Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_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: 1326839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:531278 original size:42 final size:41
Alignment explanation
Indices: 531206--531302 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
531196 TAAGTCCTTT
*
531206 GGGCCATC-AGTAAGTCTTTCGAGCATGATGATTAAATCATTC
1 GGGCCATCTA-TAAGTCTTTCGAGCAAGATGA-TAAATCATTC
* * * *
531248 GGGTCATCTATAAGTCTTTTGAGCAAGATGATAAGTCTTTC
1 GGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATCATTC
*
531289 GGGCCATCTGTAAG
1 GGGCCATCTATAAG
531303 ACCTTTGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 20 0.43
42 26 0.55
43 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (41 bp):
GGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATCATTC
Found at i:531704 original size:42 final size:41
Alignment explanation
Indices: 531640--531742 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 41
531630 AATTGGTATG
* * *
531640 TCCTTGGGGTCATC-AGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGTCATCTA-TAAGTCTTTCAAGCAAGATGA-TAAA
* * *
531682 TCCTTCGGGTCATCTATCAGTCTTTCAAGTAAGATGATAAG
1 TCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAA
* *
531723 TCATTCGGGCCATCTATAAG
1 TCCTTCGGGTCATCTATAAG
531743 ACCCTTGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 20 0.39
42 30 0.59
43 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAA
Found at i:531861 original size:16 final size:15
Alignment explanation
Indices: 531816--531866 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 15
531806 TCTCATTTAA
*
531816 AGAAAAAGAGAAAA-
1 AGAAAAAGAAAAAAG
* *
531830 AG-AATATAAAAAAG
1 AGAAAAAGAAAAAAG
531844 AGAAAAAGAAAAATAG
1 AGAAAAAGAAAAA-AG
531860 AGAAAAA
1 AGAAAAA
531867 AGAAGAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 8 0.28
14 4 0.14
15 8 0.28
16 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AGAAAAAGAAAAAAG
Found at i:532918 original size:2 final size:2
Alignment explanation
Indices: 532911--533005 Score: 93
Period size: 2 Copynumber: 47.5 Consensus size: 2
532901 TATTATTACC
* * *
532911 TA TA TA TA TG TA TG TA TGA -A TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
532953 CA TA TA TA TA TA TA CA CA CA CA CA 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
532995 TA TA TA TA TA T
1 TA TA TA TA TA T
533006 TATCATTAGT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.01
2 79 0.98
3 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (2 bp):
TA
Found at i:537705 original size:43 final size:43
Alignment explanation
Indices: 537650--538033 Score: 354
Period size: 43 Copynumber: 8.9 Consensus size: 43
537640 TTTTTTAACA
* * *
537650 AAAAACGCCGTAATAGGTATTGATATTTAGCGGCGTTTGTGTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTATG
* * *
537693 ACAAACGTCGTAATAGGTGTTGATATTTAGCGGCGTTTGTCAT-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-ATG
* *
537736 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTTTCA-G
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-ATG
* * *
537779 ACAAACGCCGCAATAGGTGTTGATATTTAGTGGTGTTTGTTAT-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTG-TATG
537822 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-ATG
* * * *
537865 AAAAACGCTGCAATAGGTGTTAATATTTAGCAGCGTTTTTCA-G
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-ATG
* * * *
537908 ACAAACGCCGCAATAGGT-TATGATGTTTAGCGGCATTT-TTTG
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTGTATG
* * * *
537950 CTAAAAA-GCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTTGT-TC
1 --AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCG---TTTGTATG
* * * * *
537996 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
538034 TTTTCACAAA
Statistics
Matches: 290, Mismatches: 35, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
42 7 0.02
43 239 0.82
44 11 0.04
45 28 0.10
46 4 0.01
47 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTATG
Found at i:537795 original size:129 final size:128
Alignment explanation
Indices: 537652--537988 Score: 464
Period size: 129 Copynumber: 2.6 Consensus size: 128
537642 TTTTAACAAA
* * * *
537652 AAACGCCGTAATAGGTATTGATATTTAGCGGCGTTTGTGT-GACAAACGTCGTAATAGGTGTTGA
1 AAACGCCGCAATAGGT-TTGATATTTAGCGGCGTTTGT-TAGAAAAACGCCGCAATAGGTGTTGA
*
537716 TATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTTTCAGAC
64 TATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTTTCAGAC
* * *
537781 AAACGCCGCAATAGGTGTTGATATTTAGTGGTGTTTGTTATAAAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATAGGT-TTGATATTTAGCGGCGTTTGTTAGAAAAACGCCGCAATAGGTGTTGAT
*
537846 ATTTAGCGGCGTTTGTCATAAAAACGCTGCAATAGGTGTTAATATTTAGCAGCGTTTTTCAGAC
65 ATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTTTCAGAC
* * * *
537910 AAACGCCGCAATAGGTTATGATGTTTAGCGGCATTT-TTTGCTAAAAA-GCCGCAGTAGGTGTTG
1 AAACGCCGCAATAGGTT-TGATATTTAGCGGCGTTTGTTAG--AAAAACGCCGCAATAGGTGTTG
* *
537973 ATGTTTTGCGGCGTTT
63 ATATTTAGCGGCGTTT
537989 TTTGTTCACA
Statistics
Matches: 185, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
128 4 0.02
129 176 0.95
130 5 0.03
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (128 bp):
AAACGCCGCAATAGGTTTGATATTTAGCGGCGTTTGTTAGAAAAACGCCGCAATAGGTGTTGATA
TTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTTTCAGAC
Found at i:538021 original size:45 final size:45
Alignment explanation
Indices: 537908--538076 Score: 222
Period size: 43 Copynumber: 3.8 Consensus size: 45
537898 CGTTTTTCAG
* * * *
537908 ACAAACGCCGCAATAGGT-TATGATGTTTAGCGGCATTTTTTGCT-
1 ACAAACGCCGCAGTAGGTAT-TGATGTTTTGCGGCGTTTTTTGTTC
* *
537952 A-AAAAGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTTGTTC
1 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTTGTTC
537996 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCG-TTTTT-TTC
1 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTTGTTC
* *
538039 ACAAACACCGCAGTAGGTATTGATGTTTTGTGGCGTTT
1 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTT
538077 CTGCTAAAAA
Statistics
Matches: 112, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
43 71 0.63
44 10 0.09
45 31 0.28
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (45 bp):
ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTTGTTC
Found at i:538023 original size:88 final size:88
Alignment explanation
Indices: 537908--538076 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 88
537898 CGTTTTTCAG
*
537908 ACAAACGCCGCAATAGGTTATGATGTTTAGCGGCATTTTTTGCTA-AAA-AGCCGCAGTAGGTGT
1 ACAAACGCCGCAATAGGTTATGATGTTTAGCGGCATTTTTTGC-ACAAACA-CCGCAGTAGGTAT
537971 TGATGTTTTGCGGCGTTTTTTGTTC
64 TGATGTTTTGCGGCGTTTTTTGTTC
* * * *
537996 ACAAACGCCGCAGTAGG-TATTGATGTTTTGCGGCGTTTTTTTCACAAACACCGCAGTAGGTATT
1 ACAAACGCCGCAATAGGTTA-TGATGTTTAGCGGCATTTTTTGCACAAACACCGCAGTAGGTATT
*
538060 GATGTTTTGTGGCGTTT
65 GATGTTTTGCGGCGTTT
538077 CTGCTAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 3 0.04
88 68 0.94
89 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (88 bp):
ACAAACGCCGCAATAGGTTATGATGTTTAGCGGCATTTTTTGCACAAACACCGCAGTAGGTATTG
ATGTTTTGCGGCGTTTTTTGTTC
Found at i:538501 original size:21 final size:21
Alignment explanation
Indices: 538476--538562 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
538466 ATTCTTCACA
*
538476 TCTCTGCTGATA-TGCTGCTTC
1 TCTCTG-TGATACCGCTGCTTC
*
538497 TCTCTGTGTTACCGCTGCTTC
1 TCTCTGTGATACCGCTGCTTC
* *
538518 TCTCTGTGCTGCCGCTGCTTC
1 TCTCTGTGATACCGCTGCTTC
* * * * *
538539 TTTCTCTGCTTCCGCTGCTGC
1 TCTCTGTGATACCGCTGCTTC
538560 TCT
1 TCT
538563 GGTTGCTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.07
21 52 0.93
ACGTcount: A:0.03, C:0.34, G:0.20, T:0.43
Consensus pattern (21 bp):
TCTCTGTGATACCGCTGCTTC
Found at i:543828 original size:41 final size:43
Alignment explanation
Indices: 543750--543837 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
543740 AAAACACCGC
543750 AAAATATTATATATATTGCGGCGTTTATCTAAAAAAACGCCA-T
1 AAAATATTATATATATTGCGGCGTTTATCT-AAAAAACGCCACT
*
543793 AAAATATTATATATATTGTGGCGTTTATCT-AAAAACGCCACT
1 AAAATATTATATATATTGCGGCGTTTATCTAAAAAACGCCACT
543835 AAA
1 AAA
543838 GTATGAGTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
41 10 0.23
42 4 0.09
43 29 0.67
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (43 bp):
AAAATATTATATATATTGCGGCGTTTATCTAAAAAACGCCACT
Found at i:543857 original size:41 final size:41
Alignment explanation
Indices: 543812--544048 Score: 242
Period size: 42 Copynumber: 5.7 Consensus size: 41
543802 TATATATTGT
*
543812 GGCGTTTATCTAAAAACGCCACTAAAGTATGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAGTATGAGTCTATAGC
* * *
543853 GGCGTTTGTATAAAAATGCCACTAGAGTACT-AGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAGTA-TGAGTCTATAGC
* ** ** *
543894 GGCGTTTATATAAAAAACACTGCTAAAGTACAAGTCTTTAGC
1 GGCGTTTATAT-AAAAACGCCACTAAAGTATGAGTCTATAGC
* * * * *
543936 GACGTTTACATTCAAAACGCCACTAAAGTACGAGTTTATAGC
1 GGCGTTTATA-TAAAAACGCCACTAAAGTATGAGTCTATAGC
* * *
543978 GGCGTTTATATTCAAAACGCCACTAAAGTATGAGTATATAGT
1 GGCGTTTATA-TAAAAACGCCACTAAAGTATGAGTCTATAGC
* * *
544020 GGAGTTTGTATAGAAACGCCACTAAAGTA
1 GGCGTTTATATAAAAACGCCACTAAAGTA
544049 CTAGTATATT
Statistics
Matches: 162, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
41 62 0.38
42 99 0.61
43 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (41 bp):
GGCGTTTATATAAAAACGCCACTAAAGTATGAGTCTATAGC
Found at i:548564 original size:1 final size:1
Alignment explanation
Indices: 548560--548616 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
548550 AAATTTTGGC
* * *** * *
548560 TTTTTTTTTTGTTTTTTTGTTTTTTTTGCCTTTTTTGTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
548617 GAAAAAATAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:548574 original size:9 final size:9
Alignment explanation
Indices: 548562--548615 Score: 67
Period size: 9 Copynumber: 5.9 Consensus size: 9
548552 ATTTTGGCTT
548562 TTTTTTTTG
1 TTTTTTTTG
548571 -TTTTTTTG
1 TTTTTTTTG
548579 TTTTTTTTG
1 TTTTTTTTG
548588 CCTTTTTTGTT-
1 --TTTTTT-TTG
548599 TTTTTTTTG
1 TTTTTTTTG
548608 TTTTTTTT
1 TTTTTTTT
548616 TGAAAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 10 0.25
9 22 0.55
11 6 0.15
12 2 0.05
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:548574 original size:11 final size:11
Alignment explanation
Indices: 548560--548616 Score: 69
Period size: 11 Copynumber: 4.8 Consensus size: 11
548550 AAATTTTGGC
548560 TTTTTTTTTTG
1 TTTTTTTTTTG
*
548571 TTTTTTTGTTTT
1 TTTTTTT-TTTG
548583 TTTTGCCTTTTTTG
1 TTTT---TTTTTTG
548597 TTTTTTTTTTG
1 TTTTTTTTTTG
548608 TTTTTTTTT
1 TTTTTTTTT
548617 GAAAAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 23 0.57
12 7 0.17
14 7 0.17
15 3 0.08
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:548582 original size:18 final size:19
Alignment explanation
Indices: 548560--548614 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 19
548550 AAATTTTGGC
548560 TTTTTTTTTTGTTTTTTTG
1 TTTTTTTTTTGTTTTTTTG
*
548579 --TTTTTTTTGCCTTTTTTG
1 TTTTTTTTTTG-TTTTTTTG
548597 TTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTGTTTTTTT
548615 TTGAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 6 0.19
20 9 0.29
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTTTTG
Found at i:548617 original size:30 final size:30
Alignment explanation
Indices: 548553--548615 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
548543 TTTTTTGAAA
* *
548553 TTTTGGCTTTTTTTTTTGTTTTTTTGTTTT
1 TTTTGCCTTTTTTGTTTGTTTTTTTGTTTT
548583 TTTTGCCTTTTTTGTTT-TTTTTTTGTTTT
1 TTTTGCCTTTTTTGTTTGTTTTTTTGTTTT
548612 TTTT
1 TTTT
548616 TGAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (30 bp):
TTTTGCCTTTTTTGTTTGTTTTTTTGTTTT
Found at i:549915 original size:41 final size:41
Alignment explanation
Indices: 549868--549952 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
549858 TATAGAAGCA
* * *
549868 TTTGTATAAAAACGCCACTAACGTATG-ATTCTATAGCGGCG
1 TTTGTATAAAAACGCCACTAAAGTACGTACT-TATAGCGGCG
549909 TTTGTATAAAAACGCCACTAAAGTACGTACTTATAGCGGCG
1 TTTGTATAAAAACGCCACTAAAGTACGTACTTATAGCGGCG
549950 TTT
1 TTT
549953 ATTGGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAAAGTACGTACTTATAGCGGCG
Found at i:551426 original size:41 final size:41
Alignment explanation
Indices: 551359--551469 Score: 181
Period size: 41 Copynumber: 2.7 Consensus size: 41
551349 GTTTATACAA
551359 AAAAAATGCCACTATTGATT-ACACTATTGTGGCATTTGTT-
1 AAAAAATGCCACTATTGATTAACACTATTGTGGCATTT-TTC
*
551399 AAAAAATGCCACTATTGATTAAAACTATTGTGGCATTTTTC
1 AAAAAATGCCACTATTGATTAACACTATTGTGGCATTTTTC
*
551440 TAAAAATGCCACTATTGATTAACACTATTG
1 AAAAAATGCCACTATTGATTAACACTATTG
551470 CGATGTTTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
40 22 0.33
41 44 0.67
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (41 bp):
AAAAAATGCCACTATTGATTAACACTATTGTGGCATTTTTC
Found at i:551483 original size:41 final size:39
Alignment explanation
Indices: 551360--551512 Score: 157
Period size: 41 Copynumber: 3.8 Consensus size: 39
551350 TTTATACAAA
* *
551360 AAAAATGCCACTATTGATT-ACACTATTGTGGCATTTGTT-A
1 AAAAATGCCACTATTGATTAACACTATTG-CG-ATTT-TTCT
* *
551400 AAAAATGCCACTATTGATTAAAACTATTGTGGCATTTTTCT
1 AAAAATGCCACTATTGATTAACACTATTG-CG-ATTTTTCT
551441 AAAAATGCCACTATTGATTAACACTATTGCGATGTTTATCT
1 AAAAATGCCACTATTGATTAACACTATTGCGAT-TTT-TCT
* * * *
551482 AAAAACGCCACTATTTATTATCATTATTGCG
1 AAAAATGCCACTATTGATTAACACTATTGCG
551513 GCGTTTTAAG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
39 2 0.02
40 25 0.25
41 74 0.73
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (39 bp):
AAAAATGCCACTATTGATTAACACTATTGCGATTTTTCT
Found at i:551510 original size:82 final size:81
Alignment explanation
Indices: 551360--551537 Score: 187
Period size: 82 Copynumber: 2.2 Consensus size: 81
551350 TTTATACAAA
* * * *
551360 AAAAATGCCACTATTGATTACACTATTGTGGCATTTGTTAAAAAATGCCACTATTGATTAAAACT
1 AAAAATGCCACTATTGATTACACTATTGCGACATTTATTAAAAAACGCCACTATTGATTAAAACT
* ***
551425 ATTGTGGCATTTTTCT
66 ATTGCGGCATTTTAAG
** * **
551441 AAAAATGCCACTATTGATTAACACTATTGCGATGTTTATCT-AAAAACGCCACTATTTATTATCA
1 AAAAATGCCACTATTGATT-ACACTATTGCGACATTTAT-TAAAAAACGCCACTATTGATTAAAA
* *
551505 TTATTGCGGCGTTTTAAG
64 CTATTGCGGCATTTTAAG
551523 AATAAATGCCACTAT
1 AA-AAATGCCACTAT
551538 ATGTGTAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 19 0.24
82 47 0.59
83 13 0.16
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (81 bp):
AAAAATGCCACTATTGATTACACTATTGCGACATTTATTAAAAAACGCCACTATTGATTAAAACT
ATTGCGGCATTTTAAG
Found at i:551552 original size:42 final size:39
Alignment explanation
Indices: 551484--551643 Score: 128
Period size: 42 Copynumber: 3.9 Consensus size: 39
551474 GTTTATCTAA
* *
551484 AAACGCCACTATTTATT-ATCATTATTGCGGCGTTTTAAGAAT
1 AAACGCCACTATATGTTAATC--TATTGCGGCGTTTT-AG-AT
* *
551526 AAATGCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTAT
1 AAACGCCACTATATGT-TAATCTATTGCGGCGTTT-TAG-AT
* *
551568 AAACGCCGCTA-AT-TTACCGATCTATTGCGGCGTTTTAGCT
1 AAACGCCACTATATGTTA---ATCTATTGCGGCGTTTTAGAT
* *
551608 AAAACACCACTATATGTTAATCTATTGCGGGGTTTT
1 -AAACGCCACTATATGTTAATCTATTGCGGCGTTTT
551644 TGGTATAAAC
Statistics
Matches: 97, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
39 2 0.02
40 18 0.19
41 13 0.13
42 56 0.58
43 5 0.05
44 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (39 bp):
AAACGCCACTATATGTTAATCTATTGCGGCGTTTTAGAT
Found at i:551652 original size:82 final size:83
Alignment explanation
Indices: 551531--551684 Score: 258
Period size: 82 Copynumber: 1.9 Consensus size: 83
551521 AGAATAAATG
551531 CCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCGA-TCTATTG
1 CCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACC-ACTCTATTG
551595 CGGCGTTTTAGCTAAAACA
65 CGGCGTTTTAGCTAAAACA
* * *
551614 CCACTATATGT-TAATCTATTGCGGGGTTTTTGGTATAAACGCCGTTAATTTACCACTCTATTGC
1 CCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGC
551678 GGCGTTT
66 GGCGTTT
551685 GTTAAAAACG
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 1 0.01
82 55 0.82
83 11 0.16
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (83 bp):
CCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGC
GGCGTTTTAGCTAAAACA
Found at i:551677 original size:42 final size:41
Alignment explanation
Indices: 551545--551684 Score: 160
Period size: 42 Copynumber: 3.4 Consensus size: 41
551535 TATATGTGTA
*
551545 ATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACC
1 ATCTATTGCGGCGTTTTTGGTATAAACGCCGCTAATTTACC
* * * *
551586 GATCTATTGCGGCGTTTTAGCTA-AAACACCACTATATGTTA--
1 -ATCTATTGCGGCGTTTTTGGTATAAACGCCGCTA-AT-TTACC
* *
551627 ATCTATTGCGGGGTTTTTGGTATAAACGCCGTTAATTTACC
1 ATCTATTGCGGCGTTTTTGGTATAAACGCCGCTAATTTACC
551668 ACTCTATTGCGGCGTTT
1 A-TCTATTGCGGCGTTT
551685 GTTAAAAACG
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
39 3 0.04
40 21 0.26
41 18 0.22
42 35 0.44
43 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (41 bp):
ATCTATTGCGGCGTTTTTGGTATAAACGCCGCTAATTTACC
Found at i:552683 original size:3 final size:3
Alignment explanation
Indices: 552675--552757 Score: 130
Period size: 3 Copynumber: 26.7 Consensus size: 3
552665 TTTGTTCGGG
*
552675 TTA TTA TTA ATA TTTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
552722 TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT
552758 GCATGCCTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
3 67 0.89
4 8 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:552703 original size:22 final size:22
Alignment explanation
Indices: 552675--552754 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
552665 TTTGTTCGGG
*
552675 TTATTATTAATATTTATTATTA
1 TTATTATTATTATTTATTATTA
552697 TTATTATTATTA-TTATTAATTA
1 TTATTATTATTATTTATT-ATTA
*
552719 TTATTATTATTAATTATTATTA
1 TTATTATTATTATTTATTATTA
552741 TTATTATTATTATT
1 TTATTATTATTATT
552755 ATTGCATGCC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.09
22 44 0.81
23 5 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTATTATTATTTATTATTA
Found at i:552708 original size:25 final size:25
Alignment explanation
Indices: 552675--552757 Score: 132
Period size: 25 Copynumber: 3.3 Consensus size: 25
552665 TTTGTTCGGG
*
552675 TTATTATTAATATTTATTATTATTA
1 TTATTATTATTATTTATTATTATTA
*
552700 TTATTATTATTATTAATTATTATTA
1 TTATTATTATTATTTATTATTATTA
552725 TTATTAATTATTA-TTATTATTATTA
1 TTATT-ATTATTATTTATTATTATTA
552750 TTATTATT
1 TTATTATT
552758 GCATGCCTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
24 3 0.06
25 44 0.81
26 7 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTATTATTATTTATTATTATTA
Found at i:554895 original size:14 final size:14
Alignment explanation
Indices: 554876--554915 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
554866 TTTATCTTTT
554876 AAAATTATTTTTAA
1 AAAATTATTTTTAA
554890 AAAATTA-TTTTAA
1 AAAATTATTTTTAA
554903 AAGATATTATTTT
1 AA-A-ATTATTTT
554916 AGGTATTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
14 8 0.35
15 4 0.17
16 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AAAATTATTTTTAA
Found at i:554913 original size:15 final size:13
Alignment explanation
Indices: 554876--554916 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 13
554866 TTTATCTTTT
554876 AAAATTATTTTTAA
1 AAAATTA-TTTTAA
554890 AAAATTATTTTAA
1 AAAATTATTTTAA
554903 AAGATATTATTTTA
1 AA-A-ATTATTTTA
554917 GGTATTCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
14 8 0.32
15 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
AAAATTATTTTAA
Found at i:563689 original size:21 final size:19
Alignment explanation
Indices: 563661--563706 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
563651 TCATTGAATC
563661 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
563681 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
563700 ACTTAGT
1 A-TTAGT
563707 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:577977 original size:256 final size:256
Alignment explanation
Indices: 577520--578203 Score: 978
Period size: 256 Copynumber: 2.7 Consensus size: 256
577510 TAAGATTTTC
* * *
577520 TGAAAATGAGAAAGCGATTTCCAAATTTTTTCATTTATTGTTTTCAAAAAATGAAATTTTTGAAA
1 TGAAAATGAGAAAGCGATTTCCAAAGTTTTTCATTTAATGTTTTCAAAAAATGAAATTTTTTAAA
* * * * *
577585 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTACGC-AAATTGGTAAATCCTTC
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTC-CAAAATTAGTAAGTCCTTC
* *
577649 AGACCATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGAGTCATCTATAAGTCTTTCGAG
130 -GACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGACTCATCTATAAGTCTTTCGAG
* * * * *
577714 TGAGATGACAAGTCCTTCGGGCCATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGA-ATT
194 CGAGATGACAAGTCCTTCAGGCCATCCGTAAGACCTTCAGGCAGGATATTTCCACATGATATT
* * *
577776 TGAAAATAAGAAAGCGATTTCCATAGTTTTTCATTTAATGTTTTCAGAAAATGAAATTTTTTAAA
1 TGAAAATGAGAAAGCGATTTCCAAAGTTTTTCATTTAATGTTTTCAAAAAATGAAATTTTTTAAA
* * * * *
577841 ACTAAGAAAGCGATTTCCAACGTTTATTACCCAGTAAATTATTTCCAAAATAAGTAAGTCCTTCG
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCCTTCG
* * * *
577906 TACCATCAGTAAGTCTTTCGAGCATGTTGATTAAATCCTTCTACTCATCTGTAAGTCTTTTGAGC
131 -ACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGACTCATCTATAAGTCTTTCGAGC
* *
577971 GAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCAGGCAGGATATTTCCACATGATTTT
195 GAGATGACAAGTCCTTCAGGCCATCCGTAAGACCTTCAGGCAGGATATTTCCACATGATATT
* **
578033 TGAAAAATGAGAAAGAGATTTCCAAAGTTTCACATTTAATGTTTTCAAAAAAATGAAA-TTTTTA
1 TG-AAAATGAGAAAGCGATTTCCAAAGTTTTTCATTTAATGTTTTC-AAAAAATGAAATTTTTTA
* *
578097 AAAGTAAGAAAGTGATTTTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCATT
64 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCCTT
*
578162 CGAGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTT
129 CGA-CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
578204 GGCGTTATCT
Statistics
Matches: 378, Mismatches: 44, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
255 2 0.01
256 221 0.58
257 5 0.01
258 140 0.37
259 10 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (256 bp):
TGAAAATGAGAAAGCGATTTCCAAAGTTTTTCATTTAATGTTTTCAAAAAATGAAATTTTTTAAA
AGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCCTTCG
ACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGACTCATCTATAAGTCTTTCGAGCG
AGATGACAAGTCCTTCAGGCCATCCGTAAGACCTTCAGGCAGGATATTTCCACATGATATT
Found at i:578346 original size:3 final size:3
Alignment explanation
Indices: 578340--578378 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
578330 TTTTTTTAGG
578340 TTA TTA TTCA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
578379 TTAAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 29 0.88
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:579919 original size:258 final size:257
Alignment explanation
Indices: 579410--580387 Score: 900
Period size: 258 Copynumber: 3.9 Consensus size: 257
579400 TCATTTTGGA
* * * *
579410 ATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTCCGGGTCATCTGTAAGCCTTTTAAGCAAGA
1 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
* * * *
579475 TGATAAGTCATTCGGGCCATCTATAAAATCTTCAGGCATGATGTTTTCACATGATTTTAAAAAAA
66 TGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATAATTTT--AAAAA
*
579540 ATGAGAAAGCGATTTCCAAAGTTTCTCATTTCATGTTTTTAGAAAATGAAATTTTTGAAAAGTAA
129 ATGAGAAAGCGATTTTCAAAGTTTCTCATTTCATGTTTTTAGAAAATGAAATTTTTGAAAAGTAA
*
579605 GAAAGTGATTTCTAAAGTGTTTTACCCAGTAAACTATTTCCAAAATCGATAAGTCATTCAAGCC
194 GAAAGTGATTTCCAAAGTGTTTTACCCAGTAAACTATTTCCAAAATCGATAAGTCATTCAAGCC
* * * * * * * *
579669 ATCAATAAGTCTTTTGAGCATGCTGATTAAATCCTTCAGGTCAACTGTCAGGCTTTCGAGCAATA
1 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
* * *
579734 TGATAAGTCCTTCGAGCCATCTATAAGACCTTCAGGCATGATATTTTCACATAATTTTCAAAAAC
66 TGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATAATTTT-AAAAAA
* * * * *
579799 TGAGAAAGCGATTTTTAAAATTTCTCATTT-A-GTATTTTCAGAAAGTGAATTTTTTGTAAAGTA
130 TGAGAAAGCGATTTTCAAAGTTTCTCATTTCATGT-TTTT-AGAAAATGAAATTTTTGAAAAGTA
* * * * *
579862 ATAAAGTGATTTCCAAAGT-TTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCTAGC
193 AGAAAGTGATTTCCAAAGTGTT-TTACCCAGTAAACTATTTCCAAAATCGATAAGTCATTCAAGC
579926 C
257 C
*
579927 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGA
1 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
** ** * * * *
579992 TGATAAGTCCTTCGGGAAATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAA-TTTGAAAAA
66 TGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACAT-AATTTTAAAAAA
* * * * * *
580056 T-AGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCT-GAAAATGAAGTTTTCGAAAAGTA
130 TGA-GAAAGCGATTTTCAAAGTTTCTCATTTCATGTTTT-TAGAAAATGAAATTTTTGAAAAGTA
* ** ** * ** *
580119 AGAAA---A----C--A--GTTTT-----G-AAA--GTTTCTTACTTAG-TAAGTCATTCGGGTC
193 AGAAAGTGATTTCCAAAGTGTTTTACCCAGTAAACTATTTCCAAAATCGATAAGTCATTCAAGCC
* * * * * * * *
580164 ATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTTGCGTCATCTATAAGTCTTTCGAGCAAGA
1 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
* * * * * * * * *
580229 TGATAAGTCTTTTGGCCCATTTGTATGACCTTCGGGTATGATGTTTTCACATGAA-TTTGAAAAA
66 TGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACAT-AATTTTAAAAAA
* ** * * * *
580293 TGGGAAAGTAATTTTCAAAGTTTCCCATTTAATCTTTTCT-GAAAATGAAATTTTCG-AAAGTAA
130 TGAGAAAGCGATTTTCAAAGTTTCTCATTTCATGTTTT-TAGAAAATGAAATTTTTGAAAAGTAA
** *
580356 GAAAACGATTTCCAAAGT-TTCTTACTCAGTAA
194 GAAAGTGATTTCCAAAGTGTT-TTACCCAGTAA
580388 GTCATTCGGG
Statistics
Matches: 600, Mismatches: 91, Indels: 62
0.80 0.12 0.08
Matches are distributed among these distances:
236 11 0.02
237 175 0.29
238 7 0.01
239 1 0.00
240 3 0.00
241 1 0.00
243 1 0.00
245 1 0.00
246 4 0.01
247 4 0.01
248 1 0.00
250 1 0.00
252 1 0.00
253 2 0.00
254 1 0.00
256 3 0.00
257 58 0.10
258 216 0.36
259 109 0.18
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (257 bp):
ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
TGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATAATTTTAAAAAAT
GAGAAAGCGATTTTCAAAGTTTCTCATTTCATGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGA
AAGTGATTTCCAAAGTGTTTTACCCAGTAAACTATTTCCAAAATCGATAAGTCATTCAAGCC
Found at i:580018 original size:41 final size:42
Alignment explanation
Indices: 579932--580018 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
579922 TAGCCATCAA
* * ** *
579932 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTG
1 TAAGTCTTTCAAGCAAGATGATTAAATCCTTCGGGAAATCCG
*
579974 TAAGTCTTTCAAGCAAGATGA-TAAGTCCTTCGGGAAATCCG
1 TAAGTCTTTCAAGCAAGATGATTAAATCCTTCGGGAAATCCG
580015 TAAG
1 TAAG
580019 ACCTTCGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGTCTTTCAAGCAAGATGATTAAATCCTTCGGGAAATCCG
Found at i:580328 original size:237 final size:236
Alignment explanation
Indices: 579911--580622 Score: 924
Period size: 237 Copynumber: 3.0 Consensus size: 236
579901 TCCAAAATTG
** * *
579911 GTAAGTCATTCTAGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTA
* ** * *
579976 AGTCTTTCAAGCAAGATGATAAGTCCTTCGGGAAATCCGTAAGACCTTCGGGTAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTC-GGCCATCTGTAAGACCTTCGGGTATGATGTTTTCA
* * *
580041 CATGAATTTGAAAAATAGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAG
130 CATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAA
** *
580106 TTTTCGAAAAGTAAGAAAAC-AGTTTTGAAAGTTTCTTACTTA
195 TTTTCGAAAAGTAAGAAAACGA-TTTCCAAAGTTTCTTACTCA
* * * * *
580148 GTAAGTCATTCGGGTCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTTGCGTCATCTATA
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTA
* * * *
580213 AGTCTTTCGAGCAAGATGATAAGTCTTTTGGCCCATTTGTATGACCTTCGGGTATGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGG-CCATCTGTAAGACCTTCGGGTATGATGTTTTCA
**
580278 CATGAATTTGAAAAATGGGAAAGTAATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAA
130 CATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAA
580343 TTTTCG-AAAGTAAGAAAACGATTTCCAAAGTTTCTTACTCA
195 TTTTCGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTCA
* * * *
580384 GTAAGTCATTCGGGCCATCGGTAAGTCTTTCAAGCATGATGATTAAATCCTTTGGGTCATTTGTC
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTA
* ** * *
580449 AGTCTTTCGAGCAAGATGATAAGTCCTTCGTGCCATCTATAAGACCTTCAAGCATAATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCG-GCCATCTGTAAGACCTTCGGGTATGATGTTTTCA
* * * ** * *
580514 CATGAATTTTTAAAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTTGTGTTTTCAGAAAA
130 CATGAA--TTT---GAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAA
* **
580579 TGAAATTTTCGAAATGTAAGAAAGTGATTTCCAAAGTTTCTTAC
190 TGAAATTTTCGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTAC
580623 CTATTAAACT
Statistics
Matches: 410, Mismatches: 56, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
236 148 0.36
237 177 0.43
238 3 0.01
241 53 0.13
242 29 0.07
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (236 bp):
GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTA
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGCCATCTGTAAGACCTTCGGGTATGATGTTTTCAC
ATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAAT
TTTCGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTCA
Found at i:580851 original size:12 final size:13
Alignment explanation
Indices: 580825--580869 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
580815 TTTCTCATTT
580825 AAAAAAAGA-AGAG
1 AAAAAAA-ATAGAG
580838 AAAAAAAATA-AG
1 AAAAAAAATAGAG
580850 AAAAAAAAATAGAG
1 -AAAAAAAATAGAG
580864 AAAAAA
1 AAAAAA
580870 TGAGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 24 0.83
14 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (13 bp):
AAAAAAAATAGAG
Found at i:580853 original size:24 final size:24
Alignment explanation
Indices: 580825--580875 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
580815 TTTCTCATTT
580825 AAAAAAAGAAGAGAAAAAAAATAAG
1 AAAAAAA-AAGAGAAAAAAAATAAG
* * *
580850 AAAAAAAAATAGAGAAAAAATGAG
1 AAAAAAAAAGAGAAAAAAAATAAG
580874 AA
1 AA
580876 GGAAGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAAAAAAAGAGAAAAAAAATAAG
Found at i:581929 original size:2 final size:2
Alignment explanation
Indices: 581922--581952 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
581912 TGTGCATGTG
581922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
581953 TATTTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:583180 original size:12 final size:12
Alignment explanation
Indices: 583163--583197 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
583153 GCCGGCTTGA
583163 AGAAAGAAAGAG
1 AGAAAGAAAGAG
583175 AGAAAGAAAGAG
1 AGAAAGAAAGAG
*
583187 TGAAAGAAAGA
1 AGAAAGAAAGA
583198 AAATACAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (12 bp):
AGAAAGAAAGAG
Found at i:583425 original size:22 final size:21
Alignment explanation
Indices: 583373--583425 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
583363 CGATTCAACC
*
583373 TAAATTTTTTTTATTTTTTAT
1 TAAATTTTTTTGATTTTTTAT
*
583394 TAAATATTTTTGATATTTTTAT
1 TAAATTTTTTTGAT-TTTTTAT
*
583416 TTAATTTTTT
1 TAAATTTTTT
583426 AAATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TAAATTTTTTTGATTTTTTAT
Found at i:584169 original size:39 final size:37
Alignment explanation
Indices: 584121--584249 Score: 122
Period size: 39 Copynumber: 3.4 Consensus size: 37
584111 CTATTTCTTT
*
584121 TTTTTTTTCATGCATGTTTATATATTTATTTATGTCGC
1 TTTTATTTCATGCATGTTTAT-TATTTATTTATGTCGC
* * *
584159 ATTTTATTTCATGCAT-TTTAGTCA-TTATACTATTTC-C
1 -TTTTATTTCATGCATGTTTA-TTATTTAT-TTATGTCGC
*
584196 TTTT-TTTCATGCATGTTTATGTATTTATTTATGTTGC
1 TTTTATTTCATGCATGTTTAT-TATTTATTTATGTCGC
*
584233 GTTTTATTTCTTGCATG
1 -TTTTATTTCATGCATG
584250 ACTGGACGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
35 11 0.15
36 13 0.18
37 10 0.14
38 14 0.19
39 25 0.34
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.59
Consensus pattern (37 bp):
TTTTATTTCATGCATGTTTATTATTTATTTATGTCGC
Found at i:584317 original size:2 final size:2
Alignment explanation
Indices: 584312--584339 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
584302 TGTGTGCTCA
584312 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
584340 TCTATGAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:586509 original size:259 final size:253
Alignment explanation
Indices: 586132--587385 Score: 1077
Period size: 237 Copynumber: 5.0 Consensus size: 253
586122 GTCATTTTGG
* * * * * *
586132 CATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGCCTTTCAACCAAG
1 CATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAG
* * * *
586197 ATGATAAGTCATTCGAGCCATCTATAAGACCTT-ATGGCAGGATGTTCTCACATGATTTTTAAAA
66 ATGATAAGTCATTCGGGCCATCTATAAGACCTTCA-GGTAGGATGTTTTCACATGA-ATTT-AAA
* * * * * *
586261 AAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAGTGTTTTCAAAAAATGGAATTTTTGAAAAGT
128 AAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTCGAAAAGT
*
586326 AAGAAAGCGATTTCCAATGTTATTTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGGGC
193 AAGAAAGCGATTTCCAAAGTT-TTTA-CC-ATAAACTATTT-CAAAATCGGTAAGTCATTCGGGC
* * * ** * * * *
586391 CATCAATAAGTCTTTCGAGCATGCTGATTAAATCCTTCAGGTCAAGTGTCAGGCTTTCGAGAAAT
1 CATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAG
*
586456 ATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGACTTTCAAAAA
66 ATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGAATTT-AAAAA
* ** * * * * **
586521 CTGAGAAAGTGATTTTTAAAATTTCTCATTTAGTATTTTCA-AAAAGTGAAATTTTTTAAAAGTA
130 ATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAA-TGAAATTTTCGAAAAGTA
* * * * **
586585 AGAAAGTGATTTCCAAAGTTTCTTACTGAGTAAACTATTTCCAAAATTGGTAATTCATTCTAGC
194 AGAAAGCGATTTCCAAAGTTT-TTAC-CA-TAAACTATTT-CAAAATCGGTAAGTCATTCGGGC
* * *
586649 CATCAATATGTCTTTCAAGCATGATGATTAAATCTTTCGGGTCATCTGTAAGTCTTTCGAGCAAG
1 CATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAG
* * ** * * * * * *
586714 ATGATAAGTCCTTCGGGCAATCCGTAAGACCTTCGGGTAGGATTTTTTTACACGAATTTGAAAAT
66 ATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTAAAAAA
* * * * * *
586779 TGTGAAAGCAATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAATTTTCAAAAAGCAAG
131 TGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTCGAAAAGTAAG
* * * *
586844 AAAACAATTTCCAAAG--TTT--C-T----TACTT----A---GTAAGTCCTTCGGGC
196 AAAGCGATTTCCAAAGTTTTTACCATAAACTATTTCAAAATCGGTAAGTCATTCGGGC
* ** * * *
586886 CGT-AAGTAAGTCTTTTTAGCATGGTGATTAAATCATTCGCGTCATTTGTAAGTCTTTCGAGCAA
1 CATCAA-TAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAA
* * * * * * * *
586950 GATGATAAGTCTTTTGGACCATTTGTAAGACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAA
65 GATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTAAAAA
* *** * * *
587015 ATGGGAAAGTGGTTTTCAAAGTCTCCCATTTAATCTTTTCTGAAAATGAAATTTTCGAAAAGTAA
130 ATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTCGAAAAGTAA
* *
587080 GTAAA-CGATTTCCAAAG--TTT--C-T----TA---C----TCAGTAAGTCGTTCGGGC
195 G-AAAGCGATTTCCAAAGTTTTTACCATAAACTATTTCAAAATCGGTAAGTCATTCGGGC
* * * *
587123 CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTATTAGTCTTTCGAGCATG
1 CATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAG
* * * ** * *
587188 ATGGTAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCATAATGTTTTCAAATGATTTTTAAAAA
66 ATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGA-ATTT--AAA
* * ** * *
587253 AAATGAGAAAGCCATTTCCAAAGTTTCTCATTTTTTGTTTTCAGAAAATGAAATTTTCGAAATGT
128 AAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTCGAAAAGT
* * * *
587318 AAGAAAGTGATTTCCAAAGTTTCTTACCTATTAAACTATTTATAAAATTGGTAAGTCCTTCGGGC
193 AAGAAAGCGATTTCCAAAGTTT-TTACC-A-TAAACTATTT-CAAAATCGGTAAGTCATTCGGGC
587383 CAT
1 CAT
587386 TGGTAAGTCC
Statistics
Matches: 813, Mismatches: 145, Indels: 73
0.79 0.14 0.07
Matches are distributed among these distances:
236 2 0.00
237 306 0.38
238 7 0.01
239 3 0.00
240 70 0.09
242 1 0.00
243 2 0.00
245 5 0.01
248 1 0.00
249 1 0.00
252 2 0.00
254 2 0.00
255 1 0.00
257 71 0.09
258 217 0.27
259 103 0.13
260 19 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (253 bp):
CATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAG
ATGATAAGTCATTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTAAAAAA
TGAGAAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTCGAAAAGTAAG
AAAGCGATTTCCAAAGTTTTTACCATAAACTATTTCAAAATCGGTAAGTCATTCGGGC
Found at i:586741 original size:41 final size:42
Alignment explanation
Indices: 586658--586741 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 42
586648 CCATCAATAT
* * *
586658 GTCTTTCAAGCATGATGATTAAATCTTTCGGGTCATCTGTAA
1 GTCTTTCAAGCAAGATGATTAAATCCTTCGGGTCATCCGTAA
* *
586700 GTCTTTCGAGCAAGATGA-TAAGTCCTTCGGG-CAATCCGTAA
1 GTCTTTCAAGCAAGATGATTAAATCCTTCGGGTC-ATCCGTAA
586741 G
1 G
586742 ACCTTCGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.03
41 19 0.53
42 16 0.44
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
GTCTTTCAAGCAAGATGATTAAATCCTTCGGGTCATCCGTAA
Found at i:587389 original size:20 final size:20
Alignment explanation
Indices: 587364--587402 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
587354 TATTTATAAA
587364 ATTGGTAAGTCCTTCGGGCC
1 ATTGGTAAGTCCTTCGGGCC
587384 ATTGGTAAGTCCTTCGGGC
1 ATTGGTAAGTCCTTCGGGC
587403 AATCAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGGTAAGTCCTTCGGGCC
Found at i:587411 original size:20 final size:20
Alignment explanation
Indices: 587368--587414 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
587358 TATAAAATTG
* **
587368 GTAAGTCCTTCGGGCCATTG
1 GTAAGTCCTTCGGGCAATCA
587388 GTAAGTCCTTCGGGCAATCA
1 GTAAGTCCTTCGGGCAATCA
587408 GTAAGTC
1 GTAAGTC
587415 TTTTGAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (20 bp):
GTAAGTCCTTCGGGCAATCA
Found at i:587586 original size:12 final size:12
Alignment explanation
Indices: 587569--587595 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
587559 TCTCATTTAA
587569 AAAAAAGAAGAG
1 AAAAAAGAAGAG
587581 AAAAAAGAAGAG
1 AAAAAAGAAGAG
587593 AAA
1 AAA
587596 GAAAATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAG
Found at i:587605 original size:16 final size:15
Alignment explanation
Indices: 587567--587610 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
587557 TTTCTCATTT
587567 AAAAA-AAAGAAGAGA
1 AAAAAGAAAGAA-AGA
587582 AAAAAGAAGAGAAAGA
1 AAAAAGAA-AGAAAGA
*
587598 AAATAGAAAGAAA
1 AAAAAGAAAGAAA
587611 AAATGAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:588601 original size:2 final size:2
Alignment explanation
Indices: 588594--588632 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
588584 TATTCGGGTT
588594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
588633 TATTTATTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:588701 original size:2 final size:2
Alignment explanation
Indices: 588694--588737 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
588684 GTGCATGTGT
*
588694 TA TA TA TA TA TA TA TA TA TA TA T- TA CTA -A TT 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
588735 TA T
1 TA T
588738 TATTTAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:591151 original size:2 final size:2
Alignment explanation
Indices: 591146--591171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
591136 TGTGTGCTCA
591146 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
591172 TCTACGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591235 original size:2 final size:2
Alignment explanation
Indices: 591230--591290 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
591220 ATATAAGTAC
* *
591230 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
591272 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
591291 ATGATTTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:593406 original size:258 final size:256
Alignment explanation
Indices: 592949--593921 Score: 988
Period size: 258 Copynumber: 3.9 Consensus size: 256
592939 GTCATTTTGA
** * * *
592949 CATCAGTAAACCTTTCGAGCATGATGATTAAATTCTTCGGGTTATCTGTAAGCCTTTCAAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTTATCTGTAAGCCTTTCGAGCAAG
* * *
593014 ATGATAAGTCATTCGGGCCATCTATAAGACCTTTGGGCAGGATATTTTCACATGATTTAAAAAAA
66 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATATTTTCACATGATTT-TAAAAA
** * *
593079 ATGAGAAAGCGATTTCCAAAGTTTCTTATTTAGTGTTTTCAAAAAATGAAATTTTTGAAAAGTAA
130 ATGAGAAAGCGATTTTTAAAGTTTCTCATTTAGTATTTTC-AAAAATGAAATTTTTGAAAAGTAA
593144 GAAAGCGATTTCCAAAGATTT-TTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTC-AGGC
194 GAAAGCGATTTCCAAAG-TTTCTTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCTA-GC
* * * * * *
593207 CATCAGTAAGTCTTTCGAGCATGCTGATTAAATCCTTCAGGTTAACTGTCAGGCTTTCGATCAAT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTTATCTGTAAGCCTTTCGAGCAAG
* *
593272 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAAA
66 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTT-AAAAA
* *
593337 CTGAGAAAGCGATTTTTAAAATTTCTCATTTAGTATTTTCAAAAAGTGAAATTTTTGAAAAGTAA
130 ATGAGAAAGCGATTTTTAAAGTTTCTCATTTAGTATTTTCAAAAA-TGAAATTTTTGAAAAGTAA
* ** * *
593402 GAAAGTGATTTCCAAAGTTTCTTACTGAGTAAACTATTTCCAAAATTGGTAAGTCATTCTAGC
194 GAAAGCGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCTAGC
* * * *
593465 AATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTTATCTGTAAGCCTTTCGAGCAAG
* * ** * * * * *
593530 ATGATAAGTCCTTCGGGCAACCCGTAAGACCTTCGGGTAGAATTTTTTCACATGAATTTGAAAAA
66 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTAAAAAA
* * * * * * *
593595 TGGGAAAGCAATTTTTCAAAGTTTCCCAAATTA-TCTTTTCTGAAAATGAAATTTTCGAAAAGTA
131 TGAGAAAGCGATTTTT-AAAGTTTCTC-ATTTAGTATTTTC-AAAAATGAAATTTTTGAAAAGTA
* * * **
593659 AGAAAACAATTTCCAAAGTTTC-T------T--AC---TT-----A---GTAAGTCCTTCGGGC
193 AGAAAGCGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCTAGC
* ** * *
593703 CATCAGTAAGTCTTTTGAGCATGATGATTAAATTATTC-GCGTCATCTGTAAGTCTTTCGAGCAA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAG-GTTATCTGTAAGCCTTTCGAGCAA
* * * * * * * * *
593767 GATGATAAGTCTTTTGGTCCATTTGTAAGACCTTCGGGTAGGATGTTTTAACATGA-ATTAGAAA
65 GATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTA-AAA
* * * * * * * *
593831 AATGGGAAAGTGATTTTCAAAGTTTCCCATTTAATCTTTTCTTAAAATGAAATTTTCGAAAAGTA
129 AATGAGAAAGCGATTTTTAAAGTTTCTCATTTAGTATTTTC-AAAAATGAAATTTTTGAAAAGTA
*
593896 AGAAAACGATTTCCAAAGTTTCTTAC
193 AGAAAGCGATTTCCAAAGTTTCTTAC
593922 TCAGTAAGTC
Statistics
Matches: 618, Mismatches: 84, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
236 4 0.01
237 64 0.10
238 134 0.22
241 1 0.00
246 2 0.00
249 2 0.00
251 1 0.00
257 27 0.04
258 374 0.61
259 9 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (256 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTTATCTGTAAGCCTTTCGAGCAAG
ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTAAAAAA
TGAGAAAGCGATTTTTAAAGTTTCTCATTTAGTATTTTCAAAAATGAAATTTTTGAAAAGTAAGA
AAGCGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCTAGC
Found at i:593557 original size:41 final size:42
Alignment explanation
Indices: 593471--593557 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
593461 TAGCAATCAA
* * * *
593471 TAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTG
1 TAAGTCTTTCGAGCAAGATGATTAAATCCTTCAGGGCACCCG
*
593513 TAAGTCTTTCGAGCAAGATGA-TAAGTCCTTC-GGGCAACCCG
1 TAAGTCTTTCGAGCAAGATGATTAAATCCTTCAGGGC-ACCCG
593554 TAAG
1 TAAG
593558 ACCTTCGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.08
41 16 0.41
42 20 0.51
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGATTAAATCCTTCAGGGCACCCG
Found at i:594052 original size:237 final size:236
Alignment explanation
Indices: 593450--594037 Score: 822
Period size: 237 Copynumber: 2.5 Consensus size: 236
593440 TCCAAAATTG
** * *
593450 GTAAGTCATTCTAGCAATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTA
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-GGTCATCTGTA
* * * *
593515 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGG-CAACCCGTAAGACCTTCGGGTAGAATTTTTTC
65 AGTCTTTCGAGCAAGATGATAAGT-CTTCGGGTC-ATCTGTAAGACCTTCGGGTAGAATGTTTTA
*
593579 ACATGAATTTGAAAAATGGGAAAGCAATTTTTCAAAGTTTCCCAAATTATCTTTTCTGAAAATGA
128 ACATGAATTAGAAAAATGGGAAAGCAATTTTTCAAAGTTTCCCAAATTATCTTTTCTGAAAATGA
*
593644 AATTTTCGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTTA
193 AATTTTCGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTCA
* * **
593688 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATTATTCGCGTCATCTGTA
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG-GTCATCTGTA
** * *
593753 AGTCTTTCGAGCAAGATGATAAGTCTTTTGGTCCATTTGTAAGACCTTCGGGTAGGATGTTTTAA
65 AGTCTTTCGAGCAAGATGATAAGTCTTCGGGT-CATCTGTAAGACCTTCGGGTAGAATGTTTTAA
** * *
593818 CATGAATTAGAAAAATGGGAAAGTGA-TTTTCAAAGTTTCCC-ATTTAATCTTTTCTTAAAATGA
129 CATGAATTAGAAAAATGGGAAAGCAATTTTTCAAAGTTTCCCAAATT-ATCTTTTCTGAAAATGA
*
593881 AATTTTCGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTCA
193 AATTTTCGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTCA
* * * *
593925 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCAAGCACGATGATTAAATCCTTCGGATCATTTGTC
1 GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG-TCATCTGTA
* *
593990 AGTCTTTCGAGCAAGAAGATAAGTCATTCGGGTCATCTATAAGACCTT
65 AGTCTTTCGAGCAAGATGATAAGTC-TTCGGGTCATCTGTAAGACCTT
594038 TAGGCATAAT
Statistics
Matches: 308, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
236 4 0.01
237 171 0.56
238 132 0.43
239 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (236 bp):
GTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTCATCTGTAA
GTCTTTCGAGCAAGATGATAAGTCTTCGGGTCATCTGTAAGACCTTCGGGTAGAATGTTTTAACA
TGAATTAGAAAAATGGGAAAGCAATTTTTCAAAGTTTCCCAAATTATCTTTTCTGAAAATGAAAT
TTTCGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTCA
Found at i:594900 original size:3 final size:3
Alignment explanation
Indices: 594892--594927 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
594882 TTTGTCTGGG
*
594892 TTA TTA TTA ATA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
594928 GCAGGCCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:596901 original size:2 final size:2
Alignment explanation
Indices: 596894--596924 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
596884 TAACAACCTT
596894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
596925 TAAAAAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597122 original size:13 final size:14
Alignment explanation
Indices: 597101--597134 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
597091 ATATCACTTT
*
597101 TTATCTTTT-AAAA
1 TTATTTTTTAAAAA
597114 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
597128 TTATTTT
1 TTATTTT
597135 AAAAGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTTTTAAAAA
Found at i:604961 original size:42 final size:41
Alignment explanation
Indices: 604914--605005 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 41
604904 CCAAAATAAG
604914 TAAATCCTTCGTGC-CATCAGTAAGTCTTTCGAGC-ATGATGA
1 TAAATCCTTCG-GCTCATCAGTAAGTCTTTCGAGCGA-GATGA
* *
604955 TTAAATCCTCCGGCTCATCTGTAAGTCTTTCGAGCGAGATGA
1 -TAAATCCTTCGGCTCATCAGTAAGTCTTTCGAGCGAGATGA
*
604997 TAAGTCCTT
1 TAAATCCTT
605006 TAGGCCATCC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 9 0.20
42 34 0.77
43 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (41 bp):
TAAATCCTTCGGCTCATCAGTAAGTCTTTCGAGCGAGATGA
Found at i:605054 original size:256 final size:256
Alignment explanation
Indices: 604542--605478 Score: 1198
Period size: 256 Copynumber: 3.7 Consensus size: 256
604532 TAAGATTTTC
* * * *
604542 TGAAAATAAGAAAGT-GATTTCCAAAGTTTTTCATTTATTATTTTCAGAAAATGAAATTTTTGAA
1 TGAAAATGAGAAA-TCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGAAATTTTTGAA
* *
604606 AAGTAAGAAAGCGATT-TCCAAAGTTTCTTACCCAGTAAACTATTTCTC-AAATTGGTAAGTCAT
65 AAGTAAGAAAGCGATTCT-CAAAGTTTCTTACCCAGTAAATTATTTC-CAAAATTAGTAAGTCAT
* *
604669 TCGAGCCATCAGTAAGTCTTTTGAGC---ATGATTAAATCATTCAGGTCATCTATAAGTCTTTCG
128 TCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTAAGTCTTTCG
* * *
604731 AGCGAGATGACAAGTCCTTCGGGCCATCCGTAAGACATTCGGGTAGGATGTTTTCACGTGAATT
193 AGCGAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATT
*
604795 TGAAAATGAGAAATCGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAAATTTTT-AA
1 TGAAAATGAGAAATCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATG-AAATTTTTGAA
* * * * * * *
604859 AAGTAAGAAAGTGACTTCT-AACGTTTATTACCCAGTAAATTCTTTCCAAAATAAGTAAATCCTT
65 AAGTAAGAAAGCGA-TTCTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCATT
* * *
604923 CGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC-CTCCGGCTCATCTGTAAGTCTTTCG
129 CGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGG-TCATCTGTAAGTCTTTCG
** *
604987 AGCGAGATGATAAGTCCTTTAGGCCATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGAATT
193 AGCGAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATT
* *
605051 TGAAAATGATAAAACGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAAA-GAAATTTTTGAA
1 TGAAAATGAGAAATCGATTTCCAAAGTTTCTCATTTAATATTTTCA-AAAAATGAAATTTTTGAA
* * * *
605115 AAGTAAGAAAGTGATTTTCAAAGTTTCTTACCCAATAAATTATTTTCAAAATTAGTAAGTCATTC
65 AAGTAAGAAAGCGATTCTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCATTC
* * * * *
605180 -AGGCCATCAGTAACTCTATCGAGCATGATAATTAAATCATTCTA-GTCATTTGTCAGTCTTTCG
130 GA-GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTC-AGGTCATCTGTAAGTCTTTCG
* * * ** * * * *
605243 AGCAAGATGATAAGTCATCCGGGCCATCTATAAGACCTTCGGGCAGGATATTTCCACATGATTTT
193 AGCGAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGA-ATT
* * *
605308 TGAAAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAATTTTT-AT
1 TG-AAAATGAGAAATCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGAAATTTTTGA-
* * * *
605372 AAAGTAAGAAAGCGATTTTCAAAGTTTCGTACCTAGTAAATTATTTCCAAAATTACTAAGTCATT
64 AAAGTAAGAAAGCGATTCTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCATT
*
605437 TGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATT
129 CGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATT
605479 AGGGTTATCT
Statistics
Matches: 593, Mismatches: 71, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
252 2 0.00
253 119 0.20
254 10 0.02
255 16 0.03
256 283 0.48
257 18 0.03
258 144 0.24
259 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (256 bp):
TGAAAATGAGAAATCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGAAATTTTTGAAA
AGTAAGAAAGCGATTCTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCATTCG
AGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGC
GAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATT
Found at i:607148 original size:256 final size:257
Alignment explanation
Indices: 606684--608096 Score: 1039
Period size: 237 Copynumber: 5.6 Consensus size: 257
606674 ATCGTTTTGG
* * * * *
606684 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTAAGCCTTTCAATCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATATGTAAGCCTTTCGAGCAAG
* * * *
606749 ATGATAAGTCATTCGGGCCATCTAAAAGACCTTCGGGCATGATGTGTTCACATGATTTTAAAAAA
66 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTC-GGCAGGATGTTTTCACATGATTTTAAAAAA
* * *
606814 ATGAGAAAACGATTTTCAAAGTTTCTCATTTAGTGTTTTCAAAAAATGAAATTTTTGAAAAGTAA
130 ATGAGAAAACGATTTTCAAAATTTCTCATTTAGTATTTTCAAAAAATGAAATATTTGAAAAGTAA
* * * * *
606879 GAAAGCGATTTCCAAAGTTTTTTTACCC-A-GAACTATTTCCAAAATCGGT-AGTCATTCGGGC
195 GAAAACAATTTCCAAAG-TTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGAGC
* * * *
606940 CATCAGTAAGTCTTTCGAGAATGTTGATTAAATCC-TCTAGGTCATATGTCAGGCTTTCGAGCAA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-AGGTCATATGTAAGCCTTTCGAGCAA
* * * *
607004 TATTATAAGTCCTTCGAGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAA
65 GATGATAAGTCCTTCGGGCCATCTATAAGACCTTC-GGCAGGATGTTTTCACATGATTTTAAAAA
** * * * * * *
607069 CCTGAGAAAACGGTTTTTAAAATTTCTCATTTAGTATTTTTAGAAAGTGAAATATTTGAAAAGTG
129 AATGAGAAAACGATTTTCAAAATTTCTCATTTAGTATTTTCAAAAAATGAAATATTTGAAAAGTA
* * * * * *
607134 TGAAAATAATTTCCAAAGTTTATTACCCAATAAACTATTTCGAAAATTGGTAAGTCCTTCTAGC
194 AGAAAACAATTTCCAAAGTTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGAGC
* * *
607198 CATCAATAAGTCTTTCGAGCATGATGATTAATTCCTTCAGGTCA-ACTGTAAGTCTTTCGAGCAA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATA-TGTAAGCCTTTCGAGCAA
* ** * * *
607262 GATGATAAGTCCTTCGGGCAATCCGTAAGACCTTCGAGTAGGATGTTTTCACATGAATTT-GAAA
65 GATGATAAGTCCTTCGGGCCATCTATAAGACCTTCG-GCAGGATGTTTTCACATGATTTTAAAAA
* * * * **
607326 AAT-AGGAAAGCGATTTTCAAAGTTTC-C-TGTATAATCTTTTCTGAAAATGAAAT-TTTCGAAA
129 AATGA-GAAAACGATTTTCAAAATTTCTCAT-T-TAGTATTTTCAAAAAATGAAATATTT-GAAA
* * *
607387 ATTAAGAAAATAATTTCCAAAG--T-TT---C--T----TA----C----TCAGTAAGTCATTCG
190 AGTAAGAAAACAATTTCCAAAGTTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCG
*
607432 GGC
255 AGC
* * * * * * **
607435 AATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCACGTCATCTGAAAGTATTTCGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATATGTAAGCCTTTCGAGCAAG
** * * * * * * *
607500 ATGATAAGT-CTTTTGGCCTATTTGTATGACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAA
66 ATGATAAGTCCTTCGGGCC-ATCTATAAGACCTTC-GGCAGGATGTTTTCACATGATTTTAAAAA
** * * * * * **
607564 TTTG-GAAAGTC-ATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAAT-TTTCGAAAAG
129 AATGAGAAA-ACGATTTTCAAAATTTCTCATTTAGTATTTTCAAAAAATGAAATATTT-GAAAAG
* * * *
607626 TAAGAAAACGATTTCCAAAG--T-TT---C--T----TA----C----TCAGTAAATCATTCGGG
192 TAAGAAAACAATTTCCAAAGTTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGAG
*
607671 T
257 C
* * * * *
607672 CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATTTGTCAGTCTTTCAAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATATGTAAGCCTTTCGAGCAAG
* * ** **
607737 ATGATAAGTCCTTCGAGACATCTATAAGACCTTCAGGCATAATGTTTTCACATGACTTTTTTTAA
66 ATGATAAGTCCTTCGGGCCATCTATAAGACCTTC-GGCAGGATGTTTTCACATGA--TTTTAAAA
* * * * *
607802 AAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTGTTTT-AAGAAAATGAAATTTTTGAAAAG
128 AAATGAGAAAACGATTTTCAAAATTTCTCATTTAGTATTTTCAA-AAAATGAAATATTTGAAAAG
* * * * * * * * * * *
607866 TAAGAAAGCAATTTCCAAAGTTTCTTAGCTATTAAACTATTTCTAAAATTGTTAAATCCTTCGGG
192 TAAGAAAACAATTTCCAAAGTTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGAG
607931 C
257 C
* * * * * *
607932 CATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTC-GGATCATCTGTCAGTCTTTCAAGCAA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGG-TCATATGTAAGCCTTTCGAGCAA
* * * * * * * *
607996 GATGATAAGTCATTCTGGCCATCTATAAGACTTTTGGGAAAGATGCTTTCATATGGTATTTGTAA
65 GATGATAAGTCCTTCGGGCCATCTATAAGAC-CTTCGGCAGGATGTTTTCACAT-G-ATTT-TAA
* *
608061 GAAAATGAGAAATCGATTTTCAAAATTTCTCATTTA
126 AAAAATGAGAAAACGATTTTCAAAATTTCTCATTTA
608097 AAAAAAAAGA
Statistics
Matches: 942, Mismatches: 164, Indels: 97
0.78 0.14 0.08
Matches are distributed among these distances:
236 6 0.01
237 294 0.31
238 13 0.01
239 10 0.01
240 62 0.07
241 3 0.00
242 1 0.00
243 2 0.00
245 2 0.00
248 1 0.00
249 1 0.00
251 1 0.00
252 2 0.00
254 2 0.00
255 13 0.01
256 183 0.19
257 80 0.08
258 112 0.12
259 4 0.00
260 113 0.12
261 36 0.04
262 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (257 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATATGTAAGCCTTTCGAGCAAG
ATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGCAGGATGTTTTCACATGATTTTAAAAAAA
TGAGAAAACGATTTTCAAAATTTCTCATTTAGTATTTTCAAAAAATGAAATATTTGAAAAGTAAG
AAAACAATTTCCAAAGTTTATTACCCAATAAACTATTTCCAAAATCGGTAAGTCATTCGAGC
Found at i:607235 original size:42 final size:41
Alignment explanation
Indices: 607184--607276 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
607174 CGAAAATTGG
* *
607184 TAAGTCCTTCTA-GCCATCAATAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTC-AGGCCAACAATAAGTCTTTCGAGCAAGATGA
* * **
607225 TTAATTCCTTCAGGTCAACTGTAAGTCTTTCGAGCAAGATGA
1 -TAAGTCCTTCAGGCCAACAATAAGTCTTTCGAGCAAGATGA
607267 TAAGTCCTTC
1 TAAGTCCTTC
607277 GGGCAATCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 10 0.23
42 33 0.77
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (41 bp):
TAAGTCCTTCAGGCCAACAATAAGTCTTTCGAGCAAGATGA
Found at i:607272 original size:21 final size:21
Alignment explanation
Indices: 607203--607282 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
607193 CTAGCCATCA
* *
607203 ATAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGAGCAAGATG
* *
607224 ATTAATTCCTTC-AGGTCAA-CTG
1 A-TAAGTCCTTCGA-G-CAAGATG
*
607246 -TAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGAGCAAGATG
*
607266 ATAAGTCCTTCGGGCAA
1 ATAAGTCCTTCGAGCAA
607283 TCCGTAAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
19 3 0.07
20 11 0.25
21 17 0.39
22 11 0.25
23 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCAAGATG
Found at i:607290 original size:41 final size:42
Alignment explanation
Indices: 607204--607299 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 42
607194 TAGCCATCAA
* * * *
607204 TAAGTCTTTCGAGCATGATGATTAATTCCTTCAGGTCAACTG
1 TAAGTCTTTCGAGCAAGATGATTAAGTCCTTCAGGGCAACCG
607246 TAAGTCTTTCGAGCAAGATGA-TAAGTCCTTC-GGGCAATCCG
1 TAAGTCTTTCGAGCAAGATGATTAAGTCCTTCAGGGCAA-CCG
* *
607287 TAAGACCTTCGAG
1 TAAGTCTTTCGAG
607300 TAGGATGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.11
41 22 0.47
42 20 0.43
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGATTAAGTCCTTCAGGGCAACCG
Found at i:607986 original size:42 final size:42
Alignment explanation
Indices: 607917--608018 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
607907 TCTAAAATTG
* * ** *
607917 TTAAATCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGA
1 TTAAATCATTCGGACCATCAGTAAGTCTTTCAAGCAAGATGA
* * *
607959 TTAAATCATTCGGATCATCTGTCAGTCTTTCAAGCAAGATGA
1 TTAAATCATTCGGACCATCAGTAAGTCTTTCAAGCAAGATGA
*
608001 -TAAGTCATTCTGG-CCATC
1 TTAAATCATTC-GGACCATC
608019 TATAAGACTT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 13 0.27
42 36 0.73
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TTAAATCATTCGGACCATCAGTAAGTCTTTCAAGCAAGATGA
Found at i:608137 original size:18 final size:18
Alignment explanation
Indices: 608100--608138 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
608090 TCATTTAAAA
*
608100 AAAAAGAGAAAAGAAGAG
1 AAAAAGAGAAAAAAAGAG
* *
608118 AAAAATAGAAAAAAATAG
1 AAAAAGAGAAAAAAAGAG
608136 AAA
1 AAA
608139 GAAAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAGAG
Found at i:608149 original size:24 final size:24
Alignment explanation
Indices: 608113--608184 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
608103 AAGAGAAAAG
608113 AAGAGAAAAATAGAAAAAAATAGA
1 AAGAGAAAAATAGAAAAAAATAGA
*
608137 AAGA-AAAATATAGAAAAAATTAGA
1 AAGAGAAAA-ATAGAAAAAAATAGA
*
608161 AGGAGGAAAGAATA-AATAAAAATA
1 AAGA-GAAA-AATAGAA-AAAAATA
608185 AACCTTCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 4 0.10
24 21 0.52
25 2 0.05
26 12 0.30
27 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (24 bp):
AAGAGAAAAATAGAAAAAAATAGA
Found at i:609150 original size:2 final size:2
Alignment explanation
Indices: 609143--609213 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
609133 TATTCGAGTT
609143 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
*
609185 TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
609214 TTATTACTAG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:610117 original size:29 final size:29
Alignment explanation
Indices: 610066--610123 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
610056 GTGTTGGTCG
*
610066 TAGGTCGCCATGCCATCCGGGCGACCTAT
1 TAGGTCGCCATGCCATCCCGGCGACCTAT
* * * *
610095 TAGGTTGCCATGTCTTCCCGGCGAGCTAT
1 TAGGTCGCCATGCCATCCCGGCGACCTAT
610124 GAGAGAGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCCCGGCGACCTAT
Found at i:610302 original size:29 final size:29
Alignment explanation
Indices: 610261--610337 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
610251 GAGGAGCAGG
610261 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
610290 AGGAATGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
610319 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
610338 TACTGGGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:618592 original size:22 final size:20
Alignment explanation
Indices: 618553--618677 Score: 130
Period size: 21 Copynumber: 5.9 Consensus size: 20
618543 ATTTATGTGC
618553 ATAGAGTATCGATACCCCTGA
1 ATAG-GTATCGATACCCCTGA
618574 TATAGGTATCGATACCCCCCTTTGA
1 -ATAGGTATCGATA--CCCC--TGA
*
618599 ATAGGTATCGATACCCCTTAA
1 ATAGGTATCGATACCCC-TGA
618620 ATAGGTATCGATACCCCTTTGA
1 ATAGGTATCGATACCCC--TGA
618642 AT-GAGTATCGATACCCCTG-
1 ATAG-GTATCGATACCCCTGA
618661 AT-GGTATCGATACCCCT
1 ATAGGTATCGATACCCCT
618678 TGTCGGGTTT
Statistics
Matches: 95, Mismatches: 2, Indels: 16
0.84 0.02 0.14
Matches are distributed among these distances:
18 14 0.15
19 3 0.03
20 2 0.02
21 30 0.32
22 26 0.27
23 4 0.04
24 13 0.14
25 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (20 bp):
ATAGGTATCGATACCCCTGA
Found at i:618624 original size:45 final size:46
Alignment explanation
Indices: 618553--618676 Score: 172
Period size: 45 Copynumber: 2.8 Consensus size: 46
618543 ATTTATGTGC
* *
618553 ATAGAGTATCGATACCCCTGATATAGGTATCGATACCCCCCTTTGA
1 ATAGAGTATCGATACCCCTTAAATAGGTATCGATACCCCCCTTTGA
618599 ATAG-GTATCGATACCCCTTAAATAGGTATCGATA--CCCCTTTGA
1 ATAGAGTATCGATACCCCTTAAATAGGTATCGATACCCCCCTTTGA
*
618642 AT-GAGTATCGATACCCC-T-GAT-GGTATCGATACCCC
1 ATAGAGTATCGATACCCCTTAAATAGGTATCGATACCCC
618677 TTGTCGGGTT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
40 10 0.14
41 2 0.03
42 4 0.06
43 24 0.33
45 28 0.39
46 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (46 bp):
ATAGAGTATCGATACCCCTTAAATAGGTATCGATACCCCCCTTTGA
Found at i:619561 original size:2 final size:2
Alignment explanation
Indices: 619554--619581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
619544 AATGTTTATT
619554 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
619582 CTTGGGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:619877 original size:21 final size:21
Alignment explanation
Indices: 619806--619873 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
619796 AATAAAAAGG
619806 GGGAGAAGTGTTAGAGTAAGA
1 GGGAGAAGTGTTAGAGTAAGA
619827 GGGAGAAGTGTTAGAGTAAGA
1 GGGAGAAGTGTTAGAGTAAGA
*
619848 GGGAGTAA-TGTTAGAGTAAGG
1 GGGAG-AAGTGTTAGAGTAAGA
619869 GGGAG
1 GGGAG
619874 TAATTTTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 43 0.96
22 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.46, T:0.19
Consensus pattern (21 bp):
GGGAGAAGTGTTAGAGTAAGA
Found at i:620302 original size:55 final size:55
Alignment explanation
Indices: 620236--620362 Score: 141
Period size: 56 Copynumber: 2.3 Consensus size: 55
620226 CCCCACAGGA
* * *
620236 GGTACCGATACCCCTATGCTAA-TTTTGACAACAAAAAATAACAG-TGTGCTCGGAG
1 GGTATCGATACCCCCATGC-AAGTTTTGACAACAAAAAATAACAGAT-TACTCGGAG
* ** * *
620291 GGTATCGATACCCCCATGCAAGTTTTTGGCTCCGAGAAATAACAGATTACTCGGAG
1 GGTATCGATACCCCCATGCAAG-TTTTGACAACAAAAAATAACAGATTACTCGGAG
620347 GGTATCGATACCCCCA
1 GGTATCGATACCCCCA
620363 GTAGGTATCG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
54 2 0.03
55 17 0.28
56 41 0.67
57 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (55 bp):
GGTATCGATACCCCCATGCAAGTTTTGACAACAAAAAATAACAGATTACTCGGAG
Found at i:620371 original size:19 final size:19
Alignment explanation
Indices: 620347--620398 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 19
620337 TTACTCGGAG
*
620347 GGTATCGATACCCCCAGTA
1 GGTATCGATACCCCCAATA
620366 GGTATCGATA-CCCCAATA
1 GGTATCGATACCCCCAATA
*
620384 GGTACCGATACCCCC
1 GGTATCGATACCCCC
620399 TGTATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTATCGATACCCCCAATA
Found at i:622540 original size:15 final size:15
Alignment explanation
Indices: 622520--622550 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
622510 GTGATGGACG
622520 GCTGCTATGTATTTA
1 GCTGCTATGTATTTA
622535 GCTGCTATGTATTTA
1 GCTGCTATGTATTTA
622550 G
1 G
622551 GGATTTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (15 bp):
GCTGCTATGTATTTA
Found at i:628985 original size:2 final size:2
Alignment explanation
Indices: 628978--629042 Score: 64
Period size: 2 Copynumber: 33.0 Consensus size: 2
628968 AAGTCTAAGA
* * *
628978 AT AT AT AT AT AT AT AT AT AT AT TT GA- AGT CT A- AG A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT
629019 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
629043 CGATACCTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:629005 original size:35 final size:35
Alignment explanation
Indices: 628962--629034 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
628952 GCATGGGAAT
628962 TATTTGAAGTCTAAGAATATATATATATATATATA
1 TATTTGAAGTCTAAGAATATATATATATATATATA
628997 TATTTGAAGTCTAAGAATATATATATATATATATA
1 TATTTGAAGTCTAAGAATATATATATATATATATA
629032 TAT
1 TAT
629035 ATATATATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (35 bp):
TATTTGAAGTCTAAGAATATATATATATATATATA
Found at i:629390 original size:13 final size:13
Alignment explanation
Indices: 629372--629398 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
629362 CCTTGTCCGG
629372 TTGTACCAACGAT
1 TTGTACCAACGAT
629385 TTGTACCAACGAT
1 TTGTACCAACGAT
629398 T
1 T
629399 CTCAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTACCAACGAT
Found at i:630159 original size:43 final size:42
Alignment explanation
Indices: 630112--630286 Score: 174
Period size: 43 Copynumber: 4.1 Consensus size: 42
630102 TATAGTGATG
*
630112 TTTTTGCCCACAAACGCCGCTAATTCTCTTGTCTTTAGTGGCA
1 TTTTTG-CCACAAACACCGCTAATTCTCTTGTCTTTAGTGGCA
630155 TTTTTTGCCACAAACACCGCTAATTCTCTTGTCTTTAGTGGTGC-
1 -TTTTTGCCACAAACACCGCTAATTCTCTTGTCTTTAGT-G-GCA
* * * * * * *
630199 TTTTGGCTATAAACGCTGCTAATTCTCCTGTCTTTAGTAGTG-T
1 TTTTTGCCACAAACACCGCTAATTCTCTTGTCTTTAGT-G-GCA
* * * *
630242 TTTTTACCACAAACACCGATAATTCTATTGTTTTTAGTGGCA
1 TTTTTGCCACAAACACCGCTAATTCTCTTGTCTTTAGTGGCA
630284 TTT
1 TTT
630287 GTAATACAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 94 0.87
44 7 0.06
45 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (42 bp):
TTTTTGCCACAAACACCGCTAATTCTCTTGTCTTTAGTGGCA
Found at i:630220 original size:86 final size:86
Alignment explanation
Indices: 630123--630281 Score: 237
Period size: 86 Copynumber: 1.8 Consensus size: 86
630113 TTTTGCCCAC
* * * * *
630123 AAACGCCGCTAATTCTCTTGTCTTTAGTGGCATTTTTTGCCACAAACACCGCTAATTCTCTTGTC
1 AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
630188 TTTAGTGGTGCTTTTGGCTAT
66 TTTAGTGGTGCTTTTGGCTAT
* ** *
630209 AAACGCTGCTAATTCTCCTGTCTTTAGTAGTGTTTTTTACCACAAACACCGATAATTCTATTGTT
1 AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
630274 TTTAGTGG
66 TTTAGTGG
630282 CATTTGTAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 64 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (86 bp):
AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
TTTAGTGGTGCTTTTGGCTAT
Found at i:630299 original size:86 final size:86
Alignment explanation
Indices: 630123--630305 Score: 217
Period size: 86 Copynumber: 2.1 Consensus size: 86
630113 TTTTGCCCAC
* * * * *
630123 AAACGCCGCTAATTCTCTTGTCTTTAGTGGCATTTTTTGCCACAAACACCGCTAATTCTCTTGTC
1 AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
* ** *
630188 TTTAGTGGTGCTTTTGGCTAT
66 TTTAGTGGTGCATTTGAATAA
* ** *
630209 AAACGCTGCTAATTCTCCTGTCTTTAGTAGTGTTTTTTACCACAAACACCGATAATTCTATTGTT
1 AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
630274 TTTAGT-G-GCATTTGTAATACA
66 TTTAGTGGTGCATTTG-AATA-A
630295 AAACGCCGCTA
1 AAACGCCGCTA
630306 TATATTATGA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
84 6 0.07
85 3 0.04
86 72 0.89
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (86 bp):
AAACGCCGCTAATTCTCCTGTCTTTAGTAGCATTTTTTACCACAAACACCGATAATTCTATTGTC
TTTAGTGGTGCATTTGAATAA
Found at i:635524 original size:18 final size:18
Alignment explanation
Indices: 635501--635598 Score: 141
Period size: 18 Copynumber: 5.7 Consensus size: 18
635491 TGTTTATGAC
635501 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
635519 GGAATTGGAATCTGT--A
1 GGAATTGGAATCTGTGAA
*
635535 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
635553 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
635571 GAAATTGGAATCTGT--A
1 GGAATTGGAATCTGTGAA
*
635587 TGAATTGGAATC
1 GGAATTGGAATC
635599 CAATTCCATA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
16 26 0.36
18 47 0.64
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:635540 original size:34 final size:35
Alignment explanation
Indices: 635501--635598 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 35
635491 TGTTTATGAC
635501 GGAATTGGAATCTGTGAAGGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTGAAGGAATTGGAATCTGTAA
*
635535 GGAATTAGAATCTGTGAAGGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAAGGAATTGGAATCTGT-AA
* *
635571 GAAATTGGAATCTGT--ATGAATTGGAATC
1 GGAATTGGAATCTGTGAAGGAATTGGAATC
635599 CAATTCCATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 44 0.76
36 14 0.24
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.30
Consensus pattern (35 bp):
GGAATTGGAATCTGTGAAGGAATTGGAATCTGTAA
Found at i:636510 original size:216 final size:208
Alignment explanation
Indices: 636136--636723 Score: 798
Period size: 216 Copynumber: 2.8 Consensus size: 208
636126 AATTATTTTT
*
636136 TTTTCGGGTCGGTCAGGTTTTTTTCACCTTAAACCCGAACCCGACCCGAATATCACACTTAAAAA
1 TTTTCGGGTCGGTCCGGTTTTTTTCACCTTAAACCCGAACCCGACCCGAATATCACACTTAAAAA
* *
636201 ACCCGACCTGACCCGATCAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATC
66 ACCCGACCCGACCCGAACAAAATAAAGTTTCATCC-A-CCGACCCGAATATATGAATTAGAAATC
*
636266 CGACCTGACCCAACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCG
129 C-A----ACCCGACCCGAAATAATAAAAAA-TATTTTTATTTAATAAAAACAGTGACTTAATCCG
*
636331 ACCCTACCCGAATTATATATA
188 ACCCGACCCGAATTATATATA
*
636352 TTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACTCGAATATCACACTT
1 TTTTCGGGTCGGTCCGGTTTTTTTCACCTTAAACCCGAACCCGA--C--C-CGAATATCACACTT
**
636417 AAAAAACCTAACCCGACCCGAACAAAATAAAGTTTCATCCAACACGACCCGAATATATGAATTAG
61 AAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC-AC-CGACCCGAATATATGAATTAG
636482 AAATCCAACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCG
124 AAATCCAACCCGACCCGAAATAAT-AAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCG
*
636547 ACCCGACCTGAATTATATATA
188 ACCCGACCCGAATTATATATA
*
636568 TTTTCGGGTCGGTCCGGTTTTTTT-ACCTTAAACCCG-A----ACCCGAATATCACAGTTAAAAA
1 TTTTCGGGTCGGTCCGGTTTTTTTCACCTTAAACCCGAACCCGACCCGAATATCACACTT-AAAA
* * * * *
636627 AACCCGATCCTACCCTACCAAAATAAAGTTTCA--C-CCGACCCGAATATATGAATTAGAAACCC
65 AACCCGACCCGACCCGAACAAAATAAAGTTTCATCCACCGACCCGAATATATGAATTAGAAATCC
* *
636689 GACCCGACCTGAAATAATAAAAACATATTTTTATT
130 AACCCGACCCGAAATAATAAAAA-ATATTTTTATT
636724 CGAATAAGTT
Statistics
Matches: 342, Mismatches: 21, Indels: 33
0.86 0.05 0.08
Matches are distributed among these distances:
200 5 0.01
201 53 0.15
202 1 0.00
204 1 0.00
205 13 0.04
206 32 0.09
208 1 0.00
210 1 0.00
214 1 0.00
215 11 0.03
216 135 0.39
217 6 0.02
218 1 0.00
220 3 0.01
221 78 0.23
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (208 bp):
TTTTCGGGTCGGTCCGGTTTTTTTCACCTTAAACCCGAACCCGACCCGAATATCACACTTAAAAA
ACCCGACCCGACCCGAACAAAATAAAGTTTCATCCACCGACCCGAATATATGAATTAGAAATCCA
ACCCGACCCGAAATAATAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACC
CGAATTATATATA
Found at i:639797 original size:122 final size:123
Alignment explanation
Indices: 639578--639819 Score: 285
Period size: 122 Copynumber: 2.0 Consensus size: 123
639568 AAAATTTGCA
* * *
639578 GCGTTTGTTTTTAAAAACGCCACTAATTCACTAACCTATTGCGGCGTTTGTTTAAAAAACGCCAC
1 GCGTTTGTATTTAAAAACGCCACTAATGCACTAACCTATTGCGGCATTTGTTTAAAAAACGCCAC
* * * *
639643 AAAGACAAGTCAATAGCGGCATTTCTG-GGAAAATG-CTGCTAATGTTACCATTTTATG
66 AAAGAAAAGGCAATAGCAGCATTTCTGAGAAAAATGTC-GCTAATGTTACCATTTTATG
* ** * *
639700 GCGTTTGTATTTAAAAACGCCACTAATGCACTGATTTATTGTGGCATTTGTTTTAAAAACGCCAC
1 GCGTTTGTATTTAAAAACGCCACTAATGCACTAACCTATTGCGGCATTTGTTTAAAAAACGCCAC
* ** *
639765 AAA-AAATGAGGCTATAGCAGTGTTTCT-AGAAAAATGTCGCTAATGTTATCATTTT
66 AAAGAAA--AGGCAATAGCAGCATTTCTGAGAAAAATGTCGCTAATGTTACCATTTT
639820 GTTTTGTTTG
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
121 2 0.02
122 60 0.60
123 37 0.37
124 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (123 bp):
GCGTTTGTATTTAAAAACGCCACTAATGCACTAACCTATTGCGGCATTTGTTTAAAAAACGCCAC
AAAGAAAAGGCAATAGCAGCATTTCTGAGAAAAATGTCGCTAATGTTACCATTTTATG
Found at i:644245 original size:20 final size:20
Alignment explanation
Indices: 644209--644246 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
644199 ATCCTATTCC
**
644209 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
644229 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
644247 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:646166 original size:44 final size:45
Alignment explanation
Indices: 646102--646216 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 45
646092 GGAAGTTTCT
* * *
646102 GCTATGTGCCAGGGTAAGACCTTACCG-TTTCTGAAGGCTCCTCT
1 GCTATGTGCTAGGGTAAGACCTTACCGTTTTCCGAAGGCTCCTCG
* * *
646146 TCTATGTGCTAGGGTAAGACCTTACCGTTTTCCGTAGGTTCCTCG
1 GCTATGTGCTAGGGTAAGACCTTACCGTTTTCCGAAGGCTCCTCG
* *
646191 GCTTTGTGCTCAGGGTAAGTCCTTAC
1 GCTATGTGCT-AGGGTAAGACCTTAC
646217 TGCAGGCTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 25 0.42
45 21 0.35
46 14 0.23
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (45 bp):
GCTATGTGCTAGGGTAAGACCTTACCGTTTTCCGAAGGCTCCTCG
Found at i:646622 original size:38 final size:38
Alignment explanation
Indices: 646580--646654 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
646570 TACGTATTAC
*
646580 CGATATTTT-ATTATGTAAATGTTTTATATGGTTTTCTA
1 CGATATTTTGA-TATGTAAATGTTTTATATAGTTTTCTA
*
646618 CGATATTTTGATATGTATATGTTTTATATAGTTTTCT
1 CGATATTTTGATATGTAAATGTTTTATATAGTTTTCT
646655 GCCATATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.56
Consensus pattern (38 bp):
CGATATTTTGATATGTAAATGTTTTATATAGTTTTCTA
Found at i:648843 original size:2 final size:2
Alignment explanation
Indices: 648836--649019 Score: 94
Period size: 2 Copynumber: 96.5 Consensus size: 2
648826 TATTCGGGTT
648836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
648877 TT TA T- TA CTA GT- TA TG TA -A GGA T- TA -A T- TA T- TA GT- TA
1 TA TA TA TA -TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
** * *
648913 T- TA T- TA CC TA TA TA TA TG TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** *
648953 TA TA TA T- TA TCA T- TA GT- TA GG TA TA T- TA T- TA GTT TA TA
1 TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
*
648991 TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
649020 TATTTAAATG
Statistics
Matches: 138, Mismatches: 22, Indels: 44
0.68 0.11 0.22
Matches are distributed among these distances:
1 16 0.12
2 113 0.82
3 9 0.07
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:650230 original size:12 final size:12
Alignment explanation
Indices: 650213--650246 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
650203 TCGGCTTGGA
650213 GAAAGAAAGAGT
1 GAAAGAAAGAGT
650225 GAAAGAAAGAGT
1 GAAAGAAAGAGT
650237 GAAAGAAAGA
1 GAAAGAAAGA
650247 AAATACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.06
Consensus pattern (12 bp):
GAAAGAAAGAGT
Found at i:650967 original size:2 final size:2
Alignment explanation
Indices: 650962--650994 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
650952 ACTTGTGTGC
650962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
650995 TATCTATGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:652523 original size:2 final size:2
Alignment explanation
Indices: 652516--652542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
652506 AAATTACTAG
652516 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
652543 TAAACTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:654032 original size:37 final size:37
Alignment explanation
Indices: 653982--654056 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
653972 AGACTCGATC
* *
653982 TTGATTTGCTTCACTACTTTTCCGTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCATGAAGGCTTAAGA
654019 TTGATTTGCTTCACTACTCTTCCATGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCATGAAGGCTTAAGA
654056 T
1 T
654057 AGCACAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (37 bp):
TTGATTTGCTTCACTACTCTTCCATGAAGGCTTAAGA
Found at i:654332 original size:41 final size:42
Alignment explanation
Indices: 654265--654387 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
654255 CATGTGAAAA
* * ** *
654265 CATCTTGCCCGAAAGTCTTATGGATGACCCGAATGACTT-AT
1 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGACTTAAT
*
654306 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
1 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGACTTAAT
* ** * *
654348 CATCATGCTCGAAAGACTTATTGATGGCCCGAAGGTCTTA
1 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGACTTA
654388 CTAAGTAAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 33 0.48
42 36 0.52
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (42 bp):
CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGACTTAAT
Found at i:654571 original size:236 final size:233
Alignment explanation
Indices: 654062--654618 Score: 807
Period size: 236 Copynumber: 2.4 Consensus size: 233
654052 AAGATAGCAC
* ** * *
654062 AAAGAACTTATCATCTTGCTCGGAATCCTGACAGATGACCCGAATGATTTAATCATCATGCTCGA
1 AAAG-ACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGA
* *
654127 AAGACTTACTGATGGCCCGAAGGTCATAGTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTGT
65 AAGACTTATTGATGGCCCGAAGGTCATACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTGT
* * *
654192 CAAAAATTTTAAAAAAAACATTAAATGGGAAACTTTGAAAATTGCTTTCTCATTTTTCAAAATCA
130 CAAAAATTTTAAAAAAAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCAATTTTCAAAATCA
*
654257 TGTGAAAACATCTTGCCCGAAAGTCTTATGGATGACCCG
195 TGTGAAAACATCTTGCCCGAAAGTCTTATGGATGACCCA
*
654296 AATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAA
1 AAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAA
* * * * *
654361 AGACTTATTGATGGCCCGAAGGTCTTACTAAGTAAGAAATTTTGGAAATCGCTTTCTTATTTTTT
66 AGACTTATTGATGGCCCGAAGGTCATACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTGTC
*
654426 AAAATTTTCATTTTAAAAAAATA-TTTAAATGAGAAACTTTGAAAATCGCTTT-T-AATTTTCAA
131 AAAA-----ATTTTAAAAAAA-ACATTAAATGAGAAACTTTGAAAATCGCTTTCTCAATTTTCAA
* *
654488 ATTCATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGACCCA
190 AATCATGTGAAAACATCTTGCCCGAAAGTCTTATGGATGACCCA
* *
654532 AAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGGATTTAATTATCATGCTCGAA
1 AAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAA
*
654597 AGACTTACTT-ATGACCCGAAGG
66 AGACTTA-TTGATGGCCCGAAGG
654619 ATTTAATCAT
Statistics
Matches: 292, Mismatches: 24, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
233 118 0.40
234 3 0.01
236 129 0.44
237 3 0.01
238 38 0.13
239 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (233 bp):
AAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAA
AGACTTATTGATGGCCCGAAGGTCATACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTGTC
AAAAATTTTAAAAAAAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCAATTTTCAAAATCAT
GTGAAAACATCTTGCCCGAAAGTCTTATGGATGACCCA
Found at i:654647 original size:42 final size:42
Alignment explanation
Indices: 654523--654650 Score: 168
Period size: 42 Copynumber: 3.1 Consensus size: 42
654513 AGGTCTTATG
* * * *
654523 GATGACCCAAAAGACTT-ATCATCTTGCTCGAAAGACTTACA
1 GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACT
*
654564 GATGACCCAAAGGATTTAATTATCATGCTCGAAAGACTTACT
1 GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACT
* * * *
654606 TATGACCCGAAGGATTTAATCATCATGCTCGGAAGGCTTACT
1 GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACT
654648 GAT
1 GAT
654651 TGCTTGCTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 15 0.20
42 60 0.80
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (42 bp):
GATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACT
Found at i:663539 original size:17 final size:17
Alignment explanation
Indices: 663517--663570 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
663507 ATATATATAT
*
663517 ATATTAAACTGAACCTA
1 ATATTAAACTAAACCTA
*
663534 ATATTAAACTAAACATA
1 ATATTAAACTAAACCTA
663551 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
663568 ATA
1 ATA
663571 GCCGTATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.30
Consensus pattern (17 bp):
ATATTAAACTAAACCTA
Found at i:664237 original size:93 final size:93
Alignment explanation
Indices: 664078--664250 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
664068 TCGTTGTTTT
*
664078 GAATGGAACAACTGGCTTATGGGACTCGGGTTTGCCATTGGTCCGGGTTTGCTCCAAACCGGGTC
1 GAATGGAACAACTGGCTTATGGGACTCAGGTTTGCCATTGGTCCGGGTTTGCTCCAAACCGGGTC
664143 TCTATTTGAGTTGAAACGGCTTCAGTAA
66 TCTATTTGAGTTGAAACGGCTTCAGTAA
* * *
664171 GAATGGAACAGCTGGCTTATGGGACTCAGGTTTGCCATTGGTCTGGGTTTGCTCCAAATCGGGTC
1 GAATGGAACAACTGGCTTATGGGACTCAGGTTTGCCATTGGTCCGGGTTTGCTCCAAACCGGGTC
664236 TCTATTTGAGTTGAA
66 TCTATTTGAGTTGAA
664251 TCAATGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
GAATGGAACAACTGGCTTATGGGACTCAGGTTTGCCATTGGTCCGGGTTTGCTCCAAACCGGGTC
TCTATTTGAGTTGAAACGGCTTCAGTAA
Found at i:664505 original size:2 final size:2
Alignment explanation
Indices: 664498--664582 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
664488 CTACAATAAG
664498 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
664540 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
664582 T
1 T
664583 GATTTATGTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:666037 original size:15 final size:15
Alignment explanation
Indices: 666017--666047 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
666007 GTGATGGACG
666017 GCTGCTATGTATTTA
1 GCTGCTATGTATTTA
666032 GCTGCTATGTATTTA
1 GCTGCTATGTATTTA
666047 G
1 G
666048 GGATTTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (15 bp):
GCTGCTATGTATTTA
Found at i:666577 original size:114 final size:117
Alignment explanation
Indices: 666353--666565 Score: 335
Period size: 114 Copynumber: 1.8 Consensus size: 117
666343 ACTAAGAGAA
*
666353 TCACTCATGACTTAAACTTTTTGTAACAAAAAAACACTATTCAATTCATCAATGTCGACCCAATA
1 TCACTCATGACCTAAACTTTTTGTAACAAAAAAACAC-ATTCAATTCATCAATGTCGACCCAATA
*
666418 ATCTTATCTATTTCTCTCTCGACCTCAACATTTTGATCTTCTGCTCATGACTC
65 ATCTTATCTATTTCTCTCTAGACCTCAACATTTTGATCTTCTGCTCATGACTC
* *
666471 TCACTCCTGACCTAAAC-TTTTGTAACAAAAAAA-A-ATTCAATTCATCATTGTCGACCCAATAA
1 TCACTCATGACCTAAACTTTTTGTAACAAAAAAACACATTCAATTCATCAATGTCGACCCAATAA
*
666533 TCTTATCTTTTTCT-TCGTAGACCTCAACATTTT
66 TCTTATCTATTTCTCTC-TAGACCTCAACATTTT
666566 TTTCTTTTGC
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
113 2 0.02
114 55 0.62
116 1 0.01
117 16 0.18
118 15 0.17
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (117 bp):
TCACTCATGACCTAAACTTTTTGTAACAAAAAAACACATTCAATTCATCAATGTCGACCCAATAA
TCTTATCTATTTCTCTCTAGACCTCAACATTTTGATCTTCTGCTCATGACTC
Found at i:667160 original size:3 final size:3
Alignment explanation
Indices: 667154--667179 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
667144 TTTTTTCGGG
667154 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
667180 GCAGGCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:669214 original size:21 final size:21
Alignment explanation
Indices: 669185--669237 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
669175 ATTCTGACTA
669185 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
669206 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
669227 TCGCAATGCGA
1 TCGCATTGCGA
669238 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:669256 original size:20 final size:20
Alignment explanation
Indices: 669227--669377 Score: 207
Period size: 20 Copynumber: 7.5 Consensus size: 20
669217 TTTTCCTAAT
669227 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
669247 TCGTAATGCGCATACGTAAA
1 TCGCAATGCGAATACGTAAA
669267 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
669287 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
669307 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
669327 TCGTAATACGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
669347 TCCCAACGCGAAT-C-TAACTA
1 TCGCAATGCGAATACGTAA--A
669367 TCGCAATGCGA
1 TCGCAATGCGA
669378 TTTACATAGC
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
18 3 0.03
20 112 0.97
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:669582 original size:22 final size:22
Alignment explanation
Indices: 669557--669622 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
669547 GGCGACATCC
669557 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
669579 GTCCCCATCTCCGAAGATATCT
1 GTCCCCATCTCCGACGAAATCA
* * *
669601 GTCTCTATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
669623 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:669984 original size:33 final size:34
Alignment explanation
Indices: 669936--670009 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
669926 ACTATCGCAA
**
669936 TGCGATTCTGTCGTTGCGATTTTCATTTT-GCGT
1 TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
*
669969 TGCGATTCT-TGCGTTGCGATAGTCATTTTCGTGT
1 TGCGATTCTGT-CGTTGCGATAGTCATTTTCGCGT
670003 TGCGATT
1 TGCGATT
670010 TTCATTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 25 0.69
34 10 0.28
ACGTcount: A:0.11, C:0.18, G:0.26, T:0.46
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
Found at i:670029 original size:20 final size:20
Alignment explanation
Indices: 669981--670030 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
669971 CGATTCTTGC
**
669981 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
670001 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
670021 GTTGCGATTT
1 GTTGCGATTT
670031 AAAGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:670038 original size:20 final size:20
Alignment explanation
Indices: 669995--670038 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
669985 CGATAGTCAT
** *
669995 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
670015 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
670035 TTTC
1 TTTC
670039 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:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:670502 original size:20 final size:20
Alignment explanation
Indices: 670458--670525 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
670448 CGATTCTTGC
** *
670458 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
* *
670478 ATTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCATTTTCGT
**
670498 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
670518 GTTGCGAT
1 GTTGCGAT
670526 TTAAAGTTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:670535 original size:20 final size:20
Alignment explanation
Indices: 670496--670535 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
670486 AGTCATTTTT
** *
670496 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTAAAGTTTC
670516 GTGTTGCGATTTAAAGTTTC
1 GTGTTGCGATTTAAAGTTTC
670536 AGAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGATTTAAAGTTTC
Found at i:672436 original size:20 final size:20
Alignment explanation
Indices: 672411--672552 Score: 123
Period size: 20 Copynumber: 7.8 Consensus size: 20
672401 AGAATAGTTT
672411 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
672431 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
672451 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
672467 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
672484 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
672500 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
672518 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
672538 ACTATCGCATTGCGA
1 ACTATCGCAATGCGA
672553 TAGTTATTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 28
0.76 0.04 0.21
Matches are distributed among these distances:
14 14 0.14
16 10 0.10
17 8 0.08
18 5 0.05
19 7 0.07
20 59 0.57
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:672491 original size:33 final size:33
Alignment explanation
Indices: 672434--672514 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
672424 GAAAATGACT
** * * *
672434 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
*
672468 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
672501 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
672515 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:673148 original size:21 final size:21
Alignment explanation
Indices: 673057--673161 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
673047 GACTCACCTG
* *
673057 TCATCGTTTAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
673079 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
673099 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
673120 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
673141 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
673162 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:673154 original size:42 final size:42
Alignment explanation
Indices: 673054--673164 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
673044 CCTGACTCAC
* * * * *
673054 CTGTCATCGTTTAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
673096 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
673138 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
673165 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:674565 original size:14 final size:14
Alignment explanation
Indices: 674546--674581 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
674536 ATTGTTTAAT
674546 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
674560 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
674574 TGATTTGT
1 TGATTTGT
674582 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:674746 original size:33 final size:34
Alignment explanation
Indices: 674706--674781 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
674696 GGAAATGACT
674706 ATCGCAACGAGAGAATCACAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
* *
674739 ATTGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
674773 ATCGCAACG
1 ATCGCAACG
674782 CGAAACTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
Found at i:674832 original size:34 final size:33
Alignment explanation
Indices: 674793--674891 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
674783 GAAACTAAAT
*
674793 TCTCGTTGCGATTTTCATTTTCGCATTGTGATTC
1 TCTCGTTGCGATTTTCA-TTTCGCATTGCGATTC
674827 TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
* * ** *
674860 TCTCATTACGATAGTCATTTCCGCGTTGCGAT
1 TCTCGTTGCGATTTTCATTT-CGCATTGCGAT
674892 AGTCAATTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 31 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
Found at i:674853 original size:33 final size:34
Alignment explanation
Indices: 674793--674891 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
674783 GAAACTAAAT
*
674793 TCTCGTTGCGATTTTCATTTTCGCATTGTGATTC
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
674827 TCTCGTTGCGATTTTCA-TTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
* * ** * *
674860 TCTCATTACGATAGTCATTTCCGCGTTGCGAT
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGAT
674892 AGTCAATTCC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.49
34 29 0.51
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (34 bp):
TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
Found at i:674893 original size:20 final size:20
Alignment explanation
Indices: 674868--674951 Score: 134
Period size: 20 Copynumber: 4.2 Consensus size: 20
674858 TCTCTCATTA
674868 CGATAGTCATTTCCGCGTTG
1 CGATAGTCATTTCCGCGTTG
*
674888 CGATAGTCAATTCCGCGTTG
1 CGATAGTCATTTCCGCGTTG
*
674908 CGATAGTCATTTCCGTGTTG
1 CGATAGTCATTTCCGCGTTG
674928 CGATAGTCATATT-CGCGTTG
1 CGATAGTCAT-TTCCGCGTTG
674948 CGAT
1 CGAT
674952 TTCCGCGTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (20 bp):
CGATAGTCATTTCCGCGTTG
Done.