Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_pilon, whole genome shotgun sequence
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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:443717 original size:12 final size:11
Alignment explanation
Indices: 443699--443730 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
443689 TTTCCTAACC
443699 CAAAAAAAATT
1 CAAAAAAAATT
443710 CAAAAAAAATT
1 CAAAAAAAATT
443721 CAAAAAAAAT
1 CAAAAAAAAT
443731 ATTTTTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:449568 original size:22 final size:23
Alignment explanation
Indices: 449543--449593 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
449533 ACAAGAGAAA
449543 AAGAATGGAGAAAAATGA-GAGG
1 AAGAATGGAGAAAAATGACGAGG
* *
449565 AAGAAT-AAGATAAATGACGAGG
1 AAGAATGGAGAAAAATGACGAGG
449587 AA-AATGG
1 AAGAATGG
449594 GAGGGAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.31, T:0.12
Consensus pattern (23 bp):
AAGAATGGAGAAAAATGACGAGG
Found at i:449990 original size:23 final size:23
Alignment explanation
Indices: 449963--450024 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
449953 AACTGTCTAA
*
449963 AGTTGACTTTGACCAACATTGAT
1 AGTTGACTTTGACCAACATTGAC
*
449986 AGTTGACTTTGACCAGCATTGAC
1 AGTTGACTTTGACCAACATTGAC
450009 AGTTGACTTTGACCAA
1 AGTTGACTTTGACCAA
450025 AAAGTCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (23 bp):
AGTTGACTTTGACCAACATTGAC
Found at i:450886 original size:27 final size:27
Alignment explanation
Indices: 450856--450909 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
450846 AAACAAGATG
* * *
450856 CCCTTGAACCCTAAAATGGCTAAAATA
1 CCCTTAAACACTAAAATGACTAAAATA
450883 CCCTTAAACACTAAAATGACTAAAATA
1 CCCTTAAACACTAAAATGACTAAAATA
450910 ACCTCGAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (27 bp):
CCCTTAAACACTAAAATGACTAAAATA
Found at i:452144 original size:23 final size:23
Alignment explanation
Indices: 452094--452144 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
452084 TTTTGAGGAC
* *
452094 AAAGAGTAACCTTACAAGTCCTT
1 AAAGAGTAACCTTACAACTCCCT
452117 AAAGAGTAACCTTACAACTCCCT
1 AAAGAGTAACCTTACAACTCCCT
*
452140 CAAGA
1 AAAGA
452145 ATTATACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (23 bp):
AAAGAGTAACCTTACAACTCCCT
Found at i:452708 original size:65 final size:66
Alignment explanation
Indices: 452595--452740 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 66
452585 GTATAAGACC
* * * * *
452595 TAGTGTATCGGTACACTAATTGCATTCGATGTTTTAATAAAGCCAGGAGTGCATCGATGTA-TCA
1 TAGTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATTCA
*
452659 G
66 A
* ** *
452660 TTGTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAATTAGGAGTGTATCGATGCATTCA
1 TAGTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATTCA
452725 A
66 A
452726 TAGTGTATCGGTACA
1 TAGTGTATCGGTACA
452741 TCCATTTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 52 0.75
66 17 0.25
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (66 bp):
TAGTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATTCA
A
Found at i:454795 original size:40 final size:40
Alignment explanation
Indices: 454726--454819 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
454716 CATTTTTGGT
* * * * *
454726 TCAATCGAACATGCTAAAAAGTTAATATTTTAGGTTGTGC
1 TCAACCGAAAATGTTAAAAAATTAATATTTTAGGTTGTAC
454766 TCAACCGAAAATGTTAAAAAATTAATATTTTAGGTTGTAC
1 TCAACCGAAAATGTTAAAAAATTAATATTTTAGGTTGTAC
*
454806 TCAACCTAAAATGT
1 TCAACCGAAAATGT
454820 CATGATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (40 bp):
TCAACCGAAAATGTTAAAAAATTAATATTTTAGGTTGTAC
Found at i:455210 original size:2 final size:2
Alignment explanation
Indices: 455203--455249 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
455193 TTGGTTTTCG
455203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
455245 GTA TA
1 -TA TA
455250 AGTAATATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:460631 original size:20 final size:20
Alignment explanation
Indices: 460606--460649 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
460596 TGACTTAAGC
460606 GGTAATGGTGGAAATGTTGA
1 GGTAATGGTGGAAATGTTGA
*
460626 GGTAATGGTGGAAATTTTGA
1 GGTAATGGTGGAAATGTTGA
460646 GGTA
1 GGTA
460650 TTGGGCTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (20 bp):
GGTAATGGTGGAAATGTTGA
Found at i:462256 original size:19 final size:19
Alignment explanation
Indices: 462234--462295 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
462224 GAAATTAAAC
462234 TATGAATCTGAAAATAAGT
1 TATGAATCTGAAAATAAGT
* * * *
462253 TATGAATTTGGAAGTAGGT
1 TATGAATCTGAAAATAAGT
* *
462272 TCTGAATC-GAGAATAAGT
1 TATGAATCTGAAAATAAGT
*
462290 TCTGAA
1 TATGAA
462296 ATGTGAAGGT
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGT
Found at i:462341 original size:19 final size:19
Alignment explanation
Indices: 462313--462356 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
462303 GGTACTAGTT
*
462313 ATGAAAATGAGATGTGAAA-
1 ATGAAAATGA-AAGTGAAAG
*
462332 ATGAATATGAAAGTGAAAG
1 ATGAAAATGAAAGTGAAAG
462351 ATGAAA
1 ATGAAA
462357 GTTCTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (19 bp):
ATGAAAATGAAAGTGAAAG
Found at i:477623 original size:31 final size:31
Alignment explanation
Indices: 477587--477664 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
477577 TAAAAAAACA
* **
477587 TAAGTTTTGGTCACTTATGTTATTGTTTT-T
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
477617 TCAAGTTTTGGTCGA-TTACGTTATCATTTTAT
1 T-AAGTTTTGGTC-ACTTACGTTATCATTTTAT
*
477649 TAAGTTTTGATCACTT
1 TAAGTTTTGGTCACTT
477665 GGATGTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 2 0.05
31 35 0.88
32 3 0.08
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCATTTTAT
Found at i:479023 original size:31 final size:31
Alignment explanation
Indices: 478988--479094 Score: 169
Period size: 31 Copynumber: 3.5 Consensus size: 31
478978 ATTCAACGTC
*
478988 CAAGTGATCAAAACTTAATAAAACGATAACG
1 CAAGTGACCAAAACTTAATAAAACGATAACG
*
479019 CAAGTGACCAAAACTTAATAAAACGATAACA
1 CAAGTGACCAAAACTTAATAAAACGATAACG
* *
479050 TAAGTGACCAAAACTTAATAAAACAATAACG
1 CAAGTGACCAAAACTTAATAAAACGATAACG
*
479081 TAAGTGACCAAAAC
1 CAAGTGACCAAAAC
479095 GTGTGTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (31 bp):
CAAGTGACCAAAACTTAATAAAACGATAACG
Found at i:482470 original size:26 final size:27
Alignment explanation
Indices: 482441--482501 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
482431 GACACGGGTC
*
482441 TAGAAAATA-TTTTCTGTTTTTATTTT
1 TAGAAAATATTTTTCTATTTTTATTTT
*
482467 TAGAAAATATTTTTTTATTTTTATTTT
1 TAGAAAATATTTTTCTATTTTTATTTT
*
482494 TTGAAAAT
1 TAGAAAAT
482502 TAGAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (27 bp):
TAGAAAATATTTTTCTATTTTTATTTT
Found at i:487975 original size:18 final size:18
Alignment explanation
Indices: 487952--487992 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
487942 AAAGGCGATG
*
487952 GCGGTATCATATATGGTT
1 GCGGTATCATATATGGCT
487970 GCGGTATCATATATGGCT
1 GCGGTATCATATATGGCT
487988 GCGGT
1 GCGGT
487993 GGCTACTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.34
Consensus pattern (18 bp):
GCGGTATCATATATGGCT
Found at i:489714 original size:17 final size:18
Alignment explanation
Indices: 489671--489711 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
489661 AAATTATATT
489671 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
489688 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
489706 ATTAAA
1 AGTAAA
489712 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:490536 original size:17 final size:17
Alignment explanation
Indices: 490494--490536 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
490484 AAAATCTAAA
*
490494 ATATTAAAATATAATTT
1 ATATTAAAATATAACTT
* *
490511 AAATAAAAATATAACTT
1 ATATTAAAATATAACTT
490528 ATATTAAAA
1 ATATTAAAA
490537 AATTATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTAAAATATAACTT
Found at i:501770 original size:60 final size:61
Alignment explanation
Indices: 501629--501813 Score: 162
Period size: 60 Copynumber: 3.1 Consensus size: 61
501619 TATATGTCCC
* *
501629 CAAAATAT-AACTCTCATT-TTAATATGATCCTTAAAACTTTTCAATATTCCAATTTCATCCT
1 CAAAATATGAAC-CTCATTCTAAAT-TAATCCTTAAAACTTTTCAATATTCCAATTTCATCCT
* *** * * *
501690 CAAACTATGATTTTCATTCTAAATTAATCCTTAAAAGTTTT-ACTATTCTAATTTCATCCT
1 CAAAATATGAACCTCATTCTAAATTAATCCTTAAAACTTTTCAATATTCCAATTTCATCCT
* * ** ** * * *
501750 TAAAATATGAACCTCTTTCTAAATTGGTCC-CCAAACTTTTGAATATTCCAATTTTATCCC
1 CAAAATATGAACCTCATTCTAAATTAATCCTTAAAACTTTTCAATATTCCAATTTCATCCT
501810 CAAA
1 CAAA
501814 TTTATCAAAA
Statistics
Matches: 96, Mismatches: 25, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
59 7 0.07
60 57 0.59
61 27 0.28
62 5 0.05
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.41
Consensus pattern (61 bp):
CAAAATATGAACCTCATTCTAAATTAATCCTTAAAACTTTTCAATATTCCAATTTCATCCT
Found at i:506140 original size:32 final size:31
Alignment explanation
Indices: 506094--506182 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 31
506084 TAGCATTTTC
506094 ATAAATTTAATGATTATTTTGTAATAGTTCTG
1 ATAAATTTAATGATTATTTTGTAATAGTTC-G
**
506126 -TAAATTTCAATGATTATTTCATAATAGTTCG
1 ATAAATTT-AATGATTATTTTGTAATAGTTCG
*
506157 ATAAAATTAATGATTCATTTTGTAAT
1 ATAAATTTAATGATT-ATTTTGTAAT
506183 TTTCAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 15 0.31
32 34 0.69
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (31 bp):
ATAAATTTAATGATTATTTTGTAATAGTTCG
Found at i:510783 original size:18 final size:18
Alignment explanation
Indices: 510760--510802 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
510750 TCCCAAACCA
*
510760 TGATCCTCGTTTTTAAAT
1 TGATCCTCATTTTTAAAT
510778 TGATCCTCATTTTTAAAT
1 TGATCCTCATTTTTAAAT
510796 TGATCCT
1 TGATCCT
510803 TAAACTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (18 bp):
TGATCCTCATTTTTAAAT
Found at i:510885 original size:60 final size:60
Alignment explanation
Indices: 510819--510946 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 60
510809 TTTAAACAAT
* * *
510819 TTTCATCCAT-AAACTATAACTTTCATTCTAAATTGGT-CCTAAAAATTCTGAA-CATTCTAA
1 TTTCATCC-TCAAACTATAACTCTCATCCTAAATCGGTCCCT-AAAATTCTGAATC-TTCTAA
* * *
510879 TTTCATCCTCAAACTATGACTCTCATCCTAAATCGGTCCCTAAACTTTTGAATCTTCTAA
1 TTTCATCCTCAAACTATAACTCTCATCCTAAATCGGTCCCTAAAATTCTGAATCTTCTAA
510939 TTTCATCC
1 TTTCATCC
510947 CCGAATTCAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 1 0.02
60 54 0.92
61 4 0.07
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
TTTCATCCTCAAACTATAACTCTCATCCTAAATCGGTCCCTAAAATTCTGAATCTTCTAA
Found at i:511199 original size:60 final size:60
Alignment explanation
Indices: 511083--511243 Score: 152
Period size: 60 Copynumber: 2.7 Consensus size: 60
511073 GTATAATTAT
* * * *
511083 GGATG-AAATGGAAATGTTCAAAAAGTTTGGGGACCAATTTAGAAGGAAGAAAATAGTTTGG
1 GGATGAAAATAGAAATGTTC-AAAAGTTTGAGGACTAATTTAGAAGGAAG-AAATAGTTTAG
* * *
511144 GGGTGAAAAT-GAAATGTTCAAAAGTTTGAGGACTAATTTAGAATGACATG-CATAGTTTAG
1 GGATGAAAATAGAAATGTTCAAAAGTTTGAGGACTAATTTAGAAGGA-A-GAAATAGTTTAG
* * *
511204 GGATGAAATTAGAATAT-TT-AAAAGTTTAAGGATTAATTTA
1 GGATGAAAATAGAA-ATGTTCAAAAGTTTGAGGACTAATTTA
511244 AAATAAATGT
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
60 59 0.69
61 19 0.22
62 7 0.08
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (60 bp):
GGATGAAAATAGAAATGTTCAAAAGTTTGAGGACTAATTTAGAAGGAAGAAATAGTTTAG
Found at i:513855 original size:41 final size:43
Alignment explanation
Indices: 513762--513858 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 43
513752 GCGCAAAAAG
* **
513762 AAACGCCGCAAAAGCTTATGCTTTTTAGTGACGTTTATTTTAC
1 AAACGCCGCTAAAGCTTATGCTTTTTAGCAACGTTTATTTTAC
* * *
513805 AAACACCGCTAAAGGTTATGC-TTTTAGCAAC-TTTTTTTTAC
1 AAACGCCGCTAAAGCTTATGCTTTTTAGCAACGTTTATTTTAC
*
513846 AAATGCCGCTAAA
1 AAACGCCGCTAAA
513859 AGATTATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 20 0.43
42 8 0.17
43 18 0.39
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (43 bp):
AAACGCCGCTAAAGCTTATGCTTTTTAGCAACGTTTATTTTAC
Found at i:513866 original size:42 final size:44
Alignment explanation
Indices: 513762--513866 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 44
513752 GCGCAAAAAG
* **
513762 AAACGCCGC-AAAAGCTTATGCTTTTTAGTGACGTTTATTTTAC
1 AAACGCCGCTAAAAGATTATGCTTTTTAGCAACGTTTATTTTAC
* * *
513805 AAACACCGCT-AAAGGTTATGC-TTTTAGCAAC-TTTTTTTTAC
1 AAACGCCGCTAAAAGATTATGCTTTTTAGCAACGTTTATTTTAC
*
513846 AAATGCCGCTAAAAGATTATG
1 AAACGCCGCTAAAAGATTATG
513867 ATCGTTAGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 17 0.33
42 17 0.33
43 18 0.35
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (44 bp):
AAACGCCGCTAAAAGATTATGCTTTTTAGCAACGTTTATTTTAC
Found at i:514439 original size:21 final size:21
Alignment explanation
Indices: 514415--514465 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
514405 CGCTTCAGTT
514415 CATTTGAGCAAATATTTCATC
1 CATTTGAGCAAATATTTCATC
514436 CATTTGAGCAAATATTTCATC
1 CATTTGAGCAAATATTTCATC
*
514457 TATTTGAGC
1 CATTTGAGC
514466 CAATTGTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (21 bp):
CATTTGAGCAAATATTTCATC
Found at i:517575 original size:42 final size:42
Alignment explanation
Indices: 517506--517820 Score: 274
Period size: 42 Copynumber: 7.6 Consensus size: 42
517496 GGATTGTACA
* * * *
517506 ATTGCGGCGTTTATTACAAAAAAGCCGCTAAGGTGCATGACT
1 ATTGTGGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
* * *
517548 ATAGTGGCGTTTATTACAAAAATGCCGCTAAAGTACATGATT
1 ATTGTGGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
*
517590 ATT-TAGGCGTTTA-T-CAAAAACGCCG--AAAGTGCATGACT
1 ATTGT-GGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
* * * * *
517628 ATTGCGGCGTTTACTGA-AAAAATGCCACTAAAGTGTATGATT
1 ATTGTGGCGTTTA-TTACAAAAACGCCGCTAAAGTGCATGATT
* ** * *
517670 ATTGCGATGTTTATTACAAAAACGCCACTAAAATGCATGATT
1 ATTGTGGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
* *
517712 ATTGTGGCGTTTA-TA-AAAAACACAGCTAAAGTGCATGATT
1 ATTGTGGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
* * * * *
517752 ATTGTGGCAATTT-TGTA-ATAAACGCCTCT-AAGTTGCTTGACT
1 ATTGTGGC-GTTTAT-TACAAAAACGCCGCTAAAG-TGCATGATT
*
517794 ATTGCGGCGTTTATTACAAAAACGCCG
1 ATTGTGGCGTTTATTACAAAAACGCCG
517821 TTTTTTGTTC
Statistics
Matches: 219, Mismatches: 40, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
38 22 0.10
40 47 0.21
41 17 0.08
42 133 0.61
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (42 bp):
ATTGTGGCGTTTATTACAAAAACGCCGCTAAAGTGCATGATT
Found at i:517813 original size:124 final size:120
Alignment explanation
Indices: 517506--517819 Score: 301
Period size: 122 Copynumber: 2.5 Consensus size: 120
517496 GGATTGTACA
* * * * * * * *
517506 ATTGCGGCGTTTATTACAAAAAAGCCGCTAAGGTGCATGACTATAGTGGCGTTTATTACAAAAAT
1 ATTGCGGCATTTATGA-AAAAACGCCACTAA-GTGCTTGACTATTGCGGCGTTTATTACAAAAAC
* * * *
517571 GCCGCTAAAGTACATGATTATTTAGGCGTTTATCAAAAACGCCGAAAGTGCATGACT
64 GCCACTAAAATACATGATTATTTAGGCGTTTATAAAAAACACCGAAAGTGCATGACT
* * * **
517628 ATTGCGGCGTTTACTGAAAAAATGCCACTAAAGTG-TATGATTATTGCGATGTTTATTACAAAAA
1 ATTGCGGCATTTA-TGAAAAAACGCCACT-AAGTGCT-TGACTATTGCGGCGTTTATTACAAAAA
* * *
517692 CGCCACTAAAATGCATGATTATTGT-GGCGTTTATAAAAAACACAGCTAAAGTGCATGATT
63 CGCCACTAAAATACATGATTATT-TAGGCGTTTATAAAAAACAC--CGAAAGTGCATGACT
* * *
517752 ATTGTGGCAATTT-TGTAATAAACGCCTCTAAGTTGCTTGACTATTGCGGCGTTTATTACAAAAA
1 ATTGCGGC-ATTTATG-AAAAAACGCCACTAAG-TGCTTGACTATTGCGGCGTTTATTACAAAAA
517816 CGCC
63 CGCC
517820 GTTTTTTGTT
Statistics
Matches: 157, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
122 83 0.53
123 10 0.06
124 60 0.38
125 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (120 bp):
ATTGCGGCATTTATGAAAAAACGCCACTAAGTGCTTGACTATTGCGGCGTTTATTACAAAAACGC
CACTAAAATACATGATTATTTAGGCGTTTATAAAAAACACCGAAAGTGCATGACT
Found at i:518180 original size:5 final size:5
Alignment explanation
Indices: 518170--518195 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
518160 AATGCACTGT
518170 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
518196 TTAGGGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:519717 original size:168 final size:168
Alignment explanation
Indices: 519438--519786 Score: 635
Period size: 168 Copynumber: 2.1 Consensus size: 168
519428 TATAGCGTTC
* *
519438 GTTTATGTTCATAGGGGTGTAAATGAACATAATGTTCCATGATATGTTCATGAACTGTTCTTATA
1 GTTTATGTTCACAGGGGTGTAAATGAACATAATATTCCATGATATGTTCATGAACTGTTCTTATA
* *
519503 ACATTCGTTTATGTTTGTTTGTTAAGTTAAAATAAACGAGTATGAACAAATTTTTATATTTAATT
66 ACATTCGCTTATGTTTGTTTGTTAAGTTAAAATAAACGAATATGAACAAATTTTTATATTTAATT
519568 AATAAACGAACGAACACGAACGGAGGTGTATTTAGTTT
131 AATAAACGAACGAACACGAACGGAGGTGTATTTAGTTT
519606 GTTTATGTTCACAGGGGTGTAAATGAACATAATATTCCATGATATGTTCATGAACTGTTCTTATA
1 GTTTATGTTCACAGGGGTGTAAATGAACATAATATTCCATGATATGTTCATGAACTGTTCTTATA
*
519671 ACGTTCGCTTATGTTTGTTTGTTAAGTTAAAATAAACGAATATGAACAAATTTTTATATTTAATT
66 ACATTCGCTTATGTTTGTTTGTTAAGTTAAAATAAACGAATATGAACAAATTTTTATATTTAATT
* *
519736 AATAAACGAACGAACATGAACGTAGGTGTATTTAGTTT
131 AATAAACGAACGAACACGAACGGAGGTGTATTTAGTTT
519774 GTTTATGTTCACA
1 GTTTATGTTCACA
519787 AATAAGCTCA
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 174 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (168 bp):
GTTTATGTTCACAGGGGTGTAAATGAACATAATATTCCATGATATGTTCATGAACTGTTCTTATA
ACATTCGCTTATGTTTGTTTGTTAAGTTAAAATAAACGAATATGAACAAATTTTTATATTTAATT
AATAAACGAACGAACACGAACGGAGGTGTATTTAGTTT
Found at i:520442 original size:64 final size:63
Alignment explanation
Indices: 520370--520559 Score: 170
Period size: 64 Copynumber: 3.1 Consensus size: 63
520360 CAAAAATACT
*
520370 TTTCAGGGTGGGCACACATATGTTAAAAACATAAAATTTTTAAATGAGATGGGTACCAATAAAA
1 TTTCAGGGTGGGCACACATATGTTAAAAACATAAAATTTTTAAATGAGAT-GGTACAAATAAAA
* * * ** * * *
520434 TTTCAGGGT-GG-ACAC---TGTCAGTAAA-AT-AAGTAATTAATTGA-A--G-A-AAACTCATA
1 TTTCAGGGTGGGCACACATATGTTA-AAAACATAAAATTTTTAAATGAGATGGTACAAA-TAAAA
*
520487 TTTCAGGGTGGGCACACATATGTTAACAACATAAAATTTTTAAATGAGATAGGTACAAATAAAA
1 TTTCAGGGTGGGCACACATATGTTAAAAACATAAAATTTTTAAATGAGAT-GGTACAAATAAAA
520551 TTTCAGGGT
1 TTTCAGGGT
520560 AGACACTGTC
Statistics
Matches: 93, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
52 2 0.02
53 13 0.14
54 3 0.03
55 4 0.04
57 3 0.03
58 16 0.17
59 16 0.17
60 4 0.04
62 4 0.04
63 3 0.03
64 22 0.24
65 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (63 bp):
TTTCAGGGTGGGCACACATATGTTAAAAACATAAAATTTTTAAATGAGATGGTACAAATAAAA
Found at i:520495 original size:53 final size:53
Alignment explanation
Indices: 520433--520666 Score: 168
Period size: 53 Copynumber: 4.2 Consensus size: 53
520423 TACCAATAAA
* *
520433 ATTTCAGGGTGGACACTGTCAGTAAAATAAGTAATTAATTGAAGAAAACTCAT
1 ATTTCAGGGTGGACACTGTCAGTAAAATAAGTAATTAATCGAAGAAAACTCAG
* ** * * ** * * *
520486 ATTTCAGGGTGGGCACACATATGTTAACAACATAAAATTTTTAAATGAGATAGGTACAAA-TAAA
1 ATTTCAGGGT-GG-ACAC---TGTCAGTAAAAT-AAGTAATT-AAT-CGA-A-G-A-AAACTCAG
*
520550 ATTTCAGGGTAGACACTGTCAGT-AAATAAGTAATTAATCGAAGAAAACTCAG
1 ATTTCAGGGTGGACACTGTCAGTAAAATAAGTAATTAATCGAAGAAAACTCAG
** * * *
520602 ATTTCAGGGTGGGA-ACCATCAGTAAAATAAGTAACTAATCGAAAAAAATTCAG
1 ATTTCAGGGT-GGACACTGTCAGTAAAATAAGTAATTAATCGAAGAAAACTCAG
520655 ATTTCAGGGTGG
1 ATTTCAGGGTGG
520667 GCACAACCCG
Statistics
Matches: 139, Mismatches: 27, Indels: 31
0.71 0.14 0.16
Matches are distributed among these distances:
51 3 0.02
52 22 0.16
53 49 0.35
54 3 0.02
55 6 0.04
56 3 0.02
57 5 0.04
58 11 0.08
59 9 0.06
60 3 0.02
61 2 0.01
62 5 0.04
63 2 0.01
64 13 0.09
65 3 0.02
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (53 bp):
ATTTCAGGGTGGACACTGTCAGTAAAATAAGTAATTAATCGAAGAAAACTCAG
Found at i:522784 original size:29 final size:32
Alignment explanation
Indices: 522751--522819 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 32
522741 CTATTTTTAT
*
522751 TTTATTTAGATTTAG-CCAT-TTA-ATTTC-AA
1 TTTATTTA-ATTTAGCCCATATTATATGTCTAA
522780 TTTATTTTAATTTAGCCCATATTATATGTCTAA
1 TTTA-TTTAATTTAGCCCATATTATATGTCTAA
522813 TTTATTT
1 TTTATTT
522820 TTTAGCTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 10 0.29
30 8 0.24
31 3 0.09
32 7 0.21
33 6 0.18
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTATTTAATTTAGCCCATATTATATGTCTAA
Found at i:528362 original size:30 final size:30
Alignment explanation
Indices: 528328--528400 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
528318 GATCGAACCA
* *
528328 AATTAGTTCGGTTAATTTAGTCTGTCACCG
1 AATTAGTTCGGTTAATTCAGTCTGCCACCG
528358 AATTAGTTCGGTTAATTCAGTCTGCCACCG
1 AATTAGTTCGGTTAATTCAGTCTGCCACCG
528388 AATTAGTTCGGTT
1 AATTAGTTCGGTT
528401 GGAGAACGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (30 bp):
AATTAGTTCGGTTAATTCAGTCTGCCACCG
Found at i:528613 original size:17 final size:17
Alignment explanation
Indices: 528591--528629 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
528581 TGAATCAAAT
528591 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
528608 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
528625 -AATTA
1 TAATTA
528630 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:538468 original size:18 final size:19
Alignment explanation
Indices: 538433--538469 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
538423 CACGGAATGT
538433 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
538453 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
538470 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:543022 original size:20 final size:21
Alignment explanation
Indices: 542997--543043 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
542987 ATATTAAGTC
542997 ATTTAATAAAG-TAAAGGAGA
1 ATTTAATAAAGATAAAGGAGA
*
543017 ATTTAA-AAAGATAGAGGAGA
1 ATTTAATAAAGATAAAGGAGA
543037 ATTTAAT
1 ATTTAAT
543044 TAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (21 bp):
ATTTAATAAAGATAAAGGAGA
Found at i:551373 original size:21 final size:21
Alignment explanation
Indices: 551333--551373 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
551323 CCGAAAAAAC
*
551333 TAAGGAGAAAATTATATTTTA
1 TAAGGAGAAAAATATATTTTA
551354 TAAGGAGAGAAAATAT-TTTT
1 TAAGGAGA-AAAATATATTTT
551374 CAAGAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
TAAGGAGAAAAATATATTTTA
Found at i:553259 original size:81 final size:81
Alignment explanation
Indices: 553148--553776 Score: 924
Period size: 81 Copynumber: 7.8 Consensus size: 81
553138 CGTTTAGCCT
* * * * *
553148 TTCATCTAACTTGCATACTTGACACCTTTCTGCCAAGTGCACAGCTAGGTCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
553213 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
* * * * * *
553229 ATCATCTAACTGACATAATTGACACATTTCTTCCAAATGCATAACTAGGTCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
553294 CAACGTTATTTAACCG
66 CAACGGTATTTAACCG
*
553310 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
553375 CAACGATATTTAACCG
66 CAACGGTATTTAACCG
* * *
553391 TTCATCTAACTGACATAATTGACACATTTCTGCCAAATACACAACTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
553456 CAACGTTATTTAACCG
66 CAACGGTATTTAACCG
* * *
553472 TTCATCTAACTGGCATAATTGACACATTTCTGCC--A-GCACAACTATGCTATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
553534 CAACTGTATTTAACCG
66 CAACGGTATTTAACCG
*
553550 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
553615 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
* * *
553631 TTCATCTAACTGGCATAATTAACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
553696 CAATGGTATTTAACTG
66 CAACGGTATTTAACCG
* * * * *
553712 ATCATCTAACCGGCATAATTGACA-ACTTTCTTCCAAATGCACATCTAGGCCATTAATTTTTTAC
1 TTCATCTAACTGGCATAATTGACACA-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTAC
553776 T
65 T
553777 TTAAAATTGT
Statistics
Matches: 498, Mismatches: 46, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
78 71 0.14
79 1 0.00
80 1 0.00
81 425 0.85
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
CAACGGTATTTAACCG
Found at i:553616 original size:240 final size:241
Alignment explanation
Indices: 553148--553776 Score: 937
Period size: 240 Copynumber: 2.6 Consensus size: 241
553138 CGTTTAGCCT
* *
553148 TTCATCTAACTTGCATACTTGACACCTTTCTGCCAAGTGCACAGCTAGGTCATTAATCTTTTACT
1 TTCATCTAAC-TGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACT
* * * *
553213 CAACGGTATTTAACCGATCATCTAACTGACATAATTGACACATTTCTTCCAAATGCATAACTAGG
65 CAACGGTATTTAACCGATCATCTAACTGGCATAATTGACACATTTCTGCC-AATGCACAACTAGC
553278 TCATTAATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGC
129 TCATTAATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGC
553343 CAAATACACAGCTAGGCCATTAATCTTTTACTCAACGATATTTAACCG
194 CAAATACACAGCTAGGCCATTAATCTTTTACTCAACGATATTTAACCG
* * * *
553391 TTCATCTAACTGACATAATTGACACATTTCTGCCAAATACACAACTAGGCCATTAATCTTTTACT
1 TTCATCTAACTG-CATAATTGACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACT
* *
553456 CAACGTTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCC-A-GCACAACTATGC
65 CAACGGTATTTAACCGATCATCTAACTGGCATAATTGACACATTTCTGCCAATGCACAACTA-GC
553519 T-ATTAATCTTTTACTCAAC-TGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTG
129 TCATTAATCTTTTACTCAACGT-TATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTG
* * *
553582 TCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCG
193 CCAAATACACAGCTAGGCCATTAATCTTTTACTCAACGATATTTAACCG
*
553631 TTCATCTAACTGGCATAATTAACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACT
1 TTCATCTAACT-GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACT
* * * * *
553696 CAATGGTATTTAACTGATCATCTAACCGGCATAATTGACA-ACTTTCTTCCAAATGCACATCTAG
65 CAACGGTATTTAACCGATCATCTAACTGGCATAATTGACACA-TTTCTGCC-AATGCACAACTA-
*
553760 GC-CATTAATTTTTTACT
127 GCTCATTAATCTTTTACT
553777 TTAAAATTGT
Statistics
Matches: 348, Mismatches: 29, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
239 2 0.01
240 214 0.61
241 4 0.01
242 3 0.01
243 125 0.36
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (241 bp):
TTCATCTAACTGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGTCATTAATCTTTTACTC
AACGGTATTTAACCGATCATCTAACTGGCATAATTGACACATTTCTGCCAATGCACAACTAGCTC
ATTAATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
AATACACAGCTAGGCCATTAATCTTTTACTCAACGATATTTAACCG
Found at i:553802 original size:18 final size:17
Alignment explanation
Indices: 553769--553802 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
553759 GGCCATTAAT
*
553769 TTTTTACTTTAAAATTG
1 TTTTTACTCTAAAATTG
553786 TTTTTACTCTAATAATT
1 TTTTTACTCTAA-AATT
553803 ATTCATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTACTCTAAAATTG
Found at i:554030 original size:57 final size:57
Alignment explanation
Indices: 553937--554082 Score: 247
Period size: 57 Copynumber: 2.6 Consensus size: 57
553927 AAATTCATAT
* *
553937 AATTTCTTAACTTTTTACACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAAATAATTATG
* *
553994 AATTTCTCAACTTTTTGCACACAAAGTGCCCCTATGGAAATTCATAAAATAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAAATAATTATG
*
554051 AATTTCTTAATTTTTTGCACACAAAGTGCCCA
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCA
554083 CTGGGTAATC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 82 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAAATAATTATG
Found at i:554535 original size:20 final size:20
Alignment explanation
Indices: 554496--554547 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
554486 TCTGTTAACT
*
554496 ATGGTATTGATACCATCCTC
1 ATGGTATTGATACCACCCTC
554516 ATGGTATTGATACTC-CCCTC
1 ATGGTATTGATAC-CACCCTC
* *
554536 TTGGTATCGATA
1 ATGGTATTGATA
554548 TCACTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGGTATTGATACCACCCTC
Found at i:554693 original size:20 final size:20
Alignment explanation
Indices: 554654--554705 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
554644 TCTGTTAACT
*
554654 ATGGTATTGATACCATCCTC
1 ATGGTATTGATACCACCCTC
554674 ATGGTATTGATACTC-CCCTC
1 ATGGTATTGATAC-CACCCTC
* *
554694 TTGGTATCGATA
1 ATGGTATTGATA
554706 TCACTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGGTATTGATACCACCCTC
Found at i:554754 original size:158 final size:158
Alignment explanation
Indices: 554466--554794 Score: 640
Period size: 158 Copynumber: 2.1 Consensus size: 158
554456 TCTATTACGG
554466 TACCGATACCATTTCTGCATTCTGTTAACTATGGTATTGATACCATCCTCATGGTATTGATACTC
1 TACCGATACCATTTCTGCATTCTGTTAACTATGGTATTGATACCATCCTCATGGTATTGATACTC
*
554531 CCCTCTTGGTATCGATATCACTTGAATCGGTATCGATACTACTCAGTGAATTCTTCTGATTTTAA
66 CCCTCTTGGTATCGATATCACTTGAATCGGTATCGATACTACTCAATGAATTCTTCTGATTTTAA
554596 GCCTATAGTATCAATATTGTTCTATCAA
131 GCCTATAGTATCAATATTGTTCTATCAA
554624 TACCGATACCATTTCTGCATTCTGTTAACTATGGTATTGATACCATCCTCATGGTATTGATACTC
1 TACCGATACCATTTCTGCATTCTGTTAACTATGGTATTGATACCATCCTCATGGTATTGATACTC
*
554689 CCCTCTTGGTATCGATATCACTTGAATCGGTATCGATATTACTCAATGAATTCTTCTGATTTTAA
66 CCCTCTTGGTATCGATATCACTTGAATCGGTATCGATACTACTCAATGAATTCTTCTGATTTTAA
554754 GCCTATAGTATCAATATTGTTCTATCAA
131 GCCTATAGTATCAATATTGTTCTATCAA
554782 TACCGATACCATT
1 TACCGATACCATT
554795 ACCTATATTT
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 169 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (158 bp):
TACCGATACCATTTCTGCATTCTGTTAACTATGGTATTGATACCATCCTCATGGTATTGATACTC
CCCTCTTGGTATCGATATCACTTGAATCGGTATCGATACTACTCAATGAATTCTTCTGATTTTAA
GCCTATAGTATCAATATTGTTCTATCAA
Found at i:558990 original size:3 final size:3
Alignment explanation
Indices: 558969--559006 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
558959 TGAAGAAATG
* *
558969 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
559007 TGTAGGCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:559500 original size:19 final size:20
Alignment explanation
Indices: 559476--559513 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
559466 TAAAGATAAT
559476 TTGATTTT-AAAAGCAAAAG
1 TTGATTTTGAAAAGCAAAAG
*
559495 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAAGCAAAA
559514 AGAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAAGCAAAAG
Found at i:560675 original size:18 final size:18
Alignment explanation
Indices: 560644--560701 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 18
560634 CAACAATTGG
* *
560644 TAACAATAGGTATCTTTT
1 TAACAATTGATATCTTTT
*
560662 TAACAATTTATATCCTTTTGT
1 TAACAATTGATAT-C-TTT-T
560683 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
560701 T
1 T
560702 CATTAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 4 0.12
21 13 0.39
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:560687 original size:21 final size:21
Alignment explanation
Indices: 560661--560701 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
560651 AGGTATCTTT
*
560661 TTAACAATTTATATCCTTTTG
1 TTAACAATTGATATCCTTTTG
*
560682 TTAACAATTGATATCTTTTT
1 TTAACAATTGATATCCTTTT
560702 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (21 bp):
TTAACAATTGATATCCTTTTG
Found at i:561082 original size:21 final size:21
Alignment explanation
Indices: 561053--561148 Score: 174
Period size: 21 Copynumber: 4.6 Consensus size: 21
561043 TAATGGAGGA
561053 GTACCGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGG
*
561074 GTACTGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGG
561095 GTACCGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGG
*
561116 GTACTGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGG
561137 GTACCGATACCC
1 GTACCGATACCC
561149 CCTATTATGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
GTACCGATACCCTATGTAGGG
Found at i:561112 original size:42 final size:42
Alignment explanation
Indices: 561053--561148 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
561043 TAATGGAGGA
561053 GTACCGATACCCTATGTAGGGGTACTGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGGGTACTGATACCCTATGTAGGG
561095 GTACCGATACCCTATGTAGGGGTACTGATACCCTATGTAGGG
1 GTACCGATACCCTATGTAGGGGTACTGATACCCTATGTAGGG
561137 GTACCGATACCC
1 GTACCGATACCC
561149 CCTATTATGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (42 bp):
GTACCGATACCCTATGTAGGGGTACTGATACCCTATGTAGGG
Found at i:561215 original size:20 final size:22
Alignment explanation
Indices: 561177--561216 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
561167 TTTGAGTAGA
561177 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
561199 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
561217 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:562328 original size:30 final size:30
Alignment explanation
Indices: 562294--562397 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 30
562284 AGAAGTTAGT
562294 TGGGATGCTCTTCTATGTTTCTTAGCCATG
1 TGGGATGCTCTTCTATGTTTCTTAGCCATG
* * * * * *
562324 TGGGATTGTTTTATTCTCATATTTTCTCTTTAGACTTT
1 TGGGA-TG--CT-CT-TC-TATGTT-TC-TTAGCCATG
562362 TGGGATGCTCTTCTATGTTTCTTAGCCATG
1 TGGGATGCTCTTCTATGTTTCTTAGCCATG
562392 TGGGAT
1 TGGGAT
562398 TGTTTTTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
30 17 0.31
31 4 0.07
32 5 0.09
33 3 0.06
34 2 0.04
35 3 0.06
36 5 0.09
37 4 0.07
38 11 0.20
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.48
Consensus pattern (30 bp):
TGGGATGCTCTTCTATGTTTCTTAGCCATG
Found at i:566482 original size:21 final size:21
Alignment explanation
Indices: 566456--566500 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
566446 GATTTCTGGG
*
566456 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
566477 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
566498 CAA
1 CAA
566501 ACGAACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:567036 original size:23 final size:24
Alignment explanation
Indices: 566993--567039 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
566983 ATATGGCATG
*
566993 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
567017 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
567040 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:567255 original size:31 final size:31
Alignment explanation
Indices: 567217--567372 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
567207 AGGGTCGAGG
567217 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
567248 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
567279 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
567310 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
567341 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
567372 G
1 G
567373 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:570668 original size:21 final size:21
Alignment explanation
Indices: 570642--570686 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
570632 GATTTCTGGG
* *
570642 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
570663 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
570684 CAA
1 CAA
570687 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:571223 original size:23 final size:24
Alignment explanation
Indices: 571180--571226 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
571170 ATATGGCATG
*
571180 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
571204 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
571227 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:571442 original size:31 final size:31
Alignment explanation
Indices: 571404--571559 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
571394 AGGGTCGAGG
571404 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
571435 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
571466 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
571497 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
571528 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
571559 G
1 G
571560 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:578966 original size:14 final size:14
Alignment explanation
Indices: 578949--578986 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
578939 AGGGGGAAAG
*
578949 AGTACAAATAAAAA
1 AGTAAAAATAAAAA
*
578963 AGTAAAAATGAAAA
1 AGTAAAAATAAAAA
578977 AGTAAAAATA
1 AGTAAAAATA
578987 GTTTATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.16
Consensus pattern (14 bp):
AGTAAAAATAAAAA
Found at i:580455 original size:42 final size:42
Alignment explanation
Indices: 580409--580498 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
580399 TTCGAGTTAC
* *
580409 TCGAGTAACTCGAAATTGAAAATTTTGATTTTTCGAGTCAAG
1 TCGAGTAACTCGAAATTAAAAAATTTGATTTTTCGAGTCAAG
580451 TCGAGTAACTCGAAATTAAAAAATTTGATTTTTCGAGTCAAG
1 TCGAGTAACTCGAAATTAAAAAATTTGATTTTTCGAGTCAAG
580493 TCGAGT
1 TCGAGT
580499 TTTACTCACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (42 bp):
TCGAGTAACTCGAAATTAAAAAATTTGATTTTTCGAGTCAAG
Found at i:584892 original size:2 final size:2
Alignment explanation
Indices: 584885--584930 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
584875 ACCCTAACCC
584885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
584927 TA TA
1 TA TA
584931 AAAGACGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:586854 original size:32 final size:32
Alignment explanation
Indices: 586788--586877 Score: 121
Period size: 31 Copynumber: 2.8 Consensus size: 32
586778 CTTTTTTTAA
*
586788 ATTATAAAATGATCATTAAATTTATC-AAGCT
1 ATTATAAAATGATTATTAAATTTATCGAAGCT
* *
586819 ATTACAAAATGATTATTAAAATTTATCGAA-TT
1 ATTATAAAATGATTATT-AAATTTATCGAAGCT
*
586851 ATTATAAAATAATTATTAAATTTATCG
1 ATTATAAAATGATTATTAAATTTATCG
586878 GATTTTATTC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 25 0.48
32 25 0.48
33 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (32 bp):
ATTATAAAATGATTATTAAATTTATCGAAGCT
Found at i:588183 original size:57 final size:57
Alignment explanation
Indices: 588118--588229 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
588108 GCTGGAAACA
* *
588118 GGAGGAGAAACGAATGC-CTGCTTTGCAACATCCTTCTGCTC-AGTGTTCTGTTCGTGG
1 GGAGGAGAAACAAATGCAC-GCTTTGCAACATCCTTCTGCTCTA-AGTTCTGTTCGTGG
* *
588175 GGAGGAGAATCAAATGCACGCTTTGCAACATCTTTCTGCTCTAAGTTCTGTTCGT
1 GGAGGAGAAACAAATGCACGCTTTGCAACATCCTTCTGCTCTAAGTTCTGTTCGT
588230 CAGAGGCAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 47 0.96
58 2 0.04
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (57 bp):
GGAGGAGAAACAAATGCACGCTTTGCAACATCCTTCTGCTCTAAGTTCTGTTCGTGG
Found at i:588775 original size:33 final size:33
Alignment explanation
Indices: 588733--588851 Score: 130
Period size: 33 Copynumber: 3.6 Consensus size: 33
588723 ACCGCCAGGG
* *
588733 CCACCAAAACTACCATCCCTAATACTGCCGCGC
1 CCACCAAAACCACCATCCCTAATACCGCCGCGC
* *
588766 CCACCAAAACCACCATCCCTTATACCGCCGCGT
1 CCACCAAAACCACCATCCCTAATACCGCCGCGC
* * * * * * *
588799 CCGCCAAAGCCACCATCCCTCATTCCACCACGT
1 CCACCAAAACCACCATCCCTAATACCGCCGCGC
*
588832 CCACCAAAGCCACCATCCCT
1 CCACCAAAACCACCATCCCT
588852 CATTCCACCA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.28, C:0.50, G:0.08, T:0.14
Consensus pattern (33 bp):
CCACCAAAACCACCATCCCTAATACCGCCGCGC
Found at i:588852 original size:33 final size:33
Alignment explanation
Indices: 588766--588863 Score: 142
Period size: 33 Copynumber: 3.0 Consensus size: 33
588756 ACTGCCGCGC
* * * * *
588766 CCACCAAAACCACCATCCCTTATACCGCCGCGT
1 CCACCAAAGCCACCATCCCTCATTCCACCACGT
*
588799 CCGCCAAAGCCACCATCCCTCATTCCACCACGT
1 CCACCAAAGCCACCATCCCTCATTCCACCACGT
588832 CCACCAAAGCCACCATCCCTCATTCCACCACG
1 CCACCAAAGCCACCATCCCTCATTCCACCACG
588864 GCCTCCATTG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.27, C:0.51, G:0.08, T:0.14
Consensus pattern (33 bp):
CCACCAAAGCCACCATCCCTCATTCCACCACGT
Found at i:594597 original size:21 final size:20
Alignment explanation
Indices: 594511--594667 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
594501 AAATGACCAA
**
594511 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
594530 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
594550 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
594570 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
594591 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
594611 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
594631 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
594652 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
594668 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:594620 original size:41 final size:41
Alignment explanation
Indices: 594511--594667 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
594501 AAATGACCAA
* **
594511 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
594550 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
594591 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
594632 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
594668 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:594709 original size:20 final size:20
Alignment explanation
Indices: 594634--594843 Score: 183
Period size: 20 Copynumber: 10.5 Consensus size: 20
594624 CGATTTTCCA
* ** *
594634 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
594654 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
594674 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
594694 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
594714 AAATCGCAACGTGTTTCCGT
1 AAATCGCAACGCGTATCCGT
*
594734 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
594754 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
594774 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
594794 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
594814 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
594834 AAATCACAAC
1 AAATCGCAAC
594844 ACTGAAATTT
Statistics
Matches: 154, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 150 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:595570 original size:24 final size:24
Alignment explanation
Indices: 595526--595572 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
595516 AAATTTGGTC
*
595526 TTGGTCAATATCTGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
595550 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
595573 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:595764 original size:12 final size:12
Alignment explanation
Indices: 595747--595771 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
595737 ATATAATCCT
595747 GAAGAAGAAAAA
1 GAAGAAGAAAAA
595759 GAAGAAGAAAAA
1 GAAGAAGAAAAA
595771 G
1 G
595772 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:598076 original size:19 final size:19
Alignment explanation
Indices: 598054--598289 Score: 278
Period size: 19 Copynumber: 13.4 Consensus size: 19
598044 CGGAAATTAC
*
598054 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
598073 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
598087 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
598106 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
598120 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
598139 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
598158 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
598177 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
598191 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
598210 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
598230 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
598244 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
598263 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
598282 AATCGCAA
1 AATCGCAA
598290 CGAGAGAATC
Statistics
Matches: 188, Mismatches: 8, Indels: 42
0.79 0.03 0.18
Matches are distributed among these distances:
14 42 0.22
15 3 0.02
16 7 0.04
17 6 0.03
18 4 0.02
19 110 0.59
20 16 0.09
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:598100 original size:33 final size:34
Alignment explanation
Indices: 598054--598311 Score: 282
Period size: 33 Copynumber: 7.5 Consensus size: 34
598044 CGGAAATTAC
* *
598054 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
598087 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
598120 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
598158 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
598191 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--ATGAA
*
598230 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
598263 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
598296 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
598312 TATAAACGCA
Statistics
Matches: 199, Mismatches: 9, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
33 118 0.59
34 16 0.08
35 6 0.03
36 5 0.03
37 4 0.02
38 40 0.20
39 10 0.05
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:598114 original size:52 final size:52
Alignment explanation
Indices: 598054--598311 Score: 371
Period size: 52 Copynumber: 4.9 Consensus size: 52
598044 CGGAAATTAC
* * *
598054 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAA
* * * * *
598106 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
598158 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
598210 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
598263 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
598312 TATAAACGCA
Statistics
Matches: 188, Mismatches: 10, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
50 7 0.04
51 7 0.04
52 110 0.59
53 59 0.31
54 4 0.02
55 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:598327 original size:105 final size:105
Alignment explanation
Indices: 598054--598311 Score: 375
Period size: 105 Copynumber: 2.5 Consensus size: 105
598044 CGGAAATTAC
* * *
598054 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCG
* * *
598116 AGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
65 -GA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
598158 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
598223 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
598263 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
598312 TATAAACGCA
Statistics
Matches: 142, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
103 7 0.05
104 62 0.44
105 71 0.50
106 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:598422 original size:19 final size:19
Alignment explanation
Indices: 598336--598414 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
598326 GGTTCTCTCG
598336 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
598356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
598375 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
598389 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
598408 TTGCGAT
1 TTGCGAT
598415 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:598540 original size:14 final size:14
Alignment explanation
Indices: 598521--598557 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
598511 CATCAATTAC
598521 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
598535 ACAAATCATCTTTT
1 ACAAATCAACTTTT
598549 ACAAATCAA
1 ACAAATCAA
598558 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:600521 original size:19 final size:19
Alignment explanation
Indices: 600481--600609 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
600471 TAGTTTACTT
* *
600481 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
600501 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
600520 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
600539 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
600553 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
600572 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
600586 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
600605 TCGCA
1 TCGCA
600610 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:600560 original size:33 final size:32
Alignment explanation
Indices: 600517--600609 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
600507 CGCGAAACCA
**
600517 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
600549 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
600582 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
600610 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:600607 original size:52 final size:52
Alignment explanation
Indices: 600481--600609 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
600471 TAGTTTACTT
**
600481 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
600533 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
600586 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
600610 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:600627 original size:19 final size:19
Alignment explanation
Indices: 600605--600739 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
600595 GAAACCAAAA
*
600605 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
600624 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
600640 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
600657 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
600673 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
600690 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
600709 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
600729 TCGTGTTGCGA
1 TCGCGTTGCGA
600740 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:600646 original size:14 final size:14
Alignment explanation
Indices: 600627--600683 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
600617 TTTCATTTCG
600627 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
600641 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
600658 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
600674 CGTTGCGATT
1 CGTTGCGATT
600684 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:600652 original size:33 final size:33
Alignment explanation
Indices: 600610--600702 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
600600 CAAAATCGCA
*
600610 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
600643 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
600676 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
600703 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:600903 original size:93 final size:93
Alignment explanation
Indices: 600787--601162 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
600777 ATGGATTGCA
600787 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
600851 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
600879 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
600944 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
600972 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
601037 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
601065 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACATTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
601130 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
601158 TTACT
1 TTACT
601163 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 277 0.99
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:602888 original size:14 final size:14
Alignment explanation
Indices: 602869--602958 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
602859 TTGAAATGAA
602869 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
602883 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
602902 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
602916 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
602935 AATCGCAACGAGAG
1 AATCGCAACGAGAG
602949 AATCGCAACG
1 AATCGCAACG
602959 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:602906 original size:33 final size:33
Alignment explanation
Indices: 602861--602975 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
602851 TCTTTTGGTT
602861 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
602894 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
602927 GATATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
602960 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
602976 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:602907 original size:19 final size:18
Alignment explanation
Indices: 602863--602980 Score: 80
Period size: 19 Copynumber: 7.1 Consensus size: 18
602853 TTTTGGTTGA
602863 AATGAAAATCGCAA--CG
1 AATGAAAATCGCAACGCG
*
602879 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
602895 AAATGACAATCGCAA--CG
1 -AATGAAAATCGCAACGCG
*
602912 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
602928 ATATGAAAATCGCAA--CG
1 A-ATGAAAATCGCAACGCG
*
602945 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
602961 AAATGAAAATCGCAATGCG
1 -AATGAAAATCGCAACGCG
602980 A
1 A
602981 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
14 30 0.38
15 3 0.04
16 6 0.08
17 4 0.05
18 4 0.05
19 33 0.41
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (18 bp):
AATGAAAATCGCAACGCG
Found at i:603011 original size:14 final size:14
Alignment explanation
Indices: 602992--603048 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
602982 TTTGGTTTCG
602992 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
603006 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
603025 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
603039 CGTTGCGATT
1 CGTTGCGATT
603049 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:603026 original size:33 final size:33
Alignment explanation
Indices: 602989--603053 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
602979 GATTTTGGTT
*
602989 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTGTCATA
603022 TCGCGTTGCGATTCTCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTGTCAT
603054 TTCTCTCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTGTCATA
Found at i:603089 original size:41 final size:41
Alignment explanation
Indices: 603032--603109 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
603022 TCGCGTTGCG
*
603032 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
603073 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
603110 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:603094 original size:20 final size:21
Alignment explanation
Indices: 603033--603108 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
603023 CGCGTTGCGA
603033 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
603054 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
603074 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
603095 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
603109 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:603230 original size:33 final size:33
Alignment explanation
Indices: 603188--603258 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
603178 AATACTAACT
603188 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
603221 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
603254 TGAAA
1 TGAAA
603259 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:603492 original size:22 final size:22
Alignment explanation
Indices: 603440--603494 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
603430 TGGTTGTGAG
**
603440 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
603462 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
603484 GGATTTCTTCG
1 GGATTTCTTCG
603495 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:603666 original size:20 final size:20
Alignment explanation
Indices: 603641--603834 Score: 185
Period size: 20 Copynumber: 9.7 Consensus size: 20
603631 CTTTAAATAT
603641 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
603661 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
603683 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
* *
603702 CGCGTTGCGATATACGGATG
1 CGCGTTGCGATTTACGGATA
* **
603722 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
603742 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
603762 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
603782 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
603802 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
603822 CGCGTTGCGATTT
1 CGCGTTGCGATTT
603835 TGGAAAATCG
Statistics
Matches: 139, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
19 2 0.01
20 120 0.86
21 15 0.11
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:603806 original size:60 final size:60
Alignment explanation
Indices: 603643--603814 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 60
603633 TTAAATATCG
* ** *
603643 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* * *** * * *
603704 CGTTGCGATATACGGATGCGCATTGCGATTTACCCATACGCGTTGTGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
603764 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
603815 TCATATTCGC
Statistics
Matches: 91, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 66 0.73
61 25 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:603851 original size:21 final size:20
Alignment explanation
Indices: 603801--603898 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
603791 ATTTATGTGT
* * * *
603801 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
603821 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
603842 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
603862 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
603883 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
603899 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:603874 original size:61 final size:60
Alignment explanation
Indices: 603801--603957 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
603791 ATTTATGTGT
*
603801 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
603862 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
603923 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
603958 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:603893 original size:41 final size:41
Alignment explanation
Indices: 603801--603957 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
603791 ATTTATGTGT
* * *
603801 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
603842 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
603883 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
603923 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
603958 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:604646 original size:31 final size:31
Alignment explanation
Indices: 604583--604647 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
604573 TGACCACGTC
* * * * *
604583 TTAATTAAATAAAAACGAACATTACCACATA
1 TTAATGAAATAAAAACAAAAATGACCAAATA
*
604614 TTAATGAAATAAAAACAAAAATGATCAAATA
1 TTAATGAAATAAAAACAAAAATGACCAAATA
604645 TTA
1 TTA
604648 TATTTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (31 bp):
TTAATGAAATAAAAACAAAAATGACCAAATA
Found at i:611391 original size:3 final size:3
Alignment explanation
Indices: 611377--611408 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
611367 AGAGATATTC
*
611377 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
611409 ATGTACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:612797 original size:31 final size:31
Alignment explanation
Indices: 612759--612850 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
612749 GGTCGAGGGT
612759 TTACCTATGTTCTTCGGGACATATGGACTGC
1 TTACCTATGTTCTTCGGGACATATGGACTGC
*
612790 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGC
*
612821 TTACCTAGGTTCTTCGGGATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
612851 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGC
Found at i:616743 original size:2 final size:2
Alignment explanation
Indices: 616736--616769 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
616726 ATAAACACAG
616736 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
616770 AGTTTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:617270 original size:36 final size:36
Alignment explanation
Indices: 617217--617286 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
617207 ACTTAACGTT
*
617217 AAATTTTGAACGAGTACTAAAATGAAACAAAAACTA
1 AAATTTTGAACGAGTACTAAAATAAAACAAAAACTA
* *
617253 AAATTTTTAACGGGTACTAAAATAAAACAAAAAC
1 AAATTTTGAACGAGTACTAAAATAAAACAAAAAC
617287 ATGATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.23
Consensus pattern (36 bp):
AAATTTTGAACGAGTACTAAAATAAAACAAAAACTA
Found at i:618397 original size:42 final size:41
Alignment explanation
Indices: 618307--618403 Score: 151
Period size: 41 Copynumber: 2.3 Consensus size: 41
618297 GGTAGACTTG
*
618307 AATTTGCAGATTTTGGTTTAGTGTTCATGTGATTTGGTTTT
1 AATTTGCAGAATTTGGTTTAGTGTTCATGTGATTTGGTTTT
*
618348 AATTTGCAGAATTTGGTTTAGTTTTTCATGGTGATTTGGTTTT
1 AATTTGCAGAATTTGGTTTAG-TGTTCAT-GTGATTTGGTTTT
618391 AA-TTGCAGAATTT
1 AATTTGCAGAATTT
618404 TAAGGAATGG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 20 0.38
42 17 0.33
43 15 0.29
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.52
Consensus pattern (41 bp):
AATTTGCAGAATTTGGTTTAGTGTTCATGTGATTTGGTTTT
Found at i:619554 original size:13 final size:14
Alignment explanation
Indices: 619538--619570 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
619528 TAATCTAATT
619538 AATAAAATT-TCAA
1 AATAAAATTATCAA
619551 AAT-AAATTATCAA
1 AATAAAATTATCAA
619564 AATAAAA
1 AATAAAA
619571 AGGACAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 10 0.56
14 3 0.17
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAAATTATCAA
Found at i:621170 original size:20 final size:22
Alignment explanation
Indices: 621137--621178 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
621127 CCGGAAATGT
621137 TAAAAAATATTAATATTTTAGG
1 TAAAAAATATTAATATTTTAGG
*
621159 TAAAAAA-A-TAATGTTTTAGG
1 TAAAAAATATTAATATTTTAGG
621179 CAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (22 bp):
TAAAAAATATTAATATTTTAGG
Found at i:623037 original size:16 final size:16
Alignment explanation
Indices: 623012--623054 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
623002 GTCTCCAACG
*
623012 TTTATATTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
623028 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
623044 TTTATGTTCGT
1 TTTATGTTCGT
623055 TAATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:623143 original size:16 final size:16
Alignment explanation
Indices: 623122--623162 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
623112 CAAAAAAAAT
623122 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
623138 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
623154 T-TT-GTTTAT
1 TGTTCGTTTAT
623163 TAAATGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.24
15 2 0.08
16 17 0.68
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:623515 original size:12 final size:12
Alignment explanation
Indices: 623498--623531 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
623488 ATTTTTTTAG
623498 TATTAATTTATA
1 TATTAATTTATA
*
623510 TATTAATTTGTA
1 TATTAATTTATA
623522 TATT-ATTTAT
1 TATTAATTTAT
623532 TTAATTAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TATTAATTTATA
Found at i:625334 original size:18 final size:19
Alignment explanation
Indices: 625293--625331 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
625283 TTAGTTCACA
625293 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAG-GG
625313 GAATGTAAGATTACCAGGG
1 GAATGTAAGATTACCAGGG
625332 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:632507 original size:4 final size:4
Alignment explanation
Indices: 632498--632578 Score: 78
Period size: 4 Copynumber: 21.0 Consensus size: 4
632488 TTTACAAGTT
* * * *
632498 TATG TATG TATG TATG CATG TATG CATG TATG CATG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
632546 -CTG TATG CATG TATG TATG --TG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
632579 AACATTAACT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.03
3 2 0.03
4 56 0.93
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:632509 original size:8 final size:8
Alignment explanation
Indices: 632499--632578 Score: 117
Period size: 8 Copynumber: 9.9 Consensus size: 8
632489 TTACAAGTTT
*
632499 ATGTATGT
1 ATGTATGC
632507 ATGTATGC
1 ATGTATGC
632515 ATGTATGC
1 ATGTATGC
632523 ATGTATGC
1 ATGTATGC
632531 ATGTATGC
1 ATGTATGC
632539 ATGTATGC
1 ATGTATGC
632547 -TGTATGC
1 ATGTATGC
*
632554 ATGTATGT
1 ATGTATGC
632562 ATGTGTATGC
1 A--TGTATGC
632572 ATGTATG
1 ATGTATG
632579 AACATTAACT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.11
8 52 0.79
10 7 0.11
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (8 bp):
ATGTATGC
Found at i:633824 original size:17 final size:17
Alignment explanation
Indices: 633802--633839 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
633792 ATATGGATAT
* *
633802 TTATTCATTTATTTTTA
1 TTATTCATGTATTATTA
633819 TTATTCATGTATTATTA
1 TTATTCATGTATTATTA
633836 TTAT
1 TTAT
633840 ATGTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTCATGTATTATTA
Found at i:637397 original size:21 final size:20
Alignment explanation
Indices: 637373--637411 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
637363 CTAATCAAGA
*
637373 CAAAAAAAAGAAGCAAAAAAG
1 CAAAAAAAACAAG-AAAAAAG
637394 CAAAAAAAACAAGAAAAA
1 CAAAAAAAACAAGAAAAA
637412 GAGAAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
CAAAAAAAACAAGAAAAAAG
Found at i:637437 original size:15 final size:17
Alignment explanation
Indices: 637400--637443 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
637390 AAAGCAAAAA
637400 AAACAAG-A-AAAAGAG
1 AAACAAGAACAAAAGAG
637415 AAACAAGAACAAAAG-G
1 AAACAAGAACAAAAGAG
*
637431 AAA-AAGAGCAAAA
1 AAACAAGAACAAAA
637444 TCAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 16 0.62
16 5 0.19
17 5 0.19
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (17 bp):
AAACAAGAACAAAAGAG
Found at i:638151 original size:22 final size:22
Alignment explanation
Indices: 638082--638152 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
638072 CCATCAATCT
*
638082 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
* *
638104 TTTAAGCATCAAATGTTAAACC
1 TTTGAGCATCAAATGTCAAACC
*
638126 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
638148 TTTGA
1 TTTGA
638153 CCAAACACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:639119 original size:37 final size:36
Alignment explanation
Indices: 639034--639138 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
639024 GTGCTCACCA
639034 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
639070 TTGTCTCTCTTGAGACAGTTTCCTTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
*
639107 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACA
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA
639139 TAAACATTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.49
37 31 0.49
38 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:639207 original size:36 final size:36
Alignment explanation
Indices: 639154--639238 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
639144 ATTGAAAACA
** *
639154 TTCCCTTGAAATGAATTTCGTCT-CTCTTGAGATAAT
1 TTCCCTTGAAACAAATTTCGTCTCCT-TTGAGACAAT
* *
639190 TTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAGT
1 TTCCCTTGAAACAAATTTCGTCTCCTTTGAGACAAT
*
639226 TTCTCTTGAAACA
1 TTCCCTTGAAACA
639239 CAAAATCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 40 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTCCCTTGAAACAAATTTCGTCTCCTTTGAGACAAT
Found at i:639252 original size:31 final size:31
Alignment explanation
Indices: 639214--639317 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 31
639204 ATTTTGTCTC
639214 CTTTGAGACAGTTTCTCTTGAAACACAAAAT
1 CTTTGAGACAGTTTCTCTTGAAACACAAAAT
** * * **
639245 CTTTGAGATTGTTTCCCTCGAAACA-AATTTTGT
1 CTTTGAGACAGTTTCTCTTGAAACACAA---AAT
639278 CTCCTATGAGACAGTTTCTCTTGAAACACAAAAT
1 CT--T-TGAGACAGTTTCTCTTGAAACACAAAAT
639312 CTTTGA
1 CTTTGA
639318 ATTTATCTCC
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
30 2 0.04
31 24 0.44
32 1 0.02
33 3 0.06
34 3 0.06
35 1 0.02
36 18 0.33
37 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (31 bp):
CTTTGAGACAGTTTCTCTTGAAACACAAAAT
Found at i:639329 original size:67 final size:67
Alignment explanation
Indices: 639180--639338 Score: 241
Period size: 67 Copynumber: 2.4 Consensus size: 67
639170 TTCGTCTCTC
** *
639180 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCTATGAGACAGTTTCTCTTGAAACACAAAAT
639245 CT
66 CT
*
639247 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCTATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCTATGAGACAGTTTCTCTTGAAACACAAAAT
639312 CT
66 CT
*
639314 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
639339 ATTTCGTTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 79 0.94
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCTATGAGACAGTTTCTCTTGAAACACAAAAT
CT
Found at i:640205 original size:105 final size:105
Alignment explanation
Indices: 640080--641122 Score: 1585
Period size: 105 Copynumber: 10.0 Consensus size: 105
640070 ATATCGTGGC
* * * * *
640080 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
*
640145 AATTTCAGAGCCAA-TTCAACTTCACAACGAAGGATATTGG
65 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
640185 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAA-CTTCC
* *
640250 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
64 CAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
640292 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
640357 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
640397 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
640462 ATCTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
640502 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
640567 ATCTCAGAGCCAATTTCAACTTCACAACGAAGG--ATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
640605 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
640670 ATCTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
640710 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
640771 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
640810 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
640875 ATCCCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
640915 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
**
640976 AT-TCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
641015 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC-ACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
** * *
641079 GGT-TCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATCT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
641120 ACT
1 ACT
641123 TGGAACAATG
Statistics
Matches: 870, Mismatches: 52, Indels: 32
0.91 0.05 0.03
Matches are distributed among these distances:
99 2 0.00
100 168 0.19
101 8 0.01
102 6 0.01
103 105 0.12
104 8 0.01
105 474 0.54
106 23 0.03
107 76 0.09
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Done.