Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 184 of 210
Found at i:54514913 original size:21 final size:21
Alignment explanation
Indices: 54514868--54514944 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
54514858 ATCAGTAAAA
* * *
54514868 ACCTTAAAATAGTAACCCCTAT
1 ACCTTAAACTA-TAAACCATAT
54514890 ACCTTAAACTATAAACCATAT
1 ACCTTAAACTATAAACCATAT
* * * * *
54514911 ACCCTAAACCAAAAACCAAAA
1 ACCTTAAACTATAAACCATAT
54514932 ACCTTAAACTATA
1 ACCTTAAACTATA
54514945 GTGATAAATC
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
21 34 0.77
22 10 0.23
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.22
Consensus pattern (21 bp):
ACCTTAAACTATAAACCATAT
Found at i:54515169 original size:41 final size:41
Alignment explanation
Indices: 54515105--54515402 Score: 490
Period size: 41 Copynumber: 7.3 Consensus size: 41
54515095 CTAAAAGTGA
* *
54515105 CGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
* *
54515146 CGCTTCTTCAAAAACGCCACTAAAGCCCCGACCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
*
54515187 CGCTTCTTCAAAAACGTCGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
* * * *
54515228 CGGTTCTTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCAG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
*
54515269 CGCTGCTTCAAAAACGCCAG-TAAAGCCCCGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCC-GCTAAAGCCCCGAGCATTAGCGG
54515310 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
54515351 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
54515392 CGCTTCTTCAA
1 CGCTTCTTCAA
54515403 TTAGAAATTA
Statistics
Matches: 237, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
40 1 0.00
41 235 0.99
42 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (41 bp):
CGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
Found at i:54515963 original size:12 final size:12
Alignment explanation
Indices: 54515946--54515971 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54515936 ATTAAAATAT
54515946 TTATAATTTCGA
1 TTATAATTTCGA
54515958 TTATAATTTCGA
1 TTATAATTTCGA
54515970 TT
1 TT
54515972 TATGATGAAG
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATAATTTCGA
Found at i:54520571 original size:22 final size:22
Alignment explanation
Indices: 54520541--54520584 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54520531 TACACCAAAA
* * *
54520541 TAGGTCTTTAGTGGCGTTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
54520563 TAGGCCTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
54520585 AACGCCACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCGCTTTTT
Found at i:54520733 original size:42 final size:42
Alignment explanation
Indices: 54520676--54520883 Score: 319
Period size: 42 Copynumber: 4.9 Consensus size: 42
54520666 GTTTACAAAC
54520676 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
54520718 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
54520760 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * * *
54520802 GAAAAA-GCCGCTAAAGATCATGTTCTTCAGTGGCGCTTAAAAAA
1 -AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT--AGAA
*
54520846 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
54520884 TTATACAAAA
Statistics
Matches: 150, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
42 109 0.73
43 10 0.07
44 31 0.21
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:54527534 original size:445 final size:445
Alignment explanation
Indices: 54526588--54527759 Score: 2136
Period size: 445 Copynumber: 2.6 Consensus size: 445
54526578 CTTACAGGGG
*
54526588 CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAATGCCACTAAAAGATTCCATCCTTCAACT
1 CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATCCTTCAACT
54526653 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
66 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
*
54526718 ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCGATAAATATTTGTGGCGCTT
131 ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
*
54526783 TTTATAAAAACACCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
196 TTTATAAAAACGCCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
* ** * *
54526848 --CT-C-CTAAGAAACGGCGCCGTTTAACGTAATTTTAAGTCAGAGTTGTGGCGTTTTAGTTAAA
261 AAGTACAGAAAGAAACGGCGCCGTTTAAAGTAATTTTAAGTCAGAGTTGCGGCGTTTTAGTTAAA
54526909 AACGCCACTAAAATTTCAAGTCATTAATGGAAACGGCGCCGTTTTATAAAAATACAAGAAAACCT
326 AACGCCACTAAAATTTCAAGTCATTAATGGAAACGGCGCCGTTTTATAAAAATACAAGAAAACCT
* * *
54526974 GGTGTTTTCCCAAACACGCCACAATCAATATATTATCGAATCGGCGTCGTTTTCA
391 GGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCAGCGTCGTTTTCA
*
54527029 CAAAATTTTATACATATTTGCGACGTTTTTAATAAAACGCCACTAAAAGATTCCATCCTTCAACT
1 CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATCCTTCAACT
*
54527094 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAATGCCACAAG
66 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
54527159 ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
131 ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
* * *
54527224 TTTATAAAAACGCCGGTAATGTCAAACTTTTTACGGTGTTTAATTGGAAATGCCACTAAAATTTC
196 TTTATAAAAACGCCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
*
54527289 AAGTACAGAAAGAAATGGCGCCGTTTAAAGTAATTTTAAGTCAGAGTTGCGGCGTTTTAGTTAAA
261 AAGTACAGAAAGAAACGGCGCCGTTTAAAGTAATTTTAAGTCAGAGTTGCGGCGTTTTAGTTAAA
54527354 AACGCCACTAAAATTTCAAGTCATTAATGGAAACGGCGCCGTTTTATAAAAATACAAGAAAACCT
326 AACGCCACTAAAATTTCAAGTCATTAATGGAAACGGCGCCGTTTTATAAAAATACAAGAAAACCT
*
54527419 GGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCAGCGTTGTTTTCA
391 GGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCAGCGTCGTTTTCA
*
54527474 CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCTATCCTTCAACT
1 CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATCCTTCAACT
54527539 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
66 AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
*
54527604 ATAAATTTATCCCCTCAGTCGAAACGACGATGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
131 ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
54527669 TTTATAAAAACGCCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
196 TTTATAAAAACGCCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
54527734 AAGTACAGAAAGAAACGGCGCCGTTT
261 AAGTACAGAAAGAAACGGCGCCGTTT
54527760 TATAAAAATA
Statistics
Matches: 701, Mismatches: 26, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
441 252 0.36
443 1 0.00
444 1 0.00
445 447 0.64
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (445 bp):
CAAAATTTTATACATATTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATCCTTCAACT
AAAACAGCGTCGTTTTCGCAGAGTACTTCATATCTTTACGGCGCTTTAAGGAAAAACGCCACAAG
ATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAATAAATATTTGTGGCGCTT
TTTATAAAAACGCCGGTAATGTCAAACTTTTTGCGGCGTTTAATTGGAAACGCCACTAAAATTTC
AAGTACAGAAAGAAACGGCGCCGTTTAAAGTAATTTTAAGTCAGAGTTGCGGCGTTTTAGTTAAA
AACGCCACTAAAATTTCAAGTCATTAATGGAAACGGCGCCGTTTTATAAAAATACAAGAAAACCT
GGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCAGCGTCGTTTTCA
Found at i:54528118 original size:24 final size:24
Alignment explanation
Indices: 54528091--54528171 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
54528081 TGTATCATTC
54528091 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTATCT
*
54528115 ATTTAAACAATTAATTACCTA-CAAATT
1 ATTTAAATAATTAATTACCTATC----T
*
54528142 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTATCT
54528167 ATTTA
1 ATTTA
54528172 TTTGTTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.02
24 25 0.52
25 1 0.02
27 1 0.02
28 20 0.42
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATCT
Found at i:54528174 original size:28 final size:26
Alignment explanation
Indices: 54528091--54528174 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 26
54528081 TGTATCATTC
*
54528091 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
54528115 ATTTAAACAATTAATTACCTACAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
54528143 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
54528171 ATTT
1 ATTT
54528175 GTTTATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 28 0.60
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:54528582 original size:29 final size:29
Alignment explanation
Indices: 54528544--54528611 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
54528534 ACCTTTGAAA
*
54528544 CCCTAAACCCTAAACCCCAAATCTATTAC
1 CCCTAAACCCTAAACCCCAAATCCATTAC
*
54528573 CCCTAAACCCTAAACCTCAAATCCATTAC
1 CCCTAAACCCTAAACCCCAAATCCATTAC
54528602 CCCTAAACCC
1 CCCTAAACCC
54528612 GATCCTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (29 bp):
CCCTAAACCCTAAACCCCAAATCCATTAC
Found at i:54528758 original size:12 final size:12
Alignment explanation
Indices: 54528741--54528779 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
54528731 CTCTTAACAT
54528741 CTAACCCCTAAC
1 CTAACCCCTAAC
54528753 CTAACCCCTAACCC
1 CTAACCCCTAA--C
*
54528767 CTAACCCTTAAC
1 CTAACCCCTAAC
54528779 C
1 C
54528780 CATAAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:54528780 original size:14 final size:14
Alignment explanation
Indices: 54528752--54528791 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54528742 TAACCCCTAA
*
54528752 CCTAACCCCTAACC
1 CCTAACCCTTAACC
54528766 CCTAACCCTTAACC
1 CCTAACCCTTAACC
* *
54528780 CATAAACCTTAA
1 CCTAACCCTTAA
54528792 ATCACATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTAACCCTTAACC
Found at i:54528837 original size:14 final size:14
Alignment explanation
Indices: 54528772--54528837 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
54528762 AACCCCTAAC
* *
54528772 CCTTAACCCATAAA
1 CCTTAATCCATAAT
*
54528786 CCTTAAATCACATTAAC
1 CCTT-AATC-CA-TAAT
* *
54528803 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
54528817 CCCTAATCCATAAT
1 CCTTAATCCATAAT
54528831 CCTTAAT
1 CCTTAAT
54528838 TCTATAATCT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
14 23 0.57
15 5 0.12
16 5 0.12
17 7 0.17
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:54529516 original size:113 final size:112
Alignment explanation
Indices: 54529393--54529721 Score: 362
Period size: 113 Copynumber: 2.9 Consensus size: 112
54529383 ATTACTGAGC
* * *
54529393 ATTAGCGGCGCTTTACAAAAAAACGCCACTAAAT-CCTGAAAGCTCAGAAAACGGCGTCGTTGTG
1 ATTAGCGGCGCTTTACAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
54529457 CTTAGGTTATTTGTGGCGCTTTATCTAAAACGCCGCTAAAGCCCTAGAT
66 CTTAGGTT-TTTGTGGCGCTTT-TCTAAAACGCCGCTAAAGCCCTAGAT
** * *
54529506 ATTAGCGGCGC-TTACTTGAAAAACGCCGCTAAATCCCCGAAAGCTC-GAAAACGACATCGTTGG
1 ATTAGCGGCGCTTTAC-AAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
* * * * * * *
54529569 GCTCAGTTTTTTTTGTGGCGCTTTGCTGAAAACTCCGCT-AAGTCCTGGGT
65 GCTTAG--GTTTTTGTGGCGCTTTTCT-AAAACGCCGCTAAAGCCCTAGAT
* * *
54529619 ATTAGCGTCGCTTCA-AAAAAAACGCCGCTAATTCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
1 ATTAGCGGCGCTTTACAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
* * * *
54529683 ATTAGGTGTTTTGCGGTGCTTTCTCGAAAACGCCGCTAA
66 CTTAGGT-TTTTGTGGCGCTTT-TCTAAAACGCCGCTAA
54529722 TGCTTATTTT
Statistics
Matches: 177, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
111 1 0.01
112 53 0.30
113 86 0.49
114 35 0.20
115 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (112 bp):
ATTAGCGGCGCTTTACAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
CTTAGGTTTTTGTGGCGCTTTTCTAAAACGCCGCTAAAGCCCTAGAT
Found at i:54532298 original size:19 final size:18
Alignment explanation
Indices: 54532262--54532300 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54532252 TTCAAAATTC
* *
54532262 AAAATATTTTTCATTTGA
1 AAAATACTTTTCAGTTGA
54532280 AAAATACTTTTCAAGTTGA
1 AAAATACTTTTC-AGTTGA
54532299 AA
1 AA
54532301 TCAAATCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (18 bp):
AAAATACTTTTCAGTTGA
Found at i:54532802 original size:8 final size:8
Alignment explanation
Indices: 54532791--54532829 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
54532781 ATTTGGTTAT
54532791 TTTTTTTA
1 TTTTTTTA
54532799 TTTTTTTGA
1 TTTTTTT-A
**
54532808 TTTGGTTA
1 TTTTTTTA
54532816 TTTTTTTA
1 TTTTTTTA
54532824 TTTTTT
1 TTTTTT
54532830 CTTATTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:54532808 original size:26 final size:25
Alignment explanation
Indices: 54532778--54532839 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
54532768 AAGATTTTGA
54532778 TTGATTTGGTTATTTTTTTTATTTTT
1 TTGATTTGGTTA-TTTTTTTATTTTT
54532804 TTGATTTGGTTATTTTTTTATTTTT
1 TTGATTTGGTTATTTTTTTATTTTT
*
54532829 TCTTATTTGGT
1 T-TGATTTGGT
54532840 ATTATTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.74
Consensus pattern (25 bp):
TTGATTTGGTTATTTTTTTATTTTT
Found at i:54532834 original size:10 final size:9
Alignment explanation
Indices: 54532787--54532836 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
54532777 ATTGATTTGG
54532787 TTATTTTTT
1 TTATTTTTT
54532796 TTATTTTTT
1 TTATTTTTT
* **
54532805 TGA-TTTGG
1 TTATTTTTT
54532813 TTA-TTTTT
1 TTATTTTTT
54532821 TTATTTTTT
1 TTATTTTTT
54532830 CTTATTT
1 -TTATTT
54532837 GGTATTATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 11 0.33
9 16 0.48
10 6 0.18
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (9 bp):
TTATTTTTT
Found at i:54533962 original size:20 final size:18
Alignment explanation
Indices: 54533916--54533963 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
54533906 TAAATTTACG
*
54533916 ATCATTTTGTTGCATTTC
1 ATCATTTTGTTACATTTC
*
54533934 ATTCGTTTTGTTACGATTTTC
1 A-TCATTTTGTTAC-A-TTTC
54533955 ATCATTTTG
1 ATCATTTTG
54533964 GTCTATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 10 0.42
20 8 0.33
21 5 0.21
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (18 bp):
ATCATTTTGTTACATTTC
Found at i:54539349 original size:143 final size:142
Alignment explanation
Indices: 54539145--54539809 Score: 963
Period size: 143 Copynumber: 4.6 Consensus size: 142
54539135 GATTGAAGTC
* * * **
54539145 ATTATGGCGAATCTTCTCTTCCTGAAGTTGCAGCGGAGCAGATTAAAGCCACCAGCCTTATCTTT
1 ATTATGGCG-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
54539210 CTGAAGTTGCAGCAGAGCAGACTGAAAACAACGAATCTTATTTCCCCGGCGTTGTAGTGGAATAG
65 CTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
54539275 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* *
54539288 ATTATGGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCCCC
1 ATTATGGC-GATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * *
54539353 CTGAAGTTGCAGCTGAGCAGACTGAAGACAGTGAATCTTATTTCTCTGGCGTTGCAGTGGAACAG
65 CTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
54539418 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* *
54539431 TTTATGGTGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGG-CGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * ** * *
54539496 CTAAAGTTGTAGTGGAGCAGACTGAAGACAGCGAATCTTATTTTCCTGGCGTTGCAGTGGAATAG
65 CTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
54539561 ATTAAAGCTACAA
130 ATTAAAGCTACAA
*
54539574 ATTATGTCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGC-GATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
54539639 CTAAAGTTGTAGCAGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAG
65 CTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
54539704 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* * * * *
54539717 ATTATTGCGAATCTTATCTTTCTGAAGTTGCAGTGGAGCATATTGAAGCCACTAGTCTTATCTCC
1 ATTATGGCG-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
*
54539782 CTGAAGTTGCAG-TGAGGCAGACTGAAGA
65 CTGAAGTTGCAGCAGA-GCAGACTGAAGA
54539810 TAGTAAATCT
Statistics
Matches: 471, Mismatches: 46, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
142 3 0.01
143 467 0.99
144 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (142 bp):
ATTATGGCGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTGCAGCAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGA
TTAAAGCTACAA
Found at i:54539953 original size:44 final size:44
Alignment explanation
Indices: 54539726--54539982 Score: 189
Period size: 44 Copynumber: 5.9 Consensus size: 44
54539716 AATTATTGCG
** * ** *
54539726 AATCTTATCTTTCTGAAGTTGCAGTGGAGCATATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * *
54539770 AGTCTTATCTCCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAAGATA-CA
** ** * *
54539815 AATCTTATCTCTTTGAAGTTGCAGAAGAGCAGA-T-CACAT-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * ** * * * *
54539856 AACCTTATCTCCCTAAAGTTGCAGTGGAATAGGTTAAAGTTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* *
54539900 AATCATATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGATACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * * **
54539944 AGTCGTATCTCTCTGAAGTTACAGTGGAGTGGATTGAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
54539983 CAACAAGACG
Statistics
Matches: 161, Mismatches: 46, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
41 25 0.16
42 1 0.01
43 7 0.04
44 100 0.62
45 26 0.16
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
Found at i:54540195 original size:30 final size:30
Alignment explanation
Indices: 54540159--54540215 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
54540149 CGAGGTCCAA
54540159 TAAAACCCAAACAAAACCAAATACAAAAAT
1 TAAAACCCAAACAAAACCAAATACAAAAAT
* * *
54540189 TAAAACCCAAACATAACTAAATCCAAA
1 TAAAACCCAAACAAAACCAAATACAAA
54540216 CCCAACAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.63, C:0.25, G:0.00, T:0.12
Consensus pattern (30 bp):
TAAAACCCAAACAAAACCAAATACAAAAAT
Found at i:54541513 original size:26 final size:23
Alignment explanation
Indices: 54541484--54541538 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
54541474 ACATTATTTG
54541484 TTTTAAAATATCTTGTATATAATAT
1 TTTTAAAAT-T-TTGTATATAATAT
* *
54541509 CTTTTAAAATTTTTTATATATTAT
1 -TTTTAAAATTTTGTATATAATAT
54541533 TTTTAA
1 TTTTAA
54541539 TAAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 1 0.04
26 9 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTAAAATTTTGTATATAATAT
Found at i:54541679 original size:11 final size:11
Alignment explanation
Indices: 54541663--54541697 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
54541653 TTCTCATCAT
54541663 TTATTTATTTA
1 TTATTTATTTA
*
54541674 TTATTTATGTA
1 TTATTTATTTA
*
54541685 CTATTTATTTA
1 TTATTTATTTA
54541696 TT
1 TT
54541698 TACTGTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:54541701 original size:15 final size:16
Alignment explanation
Indices: 54541661--54541701 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
54541651 ATTTCTCATC
*
54541661 ATTTATTTA-TTTATT
1 ATTTATTTACTATATT
*
54541676 ATTTATGTACTAT-TT
1 ATTTATTTACTATATT
54541691 ATTTATTTACT
1 ATTTATTTACT
54541702 GTTATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTTATTTACTATATT
Found at i:54543004 original size:2 final size:2
Alignment explanation
Indices: 54542997--54543067 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
54542987 GATTCACATA
54542997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54543039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54543068 ATTCCACTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54545842 original size:3 final size:3
Alignment explanation
Indices: 54545834--54545861 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54545824 AATGATACCA
54545834 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54545862 TTGATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54546670 original size:19 final size:19
Alignment explanation
Indices: 54546624--54546670 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
54546614 GAAAAAAATT
54546624 AAGGGTTT-GGGAAAGTAA
1 AAGGGTTTGGGGAAAGTAA
**
54546642 AAGTTTTTTGGGGAAAGTAA
1 AAG-GGTTTGGGGAAAGTAA
54546662 AAGGGTTTG
1 AAGGGTTTG
54546671 AGAAAGGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (19 bp):
AAGGGTTTGGGGAAAGTAA
Found at i:54547057 original size:3 final size:3
Alignment explanation
Indices: 54547049--54547097 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
54547039 AATGATACCA
54547049 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54547096 TA
1 TA
54547098 ATAAATATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:54550937 original size:29 final size:29
Alignment explanation
Indices: 54550881--54550937 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
54550871 GTAATATGGG
* *
54550881 TGCTTAAATTGCAAAATTTTTATTTTGGA
1 TGCTTAAAATGCAAAATTTTTATGTTGGA
*
54550910 TGCTTAAAATG-AAATTTTTTATAGTTGG
1 TGCTTAAAATGCAAAATTTTTAT-GTTGG
54550938 GTGATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (29 bp):
TGCTTAAAATGCAAAATTTTTATGTTGGA
Found at i:54551028 original size:26 final size:26
Alignment explanation
Indices: 54550983--54551046 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
54550973 ATATTAGAAA
* * *
54550983 AATAATTTAATTATTAAAATAATTGT
1 AATATTTTAATTACTAAAATAATTAT
* *
54551009 AATATTTTAATTACTGAAATAGTTAT
1 AATATTTTAATTACTAAAATAATTAT
*
54551035 CATATTTTAATT
1 AATATTTTAATT
54551047 GTAATCAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
AATATTTTAATTACTAAAATAATTAT
Found at i:54553222 original size:19 final size:18
Alignment explanation
Indices: 54553178--54553222 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
54553168 ATTGTTTTGG
54553178 GGGTTTGGGGAAGTAAAA
1 GGGTTTGGGGAAGTAAAA
**
54553196 GTTTTTTGGGGAAAGTAAAA
1 G-GGTTTGGGG-AAGTAAAA
54553216 GGGTTTG
1 GGGTTTG
54553223 AGAAAGGGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (18 bp):
GGGTTTGGGGAAGTAAAA
Found at i:54553537 original size:3 final size:3
Alignment explanation
Indices: 54553529--54553557 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54553519 NNNNNNNNNN
54553529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54553558 TTGATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54553648 original size:13 final size:13
Alignment explanation
Indices: 54553618--54553656 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
54553608 TGCTCCCCCC
54553618 AAAACAAATAAAACA
1 AAAACAAA-AAAA-A
54553633 AAAACCAAAAAAAA
1 AAAA-CAAAAAAAA
54553647 AAAACAAAAA
1 AAAACAAAAA
54553657 CTAATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.26
14 5 0.22
15 8 0.35
16 4 0.17
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:54553652 original size:20 final size:21
Alignment explanation
Indices: 54553616--54553657 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
54553606 TTTGCTCCCC
*
54553616 CCAAAACAAATAAAACAAAAA
1 CCAAAACAAAAAAAACAAAAA
54553637 CCAAAA-AAAAAAAACAAAAA
1 CCAAAACAAAAAAAACAAAAA
54553657 C
1 C
54553658 TAATAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.79, C:0.19, G:0.00, T:0.02
Consensus pattern (21 bp):
CCAAAACAAAAAAAACAAAAA
Found at i:54557726 original size:28 final size:28
Alignment explanation
Indices: 54557686--54557876 Score: 133
Period size: 27 Copynumber: 7.0 Consensus size: 28
54557676 CCAAGTCCCT
54557686 CAATTTACAAAAATTACTGAAATACCCC
1 CAATTTACAAAAATTACTGAAATACCCC
*
54557714 CAATTTACAAAAATTACT-AAAAACCCC
1 CAATTTACAAAAATTACTGAAATACCCC
*** ** *
54557741 TGGTTT-GTAAAATTACTGAAATACCCT
1 CAATTTACAAAAATTACTGAAATACCCC
* * *
54557768 CAATTT-GAAAAATTA-TCAAAATACCCT
1 CAATTTACAAAAATTACT-GAAATACCCC
* * **
54557795 CGATTTACAAAAATTATTGAAATACCTT
1 CAATTTACAAAAATTACTGAAATACCCC
* * **
54557823 TAATTTTC-AAAATTACCAAAATACCCC
1 CAATTTACAAAAATTACTGAAATACCCC
* **
54557850 CAATATGTAAAAATTA-TCGAAATACCC
1 CAATTTACAAAAATTACT-GAAATACCC
54557877 TTAATTTGTG
Statistics
Matches: 126, Mismatches: 31, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
26 10 0.08
27 61 0.48
28 54 0.43
29 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.29
Consensus pattern (28 bp):
CAATTTACAAAAATTACTGAAATACCCC
Found at i:54557820 original size:55 final size:55
Alignment explanation
Indices: 54557682--54557910 Score: 198
Period size: 55 Copynumber: 4.2 Consensus size: 55
54557672 GTCGCCAAGT
* *
54557682 CCCTCAATTTACAAAAATTACTGAAATACCCCCAATTTACAAAAATTA-CTAAAA-A
1 CCCTCAATTTACAAAAATTACTGAAATACCCTCAATTT-GAAAAATTATC-AAAATA
** **
54557737 CCC-CTGGTTT-GTAAAATTACTGAAATACCCTCAATTTGAAAAATTATCAAAATA
1 CCCTC-AATTTACAAAAATTACTGAAATACCCTCAATTTGAAAAATTATCAAAATA
* * * * ** *
54557791 CCCTCGATTTACAAAAATTATTGAAATACCTTTAATTTTCAAAATTACCAAAATA
1 CCCTCAATTTACAAAAATTACTGAAATACCCTCAATTTGAAAAATTATCAAAATA
* * ** * **
54557846 CCCCCAATATGTAAAAATTA-TCGAAATACCCTTAATTTGTGAAATTATCAAAATA
1 CCCTCAATTTACAAAAATTACT-GAAATACCCTCAATTTGAAAAATTATCAAAATA
*
54557901 CCCTTAATTT
1 CCCTCAATTT
54557911 GTAGAATTAC
Statistics
Matches: 140, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
53 12 0.09
54 35 0.25
55 93 0.66
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.31
Consensus pattern (55 bp):
CCCTCAATTTACAAAAATTACTGAAATACCCTCAATTTGAAAAATTATCAAAATA
Found at i:54557844 original size:27 final size:26
Alignment explanation
Indices: 54557759--54557919 Score: 115
Period size: 27 Copynumber: 5.9 Consensus size: 26
54557749 AAAATTACTG
* *
54557759 AAATACCCTCAATTTGAAAAATTATCA
1 AAATACCCTTAATTT-TAAAATTATCA
** * **
54557786 AAATACCCTCGATTTACAAAAATTATTG
1 AAATACCCTTAATTT--TAAAATTATCA
* *
54557814 AAATACCTTTAATTTTCAAAATTACCA
1 AAATACCCTTAATTTT-AAAATTATCA
** * *
54557841 AAATACCCCCAATATGTAAAAATTATCG
1 AAATACCCTTAAT-T-TTAAAATTATCA
*
54557869 AAATACCCTTAATTTGTGAAATTATCA
1 AAATACCCTTAATTT-TAAAATTATCA
*
54557896 AAATACCCTTAATTTGTAGAATTA
1 AAATACCCTTAATTT-TAAAATTA
54557920 CCGACATACC
Statistics
Matches: 105, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
26 1 0.01
27 62 0.59
28 41 0.39
29 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (26 bp):
AAATACCCTTAATTTTAAAATTATCA
Found at i:54557919 original size:82 final size:82
Alignment explanation
Indices: 54557705--54557930 Score: 226
Period size: 82 Copynumber: 2.8 Consensus size: 82
54557695 AAAATTACTG
* * ** * *
54557705 AAATACCCCCAATTTACAAAAATTA-CTAAAA-ACCCCTGGTTTGTAAAATTACTGAAATACCCT
1 AAATACCCTCAATTTACAAAAATTATC-AAAATACCCTTAATTTGTAAAATTACCGAAATACCCC
*
54557768 CAATTTGAAAAATTATCA
65 CAATATGAAAAATTATCA
* ** * *
54557786 AAATACCCTCGATTTACAAAAATTATTGAAATACCTTTAATTT-TCAAAATTACCAAAATACCCC
1 AAATACCCTCAATTTACAAAAATTATCAAAATACCCTTAATTTGT-AAAATTACCGAAATACCCC
*
54557850 CAATATGTAAAAATTATCG
65 CAATATG-AAAAATTATCA
* *** * *
54557869 AAATACCCTTAATTT-GTGAAATTATCAAAATACCCTTAATTTGTAGAATTACCGACATACCC
1 AAATACCCTCAATTTACAAAAATTATCAAAATACCCTTAATTTGTAAAATTACCGAAATACCC
54557931 ATATAGGGTA
Statistics
Matches: 116, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
81 27 0.23
82 65 0.56
83 24 0.21
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (82 bp):
AAATACCCTCAATTTACAAAAATTATCAAAATACCCTTAATTTGTAAAATTACCGAAATACCCCC
AATATGAAAAATTATCA
Found at i:54557928 original size:27 final size:27
Alignment explanation
Indices: 54557744--54557930 Score: 110
Period size: 27 Copynumber: 6.9 Consensus size: 27
54557734 AAACCCCTGG
* *
54557744 TTTGTAAAATTA-CTGAAATACCCTCAA
1 TTTGTGAAATTATC-GAAATACCCTTAA
** * **
54557771 TTTGAAAAATTATCAAAATACCCTCGA
1 TTTGTGAAATTATCGAAATACCCTTAA
*** * *
54557798 TTTACAAAAATTATTGAAATACCTTTAA
1 TTT-GTGAAATTATCGAAATACCCTTAA
* * * **
54557826 TTT-TCAAAATTACCAAAATACCCCCAA
1 TTTGT-GAAATTATCGAAATACCCTTAA
* *
54557853 TATGTAAAAATTATCGAAATACCCTTAA
1 TTTGT-GAAATTATCGAAATACCCTTAA
*
54557881 TTTGTGAAATTATCAAAATACCCTTAA
1 TTTGTGAAATTATCGAAATACCCTTAA
* *
54557908 TTTGT-AGAATTACCGACATACCC
1 TTTGTGA-AATTATCGAAATACCC
54557931 ATATAGGGTA
Statistics
Matches: 127, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.64
28 45 0.35
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (27 bp):
TTTGTGAAATTATCGAAATACCCTTAA
Found at i:54565259 original size:50 final size:50
Alignment explanation
Indices: 54565111--54565356 Score: 128
Period size: 50 Copynumber: 5.1 Consensus size: 50
54565101 ATACCTTTGT
* * * * *
54565111 AGTTGTAGTGCGTCGGATTGAATCTACCATAGCGAGTCTTATCTCCCTAA
1 AGTTGCAGTGGGTAGGATTGAATCTACCATAGCAAATCTTATCTCCCTAA
* * * * *
54565161 AGTTACAGTGGAGTAAGATTG-A---AGC-TA-CAAATCCTATAC-CCCTGA
1 AGTTGCAGTGG-GTAGGATTGAATCTACCATAGCAAATCTTAT-CTCCCTAA
* *
54565206 AGTTGCAGTGGGTTGGATTGAATCTACCATAGCAAATGTTATCTCCCTAA
1 AGTTGCAGTGGGTAGGATTGAATCTACCATAGCAAATCTTATCTCCCTAA
* * * * *
54565256 AGTTGCGGTGGAGCA-GATTGAA-GT----TA-CAAATCCTATAC-CTCTAA
1 AGTTGCAGTGG-GTAGGATTGAATCTACCATAGCAAATCTTAT-CTCCCTAA
* * * * * *
54565300 AGTTGTAGTGGGTCA-AATAGAATCTACCAAAGCGAATCTTATCTCTCTAA
1 AGTTGCAGTGGGT-AGGATTGAATCTACCATAGCAAATCTTATCTCCCTAA
54565350 AGTTGCA
1 AGTTGCA
54565357 ATAGAGCAAA
Statistics
Matches: 143, Mismatches: 34, Indels: 38
0.67 0.16 0.18
Matches are distributed among these distances:
43 1 0.01
44 35 0.24
45 27 0.19
46 3 0.02
47 2 0.01
48 2 0.01
49 6 0.04
50 59 0.41
51 8 0.06
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (50 bp):
AGTTGCAGTGGGTAGGATTGAATCTACCATAGCAAATCTTATCTCCCTAA
Found at i:54565323 original size:94 final size:95
Alignment explanation
Indices: 54565085--54565356 Score: 357
Period size: 95 Copynumber: 2.9 Consensus size: 95
54565075 AATAAATGGG
* * * * *
54565085 TGAAACTACAAATCCTATACCTTTGTAGTTGTAGTGCGTCGGATTGAATCTACCATAGCGAGTCT
1 TGAAGCTACAAATCCTATACCTCTGAAGTTGTAGTGGGTCGGATTGAATCTACCATAGCGAATCT
*
54565150 TATCTCCCTAAAGTTACAGTGGAGTAAGAT
66 TATCTCCCTAAAGTTGCAGTGGAGTAAGAT
* * * * *
54565180 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTTGGATTGAATCTACCATAGCAAATGT
1 TGAAGCTACAAATCCTATACCTCTGAAGTTGTAGTGGGTCGGATTGAATCTACCATAGCGAATCT
* *
54565245 TATCTCCCTAAAGTTGCGGTGGAG-CAGAT
66 TATCTCCCTAAAGTTGCAGTGGAGTAAGAT
* * ** * *
54565274 TGAAGTTACAAATCCTATACCTCTAAAGTTGTAGTGGGTCAAATAGAATCTACCAAAGCGAATCT
1 TGAAGCTACAAATCCTATACCTCTGAAGTTGTAGTGGGTCGGATTGAATCTACCATAGCGAATCT
*
54565339 TATCTCTCTAAAGTTGCA
66 TATCTCCCTAAAGTTGCA
54565357 ATAGAGCAAA
Statistics
Matches: 151, Mismatches: 26, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
94 74 0.49
95 77 0.51
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (95 bp):
TGAAGCTACAAATCCTATACCTCTGAAGTTGTAGTGGGTCGGATTGAATCTACCATAGCGAATCT
TATCTCCCTAAAGTTGCAGTGGAGTAAGAT
Found at i:54565913 original size:21 final size:20
Alignment explanation
Indices: 54565887--54565933 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
54565877 CTTTGCCTAC
*
54565887 TTATTTTATTTTTTATTATCA
1 TTATTTTATTATTTATT-TCA
*
54565908 TTATTTTATTATTTATTTTA
1 TTATTTTATTATTTATTTCA
54565928 TTATTT
1 TTATTT
54565934 CCGGCACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTATTATTTATTTCA
Found at i:54565925 original size:12 final size:12
Alignment explanation
Indices: 54565897--54565933 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
54565887 TTATTTTATT
54565897 TTTTATTATCATTA
1 TTTTATTAT--TTA
54565911 TTTTATTATTTA
1 TTTTATTATTTA
54565923 TTTTATTATTT
1 TTTTATTATTT
54565934 CCGGCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.61
14 9 0.39
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:54568359 original size:35 final size:34
Alignment explanation
Indices: 54568303--54568368 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
54568293 GAAATGATAC
*
54568303 AAATATAAAAGATATATAAACATAAATATGTATA
1 AAATATAAAAGATATAAAAACATAAATATGTATA
*
54568337 AAATAATAAAA-ATATGAAAAACATATATATGT
1 AAAT-ATAAAAGATAT-AAAAACATAAATATGT
54568369 GCATGTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (34 bp):
AAATATAAAAGATATAAAAACATAAATATGTATA
Found at i:54568428 original size:15 final size:15
Alignment explanation
Indices: 54568408--54568437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54568398 ATATATATAT
*
54568408 ATATAAAATTATACA
1 ATATAAAAATATACA
54568423 ATATAAAAATATACA
1 ATATAAAAATATACA
54568438 TAAGTATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAAAAATATACA
Found at i:54570992 original size:208 final size:208
Alignment explanation
Indices: 54570595--54571041 Score: 734
Period size: 208 Copynumber: 2.1 Consensus size: 208
54570585 CCGCTCCATG
* ** *
54570595 CTTCAACCTATTCCGCTACAACTTCAGGGAAATAAATATGATTCGTAGCCGATCTGCTCCATGCT
1 CTTCAACCTACTCTACTACAACTTCAGGG----AAATAGGATTCGTAGCCGATCTGCTCCATGCT
*
54570660 TCAACCTAATCCGCTGTAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGT
62 TCAACCTAATCCGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGT
*
54570725 TTGCTCCACTACAACTTTAGGGAGACATGACTTGTTGTTTTTAGTCTACTCCACTGCATCTTCAG
127 TTGCTCCACTACAACTTTAGGAAGACATGACTTGTTGTTTTTAGTCTACTCCACTGCATCTTCAG
*
54570790 GGAAATAACACTTGTAT
192 GGAAATAACACTTGTAA
* *
54570807 CTTCGACCTACTAC-ACTGCAACTTCAGGGAAATAGGATTCGTAGCCGATCTGCTCCATGCTTCA
1 CTTCAACCTACT-CTACTACAACTTCAGGGAAATAGGATTCGTAGCCGATCTGCTCCATGCTTCA
*
54570871 ACCTAATCCGCTGCAACTTCAGGGAAATAAGATTCGACATGGTAAGAACCGCTATCTACTGTTTG
65 ACCTAATCCGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTTTG
54570936 CTCCACTACAACTTTAGGAAGACATGACTTGTTGTTTTTAGTCTACTCCACTGCATCTTCAGGGA
130 CTCCACTACAACTTTAGGAAGACATGACTTGTTGTTTTTAGTCTACTCCACTGCATCTTCAGGGA
*
54571001 AATAAGACTTGTAA
195 AATAACACTTGTAA
*
54571015 CTTCAACCTGCTCTACTACAACTTCAG
1 CTTCAACCTACTCTACTACAACTTCAG
54571042 AGAGACAAGG
Statistics
Matches: 220, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
207 1 0.00
208 195 0.89
212 23 0.10
213 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (208 bp):
CTTCAACCTACTCTACTACAACTTCAGGGAAATAGGATTCGTAGCCGATCTGCTCCATGCTTCAA
CCTAATCCGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTTTGC
TCCACTACAACTTTAGGAAGACATGACTTGTTGTTTTTAGTCTACTCCACTGCATCTTCAGGGAA
ATAACACTTGTAA
Found at i:54579130 original size:23 final size:23
Alignment explanation
Indices: 54579095--54579206 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
54579085 CAGTTTTGGG
* *
54579095 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
54579118 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
54579141 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
54579164 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
54579187 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
54579207 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:54579157 original size:46 final size:46
Alignment explanation
Indices: 54579095--54579206 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
54579085 CAGTTTTGGG
*
54579095 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
54579141 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
54579187 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
54579207 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:54584749 original size:35 final size:34
Alignment explanation
Indices: 54584693--54584758 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
54584683 GAAATGATAC
*
54584693 AAATATAAAAGATATATAAACATAAATATGTATA
1 AAATATAAAAGATATAAAAACATAAATATGTATA
*
54584727 AAATAATAAAA-ATATGAAAAACATATATATGT
1 AAAT-ATAAAAGATAT-AAAAACATAAATATGT
54584759 GCATGTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (34 bp):
AAATATAAAAGATATAAAAACATAAATATGTATA
Found at i:54587394 original size:2 final size:2
Alignment explanation
Indices: 54587387--54587428 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54587377 GATTCACATA
54587387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54587429 CAGCAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54595049 original size:19 final size:18
Alignment explanation
Indices: 54595021--54595070 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
54595011 GGGATTTTTT
54595021 AATATTAATATAATTA-A
1 AATATTAATATAATTATA
*
54595038 AATTATTTAATATTATTATA
1 AA-TA-TTAATATAATTATA
54595058 AATATTAATATAA
1 AATATTAATATAA
54595071 AATTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 10 0.36
19 13 0.46
20 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTAATATAATTATA
Found at i:54595462 original size:26 final size:26
Alignment explanation
Indices: 54595428--54595491 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
54595418 ATATTAGAAA
* * *
54595428 AATAATTTAATTATTAAAATAATTGT
1 AATATTTTAATTACTAAAATAATTAT
* * *
54595454 AATATTTTAAATACTGAAATAGTTAT
1 AATATTTTAATTACTAAAATAATTAT
*
54595480 CATATTTTAATT
1 AATATTTTAATT
54595492 GTATTCAACA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (26 bp):
AATATTTTAATTACTAAAATAATTAT
Found at i:54606942 original size:42 final size:43
Alignment explanation
Indices: 54606836--54606944 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
54606826 AACGCTAAAT
*
54606836 CTAAAGAACATGATATTTAGCGGCGCTTTTCCTACAAACGCCA
1 CTAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAACGCCA
* * * * *
54606879 CTAAA-AATCAT-ATTCTATAGCGGTGGTTTT-TTACAAACGCCG
1 CTAAAGAA-CATGA-TCTTTAGCGGCGCTTTTCCTACAAACGCCA
54606921 CTAAAGAACATGATCTTTAGCGGC
1 CTAAAGAACATGATCTTTAGCGGC
54606945 ATTTTCTATG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
42 30 0.56
43 24 0.44
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
CTAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAACGCCA
Found at i:54606967 original size:44 final size:43
Alignment explanation
Indices: 54606917--54607014 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 43
54606907 TTTTACAAAC
*
54606917 GCCGCTAAAGAACATGATCTTTAGCGGCATTTTCTA-TGAGAAGT
1 GCCGCTAAAGAACATGATCTTTAGCGGCATTTT-TAGT-AGAAGA
* * *
54606961 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTAGTAGAAGA
1 GCCGCTAAAGAACATGATCTTTAGCGGCATTTTTAGTAGAAGA
*
54607004 GCTGCTAAAGA
1 GCCGCTAAAGA
54607015 CCATATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 17 0.35
44 31 0.65
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCATTTTTAGTAGAAGA
Found at i:54611219 original size:28 final size:27
Alignment explanation
Indices: 54611179--54611280 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 27
54611169 AGCCTACAAC
* *
54611179 ATGCAGTAACAGTCTGGGCTTGAGCCCT
1 ATGCAGTAACAGTGTGGGCTT-AGCCCG
54611207 ATGCAGTAACAGTGTGTGGGTCTTAGCCCG
1 ATGCAGTAACA--GTGTGGG-CTTAGCCCG
* **
54611237 ATACAGTAACAGTGTGGGCCTTAGCCTA
1 ATGCAGTAACAGTGTGGG-CTTAGCCCG
* *
54611265 ATACAATAACAGTGTG
1 ATGCAGTAACAGTGTG
54611281 ATAATGCAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
28 40 0.62
30 21 0.33
31 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (27 bp):
ATGCAGTAACAGTGTGGGCTTAGCCCG
Found at i:54611244 original size:30 final size:29
Alignment explanation
Indices: 54611193--54611280 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
54611183 AGTAACAGTC
* *
54611193 TGGGCTTGAGCCCTATGCAGTAACAGTGTG
1 TGGGCTT-AGCCCAATACAGTAACAGTGTG
*
54611223 TGGGTCTTAGCCCGATACAGTAACAGTGTG
1 TGGG-CTTAGCCCAATACAGTAACAGTGTG
* * *
54611253 -GGCCTTAGCCTAATACAATAACAGTGTG
1 TGGGCTTAGCCCAATACAGTAACAGTGTG
54611281 ATAATGCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
28 22 0.43
29 2 0.04
30 24 0.47
31 3 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGGCTTAGCCCAATACAGTAACAGTGTG
Found at i:54611798 original size:27 final size:27
Alignment explanation
Indices: 54611618--54611798 Score: 247
Period size: 27 Copynumber: 6.7 Consensus size: 27
54611608 AGTATAGCAG
54611618 TCATTTTACCCTATC-GGGGTATTTCGA
1 TCATTTTACCCT-TCGGGGGTATTTCGA
* *
54611645 TCATTTTACCCTTCGGGGGTATTTTGG
1 TCATTTTACCCTTCGGGGGTATTTCGA
* * * *
54611672 TCATTTTACCATTTGGGGATATTTTGA
1 TCATTTTACCCTTCGGGGGTATTTCGA
* *
54611699 TCATTTTACCCTTCGGGGGTATTTTGG
1 TCATTTTACCCTTCGGGGGTATTTCGA
* * *
54611726 TCATTTTGCACTTCGGGGGTAGTTCGA
1 TCATTTTACCCTTCGGGGGTATTTCGA
54611753 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGGGGGTATTTCGA
54611780 TCATTTTACCCTTCGGGGG
1 TCATTTTACCCTTCGGGGG
54611799 CAAGTTGAGC
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 133 0.99
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGGGGGTATTTCGA
Found at i:54613091 original size:95 final size:95
Alignment explanation
Indices: 54612969--54613151 Score: 215
Period size: 95 Copynumber: 1.9 Consensus size: 95
54612959 GATTTCACTT
* * * * *
54612969 GTAGCTTTAATCTATTCCACTGCAACTTCAAGGAAATAAGATTCGCATCCTCAATCTGCTCCACT
1 GTAGCTTGAATCTATTCCACTGCAACTTCAAGGAAACAAGATTCACAGCCTCAATCTACTCCACT
54613034 GCAACCTCA-AGAAGATAAGATTTATAACAC
66 GCAACCTCAGAG-AGATAAGATTTATAACAC
* * * * * * * * * *
54613064 GTAGCTTGGATCTATTTCACTGTAACTTTAGGGAAACAAGGTTTACAGCTTTAATCTACTCTACT
1 GTAGCTTGAATCTATTCCACTGCAACTTCAAGGAAACAAGATTCACAGCCTCAATCTACTCCACT
54613129 GCAACCTCAGAGAGATAAGATTT
66 GCAACCTCAGAGAGATAAGATTT
54613152 GCTATCTGCG
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
95 70 0.97
96 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (95 bp):
GTAGCTTGAATCTATTCCACTGCAACTTCAAGGAAACAAGATTCACAGCCTCAATCTACTCCACT
GCAACCTCAGAGAGATAAGATTTATAACAC
Found at i:54628616 original size:11 final size:11
Alignment explanation
Indices: 54628600--54628627 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54628590 GATTTTCAAG
54628600 CATTGTTTAAA
1 CATTGTTTAAA
54628611 CATTGTTTAAA
1 CATTGTTTAAA
54628622 CATTGT
1 CATTGT
54628628 AACCATTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (11 bp):
CATTGTTTAAA
Found at i:54629054 original size:34 final size:34
Alignment explanation
Indices: 54629015--54629085 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
54629005 AACAATGCAC
*
54629015 AAAAATGTTAGCATTGACAGCAATCGTAGCACCA
1 AAAAATGTTAGCATTGACAGCAACCGTAGCACCA
54629049 AAAAATGTTAGCATTGACAGCAACCGTAGCACCA
1 AAAAATGTTAGCATTGACAGCAACCGTAGCACCA
54629083 AAA
1 AAA
54629086 CCTTGGGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (34 bp):
AAAAATGTTAGCATTGACAGCAACCGTAGCACCA
Found at i:54629332 original size:37 final size:37
Alignment explanation
Indices: 54629286--54629359 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
54629276 AATAGATATT
*
54629286 TATTGCTCAATAGAAGAGGAGGAAGAGAAAATTACCA
1 TATTACTCAATAGAAGAGGAGGAAGAGAAAATTACCA
54629323 TATTACTCAATAGAAGAGGAGGAAGAGAAAATTACCA
1 TATTACTCAATAGAAGAGGAGGAAGAGAAAATTACCA
54629360 GAAATGCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (37 bp):
TATTACTCAATAGAAGAGGAGGAAGAGAAAATTACCA
Found at i:54643856 original size:41 final size:41
Alignment explanation
Indices: 54643806--54643963 Score: 235
Period size: 41 Copynumber: 3.9 Consensus size: 41
54643796 TTCTGACCTT
* * *
54643806 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGTGCCACTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
*
54643847 TAGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
* *
54643888 TCGGTGCTTGAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
* **
54643929 TCGGTGCTTTAGCGGTGTTTTTGAAAAAGCGCCGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGC
54643964 AAAAAACATT
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
Found at i:54644323 original size:15 final size:14
Alignment explanation
Indices: 54644305--54644342 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
54644295 ACTATTTTAA
54644305 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
54644319 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
54644334 GGTTTATGG
1 GGTTTATGG
54644343 TTTAAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:54644325 original size:22 final size:21
Alignment explanation
Indices: 54644300--54644352 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
54644290 GAGTTACTAT
*
54644300 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
54644322 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
54644343 TTTAAGGATT
1 TTTAAGGATT
54644353 GGGGTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:54644412 original size:36 final size:35
Alignment explanation
Indices: 54644354--54644436 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
54644344 TTAAGGATTG
* *
54644354 GGGTTTAAGGTTTAGGGGTTAGGGGTTAGGGGTTAA
1 GGGTTT-AGATTTAGGGGTTAGGGGTTAGGGATTAA
* * *
54644390 GGGTTTATGATTTATGGTTTAGGGGTTAGGGATTTA
1 GGGTTTA-GATTTAGGGGTTAGGGGTTAGGGATTAA
54644426 GGGTTTAGATT
1 GGGTTTAGATT
54644437 AATTAGTGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.40
Consensus pattern (35 bp):
GGGTTTAGATTTAGGGGTTAGGGGTTAGGGATTAA
Found at i:54644432 original size:7 final size:7
Alignment explanation
Indices: 54644300--54644433 Score: 88
Period size: 7 Copynumber: 18.7 Consensus size: 7
54644290 GAGTTACTAT
*
54644300 TTTAAGG
1 TTTAGGG
*
54644307 TTTATGG
1 TTTAGGG
*
54644314 ATTATGGG
1 TTTA-GGG
54644322 TTTAGGG
1 TTTAGGG
* *
54644329 ATTATGG
1 TTTAGGG
*
54644336 TTTATGG
1 TTTAGGG
*
54644343 TTTAAGG
1 TTTAGGG
* *
54644350 ATTGGGG
1 TTTAGGG
*
54644357 TTTAAGG
1 TTTAGGG
54644364 TTTAGGG
1 TTTAGGG
*
54644371 GTTAGGG
1 TTTAGGG
*
54644378 GTTAGGGG
1 TTTA-GGG
*
54644386 TTAAGGG
1 TTTAGGG
* *
54644393 TTTATGA
1 TTTAGGG
*
54644400 TTTATGG
1 TTTAGGG
54644407 TTTAGGG
1 TTTAGGG
*
54644414 GTTAGGG
1 TTTAGGG
54644421 ATTTAGGG
1 -TTTAGGG
54644429 TTTAG
1 TTTAG
54644434 ATTAATTAGT
Statistics
Matches: 99, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
7 83 0.84
8 16 0.16
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:54644585 original size:15 final size:15
Alignment explanation
Indices: 54644565--54644613 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
54644555 TTACTATTTA
54644565 AGGTTTATGGATTAT
1 AGGTTTATGGATTAT
*
54644580 AGGTTTAAGGATTAT
1 AGGTTTATGGATTAT
* *
54644595 -GGTTTATGGTTTAA
1 AGGTTTATGGATTAT
54644609 AGGTT
1 AGGTT
54644614 GGAGTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (15 bp):
AGGTTTATGGATTAT
Found at i:54644653 original size:24 final size:24
Alignment explanation
Indices: 54644619--54644664 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54644609 AGGTTGGAGT
*
54644619 TTAAGGTTTAGGGGTTAAGGGTAC
1 TTAAGGGTTAGGGGTTAAGGGTAC
54644643 TTAAGGGTTAGGGGTTAAGGGT
1 TTAAGGGTTAGGGGTTAAGGGT
54644665 TTATGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.02, G:0.41, T:0.33
Consensus pattern (24 bp):
TTAAGGGTTAGGGGTTAAGGGTAC
Found at i:54644749 original size:271 final size:271
Alignment explanation
Indices: 54644174--54645034 Score: 1270
Period size: 271 Copynumber: 3.3 Consensus size: 271
54644164 TTTTTGGGTA
* * *
54644174 AATTACTGATTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGATAT-AGTATT
1 AATTAGTG-TTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGA-TATT
* * *
54644238 AATTTTAAAATATTGAATTAATTATCATTATAGTTTAGGGTTTAAGGTTTAAGAGTTACTATTTT
64 AATTTTAAAATATTGAATTAATTATCAATATAGTTTAGGGTTTAAAGTTTAGGAGTTACTA-TTT
* * * *
54644303 AAGGTTTATGGATTATGGGTTTAGGGATTATGGTTTATGGTTT-AAGGATTGGGGTTTAAGGTTT
128 AAGGTTTAGGGATTATAGGTTTAAGGATTATGGTTTATGGTTTAAAGG-TTGGAGTTTAAGGTTT
*
54644367 AGGGGTT-A--G-------GGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGA
192 AGGGGTTAAGGGTACTCAAGGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGG
54644422 TTTAGGGTTTAGATT
257 TTTAGGGTTTAGATT
*
54644437 AATTAGTGTTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGGTATTAA
1 AATTAGTGTTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGATATTAA
54644502 TTTTAAAATATTGAATTAATTATCAATATAGTTTAGGGTTTAAAGTTTAGGAGTTACTATTTAAG
66 TTTTAAAATATTGAATTAATTATCAATATAGTTTAGGGTTTAAAGTTTAGGAGTTACTATTTAAG
*
54644567 GTTTATGGATTATAGGTTTAAGGATTATGGTTTATGGTTTAAAGGTTGGAGTTTAAGGTTTAGGG
131 GTTTAGGGATTATAGGTTTAAGGATTATGGTTTATGGTTTAAAGGTTGGAGTTTAAGGTTTAGGG
*
54644632 GTTAAGGGTACTTAAGGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGGTTTA
196 GTTAAGGGTACTCAAGGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGGTTTA
54644697 GGGTTTAGATT
261 GGGTTTAGATT
*
54644708 AATTAGTATTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGATATTAA
1 AATTAGTGTTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGATATTAA
** *
54644773 TTTTAAAATATTGAATTGGTTATCATTATAGTTTAGGGTTTAAAGTTTAGGAGTTACTATTTAAG
66 TTTTAAAATATTGAATTAATTATCAATATAGTTTAGGGTTTAAAGTTTAGGAGTTACTATTTAAG
* * *
54644838 GTTTAGGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAAGGTTGGGGTTTAAGGTTTAGGG
131 GTTTAGGGATTATAGGTTTAAGGATTATGGTTTATGGTTTAAAGGTTGGAGTTTAAGGTTTAGGG
* *
54644903 GTTAGGGGTACTCAA--G--A---GTTAAAGGTTTATG----A---TTTAGGGGTTAGGGGTTTA
196 GTTAAGGGTACTCAAGGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGGTTTA
54644954 GGGTTTAGATT
261 GGGTTTAGATT
* * *
54644965 AATTAGTGTTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTAAAAGAGATAATATTAA
1 AATTAGTGTTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGATATTAA
54645030 TTTTA
66 TTTTA
54645035 TTATATTAAC
Statistics
Matches: 559, Mismatches: 27, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
257 96 0.17
260 1 0.00
261 66 0.12
262 114 0.20
263 7 0.01
264 14 0.03
267 1 0.00
269 1 0.00
271 259 0.46
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (271 bp):
AATTAGTGTTTTTGAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATGATATTAA
TTTTAAAATATTGAATTAATTATCAATATAGTTTAGGGTTTAAAGTTTAGGAGTTACTATTTAAG
GTTTAGGGATTATAGGTTTAAGGATTATGGTTTATGGTTTAAAGGTTGGAGTTTAAGGTTTAGGG
GTTAAGGGTACTCAAGGGTTAGGGGTTAAGGGTTTATGATTTATGGTTTAGGGGTTAGGGGTTTA
GGGTTTAGATT
Found at i:54644871 original size:14 final size:15
Alignment explanation
Indices: 54644837--54644871 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
54644827 TACTATTTAA
54644837 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
54644852 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
54644866 GGTTTA
1 GGTTTA
54644872 TGGTTTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:54644897 original size:7 final size:7
Alignment explanation
Indices: 54644832--54644909 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
54644822 GGAGTTACTA
*
54644832 TTTAAGG
1 TTTAGGG
54644839 TTTAGGG
1 TTTAGGG
*
54644846 ATTATGGG
1 TTTA-GGG
54644854 TTTAGGG
1 TTTAGGG
* *
54644861 ATTATGG
1 TTTAGGG
*
54644868 TTTATGG
1 TTTAGGG
*
54644875 TTTAAAGG
1 TTT-AGGG
*
54644883 -TTGGGG
1 TTTAGGG
*
54644889 TTTAAGG
1 TTTAGGG
54644896 TTTAGGG
1 TTTAGGG
*
54644903 GTTAGGG
1 TTTAGGG
54644910 GTACTCAAGA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
6 2 0.04
7 44 0.80
8 9 0.16
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:54644905 original size:15 final size:14
Alignment explanation
Indices: 54644832--54644902 Score: 63
Period size: 14 Copynumber: 5.0 Consensus size: 14
54644822 GGAGTTACTA
54644832 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
* *
54644846 ATTATGGGTTTAGGG
1 TTTA-AGGTTTAGGG
* * *
54644861 ATTATGGTTTATGG
1 TTTAAGGTTTAGGG
*
54644875 TTTAAAGG-TTGGGG
1 TTT-AAGGTTTAGGG
54644889 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
54644903 GTTAGGGGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
13 4 0.09
14 25 0.56
15 16 0.36
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:54644905 original size:21 final size:21
Alignment explanation
Indices: 54644852--54644911 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
54644842 AGGGATTATG
* ** *
54644852 GGTTTAGGGATTATGGTTTAT
1 GGTTTAGGGGTTGGGGTTTAA
**
54644873 GGTTTAAAGGTTGGGGTTTAA
1 GGTTTAGGGGTTGGGGTTTAA
54644894 GGTTTAGGGGTTAGGGGT
1 GGTTTAGGGGTT-GGGGT
54644912 ACTCAAGAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.42, T:0.40
Consensus pattern (21 bp):
GGTTTAGGGGTTGGGGTTTAA
Found at i:54645776 original size:76 final size:77
Alignment explanation
Indices: 54645696--54645849 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 77
54645686 TTTTTCCGCA
54645696 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTA-TTCCCCCCCAATTTCCCCA
1 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTATTTCCCCCCCAATTTCCCCA
*
54645760 ATTCGGCAGCCC
66 AATCGGCAGCCC
**
54645772 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCA
1 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTATTTCCCCCCCAATTTCCCCA
54645837 AATCGGCAGCCC
66 AATCGGCAGCCC
54645849 T
1 T
54645850 CTGCATCTCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 45 0.61
77 29 0.39
ACGTcount: A:0.18, C:0.42, G:0.05, T:0.36
Consensus pattern (77 bp):
TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTATTTCCCCCCCAATTTCCCCA
AATCGGCAGCCC
Found at i:54645823 original size:40 final size:40
Alignment explanation
Indices: 54645697--54645824 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
54645687 TTTTCCGCAT
54645697 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
1 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
** * * ** * *
54645737 TTTA---TTCCC-CCCCAATT-TCCCCAATTCGGCA-GCCC
1 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCG-ATTCCC
54645772 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
1 -TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
54645813 TTTATTTTTCCC
1 TTTATTTTTCCC
54645825 CCAATTTCCC
Statistics
Matches: 64, Mismatches: 16, Indels: 16
0.67 0.17 0.17
Matches are distributed among these distances:
35 11 0.17
36 10 0.16
37 5 0.08
39 5 0.08
40 22 0.34
41 11 0.17
ACGTcount: A:0.16, C:0.41, G:0.04, T:0.38
Consensus pattern (40 bp):
TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
Found at i:54646454 original size:86 final size:86
Alignment explanation
Indices: 54646278--54646502 Score: 240
Period size: 86 Copynumber: 2.6 Consensus size: 86
54646268 ACTTACACCG
* * * **
54646278 GGTAAATGCATGAACTTGAACCATTTATTTTTGCTAATTTGTTGCATATAAGTTGTTATAAATAT
1 GGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAATCATTATAAATAT
* ****
54646343 TGAAAAATTAGTCTGATTTTT
66 TGAAAAATTAGCCTGATGGCC
54646364 GGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAATCATTATAGAA-A
1 GGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAATCATTATA-AATA
* *
54646428 TTGAAGATTTAGCCCT-ATGGCC
65 TTGAAAAATTAG-CCTGATGGCC
* * * * *
54646450 GGTAAATATATGAACTATGAA-TAGTTGATTTGTGCTAATTTGTTTCACATAAA
1 GGTAAATACATGAACT-TGAACCA-TTGATTTTTGCTAATTTGTTGCATATAAA
54646503 CTGTTGTAAG
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
86 84 0.71
87 34 0.29
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (86 bp):
GGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAATCATTATAAATAT
TGAAAAATTAGCCTGATGGCC
Found at i:54646542 original size:40 final size:40
Alignment explanation
Indices: 54646457--54646598 Score: 121
Period size: 40 Copynumber: 3.6 Consensus size: 40
54646447 GCCGGTAAAT
* * * * *
54646457 ATATGAACTA-TG-AATAGTTGATTTGTGCTAATTTGTTTC
1 ATATAAACTATTGAAAT-GTTGATTTTTGATAATTTCTTAC
* * * *
54646496 ACATAAACTGTTGTAA-GATTGATTTTTGTTAATTTCTTAC
1 ATATAAACTATTGAAATG-TTGATTTTTGATAATTTCTTAC
* *
54646536 ATATAAATTATTGAAATGTTGATTTTTGATAATTCCTTAC
1 ATATAAACTATTGAAATGTTGATTTTTGATAATTTCTTAC
*
54646576 ATATTAAA-TATTGAAGTGTTGAT
1 ATA-TAAACTATTGAAATGTTGAT
54646599 ATTCAAGCTA
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
39 8 0.10
40 69 0.82
41 7 0.08
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (40 bp):
ATATAAACTATTGAAATGTTGATTTTTGATAATTTCTTAC
Found at i:54647379 original size:21 final size:21
Alignment explanation
Indices: 54647353--54647405 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
54647343 AGCGGTGGCG
*
54647353 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
*
54647374 GTGAGATTGGATACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
54647395 GTGAGATTAGA
1 GTGAGATTAGA
54647406 AACAGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:54647528 original size:9 final size:9
Alignment explanation
Indices: 54647514--54647548 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
54647504 ATAGAAGTTT
54647514 TTTAAATTA
1 TTTAAATTA
54647523 TTTAAATTA
1 TTTAAATTA
54647532 TTTAAAATTA
1 TTT-AAATTA
*
54647542 TTAAAAT
1 TTTAAAT
54647549 ATGTGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAAATTA
Found at i:54657937 original size:43 final size:41
Alignment explanation
Indices: 54657826--54657979 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 41
54657816 AAATATTTTT
* * *
54657826 TAAAAGTTATG-TTTTTAGCGGCGTTTGTGAAAAAGCGCCGC
1 TAAAAGTCATGATTTTTAGCGGCGTTTGTG-TAAAGCGCTGC
** * * * **
54657867 TAAAAGTCATTCTTTATAGTGGTGTTTGTAGTAATAGCATTGC
1 TAAAAGTCATGATTTTTAGCGGCGTTTGT-GTAA-AGCGCTGC
54657910 TAAAAGTCATGATTTTTAGCGGCGTTTGTGGTAGAAGCGCTGC
1 TAAAAGTCATGATTTTTAGCGGCGTTTGT-GTA-AAGCGCTGC
* * *
54657953 TAAAGGTCATTATCTTTAGCGGCGTTT
1 TAAAAGTCATGATTTTTAGCGGCGTTT
54657980 TTTCACATAA
Statistics
Matches: 89, Mismatches: 20, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
41 9 0.10
42 16 0.18
43 63 0.71
44 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (41 bp):
TAAAAGTCATGATTTTTAGCGGCGTTTGTGTAAAGCGCTGC
Found at i:54661778 original size:25 final size:25
Alignment explanation
Indices: 54661747--54661801 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
54661737 AAAAGTAAGT
*
54661747 TTTAGGAGATCTTCGTTGTTTAAAG
1 TTTAGGAGATCTTCGCTGTTTAAAG
*
54661772 TTTAGGAGATCTTTGCTGTTTAAAG
1 TTTAGGAGATCTTCGCTGTTTAAAG
*
54661797 CTTAG
1 TTTAG
54661802 TGGTGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (25 bp):
TTTAGGAGATCTTCGCTGTTTAAAG
Found at i:54662582 original size:14 final size:14
Alignment explanation
Indices: 54662560--54662599 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54662550 TCAATCCGGC
*
54662560 CAAATCCAAAATGT
1 CAAAACCAAAATGT
*
54662574 CAAAACCAAAATTT
1 CAAAACCAAAATGT
*
54662588 CAAAATCAAAAT
1 CAAAACCAAAAT
54662600 CCAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (14 bp):
CAAAACCAAAATGT
Found at i:54664192 original size:44 final size:44
Alignment explanation
Indices: 54664144--54664234 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
54664134 GCTAATAAAA
* *
54664144 AATAGAATTTATGATAATTATACATTTAAGAATAATTATAATTT
1 AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
* * *
54664188 AATAGAAGTTGTGATAATTTTACATTTAAAAATATTTATAATTT
1 AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
54664232 AAT
1 AAT
54664235 TTACAATTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (44 bp):
AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
Found at i:54665954 original size:34 final size:35
Alignment explanation
Indices: 54665888--54665954 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
54665878 CAAACACTAG
* * *
54665888 AAAATATTTTCCAGTAATTTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
54665923 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
54665955 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:54669149 original size:25 final size:25
Alignment explanation
Indices: 54669121--54669169 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
54669111 AAGTTTTAAA
*
54669121 AGATCTTCGTTGTTTAAAGTTTAGG
1 AGATCTTCGTTGTTTAAAGCTTAGG
54669146 AGATCTTCGTTGTTTAAAGCTTAG
1 AGATCTTCGTTGTTTAAAGCTTAG
54669170 TGGTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (25 bp):
AGATCTTCGTTGTTTAAAGCTTAGG
Found at i:54670839 original size:22 final size:22
Alignment explanation
Indices: 54670813--54670877 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
54670803 CGTGCTTAGC
54670813 AGGCTTTGTGCCAGTGATATTT
1 AGGCTTTGTGCCAGTGATATTT
**
54670835 AGGCTTTGTGCC-----TA-GC
1 AGGCTTTGTGCCAGTGATATTT
54670851 AGGCTTTGTGCCAGTGATATTT
1 AGGCTTTGTGCCAGTGATATTT
54670873 AGGCT
1 AGGCT
54670878 GTGTACCTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 12 0.36
17 2 0.06
21 2 0.06
22 17 0.52
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (22 bp):
AGGCTTTGTGCCAGTGATATTT
Found at i:54671001 original size:114 final size:112
Alignment explanation
Indices: 54670795--54671099 Score: 353
Period size: 114 Copynumber: 2.7 Consensus size: 112
54670785 GTAACGTTAC
* * * *
54670795 TCGGGCTCCGTGCTTAGCAGGCTTTGTGCCAGTGATATTTAGGCTT-TGTGCCTAGCAGGCTTTG
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATATTT-GG-TTCTATGCCTAGCAGGCTTTG
54670859 TGCCAGTGATATTTAGGCTGTGTACCTAGCAGGCTTTGTGCCAG-TGATAT
64 TGCCA-TGATATTTAGGCTGTGTACCTAGCAGGCTTTGTG-CAGATGATAT
* * * *
54670909 TCGGGCTCTGTGCCTAGCAGGCTTTGTACCGGTGATATTATGGTTCTATGCCTAGTAGCCTTTTT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATATT-TGGTTCTATGCCTAGCAGGCTTTGT
* * * *
54670974 GCCTATGATATTTAGGCTTTGTGCCTAGTAGGCTTTGTGCTGATGATAT
65 GCC-ATGATATTTAGGCTGTGTACCTAGCAGGCTTTGTGCAGATGATAT
* * * * * * *
54671023 TCGGGTTCTGTGCCTAGAAAGCTCTGTGCTGGTGATATTCGGGCTCTATGCCTAGCAGGCTTTGT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATATT-TGGTTCTATGCCTAGCAGGCTTTGT
54671088 GCCAATGATATT
65 GCC-ATGATATT
54671100 CGGTCTTTGT
Statistics
Matches: 162, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
113 4 0.02
114 156 0.96
115 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (112 bp):
TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATATTTGGTTCTATGCCTAGCAGGCTTTGTG
CCATGATATTTAGGCTGTGTACCTAGCAGGCTTTGTGCAGATGATAT
Found at i:54671100 original size:38 final size:38
Alignment explanation
Indices: 54670795--54671102 Score: 305
Period size: 38 Copynumber: 8.1 Consensus size: 38
54670785 GTAACGTTAC
* *
54670795 TCGGGCTCCGTGCTTAGCAGGCTTTGTGCCAGTGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
** *
54670833 TTAGGCTTTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
** * *
54670871 TTAGGCTGTGTACCTAGCAGGCTTTGTGCCAGTGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
* *
54670909 TCGGGCTCTGTGCCTAGCAGGCTTTGTACCGGTGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
** * * * * *
54670947 TATGGTTCTATGCCTAGTAGCCTTTTTGCCTA-TGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCC-AGTGATAT
** * * *
54670985 TTAGGCTTTGTGCCTAGTAGGCTTTGTG-CTGATGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAG-TGATAT
* * * * **
54671023 TCGGGTTCTGTGCCTAGAAAGCTCTGTGCTGGTGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
* *
54671061 TCGGGCTCTATGCCTAGCAGGCTTTGTGCCAATGATAT
1 TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
54671099 TCGG
1 TCGG
54671103 TCTTTGTGTC
Statistics
Matches: 219, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
37 1 0.00
38 217 0.99
39 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (38 bp):
TCGGGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
Found at i:54673084 original size:6 final size:6
Alignment explanation
Indices: 54673075--54673136 Score: 99
Period size: 6 Copynumber: 10.3 Consensus size: 6
54673065 CAAATTCTAG
*
54673075 TTCTTT TTCTTT CT-TTT TTCTTT TTCTTT TTCTTT TTCTTT TTCATTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT
54673123 TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TT
54673137 TTAAATCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.08
6 42 0.81
7 6 0.12
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:54673108 original size:19 final size:18
Alignment explanation
Indices: 54673075--54673136 Score: 99
Period size: 19 Copynumber: 3.4 Consensus size: 18
54673065 CAAATTCTAG
*
54673075 TTCTTTTTCTTTCT-TTT
1 TTCTTTTTCTTTTTCTTT
54673092 TTCTTTTTCTTTTTCTTT
1 TTCTTTTTCTTTTTCTTT
54673110 TTCTTTTTCATTTTTCTTT
1 TTCTTTTTC-TTTTTCTTT
54673129 TTCTTTTT
1 TTCTTTTT
54673137 TTAAATCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
17 13 0.31
18 12 0.29
19 17 0.40
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTCTTTTTCTTTTTCTTT
Found at i:54677881 original size:26 final size:25
Alignment explanation
Indices: 54677830--54677897 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 25
54677820 AACTATCCTT
* *
54677830 GATAGTATATCCTGAAATTGCTATA
1 GATAGTATATACTGAAATTACTATA
*
54677855 GGTAGTATATACTGAGAATTACTATA
1 GATAGTATATACTGA-AATTACTATA
**
54677881 GATAGCCTATACTGAAA
1 GATAGTATATACTGAAA
54677898 ACACTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (25 bp):
GATAGTATATACTGAAATTACTATA
Found at i:54684224 original size:6 final size:6
Alignment explanation
Indices: 54684213--54684241 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54684203 TAAGTGCTTA
54684213 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
54684242 ATATTGGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:54690071 original size:27 final size:27
Alignment explanation
Indices: 54690022--54690135 Score: 156
Period size: 27 Copynumber: 4.2 Consensus size: 27
54690012 ATGAGGCCTC
* *
54690022 AAATGATCGAAATACCCCCGAAGGGTA
1 AAATGATCGAATTACCCTCGAAGGGTA
* *
54690049 AAATGATCGAATTATCCTTGAAGGGTA
1 AAATGATCGAATTACCCTCGAAGGGTA
* * *
54690076 AAATGATTGAATTACCCTTGAAGGGCA
1 AAATGATCGAATTACCCTCGAAGGGTA
*
54690103 AAATGATCGAATTACCCTCGAAGGGGA
1 AAATGATCGAATTACCCTCGAAGGGTA
54690130 AAATGA
1 AAATGA
54690136 CTGTTATACT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (27 bp):
AAATGATCGAATTACCCTCGAAGGGTA
Found at i:54690343 original size:26 final size:26
Alignment explanation
Indices: 54690314--54690385 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
54690304 CCACATATAT
* *
54690314 TGTTACTAGCAGCTTTGTTGCATTAC
1 TGTTACTAGCAGCTTTGCTGCATCAC
*
54690340 TGTTACTGGCAGCTTTGCTGCATCAC
1 TGTTACTAGCAGCTTTGCTGCATCAC
* *
54690366 TATTACTAGCACCTTTGCTG
1 TGTTACTAGCAGCTTTGCTG
54690386 TGATATTGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (26 bp):
TGTTACTAGCAGCTTTGCTGCATCAC
Found at i:54692653 original size:22 final size:23
Alignment explanation
Indices: 54692619--54692663 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
54692609 CTACCAAAAG
54692619 AAAATAAACTAAAAACAAATAAA
1 AAAATAAACTAAAAACAAATAAA
* *
54692642 AAAAT-AATTAAAGACAAATAAA
1 AAAATAAACTAAAAACAAATAAA
54692664 GAAAGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAATAAACTAAAAACAAATAAA
Found at i:54692670 original size:4 final size:4
Alignment explanation
Indices: 54692661--54692692 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54692651 AAAGACAAAT
*
54692661 AAAG AAAG AAAG AAAG AAAG AAAG AAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
54692693 GGAAGGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:54692676 original size:22 final size:22
Alignment explanation
Indices: 54692633--54692677 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54692623 TAAACTAAAA
* **
54692633 ACAAATAAAAAAATAATTAAAG
1 ACAAATAAAAAAAGAAAGAAAG
*
54692655 ACAAATAAAGAAAGAAAGAAAG
1 ACAAATAAAAAAAGAAAGAAAG
54692677 A
1 A
54692678 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.11
Consensus pattern (22 bp):
ACAAATAAAAAAAGAAAGAAAG
Found at i:54699044 original size:17 final size:17
Alignment explanation
Indices: 54699024--54699067 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
54699014 GAAAAATTAG
*
54699024 AAAAAAAAATTAAACTA
1 AAAAAAAAATTAAAATA
54699041 AAAACAAAAA-TAAAATA
1 AAAA-AAAAATTAAAATA
*
54699058 AAATAAAAAT
1 AAAAAAAAAT
54699068 AAATTGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAAAAAATTAAAATA
Found at i:54699059 original size:22 final size:22
Alignment explanation
Indices: 54699024--54699066 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54699014 GAAAAATTAG
*
54699024 AAAAAAAAATTAAACTAAAAAC
1 AAAAAAAAATTAAAATAAAAAC
54699046 AAAAATAAAA-TAAAATAAAAA
1 AAAAA-AAAATTAAAATAAAAA
54699067 TAAATTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAAAAAATTAAAATAAAAAC
Found at i:54699066 original size:11 final size:11
Alignment explanation
Indices: 54699006--54699070 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
54698996 TGCCAGAAGC
*
54699006 AAATAAAAGAA
1 AAATAAAATAA
*
54699017 AAATTAGAAAAAA
1 AAA-TA-AAATAA
*
54699030 AAATTAAACTAA
1 AAA-TAAAATAA
*
54699042 AAACAAAA-ATA
1 AAATAAAATA-A
54699053 AAATAAAATAA
1 AAATAAAATAA
54699064 AAATAAA
1 AAATAAA
54699071 TTGCTAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.02
11 22 0.50
12 10 0.23
13 11 0.25
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.15
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:54700981 original size:15 final size:15
Alignment explanation
Indices: 54700926--54700982 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
54700916 TTTATACAAC
*
54700926 AAAATATTTATTATT
1 AAAATATTTATTTTT
* *
54700941 AATATATTTATAATTGTA
1 AAAATATTTAT--TT-TT
54700959 ATAAATATTTATTTTT
1 A-AAATATTTATTTTT
54700975 AAAATATT
1 AAAATATT
54700983 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 3 0.09
18 2 0.06
19 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTTTT
Found at i:54701037 original size:15 final size:16
Alignment explanation
Indices: 54701017--54701049 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
54701007 TGAAGAATAT
54701017 TTTTTAAAA-TTATTA
1 TTTTTAAAATTTATTA
54701032 TTTTTAAAATTTATTA
1 TTTTTAAAATTTATTA
54701048 TT
1 TT
54701050 AACATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAAATTTATTA
Found at i:54701076 original size:33 final size:33
Alignment explanation
Indices: 54701039--54701135 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 33
54701029 TTATTTTTAA
54701039 AATTTATTATTAACATAAAATTAAATATTAAAT
1 AATTTATTATTAACATAAAATTAAATATTAAAT
54701072 AATTTATTA--AA-ATAATAAATT--ATATT-AAT
1 AATTTATTATTAACAT-A-AAATTAAATATTAAAT
*
54701101 AATTTATTATATGAC-T-AAATATAAATAATTAAAT
1 AATTTATTAT-TAACATAAAAT-TAAAT-ATTAAAT
54701135 A
1 A
54701136 TGTATGTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 21
0.70 0.01 0.28
Matches are distributed among these distances:
29 16 0.31
30 8 0.15
31 3 0.06
32 9 0.17
33 12 0.23
34 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTTATTATTAACATAAAATTAAATATTAAAT
Found at i:54701109 original size:16 final size:16
Alignment explanation
Indices: 54701063--54701112 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
54701053 ATAAAATTAA
54701063 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
54701080 A-A--AATAATAAATT
1 ATATTAATAATTTATT
54701093 ATATTAATAATTTATT
1 ATATTAATAATTTATT
54701109 ATAT
1 ATAT
54701113 GACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:54725893 original size:22 final size:22
Alignment explanation
Indices: 54725868--54725914 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
54725858 CTTCTTTGCC
54725868 CTCGATTGTTCTTAACTTTACT
1 CTCGATTGTTCTTAACTTTACT
*
54725890 CTCGGTTGTTCTTAACTTTACT
1 CTCGATTGTTCTTAACTTTACT
54725912 CTC
1 CTC
54725915 TTTGTGGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.49
Consensus pattern (22 bp):
CTCGATTGTTCTTAACTTTACT
Found at i:54738170 original size:47 final size:47
Alignment explanation
Indices: 54738101--54738194 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
54738091 ATCGATACTT
54738101 GTAAAAAAGTATCGATACCAAATTCAGTTACTGTTTTCCTGCACATA
1 GTAAAAAAGTATCGATACCAAATTCAGTTACTGTTTTCCTGCACATA
54738148 GTAAAAAAGTATCGATACCAAATTCAGTTACTGTTTTCCTGCACATA
1 GTAAAAAAGTATCGATACCAAATTCAGTTACTGTTTTCCTGCACATA
54738195 CATTTTAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (47 bp):
GTAAAAAAGTATCGATACCAAATTCAGTTACTGTTTTCCTGCACATA
Found at i:54738693 original size:35 final size:35
Alignment explanation
Indices: 54738654--54738723 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
54738644 GCAATGCGCC
54738654 ATATTTAATATAGATCAAGTATGATAGCAATTAAT
1 ATATTTAATATAGATCAAGTATGATAGCAATTAAT
54738689 ATATTTAATATAGATCAAGTATGATAGCAATTAAT
1 ATATTTAATATAGATCAAGTATGATAGCAATTAAT
54738724 GCACTAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (35 bp):
ATATTTAATATAGATCAAGTATGATAGCAATTAAT
Found at i:54739691 original size:22 final size:23
Alignment explanation
Indices: 54739649--54739691 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54739639 CAGGTTCGAG
54739649 ATGGAAAATAATATTTCACAACA
1 ATGGAAAATAATATTTCACAACA
54739672 ATGGAGAAA-AATA-TTCACAA
1 ATGGA-AAATAATATTTCACAA
54739692 ATGGAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (23 bp):
ATGGAAAATAATATTTCACAACA
Found at i:54747506 original size:26 final size:26
Alignment explanation
Indices: 54747468--54747529 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
54747458 GCTCACCCCC
54747468 AATATAGCCTAGCCATTTCAGTGGCT
1 AATATAGCCTAGCCATTTCAGTGGCT
** **
54747494 AATATAGTTTAGCCATTTTGGTGGCT
1 AATATAGCCTAGCCATTTCAGTGGCT
*
54747520 AATGTAGCCT
1 AATATAGCCT
54747530 TCTCAATCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (26 bp):
AATATAGCCTAGCCATTTCAGTGGCT
Found at i:54754653 original size:21 final size:22
Alignment explanation
Indices: 54754627--54754673 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
54754617 TCCTTCCTCC
*
54754627 TTTTTTTTTTTTAT-TTTAAAA
1 TTTTTTATTTTTATATTTAAAA
*
54754648 TTTTTTATTTTTATATTTCAAA
1 TTTTTTATTTTTATATTTAAAA
54754670 TTTT
1 TTTT
54754674 AAAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTATTTTTATATTTAAAA
Found at i:54754658 original size:22 final size:21
Alignment explanation
Indices: 54754628--54754673 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
54754618 CCTTCCTCCT
54754628 TTTTTTTTTTTAT-TTTAAAA
1 TTTTTTTTTTTATATTTAAAA
*
54754648 TTTTTTATTTTTATATTTCAAA
1 TTTTTT-TTTTTATATTTAAAA
54754670 TTTT
1 TTTT
54754674 AAAATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTTTTTATATTTAAAA
Found at i:54761156 original size:21 final size:23
Alignment explanation
Indices: 54761113--54761157 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54761103 TTATATTATA
*
54761113 TAAATAAAAAATTAGGAGTTAAT
1 TAAATAAAAAATTAGGAGATAAT
*
54761136 TAAATAAAATATTA-GA-ATAAT
1 TAAATAAAAAATTAGGAGATAAT
54761157 T
1 T
54761158 GGAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (23 bp):
TAAATAAAAAATTAGGAGATAAT
Found at i:54762633 original size:28 final size:28
Alignment explanation
Indices: 54762595--54762664 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
54762585 TGGTTATACA
* *
54762595 TATATTATATATGTGCATGACTTTATCT
1 TATATAATATATATGCATGACTTTATCT
* *
54762623 TATATAATATATATGCATGTCTTTATTT
1 TATATAATATATATGCATGACTTTATCT
**
54762651 TACCTAATATATAT
1 TATATAATATATAT
54762665 TAATGGATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (28 bp):
TATATAATATATATGCATGACTTTATCT
Found at i:54762691 original size:5 final size:5
Alignment explanation
Indices: 54762681--54762719 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
54762671 ATTTTGGTAT
54762681 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
54762720 TACGCATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:54763084 original size:18 final size:18
Alignment explanation
Indices: 54763056--54763111 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
54763046 TATTATAACG
* *
54763056 AACTGTGTTAATTTGGTA
1 AACTGTATTAATTTGGCA
* *
54763074 ATCTGTATTAATATGGCA
1 AACTGTATTAATTTGGCA
* *
54763092 AACTGCATTAATTTGTCA
1 AACTGTATTAATTTGGCA
54763110 AA
1 AA
54763112 ATGTGTATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (18 bp):
AACTGTATTAATTTGGCA
Found at i:54763769 original size:17 final size:17
Alignment explanation
Indices: 54763749--54763822 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
54763739 TTATGATGGA
*
54763749 GCATGAACTTTTATTTC
1 GCATGAACTGTTATTTC
*
54763766 GCATGAAGTGTTA-TTC
1 GCATGAACTGTTATTTC
* *
54763782 GATATGAACTGATATTTC
1 G-CATGAACTGTTATTTC
** * *
54763800 ATATGAACTATTATTTT
1 GCATGAACTGTTATTTC
54763817 GCATGA
1 GCATGA
54763823 GTTGTCGTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
16 4 0.09
17 37 0.84
18 3 0.07
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (17 bp):
GCATGAACTGTTATTTC
Found at i:54763807 original size:51 final size:51
Alignment explanation
Indices: 54763751--54763858 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
54763741 ATGATGGAGC
* * *
54763751 ATGAACTTTTATTTCGCATGAAG-TGTTATTCGATATGAACTGATATTTCAT
1 ATGAACTATTATTTCGCATG-AGTTGTCATTCGATAAGAACTGATATTTCAT
* * * * *
54763802 ATGAACTATTATTTTGCATGAGTTGTCGTTTGGTAAGAACTGTTATTTCAT
1 ATGAACTATTATTTCGCATGAGTTGTCATTCGATAAGAACTGATATTTCAT
54763853 ATGAAC
1 ATGAAC
54763859 AGATGTTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.04
51 46 0.96
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (51 bp):
ATGAACTATTATTTCGCATGAGTTGTCATTCGATAAGAACTGATATTTCAT
Found at i:54771746 original size:26 final size:26
Alignment explanation
Indices: 54771717--54771778 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
54771707 CTCACCCCCC
*
54771717 AATATAGCCTAGTCATTTCGATGGCT
1 AATATAGCCTAGCCATTTCGATGGCT
* *
54771743 AATATAGCTTAGCCATTTCGGTGGCT
1 AATATAGCCTAGCCATTTCGATGGCT
*
54771769 AATGTAGCCT
1 AATATAGCCT
54771779 TCTCAATCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
AATATAGCCTAGCCATTTCGATGGCT
Found at i:54774117 original size:28 final size:28
Alignment explanation
Indices: 54774059--54774119 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
54774049 AAATAAAAGG
*
54774059 AAAAACTAAACTAATGAAAAACTTAATT
1 AAAAACTAAACTAATGAAAAACTTAAAT
*
54774087 AAAAACTAAACTGAAT-ACAAAGC-TAAAT
1 AAAAACTAAACT-AATGA-AAAACTTAAAT
54774115 AAAAA
1 AAAAA
54774120 TTGTTCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (28 bp):
AAAAACTAAACTAATGAAAAACTTAAAT
Found at i:54777306 original size:22 final size:23
Alignment explanation
Indices: 54777264--54777306 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54777254 TAGGTTCAGG
54777264 ATGGAAAATAATATTTCACAACA
1 ATGGAAAATAATATTTCACAACA
54777287 ATGGAGAAA-AATA-TTCACAA
1 ATGGA-AAATAATATTTCACAA
54777307 ATGGAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (23 bp):
ATGGAAAATAATATTTCACAACA
Done.