Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009621.1 Hibiscus syriacus cultivar Beakdansim tig00117010_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: 839111
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 4
Found at i:463022 original size:28 final size:26
Alignment explanation
Indices: 462990--463047 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
462980 TAATTCTTTC
462990 TTTTCAAAAGT-TTTATATATACTTATTA
1 TTTTCAAAA-TATTTATATATA--TATTA
* *
463018 TTTTCATAATATTTATATGTATATTA
1 TTTTCAAAATATTTATATATATATTA
463044 TTTT
1 TTTT
463048 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.33
27 1 0.04
28 17 0.63
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTTCAAAATATTTATATATATATTA
Found at i:465318 original size:15 final size:13
Alignment explanation
Indices: 465290--465335 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
465280 ATTTTAAATA
465290 ATTTACATTTTTGC
1 ATTTACA-TTTTGC
465304 ATTTATGCATTTTGC
1 ATTTA--CATTTTGC
*
465319 ATTTACATTTTTC
1 ATTTACATTTTGC
465332 ATTT
1 ATTT
465336 GTTAAAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.38
14 5 0.17
15 11 0.38
16 2 0.07
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:471914 original size:22 final size:22
Alignment explanation
Indices: 471884--471962 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
471874 ATATCTACAT
471884 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
* *
471906 TCTTCAAAGATGATATATTCTC
1 TTTTCAAAGATGATAGATTCTC
*
471928 TTTTTAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
471950 TTTTCAAAGATGA
1 TTTTCAAAGATGA
471963 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTC
Found at i:472881 original size:74 final size:74
Alignment explanation
Indices: 472637--473261 Score: 1015
Period size: 74 Copynumber: 8.4 Consensus size: 74
472627 CTATTTCCAA
*
472637 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-CTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
472701 CCTCAGGGT
66 CCTCAGGGT
*
472710 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTTGATGCTTAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGCTTAAA
472775 CCCTCAGGGT
65 CCCTCAGGGT
472785 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
472850 CCTCAGGGT
66 CCTCAGGGT
472859 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
472924 CCTCAGGGT
66 CCTCAGGGT
472933 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
472998 CCTCAGGGT
66 CCTCAGGGT
*
473007 CATTTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
*
473072 CCTTA-GGT
66 CCTCAGGGT
* * *
473080 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-CTT-AA
* *
473145 AGCCTTAGGGT
64 ACCCTCAGGGT
* * * *
473156 CATCTTTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGATTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-CTT--A
*
473221 AACCTTCA-GGT
63 AACCCTCAGGGT
**
473232 CATCTGTAAG-CCTTTTAGTGCATGATGTTT
1 CATCTGTAAGACC-TACAGTGCATGATGTTT
473262 TCAACATTTC
Statistics
Matches: 526, Mismatches: 19, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
73 105 0.20
74 251 0.48
75 74 0.14
76 90 0.17
77 6 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (74 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTAAAC
CCTCAGGGT
Found at i:473400 original size:3 final size:3
Alignment explanation
Indices: 473392--473444 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
473382 TCATTTCGTT
* **
473392 TTA TTA TTA ATA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
473440 TTA TT
1 TTA TT
473445 TAAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:476300 original size:30 final size:30
Alignment explanation
Indices: 476260--476325 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
476250 AGGTTTTGCA
*
476260 AAGAAGGACTGAAGAGGCTGCTATGGCTAC
1 AAGAAAGACTGAAGAGGCTGCTATGGCTAC
476290 AAGAAAGACTGAAGAGGCTGCTATGGCTAC
1 AAGAAAGACTGAAGAGGCTGCTATGGCTAC
476320 AA-AAAG
1 AAGAAAG
476326 GCTAAAGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.15
Consensus pattern (30 bp):
AAGAAAGACTGAAGAGGCTGCTATGGCTAC
Found at i:484771 original size:36 final size:36
Alignment explanation
Indices: 484731--484799 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
484721 CAAATTAAGT
*
484731 TGGGGCAAGTCGAATATAAATAATATATTTTTAGGG
1 TGGGGCAAGTCGAATATAAACAATATATTTTTAGGG
** * *
484767 TGGGGCGGGTTGAATATAAACAATATGTTTTTA
1 TGGGGCAAGTCGAATATAAACAATATATTTTTA
484800 AAATATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (36 bp):
TGGGGCAAGTCGAATATAAACAATATATTTTTAGGG
Found at i:490457 original size:93 final size:93
Alignment explanation
Indices: 490298--490818 Score: 452
Period size: 93 Copynumber: 5.5 Consensus size: 93
490288 AGAAAACATT
* * *
490298 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAGGGTCCGGAACCAGTGGGAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCCAGAACCAGTGGCAGA
* *
490363 AAACAAAACTGATCAGAAATC-TTTGTCC
66 AAACAAAGCTGATAAGAAA-CATTTGTCC
* *
490391 GTTGATTCTGATTCAATCTACAAGCTTGATGGTGATTCCGAAAAGGGTCTAGAACCAGTGGCAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCCAGAACCAGTGGCAGA
* * *
490456 AAACAAAGCTGATAAGAAATATTCGTCT
66 AAACAAAGCTGATAAGAAACATTTGTCC
* * **
490484 GTTGCTTCTGATTCAAGCTTCAAGCTTCAAGCTTCAAGCTTGATGGTGATTCCGAAAAGGATCTG
1 GTTGATTCTG-----A--TTCAAGC-T--A----CAAGCTTGATGGTGATTCCGAAAAGGGTCCA
* * *
490549 GAAACGGTGACAGAAAACAAAGCTGATAAGAAACATTTGTCC
52 GAACCAGTGGCAGAAAACAAAGCTGATAAGAAACATTTGTCC
* * * *
490591 GTTGATTCTGATTCAAGCTATAAGCTTGATGTTCATTCCGAAAAGGGTCCAGAACCAGTGGGAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCCAGAACCAGTGGCAG-
* * *
490656 AAAACAAAGCTGATATGGAACATTTGTCT
65 AAAACAAAGCTGATAAGAAACATTTGTCC
* * * * *
490685 GTTGCTTCTGATTCAAGCTAC-A-----A--G-GATTCTGAAAAGGTTCCGGAA-CAGGTGGGAG
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCCAGAACCA-GTGGCAG
* * *
490740 AAAACAAGGCTTATAAGAAATATTTGTCC
65 AAAACAAAGCTGATAAGAAACATTTGTCC
* * * * * * * *
490769 GGTGCTTCTGATTCAAGCTAGAAGCCTAACGGTGATACCGAAAAGAGTCC
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCC
490819 GAAACCGATG
Statistics
Matches: 349, Mismatches: 53, Indels: 52
0.77 0.12 0.11
Matches are distributed among these distances:
84 44 0.13
85 25 0.07
88 1 0.00
90 1 0.00
92 1 0.00
93 139 0.40
94 45 0.13
97 1 0.00
98 1 0.00
99 1 0.00
100 13 0.04
101 1 0.00
102 1 0.00
103 1 0.00
107 74 0.21
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (93 bp):
GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGGTCCAGAACCAGTGGCAGA
AAACAAAGCTGATAAGAAACATTTGTCC
Found at i:490507 original size:7 final size:7
Alignment explanation
Indices: 490495--490524 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
490485 TTGCTTCTGA
490495 TTCAAGC
1 TTCAAGC
490502 TTCAAGC
1 TTCAAGC
490509 TTCAAGC
1 TTCAAGC
490516 TTCAAGC
1 TTCAAGC
490523 TT
1 TT
490525 GATGGTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (7 bp):
TTCAAGC
Found at i:490600 original size:107 final size:107
Alignment explanation
Indices: 490402--490617 Score: 317
Period size: 107 Copynumber: 2.0 Consensus size: 107
490392 TTGATTCTGA
* * * *
490402 TTCAATCTACAAGCTTGATGGTGATTCCGAAAAGGGTCTAGAACCAGTGGCAGAAAACAAAGCTG
1 TTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGATCTAGAAACAGTGACAGAAAACAAAGCTG
* * *
490467 ATAAGAAATATTCGTCTGTTGCTTCTGATTCAAGCT-TCAAGC
66 ATAAGAAACATTCGTCCGTTGATTCTGATTCAAGCTAT-AAGC
* * *
490509 TTCAAGCTTCAAGCTTGATGGTGATTCCGAAAAGGATCTGGAAACGGTGACAGAAAACAAAGCTG
1 TTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGATCTAGAAACAGTGACAGAAAACAAAGCTG
*
490574 ATAAGAAACATTTGTCCGTTGATTCTGATTCAAGCTATAAGC
66 ATAAGAAACATTCGTCCGTTGATTCTGATTCAAGCTATAAGC
490616 TT
1 TT
490618 GATGTTCATT
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 96 0.99
108 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (107 bp):
TTCAAGCTACAAGCTTGATGGTGATTCCGAAAAGGATCTAGAAACAGTGACAGAAAACAAAGCTG
ATAAGAAACATTCGTCCGTTGATTCTGATTCAAGCTATAAGC
Found at i:490700 original size:94 final size:94
Alignment explanation
Indices: 490509--490788 Score: 253
Period size: 94 Copynumber: 3.1 Consensus size: 94
490499 AGCTTCAAGC
* ** *
490509 TTCAAGCT-TCAAGCTTGATGGTGATTCCGAAAAGGATCTGGAAACGGTGACAGAAAACAAAGCT
1 TTCAAGCTATCAAGCTTGATGGTCATTCCGAAAAGGATCCAGAAACAGTGACAGAAAACAAAGCT
490573 GATAAGAAACATTTGTCCGTTGATTCTGA
66 GATAAGAAACATTTGTCCGTTGATTCTGA
* * * **
490602 TTCAAGCTAT-AAGCTTGATGTTCATTCCGAAAAGGGTCCAGAACCAGTGGGAGAAAAACAAAGC
1 TTCAAGCTATCAAGCTTGATGGTCATTCCGAAAAGGATCCAGAAACAGTGACAG-AAAACAAAGC
* * * *
490666 TGATATGGAACATTTGTCTGTTGCTTCTGA
65 TGATAAGAAACATTTGTCCGTTGATTCTGA
* * ** *
490696 TTCAAGCTA-CAAG---GAT--TC--T--GAAAAGGTTCC-GGAACAGGTGGGAGAAAACAAGGC
1 TTCAAGCTATCAAGCTTGATGGTCATTCCGAAAAGGATCCAGAAACA-GTGACAGAAAACAAAGC
* * * *
490750 TTATAAGAAATATTTGTCCGGTGCTTCTGA
65 TGATAAGAAACATTTGTCCGTTGATTCTGA
490780 TTCAAGCTA
1 TTCAAGCTA
490789 GAAGCCTAAC
Statistics
Matches: 160, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
84 46 0.29
85 17 0.11
87 1 0.01
89 2 0.01
91 3 0.02
93 42 0.26
94 49 0.31
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (94 bp):
TTCAAGCTATCAAGCTTGATGGTCATTCCGAAAAGGATCCAGAAACAGTGACAGAAAACAAAGCT
GATAAGAAACATTTGTCCGTTGATTCTGA
Found at i:490775 original size:84 final size:85
Alignment explanation
Indices: 490625--490788 Score: 215
Period size: 84 Copynumber: 1.9 Consensus size: 85
490615 CTTGATGTTC
* * * *
490625 ATTCCGAAAAGGGTCCAGAACCAGTGGGAGAAAAACAAAGCTGATATGGAACATTTGTCTGTTGC
1 ATTCCGAAAAGGGTCCAGAACCAGTGGGAGAAAAACAAAGCTGATAAGAAACATTTGTCCGGTGC
490690 TTCTGATTCAAGCTACAAGG
66 TTCTGATTCAAGCTACAAGG
* * * * * *
490710 ATTCTGAAAAGGTTCCGGAA-CAGGTGGGAG-AAAACAAGGCTTATAAGAAATATTTGTCCGGTG
1 ATTCCGAAAAGGGTCCAGAACCA-GTGGGAGAAAAACAAAGCTGATAAGAAACATTTGTCCGGTG
490773 CTTCTGATTCAAGCTA
65 CTTCTGATTCAAGCTA
490789 GAAGCCTAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 44 0.65
85 24 0.35
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (85 bp):
ATTCCGAAAAGGGTCCAGAACCAGTGGGAGAAAAACAAAGCTGATAAGAAACATTTGTCCGGTGC
TTCTGATTCAAGCTACAAGG
Found at i:490897 original size:66 final size:66
Alignment explanation
Indices: 490774--490901 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
490764 TGTCCGGTGC
* *
490774 TTCTGATTCAAGCTAGAAGCCTAACGGTGATACCGAAAAGAGTCCGAAACCGATGGGAGAAATTC
1 TTCTGATTCAAGCTACAAGCCTAACAGTGATACCGAAAAGAGTCCGAAACCGATGGGAGAAATTC
490839 A
66 A
* * * * * * *
490840 TTCTGATTCAAGCTACAAGCTTGACATTGATTCCGAACAGGGTCCAGAAA-CGGTGGGAGAAA
1 TTCTGATTCAAGCTACAAGCCTAACAGTGATACCGAAAAGAGTCC-GAAACCGATGGGAGAAA
490902 ACAAAGCTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 48 0.92
67 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (66 bp):
TTCTGATTCAAGCTACAAGCCTAACAGTGATACCGAAAAGAGTCCGAAACCGATGGGAGAAATTC
A
Found at i:490944 original size:93 final size:93
Alignment explanation
Indices: 490840--491021 Score: 269
Period size: 93 Copynumber: 2.0 Consensus size: 93
490830 GAGAAATTCA
*
490840 TTCTGATTCAAGCTACAAGCTTGACATTGATTC-CGAACAGGGTCCAGAAACGGTGGGAGAAAAC
1 TTCTGATTCAAGCCACAAGCTTGACATTGATTCACGAA-AGGGTCCAGAAACGGTGGGAGAAAAC
*
490904 AAAGCTGATAAGAAA-CATTTGTCCGTTGC
65 AAAGATGATAAGAAATC-TTTGTCCGTTGC
** * * *
490933 TTCTGATTCAAGCCACAAGCTTGATGTTGATTCAGGAAAGGGTCCGGAACCGGTGGGAGAAAACA
1 TTCTGATTCAAGCCACAAGCTTGACATTGATTCACGAAAGGGTCCAGAAACGGTGGGAGAAAACA
490998 AAGATGATAAGAAATCTTTGTCCG
66 AAGATGATAAGAAATCTTTGTCCG
491022 AGACAGCAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 76 0.95
94 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (93 bp):
TTCTGATTCAAGCCACAAGCTTGACATTGATTCACGAAAGGGTCCAGAAACGGTGGGAGAAAACA
AAGATGATAAGAAATCTTTGTCCGTTGC
Found at i:494653 original size:16 final size:16
Alignment explanation
Indices: 494632--494663 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
494622 AAAAAATTAA
494632 GAGCTCGATTAAAGCT
1 GAGCTCGATTAAAGCT
*
494648 GAGCTCGATTGAAGCT
1 GAGCTCGATTAAAGCT
494664 CGATTAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (16 bp):
GAGCTCGATTAAAGCT
Found at i:494663 original size:11 final size:11
Alignment explanation
Indices: 494649--494748 Score: 89
Period size: 11 Copynumber: 8.8 Consensus size: 11
494639 ATTAAAGCTG
494649 AGCTCGATTGA
1 AGCTCGATTGA
*
494660 AGCTCGATTAA
1 AGCTCGATTGA
494671 AGCTCGATTCTG-
1 AGCTCGA-T-TGA
494683 AGCTCGATTGA
1 AGCTCGATTGA
494694 AGCTCGATTCTG-
1 AGCTCGA-T-TGA
*
494706 AGCTCGATTCA
1 AGCTCGATTGA
494717 AGCTCGATTCTG-
1 AGCTCGA-T-TGA
* *
494729 AGCTCGTTTCA
1 AGCTCGATTGA
494740 AGCTCGATT
1 AGCTCGATT
494749 CTGAGCTCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
10 4 0.05
11 42 0.58
12 23 0.32
13 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:494690 original size:23 final size:23
Alignment explanation
Indices: 494660--494758 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
494650 GCTCGATTGA
*
494660 AGCTCGATTAAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
*
494683 AGCTCGATTGAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
494706 AGCTCGATTCAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
*
494729 AGCTCGTTTCAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
494752 AGCTCGA
1 AGCTCGA
494759 CATTGCTCCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTCTG
Found at i:496664 original size:7 final size:7
Alignment explanation
Indices: 496654--496734 Score: 63
Period size: 7 Copynumber: 11.6 Consensus size: 7
496644 CAATTTGAGA
496654 GTTTAGG
1 GTTTAGG
*
496661 GTTTATG
1 GTTTAGG
*
496668 GTTTAAG
1 GTTTAGG
**
496675 GTTTATA
1 GTTTAGG
*
496682 GTTTATG
1 GTTTAGG
*
496689 CTTTAGG
1 GTTTAGG
**
496696 GTTTATA
1 GTTTAGG
*
496703 GTTGAGG
1 GTTTAGG
*
496710 GTTTATG
1 GTTTAGG
*
496717 GATTAGG
1 GTTTAGG
496724 GTTTAGG
1 GTTTAGG
496731 GTTT
1 GTTT
496735 TATTTTTCTT
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:496685 original size:21 final size:21
Alignment explanation
Indices: 496661--496714 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
496651 AGAGTTTAGG
496661 GTTTATGGTTTAAGGTTTATA
1 GTTTATGGTTTAAGGTTTATA
* *
496682 GTTTATGCTTTAGGGTTTATA
1 GTTTATGGTTTAAGGTTTATA
* *
496703 GTTGAGGGTTTA
1 GTTTATGGTTTA
496715 TGGATTAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (21 bp):
GTTTATGGTTTAAGGTTTATA
Found at i:496839 original size:11 final size:11
Alignment explanation
Indices: 496823--496885 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
496813 GTATTATAGA
496823 ATTTTTAATAT
1 ATTTTTAATAT
496834 ATTTTTAA-A-
1 ATTTTTAATAT
496843 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
496854 ATAAATAGTGT
1 ATTTTTAATAT
496865 ATTTTTAATAT
1 ATTTTTAATAT
496876 ATTTTTAATA
1 ATTTTTAATA
496886 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:497647 original size:31 final size:31
Alignment explanation
Indices: 497611--497672 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
497601 GTCATAAGAA
497611 ATTTAAGAGGATAAAAATATGTATATATATT
1 ATTTAAGAGGATAAAAATATGTATATATATT
497642 ATTTAAGAGGATAAAAATATGTATATATATT
1 ATTTAAGAGGATAAAAATATGTATATATATT
497673 GTTCTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (31 bp):
ATTTAAGAGGATAAAAATATGTATATATATT
Found at i:499859 original size:2 final size:2
Alignment explanation
Indices: 499852--499886 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
499842 CCTTTGAATG
499852 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
499887 GTGAAGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:500075 original size:24 final size:24
Alignment explanation
Indices: 500047--500103 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
500037 TCTTATTTAT
500047 GTTTGAATTTATCTTTCAAGCTTA
1 GTTTGAATTTATCTTTCAAGCTTA
*
500071 GTTTGAATTTATCTTTCAGGCTTA
1 GTTTGAATTTATCTTTCAAGCTTA
* *
500095 ATTTAAATT
1 GTTTGAATT
500104 AATATTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (24 bp):
GTTTGAATTTATCTTTCAAGCTTA
Found at i:506468 original size:39 final size:39
Alignment explanation
Indices: 506414--506494 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
506404 TAATAAAAAA
506414 AATTAAAAATATAATACAAATATAACACCAATTATACCG
1 AATTAAAAATATAATACAAATATAACACCAATTATACCG
506453 AATTAAAAATATAATACAAATATAACACCAATTATACCG
1 AATTAAAAATATAATACAAATATAACACCAATTATACCG
506492 AAT
1 AAT
506495 CAAATAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (39 bp):
AATTAAAAATATAATACAAATATAACACCAATTATACCG
Found at i:509796 original size:26 final size:28
Alignment explanation
Indices: 509767--509832 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
509757 TAAAATTTTA
509767 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCAGCAGAGTTTTCGAGTCGAGTCG
*
509793 AGCTCAATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCTC-A--GCAGAGTTTTCGAGTCGAGTCG
*
509824 AGTTCAGCA
1 AGCTCAGCA
509833 ATACTCGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
26 5 0.16
28 2 0.06
30 2 0.06
31 23 0.72
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCAGCAGAGTTTTCGAGTCGAGTCG
Found at i:510271 original size:21 final size:21
Alignment explanation
Indices: 510245--510284 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
510235 AGCATTTATT
* *
510245 TTTTTATTTTTTAAAATAATA
1 TTTTTATTATTAAAAATAATA
510266 TTTTTATTATTAAAAATAA
1 TTTTTATTATTAAAAATAA
510285 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTATTATTAAAAATAATA
Found at i:513874 original size:2 final size:2
Alignment explanation
Indices: 513867--513899 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
513857 GTGAGACATA
513867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
513900 ACAATGCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:514175 original size:18 final size:18
Alignment explanation
Indices: 514152--514222 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
514142 TGAATATTTT
514152 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
514170 TCCCGAGGGACCATTGATTG
1 TCCCGAAGGACCACT-A-TG
* *
514190 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
514208 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
514223 GATAATCCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 28 0.65
19 2 0.05
20 13 0.30
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:514883 original size:45 final size:46
Alignment explanation
Indices: 514816--514919 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 46
514806 GCACAATCTA
* * **
514816 TGCATCGGTACA-TAAATCACATTCAATGTTTGTATTTTAAGGGGG
1 TGCATCGATACACTAAATCACATTCAATGTTTGTATTTTAAAGAAG
* * *
514861 TGCATCGATACACT-AATGACATTCGATGTTTTTATTTTAAAGAAG
1 TGCATCGATACACTAAATCACATTCAATGTTTGTATTTTAAAGAAG
*
514906 TGCATCGATGCACT
1 TGCATCGATACACT
514920 TCATGTGCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (46 bp):
TGCATCGATACACTAAATCACATTCAATGTTTGTATTTTAAAGAAG
Found at i:515902 original size:13 final size:13
Alignment explanation
Indices: 515884--515908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515874 AAGGATTTAG
515884 AAATAATAATAAT
1 AAATAATAATAAT
515897 AAATAATAATAA
1 AAATAATAATAA
515909 AATGATGAGA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:522408 original size:81 final size:81
Alignment explanation
Indices: 522348--522671 Score: 479
Period size: 81 Copynumber: 4.0 Consensus size: 81
522338 CAGCTAATCC
* * * *
522348 ATTATTCTTTTACTCAACAGTGTTTAACCGTTCACCTAATTGGCATAATTGACACCTTTCTGCCA
1 ATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
* *
522413 ATTGCATATTTAGGCT
66 ATTGCACAGTTAGGCT
* *
522429 ATTATTCTTTTACTTAA-AGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCC
1 ATTATTCTTTTACTCAACA-GTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCC
522493 AATTGCACAGTTAGGCT
65 AATTGCACAGTTAGGCT
* * *
522510 ATTATTCTTTTCCTCAACAGTATTTAAGCGTTCATCTAACTGGCATAATTGACACATTTCTTCCA
1 ATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
* *
522575 ATTTCACAATTAGGCT
66 ATTGCACAGTTAGGCT
* *
522591 ATTATTCTTATTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTTCC
1 ATTATTCTT-TTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCC
*
522656 AATTGCATAGTTAGGC
65 AATTGCACAGTTAGGC
522672 CTCAAAGGCA
Statistics
Matches: 221, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.00
81 154 0.70
82 66 0.30
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (81 bp):
ATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
ATTGCACAGTTAGGCT
Found at i:522713 original size:68 final size:68
Alignment explanation
Indices: 522622--522945 Score: 470
Period size: 68 Copynumber: 4.8 Consensus size: 68
522612 TATTTAACCG
* * *
522622 TTCATCTAACTGGCATAATTGACACATTTCT-TCCAATTGCATAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTGT-CAAATGCACAGTTAGGCCTCAAAGGCACTTA
522686 GCCT
65 GCCT
* * * * ** *
522690 TTTATCTAGCTGACATAAATGACACCTTTCTGTCAAATATACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
522755 CCT
66 CCT
* * * *
522758 TTCATCTAACTGACATAAATGACACATTTCTTTTAAATGCACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
522823 CCT
66 CCT
* * *
522826 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATACACAGTTAGACCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
522891 CCT
66 CCT
*
522894 TTCATGTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCT
522946 ATTAATCTTT
Statistics
Matches: 226, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 225 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:523282 original size:59 final size:58
Alignment explanation
Indices: 523161--523376 Score: 293
Period size: 59 Copynumber: 3.8 Consensus size: 58
523151 TTTCCCATAA
* * *
523161 GGAAATTCATACAATT-GATATGAATTTCTT---A-TTTCGCACACATAGTGCTC-ATAC
1 GGAAATTCATACACTTAG-TATGAATTTCTTAACATTTTAGCACACAAAGTGC-CAATAC
523215 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCAAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCC-AATAC
* *
523274 GGAAATTCATACACTTAGTATGAATTTCTTAACCTTTTAGCACACAAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTG-CCAATAC
*
523333 GAAAATTCATACACTTAGTATGAATTTCTTAACATTTT-GCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
523377 TTAGTGACAT
Statistics
Matches: 147, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
54 27 0.18
55 1 0.01
57 2 0.01
58 21 0.14
59 94 0.64
60 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCAATAC
Found at i:523924 original size:32 final size:32
Alignment explanation
Indices: 523859--523928 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
523849 TGCTCCATGG
**
523859 GATTACCCGGCGTCTTTAGTTTTTTCTCCTAT
1 GATTACCCGGCGTCTTTAGTTAATTCTCCTAT
*
523891 GATTACCCGGCGTCTTTAGTTAAATTCT-TTAT
1 GATTACCCGGCGTCTTTAGTT-AATTCTCCTAT
523923 GATTAC
1 GATTAC
523929 TGTGCATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (32 bp):
GATTACCCGGCGTCTTTAGTTAATTCTCCTAT
Found at i:528812 original size:21 final size:22
Alignment explanation
Indices: 528783--528824 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
528773 TGTTTAAACC
* *
528783 TTTTTTTAAAT-AAAATTAGAA
1 TTTTATTAAATGAAAAATAGAA
528804 TTTTATTAAATGAAAAATAGA
1 TTTTATTAAATGAAAAATAGA
528825 GCATAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTTATTAAATGAAAAATAGAA
Found at i:530097 original size:23 final size:24
Alignment explanation
Indices: 530069--530119 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
530059 AGATTGATTA
*
530069 TAAAATTATG-GATT-ATAATATTT
1 TAAAATTATGCAATTAATAA-ATTT
530092 TAAAATTATGCAATTAATAAATTT
1 TAAAATTATGCAATTAATAAATTT
530116 TAAA
1 TAAA
530120 GTGTAAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 10 0.40
24 11 0.44
25 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
TAAAATTATGCAATTAATAAATTT
Found at i:532616 original size:13 final size:13
Alignment explanation
Indices: 532598--532627 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
532588 GATAATTAAA
532598 AAAATATTTTTAC
1 AAAATATTTTTAC
*
532611 AAAATATTTTTAG
1 AAAATATTTTTAC
532624 AAAA
1 AAAA
532628 GATATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (13 bp):
AAAATATTTTTAC
Found at i:538327 original size:170 final size:168
Alignment explanation
Indices: 538029--538402 Score: 444
Period size: 170 Copynumber: 2.2 Consensus size: 168
538019 TTAAAATCTT
* * * * **
538029 TGTCATGTCATAGTGTATCATCCCATCAAACATAAATGGGGTTGATGTGAACAGTTTTCGATTGG
1 TGTCATGTCATAGTGTCTCAT-CCATCAAACATAAATGAGGTTGATGTGAACAGTTCTCGACTAA
* * * * *
538094 GAACATCAAATATGCATATAATTGACTGAAATATAAAGATAAAATTTGACAAATAGGGAAGGCTC
65 GAACATCAAATATACAAATAATTGACTGAAATATAAAGATAAAATCTAACAAAAAGGGAAGGCTC
* * *
538159 GTTCCACAAGAAGCACTTT-TCACTTTTTTAGAGAATATC
130 ATTCCACAAGAAG-ACTTTGCCACCTTTTTAGAGAATATC
* *
538198 TGTCATATCATAGTGTCTCATCTCATCAAACATAAATGAGGTTGATGTGAATAGTTCCTCGACTA
1 TGTCATGTCATAGTGTCTCATC-CATCAAACATAAATGAGGTTGATGTGAACAGTT-CTCGACTA
* * * * * **
538263 AGAACATCATATCTACAAATAATTGTCTGAAATATGAAGATAAAATCTAATAAAAATTGAAGGCT
64 AGAACATCAAATATACAAATAATTGACTGAAATATAAAGATAAAATCTAACAAAAAGGGAAGGCT
** * *
538328 CATTCCACAAGAAGTGTTTGCCCCCTTTTTAGAGAATCTC
129 CATTCCACAAGAAGACTTTGCCACCTTTTTAGAGAATATC
*
538368 TTTCATGTCATAGTGTCTCATACCATCAAACATAA
1 TGTCATGTCATAGTGTCTCAT-CCATCAAACATAA
538403 TTAAATAGGG
Statistics
Matches: 172, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
168 1 0.01
169 53 0.31
170 117 0.68
171 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (168 bp):
TGTCATGTCATAGTGTCTCATCCATCAAACATAAATGAGGTTGATGTGAACAGTTCTCGACTAAG
AACATCAAATATACAAATAATTGACTGAAATATAAAGATAAAATCTAACAAAAAGGGAAGGCTCA
TTCCACAAGAAGACTTTGCCACCTTTTTAGAGAATATC
Found at i:545996 original size:21 final size:21
Alignment explanation
Indices: 545970--546009 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
545960 CCCCCTTTGA
*
545970 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
545991 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
546010 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:549591 original size:21 final size:22
Alignment explanation
Indices: 549562--549611 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
549552 ATATTTTAAT
549562 TTTAATCT-AACCCTAAACCAC
1 TTTAATCTAAACCCTAAACCAC
* *
549583 TTTACTCTAAAAACCCTAAACCAT
1 TTTAATCT--AAACCCTAAACCAC
549607 TTTAA
1 TTTAA
549612 CATAAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
24 16 0.70
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAATCTAAACCCTAAACCAC
Found at i:549617 original size:24 final size:25
Alignment explanation
Indices: 549571--549660 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 25
549561 TTTTAATCTA
549571 ACCCTAAACCACTTT-ACTCTAAAA-
1 ACCCTAAACCACTTTAAC-CTAAAAC
* *
549595 ACCCTAAACCATTTTAACATAAAAATC
1 ACCCTAAACCACTTTAACCT-AAAA-C
549622 GTAGCCCTAAACCACTTTAACCTAAAAC
1 --A-CCCTAAACCACTTTAACCTAAAAC
549650 ACCCTAAACCA
1 ACCCTAAACCA
549661 TTCAGCCTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 15 0.27
25 16 0.29
26 1 0.02
28 1 0.02
29 5 0.09
30 17 0.31
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.22
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTAAAAC
Found at i:551591 original size:17 final size:17
Alignment explanation
Indices: 551571--551611 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
551561 AGTTTTGAAA
551571 TTGACCATGCTTTGAGC
1 TTGACCATGCTTTGAGC
551588 TTGACCATGCTTTGAGC
1 TTGACCATGCTTTGAGC
551605 TTGACCA
1 TTGACCA
551612 AATAGGCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (17 bp):
TTGACCATGCTTTGAGC
Found at i:555236 original size:2 final size:2
Alignment explanation
Indices: 555187--555220 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
555177 ATGTAAAATG
555187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555221 GACTCTGAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559199 original size:24 final size:24
Alignment explanation
Indices: 559167--559226 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
559157 TTATAAGGAT
559167 CGTGTCATAAGAGTAAAGAAAACA
1 CGTGTCATAAGAGTAAAGAAAACA
559191 CGTGTCATAAGAGTAAAGAAAACA
1 CGTGTCATAAGAGTAAAGAAAACA
*
559215 CGTGTCACAAGA
1 CGTGTCATAAGA
559227 ACAAAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.17
Consensus pattern (24 bp):
CGTGTCATAAGAGTAAAGAAAACA
Found at i:559379 original size:6 final size:6
Alignment explanation
Indices: 559368--559393 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
559358 AAATTTAAAA
559368 ACAAAG ACAAAG ACAAAG ACAAAG AC
1 ACAAAG ACAAAG ACAAAG ACAAAG AC
559394 GACAGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.00
Consensus pattern (6 bp):
ACAAAG
Found at i:566559 original size:17 final size:19
Alignment explanation
Indices: 566520--566559 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
566510 TAAGATTACA
*
566520 TAAAACAAAACACCACCAG
1 TAAAACAAAACACCACAAG
566539 -AAAA-AAAACACCA-AAG
1 TAAAACAAAACACCACAAG
566555 TAAAA
1 TAAAA
566560 GACTACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 13 0.68
18 4 0.21
ACGTcount: A:0.68, C:0.23, G:0.05, T:0.05
Consensus pattern (19 bp):
TAAAACAAAACACCACAAG
Found at i:583710 original size:14 final size:14
Alignment explanation
Indices: 583669--583720 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
583659 TTCAAAACAT
583669 TATTATTTTT-ATA
1 TATTATTTTTAATA
* *
583682 TATTTAATATTAATA
1 TA-TTATTTTTAATA
583697 TATTATTTTTAATA
1 TATTATTTTTAATA
583711 TCATT-TTTTT
1 T-ATTATTTTT
583721 TTTATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 22 0.69
15 8 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTTTTAATA
Found at i:583932 original size:41 final size:41
Alignment explanation
Indices: 583827--583935 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 41
583817 TATTCCTTAA
**
583827 AATATAA--TATAATTTTTTATATTATTATTTTAATAAGTAATT
1 AATATAATTTATAA-TTTTT-TATT-TTATTTTAATAAACAATT
* * * *
583869 AATATAATTAATAATATATTATTTTATTTTAATAAACATTT
1 AATATAATTTATAATTTTTTATTTTATTTTAATAAACAATT
583910 AATAT-ATTTATAATGTTTTTATTTTA
1 AATATAATTTATAAT-TTTTTATTTTA
583936 ATAAAATATA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
40 8 0.15
41 29 0.53
42 11 0.20
43 3 0.05
44 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (41 bp):
AATATAATTTATAATTTTTTATTTTATTTTAATAAACAATT
Found at i:587985 original size:2 final size:2
Alignment explanation
Indices: 587978--588006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
587968 GCTGTAAAGA
587978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
588007 AAGATTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:588268 original size:10 final size:9
Alignment explanation
Indices: 588252--588278 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
588242 TTTTTAGTAA
588252 TAAAAAAAT
1 TAAAAAAAT
588261 TAAAAAAAT
1 TAAAAAAAT
588270 TAAAAAAAT
1 TAAAAAAAT
588279 CAAATCCTCT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:592616 original size:66 final size:63
Alignment explanation
Indices: 592496--592625 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 63
592486 CACTTGAAAG
592496 TGGCTTTCGACGATGGTTATGAACTATGGGTCTGGGATTAGGTGTTAGGAAGAACATGTTGAA
1 TGGCTTTCGACGATGGTTATGAACTATGGGTCTGGGATTAGGTGTTAGGAAGAACATGTTGAA
592559 TGGCTTTCGACGATGGTTATGAAACTATGGGTCAGTGGGATTAGGTGTTAGGAAGAACATGTTGA
1 TGGCTTTCGACGATGGTTATG-AACTATGGGTC--TGGGATTAGGTGTTAGGAAGAACATGTTGA
592624 A
63 A
592625 T
1 T
592626 TTTCTGAGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
63 21 0.33
64 11 0.17
66 32 0.50
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.32
Consensus pattern (63 bp):
TGGCTTTCGACGATGGTTATGAACTATGGGTCTGGGATTAGGTGTTAGGAAGAACATGTTGAA
Found at i:592739 original size:13 final size:13
Alignment explanation
Indices: 592723--592747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
592713 TATATTATGT
592723 TATAATATATATA
1 TATAATATATATA
592736 TATAATATATAT
1 TATAATATATAT
592748 TGCATAGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATATATATA
Found at i:593008 original size:20 final size:21
Alignment explanation
Indices: 592983--593021 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
592973 TTATTTTAGA
592983 AATTTAAATTTAG-ATAAATG
1 AATTTAAATTTAGAATAAATG
*
593003 AATTTAGATTTAGAATAAA
1 AATTTAAATTTAGAATAAA
593022 ATTTTAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTTAAATTTAGAATAAATG
Found at i:596792 original size:14 final size:14
Alignment explanation
Indices: 596773--596800 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
596763 GCATTGAATA
596773 CTCTCTCTCTCTAT
1 CTCTCTCTCTCTAT
596787 CTCTCTCTCTCTAT
1 CTCTCTCTCTCTAT
596801 ATATATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (14 bp):
CTCTCTCTCTCTAT
Found at i:600561 original size:16 final size:17
Alignment explanation
Indices: 600525--600561 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
600515 TGTTCATATT
600525 TAAAACAATAATATTAA
1 TAAAACAATAATATTAA
*
600542 -AAAACCAT-ATATTAA
1 TAAAACAATAATATTAA
600557 TAAAA
1 TAAAA
600562 TTATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAACAATAATATTAA
Found at i:609195 original size:36 final size:36
Alignment explanation
Indices: 609155--609255 Score: 184
Period size: 36 Copynumber: 2.8 Consensus size: 36
609145 GGTGCTGGAT
609155 ATTGATACACGAATGTACCAAAGCTGATATGATAAC
1 ATTGATACACGAATGTACCAAAGCTGATATGATAAC
*
609191 ATTGATACACGAATGTACCAAAGCTGATATGATAAT
1 ATTGATACACGAATGTACCAAAGCTGATATGATAAC
*
609227 ATTGATACACGAATGTATCAAAGCTGATA
1 ATTGATACACGAATGTACCAAAGCTGATA
609256 ATACTCAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (36 bp):
ATTGATACACGAATGTACCAAAGCTGATATGATAAC
Found at i:617753 original size:36 final size:36
Alignment explanation
Indices: 617713--617805 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
617703 TGCTGGGCAG
* *
617713 TGATACACGAATGTACCAATGTTGATATGATAACAT
1 TGATACACGAATGTACCAAAGATGATATGATAACAT
617749 TGATACACGAATGTACCAAAGATGATATGATAACAT
1 TGATACACGAATGTACCAAAGATGATATGATAACAT
* * * *
617785 TAATACATGAATATATCAAAG
1 TGATACACGAATGTACCAAAG
617806 CTTATAATAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
TGATACACGAATGTACCAAAGATGATATGATAACAT
Found at i:622093 original size:36 final size:36
Alignment explanation
Indices: 622048--622186 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
622038 ACGATGCTGG
*
622048 ACATTGATACACAAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
622084 ACATCGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
622120 ACATTGATACACGAATGTACCAAAGATGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
622156 ACATTGATACACGAATGTATCAAAGGTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
622187 ATACTCAACT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:625586 original size:19 final size:19
Alignment explanation
Indices: 625562--625598 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
625552 CCAAAATACA
*
625562 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
625581 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
625599 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:626051 original size:12 final size:11
Alignment explanation
Indices: 626034--626058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
626024 CGAGGGTTAG
626034 TTTTTTTTTAA
1 TTTTTTTTTAA
626045 TTTTTTTTTAA
1 TTTTTTTTTAA
626056 TTT
1 TTT
626059 GAAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:626443 original size:20 final size:20
Alignment explanation
Indices: 626330--626466 Score: 83
Period size: 20 Copynumber: 7.2 Consensus size: 20
626320 AAAATCGCAA
**
626330 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
626350 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
** *
626370 CGATTTTCA-TTTCACGTTG
1 CGATAGTCATTTTCGCGTTG
*
626389 CGAT--T-A---TCTCGTTG
1 CGATAGTCATTTTCGCGTTG
* *
626403 CGATAGTCAAATTT-GCATTG
1 CGATAGTC-ATTTTCGCGTTG
*
626423 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
* ** *
626443 CGCTTTTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
626463 CGAT
1 CGAT
626467 TTTAAGTTTC
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
14 11 0.12
16 2 0.02
17 1 0.01
18 1 0.01
19 16 0.17
20 60 0.65
21 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:626476 original size:20 final size:20
Alignment explanation
Indices: 626433--626476 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
626423 CGATAGTCAT
* * *
626433 TTTCGTGTTGCGCTTTTCAT
1 TTTCGTGTTGCGATTTTAAG
626453 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
626473 TTTC
1 TTTC
626477 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:628399 original size:20 final size:20
Alignment explanation
Indices: 628374--628442 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
628364 AAACTTAAAA
*
628374 ATCGCAATGCGAATATGACT
1 ATCGCAACGCGAATATGACT
628394 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
* *
628414 ATCGCAACACGAATTTGACT
1 ATCGCAACGCGAATATGACT
628434 ATCGCAACG
1 ATCGCAACG
628443 GGATAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:628541 original size:14 final size:14
Alignment explanation
Indices: 628519--628549 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
628509 GCAAATTTAG
628519 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
628533 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
628547 TTT
1 TTT
628550 TATTTCGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.23, T:0.52
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:628563 original size:33 final size:34
Alignment explanation
Indices: 628514--628579 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
628504 GCAACGCAAA
* * *
628514 TTTAGTTTCGCGTTGCGATTTTCTCGTTGCGATT
1 TTTAGTTTCGCATTGCGATTATCCCGTTGCGATT
628548 TTTA-TTTCGCATTGCGATTATCCCGTTGCGAT
1 TTTAGTTTCGCATTGCGATTATCCCGTTGCGAT
628580 AGTCAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTAGTTTCGCATTGCGATTATCCCGTTGCGATT
Found at i:628639 original size:20 final size:20
Alignment explanation
Indices: 628571--628630 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
628561 GCGATTATCC
**
628571 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
628591 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
628611 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
628631 TGTTACGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:628650 original size:19 final size:20
Alignment explanation
Indices: 628626--628668 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
628616 CGATAGTCAT
628626 TTTCGTGTTACGA-TTTAAG
1 TTTCGTGTTACGATTTTAAG
*
628645 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
628665 TTTC
1 TTTC
628669 AAAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:629231 original size:21 final size:21
Alignment explanation
Indices: 629207--629276 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
629197 CTATAATCCC
629207 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* ** *
629228 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
629249 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
629270 TCAAGAG
1 TCAAGAG
629277 CCCGATTCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:629231 original size:42 final size:42
Alignment explanation
Indices: 629165--629276 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
629155 TTGTCATCAT
* *
629165 TCAAGAGG-CCTCTCCTATCATTCAAGAGGCCCCTATAATCCC
1 TCAAGAGGTCC-CTCCCACCATTCAAGAGGCCCCTATAATCCC
* * * **
629207 TCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGT-CCCTCCCACCATTCAAGAGGCCCCTATAATCCC
*
629249 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCATTCAAGAG
629277 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.91
43 4 0.07
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTATAATCCC
Found at i:630682 original size:27 final size:27
Alignment explanation
Indices: 630652--630763 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
630642 GCATTTTTTG
*
630652 TTTGTTTAATTGATTTGTAAATGTTGA
1 TTTGTTTAATTGATGTGTAAATGTTGA
* *
630679 TTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTGTTTAATTGATGTGTAAAT--GT-TGA
* *
630709 TTTGTACTTACTTAATTGATTTGTAAAAGTTGA
1 TTTG----T--TTAATTGATGTGTAAATGTTGA
630742 TTTGTTTAATTGATGTGTAAAT
1 TTTGTTTAATTGATGTGTAAAT
630764 AATTCTTATT
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
27 36 0.54
29 2 0.03
30 6 0.09
33 6 0.09
34 2 0.03
36 15 0.22
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (27 bp):
TTTGTTTAATTGATGTGTAAATGTTGA
Found at i:630730 original size:63 final size:63
Alignment explanation
Indices: 630657--630799 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
630647 TTTTGTTTGT
630657 TTAATTGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTACTTAC
1 TTAATTGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTACTTAC
* * *
630720 TTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTAT
1 TTAATTGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTACTTAC
630783 TTAATTGA-TTG-AAATGT
1 TTAATTGATTTGTAAATGT
630800 AAAAGTTGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
61 5 0.07
62 3 0.04
63 68 0.89
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.52
Consensus pattern (63 bp):
TTAATTGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTACTTAC
Found at i:630734 original size:36 final size:34
Alignment explanation
Indices: 630684--630791 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 34
630674 GTTGATTTGT
630684 TTAATTGATGTGTAAATAATTCTTATTTGTACTTA
1 TTAATTGATGTGTAAATAATTCTTATTTGT-CTTA
* * *
630719 CTTAATTGATTTGT-AA-AAGT-TGATTTG---T-
1 -TTAATTGATGTGTAAATAATTCTTATTTGTCTTA
630747 TTAATTGATGTGTAAATAATTCTTATTTGTGCTTA
1 TTAATTGATGTGTAAATAATTCTTATTTGT-CTTA
630782 TTTAATTGAT
1 -TTAATTGAT
630792 TGAAATGTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
27 12 0.21
28 2 0.04
29 4 0.07
30 6 0.11
33 6 0.11
34 4 0.07
35 2 0.04
36 21 0.37
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (34 bp):
TTAATTGATGTGTAAATAATTCTTATTTGTCTTA
Found at i:630891 original size:20 final size:20
Alignment explanation
Indices: 630866--630938 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
630856 AGGTACACTT
*
630866 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
630886 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
630906 TTGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
630926 TCGCAACGCGAAA
1 TCGCAACGCGAAA
630939 ATCGCAACGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:630941 original size:14 final size:14
Alignment explanation
Indices: 630922--630952 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
630912 TGCGAAAGCC
630922 AAAATCGCAACGCG
1 AAAATCGCAACGCG
630936 AAAATCGCAACGCG
1 AAAATCGCAACGCG
630950 AAA
1 AAA
630953 GTCAATTCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGCG
Found at i:631021 original size:20 final size:20
Alignment explanation
Indices: 630947--631192 Score: 272
Period size: 20 Copynumber: 12.7 Consensus size: 20
630937 AAATCGCAAC
*
630947 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
630966 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
630986 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
631000 GCGATAGTCAAATTCCCGTT
1 GCGATAGTCAAATTCGCGTT
* *
631020 GCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
631040 GCGATAGTCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* **
631060 GTGATAGTCAAATTTACGTT
1 GCGATAGTCAAATTCGCGTT
*
631080 GCGATAGTCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
631100 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
631120 GCGATAATCATATTCGCGCT
1 GCGATAGTCAAATTCGCGTT
*
631140 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
631160 GCGATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
631180 GCGATATTCAAAT
1 GCGATAGTCAAAT
631193 GAATGTGTAA
Statistics
Matches: 193, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
14 10 0.05
16 1 0.01
18 1 0.01
19 8 0.04
20 173 0.90
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:631420 original size:140 final size:140
Alignment explanation
Indices: 631163--631445 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
631153 TCGCGTTGCG
* *
631163 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGGCAAATTCACGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
*
631228 TAGCAATGTTCAGACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
631293 AATACACATA
131 AATACACATA
*
631303 ATAGGCAAATTCGCGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
1 ATAGGCAAATTCACGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
631368 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
631433 AATACACATA
131 AATACACATA
631443 ATA
1 ATA
631446 CAACGTTTGC
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGGCAAATTCACGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:634713 original size:21 final size:21
Alignment explanation
Indices: 634687--634742 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
634677 GACAGTCAGA
634687 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
634708 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
634729 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
634743 TACATATTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:634781 original size:21 final size:21
Alignment explanation
Indices: 634757--634803 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
634747 TATTCGCATT
*
634757 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
634778 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
634799 GCGAT
1 GCGAT
634804 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:634872 original size:19 final size:19
Alignment explanation
Indices: 634848--634884 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
634838 TGCGATACTT
*
634848 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
634867 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
634885 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:638025 original size:37 final size:36
Alignment explanation
Indices: 637928--638282 Score: 200
Period size: 36 Copynumber: 10.0 Consensus size: 36
637918 CATAATTTGC
* * *
637928 AAACAGTTTGAAATTACGTATATAATATATGGTTTTTA
1 AAACATTTTGAAAATA--TATATAATATATAGTTTTTA
* *
637966 AAACACTTTTGAAAACTGTATA-ATATATATA-TTTTTT
1 AAACA-TTTTGAAAA-TATATATA-ATATATAGTTTTTA
638003 AAACATTTTGAAAATATATATAATATATAGTTTTTA
1 AAACATTTTGAAAATATATATAATATATAGTTTTTA
638039 AAACA--TT-----TATATAT--TATATAGTTTTTA
1 AAACATTTTGAAAATATATATAATATATAGTTTTTA
*
638066 AAA-AGTTTTTGAAAATAAATATAATATATAGTTTTATA
1 AAACA--TTTTGAAAATATATATAATATATAGTTTT-TA
* *
638104 AAATATTTTTAAAAAATATATATATATTATATAGTTTTTAAAA
1 AAACA-TTTT-GAAAATATATATA-A-TATATAGTTTTT---A
* *
638147 AAAAACTTTTGAAAA-ACATATAATATATA-TTTTTAA
1 AAACA-TTTTGAAAATATATATAATATATAGTTTTT-A
* *
638183 AAACATTTTTG--AA-A-A-CT-ATATA-A-TTTTGA
1 AAACA-TTTTGAAAATATATATAATATATAGTTTTTA
* * *
638212 AAACATTTTAAAAAAAATATATAATATATA-ATTTTA
1 AAACATTTT-GAAAATATATATAATATATAGTTTTTA
* * *
638248 AAATATTTTTAAAAATATATATTATATATA-TTTTT
1 AAACA-TTTTGAAAATATATATAATATATAGTTTTT
638283 GGAAAATATC
Statistics
Matches: 258, Mismatches: 26, Indels: 68
0.73 0.07 0.19
Matches are distributed among these distances:
26 1 0.00
27 16 0.06
28 4 0.02
29 13 0.05
30 7 0.03
31 7 0.03
32 2 0.01
33 2 0.01
34 6 0.02
35 23 0.09
36 62 0.24
37 26 0.10
38 30 0.12
39 25 0.10
40 4 0.02
41 17 0.07
42 4 0.02
43 9 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
AAACATTTTGAAAATATATATAATATATAGTTTTTA
Found at i:638057 original size:64 final size:64
Alignment explanation
Indices: 637991--638111 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
637981 CTGTATAATA
* * *
637991 TATATATTTTTTAAACA-TTTTGAAAATATATATAATATATAGTTTT-TAAAACATTTATATAT
1 TATATAGTTTTTAAAAAGTTTTGAAAATAAATATAATATATAGTTTTATAAAACATTTATATAT
*
638053 TATATAGTTTTTAAAAAGTTTTTGAAAATAAATATAATATATAGTTTTATAAAATATTT
1 TATATAGTTTTTAAAAAG-TTTTGAAAATAAATATAATATATAGTTTTATAAAACATTT
638112 TTAAAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 15 0.29
64 28 0.54
65 9 0.17
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (64 bp):
TATATAGTTTTTAAAAAGTTTTGAAAATAAATATAATATATAGTTTTATAAAACATTTATATAT
Found at i:638226 original size:29 final size:30
Alignment explanation
Indices: 638168--638236 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
638158 AAAAACATAT
* **
638168 AATATATATTTTTAAAAACATTTT-TGAAA
1 AATATATAATTTTAAAAACATTTTAAAAAA
* *
638197 ACTATATAATTTTGAAAACATTTTAAAAAA
1 AATATATAATTTTAAAAACATTTTAAAAAA
638227 AATATATAAT
1 AATATATAAT
638237 ATATAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (30 bp):
AATATATAATTTTAAAAACATTTTAAAAAA
Found at i:638227 original size:80 final size:81
Alignment explanation
Indices: 638072--638228 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 81
638062 TTTAAAAAGT
* *
638072 TTTTGAAAATAAATATAATATATAGTTTTATAAAATATTTTTAAAAAATATATATATATTATATA
1 TTTTGAAAATAAATATAATATATAGTTTTATAAAACATTTTTAAAAAATATATATATATTATAAA
* *
638137 GTTTTTAAAAAAAAAC
66 ATTTTAAAAAAAAAAC
* * * * *
638153 TTTTGAAAA-ACATATAATATATATTTTTA-AAAACATTTTTGAAAACTATATA-ATTTTGA-AA
1 TTTTGAAAATAAATATAATATATAGTTTTATAAAACATTTTTAAAAAATATATATATATT-ATAA
638214 ACATTTTAAAAAAAA
65 A-ATTTTAAAAAAAA
638229 TATATAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
78 6 0.09
79 32 0.49
80 18 0.28
81 9 0.14
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (81 bp):
TTTTGAAAATAAATATAATATATAGTTTTATAAAACATTTTTAAAAAATATATATATATTATAAA
ATTTTAAAAAAAAAAC
Found at i:638230 original size:144 final size:140
Alignment explanation
Indices: 638003--638282 Score: 345
Period size: 144 Copynumber: 2.0 Consensus size: 140
637993 TATATTTTTT
* * * * *
638003 AAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTATATATTATATAGTTTTTAAA
1 AAACATTTTGAAAATACATATAATATATAGTTTTTAAAACATTTATAAACTATATAATTTTGAAA
* * *
638068 AAGTTTTTGAAAATAA-ATATAATATATAGTTTTATAAAATATTTTTAAAAAATATATATATATT
66 AAG-TTTTAAAAAAAATATATAATATATA-ATTT-TAAAATATTTTT-AAAAATATATAT-TA-T
638132 ATATAGTTTTTAAAAAA
125 ATATA-TTTTTAAAAAA
*
638149 AAAC-TTTTGAAAA-ACATATAATATATA-TTTTTAAAAACATTTTTGAAAACTATATAATTTTG
1 AAACATTTTGAAAATACATATAATATATAGTTTTT-AAAACATTTAT--AAACTATATAATTTTG
638211 AAAACA-TTTTAAAAAAAATATATAATATATAATTTTAAAATATTTTTAAAAATATATATTATAT
63 AAAA-AGTTTTAAAAAAAATATATAATATATAATTTTAAAATATTTTTAAAAATATATATTATAT
638275 ATATTTTT
127 ATATTTTT
638283 GGAAAATATC
Statistics
Matches: 120, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
140 5 0.04
141 6 0.05
142 2 0.02
143 17 0.14
144 35 0.29
145 22 0.18
146 32 0.27
147 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (140 bp):
AAACATTTTGAAAATACATATAATATATAGTTTTTAAAACATTTATAAACTATATAATTTTGAAA
AAGTTTTAAAAAAAATATATAATATATAATTTTAAAATATTTTTAAAAATATATATTATATATAT
TTTTAAAAAA
Found at i:639606 original size:4 final size:4
Alignment explanation
Indices: 639599--639713 Score: 63
Period size: 4 Copynumber: 27.5 Consensus size: 4
639589 TAATTTTTTC
* *
639599 TTAT TTAT TTAT TTAT TTAT TTA- TAAT TTAAT TTAAT TTAAT TAAAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT TT-AT T-TAT
* * * * * *
639646 TTTT TTCT TTTT TTCT TTAT TTCT TTGAT TTAT TTTT TTA- TTACT ATTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTA-T -TTAT
* *
639696 TTTT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TT
639714 TTTTTATATT
Statistics
Matches: 87, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
3 5 0.06
4 59 0.68
5 20 0.23
6 3 0.03
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:639697 original size:21 final size:21
Alignment explanation
Indices: 639653--639707 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
639643 AATTTTTTTC
* *
639653 TTTTTTTCTTTATTTCTTTGA
1 TTTTTTTATTTATTACTTTGA
639674 TTTATTTT-TTTATTACTATT-A
1 TTT-TTTTATTTATTACT-TTGA
639695 TTTTTTTATTTAT
1 TTTTTTTATTTAT
639708 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.13
21 20 0.67
22 6 0.20
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTATTTATTACTTTGA
Found at i:639712 original size:19 final size:18
Alignment explanation
Indices: 639675--639724 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
639665 TTTCTTTGAT
*
639675 TTATTTTTTTA-TTACTA
1 TTATTTTTTTATTTAATA
639692 TTATTTTTTTATTTATATA
1 TTATTTTTTTATTTA-ATA
639711 TT-TTTTTTATATTT
1 TTATTTTTT-TATTT
639725 TTTGTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 9 0.31
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTTTATTTAATA
Found at i:639719 original size:13 final size:13
Alignment explanation
Indices: 639654--639727 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
639644 ATTTTTTTCT
*
639654 TTTTTTCTTTAT-
1 TTTTTTATTTATA
*
639666 TTCTTTGATTTAT-
1 TT-TTTTATTTATA
639679 TTTTTTATTACTATTA
1 TTTTTTATT--TA-TA
639695 TTTTTTTATTTATA
1 -TTTTTTATTTATA
639709 TATTTTT-TTTATA
1 T-TTTTTATTTATA
639722 TTTTTT
1 TTTTTT
639728 GTCTTTTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
12 13 0.25
13 18 0.35
14 9 0.17
15 3 0.06
17 9 0.17
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTATA
Found at i:639720 original size:17 final size:18
Alignment explanation
Indices: 639675--639717 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
639665 TTTCTTTGAT
639675 TTATTTTTTTA-TTACTA
1 TTATTTTTTTATTTACTA
639692 TTATTTTTTTATTTA-TA
1 TTATTTTTTTATTTACTA
639709 -TATTTTTTT
1 TTATTTTTTT
639718 TATATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.36
17 13 0.52
18 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTTTTATTTACTA
Found at i:643591 original size:110 final size:109
Alignment explanation
Indices: 643394--643720 Score: 444
Period size: 110 Copynumber: 3.0 Consensus size: 109
643384 TGATGGTGGT
* * * * * *
643394 AGCTCAACTTCACAGCAAAGGGGCAACTGAATGTCAACAAACAACTTTTCAATTTCATTCAAAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGTTTCATTC-GAGT
* *
643459 CAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAATACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* *
643504 AGCTCAACTTGACAGCGAAGGGGCGACTGACTGTTAACAAACAACTTTCCAGTTTCATTTCGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGTTTCA-TTCGAGT
* * *
643569 CAATTTCAACTTCACAACGAAGGATATTAGACTCTAGACAACACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
643614 AGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAACTTTCCAGTTTCA---GAGTT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGTTTCATTCGAGTC
* * *
643676 AATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAACACA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
643720 A
1 A
643721 ATATTTGGAT
Statistics
Matches: 192, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
106 43 0.22
110 146 0.76
111 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (109 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGTTTCATTCGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:643950 original size:84 final size:83
Alignment explanation
Indices: 643818--644202 Score: 524
Period size: 84 Copynumber: 4.6 Consensus size: 83
643808 GGGATCGTGC
* * * *
643818 CCACCAAAGGCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
*
643883 GTAGAGAAGGGTTATCTG
66 GTCGAGAAGGGTTATCTG
643901 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
1 CC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
643966 AGTCGAGAAGGGTTATCT-
65 AGTCGAGAAGGGTTATCTG
* * * * * * *
643984 --ACCAAAGACCCTCGAGTTCAATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTA
* *
644047 AGGCTAGAAGGGTTATCTG
65 AGTCGAGAAGGGTTATCTG
* * * *
644066 TCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTGCAACATAACTTA
1 CCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
*
644131 AGTCGAGAAGGGTTATATG
65 AGTCGAGAAGGGTTATCTG
* *
644150 CCAACCAAATAGCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 CC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
644203 TAACATCCTC
Statistics
Matches: 263, Mismatches: 32, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
80 32 0.12
81 39 0.15
83 2 0.01
84 159 0.60
85 31 0.12
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (83 bp):
CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
GTCGAGAAGGGTTATCTG
Found at i:644091 original size:165 final size:164
Alignment explanation
Indices: 643846--644201 Score: 480
Period size: 165 Copynumber: 2.1 Consensus size: 164
643836 TTTGACTACG
* ** * *
643846 CTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTAGAGAAGGGTTATCTGCCAACCAAAG
1 CTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACCAAAG
* *
643911 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
66 ACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAG
643976 GGTTATCTACCAAAGACCCTCGAGTTCAATTACA
131 GGTTATCTACCAAAGACCCTCGAGTTCAATTACA
* ** *
644010 CTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAA
1 CTCAGCTCCAA-GGCACATCATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACC-AA
*
644074 AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGA
64 AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGA
* * * * * * *
644139 AGGGTTATATGCCAACCAAATAGCTTCGAGTTCGACTACG
129 AGGG-T-TAT--CTACCAAAGACCCTCGAGTTCAATTACA
644179 CTCAGCTCCAAGGCACATCATTT
1 CTCAGCTCCAAGGCACATCATTT
644202 GTAACATCCT
Statistics
Matches: 166, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
164 13 0.08
165 106 0.64
166 1 0.01
167 3 0.02
168 12 0.07
169 31 0.19
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (164 bp):
CTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACCAAAG
ACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAG
GGTTATCTACCAAAGACCCTCGAGTTCAATTACA
Found at i:644704 original size:21 final size:20
Alignment explanation
Indices: 644665--644702 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
644655 AGATTACGCA
644665 GGGGGTACAGATTCCCCCTG
1 GGGGGTACAGATTCCCCCTG
644685 GGGGGTATC-GATTCCCCC
1 GGGGGTA-CAGATTCCCCC
644703 CTAATGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGTACAGATTCCCCCTG
Found at i:647036 original size:84 final size:82
Alignment explanation
Indices: 646854--647670 Score: 761
Period size: 84 Copynumber: 9.9 Consensus size: 82
646844 CTGGGGTATT
* * * ** *
646854 ACATCATTTGCAGCATAGCTTAAGTCGAGAATGACTATCTG-C-CAAAGACCCTT-GAGTTCGAT
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACAAAGA-CCTTCGAGTTCGAC
* *
646916 TACACTCAGCTTCGAGGGC
65 TACGCTCAGC-TCGAAGGC
* * *
646935 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAC--AAAGACCTTCGAGTTCGA
* * *
647000 CTACGCTCAACTCCATGGC
64 CTACGCTCAGCTCGAAGGC
* * * * * *
647019 ATATCATTTCCAGCATAACTTAAGTCAATAAGGGTTATATGCCAATCAAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-A-CAAAGACCTTCGAGTTCGA
*
647084 CTACGCTCAGCTCTAAGGC
64 CTACGCTCAGCTCGAAGGC
* * * * * *
647103 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG-C-CAAAGACCCTCGAATT--AC-
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGACT
*
647163 A--CTCAGCTTCGAGGGC
66 ACGCTCAGC-TCGAAGGC
* * * *
647179 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGA
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-A-CAAAGACCTTCGAGTTCGA
*
647244 CTACGCTCAGCTCCAAGGC
64 CTACGCTCAGCTCGAAGGC
* * * * * *
647263 ACATCATTTGCAGTATAGCTTAAGT-GTAGAAGGGTTATCTG-C-CAAAGACCGTCGAGTTAGAT
1 ACATCATTTACAGCATAACTTAAGTCG-AGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGAC
* *
647325 TACACTCAGCTTCGAGGGC
65 TACGCTCAGC-TCGAAGGC
* * * *
647344 ACATCATTTACAGCATAACTCAA-TGCTAGAAGGGTTATCTGTCACCAAAAAACCATCGAGTTCG
1 ACATCATTTACAGCATAACTTAAGT-CGAGAAGGGTTATCTGTCA-C-AAAGACCTTCGAGTTCG
*
647408 ACTACGCTCAGCTCTAAGGC
63 ACTACGCTCAGCTCGAAGGC
* * *
647428 ACATCATTTACAGCATAACCTAAGTCGAGAAGGGTTATC--T-ACTAAAGACCCTCGAGTTCGAT
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAC-AAAGACCTTCGAGTTCGAC
* *
647490 TACACTCAGCATCGAGGGC
65 TACGCTCAGC-TCGAAGGC
* * *
647509 ACATCATTTACAGCATAACTCAAGGT-TAGAATGGTTATCTGTCACCAAAAGACCTTCGAGTTCG
1 ACATCATTTACAGCATAACTTAA-GTCGAGAAGGGTTATCTGTCA-C-AAAGACCTTCGAGTTCG
* *
647573 ACTACGCTCAACTCCAAGGC
63 ACTACGCTCAGCTCGAAGGC
* * * *
647593 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCGAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-A-CAAAGACCTTCGAGTTCGA
* *
647658 TTACACTCAGCTC
64 CTACGCTCAGCTC
647671 AGAGGCAAAC
Statistics
Matches: 606, Mismatches: 96, Indels: 65
0.79 0.13 0.08
Matches are distributed among these distances:
75 6 0.01
76 43 0.07
77 2 0.00
78 2 0.00
80 79 0.13
81 111 0.18
82 7 0.01
83 8 0.01
84 265 0.44
85 82 0.14
86 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (82 bp):
ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCGAAGGC
Found at i:647415 original size:165 final size:165
Alignment explanation
Indices: 646895--647669 Score: 908
Period size: 165 Copynumber: 4.7 Consensus size: 165
646885 TGACTATCTG
* * * * * * *
646895 CCAAAGACCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
1 CCAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * * * * * * * *
646959 GCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCAAC-TCCATGGCATAT
64 TCGAGAAGGGTTATCTG-C-C--AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * *
647023 CATTTCCAGCATAACTTAAGTCAATAAGGGTTATATGCCAA
125 CATTTACAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAA
* *
647064 TCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * * *
647129 GAGAAGGGCTATATGCCAAAGACCCTCGA-----ATTACACTCAGCTTCGAGGGCATATCATTTG
66 GAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
* *
647189 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
131 CAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAA
* *
647224 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGT-
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* *
647288 GTAGAAGGGTTATCTGCCAAAGACCGTCGAGTTAGATTACACTCAGCTTCGAGGGCACATCATTT
66 G-AGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
*
647353 ACAGCATAACTCAA-TGCTAGAAGGGTTATCTGTC-A
130 ACAGCATAACTCAAGT-CTAGAAGGGTTATCTGCCAA
* * * * * *
647388 CCAAAAAACCATCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAACCTAAGT
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
* * *
647453 CGAGAAGGGTTATCTACTAAAGACCCTCGAGTTCGATTACACTCAGCATCGAGGGCACATCATTT
65 CGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
* *
647518 ACAGCATAACTCAAGGT-TAGAATGGTTATCTGTC-A
130 ACAGCATAACTCAA-GTCTAGAAGGGTTATCTGCCAA
*
647553 CCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
647618 CGAGAAGGGTTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCT
65 CGAGAAGGGTTATCTGCC-A---AAGACCCTCGAGTTCGATTACACTCAGCT
647670 CAGAGGCAAA
Statistics
Matches: 530, Mismatches: 59, Indels: 34
0.85 0.09 0.05
Matches are distributed among these distances:
159 10 0.02
160 132 0.25
164 15 0.03
165 274 0.52
166 3 0.01
167 2 0.00
168 44 0.08
169 50 0.09
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
CAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAA
Found at i:648361 original size:36 final size:35
Alignment explanation
Indices: 648316--648582 Score: 270
Period size: 38 Copynumber: 7.2 Consensus size: 35
648306 TGAAAATATG
*
648316 TATATAATATATGGTTTTTAAAACACTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACA-TTTTGAAAAC
* *
648352 TGTATAATATATAGTTTTTTTAAAACATTTTGAAAATA
1 TATATAATATATAG--TTTTTAAAACATTTTGAAAA-C
648390 TATATAATATATAGTTTTTAAAACATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTGAAAAC
* * *
648425 ATTTATATATTATGTAGTTTTTAAAACGTTTTTGAAAA-
1 ---TATATAATATATAGTTTTTAAAAC-ATTTTGAAAAC
* *
648463 TAAATATAATATATAGTTTTTCAAAATATTTCTGAAAAAA
1 T--ATATAATATATAGTTTTT-AAAACATTT-TG-AAAAC
* *
648503 TATATATTATATAGTTTTTAAAAACCTTTTGAAAAAC
1 TATATAATATATAGTTTTT-AAAACATTTTG-AAAAC
648540 -ATATAATATATA-TTTTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTT-AAAACA-TTTTGAAAAC
648575 TATATAAT
1 TATATAAT
648583 TTTGAAAACA
Statistics
Matches: 197, Mismatches: 19, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
35 17 0.09
36 55 0.28
37 35 0.18
38 76 0.39
39 13 0.07
40 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAAC
Found at i:648401 original size:74 final size:74
Alignment explanation
Indices: 648304--648582 Score: 302
Period size: 74 Copynumber: 3.7 Consensus size: 74
648294 TTGCAAACGG
* *
648304 TTTGAAAATATGTATATAATATATGGTTTTT-AAAACACTTTTGAAAACTGTATAATATATAGTT
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAAACA-TTTTGAAAACTATATAATATATAGTT
648368 TTTTTAAAACAT
63 TTTTTAAAACAT
* *
648380 TTTGAAAATATATATAATATATAGTTTTT-AAAACATTTTGAAAAC-AT-TTATATATTATGTAG
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTATATAATATA-TA-GT-T
*
648442 TTTTTAAAACGTT
63 TTTTTAAAAC-AT
* * * * *
648455 TTTGAAAATAAATATAATATATAGTTTTTCAAAATATTTCTGAAAAAATATATATTATATAG-TT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACATTT-TG-AAAACTATATAATATATAGTTT
* *
648519 TTTAAAAACCT
64 TTTTAAAACAT
*
648530 TTTGAAAA-ACATATAATATATA-TTTTTAAAAACATTTTTGAAAACTATATAAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACA-TTTTGAAAACTATATAAT
648583 TTTGAAAACA
Statistics
Matches: 175, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
71 6 0.03
72 14 0.08
73 24 0.14
74 50 0.29
75 38 0.22
76 27 0.15
77 2 0.01
78 5 0.03
79 4 0.02
80 5 0.03
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (74 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTATATAATATATAGTTTTT
TTAAAACAT
Found at i:648590 original size:29 final size:30
Alignment explanation
Indices: 648544--648612 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
648534 AAAAACATAT
* *
648544 AATATATATTTTTAAAAACATTTTT-GAAA
1 AATATATAATTTTAAAAACATTTTTAAAAA
* *
648573 ACTATATAATTTTGAAAACATTTTTAAAAA
1 AATATATAATTTTAAAAACATTTTTAAAAA
648603 AATATATAAT
1 AATATATAAT
648613 ATATAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
AATATATAATTTTAAAAACATTTTTAAAAA
Found at i:648602 original size:64 final size:63
Alignment explanation
Indices: 648518--648644 Score: 157
Period size: 66 Copynumber: 2.0 Consensus size: 63
648508 ATTATATAGT
* * *
648518 TTTTAAAAACCTTTTG-AAAAACATATAATATATATTTTTAAAAACATTTTTGAAAACTATATAA
1 TTTTAAAAACATTTTGAAAAAACATATAATATATAATTTT-AAAACATTTTT-AAAAATATATAA
* * * *
648582 TTTTGAAAACATTTTTAAAAAAATATATAATATATAATTTTAAAATATTTTTAAAAATATATA
1 TTTTAAAAACA-TTTTGAAAAAACATATAATATATAATTTTAAAACATTTTTAAAAATATATA
648645 TAATATAGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 19 0.35
65 14 0.26
66 21 0.39
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (63 bp):
TTTTAAAAACATTTTGAAAAAACATATAATATATAATTTTAAAACATTTTTAAAAATATATAA
Found at i:648638 original size:36 final size:37
Alignment explanation
Indices: 648575--648651 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
648565 TTTTGAAAAC
648575 TATATAATTTTGAAAACATTTTTAAAAAAATATATAA
1 TATATAATTTTGAAAACATTTTTAAAAAAATATATAA
* *
648612 TATATAATTTT-AAAATATTTTTAAAAATATATATAA
1 TATATAATTTTGAAAACATTTTTAAAAAAATATATAA
648648 TATA
1 TATA
648652 GATTTTTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 27 0.71
37 11 0.29
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATAATTTTGAAAACATTTTTAAAAAAATATATAA
Found at i:648665 original size:38 final size:37
Alignment explanation
Indices: 648575--648668 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 37
648565 TTTTGAAAAC
* *
648575 TATATAATTTTGAAAACATTTTTAAAAAAATATATAA
1 TATAGAATTTTGAAAATATTTTTAAAAAAATATATAA
* *
648612 TATATAATTTT-AAAATATTTTTAAAAATATATATAA
1 TATAGAATTTTGAAAATATTTTTAAAAAAATATATAA
*
648648 TATAGATTTTTGGAAAATATT
1 TATAGAATTTT-GAAAATATT
648669 ATTTTTTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 32 0.63
37 11 0.22
38 8 0.16
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TATAGAATTTTGAAAATATTTTTAAAAAAATATATAA
Found at i:649976 original size:12 final size:11
Alignment explanation
Indices: 649955--650036 Score: 65
Period size: 13 Copynumber: 6.6 Consensus size: 11
649945 TAAAATAATA
649955 TTTTTTTTATT
1 TTTTTTTTATT
649966 TTTTTTCTTATT
1 TTTTTT-TTATT
649978 TATTTTTTTAATT
1 T-TTTTTTT-ATT
*
649991 TAATTTAATTTATT
1 T--TTT-TTTTATT
650005 TATTTATTTTATT
1 T-TTT-TTTTATT
*
650018 TTTTCTTTATT
1 TTTTTTTTATT
650029 TCTTTTTT
1 T-TTTTTT
650037 CCTTTGATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
11 13 0.21
12 16 0.26
13 21 0.34
14 8 0.13
15 3 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:650007 original size:4 final size:4
Alignment explanation
Indices: 649960--650056 Score: 58
Period size: 4 Copynumber: 23.5 Consensus size: 4
649950 TAATATTTTT
* *
649960 TTTA TTT- TTTT TCTTA TTTA TTTT TTTAA TTTAA TTTAA TTTA TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTT-A TTT-A TTT-A TTTA TTTA
* * *
650007 TTTA TTTTA TTT- TTTC TTTA TTTC TTT- TTTCC TTTGA TTTA TTT- TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTT-A TTTA TTTA TTTA
650055 TT
1 TT
650057 ACTATTATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
3 12 0.15
4 40 0.51
5 26 0.33
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:650028 original size:16 final size:16
Alignment explanation
Indices: 649953--650069 Score: 71
Period size: 16 Copynumber: 7.1 Consensus size: 16
649943 TTTAAAATAA
*
649953 TATTTTTTTTATTTTT
1 TATTTATTTTATTTTT
*
649969 TTTCTTA-TTTATTTTTT
1 TAT-TTATTTTA-TTTTT
*
649986 TAATTTAATTTAATTTATT
1 T-ATTT-ATTTTATTT-TT
650005 TATTTATTTTATTTTT
1 TATTTATTTTATTTTT
*
650021 TCTTTATTTCT-TTTTT
1 TATTTATTT-TATTTTT
**
650037 CCTTTGA-TTTATTTTT
1 TATTT-ATTTTATTTTT
*
650053 TA-TTACTATTATTTTT
1 TATTTA-TTTTATTTTT
650069 T
1 T
650070 TATATTTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
14 1 0.01
15 3 0.04
16 41 0.51
17 20 0.25
18 9 0.11
19 6 0.08
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (16 bp):
TATTTATTTTATTTTT
Found at i:650035 original size:50 final size:50
Alignment explanation
Indices: 649953--650069 Score: 123
Period size: 52 Copynumber: 2.3 Consensus size: 50
649943 TTTAAAATAA
* * *
649953 TATTTTTTTTATTTTTTTTCTTATTTATTTTTTTAATTTAATTTAATTTATT
1 TATTTATTTTATTTTTTCTCTTATTTACTTTTTTAATTTAATTT-ATTT-TT
** *
650005 TATTTATTTTATTTTTTCT-TTATTT-CTTTTTTCCTTTGATTTATTTTT
1 TATTTATTTTATTTTTTCTCTTATTTACTTTTTTAATTTAATTTATTTTT
*
650053 TA-TTACTATTATTTTTT
1 TATTTA-TTTTATTTTTT
650070 TATATTTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
47 3 0.05
48 14 0.25
49 4 0.07
50 13 0.23
51 6 0.11
52 17 0.30
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (50 bp):
TATTTATTTTATTTTTTCTCTTATTTACTTTTTTAATTTAATTTATTTTT
Found at i:650046 original size:17 final size:15
Alignment explanation
Indices: 649960--650053 Score: 71
Period size: 17 Copynumber: 5.7 Consensus size: 15
649950 TAATATTTTT
*
649960 TTTATTTTTTTTCTTA
1 TTTATTTTTTCT-TTA
*
649976 TTTATTTTTTTAATTTAA
1 TTTA-TTTTTT-CTTT-A
*
649994 TTTAATTTATTTATTTA
1 TTT-ATTT-TTTCTTTA
650011 TTTTATTTTTTCTTTA
1 -TTTATTTTTTCTTTA
*
650027 TTTCTTTTTTCCTTTGA
1 TTTATTTTTT-CTTT-A
650044 TTTATTTTTT
1 TTTATTTTTT
650054 ATTACTATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
15 9 0.14
16 15 0.23
17 23 0.35
18 15 0.23
19 4 0.06
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTATTTTTTCTTTA
Found at i:650070 original size:50 final size:50
Alignment explanation
Indices: 649953--650070 Score: 122
Period size: 50 Copynumber: 2.4 Consensus size: 50
649943 TTTAAAATAA
*
649953 TATTT-TTT-TTATTTTTTTTCTTATTTATTTTTTTAATTTAATTTAATT
1 TATTTATTTATTATTTTTTTTCTTATTTACTTTTTTAATTTAATTTAATT
** *
650001 TATTTATTTATT-TTATTTTTTCTTTATTT-CTTTTTTCCTTTGATTT-ATT
1 TATTTATTTATTATT-TTTTTTC-TTATTTACTTTTTTAATTTAATTTAATT
650050 T-TTTATTACTATTATTTTTTT
1 TATTTATT--TATTATTTTTTT
650071 ATATTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
48 11 0.19
49 9 0.15
50 31 0.53
51 8 0.14
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (50 bp):
TATTTATTTATTATTTTTTTTCTTATTTACTTTTTTAATTTAATTTAATT
Found at i:650877 original size:51 final size:51
Alignment explanation
Indices: 650761--650937 Score: 225
Period size: 51 Copynumber: 3.5 Consensus size: 51
650751 AGATGTACAT
* *
650761 ACTTACACCGGTGTAAGTATGTATTAAGTGTTACAC--TTTT-TTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGATACACTTTTTTATTTTATTC
* *
650809 ACTTACACCGGTGTAAGTATGTGTTAACTAATACACTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGATACACTTTTTTATTTTATTC
* * * * * * *
650860 ACTTACACCGGTATAAGTATATGTTGAGTGCTACATTTTTTTATATTATGC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGATACACTTTTTTATTTTATTC
*
650911 ACTTACACCGGTGTAAGTTTGTGTTAA
1 ACTTACACCGGTGTAAGTATGTGTTAA
650938 ATTCTTCATT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
48 32 0.29
50 4 0.04
51 73 0.67
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGATACACTTTTTTATTTTATTC
Found at i:654771 original size:12 final size:12
Alignment explanation
Indices: 654728--654777 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
654718 CAAAGCATTT
654728 TTATTTTACTTG
1 TTATTTTACTTG
654740 TTTATTTT--TTG
1 -TTATTTTACTTG
654751 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
654765 TTATTTTCCTTG
1 TTATTTTACTTG
654777 T
1 T
654778 CTTTTTTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
10 1 0.03
11 5 0.16
12 13 0.41
13 9 0.28
14 4 0.12
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.68
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:660285 original size:20 final size:22
Alignment explanation
Indices: 660260--660299 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
660250 ACACTACCAC
660260 CATTCTA-TTT-CCACATCAGA
1 CATTCTATTTTGCCACATCAGA
660280 CATTCTATTTTGCCACATCA
1 CATTCTATTTTGCCACATCA
660300 TTCTCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (22 bp):
CATTCTATTTTGCCACATCAGA
Found at i:661281 original size:12 final size:12
Alignment explanation
Indices: 661264--661288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
661254 AAATATGCAT
661264 GTTGATCTACAA
1 GTTGATCTACAA
661276 GTTGATCTACAA
1 GTTGATCTACAA
661288 G
1 G
661289 AAGTAAGAAA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GTTGATCTACAA
Found at i:664241 original size:281 final size:279
Alignment explanation
Indices: 663740--664291 Score: 989
Period size: 281 Copynumber: 2.0 Consensus size: 279
663730 CACATAACCA
* *
663740 AATTAAGATACTAATCAAAGAATTATGAAAAAATTATAAGTTTATTTATATTTTTTAAATAATAT
1 AATTAAGATACTAATCAAAGAATTATGAAAAAATTATAAGTTTATTTATACTTTTAAAATAATAT
*
663805 ATAATTATATATTCTTTATACTTTTTAATATTTAAAATTATTTTTATCATTTGTACCCAATTAAG
66 ATAATTATATATTCTTTATAATTTTTAATATTTAAAATTATTTTTATCATTTGTACCCAATTAAG
663870 CTTTTAATACTAATTAAATAATTAAATAAATTCTTAATATCAAATAAAATAATTAATTAAACTCT
131 CTTTTAATACTAATTAAATAATTAAATAAATTCTTAATATCAAATAAAATAATTAATTAAACTCT
*
663935 CCACACGAGCGACACATATCATATTACATTGAAGGTTGATATTAGTTATATTAATAAAAAGAGGG
196 CCACACGAGCGACACATATCATATTACATTGAAGGTTAATATTAGTTATATTAATAAAAAGAGGG
664000 TAAAGTACACATATAAAAG
261 TAAAGTACACATATAAAAG
* *
664019 AATTAAGATACTAATCACAGAATTATCG-AAAAATTATAATTTTATTTATACTTTTAAAATAATA
1 AATTAAGATACTAATCAAAGAATTAT-GAAAAAATTATAAGTTTATTTATACTTTTAAAATAATA
*
664083 TATAATTATATATATTCTTTATAATTTTTAATATTTATAATTATTTTTATCATTTGTACCCAATT
65 TATAA-T-TATATATTCTTTATAATTTTTAATATTTAAAATTATTTTTATCATTTGTACCCAATT
*
664148 AAGCTTTTAATACTAATTAAATAATTAAATAAATTCTTAATATCAAATAAAATAGTTAATTAAAC
128 AAGCTTTTAATACTAATTAAATAATTAAATAAATTCTTAATATCAAATAAAATAATTAATTAAAC
*
664213 TCTCCGCACGAGCGACACATATCATATTACATTGAAGGTTAATATTAGTTATATTAATAAAAAGA
193 TCTCCACACGAGCGACACATATCATATTACATTGAAGGTTAATATTAGTTATATTAATAAAAAGA
664278 GGGTAAAGTACACA
258 GGGTAAAGTACACA
664292 AATGGTTCTC
Statistics
Matches: 261, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
279 63 0.24
280 2 0.01
281 196 0.75
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (279 bp):
AATTAAGATACTAATCAAAGAATTATGAAAAAATTATAAGTTTATTTATACTTTTAAAATAATAT
ATAATTATATATTCTTTATAATTTTTAATATTTAAAATTATTTTTATCATTTGTACCCAATTAAG
CTTTTAATACTAATTAAATAATTAAATAAATTCTTAATATCAAATAAAATAATTAATTAAACTCT
CCACACGAGCGACACATATCATATTACATTGAAGGTTAATATTAGTTATATTAATAAAAAGAGGG
TAAAGTACACATATAAAAG
Found at i:667393 original size:20 final size:22
Alignment explanation
Indices: 667368--667425 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
667358 TTCCCCTTGA
667368 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
667388 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
667411 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
667426 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:667504 original size:64 final size:63
Alignment explanation
Indices: 667413--667553 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
667403 TCTTTAACAT
* * *
667413 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTT-TCATTTTAAAGG
1 GTGCATCGATGCACTACCCATGAATCGATACACAAATTACATTCGATGTTTCT-ATTTTAAAGA
* * * * * * *
667476 GATGCACCGATGCACT-CCTTATGAATCGATGCACCATTTGCATTCGATGTTTCTTTTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGAATCGATACACAAATTACATTCGATGTTTCTATTTTAAAGA
667540 GTGCATCGATGCAC
1 GTGCATCGATGCAC
667554 ATTGAATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 15 0.23
64 48 0.75
65 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGAATCGATACACAAATTACATTCGATGTTTCTATTTTAAAGA
Found at i:668621 original size:64 final size:64
Alignment explanation
Indices: 668553--668672 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 64
668543 TGTTCAAGGT
* * * * *
668553 GTATCGATGCACATGAAGTGTATCGATGTGCTCCTTTAAAATAAAAACATCGAATGTCATCAGG
1 GTATCGATGCACAAGAAGTGCATCGATGTACCCCCTTAAAATAAAAACATCGAATGTCATCAGG
* *
668617 GTATCGATGCACAAGTAGTGCATCGATGTACCCCCTTAAAATACAAACATCGAATG
1 GTATCGATGCACAAGAAGTGCATCGATGTACCCCCTTAAAATAAAAACATCGAATG
668673 GGATTTAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
GTATCGATGCACAAGAAGTGCATCGATGTACCCCCTTAAAATAAAAACATCGAATGTCATCAGG
Found at i:669393 original size:23 final size:23
Alignment explanation
Indices: 669367--669423 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
669357 TAGCACTACG
669367 GTGCAATTATATGCGGCACTTCA
1 GTGCAATTATATGCGGCACTTCA
* * *
669390 GTGCAATTCTATGTGGCACTTCG
1 GTGCAATTATATGCGGCACTTCA
*
669413 GTGCATTTATA
1 GTGCAATTATA
669424 GGAGCTGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
GTGCAATTATATGCGGCACTTCA
Found at i:674754 original size:23 final size:23
Alignment explanation
Indices: 674724--674783 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
674714 CATTTTATAT
674724 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
674747 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
674770 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
674784 TTTATACAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:679415 original size:23 final size:23
Alignment explanation
Indices: 679389--679432 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
679379 ACTACAGTGC
679389 AATTCTACGCGGCACTTCGGTAT
1 AATTCTACGCGGCACTTCGGTAT
*
679412 AATTCTACGTGGCACTTCGGT
1 AATTCTACGCGGCACTTCGGT
679433 GCATTTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
AATTCTACGCGGCACTTCGGTAT
Found at i:679443 original size:23 final size:23
Alignment explanation
Indices: 679385--679435 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
679375 TAGCACTACA
679385 GTGCAATTCTACGCGGCACTTCG
1 GTGCAATTCTACGCGGCACTTCG
** *
679408 GTATAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGCGGCACTTCG
679431 GTGCA
1 GTGCA
679436 TTTATACGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTCG
Found at i:681638 original size:18 final size:18
Alignment explanation
Indices: 681615--681652 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
681605 CACCATTTGT
681615 ATCCATATTTGGTTATAA
1 ATCCATATTTGGTTATAA
*
681633 ATCCATCTTTGGTTATAA
1 ATCCATATTTGGTTATAA
681651 AT
1 AT
681653 ATCCATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
ATCCATATTTGGTTATAA
Done.