Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 173 of 240
Found at i:53722350 original size:3 final size:3
Alignment explanation
Indices: 53722342--53722390 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
53722332 CTCTTAATTT
**
53722342 TAA TAA TAA GGA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53722388 TAA
1 TAA
53722391 AGACGTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:53728911 original size:113 final size:111
Alignment explanation
Indices: 53728709--53728923 Score: 304
Period size: 113 Copynumber: 1.9 Consensus size: 111
53728699 AATAATAAAC
* * *
53728709 CGCCACGTCATTTAACTTTTAGATATATTTTTAATTGTTGGGGATAAACCTATATAAACAACGAA
1 CGCCACGTCATTTAACTTTAAAATATATTTTTAATTGTTGGGGATAAACCCATATAAACAACGAA
* *
53728774 CAAGAAAAGTAAAGAGGATTGAACACACAAATTTTACGTAAAAAAT
66 CAAGAAAAGTAAAGAAGATCGAACACACAAATTTTACGTAAAAAAT
* * * * * *
53728820 CGCCATGTCATTTAACCTTTAAAAGTATTTTTTTGATTGTTGGGGTTCAACCCGTATAAACAACG
1 CGCCACGTCATTTAA-CTTTAAAA-TATATTTTTAATTGTTGGGGATAAACCCATATAAACAACG
*
53728885 AACAAGAAAAGTAAAGAATATCGAACACACAAATTTTAC
64 AACAAGAAAAGTAAAGAAGATCGAACACACAAATTTTAC
53728924 ATGAAAAACT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
111 14 0.16
112 6 0.07
113 70 0.78
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (111 bp):
CGCCACGTCATTTAACTTTAAAATATATTTTTAATTGTTGGGGATAAACCCATATAAACAACGAA
CAAGAAAAGTAAAGAAGATCGAACACACAAATTTTACGTAAAAAAT
Found at i:53729344 original size:6 final size:6
Alignment explanation
Indices: 53729333--53729362 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53729323 ATCAAAGTGG
53729333 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
53729363 ATTATTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:53730316 original size:14 final size:14
Alignment explanation
Indices: 53730278--53730317 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53730268 ACAAAAAAGT
*
53730278 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
53730292 AAATCATTTTACGG
1 AAAACATTTTACAG
53730306 AAAACATTTTAC
1 AAAACATTTTAC
53730318 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:53732785 original size:8 final size:9
Alignment explanation
Indices: 53732767--53732793 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53732757 TATTTCTCTC
53732767 TTTATTTTT
1 TTTATTTTT
53732776 TTTATTTTT
1 TTTATTTTT
53732785 TTTATTTTT
1 TTTATTTTT
53732794 CTTTTCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTATTTTT
Found at i:53735148 original size:42 final size:41
Alignment explanation
Indices: 53735094--53735211 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 41
53735084 CTAGCACAAA
* *
53735094 CGCCGCTGAAGACTAAGACCTTTAGCGGCGCTTTAGTG-GAAG
1 CGCCGCTAAAGACTAAGATCTTTAGCGGCG-TTT-GTGAGAAG
***
53735136 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTGTGCTAGAAG
1 CGCCGCTAAAGACTAAGATCTTTAGCGGCGTTTGTG--AGAAG
* *
53735179 CGCCGCTATAGA-TCAAGGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGACT-AAGATCTTTAGCGGCGTTT
53735212 TTTTCTCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
40 3 0.05
41 3 0.05
42 25 0.40
43 31 0.50
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (41 bp):
CGCCGCTAAAGACTAAGATCTTTAGCGGCGTTTGTGAGAAG
Found at i:53735265 original size:43 final size:43
Alignment explanation
Indices: 53735218--53735491 Score: 214
Period size: 43 Copynumber: 6.3 Consensus size: 43
53735208 GTTTTTTTCT
* *
53735218 CAAACGCC-GTAATAGACCCTGATCTATAGCGGTGCTTTGACCA
1 CAAACGCCAGTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCA
* * ** * * **
53735261 CAAACGCCACTAAATAAACTAATCTTTAGCGACGCTTTCCCCTA
1 CAAACGCCAGTAAAGACCCTGATCTTTAGCGGCGCTTTGACC-A
* * * *
53735305 -AAACGCC-GCAATAGACCCTGATCTATAGCGGTGCTTCGACCA
1 CAAACGCCAGTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCA
* * * * **
53735347 CAAAATGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCA
1 C-AAACGCCAGTAAAGACCCTGATCTTTAGCGGCGCTTTGACCA
* * * **
53735391 CAAACGCCATTAAAGACCATGATCTTTAGTGGCGCTTTTTCCA
1 CAAACGCCAGTAAAGACCCTGATCTTTAGCGGCGCTTTGACCA
*
53735434 CAAACGCC-GCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCA
1 CAAACGCCAG-TAAAGACCCTGATCTTTAGCGGCGCTTTGACCA
* * *
53735477 AAAACGACACTAAAG
1 CAAACGCCAGTAAAG
53735492 GCCAACACCT
Statistics
Matches: 174, Mismatches: 49, Indels: 16
0.73 0.21 0.07
Matches are distributed among these distances:
42 3 0.02
43 135 0.78
44 34 0.20
45 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
CAAACGCCAGTAAAGACCCTGATCTTTAGCGGCGCTTTGACCA
Found at i:53735287 original size:86 final size:86
Alignment explanation
Indices: 53735197--53735471 Score: 327
Period size: 86 Copynumber: 3.2 Consensus size: 86
53735187 TAGATCAAGG
* ***
53735197 TCTTTAGCGGCGTTTTTTTCTCAAACGCCGTAATAGACCCTGATCTATAGCGGTGCTTTGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGTAATAGACCCTGATCTATAGCGGTGCTTTGACCAC
* *
53735262 AAACGCCACTAAATAAACTAA
66 AAACGCCACTAAAGAACCTAA
* * * *
53735283 TCTTTAGCGACGCTTTCCCCTAAAACGCCGCAATAGACCCTGATCTATAGCGGTGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGTAATAGACCCTGATCTATAGCGGTGCTTTGACCAC
*
53735348 AAAATGCCACTAAAGAACCTAA
66 -AAACGCCACTAAAGAACCTAA
* * * * * * **
53735370 TCTTTAGCGGCGCTTTCCCCACAAACGCCATTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCA
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCC-GTAATAGACCCTGATCTATAGCGGTGCTTTGACCA
* * *
53735434 CAAACGCCGCTAAAGACCCTTA
65 CAAACGCCACTAAAGAACCTAA
53735456 TCTTTAGCGGCGCTTT
1 TCTTTAGCGGCGCTTT
53735472 GACCAAAAAC
Statistics
Matches: 160, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
86 90 0.56
87 68 0.43
88 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCCCCTCAAACGCCGTAATAGACCCTGATCTATAGCGGTGCTTTGACCAC
AAACGCCACTAAAGAACCTAA
Found at i:53735482 original size:86 final size:86
Alignment explanation
Indices: 53735357--53735516 Score: 212
Period size: 86 Copynumber: 1.9 Consensus size: 86
53735347 CAAAATGCCA
* * * * ** *
53735357 CTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCACAAACGCCATTAAAGACCATGATCTTTAGTG
1 CTAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGACACTAAAGACCAACACCTTTAGTG
53735422 GCGCTTTTTCCACAAACGCCG
66 GCGCTTTTTCCACAAACGCCG
* * * *
53735443 CTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGACACTAAAGGCCAACACCTTTAGTG
1 CTAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGACACTAAAGACCAACACCTTTAGTG
*
53735508 GCGTTTTTT
66 GCGCTTTTT
53735517 TTAAAAAACG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 62 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (86 bp):
CTAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGACACTAAAGACCAACACCTTTAGTG
GCGCTTTTTCCACAAACGCCG
Found at i:53735863 original size:21 final size:21
Alignment explanation
Indices: 53735837--53735949 Score: 127
Period size: 21 Copynumber: 5.4 Consensus size: 21
53735827 TTTGACGCTG
53735837 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
53735858 CTCTGCTTTGCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
53735879 CTCTGTTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
53735900 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
53735921 CTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
53735942 CTCTGCTT
1 CTCTGCTT
53735950 TTCTTGCTGC
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.05, C:0.41, G:0.19, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:53735889 original size:42 final size:42
Alignment explanation
Indices: 53735837--53735970 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 42
53735827 TTTGACGCTG
*
53735837 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTTGCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTTCCTCGCTGCAGC
* ** * *
53735879 CTCTGTTTCCCTCGCTTTAGCCTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTTCCTCGCTGCAGC
* * * * * * * *
53735921 CTGTACTTCTCTAGCTGCCGCCTCTGCTTTTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTTCCTCGCTGCAGC
*
53735963 ATCTGCTT
1 CTCTGCTT
53735971 TAAGCTGCTG
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.05, C:0.40, G:0.19, T:0.37
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTGCTTTCCTCGCTGCAGC
Found at i:53736034 original size:66 final size:66
Alignment explanation
Indices: 53735941--53736106 Score: 201
Period size: 66 Copynumber: 2.5 Consensus size: 66
53735931 CTAGCTGCCG
* * * *
53735941 CCTCTGCTTTTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCATT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-ATT
53736004 GAA
64 GAA
* * *
53736007 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTATTGA
53736072 A
66 A
* * * *
53736073 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
53736107 TTGTGTAATT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTATTGA
A
Found at i:53738550 original size:9 final size:9
Alignment explanation
Indices: 53738533--53738734 Score: 96
Period size: 9 Copynumber: 24.2 Consensus size: 9
53738523 TAAGTATAAT
*
53738533 TAAGCTATG
1 TAAGTTATG
53738542 TAAGTTATG
1 TAAGTTATG
53738551 T-A-TTATG
1 TAAGTTATG
53738558 TAAGTTAT-
1 TAAGTTATG
*
53738566 TTA-TTATG
1 TAAGTTATG
* **
53738574 AAAACTATG
1 TAAGTTATG
*
53738583 TAAGTTGTG
1 TAAGTTATG
53738592 T-A-TTATG
1 TAAGTTATG
*
53738599 -AA--AAT-
1 TAAGTTATG
* *
53738604 TATGCTATG
1 TAAGTTATG
*
53738613 TAAGTTATA
1 TAAGTTATG
* *
53738622 TAAGTCATA
1 TAAGTTATG
53738631 TAAGTTATG
1 TAAGTTATG
53738640 T-A-TTATG
1 TAAGTTATG
53738647 TAAGTTATG
1 TAAGTTATG
53738656 TAAGTTAT-
1 TAAGTTATG
*
53738664 TTA-TTATG
1 TAAGTTATG
* * *
53738672 CAAATTAAG
1 TAAGTTATG
53738681 TAAGTTATG
1 TAAGTTATG
53738690 TAAGTTATG
1 TAAGTTATG
*
53738699 TATA-ATAT-
1 TA-AGTTATG
**
53738707 TAA-TTAAC
1 TAAGTTATG
53738715 TAAGTTATG
1 TAAGTTATG
*
53738724 TAATTTATG
1 TAAGTTATG
53738733 TA
1 TA
53738735 TAATATTTAT
Statistics
Matches: 145, Mismatches: 32, Indels: 32
0.69 0.15 0.15
Matches are distributed among these distances:
6 3 0.02
7 28 0.19
8 18 0.12
9 95 0.66
10 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:53738559 original size:16 final size:16
Alignment explanation
Indices: 53738538--53738657 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
53738528 ATAATTAAGC
53738538 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
53738554 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
*
53738570 TATG-AA---A---AC
1 TATGTAAGTTATGTAT
*
53738579 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
53738595 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
*
53738609 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
* *
53738627 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
53738643 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
53738658 AGTTATTTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 10 0.13
15 2 0.03
16 44 0.58
17 1 0.01
18 11 0.14
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:53738582 original size:25 final size:25
Alignment explanation
Indices: 53738552--53738688 Score: 118
Period size: 25 Copynumber: 5.6 Consensus size: 25
53738542 TAAGTTATGT
53738552 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * *
53738577 ACTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * *
53738602 ATTATGCTATGTAAGTTA-TAT--AA
1 ATTATG-TAAGTTATTTATTATGAAA
* * * * *
53738625 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
53738650 GTTATGTAAGTTATTTATTATGCAA
1 ATTATGTAAGTTATTTATTATGAAA
*
53738675 ATTAAGTAAGTTAT
1 ATTATGTAAGTTAT
53738689 GTAAGTTATG
Statistics
Matches: 86, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
22 7 0.08
23 8 0.09
25 65 0.76
26 6 0.07
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:53738732 original size:43 final size:43
Alignment explanation
Indices: 53738631--53738757 Score: 109
Period size: 43 Copynumber: 2.9 Consensus size: 43
53738621 ATAAGTCATA
* * *
53738631 TAAGTTATGT-ATTATGTAAGTTATGTA-AGTTATTTATTATGC
1 TAAGTTATGTAATTATGTAAGTTATGTATA-ATATTAATTATAC
* *
53738673 -AAATTAAGTAAGTTATGTAAGTTATGTATAATATTAATTA-AC
1 TAAGTTATGTAA-TTATGTAAGTTATGTATAATATTAATTATAC
*
53738715 TAAGTTATGTAATTTATGTATAATATTTATGTATAATATTAAT
1 TAAGTTATGTAA-TTATG--T-A-AGTTATGTATAATATTAAT
53738758 GTAAGTTATG
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
41 7 0.10
42 2 0.03
43 38 0.56
44 1 0.01
45 1 0.01
46 1 0.01
47 18 0.26
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.47
Consensus pattern (43 bp):
TAAGTTATGTAATTATGTAAGTTATGTATAATATTAATTATAC
Found at i:53738744 original size:13 final size:13
Alignment explanation
Indices: 53738726--53738760 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
53738716 AAGTTATGTA
53738726 ATTTATGTATAAT
1 ATTTATGTATAAT
53738739 ATTTATGTATAAT
1 ATTTATGTATAAT
*
53738752 ATTAATGTA
1 ATTTATGTA
53738761 AGTTATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
ATTTATGTATAAT
Found at i:53738809 original size:34 final size:33
Alignment explanation
Indices: 53738647--53738809 Score: 184
Period size: 34 Copynumber: 4.8 Consensus size: 33
53738637 ATGTATTATG
* * ***
53738647 TAAGTTATGTAAGTTATTTATTATGCAAATTAA
1 TAAGTTATGTAAGTTATGTATAATATTAATTAA
53738680 GTAAGTTATGTAAGTTATGTATAATATTAATTAA
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAA
* *
53738714 CTAAGTTATGTAATTTATGTATAATATTTATGT-A
1 -TAAGTTATGTAAGTTATGTATAATATTAAT-TAA
*
53738748 TAATATTAATGTAAGTTATGTATAATATTAATTAA
1 TAA-GTT-ATGTAAGTTATGTATAATATTAATTAA
*
53738783 TTAAGTTATGTAATTTATGTATAATAT
1 -TAAGTTATGTAAGTTATGTATAATAT
53738810 CACATCACTC
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
33 3 0.03
34 79 0.71
35 26 0.23
36 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (33 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAA
Found at i:53738892 original size:13 final size:15
Alignment explanation
Indices: 53738873--53738913 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
53738863 CATATAAGTT
53738873 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
53738887 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
53738901 TTATGTAAGTTAT
1 -TATGTAAGTTAT
53738914 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:53738908 original size:16 final size:16
Alignment explanation
Indices: 53738872--53738950 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
53738862 ACATATAAGT
53738872 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
53738887 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
53738901 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
53738919 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
53738935 TTATATAAGTCATGTA
1 TTATGTAAGTTATGTA
53738951 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 26 0.50
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:53741478 original size:27 final size:27
Alignment explanation
Indices: 53741446--53741497 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53741436 TCTTACTTTT
* *
53741446 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
53741473 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
53741498 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:53741588 original size:8 final size:10
Alignment explanation
Indices: 53741565--53741601 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
53741555 TAATAACTAT
53741565 ATATATATCC
1 ATATATATCC
*
53741575 ATATATATTC
1 ATATATATCC
53741585 ATATATATCC
1 ATATATATCC
53741595 ATATATA
1 ATATATA
53741602 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:53744050 original size:81 final size:82
Alignment explanation
Indices: 53743922--53744159 Score: 300
Period size: 81 Copynumber: 2.9 Consensus size: 82
53743912 CTAAAGGTAG
* * * *
53743922 CATTAGCGGCGCTTACATATAAAACGCCGCTAAAGGTCAGAGTATTAGTGGCGCTCAGATAAAAA
1 CATTAGCGGCGCTTAGACA-AAAACGCCGCTAAAGGACAGAGAATTAGTGGCGCTCAGATAAAAA
53743987 CGCCACTAAAAACACGAA
65 CGCCACTAAAAACACGAA
* * * * *
53744005 CTTTAGCGGCGCTTAGA-AAAAACGCCGCTAAAGAACGGAGAATTAGTGGCGCTCAGACAATAAC
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGACAGAGAATTAGTGGCGCTCAGATAAAAAC
** * *
53744069 GCCACTAATGATACGAG
66 GCCACTAAAAACACGAA
*
53744086 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGA-ACATTAGTGGCGCTCAGATAAAAA
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGACAGAGA-ATTAGTGGCGCTCAGATAAAAA
* *
53744150 CACCGCTAAA
65 CGCCACTAAA
53744160 GATCGGAGAA
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
81 70 0.53
82 47 0.36
83 15 0.11
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (82 bp):
CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGACAGAGAATTAGTGGCGCTCAGATAAAAAC
GCCACTAAAAACACGAA
Found at i:53744142 original size:82 final size:81
Alignment explanation
Indices: 53743920--53744202 Score: 320
Period size: 82 Copynumber: 3.5 Consensus size: 81
53743910 CGCTAAAGGT
* * *
53743920 AGCATTAGCGGCGCTTACATATAAAACGCCGCTAAAGGTCAGAGTATTAGTGGCGCTCAGATAAA
1 AGCATTAGCGGCGCTTAGATA-AAAACGCCGCTAAAGGACAGA-AATTAGTGGCGCTCAGATAAA
* *
53743985 AACGCCACTAAAAACACG
64 AACGCCACTAAAGATACG
* * * * * *
53744003 AACTTTAGCGGCGCTTAGA-AAAAACGCCGCTAAAGAACGGAGAATTAGTGGCGCTCAGACAATA
1 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAGA-AATTAGTGGCGCTCAGATAAAA
*
53744067 ACGCCACTAATGATACG
65 ACGCCACTAAAGATACG
* *
53744084 AGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAACATTAGTGGCGCTCAGATAAAA
1 AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAGAA-ATTAGTGGCGCTCAGATAAAA
* *
53744149 ACACCGCTAAAGAT-CGG
65 ACGCCACTAAAGATAC-G
* * *
53744166 AGAATTAGTGGCGC-TAAAGTAAAAACGCCGCTAAAGG
1 AGCATTAGCGGCGCTTAGA-TAAAAACGCCGCTAAAGG
53744203 TTTAAAAATC
Statistics
Matches: 170, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
81 74 0.44
82 80 0.47
83 16 0.09
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (81 bp):
AGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAGAAATTAGTGGCGCTCAGATAAAAA
CGCCACTAAAGATACG
Found at i:53744160 original size:41 final size:41
Alignment explanation
Indices: 53743885--53744202 Score: 226
Period size: 41 Copynumber: 7.8 Consensus size: 41
53743875 TTTTGTTACT
* *
53743885 ATTAGCGGCGCTTCGGA-AAAAACGCCGCTAAAGG-TAG--C
1 ATTAGCGGCGC-TCAGATAAAAACGCCGCTAAAGGACAGAAC
* * * **
53743923 ATTAGCGGCGCTTACATATAAAACGCCGCTAAAGGTCAGAGT
1 ATTAGCGGCGCTCAGATA-AAAACGCCGCTAAAGGACAGAAC
* * *
53743965 ATTAGTGGCGCTCAGATAAAAACGCCACTAAA-AACACGAAC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGACA-GAAC
* * * *
53744006 TTTAGCGGCGCTTAGA-AAAAACGCCGCTAAAGAACGGAGA-
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGACAGA-AC
* * * * * * *
53744046 ATTAGTGGCGCTCAGACAATAACGCCACT-AATGATACGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGACA-GAAC
* * *
53744087 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAAC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGACAGAAC
* * *
53744128 ATTAGTGGCGCTCAGATAAAAACACCGCTAAA-GATCGGAGA-
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGA-CAGA-AC
* *
53744169 ATTAGTGGCGCT-AAAGTAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTCAGA-TAAAAACGCCGCTAAAGG
53744203 TTTAAAAATC
Statistics
Matches: 220, Mismatches: 44, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
37 2 0.01
38 12 0.05
39 16 0.07
40 39 0.18
41 130 0.59
42 21 0.10
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGACAGAAC
Found at i:53749389 original size:23 final size:26
Alignment explanation
Indices: 53749327--53749388 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
53749317 AATAAAAAAA
53749327 ATTAAAATATTATAATTTTTTTATTT
1 ATTAAAATATTATAATTTTTTTATTT
53749353 ATTAAAATATTATAATTTTTTTATTT
1 ATTAAAATATTATAATTTTTTTATTT
*
53749379 ATCAAAATAT
1 ATTAAAATAT
53749389 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTAAAATATTATAATTTTTTTATTT
Found at i:53749463 original size:27 final size:27
Alignment explanation
Indices: 53749432--53749490 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
53749422 CACCCTGGTC
*
53749432 GTGCCAAGGTGATTGGCGGCACCAAAG
1 GTGCCAAAGTGATTGGCGGCACCAAAG
*
53749459 TTGCCAAAGTGATTGGCGGCACCAAAG
1 GTGCCAAAGTGATTGGCGGCACCAAAG
53749486 GTGCC
1 GTGCC
53749491 TTTTTGGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.34, T:0.17
Consensus pattern (27 bp):
GTGCCAAAGTGATTGGCGGCACCAAAG
Found at i:53749814 original size:19 final size:18
Alignment explanation
Indices: 53749772--53749814 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
53749762 ATTATTATTG
53749772 TTAGT-ATTAAGATGTTA
1 TTAGTAATTAAGATGTTA
53749789 TTAAGTAATTAAGATGTTA
1 TT-AGTAATTAAGATGTTA
53749808 CTTAGTA
1 -TTAGTA
53749815 GTATTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 3 0.13
19 16 0.70
20 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.44
Consensus pattern (18 bp):
TTAGTAATTAAGATGTTA
Found at i:53750655 original size:17 final size:18
Alignment explanation
Indices: 53750626--53750664 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
53750616 GATATGGTTA
53750626 GTGGTGAAAAAGAAGGTG
1 GTGGTGAAAAAGAAGGTG
53750644 GTGGTG-AAAAGAAGGTG
1 GTGGTGAAAAAGAAGGTG
53750661 GTGG
1 GTGG
53750665 CGATCATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.18
Consensus pattern (18 bp):
GTGGTGAAAAAGAAGGTG
Found at i:53755748 original size:29 final size:28
Alignment explanation
Indices: 53755704--53755842 Score: 75
Period size: 28 Copynumber: 5.1 Consensus size: 28
53755694 TAAAATTTAC
53755704 CTTTTTTTCTTCCTTC-CCTCTT-CTTCTT
1 CTTTTTTTCTTCCTTCTCCT-TTCCTT-TT
*
53755732 CTTTTTTTTTTCTCTTCTCCTTTCCTTTT
1 CTTTTTTTCTTC-CTTCTCCTTTCCTTTT
**
53755761 CTTTCCTTCTT--TT-T-CTTT-CTTTT
1 CTTTTTTTCTTCCTTCTCCTTTCCTTTT
* * * *
53755784 -TTCTTCTCCTTTCC-TCTTC-TTCTTCTTT
1 CTT-TTTTTC-TTCCTTCTCCTTTCCT-TTT
*
53755812 CTTTTTTT-TCCCTTCTCCTTTCCTTTT
1 CTTTTTTTCTTCCTTCTCCTTTCCTTTT
53755839 CTTT
1 CTTT
53755843 CCTTCTTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.02
23 9 0.11
24 6 0.07
25 2 0.02
26 8 0.09
27 13 0.15
28 21 0.25
29 18 0.21
30 6 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTTTTTCTTCCTTCTCCTTTCCTTTT
Found at i:53755779 original size:4 final size:4
Alignment explanation
Indices: 53755758--53755903 Score: 87
Period size: 4 Copynumber: 37.0 Consensus size: 4
53755748 CTCCTTTCCT
*
53755758 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * * *
53755803 -TTC -TTC TTTC TTT- TTT- TTCC CTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC
* *
53755848 -TT- TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
53755896 TTTC TTTC
1 TTTC TTTC
53755904 CCTCTCCTTC
Statistics
Matches: 118, Mismatches: 9, Indels: 30
0.75 0.06 0.19
Matches are distributed among these distances:
3 24 0.20
4 73 0.62
5 12 0.10
6 9 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:53755845 original size:78 final size:79
Alignment explanation
Indices: 53755705--53755912 Score: 277
Period size: 78 Copynumber: 2.7 Consensus size: 79
53755695 AAAATTTACC
* *
53755705 TTTTT-TTCTTCCTTCCCTCTTCTTCTTC-TT-TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTTTTCTTCTTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCC
53755767 TTCTTTTTCTTTCT
66 TTCTTTTTCTTTCT
53755781 TTTTTCTTC-TCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCC
1 TTTTTCTTCTTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCC
53755845 TTCTTTTTCTTTCT
66 TTCTTTTTCTTTCT
** *
53755859 TTCCTCTCCTTCCTTT-CT-TTCTTTCTTTCTTTCTTTCTTTCTTTCCC-TCTCCTT
1 TTTTTCTTCTTCCTTTCCTCTTC-TTC-TTCTTTC-TT-TTT-TTTCCCTTCTCCTT
53755913 CTCCCCCCAA
Statistics
Matches: 118, Mismatches: 5, Indels: 13
0.87 0.04 0.10
Matches are distributed among these distances:
76 23 0.19
77 8 0.07
78 56 0.47
79 13 0.11
80 2 0.02
81 10 0.08
82 6 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (79 bp):
TTTTTCTTCTTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCC
TTCTTTTTCTTTCT
Found at i:53755985 original size:27 final size:27
Alignment explanation
Indices: 53755947--53755998 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
53755937 TATTATAACA
**
53755947 TTGGTGCCGCCAATGTCTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
53755974 TTGGTGCCGCCAATCACTTTGGCAC
1 TTGGTGCCGCCAATCACTTTGGCAC
53755999 AACCAGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.31, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGTGCCGCCAATCACTTTGGCACCT
Found at i:53756094 original size:26 final size:27
Alignment explanation
Indices: 53756062--53756121 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 27
53756052 TGTTTTTGGT
53756062 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
* *
53756088 TTATTTTGGTAATTAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
53756115 ATATTTT
1 ATATTTT
53756122 AATTATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:53759746 original size:161 final size:160
Alignment explanation
Indices: 53759514--53759833 Score: 496
Period size: 161 Copynumber: 2.0 Consensus size: 160
53759504 GGGTGGTCAA
** *
53759514 AATGAAAGTGTAATTATAATGTGGAGTGTATAATTAACCTTCGTTAGAGATATAATAGTTGAATG
1 AATGAAAGTGTAAAAATAATGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGAATG
* ** * *
53759579 ATTAAAATGAAAGCGCCTTAAAAGTTGGGTGACGAAATTACAAGAATTTTATTTTGAGTGGCCAA
66 ATTAAAATGAAAGCACAGTAAAAGTTGGGTGACGAAATTACAAGAATTTGATTTTGAGTGACCAA
53759644 AATGAAAGTACACTAAAAGTGATGTGACCAC
131 AATGAAAGTACACTAAAAGTGAT-TGACCAC
* * * *
53759675 AATGAAAGTGTAAAAATGATGTGGAGTGTACAGTTAACTTTTGTTAGAGATATAATAGTTGAATG
1 AATGAAAGTGTAAAAATAATGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGAATG
* *
53759740 ATTAAAATGAAAGCATAGTAAAAGTTGGGTGACGAAATTGCAAGAATTTGATTTTGAGTGACCAA
66 ATTAAAATGAAAGCACAGTAAAAGTTGGGTGACGAAATTACAAGAATTTGATTTTGAGTGACCAA
*
53759805 AATGAAAGTGCACTAAAAGTGATTGACCA
131 AATGAAAGTACACTAAAAGTGATTGACCA
53759834 GATGGGTAGT
Statistics
Matches: 144, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
160 6 0.04
161 138 0.96
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (160 bp):
AATGAAAGTGTAAAAATAATGTGGAGTGTACAATTAACCTTCGTTAGAGATATAATAGTTGAATG
ATTAAAATGAAAGCACAGTAAAAGTTGGGTGACGAAATTACAAGAATTTGATTTTGAGTGACCAA
AATGAAAGTACACTAAAAGTGATTGACCAC
Found at i:53775259 original size:13 final size:13
Alignment explanation
Indices: 53775243--53775268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53775233 TTTTTTAACA
53775243 TTATTTAATTTTT
1 TTATTTAATTTTT
53775256 TTATTTAATTTTT
1 TTATTTAATTTTT
53775269 ATAACTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTAATTTTT
Found at i:53775932 original size:54 final size:55
Alignment explanation
Indices: 53775874--53775992 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 55
53775864 AAACGGCCCA
53775874 CTTCCATAAATAATTTCAGAAATGA-ACCTTTATTGATACTAAACCCTATTTAAG
1 CTTCCATAAATAATTTCAGAAATGACACCTTTATTGATACTAAACCCTATTTAAG
*
53775928 CTTCCATAAATAATTTCAGAAATGAGCCTCCTTTATTGATACTAAACCCTATTTAAG
1 CTTCCATAAATAATTTCAGAAATGA--CACCTTTATTGATACTAAACCCTATTTAAG
53775985 CTTCCATA
1 CTTCCATA
53775993 CATGTAATTC
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
54 25 0.41
57 36 0.59
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (55 bp):
CTTCCATAAATAATTTCAGAAATGACACCTTTATTGATACTAAACCCTATTTAAG
Found at i:53780193 original size:16 final size:16
Alignment explanation
Indices: 53780169--53780206 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53780159 ATAACTATAC
* *
53780169 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
53780185 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
53780201 TGTAAT
1 TGTAAT
53780207 AGTAAATCAA
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:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:53780241 original size:45 final size:44
Alignment explanation
Indices: 53780185--53780282 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
53780175 GGATTAGAGG
* *
53780185 TGTAATGGAATAGAGGTGTAATAGTAAATCAAT-TGTTTGATTGAA
1 TGTAATAGAATAGAGGCGTAATAGT-AATC-ATGTGTTTGATTGAA
* *
53780230 TGTAATAGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAGTAATCATGTGTTTGATTGAA
*
53780274 TCTAATAGA
1 TGTAATAGA
53780283 GGTGTAATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.49
45 23 0.49
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (44 bp):
TGTAATAGAATAGAGGCGTAATAGTAATCATGTGTTTGATTGAA
Found at i:53780461 original size:18 final size:17
Alignment explanation
Indices: 53780440--53780474 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53780430 TTATTATTAA
*
53780440 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53780458 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53780475 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53780528 original size:157 final size:157
Alignment explanation
Indices: 53780327--53780643 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
53780317 TAGAATACCC
*
53780327 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
53780392 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
53780457 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
53780484 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
53780549 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
53780614 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
53780641 TTA
1 TTA
53780644 ATATTCTTAT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:53780614 original size:16 final size:16
Alignment explanation
Indices: 53780577--53780618 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53780567 TTAATCATAT
*
53780577 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
53780593 TT-AAATATATTATAA
1 TTAAAATATATTATAA
53780608 TTAAAATATAT
1 TTAAAATATAT
53780619 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:53780625 original size:14 final size:15
Alignment explanation
Indices: 53780586--53780627 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53780576 TTTAAACATA
*
53780586 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53780601 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53780615 A-TATAATTTAATA
1 ATTATAATTAAATA
53780628 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53780715 original size:120 final size:121
Alignment explanation
Indices: 53780575--53780872 Score: 503
Period size: 120 Copynumber: 2.5 Consensus size: 121
53780565 ATTTAATCAT
*
53780575 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
53780640 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
53780697 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
53780760 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * * *
53780816 ATTTGAA-ATAATTAATATTAAATATATTTTAACTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
53780873 TAAAATAATT
Statistics
Matches: 168, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
119 3 0.02
120 160 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:53780745 original size:14 final size:15
Alignment explanation
Indices: 53780696--53780747 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53780686 GTAAAATATA
53780696 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
53780711 TATTAAATATATTAT
1 AATTAAATATATTAT
53780726 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
53780739 AATTTAATA
1 AATTAAATA
53780748 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:53780958 original size:15 final size:15
Alignment explanation
Indices: 53780913--53780966 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
53780903 TATGAATTTG
53780913 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
53780927 -ATAA-TT-ATTACA
1 TATAATTTAATAATA
53780939 TATAATTTAATAATA
1 TATAATTTAATAATA
*
53780954 TATAATTTCATAA
1 TATAATTTAATAA
53780967 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
11 1 0.03
12 4 0.13
13 8 0.26
14 2 0.06
15 16 0.52
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:53781029 original size:87 final size:88
Alignment explanation
Indices: 53780888--53781089 Score: 273
Period size: 87 Copynumber: 2.3 Consensus size: 88
53780878 TAATTATAAC
* * * * * *
53780888 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATA-A
1 TAATAAATTTTCTTATATGAA-TTATACAATTTAAAATAATAATTATTAAATATAATTTAATAGA
*
53780952 TATATAATTTCATAAAATTCTTGA
65 TATATAATTTCATAAAATTCTTAA
53780976 TAATAAATTTTCTTATATGAATTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGT
1 TAATAAATTTTCTTATATGAATTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATA--
53781040 GATATATAATTTCATAAAATTCTTAA
63 GATATATAATTTCATAAAATTCTTAA
*
53781066 TAATAAAATGTTCTTATATGAATT
1 TAAT-AAATTTTCTTATATGAATT
53781090 TACTAAAATC
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
87 34 0.34
88 21 0.21
90 28 0.28
91 18 0.18
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (88 bp):
TAATAAATTTTCTTATATGAATTATACAATTTAAAATAATAATTATTAAATATAATTTAATAGAT
ATATAATTTCATAAAATTCTTAA
Found at i:53790045 original size:59 final size:57
Alignment explanation
Indices: 53789967--53790125 Score: 146
Period size: 59 Copynumber: 2.8 Consensus size: 57
53789957 TTCAAAGTCC
* * * * *
53789967 AAAAATATTTTTTGGGTGCTGAGACACTAATGGCCGGCA-CCTCTATACCCGATTTTTTA
1 AAAAAAATTATTTGAGTGCTGAGACACTAATGGCCGGCACCCT-TATACCAGA--TTTGA
* * *
53790026 AAAAAAATTGTTTGAGTGCT-AGGACACTAATGGTCGGCACCCTTGTACCAGATTTGA
1 AAAAAAATTATTTGAGTGCTGA-GACACTAATGGCCGGCACCCTTATACCAGATTTGA
* * *
53790083 AAAAAAA--ACTTGAGTGCTGGGACACTAATGGCCGACACACCTT
1 AAAAAAATTATTTGAGTGCTGAGACACTAATGGCCGGCAC-CCTT
53790126 TACTATATAA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
55 25 0.30
56 4 0.05
57 11 0.13
58 1 0.01
59 40 0.48
60 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (57 bp):
AAAAAAATTATTTGAGTGCTGAGACACTAATGGCCGGCACCCTTATACCAGATTTGA
Found at i:53794303 original size:43 final size:43
Alignment explanation
Indices: 53794237--53794365 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
53794227 AACTAATACA
** ** * *
53794237 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCACAGATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACATAAACACAAATCG
* *
53794280 ATGCCACTGTCCCAGACAG-GGTCTTACACATAAACACAAATTG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACATAAACACAAATCG
* * * *
53794323 ATGCCAATGTCCCAGACGTGATCTTATACGTAAACACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACATAAACACAAATCG
53794366 GAAATCCTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 68 0.97
44 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACATAAACACAAATCG
Found at i:53801047 original size:26 final size:26
Alignment explanation
Indices: 53801011--53801060 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
53801001 AAGAAGAAAA
53801011 AGAAAATCGTGCCAAGCGGCAGACAG
1 AGAAAATCGTGCCAAGCGGCAGACAG
53801037 AGAAAATCGTGCCAAGCGGCAGAC
1 AGAAAATCGTGCCAAGCGGCAGAC
53801061 TTATATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.30, T:0.08
Consensus pattern (26 bp):
AGAAAATCGTGCCAAGCGGCAGACAG
Found at i:53803946 original size:31 final size:29
Alignment explanation
Indices: 53803872--53803929 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
53803862 GAATTGGATC
* *
53803872 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATC-AAAGTTCATGTATAAAATTACACA
*
53803902 AAATCAAAGTTCATGTATACAATTACAC
1 AAATCAAAGTTCATGTATAAAATTACAC
53803930 TTTAAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTACACA
Found at i:53804156 original size:21 final size:21
Alignment explanation
Indices: 53804130--53804184 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
53804120 AACAGCGGTG
*
53804130 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
53804151 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
53804172 GCGGTGAGATTAG
1 GCGGTGAGATTAG
53804185 AAATAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:53808115 original size:16 final size:16
Alignment explanation
Indices: 53808076--53808116 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
53808066 TTCTCCATTC
53808076 CCATCTCCCCTCTTCCA
1 CCAT-TCCCCTCTTCCA
*
53808093 TCATTCCCCTCTTCCA
1 CCATTCCCCTCTTCCA
*
53808109 CCGTTCCC
1 CCATTCCC
53808117 TCCTCCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.56, G:0.02, T:0.32
Consensus pattern (16 bp):
CCATTCCCCTCTTCCA
Found at i:53808179 original size:58 final size:58
Alignment explanation
Indices: 53808064--53808256 Score: 230
Period size: 60 Copynumber: 3.3 Consensus size: 58
53808054 ATACAATGCA
* * *
53808064 ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCC
1 ATTTC-CCATTCCCATCTACCCTATTCCA-CATTCCCCTCTTCCACCGTGCCCTCCTCCC
* * *
53808124 ATTTCCTATTCCCATGCAATACCC-ATTCCA-ATTTCCC-CTTCCACCGTGCCGTCCTCCC
1 ATTTCCCATTCCCAT-C--TACCCTATTCCACATTCCCCTCTTCCACCGTGCCCTCCTCCC
* *
53808182 ATTTCCCATTCCCATCTCCCCTCTTCCATCGATTCCCCTCTTCCACCGTGCCCTCCTCCC
1 ATTTCCCATTCCCATCTACCCTATTCCA-C-ATTCCCCTCTTCCACCGTGCCCTCCTCCC
53808242 ATTTCCCATTCCCAT
1 ATTTCCCATTCCCAT
53808257 TCCCATTATC
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
55 4 0.04
56 5 0.04
57 1 0.01
58 33 0.29
59 21 0.18
60 41 0.36
61 5 0.04
62 4 0.04
ACGTcount: A:0.13, C:0.50, G:0.04, T:0.33
Consensus pattern (58 bp):
ATTTCCCATTCCCATCTACCCTATTCCACATTCCCCTCTTCCACCGTGCCCTCCTCCC
Found at i:53808187 original size:28 final size:28
Alignment explanation
Indices: 53808154--53808253 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
53808144 ACCCATTCCA
* *
53808154 ATTTCCCCTTCCACCGTGCCGTCCTCCC
1 ATTTCCCATTCCACCGTGCCCTCCTCCC
* * *
53808182 ATTTCCCATTCCCATC-TCCCCTCTTCCATC
1 ATTTCCCATT-CCACCGTGCCCTCCTCC--C
* *
53808212 GATTCCCCTCTTCCACCGTGCCCTCCTCCC
1 -ATTTCCC-ATTCCACCGTGCCCTCCTCCC
53808242 ATTTCCCATTCC
1 ATTTCCCATTCC
53808254 CATTCCCATT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 21 0.39
29 10 0.19
30 2 0.04
31 10 0.19
32 11 0.20
ACGTcount: A:0.10, C:0.52, G:0.06, T:0.32
Consensus pattern (28 bp):
ATTTCCCATTCCACCGTGCCCTCCTCCC
Found at i:53810796 original size:21 final size:20
Alignment explanation
Indices: 53810772--53810834 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
53810762 GAACAAAGTA
*
53810772 AAAAAGAGGGGAGAAACTAGC
1 AAAAAGA-GGGAGAAACCAGC
* *
53810793 AAAAATGAGGGACAAACCAGT
1 AAAAA-GAGGGAGAAACCAGC
*
53810814 AAACA-AGGGAGAAACCAGC
1 AAAAAGAGGGAGAAACCAGC
53810833 AA
1 AA
53810835 GAACGAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.40
21 19 0.54
22 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAAAGAGGGAGAAACCAGC
Found at i:53812782 original size:42 final size:42
Alignment explanation
Indices: 53812703--53813056 Score: 466
Period size: 42 Copynumber: 8.4 Consensus size: 42
53812693 ACATCGCTAA
* *
53812703 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
53812747 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTGAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
53812789 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
53812831 CTTTAGCGGCGCTTAGAAAAAAAACGTCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTT
* *
53812874 CTCTAGCGGCGCTTAG-AAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
53812915 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* ** * *
53812957 CTGTAGCGGCGCTTTAGAGGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* **
53813000 CTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGA-TCA-TGTT
53813042 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
53813057 TTTCACAAAC
Statistics
Matches: 280, Mismatches: 23, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
41 40 0.14
42 153 0.55
43 74 0.26
44 13 0.05
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:53813069 original size:85 final size:85
Alignment explanation
Indices: 53812724--53813055 Score: 349
Period size: 85 Copynumber: 3.9 Consensus size: 85
53812714 CTTACATAAA
* * * *
53812724 AAAACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTGAAGATCATGT
1 AAAACGCCTCTAAAAG-TAATGTTCTATAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
* **
53812788 TCTTTAGCGGCGC-TTAGAAA
65 TCTGTAGCGGCGCTTTAGAGC
* * * *
53812808 AAAACGCCACT-AAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGTCGCTAAAGATCATG
1 AAAACGCCTCTAAAAG-TAATGTTCTATAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATG
* *
53812872 TTCTCTAGCGGCGC-TTAGA-A
64 TTCTGTAGCGGCGCTTTAGAGC
* * * *
53812892 AAAATGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
1 AAAACGCCTCTAAAAG-TAATGTTCTATAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
*
53812956 TCTGTAGCGGCGCTTTAGAGG
65 TCTGTAGCGGCGCTTTAGAGC
**
53812977 AAAACGCCTCTAAAAGTAATGTTCTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGT
1 AAAACGCCTCTAAAAGTAATGTTCTATAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGA-TCA-T
*
53813039 GTTCTTTAGCGGCGCTT
63 GTTCTGTAGCGGCGCTT
53813056 ATTTCACAAA
Statistics
Matches: 225, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
83 36 0.16
84 84 0.37
85 101 0.45
86 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (85 bp):
AAAACGCCTCTAAAAGTAATGTTCTATAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
CTGTAGCGGCGCTTTAGAGC
Found at i:53813097 original size:44 final size:44
Alignment explanation
Indices: 53813043--53813160 Score: 209
Period size: 44 Copynumber: 2.7 Consensus size: 44
53813033 AGTAGTGTTC
53813043 TTTAGCGGCGCTTATTTCACAAACGCCACTGTTTTGATATGACT
1 TTTAGCGGCGCTTATTTCACAAACGCCACTGTTTTGATATGACT
53813087 TTTAGCGGCGCTTATTTCACAAACGCCACTGTTTTGATATGACT
1 TTTAGCGGCGCTTATTTCACAAACGCCACTGTTTTGATATGACT
* * *
53813131 TTTAGCGGCGCTTTTTTAAAAAACGCCACT
1 TTTAGCGGCGCTTATTTCACAAACGCCACT
53813161 AATTTTGGGA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (44 bp):
TTTAGCGGCGCTTATTTCACAAACGCCACTGTTTTGATATGACT
Found at i:53813585 original size:20 final size:20
Alignment explanation
Indices: 53813548--53813587 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53813538 TCTCTCGCTG
* *
53813548 CTTCTCTCGCTACGGCCTCT
1 CTTCCCTCGCTACCGCCTCT
*
53813568 CTTCCCTCGCTGCCGCCTCT
1 CTTCCCTCGCTACCGCCTCT
53813588 GCTTTAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.50, G:0.15, T:0.33
Consensus pattern (20 bp):
CTTCCCTCGCTACCGCCTCT
Found at i:53819035 original size:9 final size:9
Alignment explanation
Indices: 53819010--53819148 Score: 107
Period size: 9 Copynumber: 15.9 Consensus size: 9
53819000 GATTTAGGAA
53819010 TAAGTTATG
1 TAAGTTATG
53819019 T-A-TTATG
1 TAAGTTATG
53819026 TAAGTTATG
1 TAAGTTATG
53819035 TAAGTTATG
1 TAAGTTATG
*
53819044 TAAGTTGTG
1 TAAGTTATG
*
53819053 TAAGTTGTG
1 TAAGTTATG
*
53819062 TAAGTTGTG
1 TAAGTTATG
53819071 T-A-TTATG
1 TAAGTTATG
* *
53819078 AAACTTATG
1 TAAGTTATG
*
53819087 TACGTTATG
1 TAAGTTATG
*
53819096 T--CTTATG
1 TAAGTTATG
53819103 TAAGTTATG
1 TAAGTTATG
53819112 TATTA-TTATG
1 TA--AGTTATG
53819122 TAGAG-TATG
1 TA-AGTTATG
53819131 TATTA-TTATG
1 TA--AGTTATG
53819141 TAAGTTAT
1 TAAGTTAT
53819149 TATGTAAGTA
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.15
8 5 0.05
9 72 0.67
10 14 0.13
11 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:53819039 original size:25 final size:25
Alignment explanation
Indices: 53819010--53819113 Score: 127
Period size: 25 Copynumber: 4.1 Consensus size: 25
53819000 GATTTAGGAA
53819010 TAAGTTATGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
53819035 TAAGTTATGTAAGTTGTGTAAGTTGTG
1 TAAGTTATGT-A-TTATGTAAGTTATG
* * *
53819062 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
53819087 TACGTTATGTCTTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
53819112 TA
1 TA
53819114 TTATTATGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 42 0.65
26 2 0.03
27 21 0.32
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:53819063 original size:27 final size:26
Alignment explanation
Indices: 53819010--53819148 Score: 117
Period size: 25 Copynumber: 5.3 Consensus size: 26
53819000 GATTTAGGAA
53819010 TAAGTTATGT-ATTATGTAAGTTATG
1 TAAGTTATGTAATTATGTAAGTTATG
* *
53819035 TAAGTTATGTAAGTTGTGTAAGTTGTG
1 TAAGTTATGTAA-TTATGTAAGTTATG
* * *
53819062 TAAGTTGTGT-ATTATGAAACTTATG
1 TAAGTTATGTAATTATGTAAGTTATG
* *
53819087 TACGTTATGT-CTTATGTAAGTTATG
1 TAAGTTATGTAATTATGTAAGTTATG
*
53819112 TATTA-TTATGTAGAGTATGTATTA-TTATG
1 TA--AGTTATGTA-ATTATGTA--AGTTATG
53819141 TAAGTTAT
1 TAAGTTAT
53819149 TATGTAAGTA
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
25 42 0.47
26 8 0.09
27 22 0.24
28 10 0.11
29 7 0.08
30 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.47
Consensus pattern (26 bp):
TAAGTTATGTAATTATGTAAGTTATG
Found at i:53819100 original size:16 final size:16
Alignment explanation
Indices: 53819081--53819117 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
53819071 TATTATGAAA
*
53819081 CTTATGTACGTTATGT
1 CTTATGTAAGTTATGT
53819097 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
*
53819113 ATTAT
1 CTTAT
53819118 TATGTAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:53819122 original size:19 final size:19
Alignment explanation
Indices: 53819098--53819148 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
53819088 ACGTTATGTC
53819098 TTATGTAAGTTATGTATTA
1 TTATGTAAGTTATGTATTA
53819117 TTATGTAGAG-TATGTATTA
1 TTATGTA-AGTTATGTATTA
53819136 TTATGTAAGTTAT
1 TTATGTAAGTTAT
53819149 TATGTAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.07
19 26 0.87
20 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAAGTTATGTATTA
Found at i:53819292 original size:15 final size:12
Alignment explanation
Indices: 53819133--53819294 Score: 88
Period size: 12 Copynumber: 13.8 Consensus size: 12
53819123 AGAGTATGTA
53819133 TTATTATGTAAG
1 TTATTATGTAAG
53819145 TTATTATGTAAG
1 TTATTATGTAAG
** *
53819157 -TAGGGATGTAGG
1 TTA-TTATGTAAG
*
53819169 ATATTATGTAAG
1 TTATTATGTAAG
53819181 ---TTATGTAAG
1 TTATTATGTAAG
* * * **
53819190 TTTTTGTTTTTG
1 TTATTATGTAAG
*
53819202 TGTATTATGTAAC
1 T-TATTATGTAAG
* *
53819215 TTATTTAATTTATGG
1 TTA-TT-ATGTA-AG
* *
53819230 ATGTTATGT-A-
1 TTATTATGTAAG
53819240 TTATTATGT-A-
1 TTATTATGTAAG
53819250 TTATTATGTAAG
1 TTATTATGTAAG
53819262 TTATTATGTAAG
1 TTATTATGTAAG
53819274 TTATTATGTAAG
1 TTATTATGTAAG
*
53819286 TCATTATGT
1 TTATTATGT
53819295 TGGTTATGTA
Statistics
Matches: 113, Mismatches: 26, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
9 9 0.08
10 17 0.15
11 3 0.03
12 64 0.57
13 13 0.12
14 6 0.05
15 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:53819454 original size:19 final size:19
Alignment explanation
Indices: 53819430--53819467 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53819420 ATGTATCAAT
53819430 TTTTAAAAATATATATAAA
1 TTTTAAAAATATATATAAA
*
53819449 TTTTAAATATATATATAAA
1 TTTTAAAAATATATATAAA
53819468 CTATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAAATATATATAAA
Found at i:53819499 original size:9 final size:9
Alignment explanation
Indices: 53819485--53819565 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
53819475 TAAATATTAA
53819485 TAAGTTATG
1 TAAGTTATG
53819494 TAAGTTATG
1 TAAGTTATG
* *
53819503 TATTA-TAAATT
1 TA--AGT-TATG
*
53819514 TAAGTTGTG
1 TAAGTTATG
53819523 TAAGTTATG
1 TAAGTTATG
53819532 -AA-TTATG
1 TAAGTTATG
*
53819539 TAAGATATG
1 TAAGTTATG
* *
53819548 TAAATTACG
1 TAAGTTATG
*
53819557 TAAGATATG
1 TAAGTTATG
53819566 AAATTTGAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.08
9 37 0.70
10 2 0.04
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (9 bp):
TAAGTTATG
Found at i:53819559 original size:18 final size:17
Alignment explanation
Indices: 53819522--53819570 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
53819512 TTTAAGTTGT
* *
53819522 GTAAGTTATG-AATTAT
1 GTAAGATATGAAATTAC
53819538 GTAAGATATGTAAATTAC
1 GTAAGATATG-AAATTAC
53819556 GTAAGATATGAAATT
1 GTAAGATATGAAATT
53819571 TGAACTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
18 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (17 bp):
GTAAGATATGAAATTAC
Found at i:53819636 original size:35 final size:34
Alignment explanation
Indices: 53819578--53819669 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
53819568 ATTTGAACTT
* * *
53819578 TTAAAAAAAAT-TAATATCTAAAAATATTCGTGA
1 TTAAAAAAAATAAAATATTTAAAAAAATTCGTGA
53819611 TTAAAAAAAATAAAATATTTAAAAAAATTCGTGA
1 TTAAAAAAAATAAAATATTTAAAAAAATTCGTGA
*
53819645 TTAAAATAAAATAAAAAATTTAAAA
1 TTAAAA-AAAATAAAATATTTAAAA
53819670 TATAACTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 11 0.21
34 25 0.47
35 17 0.32
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (34 bp):
TTAAAAAAAATAAAATATTTAAAAAAATTCGTGA
Found at i:53820802 original size:37 final size:37
Alignment explanation
Indices: 53820747--53820831 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
53820737 AGATTTCTAC
*
53820747 AAAACAGTAACAGACCAGTATGCCTAAAAAATGCAGG
1 AAAACAGTAACAGACCAGTATGCCAAAAAAATGCAGG
*
53820784 AAAATAGTAACAGACCAGTATGCCAAAAAAATGCAGG
1 AAAACAGTAACAGACCAGTATGCCAAAAAAATGCAGG
53820821 AAAACAGTAAC
1 AAAACAGTAAC
53820832 CCATCGACAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.13
Consensus pattern (37 bp):
AAAACAGTAACAGACCAGTATGCCAAAAAAATGCAGG
Found at i:53822601 original size:7 final size:7
Alignment explanation
Indices: 53822589--53822637 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
53822579 TTAAGCAGTC
53822589 TAAACCT
1 TAAACCT
*
53822596 TAAACCC
1 TAAACCT
*
53822603 TAAACTT
1 TAAACCT
53822610 TAAACCT
1 TAAACCT
*
53822617 CAAACTCT
1 TAAAC-CT
*
53822625 TAAACCC
1 TAAACCT
53822632 TAAACC
1 TAAACC
53822638 CAAAACACCA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:53822607 original size:14 final size:14
Alignment explanation
Indices: 53822588--53822637 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
53822578 TTTAAGCAGT
53822588 CTAAACCTTAAACC
1 CTAAACCTTAAACC
*
53822602 CTAAACTTTAAA-C
1 CTAAACCTTAAACC
53822615 CTCAAACTCTTAAACC
1 CT-AAAC-CTTAAACC
53822631 CTAAACC
1 CTAAACC
53822638 CAAAACACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 9 0.29
16 3 0.10
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:53823287 original size:88 final size:88
Alignment explanation
Indices: 53823129--53823291 Score: 281
Period size: 88 Copynumber: 1.9 Consensus size: 88
53823119 AAGCGCAGCT
* *
53823129 AATAATATGATTTAGCGGCGATTTCTCGTAAACGCCACTAATTCCAGTATACGTCAAGATCTAAA
1 AATAATATGATTTAGCGGCGATTTCTCGTAAACGCCACTAACTCCAGTATACATCAAGATCTAAA
53823194 CGCAGCGTTTAAGAAGTGCCGCA
66 CGCAGCGTTTAAGAAGTGCCGCA
* *
53823217 AATAATATGATTTAGCGGCGATTTCTCGTGAACGCCACTAACTCCAGTATACATCAAGATTTAAA
1 AATAATATGATTTAGCGGCGATTTCTCGTAAACGCCACTAACTCCAGTATACATCAAGATCTAAA
*
53823282 TGCAGCGTTT
66 CGCAGCGTTT
53823292 GCTAATAGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (88 bp):
AATAATATGATTTAGCGGCGATTTCTCGTAAACGCCACTAACTCCAGTATACATCAAGATCTAAA
CGCAGCGTTTAAGAAGTGCCGCA
Found at i:53825646 original size:41 final size:41
Alignment explanation
Indices: 53825589--53825720 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
53825579 TTCATGTGCT
*
53825589 GCTAATGCTCAGATCTTTAGGGGCGTTTTTGAAAAAGCGCC
1 GCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCC
* * * *
53825630 GCTAATGCTCAGATCTTTAGTGGCGATTTTGGAAAAGCACC
1 GCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCC
** * * *
53825671 GCTAATGCTC-GGGCTTTAGCAGCGTTTTTTAAGAAGCGCC
1 GCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCC
53825711 GCTAATGCTC
1 GCTAATGCTC
53825721 GGGGATTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 31 0.40
41 47 0.60
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
GCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCC
Found at i:53825713 original size:40 final size:39
Alignment explanation
Indices: 53825611--53825723 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
53825601 ATCTTTAGGG
** **
53825611 GCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGTG
1 GCGTTTTTG-AAAAGCGCCGCTAATGCTC-GGGCTTTAGCA
* *
53825652 GCGATTTTGGAAAAGCACCGCTAATGCTCGGGCTTTAGCA
1 GCG-TTTTTGAAAAGCGCCGCTAATGCTCGGGCTTTAGCA
*
53825692 GCGTTTTTTAAGAAGCGCCGCTAATGCTCGGG
1 GCGTTTTTGAA-AAGCGCCGCTAATGCTCGGG
53825724 GATTTAACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 6 0.10
40 29 0.48
41 21 0.34
42 5 0.08
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
GCGTTTTTGAAAAGCGCCGCTAATGCTCGGGCTTTAGCA
Found at i:53826162 original size:14 final size:15
Alignment explanation
Indices: 53826136--53826165 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
53826126 GGTTTATAGG
53826136 TTATGGAATTAGGGA
1 TTATGGAATTAGGGA
53826151 TTATGG-ATTAGGGA
1 TTATGGAATTAGGGA
53826165 T
1 T
53826166 CCTGATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (15 bp):
TTATGGAATTAGGGA
Found at i:53826345 original size:6 final size:6
Alignment explanation
Indices: 53826314--53826356 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
53826304 ATAATGTTTA
*
53826314 AGGGTT AGGGATT CAGGG-T CGGGTT AGGGTT AGGGTT AGGGTT
1 AGGGTT AGGG-TT -AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT
53826357 TATGATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 3 0.09
6 23 0.72
7 2 0.06
8 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.49, T:0.30
Consensus pattern (6 bp):
AGGGTT
Found at i:53826865 original size:17 final size:16
Alignment explanation
Indices: 53826832--53826865 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53826822 ATATTAGATT
*
53826832 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
53826848 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
53826865 T
1 T
53826866 TGATACGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:53831150 original size:43 final size:43
Alignment explanation
Indices: 53831055--53831151 Score: 140
Period size: 43 Copynumber: 2.3 Consensus size: 43
53831045 GTTATGTTTT
* *
53831055 TAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* * *
53831098 TTGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
*
53831141 TAGCAGCGTTT
1 TAGCGGCGTTT
53831152 TTTGCGGCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
Found at i:53832217 original size:115 final size:113
Alignment explanation
Indices: 53832012--53832518 Score: 773
Period size: 114 Copynumber: 4.5 Consensus size: 113
53832002 TACACAGTAC
*
53832012 AAATTTTTTTTTA-TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATTAAAATTTT
1 AAATTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAT-AAATTTT
*
53832076 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CT
65 TTTTT-TTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCA
53832125 AAATTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATTTAAATTT
1 AAATTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA--TAAATTT
*
53832190 TTTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
64 TTTTTT-TTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCA
53832241 AAATTTTTTTTT-TATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAA----
1 AAATTTTTTTTTAT-TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTT
53832301 -TTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCCA
65 TTTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA--CCA
***
53832351 AAATTTTTTTTT-TATTTTTTTCGTATTTTTATATCTGATTCTGACACG-AAAAAAATAAAAACT
1 AAATTTTTTTTTAT-TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTT
*
53832414 TTTTTTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCA
65 TTTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCA
*
53832464 AAATTTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAA
1 AAA-TTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAA
53832519 TAAAATAAAA
Statistics
Matches: 374, Mismatches: 5, Indels: 28
0.92 0.01 0.07
Matches are distributed among these distances:
108 41 0.11
109 15 0.04
110 50 0.13
113 20 0.05
114 131 0.35
115 61 0.16
116 56 0.15
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (113 bp):
AAATTTTTTTTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTT
TTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCA
Found at i:53840126 original size:13 final size:13
Alignment explanation
Indices: 53840108--53840132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53840098 TTTTATTTGT
53840108 TTATTCCCACCGA
1 TTATTCCCACCGA
53840121 TTATTCCCACCG
1 TTATTCCCACCG
53840133 GCCGAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:53841631 original size:12 final size:12
Alignment explanation
Indices: 53841614--53841647 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
53841604 GTTATTTATT
53841614 TTCTTTTGCTCG
1 TTCTTTTGCTCG
*
53841626 TTCTTTGGCTCG
1 TTCTTTTGCTCG
53841638 TTCTTTTGCT
1 TTCTTTTGCT
53841648 TAAAATGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.18, T:0.59
Consensus pattern (12 bp):
TTCTTTTGCTCG
Found at i:53841697 original size:10 final size:10
Alignment explanation
Indices: 53841682--53841706 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53841672 GTGGATTGGC
53841682 TGATTGACTG
1 TGATTGACTG
53841692 TGATTGACTG
1 TGATTGACTG
53841702 TGATT
1 TGATT
53841707 CCTTTGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (10 bp):
TGATTGACTG
Found at i:53844862 original size:49 final size:49
Alignment explanation
Indices: 53844805--53844908 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
53844795 TCATGTGTTA
* * ** * *
53844805 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
53844854 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
53844903 TAATTT
1 TAATTT
53844909 GTTTTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:53846418 original size:54 final size:54
Alignment explanation
Indices: 53846355--53846550 Score: 135
Period size: 57 Copynumber: 3.4 Consensus size: 54
53846345 TAAGAATAAG
* * * * *
53846355 AATTTTATTTAATTATTTATTATTATTAAATTATATTGAATAATAATTATTTTA
1 AATTATATTAAATTATATATTATTATTAAATTATATTTAATAACAATTATTTTA
* * ** *
53846409 AATTATATTTTAGTATTATATATTATGATTTTATTAGTAAATTTATATAAGAA-TATTTATTAA
1 AATTATA--TTA-AATTATATATTATTATTAAATTA-T--ATTTA-ATAACAATTA-TT-TT-A
* * *
53846472 CAATTTTATTAAATTATATATT-TTATTAAATTATATTTTATAACAATTATGTTA
1 -AATTATATTAAATTATATATTATTATTAAATTATATTTAATAACAATTATTTTA
* *
53846526 AAATATGATTAAATTATTTATTATT
1 AATTAT-ATTAAATTATATATTATT
53846551 TATATTAATA
Statistics
Matches: 108, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
53 4 0.04
54 21 0.19
55 4 0.04
56 9 0.08
57 24 0.22
58 1 0.01
59 1 0.01
60 14 0.13
61 18 0.17
62 5 0.05
63 1 0.01
64 6 0.06
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (54 bp):
AATTATATTAAATTATATATTATTATTAAATTATATTTAATAACAATTATTTTA
Found at i:53846488 original size:108 final size:106
Alignment explanation
Indices: 53846267--53846482 Score: 282
Period size: 109 Copynumber: 2.0 Consensus size: 106
53846257 TAATAAAGTA
*
53846267 TATTA-TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
1 TATTATTAAATTATATTGAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
* *
53846331 TTAGTAAATTCATATAAGAATAAGAATTTTATTTAATTATTTAT
66 TTAGTAAATTCATATAAGAAT---AATTTTATTAAAATATTTAT
53846375 TATTATTAAATTATATTGAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGAT
1 TATTATTAAATTATATTGAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA-
*
53846438 TTTATTAGTAAATTTATATAAGAAT-A-TTTATTAACAAT-TTTAT
64 -TT-TTAGTAAATTCATATAAGAATAATTTTATTAA-AATATTTAT
53846481 TA
1 TA
53846483 AATTATATAT
Statistics
Matches: 98, Mismatches: 4, Indels: 14
0.84 0.03 0.12
Matches are distributed among these distances:
106 14 0.14
107 3 0.03
108 23 0.23
109 25 0.26
110 13 0.13
111 20 0.20
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (106 bp):
TATTATTAAATTATATTGAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
TTAGTAAATTCATATAAGAATAATTTTATTAAAATATTTAT
Found at i:53846512 original size:15 final size:17
Alignment explanation
Indices: 53846474--53846507 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53846464 TTTATTAACA
53846474 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53846491 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53846508 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53846521 original size:16 final size:15
Alignment explanation
Indices: 53846474--53846521 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
53846464 TTTATTAACA
*
53846474 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
53846491 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
53846506 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
53846522 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:53846699 original size:39 final size:41
Alignment explanation
Indices: 53846654--53846759 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
53846644 TTTCCTTATG
* *
53846654 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
53846694 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
53846739 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
53846760 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:53846734 original size:44 final size:46
Alignment explanation
Indices: 53846671--53846761 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
53846661 ACCTCTATTC
*
53846671 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
53846715 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
53846761 C
1 C
53846762 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:53846762 original size:16 final size:16
Alignment explanation
Indices: 53846741--53846777 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
53846731 AGAATTACCT
53846741 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
53846757 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
53846773 ATTAC
1 ATTAC
53846778 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53857511 original size:22 final size:22
Alignment explanation
Indices: 53857483--53857552 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
53857473 TATACACTAT
53857483 TAAATAGAGAGCACTAAAGTGC
1 TAAATAGAGAGCACTAAAGTGC
* * *
53857505 TATATAGAGAGCACAAAATGTGT
1 TAAATAGAGAGCACTAAA-GTGC
* *
53857528 TAAATGGAGAGCACTAATGTGC
1 TAAATAGAGAGCACTAAAGTGC
53857550 TAA
1 TAA
53857553 TAATTGGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 22 0.56
23 17 0.44
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (22 bp):
TAAATAGAGAGCACTAAAGTGC
Found at i:53860433 original size:14 final size:14
Alignment explanation
Indices: 53860414--53860453 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53860404 TTGATTGCCA
53860414 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
53860428 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
53860442 GGAAAATGTTTT
1 GTAAAATGTTTT
53860454 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:53860462 original size:20 final size:20
Alignment explanation
Indices: 53860437--53860476 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53860427 CGTAAAATGA
*
53860437 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGGTTTACT
*
53860457 TTTCTGTAAAATGGTTTACT
1 TTTCTGGAAAATGGTTTACT
53860477 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGGTTTACT
Found at i:53860466 original size:34 final size:35
Alignment explanation
Indices: 53860422--53860488 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53860412 CAGTAAAATG
*
53860422 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
53860456 TTTTCTGTAAAATGGTTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
53860489 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53865734 original size:5 final size:5
Alignment explanation
Indices: 53865724--53865748 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53865714 ACTAAATTAT
53865724 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
53865749 TGAAACTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:53868109 original size:51 final size:50
Alignment explanation
Indices: 53868033--53868228 Score: 225
Period size: 51 Copynumber: 3.9 Consensus size: 50
53868023 GATACCGATT
* ***
53868033 CACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCAATA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT-TCTGGTA
* **
53868084 CACGTAGTAGCCTGCACATAGTACTACACACGTGA-TAGAAGCTATCTGGTA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CT-TCTGGTA
* * * *
53868135 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-TTCTGGTA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTTCTGGTA
* *
53868185 CACGTAGTAGCCTGCATATAGTACTACACACGTGACCACCACTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTT
53868229 TCACTTTCAC
Statistics
Matches: 120, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 3 0.03
50 43 0.36
51 72 0.60
53 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTCTGGTA
Found at i:53868213 original size:101 final size:102
Alignment explanation
Indices: 53868037--53868219 Score: 298
Period size: 101 Copynumber: 1.8 Consensus size: 102
53868027 CCGATTCACG
*
53868037 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCAATACACGTAGTAGCCTGCACA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCAATACACGTAGTAGCCTGCACA
53868102 TAGTACTACACACGTGATAGAAGCTATCTGGTACGCA
66 TAGTACTACACACGTGATAGAAGCTATCTGGTACGCA
*** *
53868139 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGCAT
1 TAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTGTCCAATACACGTAGTAGCCTGCAC
53868202 ATAGTACTACACACGTGA
65 ATAGTACTACACACGTGA
53868220 CCACCACTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
101 38 0.51
102 33 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (102 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCAATACACGTAGTAGCCTGCACA
TAGTACTACACACGTGATAGAAGCTATCTGGTACGCA
Found at i:53868242 original size:101 final size:102
Alignment explanation
Indices: 53868031--53868253 Score: 254
Period size: 101 Copynumber: 2.2 Consensus size: 102
53868021 ATGATACCGA
* *
53868031 TTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCAATACACGTAGTAGCC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCAATACACGTAGTAGCC
* * **
53868096 TGCACATAGTACTACACACGTGATAGAAGCTATCTGG
66 TGCACATAGTACTACACACGTGACACAAGCTATCACG
* * ***
53868133 TACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTGTCCAATACACGTAGTAGC
* * * *
53868196 CTGCATATAGTACTACACACGTGACCACCA-CTTTCACT
65 CTGCACATAGTACTACACACGTGA-CACAAGCTATCACG
* *
53868234 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTGCACA
53868254 CAGTCCATGC
Statistics
Matches: 100, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
101 58 0.58
102 38 0.38
103 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (102 bp):
TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCAATACACGTAGTAGCC
TGCACATAGTACTACACACGTGACACAAGCTATCACG
Found at i:53876925 original size:96 final size:96
Alignment explanation
Indices: 53876761--53876953 Score: 325
Period size: 96 Copynumber: 2.0 Consensus size: 96
53876751 GAGGAGTATT
* *
53876761 GAGAATGTGCCTTAGACTTGCTAAATAATAGGTGTAGACCAAGTATTTAGGGATTTGTTAATTTG
1 GAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAGGGATTTGTTAATTTG
*
53876826 TGGCATGATTTTAGGAGTAAGTTAGGATGTG
66 TGGCATGATTTTAGGAATAAGTTAGGATGTG
*
53876857 GAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAGGGAATTT-TTAGTTT
1 GAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAGGG-ATTTGTTAATTT
*
53876921 GTGGCATGATTTTATGAATAAGTTAGGATGTG
65 GTGGCATGATTTTAGGAATAAGTTAGGATGTG
53876953 G
1 G
53876954 TTAGATATCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 87 0.96
97 4 0.04
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (96 bp):
GAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAGGGATTTGTTAATTTG
TGGCATGATTTTAGGAATAAGTTAGGATGTG
Found at i:53877477 original size:102 final size:101
Alignment explanation
Indices: 53877344--53877554 Score: 269
Period size: 101 Copynumber: 2.1 Consensus size: 101
53877334 AAATTATTTG
* * * * * ** * *
53877344 GTTAAGTAGAAATATGAGATATAAATGAAACATTTTAAATTCAATGTTAAAAGAAAAACCCCTAA
1 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAA-AAAAACCACAAA
53877409 TACCTTAACTAATTACTAAATAGATAGTAATCAATCA
65 TACCTTAACTAATTACTAAATAGATAGTAATCAATCA
*** * **
53877446 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTGGTTGTTAAAACAAAATTACAAAT
1 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAAAAAAACCACAAAT
*
53877511 ACCTTAACTAATTACTAAATAGATAGTAATCAATCG
66 ACCTTAACTAATTACTAAATAGATAGTAATCAATCA
53877547 GTTAAATA
1 GTTAAATA
53877555 AATTACAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
101 51 0.55
102 42 0.45
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (101 bp):
GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAAAAAAACCACAAAT
ACCTTAACTAATTACTAAATAGATAGTAATCAATCA
Found at i:53878683 original size:27 final size:27
Alignment explanation
Indices: 53878625--53878683 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
53878615 GACAACCAGT
*
53878625 GTAGTTTATCGGAATAGTAAACACGAG
1 GTAGTCTATCGGAATAGTAAACACGAG
* *
53878652 ATAGTCTATCAGGAA-AGTAAACACGTG
1 GTAGTCTATC-GGAATAGTAAACACGAG
53878679 GTAGT
1 GTAGT
53878684 TCCTCACGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
GTAGTCTATCGGAATAGTAAACACGAG
Found at i:53884261 original size:195 final size:193
Alignment explanation
Indices: 53883929--53884315 Score: 512
Period size: 195 Copynumber: 2.0 Consensus size: 193
53883919 ACATTAGTTA
* * * * * *
53883929 TACATTCAAGAACTTGAGTAACAAAAATCATAAATACTACTAACAAAGATAACCAAAAAAGGTGT
1 TACATTCAAGAACTTAAGTAAAAAAAAACATAAATACTACTAACAAACAAAACCAAAAAAGGTGC
*
53883994 TTGACCTCTATTCGTTTATAAAAATGGTGAATTTCACTATAATTCCTGTAAATTCAAAATTTTTA
66 CTGACCTCTATTCGTTTATAAAAATGGTGAATTTCACTATAATTCCTGTAAATTCAAAATTTTTA
** * *
53884059 CAAATAACTTTTAAGAAATTTCCAAATATCCTCCTTTAAATTATATATATATCTGGGTTCAATTC
131 CAAATAACTTAAAACAAATTTCCAAATATCCTCATTTAAA-T-TATATATATCTGGGTTCAATTC
*
53884124 TACATTCAAGAACTTAAGTAAAAAAAAACATAAATA-TGACTAACAAAACAAAACCAAAAATGGT
1 TACATTCAAGAACTTAAGTAAAAAAAAACATAAATACT-ACTAAC-AAACAAAACCAAAAAAGGT
* * * * *
53884188 GCCTGACCTCTATTCG-TTGTGAAGATGGT-AGATTTTACTGTAATTCCTGTAAATTCCAAAA-T
64 GCCTGACCTCTATTCGTTTATAAAAATGGTGA-ATTTCACTATAATTCCTGTAAATT-CAAAATT
* * *
53884250 TTTCCAAATAACTTAAAACACATTTCCAAATATCCTCATTTAAATTATATATATCTGGTTTCAAT
127 TTTACAAATAACTTAAAACAAATTTCCAAATATCCTCATTTAAATTATATATATCTGGGTTCAAT
53884315 T
192 T
53884316 AACATGTGTT
Statistics
Matches: 168, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
193 20 0.12
194 3 0.02
195 110 0.65
196 35 0.21
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (193 bp):
TACATTCAAGAACTTAAGTAAAAAAAAACATAAATACTACTAACAAACAAAACCAAAAAAGGTGC
CTGACCTCTATTCGTTTATAAAAATGGTGAATTTCACTATAATTCCTGTAAATTCAAAATTTTTA
CAAATAACTTAAAACAAATTTCCAAATATCCTCATTTAAATTATATATATCTGGGTTCAATTC
Found at i:53884865 original size:38 final size:34
Alignment explanation
Indices: 53884823--53884895 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 34
53884813 AAATAGATAA
53884823 AAAATTTAAAAATTATTTTTTTATTAAATAAAAACATT
1 AAAATTTAAAAATTA-TTTTTTA--AAATAAAAA-ATT
* *
53884861 AAAATTTTAAATTTATTTTTTAAAATAAAAAATT
1 AAAATTTAAAAATTATTTTTTAAAATAAAAAATT
53884895 A
1 A
53884896 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.12
35 9 0.27
37 7 0.21
38 13 0.39
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
AAAATTTAAAAATTATTTTTTAAAATAAAAAATT
Found at i:53885964 original size:17 final size:18
Alignment explanation
Indices: 53885925--53885963 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53885915 TAACATTGAG
*
53885925 TTTTT-AAATTTTTTTTA
1 TTTTTAAAATATTTTTTA
53885942 TTTTTAAAATATTTTTTA
1 TTTTTAAAATATTTTTTA
53885960 TTTT
1 TTTT
53885964 ATGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAAAATATTTTTTA
Found at i:53897249 original size:41 final size:41
Alignment explanation
Indices: 53897178--53897318 Score: 126
Period size: 41 Copynumber: 3.4 Consensus size: 41
53897168 TTTAAACAGA
* * * *
53897178 TTCACTGGCACTTCA-CCTGATAGACTTATAGTCTAATTCCG
1 TTCACTGGCACTT-AGCCTGCTAGACCTATAGCCTAATTCAG
* *
53897219 TTCACTGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACTGGCACTTAGCCTGCTAGACCTATAGCCTAATTCAG
* * * * *
53897260 TTCA-TCGGCACTTAGCCTGCTGGACATATAATCC-GATTCAA
1 TTCACT-GGCACTTAGCCTGCTAGACCTAT-AGCCTAATTCAG
*
53897301 TTCACCGGCACTTAGCCT
1 TTCACTGGCACTTAGCCT
53897319 ACTGGACGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
40 2 0.02
41 79 0.94
42 3 0.04
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (41 bp):
TTCACTGGCACTTAGCCTGCTAGACCTATAGCCTAATTCAG
Found at i:53897324 original size:41 final size:41
Alignment explanation
Indices: 53897219--53897351 Score: 162
Period size: 41 Copynumber: 3.2 Consensus size: 41
53897209 TCTAATTCCG
* * * *
53897219 TTCACTGGCACTTAGCCTGCTAGG-CCTAT-AGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCT-GGACATATAATCC-GATTCAA
*
53897260 TTCATCGGCACTTAGCCTGCTGGACATATAATCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTGGACATATAATCCGATTCAA
* * *
53897301 TTCACCGGCACTTAGCCTACTGGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTGGACATATAATCCGATTCAA
53897342 TTCACCGGCA
1 TTCACCGGCA
53897352 ATAAATCTGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.02
41 76 0.94
42 3 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTGGACATATAATCCGATTCAA
Found at i:53902125 original size:65 final size:65
Alignment explanation
Indices: 53902052--53902181 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
53902042 TGGGATGTGG
*
53902052 AATTATATTTTTCAAATTCATATAAGAAACCATTTGTTGGAGATAACTTTTTTTTAACCATCTTT
1 AATTATATTTTTCAAATTCATATAAGAAACCATTTGTTGGAGATAACTGTTTTTTAACCATCTTT
*
53902117 AATTATATTTTTCAAATTCATATTAGAAACCATTTGTTGGAGATAACTGTTTTTTAACCATCTTT
1 AATTATATTTTTCAAATTCATATAAGAAACCATTTGTTGGAGATAACTGTTTTTTAACCATCTTT
53902182 CCATCTTCAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (65 bp):
AATTATATTTTTCAAATTCATATAAGAAACCATTTGTTGGAGATAACTGTTTTTTAACCATCTTT
Found at i:53909125 original size:20 final size:21
Alignment explanation
Indices: 53909088--53909126 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53909078 GACAACAGGG
* *
53909088 AGGGAAGCAGGGGTAGCAGCA
1 AGGGAAGCAGAGGCAGCAGCA
53909109 AGGG-AGCAGAGGCAGCAG
1 AGGGAAGCAGAGGCAGCAG
53909127 AGGTATTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.15, G:0.49, T:0.03
Consensus pattern (21 bp):
AGGGAAGCAGAGGCAGCAGCA
Found at i:53912006 original size:71 final size:71
Alignment explanation
Indices: 53911890--53912032 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
53911880 CTTAAAAGTA
53911890 TGTTCACATTAGGATAAGATTCTCTTATGAACACGGGTGATAGGTTCCATTTGAAGTGGGTCAGA
1 TGTTCACATTAGGATAAGATTCTCTTATGAACACGGGTGATAGGTTCCATTTGAAGTGGGTCAGA
53911955 TGATTG
66 TGATTG
53911961 TGTTCACATTAGGATAAGATTCTCTTATGAACACGGGTGATAGGTTCCATTTGAAGTGGGTCAGA
1 TGTTCACATTAGGATAAGATTCTCTTATGAACACGGGTGATAGGTTCCATTTGAAGTGGGTCAGA
53912026 TGATTG
66 TGATTG
53912032 T
1 T
53912033 TCTCAAAGGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (71 bp):
TGTTCACATTAGGATAAGATTCTCTTATGAACACGGGTGATAGGTTCCATTTGAAGTGGGTCAGA
TGATTG
Found at i:53912392 original size:7 final size:7
Alignment explanation
Indices: 53912376--53912412 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
53912366 CACCGATTTC
53912376 TTTT-GA
1 TTTTAGA
53912382 TTTTAGA
1 TTTTAGA
53912389 TTTTAGA
1 TTTTAGA
53912396 TTTTAGA
1 TTTTAGA
*
53912403 TTTTATA
1 TTTTAGA
53912410 TTT
1 TTT
53912413 GGGCTTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (7 bp):
TTTTAGA
Found at i:53917283 original size:21 final size:19
Alignment explanation
Indices: 53917255--53917304 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
53917245 AACATGGGAA
53917255 TTAAATTATGTAAC-AATATT
1 TTAAATTAT-T-ACTAATATT
53917275 TTAAGATTATTACTAATATT
1 TTAA-ATTATTACTAATATT
*
53917295 TTAACTTATT
1 TTAAATTATT
53917305 TTATTATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (19 bp):
TTAAATTATTACTAATATT
Found at i:53927203 original size:50 final size:50
Alignment explanation
Indices: 53927121--53927297 Score: 203
Period size: 50 Copynumber: 3.4 Consensus size: 50
53927111 TATCCGAGAT
** * * * *
53927121 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCTGTGCCAATGCCATGTCCCAAAC
**
53927171 ATGGTCTTACGGGGGACCTCTCATCTCTGTGCCAACT-CCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCTGTGCCAA-TGCCATGTCCCAAAC
53927221 ATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTC---ATCTC--TG-TGCCAATGCCATGTCCCAAAC
*
53927277 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
53927298 TTACCTAAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
50 60 0.56
51 1 0.01
53 5 0.05
55 3 0.03
56 39 0.36
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCTGTGCCAATGCCATGTCCCAAAC
Found at i:53939657 original size:15 final size:16
Alignment explanation
Indices: 53939629--53939662 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
53939619 TTTCTTTAGG
53939629 TTTTGTTTTGGTTGTT
1 TTTTGTTTTGGTTGTT
53939645 TTTTGTTTT-GTTGTT
1 TTTTGTTTTGGTTGTT
53939660 TTT
1 TTT
53939663 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (16 bp):
TTTTGTTTTGGTTGTT
Found at i:53940416 original size:2 final size:2
Alignment explanation
Indices: 53940409--53940462 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
53940399 CCCCAAACAA
53940409 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53940451 CT CT CT CT CT CT
1 CT CT CT CT CT CT
53940463 AAGGCAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:53943485 original size:81 final size:81
Alignment explanation
Indices: 53943350--53943519 Score: 313
Period size: 81 Copynumber: 2.1 Consensus size: 81
53943340 GAAATTAAAA
53943350 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATACTTTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATACTTTTGGTGACAATTTAAATATAATAAA
*
53943415 GGACACTGAACCGAAG
66 AGACACTGAACCGAAG
*
53943431 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATACTTTTGGTGACAATTTAAATATAATAAA
*
53943496 AGACACTGAACTGAAG
66 AGACACTGAACCGAAG
53943512 CCAAAGAA
1 CCAAAGAA
53943520 TAATTCTTTC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (81 bp):
CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATACTTTTGGTGACAATTTAAATATAATAAA
AGACACTGAACCGAAG
Found at i:53943661 original size:24 final size:24
Alignment explanation
Indices: 53943634--53943688 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
53943624 AGTTCAATGT
53943634 ATTGAAGGATTACAAGGTGAAAAC
1 ATTGAAGGATTACAAGGTGAAAAC
53943658 ATTGAAGGATTACAAGGTGAAAAC
1 ATTGAAGGATTACAAGGTGAAAAC
53943682 ATTGAAG
1 ATTGAAG
53943689 ACTGCTGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.22
Consensus pattern (24 bp):
ATTGAAGGATTACAAGGTGAAAAC
Found at i:53953603 original size:25 final size:25
Alignment explanation
Indices: 53953574--53953621 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53953564 TATAGCCCGG
53953574 ATAAGC-TTCTTGTTACATGGCTCAC
1 ATAAGCTTTC-TGTTACATGGCTCAC
*
53953599 ATAAGCTTTCTGTTATATGGCTC
1 ATAAGCTTTCTGTTACATGGCTC
53953622 GAGAGAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (25 bp):
ATAAGCTTTCTGTTACATGGCTCAC
Found at i:53959762 original size:99 final size:99
Alignment explanation
Indices: 53959639--53959835 Score: 376
Period size: 99 Copynumber: 2.0 Consensus size: 99
53959629 CACTTGTAGC
53959639 GGATCCTCCCTTTCCAATAACCGATGAAACATCAACAGATGGTTATTAAAAGTCCACGAAGCTTC
1 GGATCCTCCCTTTCCAATAACCGATGAAACATCAACAGATGGTTATTAAAAGTCCACGAAGCTTC
53959704 ATCCACCACACGATCTATATCCACTTTAAATAAT
66 ATCCACCACACGATCTATATCCACTTTAAATAAT
* *
53959738 GGATCCTCCCTTTCCAATAACCGATGAAACATCAACAGATGGTTATTGAAAGTCCACGACGCTTC
1 GGATCCTCCCTTTCCAATAACCGATGAAACATCAACAGATGGTTATTAAAAGTCCACGAAGCTTC
53959803 ATCCACCACACGATCTATATCCACTTTAAATAA
66 ATCCACCACACGATCTATATCCACTTTAAATAA
53959836 AAATAAAATA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (99 bp):
GGATCCTCCCTTTCCAATAACCGATGAAACATCAACAGATGGTTATTAAAAGTCCACGAAGCTTC
ATCCACCACACGATCTATATCCACTTTAAATAAT
Done.