Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 180 of 221
Found at i:53734758 original size:18 final size:17
Alignment explanation
Indices: 53734737--53734770 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
53734727 AATTATAAAT
53734737 TGAAATGAAAACAAAAAC
1 TGAAATGAAAA-AAAAAC
53734755 TGAAATGAAAAAAAAA
1 TGAAATGAAAAAAAAA
53734771 TTAATATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (17 bp):
TGAAATGAAAAAAAAAC
Found at i:53734841 original size:20 final size:21
Alignment explanation
Indices: 53734805--53734843 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53734795 AATATGAAAA
53734805 AAATTGAAATGAGAAAAAATT
1 AAATTGAAATGAGAAAAAATT
*
53734826 AAATTTAAAT-AGAAAAAA
1 AAATTGAAATGAGAAAAAA
53734844 AAGATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATTGAAATGAGAAAAAATT
Found at i:53734844 original size:21 final size:20
Alignment explanation
Indices: 53734801--53734861 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
53734791 TATTAATATG
*
53734801 AAAA-AAATTGAAATGAGAAA
1 AAAAGAAATTTAAATGA-AAA
**
53734821 AAATTAAATTTAAATAGAAAA
1 AAAAGAAATTTAAAT-GAAAA
53734842 AAAAGATAATTTAAATGAAA
1 AAAAGA-AATTTAAATGAAA
53734862 TGGAAATGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.09
21 20 0.59
22 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAAGAAATTTAAATGAAAA
Found at i:53737800 original size:90 final size:90
Alignment explanation
Indices: 53737586--53737778 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 90
53737576 TAATACGCAT
* * *
53737586 TAAATTAAATTTAAACACCCAAAAAACTATAAACAGATGGGTAAATTTAATACACAAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATAGGTAAAATTAATACACAAAAATTTTA
53737651 AATTCAAACTACATATAACACAAAC
66 AATTCAAACTACATATAACACAAAC
* *
53737676 TAAATTAAATTTAAACACCCAACAAACTAAAAACAGATAGGTAAAATTAATACACGAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATAGGTAAAATTAATACACAAAAATTTTA
* ***
53737741 AATTCAAACTACATATAATACGGGC
66 AATTCAAACTACATATAACACAAAC
53737766 TAAATTAAATTTA
1 TAAATTAAATTTA
53737779 CAGATACAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (90 bp):
TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATAGGTAAAATTAATACACAAAAATTTTA
AATTCAAACTACATATAACACAAAC
Found at i:53738631 original size:112 final size:110
Alignment explanation
Indices: 53738497--53738810 Score: 452
Period size: 111 Copynumber: 2.8 Consensus size: 110
53738487 AAAAAAGGTA
* *
53738497 GTGCCGGACATCAGTGTCCCAAAGTAAAAAAAAAGTCCTTAGGAGCCGAAAAATGTACTTGGTGC
1 GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTCCTTGGGAGCCGAAAAATGTACTTGGTGC
* *
53738562 CGGCCATCTGCTGGCC-GACACCCAAAATATTTCTTTAAATGACACTG
66 TGGCCATCTACTGGCCAG-CACCC-AAAT-TTTCTTTAAATGACACTG
* * *
53738609 GTGTCGGCCATCAGTGTACCAAAGT-AAAAAAAAGTGCCTTGGGAGCCGAAACATGTACTTGGTG
1 GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGT-CCTTGGGAGCCGAAAAATGTACTTGGTG
* *
53738673 CTGACCATCTACTGGCCAGCACCCAAATTTTTTTTAAATGACACTG
65 CTGGCCATCTACTGGCCAGCACCCAAATTTTCTTTAAATGACACTG
* *
53738719 GTGCCGGCCATCAGTGTCCCAAAGTAAAATAAAAGTTCATTGGGAGCCGAAAAATGTACTTGGTG
1 GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAG-TCCTTGGGAGCCGAAAAATGTACTTGGTG
* *
53738784 CTGGCCATCTATTGACCAGCACCCAAA
65 CTGGCCATCTACTGGCCAGCACCCAAA
53738811 ATTATTTTTT
Statistics
Matches: 181, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
110 40 0.22
111 72 0.40
112 68 0.38
113 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (110 bp):
GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTCCTTGGGAGCCGAAAAATGTACTTGGTGC
TGGCCATCTACTGGCCAGCACCCAAATTTTCTTTAAATGACACTG
Found at i:53738794 original size:111 final size:111
Alignment explanation
Indices: 53738497--53738820 Score: 465
Period size: 112 Copynumber: 2.9 Consensus size: 111
53738487 AAAAAAGGTA
* *
53738497 GTGCCGGACATCAGTGTCCCAAAGTAAAAAAAAAG-TCCTTAGGAGCCGAAAAATGTACTTGGTG
1 GTGCCGGCCATCAGTGTCCCAAAGT-AAAAAAAAGTTCCTTGGGAGCCGAAAAATGTACTTGGTG
* * *
53738561 CCGGCCATCTGCTGGCC-GACACCCAAAATATTTCTTTAAATGACACTG
65 CTGGCCATCTACTGGCCAG-CACCCAAAAT-TTTTTTTAAATGACACTG
* * * *
53738609 GTGTCGGCCATCAGTGTACCAAAGTAAAAAAAAGTGCCTTGGGAGCCGAAACATGTACTTGGTGC
1 GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAGTTCCTTGGGAGCCGAAAAATGTACTTGGTGC
*
53738674 TGACCATCTACTGGCCAGCACCC-AAATTTTTTTTAAATGACACTG
66 TGGCCATCTACTGGCCAGCACCCAAAATTTTTTTTAAATGACACTG
*
53738719 GTGCCGGCCATCAGTGTCCCAAAGTAAAATAAAAGTTCATTGGGAGCCGAAAAATGTACTTGGTG
1 GTGCCGGCCATCAGTGTCCCAAAGTAAAA-AAAAGTTCCTTGGGAGCCGAAAAATGTACTTGGTG
* *
53738784 CTGGCCATCTATTGACCAGCACCCAAAATTATTTTTT
65 CTGGCCATCTACTGGCCAGCACCCAAAATT-TTTTTT
53738821 TTAAATGCCC
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
110 44 0.23
111 66 0.35
112 72 0.38
113 7 0.04
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (111 bp):
GTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAGTTCCTTGGGAGCCGAAAAATGTACTTGGTGC
TGGCCATCTACTGGCCAGCACCCAAAATTTTTTTTAAATGACACTG
Found at i:53746992 original size:30 final size:31
Alignment explanation
Indices: 53746958--53747017 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
53746948 AAACCTTTTA
53746958 TTTTTCCCCAAAA-TTTGTACTCCC-TCCCAC
1 TTTTTCCCCAAAACTTT-TACTCCCTTCCCAC
* *
53746988 TTTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTTCCCCAAAACTTTTACTCCCTTCCCA
53747018 TCCTACCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.42
Consensus pattern (31 bp):
TTTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:53754544 original size:13 final size:13
Alignment explanation
Indices: 53754526--53754555 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53754516 AGCCCAAACT
53754526 CAATTACCCAACC
1 CAATTACCCAACC
*
53754539 CAATTATCCAACC
1 CAATTACCCAACC
53754552 CAAT
1 CAAT
53754556 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:53754708 original size:9 final size:9
Alignment explanation
Indices: 53754696--53754763 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
53754686 AAATAAAAAA
53754696 AATTCGGGT
1 AATTCGGGT
*
53754705 AATTCAGGT
1 AATTCGGGT
*
53754714 ATTTTTC-GGT
1 A--ATTCGGGT
*
53754724 AATTCGGTT
1 AATTCGGGT
*
53754733 AATTCGGTT
1 AATTCGGGT
*
53754742 AATTCGGTT
1 AATTCGGGT
53754751 AATTCGGGT
1 AATTCGGGT
53754760 AATT
1 AATT
53754764 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.06
9 41 0.80
10 4 0.08
11 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGGT
Found at i:53754746 original size:18 final size:17
Alignment explanation
Indices: 53754718--53754763 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
53754708 TCAGGTATTT
53754718 TTCGGTAATTCGGTTAA
1 TTCGGTAATTCGGTTAA
53754735 TTCGGTTAATTCGGTTAA
1 TTCGG-TAATTCGGTTAA
53754753 TTCGGGTAATT
1 TTC-GGTAATT
53754764 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.19
18 20 0.74
19 2 0.07
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (17 bp):
TTCGGTAATTCGGTTAA
Found at i:53758121 original size:26 final size:26
Alignment explanation
Indices: 53758092--53758141 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53758082 AAGTTTAATT
* *
53758092 AATTTTATATTTAAATAAGTTAATAA
1 AATTATATATTTAAATAAGATAATAA
53758118 AATTATATATTTAAATAAGATAAT
1 AATTATATATTTAAATAAGATAAT
53758142 TTATTAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTATATATTTAAATAAGATAATAA
Found at i:53769115 original size:19 final size:20
Alignment explanation
Indices: 53769074--53769115 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53769064 GTTTCTATGC
* *
53769074 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
53769094 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
53769113 CAT
1 CAT
53769116 CCCATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:53774970 original size:19 final size:20
Alignment explanation
Indices: 53774929--53774970 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53774919 GTTTCTATGC
* *
53774929 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
53774949 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
53774968 CAT
1 CAT
53774971 CGCATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:53782023 original size:18 final size:17
Alignment explanation
Indices: 53781990--53782028 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53781980 TTGTATAAAT
53781990 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53782008 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53782025 TGTG
1 TGTG
53782029 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53782281 original size:23 final size:23
Alignment explanation
Indices: 53782254--53782351 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
53782244 AGTGTTATTG
53782254 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
53782277 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
53782300 -CCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53782322 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53782345 ATCAGTG
1 ATCAGTG
53782352 TGGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.28
23 48 0.72
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:53782320 original size:45 final size:45
Alignment explanation
Indices: 53782256--53782344 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
53782246 TGTTATTGAT
* * *
53782256 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
53782301 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
53782345 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:53785077 original size:217 final size:217
Alignment explanation
Indices: 53784702--53785412 Score: 1190
Period size: 217 Copynumber: 3.3 Consensus size: 217
53784692 AGTCATATCT
*
53784702 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTATGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
* *
53784767 GCAAGTCTTATCCCCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
** *
53784832 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTTCTGAAGTTGCAGTGGAACGGATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
53784897 ACCTCAAATCTTACCTCTCTGA
196 ACCTCAAATCTTACCTCTCTGA
* * *
53784919 AGTTGCAGAGAGTAAATCGCATTTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
*
53784984 GCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* **
53785049 GTTACAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
*
53785114 ACCTCAAATCGTACCTCTCTGA
196 ACCTCAAATCTTACCTCTCTGA
53785136 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
* * *
53785201 GCAAGCCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* *
53785266 GTTGCAGTGGAGTAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
* *
53785331 ACCTTAGATCTTATCCT-TCTGA
196 ACCTCAAATCTTA-CCTCTCTGA
* * *
53785353 AGTTGCAGAGAACAGATCGCATCTAGTCATATCTCTCTGAGGTTGCAGTGGAGTAGACTA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTA
53785413 AGATAGAAAA
Statistics
Matches: 461, Mismatches: 32, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
217 458 0.99
218 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
ACCTCAAATCTTACCTCTCTGA
Found at i:53785322 original size:44 final size:42
Alignment explanation
Indices: 53784731--53785330 Score: 296
Period size: 44 Copynumber: 13.8 Consensus size: 42
53784721 CATCTAGTCA
* * *
53784731 TATCTCCCTGAGGTTGCAGTGGAGCAGACTATGTAAG-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-T-T-AAAGCCAAATCT
* * * *
53784775 TATCCCCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAATCT
*
53784820 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATCT
** * * *
53784864 TATCTTTCTGAAGTTGCAGTGGAACGGATTAAAACCTCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CAAATCT
* * * * *
53784908 TACCTCTCTGAAGTTGCA---GAG-AG--TAAATCGCATTTAGTCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CA---AATCT
* * *
53784948 TATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAAG-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA---AAGCCAAATCT
* * *
53784992 TATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAATCT
* *
53785037 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATCT
* * *
53785081 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCTCAAATCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CAAATCT
* * * *** * * * *
53785125 TACCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TCTAGTCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATCT
* * **
53785165 TATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAAG-CAAGCCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA---AAGCCAAATCT
* * *
53785209 TATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAATCT
* * *
53785254 TATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATCT
**
53785298 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
53785331 ACCTTAGATC
Statistics
Matches: 430, Mismatches: 78, Indels: 96
0.71 0.13 0.16
Matches are distributed among these distances:
37 6 0.01
38 1 0.00
40 39 0.09
41 9 0.02
42 10 0.02
43 27 0.06
44 227 0.53
45 95 0.22
46 12 0.03
47 2 0.00
49 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATCT
Found at i:53787481 original size:19 final size:20
Alignment explanation
Indices: 53787440--53787481 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53787430 GTTTCTATGC
* *
53787440 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
53787460 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
53787479 CAT
1 CAT
53787482 CGCATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:53789682 original size:32 final size:32
Alignment explanation
Indices: 53789641--53789707 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
53789631 ACATGACAGC
* *
53789641 CTGGTGGAGGGCCTGCCACAGGCGGCATCGGA
1 CTGGTGGAGGGCCTGCCAAAGGCGGCACCGGA
53789673 CTGGTGGAGGGCCTGCCAAAGGCGGCACCGGA
1 CTGGTGGAGGGCCTGCCAAAGGCGGCACCGGA
53789705 CTG
1 CTG
53789708 AAATGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.16, C:0.28, G:0.43, T:0.12
Consensus pattern (32 bp):
CTGGTGGAGGGCCTGCCAAAGGCGGCACCGGA
Found at i:53793911 original size:40 final size:41
Alignment explanation
Indices: 53793865--53793947 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
53793855 AATTCATTAC
* * *
53793865 TTTAGTAATTTCACAGTTCAATGCAGTACACA-TAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
* *
53793905 TTTAGTAACTTCACAATTCAATTCAGTACTCAGAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
53793946 TT
1 TT
53793948 CAGTTCAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 28 0.76
41 9 0.24
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (41 bp):
TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
Found at i:53797662 original size:31 final size:30
Alignment explanation
Indices: 53797607--53797665 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53797597 GTAAATACTT
***
53797607 AAAATTTGAAGGGTTAAAGTGTAAATATAA
1 AAAATTTGAAGGACCAAAGTGTAAATATAA
53797637 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAA-AGTGTAAATAT
53797666 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAATTTGAAGGACCAAAGTGTAAATATAA
Found at i:53798884 original size:42 final size:42
Alignment explanation
Indices: 53798819--53799015 Score: 157
Period size: 42 Copynumber: 4.7 Consensus size: 42
53798809 CGTGTTTTAC
* * *
53798819 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* * * * * *
53798861 TTTCCGTTCAACTTTTTTGAGCTTTTGTTTAACACATACGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* * * *
53798903 TTTCCGTTTAGCTCATT-TGAGCTTCTATTTAAACT-TTATGGG
1 TTTCCGTTCAGCTC-TTATGAGCTTCTGTTT-AACTCATATGAG
* * * * * *
53798945 TTTTCGTTCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* *
53798987 TTTCTGTTTAGCT-TTCATGAGCTTCTGTT
1 TTTCCGTTCAGCTCTT-ATGAGCTTCTGTT
53799016 CAGCCTCCGG
Statistics
Matches: 122, Mismatches: 28, Indels: 10
0.76 0.17 0.06
Matches are distributed among these distances:
41 7 0.06
42 110 0.90
43 5 0.04
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
Found at i:53801067 original size:24 final size:24
Alignment explanation
Indices: 53801030--53801076 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53801020 TATATATACC
53801030 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
53801054 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
53801077 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:53801814 original size:21 final size:20
Alignment explanation
Indices: 53801777--53801817 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
53801767 TTTCGTTTGG
53801777 CTTTCTCTATTTC-TTTCTTT
1 CTTT-TCTATTTCTTTTCTTT
53801797 CTTTTCTATTTCTATTTCTTT
1 CTTTTCTATTTCT-TTTCTTT
53801818 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTTTCTATTTCTTTTCTTT
Found at i:53813626 original size:16 final size:17
Alignment explanation
Indices: 53813594--53813626 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53813584 TCAAATAAAC
*
53813594 ATTAAAAAATTACATTA
1 ATTAAAAAAATACATTA
53813611 ATTAAAAAAATA-ATTA
1 ATTAAAAAAATACATTA
53813627 CATAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAAAAATACATTA
Found at i:53826538 original size:47 final size:47
Alignment explanation
Indices: 53826418--53826629 Score: 151
Period size: 44 Copynumber: 4.6 Consensus size: 47
53826408 TTAAATGTAT
* * * **
53826418 AAATTATATATCATTATTAAATTATATTTAATATTAATTA-TTT-T-
1 AAATTATATATAATTATTAAATTATATTTATTATCAAGAATTTTATG
*
53826462 AAATTATATA-AATTCATATAAGA--AAATTTATTATCAAGAATTTTATG
1 AAATTATATATAATT-AT-TAA-ATTATATTTATTATCAAGAATTTTATG
* * * * **
53826509 AAATTACATATCATTATTAAATTATATTTAATATTAATTA-TTT-T-
1 AAATTATATATAATTATTAAATTATATTTATTATCAAGAATTTTATG
* *
53826553 AAATTATATA-AATTCATATAAGA--AAATTTATTATCAAGAATTTTACG
1 AAATTATATATAATT-AT-TAA-ATTATATTTATTATCAAGAATTTTATG
*
53826600 AAATTATATATTATTATTAAATTATATTTA
1 AAATTATATATAATTATTAAATTATATTTA
53826630 ATAATAATTA
Statistics
Matches: 127, Mismatches: 23, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
43 6 0.05
44 47 0.37
45 15 0.12
46 12 0.09
47 41 0.32
48 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (47 bp):
AAATTATATATAATTATTAAATTATATTTATTATCAAGAATTTTATG
Found at i:53826695 original size:91 final size:91
Alignment explanation
Indices: 53826418--53826676 Score: 455
Period size: 91 Copynumber: 2.8 Consensus size: 91
53826408 TTAAATGTAT
53826418 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
53826483 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
53826509 AAATTACATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
*
53826574 GAAAATTTATTATCAAGAATTTTACG
66 GAAAATTTATTATCAAGAATTTTATG
* * * * *
53826600 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAGATCCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
53826665 GAAAATTTATTA
66 GAAAATTTATTA
53826677 GTTATAATTA
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 160 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:53826809 original size:37 final size:35
Alignment explanation
Indices: 53826768--53826937 Score: 100
Period size: 37 Copynumber: 4.7 Consensus size: 35
53826758 TAGTATCATA
*
53826768 TATTATGATTTTAGTAAATTCATATAAGAATATTGAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* * *
53826805 TATTAAGAATTTTATTAAATTATAT---ATTTTAAT
1 TATTATG-ATTTTAGTAAATTATATAAAATATTAAT
* * * *
53826838 TATAAT-ATATTTAATAATTATTATGTTAAATTATCT-A-
1 TATTATGAT-TTTAGTAA--ATTAT-ATAAAATAT-TAAT
*
53826875 TATTATGATTTGAGTAAATTCATATAAGAATATTAAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* *
53826912 TATTAAGAATTTTATTAAATTATATA
1 TATTATG-ATTTTAGTAAATTATATA
53826938 TTTTAATTAT
Statistics
Matches: 100, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
31 2 0.02
32 7 0.07
33 10 0.10
34 5 0.05
35 8 0.08
36 7 0.07
37 32 0.32
38 28 0.28
39 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (35 bp):
TATTATGATTTTAGTAAATTATATAAAATATTAAT
Found at i:53826947 original size:13 final size:13
Alignment explanation
Indices: 53826929--53826982 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
53826919 AATTTTATTA
53826929 AATTATATATTTT
1 AATTATATATTTT
*
53826942 AA-T-TATA-TTA
1 AATTATATATTTT
53826952 AATTATATATTTT
1 AATTATATATTTT
53826965 AATTATAATATATTT
1 AATTAT-ATAT-TTT
53826980 AAT
1 AAT
53826983 AATTATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 5 0.15
13 10 0.29
14 4 0.12
15 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTATATATTTT
Found at i:53826950 original size:23 final size:23
Alignment explanation
Indices: 53826919--53826971 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
53826909 AATTATTAAG
*
53826919 AATTTTATTAAATTATATATTTT
1 AATTATATTAAATTATATATTTT
53826942 AATTATATTAAATTATATATTTT
1 AATTATATTAAATTATATATTTT
53826965 AATTATA
1 AATTATA
53826972 ATATATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATATTAAATTATATATTTT
Found at i:53826951 original size:18 final size:18
Alignment explanation
Indices: 53826920--53827009 Score: 50
Period size: 23 Copynumber: 5.1 Consensus size: 18
53826910 ATTATTAAGA
*
53826920 ATTTT-ATTAAATTATAT
1 ATTTTAATTATATTATAT
53826937 ATTTTAATTATATTAAATTATAT
1 ATTTTAA-T-TA-T--ATTATAT
53826960 ATTTTAATTATA--ATAT
1 ATTTTAATTATATTATAT
53826976 A-TTTAA-TA-ATTAT-T
1 ATTTTAATTATATTATAT
* *
53826990 ATGTTAAATTATATTTTAT
1 AT-TTTAATTATATTATAT
53827009 A
1 A
53827010 GTATCATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 24
0.68 0.04 0.29
Matches are distributed among these distances:
13 1 0.02
14 4 0.07
15 7 0.12
16 9 0.16
17 7 0.12
18 6 0.11
19 3 0.05
20 3 0.05
21 2 0.04
22 1 0.02
23 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
ATTTTAATTATATTATAT
Found at i:53827095 original size:14 final size:14
Alignment explanation
Indices: 53827067--53827113 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
53827057 TTAAGAATTT
53827067 TATTAAATTAT-ATA
1 TATT-AATTATAATA
*
53827081 TTTTAATTATAATA
1 TATTAATTATAATA
*
53827095 TATTAATAATAATTA
1 TATTAATTATAA-TA
53827110 TATT
1 TATT
53827114 TAAATATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.21
14 16 0.57
15 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTAATTATAATA
Found at i:53827311 original size:44 final size:45
Alignment explanation
Indices: 53827261--53827350 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
53827251 TCTCTATTCT
*
53827261 ATTCAACCAAACACA-AGA-ATACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGATATACTATTACGCCTCTATTCCAATAC
* * *
53827305 ATTCAACCAAACAATTGATTTGCTATTACGCCTCTATTCCAATAC
1 ATTCAACCAAACAATAGATATACTATTACGCCTCTATTCCAATAC
53827350 A
1 A
53827351 GCGAACCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.03
44 15 0.38
45 24 0.60
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.30
Consensus pattern (45 bp):
ATTCAACCAAACAATAGATATACTATTACGCCTCTATTCCAATAC
Found at i:53838738 original size:21 final size:21
Alignment explanation
Indices: 53838714--53838757 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53838704 CTCTTCAATT
53838714 GACACTCACAGCAGACTCAAA
1 GACACTCACAGCAGACTCAAA
53838735 GACACTCACAGCAGACTCAAA
1 GACACTCACAGCAGACTCAAA
53838756 GA
1 GA
53838758 AGCTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.32, G:0.16, T:0.09
Consensus pattern (21 bp):
GACACTCACAGCAGACTCAAA
Found at i:53841801 original size:15 final size:15
Alignment explanation
Indices: 53841781--53841812 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53841771 AAATTTCCCC
53841781 AATCATCTTATTTCT
1 AATCATCTTATTTCT
*
53841796 AATCATTTTATTTCT
1 AATCATCTTATTTCT
53841811 AA
1 AA
53841813 GAAACTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (15 bp):
AATCATCTTATTTCT
Found at i:53842524 original size:64 final size:64
Alignment explanation
Indices: 53842445--53842591 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
53842435 TATAGTATTT
53842445 AAATTAGAGGATTCGAACTTAAGATTTTAAAATTCTCAAATTTCTAACCTTATTAATTCAATCA
1 AAATTAGAGGATTCGAACTTAAGATTTTAAAATTCTCAAATTTCTAACCTTATTAATTCAATCA
*
53842509 AAATTAAAGGATTCGAACTTAAGATTTTAAAATTCTCAAATTTCTAACCTTATTAATTCAATCA
1 AAATTAGAGGATTCGAACTTAAGATTTTAAAATTCTCAAATTTCTAACCTTATTAATTCAATCA
53842573 AAATTAGAGGATTCGAACT
1 AAATTAGAGGATTCGAACT
53842592 AATATAACAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (64 bp):
AAATTAGAGGATTCGAACTTAAGATTTTAAAATTCTCAAATTTCTAACCTTATTAATTCAATCA
Found at i:53846182 original size:21 final size:21
Alignment explanation
Indices: 53846158--53846210 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
53846148 CATTGTTTCT
*
53846158 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
53846179 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
53846200 AATCTCACCGC
1 AATCTCACCGC
53846211 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:53849568 original size:14 final size:14
Alignment explanation
Indices: 53849549--53849583 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53849539 ATTGTGCAAA
*
53849549 TAAAATTTGGAAGT
1 TAAAATTTGAAAGT
53849563 TAAAATTTGAAAGT
1 TAAAATTTGAAAGT
53849577 TAAAATT
1 TAAAATT
53849584 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (14 bp):
TAAAATTTGAAAGT
Found at i:53851152 original size:9 final size:9
Alignment explanation
Indices: 53851132--53851224 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 9
53851122 TAAAACCAGT
53851132 TTAAAAATTA
1 TTAAAAA-TA
53851142 TTAAAAATA
1 TTAAAAATA
*
53851151 TT-AAAATG
1 TTAAAAATA
* *
53851159 TAAAAAAAA
1 TTAAAAATA
*
53851168 GCATAAAAATTA
1 --TTAAAAA-TA
53851180 TTAAACAATA
1 TTAAA-AATA
*
53851190 -TAAATACTA
1 TTAAA-AATA
53851199 TTAAAAAGTA
1 TTAAAAA-TA
53851209 -TAAAAATA
1 TTAAAAATA
53851217 TTAAAAAT
1 TTAAAAAT
53851225 TATATCTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
8 8 0.12
9 29 0.45
10 19 0.30
11 7 0.11
12 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
TTAAAAATA
Found at i:53851156 original size:19 final size:18
Alignment explanation
Indices: 53851133--53851224 Score: 87
Period size: 19 Copynumber: 4.9 Consensus size: 18
53851123 AAAACCAGTT
53851133 TAAAAATTATTAAAAATA
1 TAAAAATTATTAAAAATA
* ** *
53851151 TTAAAATGTAAAAAAAAGCA
1 TAAAAAT-TATTAAAAA-TA
53851171 TAAAAATTATTAAACAATA
1 TAAAAATTATTAAA-AATA
* *
53851190 TAAATACTATTAAAAAGTA
1 TAAAAATTATTAAAAA-TA
53851209 TAAAAA-TATTAAAAAT
1 TAAAAATTATTAAAAAT
53851225 TATATCTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.02
18 17 0.29
19 32 0.54
20 9 0.15
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAATTATTAAAAATA
Found at i:53851175 original size:38 final size:37
Alignment explanation
Indices: 53851133--53851224 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 37
53851123 AAAACCAGTT
*
53851133 TAAAAATTATTAAAAATATTAAA-ATGTAAAAAAAAGCA
1 TAAAAATTATTAAAAATA-TAAATA-CTAAAAAAAAGCA
** *
53851171 TAAAAATTATTAAACAATATAAATACTATTAAAAAGTA
1 TAAAAATTATTAAA-AATATAAATACTAAAAAAAAGCA
53851209 TAAAAA-TATTAAAAAT
1 TAAAAATTATTAAAAAT
53851225 TATATCTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 3 0.06
37 7 0.15
38 33 0.69
39 5 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (37 bp):
TAAAAATTATTAAAAATATAAATACTAAAAAAAAGCA
Found at i:53858235 original size:3 final size:3
Alignment explanation
Indices: 53858227--53858272 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
53858217 TAGAGGCCTG
53858227 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
53858273 TCACATTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:53859255 original size:17 final size:17
Alignment explanation
Indices: 53859233--53859266 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53859223 ATCCTTGTAT
53859233 AAGAAAATAAGCAAATA
1 AAGAAAATAAGCAAATA
* *
53859250 AAGAAACTAAGGAAATA
1 AAGAAAATAAGCAAATA
53859267 GAAATATGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (17 bp):
AAGAAAATAAGCAAATA
Found at i:53861846 original size:30 final size:30
Alignment explanation
Indices: 53861805--53861895 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
53861795 TATATAAAGC
*
53861805 TTAAGTGATATGATAAATTCTGTAGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
*
53861835 TTAAGTCATATGATAAATTCTGTTGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
53861865 TTAAGTCATATGATAAATTCTGTAGTGCTG
1 TTAAGTCATATGATAAATTCTGTAGTGCTG
53861895 T
1 T
53861896 CTAGTTTATC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (30 bp):
TTAAGTCATATGATAAATTCTGTAGTGCTG
Found at i:53862609 original size:2 final size:2
Alignment explanation
Indices: 53862604--53862644 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
53862594 AAAAAAAGGA
53862604 AG 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 AG A
53862645 CAGGTGCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53865210 original size:140 final size:139
Alignment explanation
Indices: 53864959--53865238 Score: 445
Period size: 140 Copynumber: 2.0 Consensus size: 139
53864949 TGGAATTTTC
*
53864959 ATTAGTTCTGAAATTTCAATTTTGCGTAGCCTATAATATTATGGTATCTATGTATCCATATCCAG
1 ATTAGTTCTGAAATTTCAATTTTGCATAGCCTATAATATTATGGTATCTATGTATCCATATCCAG
*
53865024 CTCTCACACACTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTTGGA
66 CTCTCACACACTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGGA
53865089 TCAAATCTA
131 TCAAATCTA
* * * *
53865098 ATTAGTTCTGAAATTTCAATTTTGTATAGTCCTATCATATTATGGTAT-TCATGTATCCTTATTC
1 ATTAGTTCTGAAATTTCAATTTTGCATAG-CCTATAATATTATGGTATCT-ATGTATCCATATCC
* ** *
53865162 AGCTCTCAGACTTTTCATAGCCTTCTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAG
64 AGCTCTCACACACTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAG
53865227 GATCAAATCTA
129 GATCAAATCTA
53865238 A
1 A
53865239 ACCATAATCC
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
139 28 0.22
140 101 0.78
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (139 bp):
ATTAGTTCTGAAATTTCAATTTTGCATAGCCTATAATATTATGGTATCTATGTATCCATATCCAG
CTCTCACACACTTCATAGCCTACTCTACTAGTCCAAAAGTTTAGATGAAAGGAGTCAACCTAGGA
TCAAATCTA
Found at i:53868876 original size:14 final size:16
Alignment explanation
Indices: 53868851--53868882 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53868841 TTTTTATAAA
53868851 AAAAATAGATAAT-TT
1 AAAAATAGATAATATT
53868866 AAAAATA-ATAATATT
1 AAAAATAGATAATATT
53868881 AA
1 AA
53868883 TTTAACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAAATAGATAATATT
Found at i:53869469 original size:17 final size:17
Alignment explanation
Indices: 53869436--53869473 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53869426 CATGTCACAT
*
53869436 AATTAAAAAATTTTAAA
1 AATTAAAAAATTATAAA
53869453 AATT-AAAAATTAATAAA
1 AATTAAAAAATT-ATAAA
53869470 AATT
1 AATT
53869474 CTAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAAAAATTATAAA
Found at i:53869914 original size:3 final size:3
Alignment explanation
Indices: 53869906--53870024 Score: 159
Period size: 3 Copynumber: 40.0 Consensus size: 3
53869896 GGGTTTAGGC
53869906 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * *
53869954 AGA AGA AGA AGA AGA AGA AGA ATA AAA AGA AGA GGA GGA GGA AG- AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
53870001 AGG AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA
53870025 GAAAAAATAG
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 105 0.98
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:53870323 original size:109 final size:109
Alignment explanation
Indices: 53870132--53870348 Score: 425
Period size: 109 Copynumber: 2.0 Consensus size: 109
53870122 TTTTTGGGTG
53870132 TAAGAAGTTTGGGAATGGGTTTCAAAAACCATGTTGTTTTTCACCTGGTTTGATCCACCATTGAT
1 TAAGAAGTTTGGGAATGGGTTTCAAAAACCATGTTGTTTTTCACCTGGTTTGATCCACCATTGAT
53870197 GCCCCGTTCACAAATTGTGTTGTTGGGTCTTCTAAAAAAAGTGT
66 GCCCCGTTCACAAATTGTGTTGTTGGGTCTTCTAAAAAAAGTGT
*
53870241 TAAGAAGTTTGGGAGTGGGTTTCAAAAACCATGTTGTTTTTCACCTGGTTTGATCCACCATTGAT
1 TAAGAAGTTTGGGAATGGGTTTCAAAAACCATGTTGTTTTTCACCTGGTTTGATCCACCATTGAT
53870306 GCCCCGTTCACAAATTGTGTTGTTGGGTCTTCTAAAAAAAGTG
66 GCCCCGTTCACAAATTGTGTTGTTGGGTCTTCTAAAAAAAGTG
53870349 AGGACATTGG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (109 bp):
TAAGAAGTTTGGGAATGGGTTTCAAAAACCATGTTGTTTTTCACCTGGTTTGATCCACCATTGAT
GCCCCGTTCACAAATTGTGTTGTTGGGTCTTCTAAAAAAAGTGT
Found at i:53871206 original size:21 final size:21
Alignment explanation
Indices: 53871180--53871233 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
53871170 GTAAGTTTGG
**
53871180 TGAGTTGGGGCAGTTTGTAAC
1 TGAGTTGGGGCAGACTGTAAC
* **
53871201 TGAGTTGGGGTAGACTGTTGC
1 TGAGTTGGGGCAGACTGTAAC
53871222 TGAGTTGGGGCA
1 TGAGTTGGGGCA
53871234 ACCACTTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.09, G:0.43, T:0.31
Consensus pattern (21 bp):
TGAGTTGGGGCAGACTGTAAC
Found at i:53873882 original size:28 final size:28
Alignment explanation
Indices: 53873824--53873883 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
53873814 TTTAAAATTC
* * *
53873824 ATTATTCTTTTATTATACTTACTTTATT
1 ATTATTATTTTATTATACTTACTTAAAT
*
53873852 ATTATTATTATTA-TATATTTACTTAAAT
1 ATTATTATT-TTATTATACTTACTTAAAT
53873880 ATTA
1 ATTA
53873884 AGAAAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTATTATTTTATTATACTTACTTAAAT
Found at i:53876867 original size:38 final size:38
Alignment explanation
Indices: 53876816--53876892 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
53876806 CAATTAGACC
53876816 TCTAATTGTACGAACTAACTATTTGATTTATATATGTG
1 TCTAATTGTACGAACTAACTATTTGATTTATATATGTG
53876854 TCTAATTGTACGAACTAACTATTTGATTTATATATGTG
1 TCTAATTGTACGAACTAACTATTTGATTTATATATGTG
53876892 T
1 T
53876893 TGAGTATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (38 bp):
TCTAATTGTACGAACTAACTATTTGATTTATATATGTG
Found at i:53879319 original size:16 final size:16
Alignment explanation
Indices: 53879289--53879319 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53879279 AAATCTAGAC
*
53879289 AACCCTAAATCAAAAT
1 AACCCTAAATAAAAAT
53879305 AACCCTAAATAAAAA
1 AACCCTAAATAAAAA
53879320 AATGAAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (16 bp):
AACCCTAAATAAAAAT
Found at i:53887798 original size:21 final size:21
Alignment explanation
Indices: 53887770--53887834 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
53887760 TCTATTGAGC
53887770 TTTT-GTTTAACCCTTATGGG
1 TTTTCGTTTAACCCTTATGGG
* * * *
53887790 TTTTCGTTTAGCTCTTACGAG
1 TTTTCGTTTAACCCTTATGGG
* * *
53887811 CTTTCGTTCAACCTTTATGGG
1 TTTTCGTTTAACCCTTATGGG
53887832 TTT
1 TTT
53887835 CTGTTTAGCT
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (21 bp):
TTTTCGTTTAACCCTTATGGG
Found at i:53887803 original size:42 final size:42
Alignment explanation
Indices: 53887706--53887862 Score: 151
Period size: 42 Copynumber: 3.7 Consensus size: 42
53887696 ACGTGTTTAC
* * * *
53887706 TTTTCGTTTAGCTCTTATGAGCTTCTGCTTAACTCATA-GTAG
1 TTTTCGTTTAGCTCTTATGAGCTTCTGTTTAACCCTTATG-GG
* * *
53887748 TTTCCGTTCAGCTC-TATTGAGCTTTTGTTTAACCCTTATGGG
1 TTTTCGTTTAGCTCTTA-TGAGCTTCTGTTTAACCCTTATGGG
* * *
53887790 TTTTCGTTTAGCTCTTACGAGCTT-TCGTTCAACCTTTATGGG
1 TTTTCGTTTAGCTCTTATGAGCTTCT-GTTTAACCCTTATGGG
*
53887832 -TTTCTGTTTAGCTCTCATGAGCTTCTGTTTA
1 TTTTC-GTTTAGCTCTTATGAGCTTCTGTTTA
53887863 GCCTTCGGGC
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 7 0.07
42 83 0.88
43 4 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTTCGTTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:53890565 original size:11 final size:11
Alignment explanation
Indices: 53890549--53890588 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
53890539 AATAGAAGTT
53890549 GAGAGAATTGA
1 GAGAGAATTGA
*
53890560 GAGAGAATTAA
1 GAGAGAATTGA
53890571 GAGAGAATTGA
1 GAGAGAATTGA
53890582 GAGAGAA
1 GAGAGAA
53890589 CTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:53897345 original size:14 final size:14
Alignment explanation
Indices: 53897328--53897358 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53897318 TTGAATATAT
53897328 ATACAAAAAAAATA
1 ATACAAAAAAAATA
*
53897342 ATACAAAAAAATTA
1 ATACAAAAAAAATA
53897356 ATA
1 ATA
53897359 TGGGAGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (14 bp):
ATACAAAAAAAATA
Found at i:53903030 original size:13 final size:12
Alignment explanation
Indices: 53903012--53903062 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
53903002 AGAAAAATTC
53903012 TCTTTTCTTTCTT
1 TCTTTT-TTTCTT
*
53903025 TCTTTTTTCACTT
1 TCTTTTTT-TCTT
53903038 TCTTTTCTTTCTT
1 TCTTTT-TTTCTT
*
53903051 TATTTTTTTCTT
1 TCTTTTTTTCTT
53903063 CAGGTCAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 8 0.24
13 23 0.70
14 2 0.06
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:53903717 original size:23 final size:23
Alignment explanation
Indices: 53903663--53903717 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
53903653 CTTGATTTTT
* * *
53903663 ACTTCGGTACTCTTGTTACTTGC
1 ACTTCGGTGCTCCTGTTACTGGC
*
53903686 ACCTT-GGTGCTCCTGTTGCTGGC
1 A-CTTCGGTGCTCCTGTTACTGGC
53903709 ACTTCGGTG
1 ACTTCGGTG
53903718 TGATCTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.09, C:0.27, G:0.25, T:0.38
Consensus pattern (23 bp):
ACTTCGGTGCTCCTGTTACTGGC
Found at i:53905039 original size:40 final size:40
Alignment explanation
Indices: 53904995--53905081 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
53904985 GAAAAACGAT
*
53904995 GCAAAAGGTAAGCAATAGCGGTGTTTTT-GTTCCAAATGCC
1 GCAAAAGGTAAGCAATAGCGGTGTTTTTGGTT-CAAACGCC
* * *
53905035 GCAAAAAGTTGAGCAATAGTGGTGTTTTTGGTTCAAACGCC
1 GC-AAAAGGTAAGCAATAGCGGTGTTTTTGGTTCAAACGCC
53905076 GCAAAA
1 GCAAAA
53905082 AGTTGAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 6 0.15
41 32 0.78
42 3 0.07
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (40 bp):
GCAAAAGGTAAGCAATAGCGGTGTTTTTGGTTCAAACGCC
Found at i:53905095 original size:41 final size:42
Alignment explanation
Indices: 53905008--53905107 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 42
53904998 AAAGGTAAGC
* * *
53905008 AATAGCGGTGTTTTT-GTTCCAAATGCCGCAAAAAGTTGAGC
1 AATAGTGGTGTTTTTGGTTCCAAACGCCGCAAAAAGTTGAGA
53905049 AATAGTGGTGTTTTTGGTT-CAAACGCCGCAAAAAGTTGAGA
1 AATAGTGGTGTTTTTGGTTCCAAACGCCGCAAAAAGTTGAGA
* *
53905090 AATAGTGGCGATTTTGGT
1 AATAGTGGTGTTTTTGGT
53905108 CTAAACACCG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
41 50 0.94
42 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (42 bp):
AATAGTGGTGTTTTTGGTTCCAAACGCCGCAAAAAGTTGAGA
Found at i:53912469 original size:33 final size:32
Alignment explanation
Indices: 53912319--53912617 Score: 145
Period size: 33 Copynumber: 9.0 Consensus size: 32
53912309 ATGGCAGTGT
* *
53912319 TTAT-ATGTAAGACCATGGCTGAGCTATGGCA
1 TTATGATGTAAGACCATAGCTGGGCTATGGCA
* * * ** *
53912350 TTCTAATGATAAGACCATAACTGGTTTATGACA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
* * * * * *
53912383 CTATGAACGTAAGACCATGGTTGGACCATGGCA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
*
53912416 GTGTTTAT-ATGTAAGACCATAGTTGGGCTATGGCA
1 ----TTATGATGTAAGACCATAGCTGGGCTATGGCA
* *
53912451 TTCTGATGATAAGACCATAGCTGGGTTATGGCA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
* * * *
53912484 CTATGAACGTAAGACCATAACTGGGTTATGGCA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
* * ** * * * * *
53912517 CTATGAACGTAAGATTATGGTTGGACCATGACA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
53912550 GTGTTTAT-ATGTAAGACCATAGCTGGGCTATGGCA
1 ----TTATGATGTAAGACCATAGCTGGGCTATGGCA
* * * *
53912585 TTCTAATGATAAGACCATAACTGGGTTATGGCA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
53912618 CTACAAATGT
Statistics
Matches: 201, Mismatches: 51, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
31 9 0.04
32 9 0.04
33 131 0.65
34 4 0.02
35 42 0.21
37 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (32 bp):
TTATGATGTAAGACCATAGCTGGGCTATGGCA
Found at i:53912498 original size:134 final size:134
Alignment explanation
Indices: 53912359--53912620 Score: 452
Period size: 134 Copynumber: 2.0 Consensus size: 134
53912349 ATTCTAATGA
* *
53912359 TAAGACCATAACTGGTTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTAT
1 TAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
* * *
53912424 ATGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGCTGGGTTATGGCACTATG
66 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTATG
53912489 AACG
131 AACG
* **
53912493 TAAGACCATAACTGGGTTATGGCACTATGAACGTAAGATTATGGTTGGACCATGACAGTGTTTAT
1 TAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
53912558 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTA
66 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTA
53912621 CAAATGTAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 120 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (134 bp):
TAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTATG
AACG
Found at i:53912516 original size:101 final size:101
Alignment explanation
Indices: 53912257--53912501 Score: 409
Period size: 101 Copynumber: 2.4 Consensus size: 101
53912247 GAATTGACGA
* *
53912257 ATAAGACCTTAACTAGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
*
53912322 TATGTAAGACCATGGCTGAGCTATGGCATTCTAATG
66 TATGTAAGACCATAGCTGAGCTATGGCATTCTAATG
*
53912358 ATAAGACCATAACTGGTTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
* * *
53912423 TATGTAAGACCATAGTTGGGCTATGGCATTCTGATG
66 TATGTAAGACCATAGCTGAGCTATGGCATTCTAATG
* *
53912459 ATAAGACCATAGCTGGGTTATGGCACTATGAACGTAAGACCAT
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCAT
53912502 AACTGGGTTA
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 134 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
TATGTAAGACCATAGCTGAGCTATGGCATTCTAATG
Found at i:53912654 original size:24 final size:24
Alignment explanation
Indices: 53912622--53912697 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
53912612 ATGGCACTAC
*
53912622 AAATGTAAAGGATGAATTGACGGG
1 AAATGTAAAGGATGAATTGACGGA
*
53912646 AAATGTAAAGGATGAATTGACGAA
1 AAATGTAAAGGATGAATTGACGGA
* ** *
53912670 AAATATAAAAAATGAATTGACGGT
1 AAATGTAAAGGATGAATTGACGGA
53912694 AAAT
1 AAAT
53912698 TACCCAAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.22
Consensus pattern (24 bp):
AAATGTAAAGGATGAATTGACGGA
Found at i:53914818 original size:43 final size:43
Alignment explanation
Indices: 53914704--53914852 Score: 120
Period size: 43 Copynumber: 3.5 Consensus size: 43
53914694 GAAAAATGAA
* * * * * * * *
53914704 GCTAAAAGTCATGTTCTTTATCGCCATTTGTGGGGAAAGCGCC
1 GCTAAAGGTCATGTTCTATAACGACGTTTATGGGAAAAGCACC
* * *
53914747 GCTAAAGATCATGTTCTTTAGCGACGTTTATGGGAAAAGCACC
1 GCTAAAGGTCATGTTCTATAACGACGTTTATGGGAAAAGCACC
* * * * *
53914790 GTTAAAGGTCATGTTCTATAATGGCGTTTTTGTGAGAAA-CACC
1 GCTAAAGGTCATGTTCTATAACGACGTTTATGGGA-AAAGCACC
* *
53914833 ACTAAATGTCATGTTCTATA
1 GCTAAAGGTCATGTTCTATA
53914853 GCGGCGATTT
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
43 83 0.97
44 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
GCTAAAGGTCATGTTCTATAACGACGTTTATGGGAAAAGCACC
Found at i:53917009 original size:50 final size:50
Alignment explanation
Indices: 53916851--53917100 Score: 344
Period size: 50 Copynumber: 4.9 Consensus size: 50
53916841 GATCATAACA
* ** *
53916851 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
*
53916902 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
53916951 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
53917001 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
53917056 ATGCCAATGCCATGTTCCAAACATGGTCTTACATGGGA--TCTCATC
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
53917101 ACCCAAATGT
Statistics
Matches: 182, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
49 41 0.23
50 63 0.35
51 33 0.18
53 5 0.03
54 4 0.02
55 2 0.01
56 34 0.19
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:53930811 original size:17 final size:17
Alignment explanation
Indices: 53930789--53930829 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
53930779 GATCTTCAAT
53930789 GAGCTT-TTAACCAAAAC
1 GAGCTTCTT-ACCAAAAC
53930806 GAGCTTCTTACCAAAAC
1 GAGCTTCTTACCAAAAC
53930823 GAGCTTC
1 GAGCTTC
53930830 CAATAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (17 bp):
GAGCTTCTTACCAAAAC
Found at i:53944470 original size:4 final size:4
Alignment explanation
Indices: 53944461--53944532 Score: 74
Period size: 4 Copynumber: 17.2 Consensus size: 4
53944451 TTATTTTTTG
* * *
53944461 TTAT TTAT TTAT TTAT TAAT TTATT TTAT TTTT TTACT TTAT TTAT TAAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTA-T TTAT TTAT TTAT
53944511 TTATT TTAT TT-T ATTAT TTAT T
1 TTA-T TTAT TTAT -TTAT TTAT T
53944533 ACTTATTTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
3 1 0.02
4 43 0.75
5 13 0.23
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:53944486 original size:30 final size:30
Alignment explanation
Indices: 53944441--53944532 Score: 129
Period size: 30 Copynumber: 3.1 Consensus size: 30
53944431 AGGCAACCCA
53944441 ATTT-TTAATTTTATTTT-TTGTTATTTATTT
1 ATTTATTAA-TTTATTTTATT-TTATTTATTT
53944471 ATTTATTAATTTATTTTATTTT-TTTACTTT
1 ATTTATTAATTTATTTTATTTTATTTA-TTT
53944501 ATTTATTAATTTATTTTATTTTA-TTATTT
1 ATTTATTAATTTATTTTATTTTATTTATTT
53944530 ATT
1 ATT
53944533 ACTTATTTGG
Statistics
Matches: 58, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
29 10 0.17
30 42 0.72
31 6 0.10
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (30 bp):
ATTTATTAATTTATTTTATTTTATTTATTT
Found at i:53946483 original size:15 final size:15
Alignment explanation
Indices: 53946458--53946492 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53946448 GACTCTATTT
*
53946458 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
53946472 TAATTAATATTAAGA
1 TAATTAATATTAAGA
53946487 TAATTA
1 TAATTA
53946493 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:53957319 original size:6 final size:6
Alignment explanation
Indices: 53957308--53957334 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53957298 CAAGAAGCAG
53957308 TGGGTT TGGGTT TGGGTT TGGGTT TGG
1 TGGGTT TGGGTT TGGGTT TGGGTT TGG
53957335 TTAAACGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
TGGGTT
Found at i:53964048 original size:21 final size:20
Alignment explanation
Indices: 53964014--53964052 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53964004 TCTGTTTTTA
53964014 TTTTATTTTATTTATCATCCC
1 TTTTATTTTATTTA-CATCCC
53964035 TTTTA-TTTATTTTACATC
1 TTTTATTTTA-TTTACATC
53964053 TCTGCACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTTTATTTACATCCC
Found at i:53965503 original size:31 final size:31
Alignment explanation
Indices: 53965465--53965546 Score: 114
Period size: 29 Copynumber: 2.7 Consensus size: 31
53965455 AAGGAGGGCT
*
53965465 TAATTAATTTTTAAATTATTTTATGAGGACA
1 TAATTAATTTTTAAATTATTTTATAAGGACA
* *
53965496 TAATTAA-TTTT-AATTATTTTTTAAGGACT
1 TAATTAATTTTTAAATTATTTTATAAGGACA
53965525 TAATTAATTTTTAAAATTATTT
1 TAATTAATTTTT-AAATTATTT
53965547 AAGTCTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.49
30 8 0.18
31 7 0.16
32 8 0.18
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (31 bp):
TAATTAATTTTTAAATTATTTTATAAGGACA
Found at i:53965903 original size:18 final size:16
Alignment explanation
Indices: 53965864--53965906 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
53965854 AAAAATTATG
*
53965864 TTTTTATATTTTATAT
1 TTTTTATATTTTATAA
53965880 TTTTTATCATTTTAATAA
1 TTTTTAT-ATTTT-ATAA
53965898 TTTTTATAT
1 TTTTTATAT
53965907 AATTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATATTTTATAA
Found at i:53965911 original size:20 final size:21
Alignment explanation
Indices: 53965878--53965930 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
53965868 TATATTTTAT
*
53965878 ATTTTT-TATCATTTTA-ATA
1 ATTTTTATATAATTTTATATA
53965897 ATTTTTATATAATTTTATATA
1 ATTTTTATATAATTTTATATA
*
53965918 ACTCTTTATATAA
1 A-TTTTTATATAA
53965931 AATTTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 9 0.31
21 4 0.14
22 10 0.34
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTATATAATTTTATATA
Found at i:53965925 original size:12 final size:10
Alignment explanation
Indices: 53965871--53965930 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
53965861 ATGTTTTTAT
53965871 ATTTTATAT-
1 ATTTTATATA
*
53965880 -TTTT-TATC
1 ATTTTATATA
53965888 ATTTTA-ATA
1 ATTTTATATA
53965897 ATTTTTATATA
1 A-TTTTATATA
53965908 ATTTTATATA
1 ATTTTATATA
53965918 ACTCTTTATATA
1 A-T-TTTATATA
53965930 A
1 A
53965931 AATTTATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 7 0.16
10 15 0.35
11 5 0.12
12 9 0.21
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTATATA
Found at i:53965934 original size:24 final size:20
Alignment explanation
Indices: 53965888--53965935 Score: 51
Period size: 24 Copynumber: 2.2 Consensus size: 20
53965878 ATTTTTTATC
*
53965888 ATTTTAATAATTTTTATATA
1 ATTTTAATAATTTTTATAAA
53965908 ATTTTATATAACTCTTTATATAAA
1 ATTTTA-ATAA-T-TTT-TATAAA
53965932 ATTT
1 ATTT
53965936 ATAAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 1 0.04
23 3 0.13
24 9 0.39
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATAATTTTTATAAA
Found at i:53966184 original size:8 final size:8
Alignment explanation
Indices: 53966171--53966261 Score: 62
Period size: 8 Copynumber: 11.0 Consensus size: 8
53966161 TCTATGGTTG
53966171 TTTTTATA
1 TTTTTATA
53966179 TTTTTATA
1 TTTTTATA
**
53966187 -ACTT-T-
1 TTTTTATA
53966192 TTTTTATA
1 TTTTTATA
53966200 TTTTTTATA
1 -TTTTTATA
*
53966209 TTTTTTTA
1 TTTTTATA
53966217 TTTTTATA
1 TTTTTATA
53966225 GTTTTTTATAA
1 --TTTTTAT-A
*
53966236 CTTTTATAA
1 TTTTTAT-A
*
53966245 TTTTCTAAA
1 TTTT-TATA
53966254 TTTTTATA
1 TTTTTATA
53966262 ATATTTTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.05
7 3 0.05
8 25 0.38
9 24 0.37
10 9 0.14
11 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:53966230 original size:10 final size:9
Alignment explanation
Indices: 53966171--53966268 Score: 74
Period size: 9 Copynumber: 10.3 Consensus size: 9
53966161 TCTATGGTTG
53966171 TTTTTATAT
1 TTTTTATAT
*
53966180 TTTTATAACTTT
1 TTTT-T-A-TAT
53966192 TTTTTATAT
1 TTTTTATAT
53966201 TTTTTATAT
1 TTTTTATAT
53966210 TTTTT-TA-
1 TTTTTATAT
53966217 TTTTTATAGT
1 TTTTTATA-T
*
53966227 TTTTTATAA
1 TTTTTATAT
*
53966236 CTTTTATAAT
1 TTTTTAT-AT
* *
53966246 TTTCTAAAT
1 TTTTTATAT
53966255 TTTTATAATAT
1 TTTT-T-ATAT
53966266 TTT
1 TTT
53966269 AATAACATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 5 0.07
8 4 0.06
9 31 0.44
10 16 0.23
11 8 0.11
12 6 0.09
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:53968790 original size:19 final size:19
Alignment explanation
Indices: 53968768--53968808 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53968758 AAGATTAATT
53968768 TTTTAAATAA-TTTAATTAA
1 TTTTAAATAATTTTAA-TAA
*
53968787 TTTTTAATAATTTTAATAA
1 TTTTAAATAATTTTAATAA
53968806 TTT
1 TTT
53968809 CTTATACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAATAATTTTAATAA
Found at i:53969455 original size:24 final size:24
Alignment explanation
Indices: 53969407--53969455 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
53969397 TATAGGTATA
* *
53969407 AGTATAAATAATCTATATAATAAT
1 AGTATAAATAATATATATAAAAAT
53969431 AGTATAATATAATATAT-TAAAAAT
1 AGTATAA-ATAATATATATAAAAAT
53969455 A
1 A
53969456 CCAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AGTATAAATAATATATATAAAAAT
Found at i:53969645 original size:17 final size:18
Alignment explanation
Indices: 53969623--53969663 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
53969613 AAAATCTTCT
* *
53969623 AATTAATAA-ATTTATTA
1 AATTAATAATATTAAATA
53969640 AATTAA-AATATTAAATA
1 AATTAATAATATTAAATA
53969657 AATTAAT
1 AATTAAT
53969664 TTTTTTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAATAATATTAAATA
Found at i:53973986 original size:71 final size:71
Alignment explanation
Indices: 53973859--53974069 Score: 368
Period size: 71 Copynumber: 3.0 Consensus size: 71
53973849 TCAAGTTTAG
* *
53973859 AAAATGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
53973924 TGAGAA
66 TGAGAA
*
53973930 AAAAAGGTTCGTGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
53973995 TGAGAA
66 TGAGAA
* * *
53974001 AAAAAGGATCGTGCCCAGTAAGTTAGGACACGATCTTCTCTTAATTCCCGAGATCGTTTAAAACT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
53974066 TGAG
66 TGAG
53974070 TTTGAAAAGA
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 133 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (71 bp):
AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAACT
TGAGAA
Found at i:53976376 original size:22 final size:22
Alignment explanation
Indices: 53976328--53976377 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
53976318 TTTTCACGTA
* *
53976328 CTATTTATTTGTTTTTTATCAC
1 CTATTTAATTGTTTTCTATCAC
*
53976350 TTATTTAAATTGTTTTCTAT-AC
1 CTATTT-AATTGTTTTCTATCAC
53976372 CTATTT
1 CTATTT
53976378 TTAAACCCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.62
Consensus pattern (22 bp):
CTATTTAATTGTTTTCTATCAC
Found at i:53976583 original size:30 final size:31
Alignment explanation
Indices: 53976549--53976650 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
53976539 TAAAAAATAA
*
53976549 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
53976579 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
53976609 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
53976639 AAATTTCATTTT
1 AAATTTCATTTT
53976651 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:53976933 original size:10 final size:10
Alignment explanation
Indices: 53976914--53976963 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
53976904 TTTTTCGAAG
*
53976914 GAAAAAAGAA
1 GAAAAGAGAA
53976924 GAAAAGAGAA
1 GAAAAGAGAA
53976934 GAAAAGAGAA
1 GAAAAGAGAA
* *
53976944 -AGAGGAGAA
1 GAAAAGAGAA
53976953 GAAAAGA-AA
1 GAAAAGAGAA
53976962 GA
1 GA
53976964 GTACTGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:53976964 original size:17 final size:19
Alignment explanation
Indices: 53976917--53976959 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
53976907 TTCGAAGGAA
53976917 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
53976935 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
53976954 AAAAGA
1 AAAAGA
53976960 AAGAGTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:53977025 original size:3 final size:3
Alignment explanation
Indices: 53977019--53977091 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
53977009 GCTAGACTTT
*
53977019 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA -AA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
* *
53977064 -AA GAAA GAA -AA AAA GAA AAA GAA -AA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA
53977092 ATAATAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
2 10 0.17
3 39 0.67
4 9 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53977037 original size:10 final size:10
Alignment explanation
Indices: 53977022--53977050 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
53977012 AGACTTTGAA
53977022 GAAGAAGAAG
1 GAAGAAGAAG
53977032 GAAGAAGAAG
1 GAAGAAGAAG
53977042 GAAGAAGAA
1 GAAGAAGAA
53977051 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:53977037 original size:13 final size:13
Alignment explanation
Indices: 53977019--53977061 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
53977009 GCTAGACTTT
53977019 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
53977032 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
53977045 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
53977056 GAAGAA
1 GAAGAA
53977062 AAAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 7 0.25
12 2 0.07
13 15 0.54
14 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:53977075 original size:11 final size:11
Alignment explanation
Indices: 53977046--53977092 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
53977036 AAGAAGGAAG
* *
53977046 AAGAAAAGAGG
1 AAGAAAAAAGA
53977057 AAGAAAAAAGA
1 AAGAAAAAAGA
53977068 AAGAAAAAAAGA
1 AAG-AAAAAAGA
53977080 AA-AAGAAAAGA
1 AAGAA-AAAAGA
53977091 AA
1 AA
53977093 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 2 0.06
11 20 0.62
12 10 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:53977101 original size:19 final size:17
Alignment explanation
Indices: 53977060--53977102 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
53977050 AAAGAGGAAG
53977060 AAAAAAGAAAGAAAAAA
1 AAAAAAGAAAGAAAAAA
*
53977077 AGAAAAAGAAAAGAAATAAT
1 A-AAAAAG-AAAGAAA-AAA
53977097 AAAAAA
1 AAAAAA
53977103 TATTATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 12 0.55
20 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAA
Found at i:53977364 original size:11 final size:10
Alignment explanation
Indices: 53977342--53977405 Score: 65
Period size: 10 Copynumber: 6.0 Consensus size: 10
53977332 GGCCCAGCAG
53977342 AGAAAAAAAA
1 AGAAAAAAAA
53977352 AGAAAAGAAAA
1 AGAAAA-AAAA
*
53977363 AGAAGAAAAAG
1 AGAA-AAAAAA
**
53977374 AGAAGGAAAA
1 AGAAAAAAAA
53977384 AGAAGGAAAAAA
1 AGAA--AAAAAA
53977396 AGAAAAAAAA
1 AGAAAAAAAA
53977406 GAGGTTCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 19 0.43
11 15 0.34
12 10 0.23
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:53977406 original size:21 final size:20
Alignment explanation
Indices: 53977342--53977407 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
53977332 GGCCCAGCAG
53977342 AGAA-AAAAAAAGAAAAGAAAA
1 AGAAGAAAAAAAG-AAA-AAAA
* *
53977363 AGAAGAAAAAGAGAAGGAAAA
1 AGAAGAAAAAAAGAA-AAAAA
53977384 AGAAGGAAAAAAAGAAAAAAA
1 AGAA-GAAAAAAAGAAAAAAA
53977405 AGA
1 AGA
53977408 GGTTCAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAAAGAAAAAAA
Found at i:53977775 original size:18 final size:18
Alignment explanation
Indices: 53977731--53977987 Score: 189
Period size: 17 Copynumber: 14.5 Consensus size: 18
53977721 TCTATAATCC
*
53977731 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
53977749 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
53977766 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
53977783 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
53977800 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
*
53977821 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
53977838 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
53977855 TCG-GTGTTTCAAAGATTT
1 TCGTGT-TTTCAAAAATTT
*
53977873 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTTCAAAAATTT
* * **
53977890 CCGGTGATTTTAAAAAAAAAT
1 TC-GTG-TTTT-CAAAAATTT
*
53977911 T-GT-TTTCTAAAAAATTT
1 TCGTGTTT-TCAAAAATTT
*
53977928 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
53977945 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
*
53977962 TCGTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
*
53977979 TCGTATTTT
1 TCGTGTTTT
53977988 AATTTTTTTA
Statistics
Matches: 193, Mismatches: 27, Indels: 39
0.75 0.10 0.15
Matches are distributed among these distances:
16 9 0.05
17 109 0.56
18 45 0.23
19 8 0.04
20 9 0.05
21 13 0.07
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:53977793 original size:16 final size:16
Alignment explanation
Indices: 53977742--53977795 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
53977732 CGTGCTTTTA
53977742 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
53977758 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
53977776 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
53977792 AAAA
1 AAAA
53977796 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:53977819 original size:72 final size:72
Alignment explanation
Indices: 53977741--53977887 Score: 217
Period size: 72 Copynumber: 2.0 Consensus size: 72
53977731 TCGTGCTTTT
*
53977741 AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTC-AAAA-TTCTAGTGTTTCAAAAATTTTCTT
1 AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTCAAAAATTTC-AGTGTTTCAAAAATTTTCGT
53977804 GTTTTCAGA
65 GTTTTCA-A
* * * *
53977813 AAAAATTTTCGTGTTTCAAAAATCTTCGTGTTTTCAAAAATTTCGGTGTTTCAAAGATTTTCGTG
1 AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTCAAAAATTTCAGTGTTTCAAAAATTTTCGTG
53977878 TTTTCAA
66 TTTTCAA
53977885 AAA
1 AAA
53977888 CTCCGGTGAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
72 37 0.54
73 28 0.41
74 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (72 bp):
AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTCAAAAATTTCAGTGTTTCAAAAATTTTCGTG
TTTTCAA
Found at i:53977852 original size:107 final size:105
Alignment explanation
Indices: 53977726--53977976 Score: 281
Period size: 107 Copynumber: 2.3 Consensus size: 105
53977716 TAATTTCTAT
* * * *
53977726 AATCCTCGTGCTTTTAAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTC-AAAATTCTAGTG-T
1 AATCTTCGTG-TTTTAAAAATT-TCGTGTTTCAAAAATCTTCGTGTTTTCAAAAACTCCAGTGAT
**** *
53977789 TTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTCAAA
64 TTCAAAAA-AAAATTGTTTTC-GAAAAAATTTCCGTGTTTCAAA
* * *
53977833 AATCTTCGTGTTTTCAAAAATTTCGGTGTTTCAAAGATTTTCGTGTTTTCAAAAACTCCGGTGAT
1 AATCTTCGTGTTTT-AAAAATTTC-GTGTTTCAAAAATCTTCGTGTTTTCAAAAACTCCAGTGAT
* *
53977898 TTTAAAAAAAAATTGTTTTCTAAAAAATTTCCGTGTTTCAAA
64 TTCAAAAAAAAATTGTTTTCGAAAAAATTTCCGTGTTTCAAA
* *
53977940 AATTTTCGTGTTTTAAAAATTTTCGTGTTTTAAAAAT
1 AATCTTCGTGTTTTAAAAA-TTTCGTGTTTCAAAAAT
53977977 TCTCGTATTT
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
106 22 0.18
107 75 0.61
108 17 0.14
109 8 0.07
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (105 bp):
AATCTTCGTGTTTTAAAAATTTCGTGTTTCAAAAATCTTCGTGTTTTCAAAAACTCCAGTGATTT
CAAAAAAAAATTGTTTTCGAAAAAATTTCCGTGTTTCAAA
Found at i:53977895 original size:35 final size:35
Alignment explanation
Indices: 53977726--53977960 Score: 171
Period size: 35 Copynumber: 6.6 Consensus size: 35
53977716 TAATTTCTAT
* *
53977726 AATCCTCGTGCTTTT-AAAAATTCTC-ATGTTTCAAA
1 AATCTTCGTG-TTTTCAAAAATTC-CGGTGTTTCAAA
**
53977761 AATCTTCGTGTTTTC-AAAATTCTAGTGTTTCAAA
1 AATCTTCGTGTTTTCAAAAATTCCGGTGTTTCAAA
* * *
53977795 AATTTTCTTGTTTTCAGAAAAAATTTTC-GTGTTTCAAA
1 AATCTTCGTGTTTTC---AAAAA-TTCCGGTGTTTCAAA
*
53977833 AATCTTCGTGTTTTCAAAAATTTCGGTGTTTCAAA
1 AATCTTCGTGTTTTCAAAAATTCCGGTGTTTCAAA
* * * *
53977868 GATTTTCGTGTTTTCAAAAACTCCGGTGATTTTAAAAA
1 AATCTTCGTGTTTTCAAAAATTCCGGTG--TTT-CAAA
** *
53977906 AAAATT-GT-TTTCTAAAAAATTTCC-GTGTTTCAAA
1 AATCTTCGTGTTT-TCAAAAA-TTCCGGTGTTTCAAA
*
53977940 AATTTTCGTGTTTT-AAAAATT
1 AATCTTCGTGTTTTCAAAAATT
53977961 TTCGTGTTTT
Statistics
Matches: 163, Mismatches: 22, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
33 2 0.01
34 49 0.30
35 54 0.33
36 6 0.04
37 14 0.09
38 36 0.22
39 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AATCTTCGTGTTTTCAAAAATTCCGGTGTTTCAAA
Found at i:53977906 original size:72 final size:71
Alignment explanation
Indices: 53977758--53977975 Score: 198
Period size: 72 Copynumber: 3.1 Consensus size: 71
53977748 CTCATGTTTC
* *
53977758 AAAAATCTTCGTGTTTTC-AAAA-TTCTAGTGTTTCAAAAATTTTCTTGTTTTCAGAAAAAATTT
1 AAAAATCTTCGTGTTTTCAAAAATTTC-AGTGTTTCAAAAATTTTCGTGTTTTC---AAAAATCT
* *
53977821 TCGTGTTT-C
62 CCGTGTTTAA
* *
53977830 AAAAATCTTCGTGTTTTCAAAAATTTCGGTGTTTCAAAGATTTTCGTGTTTTCAAAAA-CTCCGG
1 AAAAATCTTCGTGTTTTCAAAAATTTCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTCC-G
53977894 TGATTTTAA
65 TG--TTTAA
** * * * *
53977903 AAAAAAATT-GT-TTTCTAAAAAATTTCCGTGTTTCAAAAATTTTCGTGTTTT-AAAAATTTTCG
1 AAAAATCTTCGTGTTT-TCAAAAATTTCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTCCG
*
53977965 TGTTTTA
65 TGTTTAA
53977972 AAAA
1 AAAA
53977976 TTCTCGTATT
Statistics
Matches: 124, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
69 10 0.08
70 8 0.06
71 11 0.09
72 58 0.47
73 34 0.27
74 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (71 bp):
AAAAATCTTCGTGTTTTCAAAAATTTCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTCCGT
GTTTAA
Found at i:53977988 original size:17 final size:17
Alignment explanation
Indices: 53977731--53978086 Score: 182
Period size: 17 Copynumber: 20.8 Consensus size: 17
53977721 TCTATAATCC
*
53977731 TCGTGCTTTTAAAAATTC
1 TCGTG-TTTTAAAAATTT
* * *
53977749 TCATGTTTCAAAAATCT
1 TCGTGTTTTAAAAATTT
* *
53977766 TCGTGTTTTCAAAATTC
1 TCGTGTTTTAAAAATTT
* *
53977783 TAGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
*
53977800 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTT----AAAAATTT
* *
53977821 TCGTGTTTCAAAAATCT
1 TCGTGTTTTAAAAATTT
53977838 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTT-AAAAATTT
* *
53977855 TCGGTGTTTCAAAGATTT
1 TC-GTGTTTTAAAAATTT
*
53977873 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTT-AAAAATTT
* **
53977890 CCGGTGATTTTAAAAAAAAAT
1 TC-GTG-TTTT--AAAAATTT
53977911 T-GT-TTTCTAAAAAATTT
1 TCGTGTTT-T-AAAAATTT
* *
53977928 CCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
53977945 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
*
53977962 TCGTGTTTTAAAAATTC
1 TCGTGTTTTAAAAATTT
*
53977979 TCGTATTTT---AATTT
1 TCGTGTTTTAAAAATTT
** **
53977993 T--T-TTAAGAAAAAAAT
1 TCGTGTT-TTAAAAATTT
* * *
53978008 T-GTGTTTCAAAAAATG
1 TCGTGTTTTAAAAATTT
*
53978024 TCTTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
*
53978041 T-GTGTTTCT-GAAATTT
1 TCGTGTTT-TAAAAATTT
* *
53978057 CCGTG-TTTAAAAATTC
1 TCGTGTTTTAAAAATTT
53978073 TCGTGTTTTAAAAA
1 TCGTGTTTTAAAAA
53978087 AAAACTTTCA
Statistics
Matches: 255, Mismatches: 57, Indels: 53
0.70 0.16 0.15
Matches are distributed among these distances:
11 2 0.01
12 1 0.00
14 5 0.02
15 5 0.02
16 30 0.12
17 153 0.60
18 29 0.11
19 9 0.04
20 5 0.02
21 16 0.06
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTT
Found at i:53978046 original size:16 final size:16
Alignment explanation
Indices: 53978017--53978086 Score: 63
Period size: 16 Copynumber: 4.3 Consensus size: 16
53978007 TTGTGTTTCA
* *
53978017 AAAAATGTCTTGTTTT
1 AAAAATTTCGTGTTTT
*
53978033 AAAAATTTTGTGTTTCT
1 AAAAATTTCGTGTTT-T
*
53978050 -GAAATTTCCGTG-TTT
1 AAAAATTT-CGTGTTTT
53978065 AAAAATTCTCGTGTTTT
1 AAAAATT-TCGTGTTTT
53978082 AAAAA
1 AAAAA
53978087 AAAACTTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
15 1 0.02
16 29 0.67
17 13 0.30
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAAATTTCGTGTTTT
Found at i:53978124 original size:16 final size:17
Alignment explanation
Indices: 53978105--53978141 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53978095 CATTTTTTAA
53978105 AAAAATT-TCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
53978120 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
53978137 AAAAA
1 AAAAA
53978142 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:53986221 original size:66 final size:68
Alignment explanation
Indices: 53986098--53986261 Score: 192
Period size: 66 Copynumber: 2.4 Consensus size: 68
53986088 CTTTCCAAGG
* **
53986098 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAATTT-T
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCATCAAGACACGCCGAGGTATTTTAATTTAT
53986161 -TTT
65 GTTT
* * *
53986164 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATC-GGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATCAAGACACGCCGAGGTA-TTTTAATTTAT
53986228 GTTT
65 GTTT
* ** *
53986232 TAAATTGACTCATATTGCGAGAGGTGAGTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTT
53986262 AAGCCTTTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 11 0.13
66 41 0.49
67 3 0.04
68 29 0.35
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (68 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATCAAGACACGCCGAGGTATTTTAATTTATG
TTT
Found at i:53986539 original size:73 final size:72
Alignment explanation
Indices: 53986274--53986609 Score: 421
Period size: 72 Copynumber: 4.5 Consensus size: 72
53986264 GCCTTTTAAT
*
53986274 TTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCA
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCA
53986338 ATTTCTG
66 ATTTCTG
*
53986345 CTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACG-TGAGGTATTT
1 TTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
*
53986408 CAATTCCTGTTCAATTA
64 CAA----T-TTC---TG
53986425 TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTT
53986490 CAATTTCTG
64 CAATTTCTG
* * *
53986499 TTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTCA
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCA
*
53986563 AATTCT-
66 ATTTCTG
** *
53986569 ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
53986610 ACCTTTTAAT
Statistics
Matches: 235, Mismatches: 13, Indels: 33
0.84 0.05 0.12
Matches are distributed among these distances:
70 4 0.02
71 16 0.07
72 56 0.24
73 48 0.20
74 39 0.17
76 1 0.00
77 6 0.03
78 1 0.00
79 38 0.16
80 8 0.03
81 11 0.05
82 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (72 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCA
ATTTCTG
Found at i:53986556 original size:153 final size:152
Alignment explanation
Indices: 53986275--53986563 Score: 483
Period size: 153 Copynumber: 1.9 Consensus size: 152
53986265 CCTTTTAATT
*
53986275 TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAAT
1 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAAT
* *
53986340 TTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTGAGGTA
66 TTCTGCTTTTCAAGAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGACACGCGAGGTA
53986405 TTTCAATTCCTGTTCAATTATG
131 TTTCAATTCCTGTTCAATTATG
53986427 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTCA
* * *
53986492 ATTTCTGTTTTTC-A-AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCCGAG
64 ATTTCTGCTTTTCAAGAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGACACG-CGAG
53986555 GTATTTCAA
128 GTATTTCAA
53986564 ATTCTACTTT
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
152 46 0.36
153 64 0.50
154 18 0.14
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (152 bp):
TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAAT
TTCTGCTTTTCAAGAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGACACGCGAGGTA
TTTCAATTCCTGTTCAATTATG
Found at i:53986899 original size:43 final size:43
Alignment explanation
Indices: 53986834--53986921 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
53986824 CTTTTAATTT
* *
53986834 CTGTTTTCAAAATTCAATTTATATTGTGAAAAATGAGTTGAGC
1 CTGTTTTCAAAATTCAACTTATATTGCGAAAAATGAGTTGAGC
* **
53986877 CTGTTTTCAAAATTCAACTTATATTGCGAGAGGTGAGTTGAGC
1 CTGTTTTCAAAATTCAACTTATATTGCGAAAAATGAGTTGAGC
53986920 CT
1 CT
53986922 CGGGTCACGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (43 bp):
CTGTTTTCAAAATTCAACTTATATTGCGAAAAATGAGTTGAGC
Found at i:53987148 original size:76 final size:75
Alignment explanation
Indices: 53986878--53987447 Score: 737
Period size: 76 Copynumber: 7.6 Consensus size: 75
53986868 GAGTTGAGCC
* * * * * *
53986878 TGTTTTCAAAATTCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-
1 TGTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTC
53986940 TTTT-AATTTA
65 TTTTAAATTTA
* * *
53986950 TGATTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-T
1 TGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
53987012 TTTAAATTTA
66 TTTAAATTTA
**
53987022 TGTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
53987087 TTTAAATTTCCA
66 TTTAAATTT--A
*
53987099 T-TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCT
1 TGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
* *
53987163 TTTAATTTTC
66 TTTAAATTTA
* *
53987173 TGTTTTTCAAAAAATCGACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTT
1 TG-TTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
*
53987238 CTTTCAAATTT-
64 CTTTTAAATTTA
53987249 TCGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
1 T-G-TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
*
53987314 CTTTTAAATTTC
64 CTTTTAAATTTA
* ** * *
53987326 TGTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGATCACATGCCGAGGTATT
1 TGTTTTCAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGGGT--CATGCCGAGGTATT
*
53987391 TC-TTTAAATTTT
63 TCTTTTAAATTTA
* *
53987403 TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TGTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC
53987448 AGGACACACG
Statistics
Matches: 453, Mismatches: 30, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
71 39 0.09
72 82 0.18
74 2 0.00
75 31 0.07
76 159 0.35
77 124 0.27
78 16 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (75 bp):
TGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
TTTAAATTTA
Found at i:53987218 original size:77 final size:76
Alignment explanation
Indices: 53986880--53987552 Score: 721
Period size: 76 Copynumber: 8.8 Consensus size: 76
53986870 GTTGAGCCTG
* * * * * * *
53986880 TTTTCAAAATTCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TT
1 TTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
*
53986942 TT-AATTTATG-
65 TTAAATTTCTGT
* * * *
53986952 ATTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTT
1 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
*
53987014 TAAATTTATGT
66 TAAATTTCTGT
* *
53987025 TTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTTT
1 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
**
53987089 TAAATTTCCAT
66 TAAATTTCTGT
53987100 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
1 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
*
53987165 TAATTTTCTGT
66 TAAATTTCTGT
*
53987176 TTTTCAAAAAATCGACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
1 TTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
*
53987241 TCAAATTT-TCGT
65 TTAAATTTCT-GT
*
53987253 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTTT
1 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
53987318 TAAATTTCTG-
66 TAAATTTCTGT
* ** *
53987328 TTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTG-GATCACATGCCGAGGTATTT
1 TTTTCAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGAG-T--CATGCCGAGGTATTT
*
53987392 C-TTTAAATTTTTG-
62 CTTTTAAATTTCTGT
* * ** *
53987405 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTAA
1 TTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC--GAGTCATGCCGAGGTATT--
* *
53987470 GCCTTTT-GATTTCTGT
61 -TCTTTTAAATTTCTGT
* * **
53987486 TTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGTCACACCGAGGTA
1 TTTTC-----AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGA-GTCATGCCGAGGTA
53987550 TTT
59 TTT
53987553 TCCATTTCTG
Statistics
Matches: 532, Mismatches: 41, Indels: 47
0.86 0.07 0.08
Matches are distributed among these distances:
71 39 0.07
72 77 0.14
73 3 0.01
74 1 0.00
75 37 0.07
76 156 0.29
77 135 0.25
78 16 0.03
79 1 0.00
80 7 0.01
81 8 0.02
83 1 0.00
84 13 0.02
86 38 0.07
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (76 bp):
TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
TAAATTTCTGT
Found at i:53987235 original size:153 final size:151
Alignment explanation
Indices: 53986880--53987552 Score: 728
Period size: 153 Copynumber: 4.4 Consensus size: 151
53986870 GTTGAGCCTG
* * * * * * *
53986880 TTTTCAAAATTCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TT
1 TTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
* * *
53986942 TT-AATTTATGATTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
65 TTAAATTTATGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCACGCCGA
*
53987006 GGTA--T-TTTTAAATTTATGT
130 GGTATTTCTTTTAAATTTCTGT
* *
53987025 TTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTTT
1 TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
*
53987089 TAAATTTCCAT-TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCG
66 TAAATTT--ATGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCACGCCG
*
53987153 AGGTATTTCTTTTAATTTTCTGT
129 AGGTATTTCTTTTAAATTTCTGT
*
53987176 TTTTCAAAAAATCGACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
1 TTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTT
* * *
53987241 TCAAATTT-TCGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCC
65 TTAAATTTAT-G-TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCACGCC
53987305 GAGGTATTTCTTTTAAATTTCTG-
128 GAGGTATTTCTTTTAAATTTCTGT
* ** *
53987328 TTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTG-GATCACATGCCGAGGTATTT
1 TTTTCAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGAG-T--CATGCCGAGGTATTT
* * * **
53987392 C-TTTAAATTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA
62 CTTTTAAATTTATGTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC--GAGTCA
* *
53987456 CGCCGAGGTATTAAGCCTTTT-GATTTCTGT
124 CGCCGAGGTATT---TCTTTTAAATTTCTGT
* * **
53987486 TTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGTCACACCGAGGTA
1 TTTTC-----AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGA-GTCATGCCGAGGTA
53987550 TTT
59 TTT
53987553 TCCATTTCTG
Statistics
Matches: 456, Mismatches: 38, Indels: 52
0.84 0.07 0.10
Matches are distributed among these distances:
143 32 0.07
144 14 0.03
145 5 0.01
146 4 0.01
147 5 0.01
148 54 0.12
149 2 0.00
150 2 0.00
151 32 0.07
152 46 0.10
153 163 0.36
154 17 0.04
155 14 0.03
157 7 0.02
158 10 0.02
161 13 0.03
163 35 0.08
164 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (151 bp):
TTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCATGCCGAGGTATTTCTTT
TAAATTTATGTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAGTCACGCCGAG
GTATTTCTTTTAAATTTCTGT
Found at i:53987772 original size:73 final size:72
Alignment explanation
Indices: 53987588--53987841 Score: 384
Period size: 73 Copynumber: 3.5 Consensus size: 72
53987578 TTTGAAAGAA
* *
53987588 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATCGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
53987653 TCAAAAT
66 TCAAAAT
*
53987660 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
53987725 TTCAAAAT
65 TTCAAAAT
* *
53987733 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTT-
** *
53987798 TAAAAAAAAA
65 T--TCAAAAT
53987808 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
53987842 GTTCACATGT
Statistics
Matches: 168, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
72 61 0.36
73 70 0.42
74 3 0.02
75 34 0.20
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:53989072 original size:16 final size:16
Alignment explanation
Indices: 53989051--53989088 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53989041 AAAGTATGAT
* *
53989051 ATAAAAAATACAAGAA
1 ATAAAAAATAAAAAAA
53989067 ATAAAAAATAAAAAAA
1 ATAAAAAATAAAAAAA
53989083 ATAAAA
1 ATAAAA
53989089 TTTTTTACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
ATAAAAAATAAAAAAA
Found at i:53990977 original size:15 final size:17
Alignment explanation
Indices: 53990956--53990998 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
53990946 AAATCTGGAA
53990956 TGCTAGCTCGCCA-CAC
1 TGCTAGCTCGCCACCAC
* *
53990972 -GCTAGCTCACCACCTC
1 TGCTAGCTCGCCACCAC
53990988 TGCTAGCTCGC
1 TGCTAGCTCGC
53990999 GGGATCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.50
16 2 0.09
17 9 0.41
ACGTcount: A:0.16, C:0.44, G:0.19, T:0.21
Consensus pattern (17 bp):
TGCTAGCTCGCCACCAC
Found at i:54006189 original size:69 final size:70
Alignment explanation
Indices: 54006038--54006244 Score: 330
Period size: 69 Copynumber: 3.0 Consensus size: 70
54006028 CTCAGTTTAG
* *
54006038 AAAATGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCG-TTAAAACT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATC-TTTCTTAATTTCCGAGATCGTTTAAAACT
54006102 TGAGAA
65 TGAGAA
*
54006108 AAAAAGGTTCGTGCCCAGTAAGTTAGGACACAATCTTTCTTAATTTCCGAGATCGTTTAAAACTT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTCTTAATTTCCGAGATCGTTTAAAACTT
54006173 GAG-A
66 GAGAA
* *
54006177 AAAAAGGATCGTGCCCAGTAAGTTAGGACACGATCTTCTCTT-ATTCCCGAGATCGTTTAAAACT
1 AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTT-TCTTAATTTCCGAGATCGTTTAAAACT
54006241 TGAG
65 TGAG
54006245 TTTGAAAGAT
Statistics
Matches: 129, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
69 81 0.63
70 48 0.37
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (70 bp):
AAAAAGGATCGTGCCCAGTAAGTTAGGACACAATCTTTCTTAATTTCCGAGATCGTTTAAAACTT
GAGAA
Found at i:54006497 original size:17 final size:17
Alignment explanation
Indices: 54006475--54006518 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54006465 AAAATGAAAT
54006475 AAATAAATATAAAAGAC
1 AAATAAATATAAAAGAC
* *
54006492 AAATAAATCATATAATAC
1 AAATAAAT-ATAAAAGAC
*
54006510 AATTAAATA
1 AAATAAATA
54006519 AGCGAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAAATATAAAAGAC
Found at i:54008511 original size:22 final size:21
Alignment explanation
Indices: 54008464--54008512 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
54008454 GTTTCACGTA
*
54008464 CTATTTATTTGTTTTTATCAC
1 CTATTTAATTGTTTTTATCAC
*
54008485 TTATTTAAATTGTTTTCTAT-AC
1 CTATTT-AATTGTTTT-TATCAC
54008507 CTATTT
1 CTATTT
54008513 TTAAACCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.22
22 15 0.65
23 3 0.13
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.61
Consensus pattern (21 bp):
CTATTTAATTGTTTTTATCAC
Found at i:54008704 original size:30 final size:31
Alignment explanation
Indices: 54008670--54008772 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 31
54008660 TAAAAAATAA
*
54008670 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
54008700 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
54008730 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
54008760 AAATTTTCATTTT
1 AAA-TTTCATTTT
54008773 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
29 4 0.06
30 50 0.81
31 8 0.13
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Done.