Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 58 of 187
Found at i:17240067 original size:88 final size:88
Alignment explanation
Indices: 17239959--17240437 Score: 742
Period size: 88 Copynumber: 5.4 Consensus size: 88
17239949 GTTGGGGTCA
* * * *
17239959 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTATCCTACTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
*
17240024 CCAGGGAGGCAAGGCTGGTGTTT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17240047 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATATACTATTTTTAGCTTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
*
17240112 CCAGGGAGGCAAGGCTGGTGTTT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * ** * *
17240135 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAGCTTGTTCCACTGGAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
*
17240200 CAAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17240223 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATATACTATTTTTAGCTTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
17240288 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
17240311 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTGCTTCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
*
17240376 CCAAGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
17240399 TCGATTTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTG
17240438 TTATCTTCAT
Statistics
Matches: 359, Mismatches: 32, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 359 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCTTACTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:17246462 original size:36 final size:34
Alignment explanation
Indices: 17246417--17246484 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
17246407 CATATTACAA
*
17246417 AAAATGTATAAACATATAT-AAATTATAGAATATGGG
1 AAAACGTATAAACAT-TATGAAA-TATA-AATATGGG
*
17246453 AAAACGTATAAATATTATGAAATATAAATATG
1 AAAACGTATAAACATTATGAAATATAAATATG
17246485 TTTATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.21
35 7 0.24
36 16 0.55
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (34 bp):
AAAACGTATAAACATTATGAAATATAAATATGGG
Found at i:17246633 original size:20 final size:17
Alignment explanation
Indices: 17246608--17246663 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
17246598 TATGCGCACC
*
17246608 TATATATAGGTATAATAA
1 TATATATA-ATATAATAA
17246626 TATATATAATATAATAA
1 TATATATAATATAATAA
* *
17246643 TAATATTTAAAATAATAA
1 T-ATATATAATATAATAA
17246661 TAT
1 TAT
17246664 CAATACTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TATATATAATATAATAA
Found at i:17249723 original size:16 final size:16
Alignment explanation
Indices: 17249698--17249733 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
17249688 GAATTTTTAT
*
17249698 ATATTTTTTAGTATTAA
1 ATATTTTTAAG-ATTAA
17249715 ATATTTTTAAGATTAA
1 ATATTTTTAAGATTAA
17249731 ATA
1 ATA
17249734 ACATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATTTTTAAGATTAA
Found at i:17252958 original size:20 final size:20
Alignment explanation
Indices: 17252935--17253001 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
17252925 AGTGTATTTG
17252935 CAATACTGATGGCTTGTCCA
1 CAATACTGATGGCTTGTCCA
** * * *
17252955 CAATACTGACAGTTTATCTA
1 CAATACTGATGGCTTGTCCA
17252975 CAATACTGATGGCTTGTCCA
1 CAATACTGATGGCTTGTCCA
*
17252995 TAATACT
1 CAATACT
17253002 AACAGTTTAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (20 bp):
CAATACTGATGGCTTGTCCA
Found at i:17252979 original size:40 final size:40
Alignment explanation
Indices: 17252920--17253021 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
17252910 GGAGGAAGAT
* * *
17252920 CTGACAGTGTATTTGCAATACTGATGGCTTGTCCACAATA
1 CTGACAGTTTATCTACAATACTGATGGCTTGTCCACAATA
*
17252960 CTGACAGTTTATCTACAATACTGATGGCTTGTCCATAATA
1 CTGACAGTTTATCTACAATACTGATGGCTTGTCCACAATA
* *
17253000 CTAACAGTTTATCTATAATACT
1 CTGACAGTTTATCTACAATACT
17253022 TGTAACTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (40 bp):
CTGACAGTTTATCTACAATACTGATGGCTTGTCCACAATA
Found at i:17253017 original size:20 final size:20
Alignment explanation
Indices: 17252956--17253021 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
17252946 GCTTGTCCAC
*
17252956 AATACTGACAGTTTATCTAC
1 AATACTGACAGTTTATCTAT
** * * *
17252976 AATACTGATGGCTTGTCCAT
1 AATACTGACAGTTTATCTAT
*
17252996 AATACTAACAGTTTATCTAT
1 AATACTGACAGTTTATCTAT
17253016 AATACT
1 AATACT
17253022 TGTAACTTGT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
AATACTGACAGTTTATCTAT
Found at i:17253031 original size:40 final size:40
Alignment explanation
Indices: 17252935--17253036 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
17252925 AGTGTATTTG
** *
17252935 CAATACTGATGGCTTGTCCACAATACTGACAGTTTATCTA
1 CAATACTGATAACTTGTCCACAATACTAACAGTTTATCTA
** *
17252975 CAATACTGATGGCTTGTCCATAATACTAACAGTTTATCTA
1 CAATACTGATAACTTGTCCACAATACTAACAGTTTATCTA
*
17253015 TAATACTTG-TAACTTGTCCACA
1 CAATAC-TGATAACTTGTCCACA
17253037 TATTTTTGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 53 0.96
41 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (40 bp):
CAATACTGATAACTTGTCCACAATACTAACAGTTTATCTA
Found at i:17253117 original size:43 final size:41
Alignment explanation
Indices: 17253008--17253129 Score: 102
Period size: 43 Copynumber: 2.9 Consensus size: 41
17252998 TACTAACAGT
* * * *
17253008 TTATCTATAATACTTGTAACTTGTCCACATATTTTTGGCAG
1 TTATCTACAATACTAGTGACTTGTCCACATATTTGTGGCAG
* * * *
17253049 CTTGA-CTGCAAATATTGGTGGCTTGTCCACATATTTGTGGCAG
1 -TT-ATCTAC-AATACTAGTGACTTGTCCACATATTTGTGGCAG
* *
17253092 TATATCTACAATTACTAGTGACTTGTCCAAAAATTTGT
1 T-TATCTACAA-TACTAGTGACTTGTCCACATATTTGT
17253130 TTGTTTTGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
42 8 0.13
43 54 0.87
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (41 bp):
TTATCTACAATACTAGTGACTTGTCCACATATTTGTGGCAG
Found at i:17267340 original size:46 final size:46
Alignment explanation
Indices: 17267273--17267366 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
17267263 CAAAATCGTG
17267273 ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
1 ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
* *
17267319 ATGTAAACCGCGGATCTCTATCCGAAATGATGGAGACTGGTACTCC
1 ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
17267365 AT
1 AT
17267367 ACAATCTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (46 bp):
ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
Found at i:17280299 original size:21 final size:21
Alignment explanation
Indices: 17280259--17280301 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17280249 TTATACATCC
17280259 TAAATTTCATATTATAATATA
1 TAAATTTCATATTATAATATA
17280280 TAAATTTCATATTATAATATA
1 TAAATTTCATATTATAATATA
17280301 T
1 T
17280302 CTAAGCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTTCATATTATAATATA
Found at i:17280782 original size:26 final size:26
Alignment explanation
Indices: 17280735--17280787 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
17280725 AAATTAAAAG
*
17280735 ATCATTTGGTGTTTTGAAAGTAAGAAA
1 ATCATTTAGTGTTTTGAAAGT-AGAAA
**
17280762 ATCATTTAG-GTTTTGTTAGTAGAAA
1 ATCATTTAGTGTTTTGAAAGTAGAAA
17280787 A
1 A
17280788 AGCTTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 9 0.39
27 8 0.35
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (26 bp):
ATCATTTAGTGTTTTGAAAGTAGAAA
Found at i:17286652 original size:20 final size:20
Alignment explanation
Indices: 17286608--17286657 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17286598 TAAAAAAGGA
*
17286608 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
17286628 ATATCAATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
17286647 AGTATCGATAC
1 A-TATCGATAC
17286658 TGGATCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:17292934 original size:31 final size:31
Alignment explanation
Indices: 17292899--17292962 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
17292889 TAGAGTTAAT
* *
17292899 AGAACATCT-AATAATGTTAGGGACTGAACTG
1 AGAACATCTGAA-AATATTAGGGACTGAAATG
*
17292930 AGAACATCTGAAAATATTAGGGGCTGAAATG
1 AGAACATCTGAAAATATTAGGGACTGAAATG
17292961 AG
1 AG
17292963 CCAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (31 bp):
AGAACATCTGAAAATATTAGGGACTGAAATG
Found at i:17296728 original size:13 final size:12
Alignment explanation
Indices: 17296701--17296736 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
17296691 GTATATGGAA
17296701 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
17296713 AAAGGAAAAGAAG
1 AAAAGAAAA-AAG
17296726 AAAAGAAAAAA
1 AAAAGAAAAAA
17296737 AAAGAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:17296739 original size:18 final size:17
Alignment explanation
Indices: 17296699--17296743 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
17296689 ATGTATATGG
17296699 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
**
17296716 GGAAAAGAAGAAAAGAAA
1 AAAAAAGAA-AAAAGAAA
17296734 AAAAAAGAAA
1 AAAAAAGAAA
17296744 CTAGAATGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:17297423 original size:42 final size:42
Alignment explanation
Indices: 17297371--17297676 Score: 345
Period size: 42 Copynumber: 7.3 Consensus size: 42
17297361 CTTCATATAC
* *
17297371 AATGCAATGAAAAGTAAATGAACCTCCACACCTGAGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
* *
17297413 AATGTAATGAAAAGTAGATGGACCTCCACACCT-AGACCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAG-CCTCTA
* * * * *
17297455 AATGTAATGAAAAGTCAATGGAACTCCACACATCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACAC--CTGAGCCTCTA
*
17297499 AATGCAATGAAAAGTAAATGGAACTCCACACCT-AGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGA-GCCTCTA
* * *
17297541 AATGTAAT-AAAACGTAAGTGGACCTCTAC-CCT-AGGCCTCTA
1 AATGCAATGAAAA-GTAAATGGACCTCCACACCTGA-GCCTCTA
* * *
17297582 AATGCAATGAAAAGTAAATGGACCTCTACGCCCGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
* *
17297624 AATGCAATGAAAAGTAAATGGAGCTCCACA-CTGGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCT-GAGCCTCTA
17297666 AATGCAATGAA
1 AATGCAATGAA
17297677 TGTTTCCCTT
Statistics
Matches: 229, Mismatches: 25, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
41 41 0.18
42 150 0.66
43 1 0.00
44 36 0.16
45 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
Found at i:17297621 original size:83 final size:81
Alignment explanation
Indices: 17297371--17297676 Score: 328
Period size: 86 Copynumber: 3.6 Consensus size: 81
17297361 CTTCATATAC
* * * * *
17297371 AATGCAATGAAAAGTAAAT-GAACCTCCACACCTGAGCCTTTAAATGTAATGAAAAGTAGATGGA
1 AATGTAATGAAAAGT-AATGGAA-CTCCAC-CCTGGGCCTCTAAATGCAATGAAAAGTAAATGGA
17297435 CCTCCACACCTAGACCTCTA
63 CCTCCACACCTAG-CCTCTA
*
17297455 AATGTAATGAAAAGTCAATGGAACTCCACACATCTGGGCCTTTAAATGCAATGAAAAGTAAATGG
1 AATGTAATGAAAAGT-AATGGAACTCCAC-C--CTGGGCCTCTAAATGCAATGAAAAGTAAATGG
*
17297520 AACTCCACACCTAGGCCTCTA
62 ACCTCCACACCTA-GCCTCTA
* * *
17297541 AATGTAAT-AAAACGTAAGTGGACCTCTACCCTAGGCCTCTAAATGCAATGAAAAGTAAATGGAC
1 AATGTAATGAAAA-GTAA-TGGAACTCCACCCTGGGCCTCTAAATGCAATGAAAAGTAAATGGAC
* * *
17297605 CTCTACGCCCGAGCCTCTA
64 CTCCAC-ACCTAGCCTCTA
* * *
17297624 AATGCAATGAAAAGTAAATGGAGCTCCACACTGGGGCCTCTAAATGCAATGAA
1 AATGTAATGAAAAGT-AATGGAACTCCACCCT-GGGCCTCTAAATGCAATGAA
17297677 TGTTTCCCTT
Statistics
Matches: 193, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
83 63 0.33
84 53 0.27
85 10 0.05
86 66 0.34
87 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (81 bp):
AATGTAATGAAAAGTAATGGAACTCCACCCTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCT
CCACACCTAGCCTCTA
Found at i:17298121 original size:22 final size:21
Alignment explanation
Indices: 17298093--17298134 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
17298083 TTTTTTGTTT
* *
17298093 CCTTTTTGTTTTATTGTTTTTC
1 CCTTTTTCTTTT-TTCTTTTTC
17298115 CCTTTTTCTTTTTTCTTTTT
1 CCTTTTTCTTTTTTCTTTTT
17298135 TTTTCTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (21 bp):
CCTTTTTCTTTTTTCTTTTTC
Found at i:17320658 original size:101 final size:102
Alignment explanation
Indices: 17320530--17320714 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
17320520 AAAGTGATGG
* * *
17320530 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATATGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGCCACATATGTAGT
17320593 ACTATGTGCAAGCTACTATGCGTACTGGATAGCTTCAA
65 ACTATGTGCAAGCTACTATGCGTACTGGATAGCTTCAA
* * *
17320631 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGCCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGCCACATATGTAGTA
*
17320696 CTATGTGCAGGCTACTATG
66 CTATGTGCAAGCTACTATG
17320715 TGAACCGGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 39 0.52
102 32 0.43
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGCCACATATGTAGTA
CTATGTGCAAGCTACTATGCGTACTGGATAGCTTCAA
Found at i:17320674 original size:51 final size:47
Alignment explanation
Indices: 17320530--17320712 Score: 152
Period size: 51 Copynumber: 3.7 Consensus size: 47
17320520 AAAGTGATGG
* * * *
17320530 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATA-G-TA-A
* * * * *
17320580 TCGCATATGTAGTACTATGTGCAAGCTACTATGCGTACTGGATAGCTTCAA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GGATAG--T-AA
* *
17320631 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATAGTAA
17320679 TGGCCACATGTGTAGTACTATGTGCAGGCTACTA
1 T---CACATGTGTAGTACTATGTGCAGGCTACTA
17320713 TGTGAACCGG
Statistics
Matches: 107, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
48 2 0.02
49 2 0.02
50 33 0.31
51 68 0.64
52 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (47 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATAGTAA
Found at i:17320716 original size:26 final size:26
Alignment explanation
Indices: 17320636--17320716 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
17320626 TTCAATCACG
17320636 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
17320662 CGTGTA-T-CGGATAGTG-ATGGCCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCTACTA
17320687 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
17320713 TGTG
1 TGTG
17320717 AACCGGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:17320961 original size:16 final size:16
Alignment explanation
Indices: 17320940--17320971 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17320930 TGATTGAAAG
*
17320940 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
17320956 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
17320972 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:17323110 original size:16 final size:16
Alignment explanation
Indices: 17323089--17323120 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17323079 GTTTTGTTGC
*
17323089 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
17323105 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
17323121 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:17323317 original size:46 final size:43
Alignment explanation
Indices: 17323245--17323342 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 43
17323235 ATAATAACAA
*
17323245 ATACACGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATG
1 ATAC-CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAATG
* *
17323291 ATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAATG
1 ATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAATG
17323335 ATACCGGT
1 ATACCGGT
17323343 TCACATAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
43 5 0.11
44 13 0.28
45 2 0.04
46 23 0.49
47 4 0.09
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
ATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAATG
Found at i:17323424 original size:51 final size:51
Alignment explanation
Indices: 17323338--17323538 Score: 221
Period size: 51 Copynumber: 4.0 Consensus size: 51
17323328 ATTAATGATA
* * * * *
17323338 CCGGTTCACATAGTAACCTGTACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
17323389 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * *
17323440 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
* * *
17323490 CTGGTACATGTAGTAGCCTGCATATAGTACTACACACGTGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
17323539 TTCACTTTCA
Statistics
Matches: 124, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.03
50 40 0.32
51 77 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:17323528 original size:101 final size:102
Alignment explanation
Indices: 17323346--17323530 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
17323336 TACCGGTTCA
* *
17323346 CATAGTAACCTGTACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAACCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
17323411 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * * *
17323448 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACATGTAGTAGCCTGC
1 CATAGTAACCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
*
17323511 ATATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
17323531 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 38 0.51
102 33 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAACCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:17323554 original size:101 final size:102
Alignment explanation
Indices: 17323338--17323530 Score: 273
Period size: 102 Copynumber: 1.9 Consensus size: 102
17323328 ATTAATGATA
* * *
17323338 CCGGTTCACATAGTAACCTGTACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
*
17323403 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
* * * * *
17323440 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACATGTAG
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAG
*
17323503 TAGCCTGCATATAGTACTACACACGTGA
65 TAGCCTGCACATAGTACTACACACGTGA
17323531 CCATCACTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 38 0.47
102 39 0.48
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
Found at i:17325268 original size:3 final size:3
Alignment explanation
Indices: 17325260--17325298 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
17325250 TATTTGTAAA
* * *
17325260 AAT AAT AAT AAT AGT ACT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17325299 TTGGGTCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17329121 original size:15 final size:14
Alignment explanation
Indices: 17329101--17329140 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
17329091 AATAAAATAA
*
17329101 AATTCAATTTAATT
1 AATTCAATTTAAGT
17329115 CAATTCAATTTAAGT
1 -AATTCAATTTAAGT
17329130 AATTCTAATTT
1 AATTC-AATTT
17329141 TTAAATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (14 bp):
AATTCAATTTAAGT
Found at i:17334506 original size:20 final size:21
Alignment explanation
Indices: 17334471--17334509 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17334461 CAGCTCGTTG
17334471 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
17334492 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
17334510 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:17334917 original size:13 final size:13
Alignment explanation
Indices: 17334899--17334924 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17334889 TGTGTCCTAA
17334899 TATGAATTAAATT
1 TATGAATTAAATT
17334912 TATGAATTAAATT
1 TATGAATTAAATT
17334925 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:17337183 original size:30 final size:31
Alignment explanation
Indices: 17337142--17337202 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
17337132 GGGTTGGGAG
* *
17337142 GGGAGAGGAGTAAAAGCTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGCTTTGAGGGAAAAGT
*
17337173 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGCTTTGAGGGAAAAGT
17337203 AAAAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.44, T:0.18
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGCTTTGAGGGAAAAGT
Found at i:17337265 original size:9 final size:9
Alignment explanation
Indices: 17337251--17337287 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17337241 TATAGTTTAA
17337251 TATTCGAAT
1 TATTCGAAT
*
17337260 TATTCGAGT
1 TATTCGAAT
*
17337269 TATTCGAGT
1 TATTCGAAT
17337278 TATTCGAAT
1 TATTCGAAT
17337287 T
1 T
17337288 CGAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17337740 original size:46 final size:46
Alignment explanation
Indices: 17337673--17337765 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
17337663 GTAGAGCAAG
17337673 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
1 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
17337719 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
1 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
17337765 T
1 T
17337766 TCATTGTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.19, C:0.06, G:0.45, T:0.29
Consensus pattern (46 bp):
TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
Found at i:17350204 original size:11 final size:9
Alignment explanation
Indices: 17350169--17350203 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
17350159 GTAGGTAACT
17350169 TTTTTTTGC
1 TTTTTTTGC
*
17350178 ATTTTTTGC
1 TTTTTTTGC
17350187 TTTTTTTGC
1 TTTTTTTGC
17350196 TGTTTTTT
1 T-TTTTTT
17350204 TAGCTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.03, C:0.09, G:0.11, T:0.77
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:17350343 original size:76 final size:76
Alignment explanation
Indices: 17350246--17350392 Score: 260
Period size: 77 Copynumber: 1.9 Consensus size: 76
17350236 CTGATACCAA
*
17350246 CTGATGCGGAAACCCGGATCTAGACACAAGAG-AACACAAATTAGAAATAAAACGAGAATAAATA
1 CTGATGCGGAAACCCAGATCTAGACACAAGAGAAACACAAATTAGAAATAAAACGAGAATAAATA
17350310 AAATTAGTTAT
66 AAATTAGTTAT
*
17350321 CTGATGCGGAAAACCCAGATCTAGACACAAGAGAAACACAAATTAGAAATAAAATGAGAATAAAT
1 CTGATGCGG-AAACCCAGATCTAGACACAAGAGAAACACAAATTAGAAATAAAACGAGAATAAAT
17350386 AAAATTA
65 AAAATTA
17350393 TTTAAATAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
75 9 0.13
76 22 0.32
77 37 0.54
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (76 bp):
CTGATGCGGAAACCCAGATCTAGACACAAGAGAAACACAAATTAGAAATAAAACGAGAATAAATA
AAATTAGTTAT
Found at i:17352854 original size:18 final size:18
Alignment explanation
Indices: 17352823--17352857 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17352813 TTATTTTATT
17352823 TAAATTTAATTATAAAAA
1 TAAATTTAATTATAAAAA
17352841 TAAATATTAA-TATAAAA
1 TAAAT-TTAATTATAAAA
17352858 TTATATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATTTAATTATAAAAA
Found at i:17366168 original size:22 final size:22
Alignment explanation
Indices: 17366140--17366193 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
17366130 TATTCATTTA
17366140 ATTTTTTAACTA-TTCA-AATTAT
1 ATTTTTTAA-TAGTT-ATAATTAT
17366162 ATTTTTTGAATAGTTATAATTAT
1 ATTTTTT-AATAGTTATAATTAT
*
17366185 TTTTTTTAA
1 ATTTTTTAA
17366194 ATCAAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTTTTAATAGTTATAATTAT
Found at i:17370160 original size:43 final size:43
Alignment explanation
Indices: 17369960--17370145 Score: 282
Period size: 43 Copynumber: 4.3 Consensus size: 43
17369950 TTTTTTCTAA
* *
17369960 AAACGCCGCTAAAGACCAAGATCTTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
** * *
17370003 AAACGCCGCTAAAGACCGGGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
* *
17370046 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAG
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
* *
17370089 AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
17370132 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
17370146 CTTATGACCT
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
Found at i:17370167 original size:43 final size:42
Alignment explanation
Indices: 17369960--17370168 Score: 267
Period size: 43 Copynumber: 4.9 Consensus size: 42
17369950 TTTTTTCTAA
* *
17369960 AAACGCCGCTAAAGACCAAGATCTTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCG-CGCTTTTCCCAC
** *
17370003 AAACGCCGCTAAAGACCGGGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGC-GCGCTTTTCCCAC
*
17370046 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAG
1 AAACGCCGCTAAAGACCAAGACCTTTAGC-GCGCTTTTCCCAC
* *
17370089 AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCG-CGCTTTTCCCAC
* *
17370132 AAACGCCGCTAAAG-CTTATGACCTTTAGCAGCGCTTT
1 AAACGCCGCTAAAGAC-CAAGACCTTTAGC-GCGCTTT
17370169 AATTAAAAAT
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
42 1 0.01
43 145 0.98
44 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGCGCTTTTCCCAC
Found at i:17370183 original size:129 final size:127
Alignment explanation
Indices: 17369960--17370228 Score: 299
Period size: 129 Copynumber: 2.1 Consensus size: 127
17369950 TTTTTTCTAA
* * * * * *
17369960 AAACGCCGCTAAAGACCAAGATCTTTAGCGACGCTTTTTCCACAAACGCCGCTAAAGACCGGGAT
1 AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGGAC
* ** * * *
17370025 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCCAG
66 CTTTAGCAGCGCTTTAACCAAAAACGCCGCTAAA-A-CATAGACCTTTAGCGACGCTTTT-CCAC
* *
17370089 AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAG-CTTATGA
1 AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGAC-CAGGA
** * * * * *
17370153 CCTTTAGCAGCGCTTTAATTAAAAATGCCGCTATAACATTGACTTTTAGCGACGCTTTTTCAC
65 CCTTTAGCAGCGCTTTAACCAAAAACGCCGCTAAAACATAGACCTTTAGCGACGCTTTTCCAC
17370216 AAACGCCACTAAA
1 AAACGCCACTAAA
17370229 AGCATAAATT
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
127 17 0.15
128 19 0.16
129 81 0.69
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (127 bp):
AAACGCCACTAAAGAACAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGGAC
CTTTAGCAGCGCTTTAACCAAAAACGCCGCTAAAACATAGACCTTTAGCGACGCTTTTCCAC
Found at i:17372769 original size:41 final size:41
Alignment explanation
Indices: 17372711--17373067 Score: 534
Period size: 41 Copynumber: 8.7 Consensus size: 41
17372701 AATATTTTTT
* * * *
17372711 GCGGCGCTTTTTTAAAAACGCTGCTAAAGACCCGAGAATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
17372752 GCGGCACTTCTTCAAAAACGCCACTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
*
17372793 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
17372834 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * *
17372875 GCAGTGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
17372916 GCGGCGCTCCTTCAAAAACGTCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
17372957 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCCGGGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * * *
17372998 GCGGCGCTTCTTAAAAAATGACACTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
17373039 GCGACGCTTCTTCAAAAATGCCGCTAAAG
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAG
17373068 CCTCGAAAAC
Statistics
Matches: 284, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 284 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
Found at i:17373159 original size:39 final size:39
Alignment explanation
Indices: 17373105--17373198 Score: 145
Period size: 39 Copynumber: 2.4 Consensus size: 39
17373095 TAGGCTTAGG
* * * *
17373105 TTTTTTGCAGCGCTTTTTGGAAAATGCCGCTAATGCTCA
1 TTTTTAGCGGCGCTTTTTGGAAAACGCAGCTAATGCTCA
17373144 TTTTTAGCGGCGCTTTTTGGAAAACGCAGCTAATGCTCA
1 TTTTTAGCGGCGCTTTTTGGAAAACGCAGCTAATGCTCA
17373183 TTTTTAGCGGCG-TTTT
1 TTTTTAGCGGCGCTTTT
17373199 CCTAAAAGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 4 0.08
39 47 0.92
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTTTGGAAAACGCAGCTAATGCTCA
Found at i:17378043 original size:2 final size:2
Alignment explanation
Indices: 17378036--17378074 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17378026 ATCATGTGAA
17378036 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17378075 AATGGGTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17379070 original size:17 final size:17
Alignment explanation
Indices: 17379048--17379084 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
17379038 TGATTCCAGC
17379048 ATTAACTCGGTCTATGA
1 ATTAACTCGGTCTATGA
17379065 ATTAACTCGGTCTATGA
1 ATTAACTCGGTCTATGA
17379082 ATT
1 ATT
17379085 CCCCTATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (17 bp):
ATTAACTCGGTCTATGA
Found at i:17383044 original size:37 final size:37
Alignment explanation
Indices: 17382997--17383073 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
17382987 CATAGGAAAG
17382997 AAAACTACGTAAGCATATAATGCTTAGTAAGTTCAGA
1 AAAACTACGTAAGCATATAATGCTTAGTAAGTTCAGA
17383034 AAAACTACGTAAGCATATAATGCTTAGTAAGTTCAGA
1 AAAACTACGTAAGCATATAATGCTTAGTAAGTTCAGA
17383071 AAA
1 AAA
17383074 CATGAACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (37 bp):
AAAACTACGTAAGCATATAATGCTTAGTAAGTTCAGA
Found at i:17391409 original size:11 final size:12
Alignment explanation
Indices: 17391389--17391423 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
17391379 ATGTTATAAT
17391389 ATTAATATTTTA
1 ATTAATATTTTA
*
17391401 ATT-ATATTTTT
1 ATTAATATTTTA
17391412 ATTAATATTTTA
1 ATTAATATTTTA
17391424 TTGTGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTAATATTTTA
Found at i:17394531 original size:13 final size:13
Alignment explanation
Indices: 17394509--17394570 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
17394499 TTTGGCAATA
*
17394509 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
17394522 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* * *
17394535 AC-ATGGAAAAGTA
1 -CTTTTGAAAAGTG
17394548 CTTTT-AAGAAGTG
1 CTTTTGAA-AAGTG
17394561 CTTTTGAAAA
1 CTTTTGAAAA
17394571 ATTTGGTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
12 3 0.08
13 32 0.84
14 3 0.08
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:17395723 original size:15 final size:15
Alignment explanation
Indices: 17395703--17395764 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
17395693 TGTTTAATTA
*
17395703 TAATTAATTTTTAAT
1 TAATTAAATTTTAAT
*
17395718 TAATTAAAGTTTAAT
1 TAATTAAATTTTAAT
* * *
17395733 TAAATAAATTATGAT
1 TAATTAAATTTTAAT
*
17395748 TAATTAGA-TTTAAT
1 TAATTAAATTTTAAT
17395762 TAA
1 TAA
17395765 AAGTATATAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
14 7 0.19
15 30 0.81
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
TAATTAAATTTTAAT
Found at i:17398645 original size:40 final size:41
Alignment explanation
Indices: 17398589--17398742 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 41
17398579 ATATTTTTAT
* *
17398589 TTTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATATA
1 TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATATA
17398630 TTTTTATT-TTTTTTTAATTTTAAAAT-TTTTTAAAA-ATA
1 TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATATA
17398668 CTTTTT-TTAATTTTTTTAATTTTAAAATATTTTTAAAATACT-
1 -TTTTTATT-ATTTTTTTAATTTTAAAATATTTTTAAAATA-TA
*
17398710 TTTTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTTTATT-A--TTT-TTTTAA-TTTTAAAATA
17398743 AATTTTTGGT
Statistics
Matches: 100, Mismatches: 2, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
38 5 0.05
39 13 0.13
40 36 0.36
41 21 0.21
42 5 0.05
43 1 0.01
44 3 0.03
45 6 0.06
46 10 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (41 bp):
TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATATA
Found at i:17398724 original size:12 final size:12
Alignment explanation
Indices: 17398709--17398737 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17398699 TTTAAAATAC
17398709 TTTTT-TTTTAA
1 TTTTTATTTTAA
17398720 TTTTTATTTTAA
1 TTTTTATTTTAA
17398732 TTTTTA
1 TTTTTA
17398738 AAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:17399953 original size:3 final size:3
Alignment explanation
Indices: 17399945--17399987 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17399935 TTTCTAAAAC
17399945 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17399988 CGTCATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17405199 original size:11 final size:12
Alignment explanation
Indices: 17405183--17405217 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
17405173 AAGAGAGAAC
17405183 TAAAAACAAAA-
1 TAAAAACAAAAT
17405194 TAAAAACAAAAT
1 TAAAAACAAAAT
17405206 TAAACAACAAAA
1 TAAA-AACAAAA
17405218 AGGGTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 4 0.18
13 7 0.32
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (12 bp):
TAAAAACAAAAT
Found at i:17407771 original size:222 final size:223
Alignment explanation
Indices: 17407338--17407784 Score: 869
Period size: 223 Copynumber: 2.0 Consensus size: 223
17407328 TTGGAAAAGA
*
17407338 AGTGAGAACATGGATTTAGGTTGTCGTAAGAGTGCGAGTTTCAATATTTTTTTTATTTTTCTAGA
1 AGTGAGAACATGAATTTAGGTTGTCGTAAGAGTGCGAGTTTCAATATTTTTTTTATTTTTCTAGA
17407403 ACCCCAAAAGCTAGGATTTAGGTTGTTGAGTGGAAACTGACATATTTTGGCCTCAAATTGCTAAA
66 ACCCCAAAAGCTAGGATTTAGGTTGTTGAGTGGAAACTGACATATTTTGGCCTCAAATTGCTAAA
17407468 ACTGTTATCTCTCTGCATTCACTTCTATTGTTTCCTCTTCTTTCTTTGTCAATCTTAGTTGTTAC
131 ACTGTTATCTCTCTGCATTCACTTCTATTGTTTCCTCTTCTTTCTTTGTCAATCTTAGTTGTTAC
17407533 AATGTTGGTCACATGGATTGATATAGAC
196 AATGTTGGTCACATGGATTGATATAGAC
17407561 AGTGAGAACATGAATTTAGGTTGTCGTAAGAGTGCGAGTTTCAATATTTTTTTTATTTTTCTAGA
1 AGTGAGAACATGAATTTAGGTTGTCGTAAGAGTGCGAGTTTCAATATTTTTTTTATTTTTCTAGA
17407626 ACCCCAAAAGCTAGGATTTAGGTTGTTGAGTGGAAACTGACATATTTTGGCCTC-AATTGCTAAA
66 ACCCCAAAAGCTAGGATTTAGGTTGTTGAGTGGAAACTGACATATTTTGGCCTCAAATTGCTAAA
*
17407690 ACTGTTATCTCTCTGTATTCACTTCTATTGTTTCCTCTTCTTTCTTTGTCAATCTTAGTTGTTAC
131 ACTGTTATCTCTCTGCATTCACTTCTATTGTTTCCTCTTCTTTCTTTGTCAATCTTAGTTGTTAC
17407755 AATGTTGGTCACATGGATTGATATAGAC
196 AATGTTGGTCACATGGATTGATATAGAC
17407783 AG
1 AG
17407785 AAGTTAAAAC
Statistics
Matches: 222, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
222 104 0.47
223 118 0.53
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (223 bp):
AGTGAGAACATGAATTTAGGTTGTCGTAAGAGTGCGAGTTTCAATATTTTTTTTATTTTTCTAGA
ACCCCAAAAGCTAGGATTTAGGTTGTTGAGTGGAAACTGACATATTTTGGCCTCAAATTGCTAAA
ACTGTTATCTCTCTGCATTCACTTCTATTGTTTCCTCTTCTTTCTTTGTCAATCTTAGTTGTTAC
AATGTTGGTCACATGGATTGATATAGAC
Found at i:17419033 original size:17 final size:17
Alignment explanation
Indices: 17419011--17419074 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
17419001 AATCTTAAAG
17419011 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
17419028 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
17419047 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
17419064 TTTTAATTGTA
1 TTCTAATTGTA
17419075 GCATTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:17419043 original size:36 final size:36
Alignment explanation
Indices: 17419003--17419073 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
17418993 GATTATGTAA
17419003 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
17419039 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGT
17419074 AGCATTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:17419353 original size:48 final size:48
Alignment explanation
Indices: 17419278--17419373 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
17419268 TGAGGGAATT
* *
17419278 CTGTTGAATCCTTTATTATTGTAAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTA
*
17419326 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTA
17419374 AGCAAAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTA
Found at i:17421673 original size:36 final size:36
Alignment explanation
Indices: 17421624--17421692 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
17421614 GATTATGTAA
*
17421624 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGATCTAATTGTATACAGCTTCTAATTGTG
*
17421660 TCTTAGAGATCTAATTGTATACAGCTTTTAATT
1 TCTTAGAGATCTAATTGTATACAGCTTCTAATT
17421693 ATAGCCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTTAGAGATCTAATTGTATACAGCTTCTAATTGTG
Found at i:17421963 original size:48 final size:48
Alignment explanation
Indices: 17421888--17421981 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
17421878 TGAGGGAATT
* *
17421888 CTGTTGAATCCTTTATTATTGTAAGTTAGGCCGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTA
* *
17421936 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTT
17421982 AAGCAAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTA
Found at i:17433485 original size:24 final size:22
Alignment explanation
Indices: 17433458--17433512 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
17433448 AAAGCTTACA
*
17433458 AAAGAGCTTATATCGGGTAGCTCC
1 AAAGAGCTTA-AT-GGGAAGCTCC
17433482 AAAGAGAACTTAATGGGAAGCTCC
1 AAAGAG--CTTAATGGGAAGCTCC
*
17433506 GAAGAGC
1 AAAGAGC
17433513 ACTTAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
24 20 0.74
25 2 0.07
26 4 0.15
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
AAAGAGCTTAATGGGAAGCTCC
Found at i:17435704 original size:25 final size:25
Alignment explanation
Indices: 17435676--17435758 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
17435666 TGTATATAGA
17435676 GAAGCTCATGCGAGCCATAAATCGG
1 GAAGCTCATGCGAGCCATAAATCGG
* *
17435701 GAAGCTCATGCAAGCCATAAATTGG
1 GAAGCTCATGCGAGCCATAAATCGG
* * *
17435726 GAAACTCATGCGAACCA-ATTATCGG
1 GAAGCTCATGCGAGCCATA-AATCGG
17435751 GAAGCTCA
1 GAAGCTCA
17435759 AGAAAGCCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 1 0.02
25 48 0.98
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATGCGAGCCATAAATCGG
Found at i:17435799 original size:50 final size:50
Alignment explanation
Indices: 17435675--17435800 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
17435665 TTGTATATAG
* * **
17435675 AGAAGCTCATGCGAGCCATAA-ATCGGGAAGCTCATGCAAGCCATAAATTG
1 AGAAGCTCATGCGAGCCA-AATATCGGGAAGCTCAAGAAAGCCATAAATCA
* * * * *
17435725 GGAAACTCATGCGAACCAATTATCGGGAAGCTCAAGAAAGCCATTAATCA
1 AGAAGCTCATGCGAGCCAAATATCGGGAAGCTCAAGAAAGCCATAAATCA
* *
17435775 AGAAGCTCGTGAGAGCCAAATATCGG
1 AGAAGCTCATGCGAGCCAAATATCGG
17435801 ACATGTCATT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (50 bp):
AGAAGCTCATGCGAGCCAAATATCGGGAAGCTCAAGAAAGCCATAAATCA
Found at i:17439837 original size:5 final size:5
Alignment explanation
Indices: 17439827--17439879 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
17439817 TTGAAGTTTT
* *
17439827 ATCGA ATCGA ATCGA GT-GA GATAGA ATTCGA ATCGA ATCGA ATCGA ATCGA
1 ATCGA ATCGA ATCGA ATCGA -ATCGA A-TCGA ATCGA ATCGA ATCGA ATCGA
17439878 AT
1 AT
17439880 ATATTTATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 34 0.81
6 6 0.14
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (5 bp):
ATCGA
Found at i:17442673 original size:14 final size:14
Alignment explanation
Indices: 17442654--17442680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17442644 AATTAGTTTA
17442654 AAATCAAACTTAAT
1 AAATCAAACTTAAT
17442668 AAATCAAACTTAA
1 AAATCAAACTTAA
17442681 ATTTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATCAAACTTAAT
Found at i:17449415 original size:18 final size:18
Alignment explanation
Indices: 17449392--17449429 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
17449382 TCATGGTTCT
17449392 AAAGTGTTACTGATATGA
1 AAAGTGTTACTGATATGA
17449410 AAAGTGTTACTGATATGA
1 AAAGTGTTACTGATATGA
17449428 AA
1 AA
17449430 CACTATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (18 bp):
AAAGTGTTACTGATATGA
Found at i:17469932 original size:19 final size:19
Alignment explanation
Indices: 17469908--17469982 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
17469898 ATAATCTTCA
17469908 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
**
17469927 ATGATATATAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
17469946 ATGATATGCAATTTTAGAT
1 ATGATATGCAATCTTAGAT
*
17469965 ATGATATGAAATCTTAGA
1 ATGATATGCAATCTTAGA
17469983 AGATATGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:17473678 original size:21 final size:22
Alignment explanation
Indices: 17473639--17473681 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
17473629 TAAAAATGGT
17473639 TTTATATTAATATTTTATATAA
1 TTTATATTAATATTTTATATAA
17473661 TTTATAATTAA-A-TTTATATAA
1 TTTAT-ATTAATATTTTATATAA
17473682 AAATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATATTAATATTTTATATAA
Found at i:17475276 original size:27 final size:27
Alignment explanation
Indices: 17475238--17475292 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
17475228 AGATTGATAA
*
17475238 TAACATATGAAATCTAGGTGAATTCTT
1 TAACAGATGAAATCTAGGTGAATTCTT
17475265 TAACAGATGAAATCTAGGTGAATTCTT
1 TAACAGATGAAATCTAGGTGAATTCTT
17475292 T
1 T
17475293 CCTAAGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (27 bp):
TAACAGATGAAATCTAGGTGAATTCTT
Found at i:17486096 original size:23 final size:23
Alignment explanation
Indices: 17486061--17486137 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
17486051 AAGTTAGAAG
*
17486061 AGTGAAGAGACTTTAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
17486084 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
17486107 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
*
17486130 AGTTAAGA
1 AGTGAAGA
17486138 AGACACACAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.23
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:17491321 original size:21 final size:19
Alignment explanation
Indices: 17491297--17491364 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
17491287 TACAAATGTG
17491297 TTAATATCTAATTATAAATAT
1 TTAATAT-TAATT-TAAATAT
17491318 TTAATGATTATATTTAAATAT
1 TTAAT-ATTA-ATTTAAATAT
* *
17491339 TTAAAATATAATTTATATAT
1 TTAATAT-TAATTTAAATAT
17491359 TCTAAT
1 T-TAAT
17491365 TAAATTTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.30
21 23 0.57
22 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (19 bp):
TTAATATTAATTTAAATAT
Found at i:17491368 original size:33 final size:32
Alignment explanation
Indices: 17491331--17491427 Score: 85
Period size: 33 Copynumber: 2.9 Consensus size: 32
17491321 ATGATTATAT
17491331 TTAAATATTTAAAATATAATTTATATATTCTAA
1 TTAAATATTTAAAATATAATTTATATATT-TAA
17491364 TTAAAT-TTTACAAATAATTAATATT-TATTATTTAA
1 TTAAATATTTA-AAAT-A-TAAT-TTATA-TATTTAA
*
17491399 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
17491428 AAAATATTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 19
0.73 0.01 0.26
Matches are distributed among these distances:
31 4 0.07
32 10 0.19
33 20 0.37
34 5 0.09
35 9 0.17
36 6 0.11
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAATATTTAAAATATAATTTATATATTTAA
Found at i:17491397 original size:24 final size:23
Alignment explanation
Indices: 17491370--17491419 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
17491360 CTAATTAAAT
* *
17491370 TTTACAAATAATTAATATTTATTA
1 TTTAAAAATAATTAAAATTTA-TA
*
17491394 TTTAAAAATATTTAAAATTTATA
1 TTTAAAAATAATTAAAATTTATA
17491417 TTT
1 TTT
17491420 CATATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAAATAATTAAAATTTATA
Found at i:17491418 original size:30 final size:30
Alignment explanation
Indices: 17491333--17491436 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
17491323 GATTATATTT
*
17491333 AAATATTTAAAATATA-ATTTATATATTCTAA
1 AAATATTTAAAATTTATATTTAT-TATT-TAA
17491364 TTAAAT-TTTACAAATAATTAATATTTATTATTTAA
1 --AAATATTTA-AAAT--TT-ATATTTATTATTTAA
17491399 AAATATTTAAAATTTATATTTCA-TATATT-A
1 AAATATTTAAAATTTATATTT-ATTAT-TTAA
17491429 AAATATTT
1 AAATATTT
17491437 TCAATAAGTT
Statistics
Matches: 62, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
30 18 0.29
31 5 0.08
32 4 0.06
33 16 0.26
34 4 0.06
35 4 0.06
36 5 0.08
37 6 0.10
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
AAATATTTAAAATTTATATTTATTATTTAA
Found at i:17491643 original size:26 final size:25
Alignment explanation
Indices: 17491610--17491680 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
17491600 ATTTTAAACC
17491610 AAAC-TTTTTCAAAAGTATTTTTCAA
1 AAACATTTTTCAAAAGTATTTTTC-A
* *
17491635 AAATATTTTTCAAAAATATTTTTTCA
1 AAACATTTTTCAAAAGTA-TTTTTCA
* *
17491661 CAACACTTTTCAAAAGTATT
1 AAACATTTTTCAAAAGTATT
17491681 GCTAGACTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 5 0.13
26 27 0.71
27 6 0.16
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (25 bp):
AAACATTTTTCAAAAGTATTTTTCA
Found at i:17491660 original size:14 final size:13
Alignment explanation
Indices: 17491614--17491657 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
17491604 TAAACCAAAC
*
17491614 TTTTTCAAAAGTA
1 TTTTTCAAAAATA
17491627 TTTTTCAAAAATA
1 TTTTTCAAAAATA
17491640 TTTTTCAAAAATA
1 TTTTTCAAAAATA
17491653 TTTTT
1 TTTTT
17491658 TCACAACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (13 bp):
TTTTTCAAAAATA
Found at i:17502910 original size:56 final size:55
Alignment explanation
Indices: 17502811--17502922 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 55
17502801 TAAATGTATA
* * *
17502811 TGTTTTATACATTTTTGAATTTGATTAATTATAGATATACATTGCCGAATTTGAT
1 TGTTTTATACATTTCTGAATTCGATTAATTATAGATATACATTGCCGAAATTGAT
* ** * *
17502866 TGTTTTATATATTTCTGAATTCGAATTGTTTATAGTTATACATTGTCGAAATTGAT
1 TGTTTTATACATTTCTGAATTCG-ATTAATTATAGATATACATTGCCGAAATTGAT
17502922 T
1 T
17502923 TGCATATAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 20 0.42
56 28 0.58
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.50
Consensus pattern (55 bp):
TGTTTTATACATTTCTGAATTCGATTAATTATAGATATACATTGCCGAAATTGAT
Found at i:17503001 original size:92 final size:92
Alignment explanation
Indices: 17502900--17503396 Score: 735
Period size: 92 Copynumber: 5.4 Consensus size: 92
17502890 ATTGTTTATA
* * * * * *
17502900 GTTATACATTGTCGAAATTGATTTGCATATAGATATAAGTTGCCTAATTGATTTGTATATGATTG
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
*
17502965 TACATTGCTGAAATTAATTTGTACATG
66 TATATTGCTGAAATTAATTTGTACATG
* * *
17502992 GTTATACATTTTTGAAATTAAATTGTATATGGATATAAGTTGTCGAATTGATTTGTATATGATTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
*
17503057 TATATTGCTGAATTTAATTTGTACATG
66 TATATTGCTGAAATTAATTTGTACATG
* * *
17503084 GTTATACATTATTGAACTTGAATTGTATATGGATATAAGTTGTCGAATTGATTTGTATATGATTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
17503149 TATATTGCTGAAATTAATTTGTACATG
66 TATATTGCTGAAATTAATTTGTACATG
*
17503176 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTACCGAATTGATTTGTATATGATTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
*
17503241 TATATTGCTGAAATTAATTTGTAAATG
66 TATATTGCTGAAATTAATTTGTACATG
* * *
17503268 GTTATACACTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGTATATGGTTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
* * *
17503333 TACATTGCTGAATTTAATTTGTATATG
66 TATATTGCTGAAATTAATTTGTACATG
* ** * *
17503360 ATTATACATTGCCGAACTTG-ATTCGTATATGGTTATA
1 GTTATACATTGTTGAAATTGAATT-GTATATGGATATA
17503397 CATTATCGAT
Statistics
Matches: 371, Mismatches: 33, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
91 3 0.01
92 368 0.99
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
TATATTGCTGAAATTAATTTGTACATG
Found at i:17503457 original size:31 final size:31
Alignment explanation
Indices: 17503016--17503463 Score: 175
Period size: 31 Copynumber: 14.6 Consensus size: 31
17503006 AAATTAAATT
* * *
17503016 GTATATGGATATA-AGTTGTCGAA-TTGATTT
1 GTATATGAATATACA-TTGCCGAATTTGATTC
* * * * *
17503046 GTATATGATTATATATTGCTGAATTTAATTT
1 GTATATGAATATACATTGCCGAATTTGATTC
* ** *** *
17503077 GTACATGGTTATACATTATTGAACTTGAATT-
1 GTATATGAATATACATTGCCGAATTTG-ATTC
* * *
17503108 GTATATGGATATA-AGTTGTCGAA-TTGATTT
1 GTATATGAATATACA-TTGCCGAATTTGATTC
* * * * * *
17503138 GTATATGATTATATATTGCTGAAATTAATTT
1 GTATATGAATATACATTGCCGAATTTGATTC
* ** ** *
17503169 GTACATGGTTATACATTGTTGAAATTGAATT-
1 GTATATGAATATACATTGCCGAATTTG-ATTC
* * *
17503200 GTATATGGATATA-AGTTACCGAA-TTGATTT
1 GTATATGAATATACA-TTGCCGAATTTGATTC
* * * * * *
17503230 GTATATGATTATATATTGCTGAAATTAATTT
1 GTATATGAATATACATTGCCGAATTTGATTC
* ** * ** *
17503261 GTAAATGGTTATACACTGTTGAAATTGAATT-
1 GTATATGAATATACATTGCCGAATTTG-ATTC
*
17503292 GTATATGGATATA-AGTTGCCGAA-TTGATTC
1 GTATATGAATATACA-TTGCCGAATTTGATTC
** * * *
17503322 GTATATGGTTATACATTGCTGAATTTAATTT
1 GTATATGAATATACATTGCCGAATTTGATTC
* *
17503353 GTATATGATTATACATTGCCGAACTTGATTC
1 GTATATGAATATACATTGCCGAATTTGATTC
** ** * *
17503384 GTATATGGTTATACATTATCG-ATTTTATTT
1 GTATATGAATATACATTGCCGAATTTGATTC
*
17503414 GTATAT-AGATATACATTGCCGAATTTGGTTC
1 GTATATGA-ATATACATTGCCGAATTTGATTC
*
17503445 GTATATGAATATATATTGC
1 GTATATGAATATACATTGC
17503464 TTAATTGATT
Statistics
Matches: 328, Mismatches: 70, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
29 9 0.03
30 104 0.32
31 205 0.62
32 10 0.03
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (31 bp):
GTATATGAATATACATTGCCGAATTTGATTC
Found at i:17503475 original size:61 final size:59
Alignment explanation
Indices: 17502900--17503475 Score: 353
Period size: 61 Copynumber: 9.4 Consensus size: 59
17502890 ATTGTTTATA
* * *
17502900 GTTATACATTG-TCGAAATTGATTTGCATATAGATATA-AGTTGCCTAATTGATTTGTATATG
1 GTTATACATTGCT-G-AATTGATTTGTATAT-GATATACA-TTGCCGAATTGATTCGTATATG
* * * * * *** *
17502961 ATTGTACATTGCTGAAATTAATTTGTACATGGTTATACATTTTTGAAATTAAATT-GTATATG
1 GTTATACATTGCTG-AATTGATTTGTATAT-GATATACATTGCCG-AATT-GATTCGTATATG
* * * * * *
17503023 GATATA-AGTTG-TCGAATTGATTTGTATATGATTATATATTGCTGAATTTAATTTGTACATG
1 GTTATACA-TTGCT-GAATTGATTTGTATATGA-TATACATTGCCGAA-TTGATTCGTATATG
** * * *
17503084 GTTATACATTATTGAACTTGAATTGTATATGGATATA-AGTTGTCGAATTGATTTGTATATG
1 GTTATACATTGCTGAA-TTGATTTGTATAT-GATATACA-TTGCCGAATTGATTCGTATATG
* * * * * **
17503145 ATTATATATTGCTGAAATTAATTTGTACATGGTTATACATTGTTGAAATTGAATT-GTATATG
1 GTTATACATTGCTG-AATTGATTTGTATAT-GATATACATTGCCG-AATTG-ATTCGTATATG
* * * * * * * *
17503207 GATATA-AGTTACCGAATTGATTTGTATATGATTATATATTGCTGAAATTAATTTGTAAATG
1 GTTATACA-TTGCTGAATTGATTTGTATATGA-TATACATTGCCG-AATTGATTCGTATATG
* * *
17503268 GTTATACACTGTTGAAATTGAATTGTATATGGATATA-AGTTGCCGAATTGATTCGTATATG
1 GTTATACATTGCTG-AATTGATTTGTATAT-GATATACA-TTGCCGAATTGATTCGTATATG
*
17503329 GTTATACATTGCTGAATTTAATTTGTATATGATTATACATTGCCGAACTTGATTCGTATATG
1 GTTATACATTGCTGAA-TTGATTTGTATATGA-TATACATTGCCGAA-TTGATTCGTATATG
* * * *
17503391 GTTATACATT-ATCGATTTTATTTGTATATAGATATACATTGCCGAATTTGGTTCGTATATG
1 GTTATACATTGCT-GAATTGATTTGTATAT-GATATACATTGCCGAA-TTGATTCGTATATG
** * *
17503452 AATATATATTGCTTAATTGATTTG
1 GTTATACATTGCTGAATTGATTTG
17503476 AGCATTGGAT
Statistics
Matches: 408, Mismatches: 75, Indels: 64
0.75 0.14 0.12
Matches are distributed among these distances:
60 15 0.04
61 262 0.64
62 121 0.30
63 10 0.02
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (59 bp):
GTTATACATTGCTGAATTGATTTGTATATGATATACATTGCCGAATTGATTCGTATATG
Found at i:17507392 original size:10 final size:10
Alignment explanation
Indices: 17507377--17507401 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17507367 CATAAGTATT
17507377 TTTATAAATA
1 TTTATAAATA
17507387 TTTATAAATA
1 TTTATAAATA
17507397 TTTAT
1 TTTAT
17507402 GGAGTGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATAAATA
Found at i:17508125 original size:18 final size:18
Alignment explanation
Indices: 17508082--17508127 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
17508072 TAGGGAAAGT
*
17508082 ATTAATTAAGAAAATTAG
1 ATTAATTGAGAAAATTAG
17508100 ATTAATTGAGAAAATTAG
1 ATTAATTGAGAAAATTAG
17508118 ATTAATTGAG
1 ATTAATTGAG
17508128 GGATTAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (18 bp):
ATTAATTGAGAAAATTAG
Found at i:17509588 original size:36 final size:36
Alignment explanation
Indices: 17509542--17509651 Score: 202
Period size: 36 Copynumber: 3.1 Consensus size: 36
17509532 GGTAGCTTTA
* *
17509542 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
17509578 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
17509614 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
17509650 GC
1 GC
17509652 CAAAATTGAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:17509598 original size:21 final size:20
Alignment explanation
Indices: 17509570--17509635 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
17509560 AGTGAAAAAG
17509570 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
*
17509590 TGATCAAGTGAC-A-A---A-G
1 TGAT-AAGTG-CTATACTTATC
17509606 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
17509626 TGATCAAGTG
1 TGAT-AAGTG
17509636 ACAAAGTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 17
0.65 0.04 0.31
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 5 0.14
17 1 0.03
19 1 0.03
20 9 0.26
21 11 0.31
22 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:17514778 original size:25 final size:26
Alignment explanation
Indices: 17514740--17514789 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
17514730 TAATTATAGA
* *
17514740 TATACATTGTCGAATTTG-ATTGTTT
1 TATACATTGCCGAATTCGAATTGTTT
*
17514765 TATATATTGCCGAATTCGAATTGTT
1 TATACATTGCCGAATTCGAATTGTT
17514790 CATAGTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (26 bp):
TATACATTGCCGAATTCGAATTGTTT
Found at i:17514871 original size:61 final size:62
Alignment explanation
Indices: 17514764--17515369 Score: 466
Period size: 61 Copynumber: 9.9 Consensus size: 62
17514754 TTTGATTGTT
* * * * *
17514764 TTATATATTGCCG-AATTCGAATTGT-TCATAGTTATACATTGTTGAAATTGATTTGCATATGG
1 TTATACATTGCCGAAATT-GATTTGTAT-ATGGTTATACATTGCTGAAATTGATTTGTATATGG
* * * * *
17514826 GTATA-AGTTGCCG-AATTGATTTGTATATGATTGTACATTGCTGAAATTAATTTGTACATGG
1 TTATACA-TTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
* * * * * *
17514887 TTATACATTGTCGAAATTGATTTGCATATGGGTATA-AGTTACCG-AATTGATTTGTATATGA
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACA-TTGCTGAAATTGATTTGTATATGG
* * * * * * *
17514948 TTGTACATTGCTGAAATTAATTTGTACATGGTTATAAATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
* * * * *
17515010 ATATA-AGTTGCCG-AATTGATTTGTATATGATTATATATTGCTGAAATTAATTTGTACATGG
1 TTATACA-TTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
** * * * *
17515071 TTATACATTGTTGAAATTGAATTGTATATGGATATA-AGTTGCCG-AATTGATTTGTATATGA
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACA-TTGCTGAAATTGATTTGTATATGG
* * * * * *
17515132 TTATATATTGCTGAAATTAATTTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
* * * * * *
17515194 ATATA-AGTTGCCG-AATCGATTCGTATATGGTTATACATTGCTGAATTTAATTTGTATATGA
1 TTATACA-TTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
** * * ** * ** *
17515255 TTATACATTTTCGAACTAGATTCATATATGGTTATACATTGCTG-ATTTTTTTTGTATATAG
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
* * * * * ** * *
17515316 ATATACATTGCTGAATTTGGTTCGTATATGAATATATATTGCTG-AATTTATTTG
1 TTATACATTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTG
17515370 AGCATTGGAT
Statistics
Matches: 431, Mismatches: 97, Indels: 33
0.77 0.17 0.06
Matches are distributed among these distances:
61 291 0.68
62 140 0.32
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (62 bp):
TTATACATTGCCGAAATTGATTTGTATATGGTTATACATTGCTGAAATTGATTTGTATATGG
Found at i:17514879 original size:31 final size:31
Alignment explanation
Indices: 17514795--17515369 Score: 366
Period size: 31 Copynumber: 18.8 Consensus size: 31
17514785 TTGTTCATAG
* * * *
17514795 TTATACATTGTTGAAATTGATTTGCATATGG
1 TTATACATTGCTGAAATTAATTTGTATATGA
* * *
17514826 GTATA-AGTTGCCG-AATTGATTTGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGA
* * *
17514856 TTGTACATTGCTGAAATTAATTTGTACATGG
1 TTATACATTGCTGAAATTAATTTGTATATGA
* * *
17514887 TTATACATTG-TCGAAATTGATTTGCATATGG
1 TTATACATTGCT-GAAATTAATTTGTATATGA
* * * *
17514918 GTATA-AGTTACCG-AATTGATTTGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGA
* * *
17514948 TTGTACATTGCTGAAATTAATTTGTACATGG
1 TTATACATTGCTGAAATTAATTTGTATATGA
* *
17514979 TTATAAATTGTTGAAATTGAA-TTGTATATGGA
1 TTATACATTGCTGAAATT-AATTTGTATAT-GA
* *
17515011 -TATA-AGTTGCCG-AATTGATTTGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGA
* * *
17515040 TTATATATTGCTGAAATTAATTTGTACATGG
1 TTATACATTGCTGAAATTAATTTGTATATGA
*
17515071 TTATACATTGTTGAAATTGAA-TTGTATATGGA
1 TTATACATTGCTGAAATT-AATTTGTATAT-GA
* *
17515103 -TATA-AGTTGCCG-AATTGATTTGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGA
* * *
17515132 TTATATATTGCTGAAATTAATTTGTACATGG
1 TTATACATTGCTGAAATTAATTTGTATATGA
*
17515163 TTATACATTGTTGAAATTGAA-TTGTATATGGA
1 TTATACATTGCTGAAATT-AATTTGTATAT-GA
* ** * *
17515195 -TATA-AGTTGCCG-AATCGATTCGTATATGG
1 TTATACA-TTGCTGAAATTAATTTGTATATGA
*
17515224 TTATACATTGCTGAATTTAATTTGTATATGA
1 TTATACATTGCTGAAATTAATTTGTATATGA
* * ** *
17515255 TTATACATT-TTCG-AACTAGATTCATATATGG
1 TTATACATTGCT-GAAATTA-ATTTGTATATGA
* **
17515286 TTATACATTGCTG-ATTTTTTTTGTATATAGA
1 TTATACATTGCTGAAATTAATTTGTATAT-GA
* ** *
17515317 -TATACATTGCTGAATTTGGTTCGTATATGA
1 TTATACATTGCTGAAATTAATTTGTATATGA
* * *
17515347 ATATATATTGCTG-AATTTATTTG
1 TTATACATTGCTGAAATTAATTTG
17515370 AGCATTGGAT
Statistics
Matches: 421, Mismatches: 88, Indels: 71
0.73 0.15 0.12
Matches are distributed among these distances:
29 8 0.02
30 143 0.34
31 260 0.62
32 10 0.02
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (31 bp):
TTATACATTGCTGAAATTAATTTGTATATGA
Found at i:17515285 original size:184 final size:183
Alignment explanation
Indices: 17514785--17515330 Score: 765
Period size: 184 Copynumber: 3.0 Consensus size: 183
17514775 CGAATTCGAA
* * * * *
17514785 TTGTTCATAGTTATACATTGTTGAAATTGATTTGCATATGGGTATAAGTTGCCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
* * *
17514850 ATATGATTGTACATTGCTGAAATTAATTTGTACATGGTTATACATTGTCGAAATTGATTTGCATA
66 ATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATACATTTTCGAAATTGA-TTGTATA
* * *
17514915 TGGGTATAAGTTACCGAATTGATTTGTATATGATTGTACATTGCTGAAATTAAT
130 TGGATATAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAAT
*
17514969 TTGTACATGGTTATAAATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
*
17515034 ATATGATTATATATTGCTGAAATTAATTTGTACATGGTTATACATTGTT-GAAATTGAATTGTAT
66 ATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATACATT-TTCGAAATTG-ATTGTAT
*
17515098 ATGGATATAAGTTGCCGAATTGATTTGTATATGATTATATATTGCTGAAATTAAT
129 ATGGATATAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAAT
* *
17515153 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATCGATTCGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
* * * * * * *
17515218 ATATGGTTATACATTGCTGAATTTAATTTGTATATGATTATACATTTTCGAACTAGATTCATATA
66 ATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATACATTTTCGAAATTGATT-GTATA
* * * **
17515283 TGGTTATACA-TTGCTGATTTTTTTTGTATATAGA-TATACATTGCTGAA
130 TGGATATA-AGTTGCCGAATTGATTTGTATAT-GATTATACATTGCTGAA
17515331 TTTGGTTCGT
Statistics
Matches: 325, Mismatches: 31, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
183 5 0.02
184 315 0.97
185 5 0.02
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.43
Consensus pattern (183 bp):
TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
ATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATACATTTTCGAAATTGATTGTATAT
GGATATAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAAT
Found at i:17515285 original size:276 final size:277
Alignment explanation
Indices: 17514764--17515330 Score: 770
Period size: 276 Copynumber: 2.1 Consensus size: 277
17514754 TTTGATTGTT
* * * *
17514764 TTATATATTGCCG-AATTCGAATTGTTCATAGTTATACATTGTTGAAATTGATTTGCATATGGGT
1 TTATATATTGCTGAAATTC-AATTGTACATAGTTATACATTGTTGAAATTGAATTGCATATGGAT
*
17514828 ATAAGTTGCCGAATTGATTTGTATATGATTGTACATTGCTGAAATTAATTTGTACATGGTTATAC
65 ATAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATAC
* * * * *
17514893 ATTGTCGAAATTGATTTGCATATGGGTATAAGTTACCGAATTGATTTGTATATGATTGTACATTG
130 ATTGTCGAAATTGAATTGCATATGGATATAAGTTACCGAATCGATTCGTATATGATTATACATTG
* * *
17514958 CTGAAATTAATTTGTACATGGTTATAAATTGTTGAAATTGAATTGTATATGGATATA-AGTTGCC
195 CTGAAATTAATTTGTACATGATTATAAATTGTTGAAATAGAATTATATATGGATATACA-TTGCC
17515022 GAATTGATTTGTATAT-GA
259 GAATTGATTTGTATATAGA
* *
17515040 TTATATATTGCTGAAATT-AATTTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGAT
1 TTATATATTGCTGAAATTCAA-TTGTACATAGTTATACATTGTTGAAATTGAATTGCATATGGAT
*
17515104 ATAAGTTGCCGAATTGATTTGTATATGATTATATATTGCTGAAATTAATTTGTACATGGTTATAC
65 ATAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATAC
* * * *
17515169 ATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATCGATTCGTATATGGTTATACATTG
130 ATTGTCGAAATTGAATTGCATATGGATATAAGTTACCGAATCGATTCGTATATGATTATACATTG
* * * * *
17515234 CTGAATTTAATTTGTATATGATTATACATT-TTCGAACTAG-ATTCATATATGGTTATACATTGC
195 CTGAAATTAATTTGTACATGATTATAAATTGTT-GAAATAGAATT-ATATATGGATATACATTGC
* * **
17515297 TGATTTTTTTTGTATATAGA
258 CGAATTGATTTGTATATAGA
*
17515317 -TATACATTGCTGAA
1 TTATATATTGCTGAA
17515331 TTTGGTTCGT
Statistics
Matches: 255, Mismatches: 30, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
275 7 0.03
276 241 0.95
277 7 0.03
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (277 bp):
TTATATATTGCTGAAATTCAATTGTACATAGTTATACATTGTTGAAATTGAATTGCATATGGATA
TAAGTTGCCGAATTGATTTGTATATGATTATACATTGCTGAAATTAATTTGTACATGGTTATACA
TTGTCGAAATTGAATTGCATATGGATATAAGTTACCGAATCGATTCGTATATGATTATACATTGC
TGAAATTAATTTGTACATGATTATAAATTGTTGAAATAGAATTATATATGGATATACATTGCCGA
ATTGATTTGTATATAGA
Found at i:17515333 original size:92 final size:92
Alignment explanation
Indices: 17514785--17515263 Score: 769
Period size: 92 Copynumber: 5.2 Consensus size: 92
17514775 CGAATTCGAA
* * * * *
17514785 TTGTTCATAGTTATACATTGTTGAAATTGATTTGCATATGGGTATAAGTTGCCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
*
17514850 ATATGATTGTACATTGCTGAAATTAAT
66 ATATGATTATACATTGCTGAAATTAAT
* * * * *
17514877 TTGTACATGGTTATACATTGTCGAAATTGATTTGCATATGGGTATAAGTTACCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
*
17514942 ATATGATTGTACATTGCTGAAATTAAT
66 ATATGATTATACATTGCTGAAATTAAT
*
17514969 TTGTACATGGTTATAAATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
*
17515034 ATATGATTATATATTGCTGAAATTAAT
66 ATATGATTATACATTGCTGAAATTAAT
17515061 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
*
17515126 ATATGATTATATATTGCTGAAATTAAT
66 ATATGATTATACATTGCTGAAATTAAT
* *
17515153 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATCGATTCGT
1 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
* *
17515218 ATATGGTTATACATTGCTGAATTTAAT
66 ATATGATTATACATTGCTGAAATTAAT
* *
17515245 TTGTATATGATTATACATT
1 TTGTACATGGTTATACATT
17515264 TTCGAACTAG
Statistics
Matches: 367, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 367 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (92 bp):
TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
ATATGATTATACATTGCTGAAATTAAT
Found at i:17528053 original size:16 final size:16
Alignment explanation
Indices: 17528032--17528065 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17528022 TGTATTCTTT
17528032 TTTTGGTTAATCTAAC
1 TTTTGGTTAATCTAAC
**
17528048 TTTTGGTTCCTCTAAC
1 TTTTGGTTAATCTAAC
17528064 TT
1 TT
17528066 GTCGGCTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTTGGTTAATCTAAC
Found at i:17531394 original size:57 final size:57
Alignment explanation
Indices: 17531306--17531478 Score: 346
Period size: 57 Copynumber: 3.0 Consensus size: 57
17531296 TAAAATTAGG
17531306 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
1 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
17531363 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
1 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
17531420 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
1 TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
17531477 TT
1 TT
17531479 TTATCTGGTC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 116 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.46
Consensus pattern (57 bp):
TTAATTTTTGTCATTAATCCCTGTACTTTGCAAAAGTTATGGATTTGATCCTTGTGC
Found at i:17534473 original size:30 final size:31
Alignment explanation
Indices: 17534434--17534493 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
17534424 GGAGGTGGGA
*
17534434 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
17534465 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
17534494 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:17534727 original size:9 final size:9
Alignment explanation
Indices: 17534709--17534754 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
17534699 TATAGTTTGA
*
17534709 TATTCAAAT
1 TATTCGAAT
17534718 TATTCGAAT
1 TATTCGAAT
*
17534727 TATTCAAAT
1 TATTCGAAT
**
17534736 TATTCGAGC
1 TATTCGAAT
17534745 TATTCGAAT
1 TATTCGAAT
17534754 T
1 T
17534755 CGAAAACTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17534748 original size:18 final size:18
Alignment explanation
Indices: 17534709--17534754 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
17534699 TATAGTTTGA
*
17534709 TATTCAAATTATTCGAAT
1 TATTCAAATTATTCGAAC
*
17534727 TATTCAAATTATTCGAGC
1 TATTCAAATTATTCGAAC
*
17534745 TATTCGAATT
1 TATTCAAATT
17534755 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (18 bp):
TATTCAAATTATTCGAAC
Found at i:17534855 original size:107 final size:107
Alignment explanation
Indices: 17534743--17534956 Score: 401
Period size: 107 Copynumber: 2.0 Consensus size: 107
17534733 AATTATTCGA
17534743 GCTATTCGAATTCGAAAACTCAACTCGATTCGAACTCGAAATTTGAAAAAAAAATTCAAGTTGAT
1 GCTATTCGAATTCGAAAACTCAACTCGATTCGAACTCGAAATTTGAAAAAAAAATTCAAGTTGAT
*
17534808 TTGAATAACTCGATTAACTCGAATAACTCGATTCGTTTAACT
66 TTGAATAACTCGATTAACTCGAATAACTCGATTCGGTTAACT
17534850 GCTATTCGAATTCGAAAACTCAACTCGATTCGAACTCGAAATTTGAAAAAAAAATTCAAGTTGAT
1 GCTATTCGAATTCGAAAACTCAACTCGATTCGAACTCGAAATTTGAAAAAAAAATTCAAGTTGAT
* *
17534915 TTGAATAACTCGATTAACTCGAATAAGTCGATTTGGTTAACT
66 TTGAATAACTCGATTAACTCGAATAACTCGATTCGGTTAACT
17534957 CGAAATTCAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (107 bp):
GCTATTCGAATTCGAAAACTCAACTCGATTCGAACTCGAAATTTGAAAAAAAAATTCAAGTTGAT
TTGAATAACTCGATTAACTCGAATAACTCGATTCGGTTAACT
Found at i:17539655 original size:12 final size:12
Alignment explanation
Indices: 17539638--17539663 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17539628 TATTCATGTA
17539638 AACACTTCATAT
1 AACACTTCATAT
17539650 AACACTTCATAT
1 AACACTTCATAT
17539662 AA
1 AA
17539664 TTATTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (12 bp):
AACACTTCATAT
Found at i:17540284 original size:16 final size:16
Alignment explanation
Indices: 17540263--17540296 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17540253 CAAAAATACA
17540263 GAACAAATGTATATTC
1 GAACAAATGTATATTC
17540279 GAACAAATGTATATTC
1 GAACAAATGTATATTC
17540295 GA
1 GA
17540297 GTCTGCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (16 bp):
GAACAAATGTATATTC
Found at i:17542814 original size:20 final size:22
Alignment explanation
Indices: 17542786--17542826 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17542776 TAAGAAATGT
17542786 GGAAAAAG-A-AAGAAAAAAAG
1 GGAAAAAGAAGAAGAAAAAAAG
*
17542806 GGAAGAAGAAGAAGAAAAAAA
1 GGAAAAAGAAGAAGAAAAAAA
17542827 TAAAGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
GGAAAAAGAAGAAGAAAAAAAG
Found at i:17543642 original size:10 final size:10
Alignment explanation
Indices: 17543629--17543658 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17543619 AATATAAAAA
*
17543629 ATAATTTATT
1 ATAACTTATT
17543639 ATAACTTATT
1 ATAACTTATT
17543649 ATAACTTATT
1 ATAACTTATT
17543659 TTTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (10 bp):
ATAACTTATT
Found at i:17544130 original size:21 final size:21
Alignment explanation
Indices: 17544106--17544145 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17544096 TTTGATTCAC
*
17544106 CGTCATCATCATTATCATCGT
1 CGTCATCATCATCATCATCGT
* *
17544127 CGTCGTCGTCATCATCATC
1 CGTCATCATCATCATCATC
17544146 ACTTTCTCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (21 bp):
CGTCATCATCATCATCATCGT
Found at i:17545630 original size:72 final size:73
Alignment explanation
Indices: 17545538--17545712 Score: 239
Period size: 72 Copynumber: 2.4 Consensus size: 73
17545528 TCACATATAA
* * *
17545538 ATAAACAACTATTGATAAAACTAATTTAGTA-AAAAATAAGTAGAATATAAATTCAATATCTAAA
1 ATAAACAACTATTGATAAAACTAATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
17545602 GACCAAAC
66 AACCAAAC
* * *
17545610 ATAAACAACTTTTAATAAAACTAGA-TTA-CACATAAATAAGTAGAACATAAATTCAATATCCAA
1 ATAAACAACTATTGATAAAACTA-ATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAA
17545673 AAACCAAAC
65 AAACCAAAC
* *
17545682 ATAAATAACTATTGATAAAACTAGTTTAGCA
1 ATAAACAACTATTGATAAAACTAATTTAGCA
17545713 TTATTGTTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
71 1 0.01
72 84 0.95
73 3 0.03
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.26
Consensus pattern (73 bp):
ATAAACAACTATTGATAAAACTAATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAAA
AACCAAAC
Found at i:17547498 original size:44 final size:45
Alignment explanation
Indices: 17547433--17547531 Score: 168
Period size: 44 Copynumber: 2.2 Consensus size: 45
17547423 ACGCCTCCTC
17547433 CTTTTACCT-ATTGCTATCTTCTTCTTTTTC-TTTTTCTCCC-CTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTTC-CCCACTT
17547476 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTTCCCCACTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTTCCCCACTT
17547521 CTTTTACCTAA
1 CTTTTACCTAA
17547532 ATCAGATTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
43 9 0.17
44 24 0.45
45 20 0.38
ACGTcount: A:0.11, C:0.29, G:0.02, T:0.58
Consensus pattern (45 bp):
CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTTCCCCACTT
Found at i:17549234 original size:25 final size:25
Alignment explanation
Indices: 17549187--17549234 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17549177 AACCAACACC
*
17549187 AGCACCAACAGAAGAACAGAGAACT
1 AGCACCAACAGAAGAACAAAGAACT
* * *
17549212 AGCACCAGCAGAGGATCAAAGAA
1 AGCACCAACAGAAGAACAAAGAA
17549235 GCAGCGATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.23, G:0.23, T:0.04
Consensus pattern (25 bp):
AGCACCAACAGAAGAACAAAGAACT
Found at i:17564527 original size:45 final size:45
Alignment explanation
Indices: 17564452--17564585 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
17564442 ACGTGTACCG
* * *
17564452 GGTACCATTGATTATAAAGGTGGTTATTGTGTGCTGATTCCTCCT
1 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
* ** *
17564497 GGTATCATTGATTATAAAGGTGACTGTTGTGTGTTGATTCCACCA
1 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
* *
17564542 GGTACCATTGATTATGAAGGTGGTTGTTATGTGCTGATTCCACC
1 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACC
17564586 GTGTATCTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (45 bp):
GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
Found at i:17568228 original size:20 final size:20
Alignment explanation
Indices: 17568173--17568221 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
17568163 AACATGATTG
17568173 AAATCATTTTGACTTGGTTA
1 AAATCATTTTGACTTGGTTA
17568193 AAATCATTTTGACTTGGTTA
1 AAATCATTTTGACTTGGTTA
17568213 AAATCATTT
1 AAATCATTT
17568222 CCACTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
AAATCATTTTGACTTGGTTA
Found at i:17570686 original size:20 final size:21
Alignment explanation
Indices: 17570633--17570686 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
17570623 GATAATGAAT
*
17570633 ATAA-CAATGACATAGAGATA
1 ATAATCAATGACATAGAGAAA
* *
17570653 AT-ATAAATATACATA-AGAAA
1 ATAATCAAT-GACATAGAGAAA
17570673 ATAATCAATGACAT
1 ATAATCAATGACAT
17570687 GCAAAATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (21 bp):
ATAATCAATGACATAGAGAAA
Found at i:17571080 original size:26 final size:29
Alignment explanation
Indices: 17571019--17571082 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
17571009 TACACGTAAA
17571019 ATATAT-TAAAAATAATTAAATAATATCT
1 ATATATATAAAAATAATTAAATAATATCT
* *
17571047 ACAT-TATAAAAA-AA-TAAAT-ATATGT
1 ATATATATAAAAATAATTAAATAATATCT
17571072 ATATATATAAA
1 ATATATATAAA
17571083 CATGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.26
26 11 0.35
27 3 0.10
28 9 0.29
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
ATATATATAAAAATAATTAAATAATATCT
Found at i:17575530 original size:11 final size:11
Alignment explanation
Indices: 17575494--17575540 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
17575484 TTTTTTATGC
17575494 TTTT-TAAATT
1 TTTTATAAATT
*
17575504 TTTTATATATT
1 TTTTATAAATT
* *
17575515 CTTTAGAAATT
1 TTTTATAAATT
*
17575526 TTTTATTAATT
1 TTTTATAAATT
17575537 TTTT
1 TTTT
17575541 TAGTTATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTATAAATT
Found at i:17584494 original size:13 final size:13
Alignment explanation
Indices: 17584476--17584509 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17584466 ATTATTAAAT
*
17584476 ATTTATAAACAAA
1 ATTTATAAAAAAA
17584489 ATTTATAAAAAAA
1 ATTTATAAAAAAA
*
17584502 AGTTATAA
1 ATTTATAA
17584510 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (13 bp):
ATTTATAAAAAAA
Found at i:17588539 original size:16 final size:17
Alignment explanation
Indices: 17588518--17588549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17588508 AAATATGCAA
17588518 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
17588534 TCACATAACTTCATAT
1 TCACATAACTTCATAT
17588550 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:17588776 original size:43 final size:43
Alignment explanation
Indices: 17588709--17588878 Score: 199
Period size: 43 Copynumber: 4.0 Consensus size: 43
17588699 AGACTCGTAT
*
17588709 AATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATC
1 AATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATC
*
17588752 AATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-C
1 AATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATC
* * * *
17588793 GATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTC
1 AATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-TC
*
17588836 GATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATATC
1 AATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATATC
17588879 GGAAATCCTA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 27 0.25
42 16 0.15
43 61 0.56
44 5 0.05
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
AATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATC
Found at i:17588851 original size:84 final size:84
Alignment explanation
Indices: 17588710--17588867 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
17588700 GACTCGTATA
* * *
17588710 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGAC-GTGG
17588774 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
* *
17588794 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCAATGCC-ACTGTCCCAGACGTG
17588857 GTCTTACACGA
64 GTCTTACACGA
17588868 TAACACATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 62 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:17590127 original size:35 final size:35
Alignment explanation
Indices: 17590081--17590149 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
17590071 TCCCAAAACC
17590081 ACTGTTCCGATTAGGGTCAAAATCGGGCTGTTACT
1 ACTGTTCCGATTAGGGTCAAAATCGGGCTGTTACT
17590116 ACTGTTCCGATTAGGGTCAAAATCGGGCTGTTAC
1 ACTGTTCCGATTAGGGTCAAAATCGGGCTGTTAC
17590150 ATTTATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (35 bp):
ACTGTTCCGATTAGGGTCAAAATCGGGCTGTTACT
Found at i:17590303 original size:19 final size:19
Alignment explanation
Indices: 17590281--17590318 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17590271 TCACTGTCAC
17590281 CCACCATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
*
17590300 CCACCGTAATCAAATTTGT
1 CCACCATAATCAAATTTGT
17590319 TATTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:17590475 original size:18 final size:18
Alignment explanation
Indices: 17590431--17590468 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17590421 ATGTATTTTG
*
17590431 AAAT-TAAAACATATATT
1 AAATGTAAAAAATATATT
*
17590448 AAATGTAAAAAATATCTT
1 AAATGTAAAAAATATATT
17590466 AAA
1 AAA
17590469 GATAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATGTAAAAAATATATT
Found at i:17590843 original size:30 final size:32
Alignment explanation
Indices: 17590798--17590863 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 32
17590788 GGTGTGATGG
17590798 GAGGAGAGCAAAAGTTATGGGGA-GAAAGTG-A
1 GAGGAGAGCAAAAGTT-TGGGGAGGAAAGTGAA
* *
17590829 GAGG-GAGTAAAAGTTTTGGGAGGAAAGTGAA
1 GAGGAGAGCAAAAGTTTGGGGAGGAAAGTGAA
17590860 GAGG
1 GAGG
17590864 TTTAGGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.16
30 17 0.55
31 9 0.29
ACGTcount: A:0.39, C:0.02, G:0.44, T:0.15
Consensus pattern (32 bp):
GAGGAGAGCAAAAGTTTGGGGAGGAAAGTGAA
Found at i:17591603 original size:27 final size:27
Alignment explanation
Indices: 17591572--17591623 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
17591562 AATAAACTAA
17591572 AATATAACAATATAATAACATTTAAAT
1 AATATAACAATATAATAACATTTAAAT
*** *
17591599 AATATCTTAATATATTAACATTTAA
1 AATATAACAATATAATAACATTTAA
17591624 CAATTCCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (27 bp):
AATATAACAATATAATAACATTTAAAT
Found at i:17596957 original size:28 final size:30
Alignment explanation
Indices: 17596923--17596999 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 30
17596913 AGTGTTGGAA
*
17596923 AGAAAATGAGAGGAGAAAAAT-ATGTT-GG
1 AGAAAATGAGAGAAGAAAAATGATGTTAGG
* *
17596951 GGAAAATGGGAGAAGAAAAATGATGTTAGG
1 AGAAAATGAGAGAAGAAAAATGATGTTAGG
*
17596981 AGAAATTGAGAGAAGAAAA
1 AGAAAATGAGAGAAGAAAA
17597000 TTTTTTTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 18 0.44
29 5 0.12
30 18 0.44
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (30 bp):
AGAAAATGAGAGAAGAAAAATGATGTTAGG
Found at i:17602845 original size:41 final size:41
Alignment explanation
Indices: 17602800--17602914 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
17602790 TGATTCAGTA
* *
17602800 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAAT-GTAT
1 CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATACT-T
*
17602841 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATACTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATACTT
* *
17602882 CACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTG
17602915 TATTACATTC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 64 0.96
42 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATACTT
Done.