alignment explanation
Indices: 52321661--52321692 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52321651 GTGAGAACAC
52321661 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
52321673 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
52321687 ATGTGT
1 ATGTGT
52321693 TTAAGACGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:52321934 original size:151 final size:152
Alignment explanation
Indices: 52321658--52321959 Score: 446
Period size: 151 Copynumber: 2.0 Consensus size: 152
52321648 GTTGTGAGAA
* * * * * *
52321658 CACATGTGTAGTACTATGTGTAGGCTACTATGTGTTTAAGACGGTTTTAGGTCATGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAAGCTACTACGTGTATAAGACGG-TTTAGGTCAAGTGTGTAGTA
** * *
52321723 CTAAGTGCAGGCTGCCACATGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
65 CTAAGTGCAGGCCACCACATGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAATGCAGGCTAC
* *
52321788 TATGCGTACCCGATAGCTTCAAT
130 TATGCGTACCAGAGAGCTTCAAT
* *
52321811 CACATGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGG-TTAGGTCAAGTGTGTAGTAC
1 CACATGTGTAGTACTAAGTGCAAGCTACTACGTGTATAAGACGGTTTAGGTCAAGTGTGTAGTAC
52321875 TAAGTGCAGGCCACTC-CATGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAATGCAGGCTAC
66 TAAGTGCAGGCCAC-CACATGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAATGCAGGCTAC
52321939 TATGCGTACCAGAGAGCTTCA
130 TATGCGTACCAGAGAGCTTCA
52321960 GTTACAAGGG
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
151 96 0.72
152 1 0.01
153 37 0.28
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (152 bp):
CACATGTGTAGTACTAAGTGCAAGCTACTACGTGTATAAGACGGTTTAGGTCAAGTGTGTAGTAC
TAAGTGCAGGCCACCACATGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAATGCAGGCTACT
ATGCGTACCAGAGAGCTTCAAT
Found at i:52321948 original size:50 final size:50
Alignment explanation
Indices: 52321714--52321951 Score: 241
Period size: 50 Copynumber: 4.7 Consensus size: 50
52321704 TTAGGTCATG
* * ***
52321714 TGTGTAGTACTAAGTGCAGGCTGCCACATGTACCAGATTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGTTAGGTCGCA
* * * *
52321764 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCA-ATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG-TT-AGGTCGCA
* * * * * *
52321815 TGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAGGTC-AA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGTTAGGTCGCA
* *
52321864 GTGTGTAGTACTAAGTGCAGGCCACTCCAT--GTACCAAATTGTTAGGTCGCA
1 -TGTGTAGTACTAAGTGCAGGCTACT--ATGCGTACCAGATTGTTAGGTCGCA
*
52321915 TGTGTAGTACTAAATGCAGGCTACTATGCGTACCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
52321952 GAGCTTCAGT
Statistics
Matches: 152, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
48 2 0.01
49 2 0.01
50 105 0.69
51 41 0.27
52 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGTTAGGTCGCA
Found at i:52338187 original size:48 final size:48
Alignment explanation
Indices: 52338072--52338349 Score: 193
Period size: 48 Copynumber: 5.7 Consensus size: 48
52338062 TACGTGAGGT
* ** *
52338072 AGTGTAAGACCATGTTCGGGACATGG--TAGCGACACCGTTGTGTGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATAG-G-CATTGTTATGT--GAGCC
*
52338122 AATGTAAGACCATGTTTGGGACATGGCATAGGCATTGTTATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATAGGCATTGTTATGTGAGCC
* * * * * *
52338170 AGTGTAAGACCATGTTTGGAACATGGCATCGGCGTTGATATGTGTGTGCA
1 AGTGTAAGACCATGTTTGGGACATGGCATAGGCATTG-T-TATGTGAGCC
* * * ** * * *
52338220 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATAGGCATTGTTATGTGAGCC
* * * ** * * **
52338268 AGTGTAAGTCCATGTCTAGGACACAGCATCAGTC-TCGACATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCAT-AGGCATTGTTATGTGAGCC
* * *
52338316 AATGTAAGACCATGTTTGAGACATGGCATCGGCA
1 AGTGTAAGACCATGTTTGGGACATGGCATAGGCA
52338350 ATTTACCTTC
Statistics
Matches: 179, Mismatches: 43, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
47 2 0.01
48 98 0.55
49 3 0.02
50 72 0.40
51 1 0.01
52 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATAGGCATTGTTATGTGAGCC
Found at i:52338297 original size:98 final size:95
Alignment explanation
Indices: 52338117--52338346 Score: 248
Period size: 98 Copynumber: 2.4 Consensus size: 95
52338107 CGTTGTGTGA
* * ** * *
52338117 GAGCCAATGTAAGACCATGTTTGGGACATGGCATAGGCATTGTTATGTGAGCCAGTGTAAGACCA
1 GAGCCAATGTAAGACCATGTTTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACCA
* * *
52338182 TGTTTGGAACATGGCATC-GGCGTTGATATGT
66 TGTTAGGAACA-GGCATCAGGC-TCGACATGT
* * * * *
52338213 GTGTGCAAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGTC
1 GAG-CCAA-TGTAAGACCATGTTTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGAC
*
52338278 CATGTCTAGGACACA-GCATCAGTCTCGACATGT
64 CATGT-TAGGA-ACAGGCATCAGGCTCGACATGT
*
52338311 GAGCCAATGTAAGACCATGTTTGAGACATGGCATCG
1 GAGCCAATGTAAGACCATGTTTGGGACATGGCATCG
52338347 GCAATTTACC
Statistics
Matches: 110, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
96 29 0.26
97 6 0.05
98 66 0.60
99 6 0.05
100 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (95 bp):
GAGCCAATGTAAGACCATGTTTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACCA
TGTTAGGAACAGGCATCAGGCTCGACATGT
Found at i:52340352 original size:24 final size:23
Alignment explanation
Indices: 52340325--52340370 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
52340315 CATTCCGCCT
* *
52340325 TGTTTCAATTCTAGAAATTCTTTA
1 TGTTTCAAATCAAGAAA-TCTTTA
52340349 TGTTTCAAATCAAGAAATCTTT
1 TGTTTCAAATCAAGAAATCTTT
52340371 GACTTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (23 bp):
TGTTTCAAATCAAGAAATCTTTA
Found at i:52342686 original size:43 final size:43
Alignment explanation
Indices: 52342639--52342733 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
52342629 TACCAAACAG
* * * *
52342639 GGTCTTACACGAAATC-GATTAACAATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAATCTCAAT-ACAATACCAATATCCCAGACAT
* * *
52342682 GGTCTTACATGTAATCTCAATACAATATCAATATCCCAGACAT
1 GGTCTTACACGAAATCTCAATACAATACCAATATCCCAGACAT
52342725 GGTCTTACA
1 GGTCTTACA
52342734 TGTTATCACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 42 0.95
44 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGAAATCTCAATACAATACCAATATCCCAGACAT
Found at i:52346460 original size:40 final size:40
Alignment explanation
Indices: 52346418--52346561 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
52346408 TGGCTAATTT
* *
52346418 CGGGCTAAGTCCCGAAGGCGTTCGTGCGAGCTACTATATT
1 CGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTACTATATC
*
52346458 CGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATATC
1 CGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTACTATATC
* * * *
52346498 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTACTATATC
*
52346538 CGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCGTTTG
52346562 AGCTAGTGGC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTACTATATC
Found at i:52346575 original size:40 final size:39
Alignment explanation
Indices: 52346377--52346584 Score: 206
Period size: 40 Copynumber: 5.2 Consensus size: 39
52346367 CGGATGATAA
* * *
52346377 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTATA-T
* * *
52346417 TCGGGCTAAGTCCCGAAGGCGTTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
52346457 TCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
52346497 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
52346537 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATAT
52346577 CC-GGCTAA
1 CCGGGCTAA
52346585 ACTCCGAAGG
Statistics
Matches: 146, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
39 7 0.05
40 135 0.92
41 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:52346576 original size:80 final size:80
Alignment explanation
Indices: 52346373--52346584 Score: 261
Period size: 80 Copynumber: 2.7 Consensus size: 80
52346363 TGTTCGGATG
*
52346373 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTTCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTATA-TCCGGGCTAAGTCCCGAAGG
* *
52346436 CGTTCGTGCGAGCTACT
64 CATTCGTGCAAGCTACT
** * * * **
52346453 ATATTCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCT-ATTATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TGGCTATATCCGGGCTAAGTCCCGAAGGC
* *
52346517 ATTTGTGCAAGTTACT
65 ATTCGTGCAAGCTACT
52346533 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAA
52346585 ACTCCGAAGG
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
79 7 0.06
80 98 0.90
81 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACT
Found at i:52354527 original size:40 final size:40
Alignment explanation
Indices: 52354429--52354678 Score: 324
Period size: 40 Copynumber: 6.3 Consensus size: 40
52354419 TCCTCGTTCA
* * * ** *
52354429 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
52354468 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
52354508 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
52354548 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
52354588 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * ** * *
52354628 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAACAACTCGCACG
52354668 AATGCCTTCGG
1 AATGCCTTCGG
52354679 ATCTTAGTCC
Statistics
Matches: 196, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
39 34 0.17
40 158 0.81
41 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:52354572 original size:80 final size:79
Alignment explanation
Indices: 52354429--52354731 Score: 349
Period size: 80 Copynumber: 3.8 Consensus size: 79
52354419 TCCTCGTTCA
* * * * *
52354429 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
52354494 TAACAACTCGCACG
66 TAACAACTCGCACG
**
52354508 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
52354573 TTAACAACTCGCACG
65 TTAACAACTCGCACG
* * *
52354588 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGG-A
** * *
52354653 TTT-GTATCTCGCACA
64 TTTAACAACTCGCACG
** * * * * * *
52354668 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
52354732 CAGCATTCAA
Statistics
Matches: 193, Mismatches: 27, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
79 37 0.19
80 147 0.76
81 9 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:52354691 original size:120 final size:119
Alignment explanation
Indices: 52354427--52354731 Score: 337
Period size: 120 Copynumber: 2.5 Consensus size: 119
52354417 GCTCCTCGTT
* * ** * *
52354427 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
* *
52354492 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
66 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* *
52354546 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAACAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** * * ** *
52354611 ATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
65 ATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGG-ATTTAACAACTCGCA
* * * * * *
52354666 CAAATGCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTA-ACAAC-TCGCACAATGCCTTCGGGACTTAACCC
52354729 GGA
63 GGA
52354732 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.24
120 109 0.70
121 10 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:52354740 original size:41 final size:41
Alignment explanation
Indices: 52354663--52354740 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52354653 TTTGTATCTC
* * *
52354663 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52354704 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52354741 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52360601 original size:29 final size:29
Alignment explanation
Indices: 52360566--52360643 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
52360556 CATATTTTAT
*
52360566 TGATTTGGCTTCGGGCCATGCATATCGAA
1 TGATTTGGCTTCGAGCCATGCATATCGAA
52360595 TGATTTGGCTTCGAGCCATGCATATCGAA
1 TGATTTGGCTTCGAGCCATGCATATCGAA
* *
52360624 TGATTTGGCTTTGAGACATG
1 TGATTTGGCTTCGAGCCATG
52360644 ATAATAGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (29 bp):
TGATTTGGCTTCGAGCCATGCATATCGAA
Found at i:52366941 original size:93 final size:93
Alignment explanation
Indices: 52366782--52366968 Score: 288
Period size: 93 Copynumber: 2.0 Consensus size: 93
52366772 ACACGGGGTT
* *
52366782 GAAGAAGCTACGTGGGAACCCGACGATGCTATGGGAAAGCAATACCTGGACCTATTCACTGATAA
1 GAAGAAGCTACATGGGAACCCGACGATGCTATGAGAAAGCAATACCTGGACCTATTCACTGATAA
** *
52366847 GATT-TTTTGAGGATGAAAATCCCTAAGG
66 GATTGTTCAG-GGACGAAAATCCCTAAGG
*
52366875 GAAGAAGCTACATGGGAACCCGACGATG-TAATGAGAAAGCAATACCTGGACCTATTCACTGGTA
1 GAAGAAGCTACATGGGAACCCGACGATGCT-ATGAGAAAGCAATACCTGGACCTATTCACTGATA
52366939 AGATTGTTCAGGGACGAAAATCCCTAAGG
65 AGATTGTTCAGGGACGAAAATCCCTAAGG
52366968 G
1 G
52366969 GGGAGAGTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
92 1 0.01
93 82 0.95
94 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (93 bp):
GAAGAAGCTACATGGGAACCCGACGATGCTATGAGAAAGCAATACCTGGACCTATTCACTGATAA
GATTGTTCAGGGACGAAAATCCCTAAGG
Found at i:52381790 original size:28 final size:28
Alignment explanation
Indices: 52381745--52381847 Score: 152
Period size: 28 Copynumber: 3.7 Consensus size: 28
52381735 TGGCCCCTTT
* * *
52381745 AGGCCTAATCTCATTCATATGGCCTATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
52381773 GGGTCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
52381801 AGGCCCAATCACTTTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
52381829 AGGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
52381848 GTCATGCAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:52385767 original size:23 final size:23
Alignment explanation
Indices: 52385740--52385911 Score: 177
Period size: 23 Copynumber: 7.4 Consensus size: 23
52385730 TCATCTCATA
*
52385740 AGAGCTTACTATTTCAGCTCATT
1 AGAGCTTACTATTTCAGCTCAAT
* * *
52385763 GGAGCTTACCA-TTCAGCTCGAT
1 AGAGCTTACTATTTCAGCTCAAT
*
52385785 AGAGCTTACTGTTT-AGCTCAAT
1 AGAGCTTACTATTTCAGCTCAAT
*
52385807 AGAGCTTACCATTTCAGCTCAAT
1 AGAGCTTACTATTTCAGCTCAAT
* *
52385830 AGAGCTTACTGTTTTAGCTCAAT
1 AGAGCTTACTATTTCAGCTCAAT
* ** *
52385853 AGAGCTTACCAACTCAGCTCATT
1 AGAGCTTACTATTTCAGCTCAAT
* *
52385876 AGAGCTTACTATTCATTAGCTCAAG
1 AGAGCTTACTATT--TCAGCTCAAT
52385901 AGGAGCTTACT
1 A-GAGCTTACT
52385912 GATCATGGCT
Statistics
Matches: 119, Mismatches: 25, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
22 36 0.30
23 66 0.55
25 8 0.07
26 9 0.08
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (23 bp):
AGAGCTTACTATTTCAGCTCAAT
Found at i:52385863 original size:46 final size:45
Alignment explanation
Indices: 52385740--52385910 Score: 209
Period size: 46 Copynumber: 3.7 Consensus size: 45
52385730 TCATCTCATA
* * * *
52385740 AGAGCTTACTATTTCAGCTCATTGGAGCTTACCATTCAGCTCGAT
1 AGAGCTTACTATTTTAGCTCAATAGAGCTTACCATTCAGCTCAAT
*
52385785 AGAGCTTACT-GTTTAGCTCAATAGAGCTTACCATTTCAGCTCAAT
1 AGAGCTTACTATTTTAGCTCAATAGAGCTTACCA-TTCAGCTCAAT
* * *
52385830 AGAGCTTACTGTTTTAGCTCAATAGAGCTTACCAACTCAGCTCATT
1 AGAGCTTACTATTTTAGCTCAATAGAGCTTACC-ATTCAGCTCAAT
*
52385876 AGAGCTTACTATTCATTAGCTCAAGAGGAGCTTAC
1 AGAGCTTACTATT--TTAGCTCAATA-GAGCTTAC
52385911 TGATCATGGC
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
44 19 0.17
45 30 0.27
46 42 0.38
47 1 0.01
48 10 0.09
49 8 0.07
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
AGAGCTTACTATTTTAGCTCAATAGAGCTTACCATTCAGCTCAAT
Found at i:52388143 original size:41 final size:41
Alignment explanation
Indices: 52388086--52388167 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
52388076 AGGACATCGG
* *
52388086 AAGAGATCTCAGTAGTAGTCGTCGCGAATCAGGTGTGTACC
1 AAGAGATCTCAGTAGTAGTCATCGCGAATCAGGGGTGTACC
52388127 AAGAGATCTCAGTAGTAGTCATCGCGAATCAGGGGTGTACC
1 AAGAGATCTCAGTAGTAGTCATCGCGAATCAGGGGTGTACC
52388168 GAACACCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
AAGAGATCTCAGTAGTAGTCATCGCGAATCAGGGGTGTACC
Found at i:52388369 original size:20 final size:21
Alignment explanation
Indices: 52388330--52388369 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52388320 GTACTTCGGG
*
52388330 AAAACAGGGCCTCGATGGGCC
1 AAAACAGGGCCTCAATGGGCC
*
52388351 AAAACTGGGCC-CAATGGGC
1 AAAACAGGGCCTCAATGGGC
52388370 TTACGGACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.28, G:0.33, T:0.10
Consensus pattern (21 bp):
AAAACAGGGCCTCAATGGGCC
Found at i:52391678 original size:45 final size:45
Alignment explanation
Indices: 52391623--52391712 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
52391613 TGGAAGTGGG
52391623 AAAGAATAACAATGGACTTTGTGAGTGGGTTACCTGTGACACCCA
1 AAAGAATAACAATGGACTTTGTGAGTGGGTTACCTGTGACACCCA
* *
52391668 AAAGAGTAACAATGGACTTTGTGAGTGGGTTACCTTTGACACCCA
1 AAAGAATAACAATGGACTTTGTGAGTGGGTTACCTGTGACACCCA
52391713 CCAAGAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (45 bp):
AAAGAATAACAATGGACTTTGTGAGTGGGTTACCTGTGACACCCA
Found at i:52396294 original size:13 final size:13
Alignment explanation
Indices: 52396276--52396303 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52396266 ACATATTATA
52396276 AATATTTTGTGTT
1 AATATTTTGTGTT
52396289 AATATTTTGTGTT
1 AATATTTTGTGTT
52396302 AA
1 AA
52396304 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
AATATTTTGTGTT
Found at i:52397089 original size:12 final size:12
Alignment explanation
Indices: 52397068--52397110 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
52397058 ACCACATAAG
52397068 TATATATATACT
1 TATATATATACT
* *
52397080 TATATGTATAAGT
1 TATATATAT-ACT
52397093 ATATATATATACT
1 -TATATATATACT
52397106 TATAT
1 TATAT
52397111 GTATGTTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 13 0.52
13 4 0.16
14 8 0.32
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (12 bp):
TATATATATACT
Found at i:52397790 original size:40 final size:40
Alignment explanation
Indices: 52397742--52397907 Score: 257
Period size: 40 Copynumber: 4.2 Consensus size: 40
52397732 GGACTAAGAT
52397742 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
52397782 CCGAAGGCATTTGTGCTAGTTACTATAAT-CGGACTAAGAT-
1 CCGAAGGCATTTGTGCTAGTTACTAT-ATCCGGGCTAAG-TC
52397822 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * *
52397862 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
52397901 CCGAAGG
1 CCGAAGG
52397908 TACTTGGGTT
Statistics
Matches: 117, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
39 18 0.15
40 96 0.82
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:52397864 original size:80 final size:80
Alignment explanation
Indices: 52397726--52397907 Score: 305
Period size: 80 Copynumber: 2.3 Consensus size: 80
52397716 TATTCGGATG
52397726 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
52397791 TTTGTGCTAGTTACT
66 TTTGTGCGAGTTACT
*
52397806 ATAATCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
52397871 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTACT
*
52397886 ATATCCGG-CTAA-ATCCCGAAGG
1 ATAACCGGACTAAGAT-CCGAAGG
52397908 TACTTGGGTT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
78 2 0.02
79 11 0.11
80 83 0.86
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (80 bp):
ATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:52414082 original size:23 final size:23
Alignment explanation
Indices: 52414056--52414113 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
52414046 ATCACAGTGT
*
52414056 AGCTGCTAATAGTAATGCAGCAA
1 AGCTGCTAATAGAAATGCAGCAA
*
52414079 AGCTGCTAATAAAAATGCAGCAA
1 AGCTGCTAATAGAAATGCAGCAA
52414102 AGCTGCTAATAG
1 AGCTGCTAATAG
52414114 CGGTAAACGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (23 bp):
AGCTGCTAATAGAAATGCAGCAA
Found at i:52414749 original size:18 final size:18
Alignment explanation
Indices: 52414726--52414760 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52414716 CAGAGAAGCA
52414726 GGCCCATGTGGCCCATTG
1 GGCCCATGTGGCCCATTG
*
52414744 GGCCCATTTGGCCCATT
1 GGCCCATGTGGCCCATT
52414761 AAGGCCCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.29, T:0.26
Consensus pattern (18 bp):
GGCCCATGTGGCCCATTG
Found at i:52422522 original size:33 final size:33
Alignment explanation
Indices: 52422484--52422546 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
52422474 TACAGTAACG
* * *
52422484 GTCTAGGCCTGAGCCCTATTCATTAACAGTATA
1 GTCTAGGCCTAAGCCCTATGCAGTAACAGTATA
52422517 GTCTAGGCCTAAGCCCTATGCAGTAACAGT
1 GTCTAGGCCTAAGCCCTATGCAGTAACAGT
52422547 GTGGGCCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (33 bp):
GTCTAGGCCTAAGCCCTATGCAGTAACAGTATA
Found at i:52430231 original size:40 final size:40
Alignment explanation
Indices: 52430148--52430410 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
52430138 TTGAATGCTG
* * * * * *
52430148 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
52430188 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
52430228 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
52430268 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
52430308 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52430348 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52430387 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52430411 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:52430430 original size:79 final size:80
Alignment explanation
Indices: 52430187--52430445 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
52430177 AAGTGAATAT
* * * * * *
52430187 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
52430251 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
52430267 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
52430332 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
52430347 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
52430411 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
52430426 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
52430446 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:52438304 original size:39 final size:40
Alignment explanation
Indices: 52438100--52438322 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
52438090 TTGAATGCTG
* * * * * *
52438100 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
52438140 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
52438180 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
52438220 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
52438260 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
52438299 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52438323 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:52438342 original size:79 final size:80
Alignment explanation
Indices: 52438175--52438357 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
52438165 GTGCGAGATA
* * *
52438175 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
52438240 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
52438255 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
52438319 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
52438334 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
52438358 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:52442963 original size:20 final size:20
Alignment explanation
Indices: 52442897--52442963 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
52442887 ATTTTGATAA
*
52442897 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
52442917 ACGTGACATGTATGATATGC
1 ACATGATATGTATGATATGC
52442937 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52442957 ACATGAT
1 ACATGAT
52442964 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52443081 original size:25 final size:24
Alignment explanation
Indices: 52443013--52443089 Score: 120
Period size: 23 Copynumber: 3.2 Consensus size: 24
52443003 GAGGAAGTAC
*
52443013 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
52443037 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
52443060 AAAAGGGCTTTTTGCCCCAGTTATT
1 AAAAGGGC-TTATGCCCCAGTTATT
52443085 AAAAG
1 AAAAG
52443090 AGACTAGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
23 22 0.45
24 7 0.14
25 20 0.41
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:52443339 original size:31 final size:31
Alignment explanation
Indices: 52443298--52443360 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
52443288 CGTTTACAGT
*
52443298 AAAGACTTCGGCCTAGTAATATGAAATATGA
1 AAAGACTTCGGCCCAGTAATATGAAATATGA
* **
52443329 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGACTTCGGCCCAGTAATATGAAATATGA
52443360 A
1 A
52443361 GTGTTAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGACTTCGGCCCAGTAATATGAAATATGA
Found at i:52443693 original size:37 final size:37
Alignment explanation
Indices: 52443652--52443731 Score: 160
Period size: 37 Copynumber: 2.2 Consensus size: 37
52443642 CAATTCATCA
52443652 CATACTCTTTTAACCATTCCAACAAGTATCAAATGGC
1 CATACTCTTTTAACCATTCCAACAAGTATCAAATGGC
52443689 CATACTCTTTTAACCATTCCAACAAGTATCAAATGGC
1 CATACTCTTTTAACCATTCCAACAAGTATCAAATGGC
52443726 CATACT
1 CATACT
52443732 AACACATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (37 bp):
CATACTCTTTTAACCATTCCAACAAGTATCAAATGGC
Done.