Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_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: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:464390 original size:65 final size:64
Alignment explanation
Indices: 464302--464456 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 64
464292 ACACCTGGGG
* * * *
464302 TGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTTT
1 TGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGG-CT
464366 C
64 C
* * * * ** *
464367 TGCATCGGTACATAAAATGCATTCAATGTTTTAATATATTCAAGAGTGCATCGATGCATGGCTG
1 TGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTC
*
464431 TGCATCGGTACACAAAATGCATTCGA
1 TGCATCGGTACATAAAATGCATTCGA
464457 AATAGGGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 26 0.34
65 50 0.66
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (64 bp):
TGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTC
Found at i:464912 original size:20 final size:20
Alignment explanation
Indices: 464887--464979 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
464877 TTTTCCCAAT
*
464887 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
464907 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
*
464928 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
464948 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
464969 TCGCAATGCGA
1 TCGCAATGCGA
464980 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:464932 original size:41 final size:41
Alignment explanation
Indices: 464887--464979 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
464877 TTTTCCCAAT
464887 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
*
464928 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
464969 TCGCAATGCGA
1 TCGCAATGCGA
464980 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
Found at i:464992 original size:41 final size:41
Alignment explanation
Indices: 464906--465040 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 41
464896 GAATAAGTAA
* *
464906 ATCGCAACGCGAATTGGAAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCG-ATACTG-ACT
*
464947 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
* * * * *
464988 ATCGCAATGCGATAAT--ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGA-AAAATCGCAATGCGATACTGACT
*
465029 TTCGCAACGCGA
1 ATCGCAACGCGA
465041 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
Found at i:464993 original size:20 final size:19
Alignment explanation
Indices: 464968--465082 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
464958 AATTGGGAAA
*
464968 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
464988 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
465009 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
465029 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
465049 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
465069 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
465083 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:465278 original size:22 final size:22
Alignment explanation
Indices: 465250--465293 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
465240 CACTCTCTCA
465250 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
465272 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
465294 TATATCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:465582 original size:20 final size:20
Alignment explanation
Indices: 465557--465594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
465547 CGATTCTCTC
465557 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
465577 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
465595 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:466935 original size:18 final size:18
Alignment explanation
Indices: 466914--466958 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
466904 TCCACTTCGG
*
466914 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
466932 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
466950 GAGCCATCA
1 GAGCCATCA
466959 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:467490 original size:20 final size:20
Alignment explanation
Indices: 467440--467492 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
467430 TAGTTTACTT
* *
467440 TCGCAACACAAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
467460 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
467480 TCGCAATGCGAAA
1 TCGCAACGCGAAA
467493 TGAAAATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:467547 original size:14 final size:14
Alignment explanation
Indices: 467528--467590 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
467518 ATGCGAAATG
467528 AAATCGCAACGACA
1 AAATCGCAACGACA
*
467542 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
467558 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
467574 AAATCGCAACG-CA
1 AAATCGCAACGACA
467587 AAAT
1 AAAT
467591 GAAAATCGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 6 0.14
14 20 0.47
16 8 0.19
18 9 0.21
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:467552 original size:32 final size:33
Alignment explanation
Indices: 467479--467601 Score: 187
Period size: 32 Copynumber: 3.8 Consensus size: 33
467469 GAAAATGGCT
* *
467479 ATCGCAATGCGAAATGAAAATTGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
467512 ATCACAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
467544 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
467576 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
467602 TGCGATTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 59 0.71
33 24 0.29
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:467635 original size:14 final size:14
Alignment explanation
Indices: 467618--467675 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
467608 TTATGTTTCG
*
467618 CGTTGCGAGTTTGT
1 CGTTGCGATTTTGT
*
467632 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
467648 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
467664 CGTTGCGATTTT
1 CGTTGCGATTTT
467676 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:467682 original size:33 final size:32
Alignment explanation
Indices: 467613--467691 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
467603 GCGATTTATG
*
467613 TTTCGCGTTGCGAGTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
467645 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
467678 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
467692 AGCCATTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:467690 original size:19 final size:19
Alignment explanation
Indices: 467634--467733 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
467624 GAGTTTGTCG
*
467634 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
467652 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
467666 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
***
467685 TTGCGATAGCCATTTCTGCA
1 TTGCGATTTTCATTTC-GCA
** *
467705 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
467724 TTGCGATTTT
1 TTGCGATTTT
467734 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 9 0.13
19 23 0.34
20 18 0.27
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:467707 original size:20 final size:19
Alignment explanation
Indices: 467676--467730 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
467666 TTGCGATTTT
467676 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
467695 CATTTCTGCATTGCGATAGT
1 CATTTC-GCATTGCGATAGC
*
467715 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
467731 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:468167 original size:42 final size:42
Alignment explanation
Indices: 468099--468180 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
468089 TCACCGATCA
* * *
468099 TCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATTC
1 TCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTATTC
* *
468141 TCCCTCAAGATTCCCCCCCCACCGTTCAAGAGGCCACTAT
1 TCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTAT
468181 CATCGTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.43, G:0.13, T:0.22
Consensus pattern (42 bp):
TCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTATTC
Found at i:469618 original size:14 final size:14
Alignment explanation
Indices: 469599--469634 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
469589 ATTGTTTAAT
469599 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
469613 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
469627 TGATTTGT
1 TGATTTGT
469635 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:469773 original size:19 final size:19
Alignment explanation
Indices: 469751--469818 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
469741 ATCGCAACGA
469751 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
469770 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
469789 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
469803 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
469819 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:469894 original size:20 final size:20
Alignment explanation
Indices: 469837--469894 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
469827 TCGCATTGCG
* *
469837 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
469857 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
469877 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
469895 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:470981 original size:24 final size:24
Alignment explanation
Indices: 470954--471007 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
470944 GTATTCAAAA
* *
470954 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
470978 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
471002 TTTGAT
1 TTTGAT
471008 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:471199 original size:12 final size:12
Alignment explanation
Indices: 471182--471206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
471172 ATATAATCCT
471182 GAAGAAGAAAAA
1 GAAGAAGAAAAA
471194 GAAGAAGAAAAA
1 GAAGAAGAAAAA
471206 G
1 G
471207 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:471907 original size:20 final size:20
Alignment explanation
Indices: 471882--471934 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
471872 GCGCTATGTA
471882 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
471902 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
471922 TATCTCGTTGCGA
1 AATCGCGTTGCGA
471935 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:471968 original size:20 final size:20
Alignment explanation
Indices: 471943--471996 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
471933 GATTTTGTAT
471943 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
471963 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
471983 TATCGCATTGCGAT
1 TATCGCATTGCGAT
471997 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:471981 original size:61 final size:61
Alignment explanation
Indices: 471883--471999 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
471873 CGCTATGTAA
* * * * *
471883 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
471944 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
472000 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:472015 original size:61 final size:61
Alignment explanation
Indices: 471883--472017 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
471873 CGCTATGTAA
* * * * * ** *
471883 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
471944 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
472006 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
472018 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:472107 original size:21 final size:21
Alignment explanation
Indices: 472067--472107 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
472057 ATTGTATACC
**
472067 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
472088 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
472108 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:472401 original size:14 final size:14
Alignment explanation
Indices: 472372--472408 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
472362 TAAGATTTTC
*
472372 TTTT-AAAAA-CAT
1 TTTTGAAAAATCAA
472384 TTTTGAAAAATCAA
1 TTTTGAAAAATCAA
472398 TTTTGAAAAAT
1 TTTTGAAAAAT
472409 TACTCCCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 13 0.59
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
TTTTGAAAAATCAA
Found at i:472744 original size:19 final size:18
Alignment explanation
Indices: 472713--472760 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
472703 ATTTAAGTTC
*
472713 AAATATCCAAACATCCATA
1 AAATATTCAAACATCCA-A
472732 ATAA-ATTCAAACATCCAA
1 A-AATATTCAAACATCCAA
472750 AAATATTCAAA
1 AAATATTCAAA
472761 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 13 0.50
20 2 0.08
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATATTCAAACATCCAA
Found at i:476357 original size:19 final size:19
Alignment explanation
Indices: 476333--476378 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
476323 TTCTTGAGTA
476333 TAGCCTTGAGAAACAAGTC
1 TAGCCTTGAGAAACAAGTC
476352 TAGCCTTGAGAAACAAGTC
1 TAGCCTTGAGAAACAAGTC
476371 TAGCCTTG
1 TAGCCTTG
476379 TTCCTCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGCCTTGAGAAACAAGTC
Found at i:480712 original size:64 final size:65
Alignment explanation
Indices: 480581--480716 Score: 195
Period size: 65 Copynumber: 2.1 Consensus size: 65
480571 ACACTATTCA
* * *
480581 CATTCGATGTTTCAAAAGATCCAGGAGTGCATCAGTGCATGGTTTGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAAAAGATCCAAGAGTACATCAGTGCATGGTTTGTGCATCGGTACACAAAATG
* * *
480646 CATTCGATGTTTCAATATATTCAAGAGTACATC-GTTGCATGG-TTGTGCATCGGTACACAAAAT
1 CATTCGATGTTTCAAAAGATCCAAGAGTACATCAG-TGCATGGTTTGTGCATCGGTACACAAAAT
480709 G
65 G
480710 CATTCGA
1 CATTCGA
480717 AATAGGGTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 29 0.45
65 35 0.55
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGATCCAAGAGTACATCAGTGCATGGTTTGTGCATCGGTACACAAAATG
Found at i:481279 original size:12 final size:12
Alignment explanation
Indices: 481255--481290 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
481245 GTTGTCTATA
481255 ATAGAGAGTATTG
1 ATAGAG-GTATTG
*
481268 ATAGGGGTATTG
1 ATAGAGGTATTG
481280 ATAGAGGTATT
1 ATAGAGGTATT
481291 AGTTCCCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (12 bp):
ATAGAGGTATTG
Found at i:481468 original size:23 final size:22
Alignment explanation
Indices: 481412--481471 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
481402 GCCTTCATGG
* * *
481412 GGTATTGATAGCCTTTCATAGG
1 GGTATTGATACCCATTCATAGA
*
481434 GGTA-TCAGTACCCATTCATAAGA
1 GGTATTGA-TACCCATTCAT-AGA
481457 GGTATTGATACCCAT
1 GGTATTGATACCCAT
481472 GGTATTGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.07
22 13 0.43
23 13 0.43
24 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (22 bp):
GGTATTGATACCCATTCATAGA
Found at i:481477 original size:15 final size:15
Alignment explanation
Indices: 481457--481501 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
481447 ATTCATAAGA
481457 GGTATTGATACCCAT
1 GGTATTGATACCCAT
*
481472 GGTATTGATACCCAG
1 GGTATTGATACCCAT
481487 GGTATTGATACCCAT
1 GGTATTGATACCCAT
481502 TCATAGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (15 bp):
GGTATTGATACCCAT
Found at i:483824 original size:32 final size:32
Alignment explanation
Indices: 483765--483825 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
483755 ACTCCCTAGT
* *
483765 TTTTCACGTGATAAACTATAACCTTTCCCAGC
1 TTTTCACGGGATAAACTAGAACCTTTCCCAGC
* * *
483797 TTTTCACGGGATCAGCTAGAACTTTTCCC
1 TTTTCACGGGATAAACTAGAACCTTTCCC
483826 CTTTACAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (32 bp):
TTTTCACGGGATAAACTAGAACCTTTCCCAGC
Found at i:484265 original size:22 final size:22
Alignment explanation
Indices: 484240--484302 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
484230 AATTTGAGCC
* *
484240 TTCATGGGGGTATTGATACCCT
1 TTCATAGGGGTATTGATACCCA
* *
484262 TTCATAGGGGTATCGACACCCA
1 TTCATAGGGGTATTGATACCCA
*
484284 TTCATAAGGTGTATTGATA
1 TTCAT-AGGGGTATTGATA
484303 GGGCTATTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
TTCATAGGGGTATTGATACCCA
Found at i:500514 original size:19 final size:21
Alignment explanation
Indices: 500478--500519 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
500468 TTGATTTTTG
500478 TTTAATTATATGTATAAA-AT
1 TTTAATTATATGTATAAACAT
*
500498 TTTAATT-TATTTATAAACAT
1 TTTAATTATATGTATAAACAT
500518 TT
1 TT
500520 AAAAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAATTATATGTATAAACAT
Found at i:500762 original size:23 final size:22
Alignment explanation
Indices: 500727--500773 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
500717 ATTTATCTTT
*
500727 TAAATTTTATAAAAATTATATA
1 TAAATTTTATAAAAAATATATA
500749 TAAATTTTATTAAAAAATATATA
1 TAAATTTTA-TAAAAAATATATA
500772 TA
1 TA
500774 TATTAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTATAAAAAATATATA
Found at i:502123 original size:25 final size:23
Alignment explanation
Indices: 502084--502141 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
502074 ACTTTTTGTT
502084 TTTTGTTTTGCTTTTCTT-TTCTTTTC
1 TTTT-TTTTGCTTTT-TTATTC--TTC
*
502110 TTTTTTTTGGTTTTTTATTCTTC
1 TTTTTTTTGCTTTTTTATTCTTC
502133 TTTTTTTTG
1 TTTTTTTTG
502142 TATGAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.40
24 2 0.07
25 12 0.40
26 4 0.13
ACGTcount: A:0.02, C:0.10, G:0.09, T:0.79
Consensus pattern (23 bp):
TTTTTTTTGCTTTTTTATTCTTC
Found at i:502704 original size:17 final size:17
Alignment explanation
Indices: 502682--502721 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
502672 TTAAGAAAAG
502682 GAAATGGAAATGATAAA
1 GAAATGGAAATGATAAA
502699 GAAATGGAAATGATAAA
1 GAAATGGAAATGATAAA
502716 GAAATG
1 GAAATG
502722 AAAGTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (17 bp):
GAAATGGAAATGATAAA
Found at i:503290 original size:19 final size:20
Alignment explanation
Indices: 503252--503302 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
503242 GAAACCCCTT
*
503252 TGAAAATACATGATTTTTAA
1 TGAAAATACATTATTTTTAA
503272 TGAAAATACATTA-TTTTAA
1 TGAAAATACATTATTTTTAA
*
503291 TGAAGATACATT
1 TGAAAATACATT
503303 CTCATGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (20 bp):
TGAAAATACATTATTTTTAA
Found at i:504174 original size:15 final size:15
Alignment explanation
Indices: 504154--504190 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
504144 CAATCTAAAC
504154 ATAACATTAGCTAGA
1 ATAACATTAGCTAGA
*
504169 ATAACAATAGCTAGA
1 ATAACATTAGCTAGA
504184 ATAACAT
1 ATAACAT
504191 GACATGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (15 bp):
ATAACATTAGCTAGA
Found at i:505759 original size:19 final size:20
Alignment explanation
Indices: 505722--505771 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
505712 AACCCCTTTG
505722 GAAAATACATGATTTTTAAT
1 GAAAATACATGATTTTTAAT
505742 GAAAATACATGA-TTTTAAT
1 GAAAATACATGATTTTTAAT
*
505761 GAAGATACATG
1 GAAAATACATG
505772 CTCATGGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAT
Found at i:507587 original size:24 final size:21
Alignment explanation
Indices: 507560--507603 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
507550 AATAAATCAA
507560 AATAAGTAATGAAAAACTATCGAC
1 AATAAG-AAT-AAAAA-TATCGAC
*
507584 AATATGAATAAAAATATCGA
1 AATAAGAATAAAAATATCGA
507604 ACCAGGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (21 bp):
AATAAGAATAAAAATATCGAC
Found at i:509063 original size:18 final size:19
Alignment explanation
Indices: 509036--509076 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
509026 GTAGGAGTTC
*
509036 TTTTCTTTCTTTTTTTTGT
1 TTTTCTTTCTTTCTTTTGT
509055 TTTTC-TTCTTTCTTTTGT
1 TTTTCTTTCTTTCTTTTGT
509073 TTTT
1 TTTT
509077 TCTTGATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTTGT
Found at i:509895 original size:19 final size:20
Alignment explanation
Indices: 509847--509896 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
509837 AAACCCCTTT
*
509847 GAAAATACATGATTTTTAAT
1 GAAAATACATGATTTTTAAA
*
509867 GAAAAAACATGA-TTTTAAA
1 GAAAATACATGATTTTTAAA
*
509886 GAAGATACATG
1 GAAAATACATG
509897 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAA
Found at i:514101 original size:12 final size:12
Alignment explanation
Indices: 514084--514110 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
514074 GCAAGCACTC
514084 AAAGAAGAAAAG
1 AAAGAAGAAAAG
514096 AAAGAAGAAAAG
1 AAAGAAGAAAAG
514108 AAA
1 AAA
514111 AGAAAATTGC
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):
AAAGAAGAAAAG
Found at i:521897 original size:15 final size:16
Alignment explanation
Indices: 521879--521931 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
521869 AAAGAACAAG
521879 TTATTAATATAATA-A
1 TTATTAATATAATATA
521894 TTA-TAGATATAATATA
1 TTATTA-ATATAATATA
*
521910 TATATGAATATAACTATA
1 T-TATTAATATAA-TATA
521928 TTAT
1 TTAT
521932 AACATATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 2 0.06
17 11 0.34
18 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (16 bp):
TTATTAATATAATATA
Found at i:529173 original size:17 final size:18
Alignment explanation
Indices: 529141--529176 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
529131 TAGGTTAGTG
529141 TAGAAAGGAATAGAAGAAA
1 TAGAAAGG-ATAGAAGAAA
529160 TAGAAAGG-TAGAAGAAA
1 TAGAAAGGATAGAAGAAA
529177 GGATTCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (18 bp):
TAGAAAGGATAGAAGAAA
Found at i:529581 original size:19 final size:16
Alignment explanation
Indices: 529560--529598 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
529550 TTAGGAAGAT
*
529560 GATGATGGCCTTGATG
1 GATGATGACCTTGATG
529576 GATGATGACCTTGATG
1 GATGATGACCTTGATG
529592 GATGATG
1 GATGATG
529599 TTGATGGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.36, T:0.31
Consensus pattern (16 bp):
GATGATGACCTTGATG
Found at i:529614 original size:15 final size:13
Alignment explanation
Indices: 529570--529617 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 13
529560 GATGATGGCC
529570 TTGATGGATGATG
1 TTGATGGATGATG
529583 ACCTTGATGGATGATG
1 ---TTGATGGATGATG
529599 TTGATGGAGTTGATG
1 TTGATGGA--TGATG
529614 TTGA
1 TTGA
529618 AATGGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.27
15 9 0.30
16 13 0.43
ACGTcount: A:0.23, C:0.04, G:0.35, T:0.38
Consensus pattern (13 bp):
TTGATGGATGATG
Found at i:539321 original size:20 final size:20
Alignment explanation
Indices: 539296--539345 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
539286 TGTCTGAGGA
539296 CTTTTTTTCATTTATTCATT
1 CTTTTTTTCATTTATTCATT
539316 C-TTTTTT-A-TTATTCATT
1 CTTTTTTTCATTTATTCATT
539333 -TTTCTTTTCATTT
1 CTTT-TTTTCATTT
539346 TTTCTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 7 0.27
20 3 0.12
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTTTTTTCATTTATTCATT
Found at i:539330 original size:25 final size:22
Alignment explanation
Indices: 539300--539366 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 22
539290 TGAGGACTTT
539300 TTTTCATTTATTCATTCTTTTTTA
1 TTTTCATTT-TTC-TTCTTTTTTA
*
539324 TTATTCATTTTTCTTTTCATTTTTTC
1 TT-TTCATTTTTC--TTC-TTTTTTA
539350 TTTTCATTTTTTCTTCT
1 TTTTCA-TTTTTCTTCT
539367 ATCAACTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 1 0.03
24 8 0.22
25 14 0.38
26 14 0.38
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCATTTTTCTTCTTTTTTA
Found at i:539361 original size:13 final size:13
Alignment explanation
Indices: 539300--539364 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
539290 TGAGGACTTT
*
539300 TTTTCATTTATTC
1 TTTTCATTTTTTC
* *
539313 -ATTC-TTTTTTA
1 TTTTCATTTTTTC
539324 TTATTCA-TTTTTC
1 TT-TTCATTTTTTC
539337 TTTTCATTTTTTC
1 TTTTCATTTTTTC
539350 TTTTCATTTTTTC
1 TTTTCATTTTTTC
539363 TT
1 TT
539365 CTATCAACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 5 0.12
12 7 0.16
13 31 0.72
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCATTTTTTC
Found at i:539693 original size:45 final size:45
Alignment explanation
Indices: 539571--540065 Score: 220
Period size: 44 Copynumber: 11.1 Consensus size: 45
539561 CTATGATTGT
* * * * *
539571 ATCTAG-AAGAAGAGTGACGTTGATCCAACTCCTAATATGATGGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* * * * *** *
539615 ATCGAGCAATATG-GTGAAGAAAATCTAACTCCTTATGTAATGGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* ** * * *
539659 ATCTTGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATTGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* * * * *
539704 ATCGAGC-AAAATAGTGATGTTGATCCAACACCTTATGTGATAGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* *
539748 ATCTAACAAAAAGAGTGATGTTGATCCAACTCCTTATGTGATGGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* ** * * * *
539793 ATCGAGGGAAATG-GTAATGTTGATTCAACTCCTTAT-TCGATGGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGT-AATGGA
** * * * *
539837 ATCTAGCATAAAA-AGTG-TCACTAATCCAACTCTTTATGTGATGGG
1 ATCTAGCA-AAAAGAGTGAT-GTTGATCCAACTCCTTATGTAATGGA
* * *** * * * ** *
539882 ATCAAGCAAAATG-GTGACACTGGTCCAACTTCTTACGCGATGAA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* *** * * *
539926 ATCAAATGAAATGA-TGATGTTGATCCAACTCTTTATGTGATGGA
1 ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* * * * * * *
539970 ATCTAGAGAAAAAAAAG-AATGTTGATCCACCTCTTTCTGTGATGGA
1 ATCT--AGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
* * * * *
540016 ATCTAGAAAAAAAAAAG-GAATGTTGATCCACCTCCTTTTGTGATGGA
1 ATCTAG--CAAAAAGAGTG-ATGTTGATCCAACTCCTTATGTAATGGA
540063 ATC
1 ATC
540066 GAATATGCAA
Statistics
Matches: 343, Mismatches: 91, Indels: 31
0.74 0.20 0.07
Matches are distributed among these distances:
43 1 0.00
44 164 0.48
45 104 0.30
46 45 0.13
47 29 0.08
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (45 bp):
ATCTAGCAAAAAGAGTGATGTTGATCCAACTCCTTATGTAATGGA
Found at i:539738 original size:89 final size:89
Alignment explanation
Indices: 539571--539893 Score: 246
Period size: 89 Copynumber: 3.6 Consensus size: 89
539561 CTATGATTGT
* * * * *
539571 ATCTAG-AAGAAGAGTGACGTTGATCCAACTCCTAATATG--ATGGAATCGAGCAATATGGTGAA
1 ATCTAGCAAAAAGAGTGACATGGATCCAACTCCT--TATGAAATGGAATCGAGCAAAATAGT-AA
*** * * *
539633 -GAAAATCTAACTCCTTATGTAATGGA
63 TGTTGATCCAACACCTTATGTGATGGA
* * *
539659 ATCTTGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATTGAATCGAGCAAAATAGTGATGT
1 ATCTAGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATGGAATCGAGCAAAATAGTAATGT
*
539724 TGATCCAACACCTTATGTGATAGA
66 TGATCCAACACCTTATGTGATGGA
* ** * ** ** *
539748 ATCTAACAAAAAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATCGAGGGAAATGGTAATGT
1 ATCTAGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATGGAATCGAGCAAAATAGTAATGT
* *
539813 TGATTCAACTCCTTAT-TCGATGGA
66 TGATCCAACACCTTATGT-GATGGA
* * * ** * *
539837 ATCTAGCATAAAA-AGTGTCACT-AATCCAACTCTTTATGTGATGGGATCAAGCAAAAT
1 ATCTAGCA-AAAAGAGTGACA-TGGATCCAACTCCTTATGAAATGGAATCGAGCAAAAT
539894 GGTGACACTG
Statistics
Matches: 188, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
87 4 0.02
88 7 0.04
89 172 0.91
90 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (89 bp):
ATCTAGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATGGAATCGAGCAAAATAGTAATGT
TGATCCAACACCTTATGTGATGGA
Found at i:539892 original size:178 final size:178
Alignment explanation
Indices: 539580--539972 Score: 388
Period size: 178 Copynumber: 2.2 Consensus size: 178
539570 TATCTAGAAG
* * *
539580 AAGAGTGACGTTGATCCAACTCCTAATATGATGGAATCGAGCAATATGGTGAAGAAAATCTAACT
1 AAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAATATGGTGAAGAAAATCTAACT
* * * *
539645 CCTTATGTAATGGAATCTTGCAAAAAGAGTGACATGGATCCAACTCCTTATGAAATTGAATCGAG
66 CCTTATGTAATGGAATCTAGCAAAAAGAGTGACATGAATCCAACTCCTTATGAAATGGAATCAAG
*** * * *
539710 CAAAATAGTGATGTTGATCCAACACCTTATGTGAT-AGAATCTAACAAA
131 CAAAATAGTGACACTGATCCAACACCTTACGCGATGA-AATCAAACAAA
* ***
539758 AAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATCGAGGGAA-ATGGT-AATGTTGAT-TCA
1 AAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATCGA-GCAATATGGTGAA-GAAAATCT-A
* * * ** *
539820 ACTCCTTAT-TCGATGGAATCTAGCATAAAA-AGTGTCACT-AATCCAACTCTTTATGTGATGGG
63 ACTCCTTATGT-AATGGAATCTAGCA-AAAAGAGTGACA-TGAATCCAACTCCTTATGAAATGGA
* * ** **
539882 ATCAAGCAAAATGGTGACACTGGTCCAACTTCTTACGCGATGAAATCAAATGAA
125 ATCAAGCAAAATAGTGACACTGATCCAACACCTTACGCGATGAAATCAAACAAA
* *
539936 ATGA-TGATGTTGATCCAACTCTTTATGTGATGGAATC
1 AAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATC
539973 TAGAGAAAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
177 36 0.20
178 132 0.75
179 9 0.05
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (178 bp):
AAGAGTGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAATATGGTGAAGAAAATCTAACT
CCTTATGTAATGGAATCTAGCAAAAAGAGTGACATGAATCCAACTCCTTATGAAATGGAATCAAG
CAAAATAGTGACACTGATCCAACACCTTACGCGATGAAATCAAACAAA
Found at i:539994 original size:46 final size:46
Alignment explanation
Indices: 539942--540065 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
539932 TGAAATGATG
* *
539942 ATGTTGATCCAACTCTTTATGTGATGGAATCTAGAGAAAAAAAA-GA
1 ATGTTGATCCACCTCTTT-TGTGATGGAATCTAGAAAAAAAAAAGGA
539988 ATGTTGATCCACCTCTTTCTGTGATGGAATCTAGAAAAAAAAAAGGA
1 ATGTTGATCCACCTCTTT-TGTGATGGAATCTAGAAAAAAAAAAGGA
540035 ATGTTGATCCACCTCCTTTTGTGATGGAATC
1 ATGTTGATCCACCT-CTTTTGTGATGGAATC
540066 GAATATGCAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
46 41 0.56
47 28 0.38
48 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGTTGATCCACCTCTTTTGTGATGGAATCTAGAAAAAAAAAAGGA
Found at i:546880 original size:25 final size:25
Alignment explanation
Indices: 546852--546952 Score: 130
Period size: 25 Copynumber: 4.0 Consensus size: 25
546842 ATGCGCAATA
* *
546852 TGCACTCGAAAGTTCCTCGCATAAT
1 TGCACTCGAAAGTGCCTCGTATAAT
*
546877 TGCACTCGAAAGTGCCTCGTACAAT
1 TGCACTCGAAAGTGCCTCGTATAAT
* *
546902 TGCACTCAAAAGTGCCTTGTATAAT
1 TGCACTCGAAAGTGCCTCGTATAAT
* * *
546927 TACACTCGAAAGAGCCTCATATAAT
1 TGCACTCGAAAGTGCCTCGTATAAT
546952 T
1 T
546953 ACACCATAGG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (25 bp):
TGCACTCGAAAGTGCCTCGTATAAT
Found at i:552643 original size:3 final size:3
Alignment explanation
Indices: 552635--552666 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
552625 ACCTCAAAAT
552635 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
552667 CTTTACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:553477 original size:32 final size:32
Alignment explanation
Indices: 553455--553536 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
553445 AAGCAAACGT
*
553455 GGTATCGGTTTTGTTATTGGCTAAAAAAAGGC
1 GGTACCGGTTTTGTTATTGGCTAAAAAAAGGC
553487 GGTACCGGTTTTGTTATTGGCTAAAAAAAGGC
1 GGTACCGGTTTTGTTATTGGCTAAAAAAAGGC
553519 GGTACCGGTTTTGTTATT
1 GGTACCGGTTTTGTTATT
553537 TTTGTGCATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (32 bp):
GGTACCGGTTTTGTTATTGGCTAAAAAAAGGC
Found at i:554756 original size:24 final size:24
Alignment explanation
Indices: 554729--554798 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
554719 AACATCAAAT
554729 ACAATAAAATAATATTATTTATTA
1 ACAATAAAATAATATTATTTATTA
* *
554753 ACAAAAAAATAATATTATTTTGTTA
1 ACAATAAAATAATATTA-TTTATTA
* *
554778 ACTATTAGAATAAT-TTATTTA
1 AC-AATAAAATAATATTATTTA
554799 ATATTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
24 19 0.50
25 11 0.29
26 8 0.21
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (24 bp):
ACAATAAAATAATATTATTTATTA
Found at i:554907 original size:26 final size:27
Alignment explanation
Indices: 554878--554941 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
554868 TTAAAATAAA
*
554878 ATTATTATAAATTATAT-TTATTATTT
1 ATTATTATAAATAATATATTATTATTT
*
554904 ATTATAATAAGAATAATATATTATTATTT
1 ATTATTAT-A-AATAATATATTATTATTT
554933 A-TATTATAA
1 ATTATTATAA
554942 TGAGAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 8 0.25
27 2 0.06
28 12 0.38
29 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTATTATAAATAATATATTATTATTT
Found at i:554913 original size:37 final size:36
Alignment explanation
Indices: 554829--554913 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 36
554819 ATTATTAAAA
*
554829 TATTATATCTAAAATTTTATAAATAATTATTATATTT
1 TATTATA-ATAAAATTTTATAAATAATTATTATATTT
* *
554866 TATTAAAATAAAATTATTATAAATTA-TATT-TATTATT
1 TATTATAATAAAATT-TTATAAATAATTATTATA-T-TT
554903 TATTATAATAA
1 TATTATAATAA
554914 GAATAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 2 0.05
36 12 0.29
37 27 0.66
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
TATTATAATAAAATTTTATAAATAATTATTATATTT
Found at i:554955 original size:29 final size:29
Alignment explanation
Indices: 554890--554955 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
554880 TATTATAAAT
*
554890 TATATTTATTATTTATTATAATAAGAATAA
1 TATA-TTATTATTTATTATAATAAGAAGAA
*
554920 TATATTATTATTTA-TATTATAATGAGAGAA
1 TATATTATTATTTATTATAATAA-GA-AGAA
554950 TA-ATTA
1 TATATTA
554956 AACATATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 7 0.22
29 16 0.50
30 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (29 bp):
TATATTATTATTTATTATAATAAGAAGAA
Found at i:555672 original size:21 final size:24
Alignment explanation
Indices: 555614--555675 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 24
555604 ATTTATGTCA
555614 ATATTATTATTAAAATATTATATCT
1 ATATT-TTATTAAAATATTATATCT
*
555639 ATAATTTTA-TAAATTA-T-TAT-T
1 AT-ATTTTATTAAAATATTATATCT
555660 ATATTTTATTAAAATA
1 ATATTTTATTAAAATA
555676 AAATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 3 0.09
23 1 0.03
24 6 0.18
25 5 0.15
26 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTTATTAAAATATTATATCT
Found at i:555686 original size:37 final size:36
Alignment explanation
Indices: 555641--555713 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
555631 TTATATCTAT
555641 AATTTTATAAATTAT-TATTA-TATTTTATTAAAATAA
1 AATTTTATAAATTATAT-TTATTA-TTTATTAAAATAA
*
555677 AATTATTATAAATTATATTTATTATTTATTATAATAA
1 AATT-TTATAAATTATATTTATTATTTATTAAAATAA
555714 GAATAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 26 0.79
38 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
AATTTTATAAATTATATTTATTATTTATTAAAATAA
Found at i:556321 original size:24 final size:24
Alignment explanation
Indices: 556294--556345 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
556284 AACATCAAAT
556294 ACAATAA-AATAATATTATTTATTA
1 ACAATAATAATAATATTATTT-TTA
556318 ACAA-AATAATAATATTATTTTTA
1 ACAATAATAATAATATTATTTTTA
556341 A-AATA
1 ACAATA
556346 TTAGAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.27
24 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
ACAATAATAATAATATTATTTTTA
Found at i:556459 original size:33 final size:30
Alignment explanation
Indices: 556409--556475 Score: 73
Period size: 33 Copynumber: 2.1 Consensus size: 30
556399 ATCTATAATT
*
556409 TTATAAATAAAAAATTATGATTATTATATTGTA
1 TTATAAATAAAAAATTAT-A-AATTATATT-TA
*
556442 TTAT-AATAAAATTATTATAAATTATATTTA
1 TTATAAATAAAA-AATTATAAATTATATTTA
556472 TTAT
1 TTAT
556476 TTATTATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 6 0.19
31 8 0.26
32 8 0.26
33 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATAAATAAAAAATTATAAATTATATTTA
Found at i:556612 original size:774 final size:773
Alignment explanation
Indices: 553544--556629 Score: 4407
Period size: 800 Copynumber: 4.0 Consensus size: 773
553534 ATTTTTGTGC
* *
553544 ATAACAAAACCGATAAAAATTACCGAAAACATCATTATTTTAACAAAACCGATAAAGCGCTACCG
1 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
* * * *
553609 ATTTTGTTATTTTTTTACCAGTTTTGTTATTGTTGGGCATTTGACCGGAAATATTAAAAAAATTG
66 GTTTTGTTATTTTGTTATCAGTTTTGTTATTGTTGGGCATTTTACCGGAAATATT--AAAAA---
* * * *
553674 ATGTTTTAGGTAGAAATAATAATGTTTTATGTAATTTTTATCGGTTTTGTTATACCCAACAATAA
126 A---CTT--GTAG-------AATGTTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAA
* * * *
553739 CAAATCCGGTAAGAATAGACTTTTTAATAATAAAATTAAT-AA-AC------T-CAAATTAATTT
179 CAAAACCGGTAAAAATAGACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAATTT
* *
553795 TAATTTTTTAGTTTGTAAGTTGCCACGATATAACTAATG-AAAAAAGGACACGATATTTCTATTT
244 TAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTATTTCTATTT
*
553859 CGATATTAACTTTCTAATAA-AAAAT-----A-AAAAA-AT-TATATATAATTACAATATAATTT
309 CGATATTAGCTTTCTAATAATAAAATAAAAAATAAAAATATATATATATAATTACAATATAATTT
*
553915 TAAAAAATAATCATAATTAAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAA
374 TAAAAAA-AATCATAATGAAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAA
*
553980 TACAAT-AAATAATATTATTTATTAACAAAATAATATTATTA-TTTTAAAATATATAAGAATAAT
438 TACAATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTTAAAATAT-T-AGAATAAT
554043 TTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATAAAA
501 TTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAATTTTATAAAT--AA
*
554108 ATTATGATTATTATATTTTATTAAAATAAAATTATTACAAATTATATTTATTATTTATTATAATA
564 A-T-T-ATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTTATTATAATA
554173 AGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGCGTCGATACATTTT
626 AGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGCGTCGATACATTTT
554238 CTAAAAGTATCGACACATATGTTACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAA
691 CTAAAAGTATCGACACATATGTTACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAA
*
554303 TGTATCCGGTATACAACA
756 TGTAACCGGTATACAACA
*
554321 ATAACAAAACCGGTAGAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACC-
1 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
*
554385 -------------G------GTTTTGTTATTGTTGGGCATTTTACCGGAAATGTTAAAAAA--T-
66 GTTTTGTTATTTTGTTATCAGTTTTGTTATTGTTGGGCATTTTACCGGAAATATTAAAAAACTTG
** * * *
554428 T-G-ATGTTTTAGGTAATTTTTATTGGTTTTGTTATGTCCAACAATTACAAAATCGGTAAAAATA
131 TAGAATGTTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGGTAAAAATA
554491 GACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAA-TTT--TTTTTTAGTTTGTA
196 GACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAATTTTAATTTTTTAGTTTGTA
* *
554553 AGTTGCCAAAATATAACTAATGAAAAAAA-GACACGGTATTTCTATTTCGATATTATCTTTCTAA
261 AGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTATTTCTATTTCGATATTAGCTTTCTAA
*
554617 TAATAAAATAAAAAATAAAAAAATA-ATATATAATTACAATATAAATTTT-AAAAAAATCATAAT
326 TAATAAAATAAAAAATAAAAATATATATATATAATTACAATAT-AATTTTAAAAAAAATCATAAT
554680 GAAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACAATAAAATAATATT
390 GAAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACAATAAAATAATATT
* * *
554745 ATTTATTAACAAAAAAATAATATTATTTTGTTAACTATTAGAATAATTTATTTAATATTATTTAT
455 ATTTATTAACAAAATAATAATATTATTTT-TAAAATATTAGAATAATTTATTTAATATTATTTAT
*
554810 GTCAATATTATTATTAAAATATTATATCTAAAATTTTATAAAT--A--ATTATTATATTTTATTA
519 GTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATAAATTATTATTATATTTTATTA
* *
554871 AAATAAAATTATTATAAATTATATTTATTATTTATTATAATAAGAATAATATATTATTATTTATA
584 AAATAAAATTATTATAAATTATATTTATTATTTATTATAATAAGAATAATATATCATTAATTATA
* * *
554936 TTATAATGAGAGAATAATTAAACATATGCGTCAATACAGTTTCTAAAAGTATCGACACATATGTT
649 TTATAATGAGAGAATAGTTAAACATATGCGTCGATACATTTTCTAAAAGTATCGACACATATGTT
*
555001 ACATCGAAACCGATAATTATAATGTAATAGGTAAATATACAATGTAACCGGTATACAACA
714 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATACAACA
555061 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
1 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
* *
555126 GTTTTGTTATTTTTTTA-CCGATTTTGTTATTGTTGGGCATTTTACCGGAAATATTAAAAAACAT
66 GTTTTGTTATTTTGTTATCAG-TTTTGTTATTGTTGGGCATTTTACCGGAAATATTAAAAAAC--
* *
555190 TGATGTTTTAGGTAGAAATAATAATGTTTTAGGTAATTGTTACTGGTTTTGTTATGCCCAACAAT
128 -------TT--GTAG-------AATGTTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAAT
*
555255 AACAAAACCGGTAAAAATAGACTTTTTAATGATAAAATTAGAAAACACAAATTATACAAATTAAT
177 AACAAAACCGGTAAAAATAGACTTTTTAATGATAAAATTAGTAAACACAAATTATAC--A--AA-
* *
555320 TTTAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAGAAAAATGACACGGTAT
237 -TTAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTAT
555385 TTCTATTTCGATATTAGCTTTCTAATAATAAAATAAAAAAATAAAATATATATATATATATATAA
301 TTCTATTTCGATATTAGCTTTCTAATAATAAAAT-AAAAAAT--AA-A-A-ATATATATATATAA
*
555450 TTACAATATAATTTTTAAAAAAAAATCATAATGAAATGATGAAAAATAATCATAATTACAATATA
360 TTACAATATAA-TTTT-AAAAAAAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATA
*
555515 ACTATAAACATCAAATACAATAAAATAATATTATTTATTAACAAAATAATATTATT-TTTTTAAA
423 ACTATAAACATCAAATACAATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTTAAA
555579 ATATTAGAATAATTTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAA-
488 ATATTAGAATAATTTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAAT
555643 TTT-T--ATAAATTATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTTA
553 TTTATAAATAAATTATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTTA
* * *
555705 TTATAATAAGAATAATATATCATTAATTATATTATACTTAGAGAATAGTTAAGCATATGCGTCGA
618 TTATAATAAGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGCGTCGA
* ** * *
555770 TACATTTTCTAAAAGTATAGACATTTATGTTACATCTAAACCCATAATTATAATGTAATAGGTAA
683 TACATTTTCTAAAAGTATCGACACATATGTTACATCGAAACCGATAATTATAATGTAATAGGTAA
*
555835 ATTTACAATGTAACTGGTATACAACA
748 ATTTACAATGTAACCGGTATACAACA
* * *
555861 ATAGCAAAACCGGTAAAAATTATCGAAAACATCATTATTTTAACAAAACCGGTAAAACGCTACCG
1 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
* *
555926 GTTTTGTTATTTTGTTATCAGGTTTGTTATTGTTGGGCATTTTACCGGAAATGTTAAAAAACTT-
66 GTTTTGTTATTTTGTTATCAGTTTTGTTATTGTTGGGCATTTTACCGGAAATATTAAAAAACTTG
555990 T-G-ATGTTTTAGGTAATTTTTACCGG-TTTGTTATGCCCAACAATAACAAAACCGGTAAAAATA
131 TAGAATGTTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGGTAAAAATA
556052 GACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAATTTTAATTTTTTAGTTTGTA
196 GACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAATTTTAATTTTTTAGTTTGTA
* *
556117 AGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTATTTCAATTTCGATATTAGCTTCCTAA
261 AGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTATTTCTATTTCGATATTAGCTTTCTAA
556182 TAATAAAATAAAAAATAAAAATATATATATATAATTACAATATAATTTT-AAAAAAATCATAATG
326 TAATAAAATAAAAAATAAAAATATATATATATAATTACAATATAATTTTAAAAAAAATCATAATG
*
556246 AAGTGAAGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACAATAAAATAATATTA
391 AAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACAATAAAATAATATTA
* *
556311 TTTATTAACAAAATAATAATATTATTTTTAAAATATTAGAATCATTTATTTAATTTTATTTATGT
456 TTTATTAACAAAATAATAATATTATTTTTAAAATATTAGAATAATTTATTTAATATTATTTATGT
*
556376 CAATATTATTATTAAAATATTATATCTATAATTTTATAAATAAAAAATTATGATTATTATATTGT
521 CAATATTATTATTAAAATATTATATCTATAATTTTATAAAT---AAA-T-T-ATTATTATATTTT
* *
556441 ATTATAATAAAATTATTATAAATTATATTTATTATTTATTATAATAATAATAATATATCATTAAT
580 ATTAAAATAAAATTATTATAAATTATATTTATTATTTATTATAATAAGAATAATATATCATTAAT
* * * *
556506 TATATTATAATGAGAGAATAGTTAAACATATGTGTTGATACATTTTCTAAAAGTATCGATAAATA
645 TATATTATAATGAGAGAATAGTTAAACATATGCGTCGATACATTTTCTAAAAGTATCGACACATA
* *
556571 TGTTACATTGAAACCGATAATTATAATGTAATAGATAAATTTACAATGTAACCGGTATA
710 TGTTACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATA
556630 AATATATCGG
Statistics
Matches: 2103, Mismatches: 104, Indels: 207
0.87 0.04 0.09
Matches are distributed among these distances:
735 74 0.04
736 2 0.00
737 2 0.00
740 262 0.12
741 70 0.03
742 11 0.01
743 5 0.00
744 9 0.00
745 1 0.00
747 2 0.00
748 67 0.03
749 125 0.06
750 10 0.00
751 6 0.00
752 1 0.00
755 5 0.00
757 33 0.02
759 1 0.00
760 39 0.02
763 100 0.05
764 70 0.03
765 7 0.00
766 26 0.01
767 1 0.00
768 3 0.00
769 2 0.00
771 11 0.01
772 95 0.05
773 1 0.00
774 188 0.09
775 1 0.00
776 1 0.00
777 61 0.03
778 74 0.04
779 21 0.01
783 93 0.04
785 1 0.00
787 3 0.00
788 1 0.00
789 4 0.00
790 3 0.00
791 2 0.00
792 41 0.02
793 43 0.02
794 7 0.00
796 4 0.00
797 1 0.00
798 3 0.00
799 9 0.00
800 395 0.19
801 6 0.00
802 100 0.05
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (773 bp):
ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTACCG
GTTTTGTTATTTTGTTATCAGTTTTGTTATTGTTGGGCATTTTACCGGAAATATTAAAAAACTTG
TAGAATGTTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGGTAAAAATA
GACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATTAATTTTAATTTTTTAGTTTGTA
AGTTGCCACAATATAACTAATGAAAAAAAGGACACGGTATTTCTATTTCGATATTAGCTTTCTAA
TAATAAAATAAAAAATAAAAATATATATATATAATTACAATATAATTTTAAAAAAAATCATAATG
AAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACAATAAAATAATATTA
TTTATTAACAAAATAATAATATTATTTTTAAAATATTAGAATAATTTATTTAATATTATTTATGT
CAATATTATTATTAAAATATTATATCTATAATTTTATAAATAAATTATTATTATATTTTATTAAA
ATAAAATTATTATAAATTATATTTATTATTTATTATAATAAGAATAATATATCATTAATTATATT
ATAATGAGAGAATAGTTAAACATATGCGTCGATACATTTTCTAAAAGTATCGACACATATGTTAC
ATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATACAACA
Found at i:557051 original size:198 final size:200
Alignment explanation
Indices: 556575--557056 Score: 611
Period size: 200 Copynumber: 2.4 Consensus size: 200
556565 TAAATATGTT
* *
556575 ACATTGAAACCGATAATTATAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATATCGG
1 ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGG
* *
556640 TTTTATGATG-GAATAGGT-TAACATAATGTATCGAAACAAATTTAGAAAGCGTCGATACATTTT
66 TTTTATGA-GAAAATAGGTCTAACATAATGTATCGAAACAAATTTAGAAAGCGTCAATACATTTT
* * *
556703 GTCCAGAATGAATGCCAAAGGAGGTGCACGCATAAAGTGTCGATATATTTATTAAAAGTATCGAT
130 GTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGACACATTTA-TAAAAGTATCGAT
556768 CCCAAAA
194 CCCAAAA
* * * * * *
556775 ACATCGAAACCGATAATTACAATGTAATAAGTAAATTTACAATGTAACCGGTAGAAATACACTGG
1 ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGG
* ** *** *
556840 TTTTATGAGAAAATAGGTCT-ACATAATGTATCGACAC-GTTTTAAGTTTGTGTCAATAC-TTTT
66 TTTTATGAGAAAATAGGTCTAACATAATGTATCGAAACAAATTT-AGAAAGCGTCAATACATTTT
* * *
556902 TTCCAGAATGAATGTCC-AACGAGTTGCACGCATAAAGTGTCGACACATTTA-AAATTGTATCGA
130 GTCCAGAATGAATG-CCAAACGAGGTGCACGCATAAAGTGTCGACACATTTATAAA-AGTATCGA
556965 TCCCAAAA
193 TCCCAAAA
* * *
556973 ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTTACCAGTATAAATATACCGG
1 ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGG
*
557038 -TTTAGTTAGAAAATAGGTC
66 TTTTA-TGAGAAAATAGGTC
557057 AATATAAGCG
Statistics
Matches: 243, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
197 7 0.03
198 84 0.35
199 51 0.21
200 100 0.41
201 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (200 bp):
ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGG
TTTTATGAGAAAATAGGTCTAACATAATGTATCGAAACAAATTTAGAAAGCGTCAATACATTTTG
TCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGACACATTTATAAAAGTATCGATCC
CAAAA
Found at i:557153 original size:87 final size:87
Alignment explanation
Indices: 557058--557393 Score: 600
Period size: 87 Copynumber: 3.9 Consensus size: 87
557048 AAATAGGTCA
557058 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
557123 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
*
557145 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTAATTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
557210 TCGGTTAAATACATATTTTATT
66 CCGGTTAAATACCTATTTTATT
* *
557232 ACATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
557297 CCGTTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
* *
557319 ATATAAACGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
557384 CCGGTTAAAT
66 CCGGTTAAAT
557394 GATATAACAT
Statistics
Matches: 235, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 235 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:557158 original size:23 final size:23
Alignment explanation
Indices: 557132--557183 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
557122 TCCGGTTAAA
**
557132 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
557155 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
557178 TACCTA
1 TACCTA
557184 ATATGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:557279 original size:23 final size:23
Alignment explanation
Indices: 557229--557273 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
557219 TACATATTTT
* *
557229 ATTACATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
557252 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
557274 TGTTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:557281 original size:26 final size:24
Alignment explanation
Indices: 557226--557283 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
557216 AAATACATAT
*
557226 TTTATTACATAAGCGCTACCTAT-
1 TTTATTATATAAGCGCTACCTATA
**
557249 TACATTATATAAGCGCTACCTAATA
1 TTTATTATATAAGCGCTACCT-ATA
557274 TGTTATTATA
1 T-TTATTATA
557284 CTTGATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 18 0.67
24 2 0.07
25 1 0.04
26 6 0.22
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTATTATATAAGCGCTACCTATA
Found at i:557332 original size:23 final size:23
Alignment explanation
Indices: 557306--557357 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
557296 TCCGTTTAAA
**
557306 TACCTATTTTATTATATAAACGC
1 TACCTATTACATTATATAAACGC
**
557329 TACCTATTACATTATATAAGTGC
1 TACCTATTACATTATATAAACGC
557352 TACCTA
1 TACCTA
557358 ATATGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:557879 original size:23 final size:23
Alignment explanation
Indices: 557853--557917 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
557843 TACAATAACA
557853 TATTAGGTAGCGCTTATATAATG
1 TATTAGGTAGCGCTTATATAATG
557876 TATTAGGTAGCGCTTATATAATG
1 TATTAGGTAGCGCTTATATAATG
*
557899 TAATAGGTAGCGCTTATAT
1 TATTAGGTAGCGCTTATAT
557918 TGACCTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (23 bp):
TATTAGGTAGCGCTTATATAATG
Found at i:558576 original size:200 final size:197
Alignment explanation
Indices: 557912--558634 Score: 872
Period size: 199 Copynumber: 3.6 Consensus size: 197
557902 TAGGTAGCGC
* * * *
557912 TTATATTGACCTATTTTATAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * *
557976 TTACATTATAATTATTGGTTTCGATGTTTTTTGGAT-GATACAATTT-GAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAAAAATGTATCGACACTT
* *
558039 TATGCGTGCACCTCGTTTGGGCATTCATTCTGGA-AAAAGTATCGACACAAACTTAAAAAATGTC
129 TATGCGTGCA-CTCGTTTGGGCATTCATTCTGGACAAAAGTATCGACACAAA-TTAACAAGTGTC
558103 GATACA
192 GATACA
* * * * * *
558109 TTAT-TTAGACATATTTTCTCATAAAACCGGTATATTTCTATCAGG-TACATTGAAAATTTATCT
1 TTATGTT-GACCTATTTTCTAATAAAACCGGTATATTTATA-CCGGTTACATTGTAAATTTACCT
* * * * * *
558172 ATCATATTATAATTATCGGTTTCGATGTTTTTGAGATCAATACTTTTAATAAATGTATCAAAACT
64 ATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAA-AAATGTATCGACACT
* * *
558237 TTATGCGTGCACCCGTTT-GGCATTCATTATGGACAAAATGTATTGACACAAATTTAACAAGTGT
128 TTATGCGTGCACTCGTTTGGGCATTCATTCTGGACAAAA-GTATCGACACAAA-TTAACAAGTGT
*
558301 CGATACT
191 CGATACA
* * * *
558308 TTATGCTGACCTATTTTCTCATAAAACCGGTATATTTATACCAGTTACATTGTAAATTTACATAT
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
558373 TACATTATAATTATCGGTTTCGAT-TTTATTGGGATTGATACTTTTAATAACTGTATCGACACTT
66 TACATTATAATTATCGGTTTCGATGTTT-TTGGGATCGATACTTTTAA-AAATGTATCGACACTT
* *
558437 TATGCGTGCATCTCGTTTGGGCATTCATTCTGCACAATAAGTATCGACACAAATTGCACAAGTGT
129 TATGCGTGCA-CTCGTTTGGGCATTCATTCTGGACAA-AAGTATCGACACAAATT-AACAAGTGT
*
558502 TGATACA
191 CGATACA
* * * *
558509 ATATGTTGACCTGTTTTCTAAT-TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
*
558573 TACATTATAATTATTGGTTTCGATGTTTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATG-TTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
558635 ATATTTAGGT
Statistics
Matches: 449, Mismatches: 59, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
196 3 0.01
197 95 0.21
198 22 0.05
199 165 0.37
200 94 0.21
201 65 0.14
202 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (197 bp):
TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTTA
TGCGTGCACTCGTTTGGGCATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATA
CA
Found at i:561150 original size:19 final size:19
Alignment explanation
Indices: 561105--561153 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
561095 TTAAATTCAC
561105 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
** *
561124 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
561143 ATACAAAATTA
1 ATACAAAATTA
561154 ACCCTACCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:563258 original size:155 final size:155
Alignment explanation
Indices: 562976--563265 Score: 418
Period size: 155 Copynumber: 1.9 Consensus size: 155
562966 CGTGTTGATA
* * *
562976 CATTATGTTCACCTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCT
1 CATTATGTACACCTATTCTCTCATAAAACCGGTAAAGTTATACCGGTTACATTGTAAATTTACCT
* * *
563041 ATTGCATTATAATTATCGATTTTGATATTTTTGGGATCGATACTTTTTAAAAATGTATCGACACT
66 ATTACATTATAATTATCGATTTTGATATTTCTAGGATCGATACTTTTTAAAAATGTATCGACACT
563106 TTATGTGTGCAACCCTTTTGGCATT
131 TTATGTGTGCAACCCTTTTGGCATT
* * * ** * *
563131 CATTATGTAGACCTATTCTCTCATAAAACTGGTATAGTTATATTGGTTATATTGTAAATTTATCT
1 CATTATGTACACCTATTCTCTCATAAAACCGGTAAAGTTATACCGGTTACATTGTAAATTTACCT
* * * * *
563196 ATTACATTATAATTATGGGTTTTTATGTTTCTAGGATCGATACTTTTTATAAATGTATCGACACT
66 ATTACATTATAATTATCGATTTTGATATTTCTAGGATCGATACTTTTTAAAAATGTATCGACACT
563261 TTATG
131 TTATG
563266 CGTTCACCAT
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
155 117 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (155 bp):
CATTATGTACACCTATTCTCTCATAAAACCGGTAAAGTTATACCGGTTACATTGTAAATTTACCT
ATTACATTATAATTATCGATTTTGATATTTCTAGGATCGATACTTTTTAAAAATGTATCGACACT
TTATGTGTGCAACCCTTTTGGCATT
Found at i:563502 original size:200 final size:200
Alignment explanation
Indices: 563132--563666 Score: 650
Period size: 200 Copynumber: 2.7 Consensus size: 200
563122 TTTGGCATTC
** * * * *
563132 ATTATGTAGACCTATTCTCTCATAAAACTGGTATAGTTATATTGGTTATATTGTAAATTTATCTA
1 ATTATGTAGACCTATTCTAACATAAAACCGGTATATTTATATCGGTTATATTGTAAATTTACCTA
* ** * * *
563197 TTACATTATAATTATGGGTTTTTATGTTTCT-AGGATCGATACTTTTTATAAATGTATCGACACT
66 TTACATTATAATTATAGGTTTCAATGTTTTTGA-GATCGATACTTTTTAAAAATGTATCGACATT
* * *
563261 TTATGCGTTCACCATTTTGGCCAATCATTCTGGATAAAAAGTATCGACACAAAATT-CAAAAGTG
130 TTATGCGTGCACCAGTTTGGCCAATCATTCTGGAAAAAAAGTATCGACAC-AAATTCCAAAAGTG
563325 TCGACAA
194 TCGACAA
** *
563332 ATTATGTAGACCTATTCTAACATAAAACCGGTATATTTATATCGGTTATATTACAAAATTACCTA
1 ATTATGTAGACCTATTCTAACATAAAACCGGTATATTTATATCGGTTATATTGTAAATTTACCTA
* *
563397 TTACATTATAATTATAGGTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATTTATCGACATTT
66 TTACATTATAATTATAGGTTTCAATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACATTT
* * *
563462 TATGCGTGCACCACGTTTGG-CATTCATTTTGGAAAAAAAGTATCGACACAAATTCCACAAGTGT
131 TATGCGTGCACCA-GTTTGGCCAATCATTCTGGAAAAAAAGTATCGACACAAATTCCAAAAGTGT
* *
563526 CGATAC
195 CGACAA
* * * *
563532 ATTATGTATATCTATTTTTCTTA-A-AAAACCGGTATATTTATA-CAGGTTACATTGTAAATTTA
1 ATTATGTAGACCTA---TTCTAACATAAAACCGGTATATTTATATC-GGTTATATTGTAAATTTA
* * * * * *
563594 CCTATTACATTATAATTTTTGATTTCAATGTTTTTGGGATCGAAACTTTTTAAACATGTATCGAC
62 CCTATTACATTATAATTATAGGTTTCAATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGAC
563659 ATTTTATG
127 ATTTTATG
563667 GGAAACTTTA
Statistics
Matches: 289, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
199 5 0.02
200 175 0.61
201 103 0.36
202 1 0.00
203 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (200 bp):
ATTATGTAGACCTATTCTAACATAAAACCGGTATATTTATATCGGTTATATTGTAAATTTACCTA
TTACATTATAATTATAGGTTTCAATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACATTT
TATGCGTGCACCAGTTTGGCCAATCATTCTGGAAAAAAAGTATCGACACAAATTCCAAAAGTGTC
GACAA
Found at i:568303 original size:202 final size:198
Alignment explanation
Indices: 568010--568826 Score: 1063
Period size: 202 Copynumber: 4.1 Consensus size: 198
568000 TGTTTTTTGG
* * * * * *
568010 ATCGACACTTAATGGGTGCACCCTTTT-GCCATTCCTTCTGGACAAAACATATCGACACAAATTC
1 ATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAA-GTATCGACACAAATT-
* * * *
568074 CAGAAGTGTCGATACATTTTCTAGACCTATTCTCGCATAAAACCGGTATATTTATACCGGTTACA
64 CAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACA
* * *
568139 TTGA-AAAATTACCTATTACATTATAATAATGGGTTTCGATGTTTCTGGGATCGATAC-TTTTAT
129 TT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATACTTTTTAA
568202 AAATGT
193 AAATGT
*
568208 ATCGACACTTTATGTGTGCACCATTTTTTTGGGCATTCATTCTGGACAAAATGTATCGACACATA
1 ATCGACACTTTATGCGTGCACCA---TTTTGGGCATTCATTCTGGACAAAA-GTATCGACACA-A
* * *
568273 ATTAAAAAGTGTTGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTT
61 ATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTT
* * * *
568338 ACATTACAAGATTACCTATTACATTATAATTATGGG-TTCGATGTCTCTGAGATTGACACTTTTT
126 ACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATACTTTTT
568402 AAAAATGT
191 AAAAATGT
* * * *
568410 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTAGACAAAAAGTATTGACACCAATTT
1 ATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC-AAAAGTATCGACA-CAAATT
* *
568475 CAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAA-TGGTATATTTATACCGGTTACA
64 CAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACA
568539 TTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATA-TTTTTAAA
129 TTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATACTTTTT--A
568603 AAAATGT
192 AAAATGT
* * *
568610 ATCGACACTTTATGGGTGCATCC-TTTTGGGCATTCCTTCTGGACAAACAGTATCGATACAAATT
1 ATCGACACTTTATGCGTGCA-CCATTTTGGGCATTCATTCTGGACAAA-AGTATCGACACAAA-T
* * * * **
568674 TTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATAGTTATTTCGGTTAC
63 TCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTAC
** * * * *
568739 ATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTAGGATCGATACTTTTTAT
128 ATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATACTTTTTAA
568804 AAATGT
193 AAATGT
*
568810 GTCGACACTTTATGCGT
1 ATCGACACTTTATGCGT
568827 TCAAAGGTGT
Statistics
Matches: 545, Mismatches: 57, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
198 78 0.14
199 95 0.17
200 121 0.22
201 95 0.17
202 152 0.28
203 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (198 bp):
ATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAGTATCGACACAAATTCA
AAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATT
ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATACTTTTTAAAAA
TGT
Found at i:568817 original size:400 final size:397
Alignment explanation
Indices: 568010--568829 Score: 1118
Period size: 400 Copynumber: 2.1 Consensus size: 397
568000 TGTTTTTTGG
* * * * * *
568010 ATCGACACTTAATGGGTGCACCCTTTTGCCATTCCTTCTGGACAAAACATATCGACACAAATTCC
1 ATCGACACTTTATGCGTTCACCATTTTGCCATTCATTCTAGACAAAACATATCGACACAAATTCC
* *
568075 AGAAGTGTCGATACATTTTCTAGACCTATTCTCGCATAAAACCGGTATATTTATACCGGTTACAT
66 AGAAGTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACAT
* *
568140 TGAAAAATTACCTATTACATTATAATAATGGGTTTCGATGTTTCTGGGATCGATACTTTTATAAA
131 TGAAAAATTACCTATTACATTATAATAATGGGTTTCGATGTCTCTGGGATCGATACTTTTAAAAA
*
568205 TGTATCGACACTTTATGTGTGCACCATTTTTTTGGGCATTCATTCTGGACAAAATGTATCGACAC
196 TGTATCGACACTTTATGGGTGCACC---TTTTTGGGCATTCATTCTGGACAAAATGTATCGACAC
* * *
568270 ATAATTAAAAAGTGTTGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCG
258 ATAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATAGTTATACCG
*
568335 GTTACATTACAAGATTACCTATTACATTATAATTATGGGTTCGATGTCTCTGAGATTGACACTTT
323 GTTACATTACAAGATTACCTATTACATTATAATTATGGGTTCGATGTCTCTGAGATCGACACTTT
568400 TTAAAAATGT
388 TTAAAAATGT
* * *
568410 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTAGACAAAA-AGTATTGACACCAATT
1 ATCGACACTTTATGCGTTCACCATTTT-GCCATTCATTCTAGACAAAACA-TATCGACACAAATT
* * *
568474 TCA-AATGTGTCGATACATTATGTAGACCTATTCTCACATAAAA-TGGTATATTTATACCGGTTA
64 CCAGAA-GTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTA
* *
568537 CATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGATATTTTTA
128 CATTGA-AAAATTACCTATTACATTATAATAATGGGTTTCGATGTCTCTGGGATCGATACTTTT-
*
568601 AAAAAATGTATCGACACTTTATGGGTGCATCC-TTTTGGGCATTCCTTCTGGACAAACA-GTATC
191 -AAAAATGTATCGACACTTTATGGGTGCA-CCTTTTTGGGCATTCATTCTGGACAAA-ATGTATC
* * * *
568664 GATACA-AATTTTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATAGTT
253 GACACATAA-TTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATAGTT
** ** *
568728 ATTTCGGTTACATTGTAA-ATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCT-AGGAT
317 ATACCGGTTACATTACAAGA-TTACCTATTACATTATAATTATGGG-TTCGATGTCTCTGA-GAT
* *
568791 CGATACTTTTTATAAATGT
379 CGACACTTTTTAAAAATGT
*
568810 GTCGACACTTTATGCGTTCA
1 ATCGACACTTTATGCGTTCA
568830 AAGGTGTCGA
Statistics
Matches: 372, Mismatches: 36, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
398 3 0.01
399 123 0.33
400 153 0.41
401 65 0.17
402 26 0.07
403 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (397 bp):
ATCGACACTTTATGCGTTCACCATTTTGCCATTCATTCTAGACAAAACATATCGACACAAATTCC
AGAAGTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACAT
TGAAAAATTACCTATTACATTATAATAATGGGTTTCGATGTCTCTGGGATCGATACTTTTAAAAA
TGTATCGACACTTTATGGGTGCACCTTTTTGGGCATTCATTCTGGACAAAATGTATCGACACATA
ATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATAGTTATACCGGTT
ACATTACAAGATTACCTATTACATTATAATTATGGGTTCGATGTCTCTGAGATCGACACTTTTTA
AAAATGT
Found at i:568958 original size:153 final size:153
Alignment explanation
Indices: 568680--568967 Score: 432
Period size: 153 Copynumber: 1.9 Consensus size: 153
568670 AATTTTATAA
* * ** ** **
568680 GTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATAGTTATTTCGGTTACATTGTA
1 GTGTCGATACATTATGTAGACCTATTCTCACATAAAAACAATATAGTTATACCGGTTACATTACA
* * *
568745 AATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTAGGATCGATACTTTTTATAAATGT
66 AAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTAGGATCGATACGTTTTATAAATGT
*
568810 GTCGACACTTTATGCGTTCAAAG
131 ATCGACACTTTATGCGTTCAAAG
* *
568833 GTGTCGATACATTATGTAGACCTATTCTCACATAAAAACAATATATTTATACCGGTTATATTACA
1 GTGTCGATACATTATGTAGACCTATTCTCACATAAAAACAATATAGTTATACCGGTTACATTACA
* *
568898 AAATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGATACGTTTTATAAATGT
66 AAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTAGGATCGATACGTTTTATAAATGT
568963 ATCGA
131 ATCGA
568968 TACATCTGCT
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
153 119 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (153 bp):
GTGTCGATACATTATGTAGACCTATTCTCACATAAAAACAATATAGTTATACCGGTTACATTACA
AAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTAGGATCGATACGTTTTATAAATGT
ATCGACACTTTATGCGTTCAAAG
Found at i:569025 original size:15 final size:15
Alignment explanation
Indices: 568987--569054 Score: 102
Period size: 15 Copynumber: 4.6 Consensus size: 15
568977 TTACCTATAA
*
568987 TTTAGAAACTTTACG
1 TTTAGGAACTTTACG
569002 TTT-GGAACTTTACG
1 TTTAGGAACTTTACG
569016 TTTAGGAACTTTACG
1 TTTAGGAACTTTACG
*
569031 TTTGGGAACTTTACG
1 TTTAGGAACTTTACG
*
569046 TTTGGGAAC
1 TTTAGGAAC
569055 CATACTGGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
14 13 0.26
15 37 0.74
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (15 bp):
TTTAGGAACTTTACG
Found at i:569390 original size:19 final size:19
Alignment explanation
Indices: 569366--569412 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
569356 TTACATTCAC
569366 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
569385 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
569404 ATACAAAAT
1 ATACAAAAT
569413 CAACCCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:570993 original size:18 final size:18
Alignment explanation
Indices: 570970--571008 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
570960 TCCTCTTCAT
570970 TTCCTCTATCTTTTCGTC
1 TTCCTCTATCTTTTCGTC
*
570988 TTCCTCTATCTTTTCTTC
1 TTCCTCTATCTTTTCGTC
571006 TTC
1 TTC
571009 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCCTCTATCTTTTCGTC
Found at i:571229 original size:33 final size:33
Alignment explanation
Indices: 571192--571291 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
571182 CCATCTTAAG
**
571192 TTCACCCCTCAACATTTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
571225 TTCACCCCTCAACACCTCAACTGCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
571258 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
571291 T
1 T
571292 CCATCTATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.24, C:0.46, G:0.01, T:0.29
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:571352 original size:21 final size:21
Alignment explanation
Indices: 571326--571366 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
571316 CCCTTATGCC
571326 TCTCAAGTGTCTCTTCGACTA
1 TCTCAAGTGTCTCTTCGACTA
* *
571347 TCTCAAGTTTTTCTTCGACT
1 TCTCAAGTGTCTCTTCGACT
571367 CTTGATTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.12, T:0.44
Consensus pattern (21 bp):
TCTCAAGTGTCTCTTCGACTA
Found at i:571770 original size:19 final size:22
Alignment explanation
Indices: 571742--571796 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
571732 TCAACCTGCA
571742 TTTATAATAAAATT-TA-TA-AT
1 TTTAT-ATAAAATTATACTACAT
571762 TTTATATAATAATTATACTATCAT
1 TTTATATAA-AATTATACTA-CAT
571786 TTTATATAAAA
1 TTTATATAAAA
571797 AACAAAAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 2 0.07
22 2 0.07
23 2 0.07
24 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATATAAAATTATACTACAT
Found at i:574065 original size:182 final size:182
Alignment explanation
Indices: 573758--574431 Score: 996
Period size: 182 Copynumber: 3.7 Consensus size: 182
573748 TACGCTTACT
* ** * *
573758 TATTAAAGTATCGACACTTTCAATATATCCGGTAGAGCTTTACCGGTTTTGTCATTTCA-AGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTT-AGAGACC
* * *
573822 GGTTTTGTCATATTTTTACCTGGTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACAC
* **
573887 TTTATAGGCGCTAAAACTGTTTCTCTTTTAAATTTACAAAGTGTCGATGTTTA
130 TTTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
573940 TATTAAAGCATCGACACTTTCAATATATCCGGTCGCTCTATACCGATTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
574005 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
574070 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
** *
574122 TATTAAAGTATCGACACTTTCAATATATATGGTCGCTCTATTCCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
*
574187 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
** *
574252 TTATAGGCATTAAAATTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
574304 TAATAAATTATCGACACTTTCAATATATCAGGTACCGCT-T-TACCGGTTTTATCTTTTCGAGAC
1 TATTAAAGTATCGACACTTTCAATATATCCGGT--CGCTCTATACCGGTTTTGTCCTTTAGAGAC
* *
574367 CGGTTTTGTCATATTTTTACCTGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATCGAC
64 CGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
574431 A
128 A
574432 TAAACCGACA
Statistics
Matches: 447, Mismatches: 41, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
181 1 0.00
182 439 0.98
183 3 0.01
184 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:575549 original size:19 final size:19
Alignment explanation
Indices: 575527--575593 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
575517 ATTTGTGGAT
575527 TGTTACTTTAGTTGTAATA
1 TGTTACTTTAGTTGTAATA
* *
575546 TGTTAGTTTGATGTATTTGTGGAT-
1 TGTTACTTT-A-G---TTGT-AATA
575570 TGTTACTTTAGTTGTAATA
1 TGTTACTTTAGTTGTAATA
575589 TGTTA
1 TGTTA
575594 GTTTTGTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
18 2 0.05
19 17 0.46
20 1 0.03
21 1 0.03
22 1 0.03
23 1 0.03
24 12 0.32
25 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.21, T:0.54
Consensus pattern (19 bp):
TGTTACTTTAGTTGTAATA
Found at i:575559 original size:43 final size:43
Alignment explanation
Indices: 575498--575621 Score: 214
Period size: 43 Copynumber: 2.9 Consensus size: 43
575488 AGAACGATTC
*
575498 TAATATGTTAGATTGATGTATTTGTGGATTGTTACTTTAGTTG
1 TAATATGTTAGTTTGATGTATTTGTGGATTGTTACTTTAGTTG
575541 TAATATGTTAGTTTGATGTATTTGTGGATTGTTACTTTAGTTG
1 TAATATGTTAGTTTGATGTATTTGTGGATTGTTACTTTAGTTG
*
575584 TAATATGTTAGTTTTG-TGTATTTATGGATTGTTACTTT
1 TAATATGTTAG-TTTGATGTATTTGTGGATTGTTACTTT
575622 GGAGTTTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
43 74 0.95
44 4 0.05
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (43 bp):
TAATATGTTAGTTTGATGTATTTGTGGATTGTTACTTTAGTTG
Found at i:575565 original size:24 final size:24
Alignment explanation
Indices: 575498--575565 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 24
575488 AGAACGATTC
*
575498 TAATATGTTAGATTGATGTATTTG
1 TAATATGTTAGTTTGATGTATTTG
* *
575522 TGGAT-TGTTACTTT-A-G---TTG
1 T-AATATGTTAGTTTGATGTATTTG
575541 TAATATGTTAGTTTGATGTATTTG
1 TAATATGTTAGTTTGATGTATTTG
575565 T
1 T
575566 GGATTGTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
18 2 0.06
19 12 0.38
20 1 0.03
21 1 0.03
22 1 0.03
23 1 0.03
24 12 0.38
25 2 0.06
ACGTcount: A:0.24, C:0.01, G:0.22, T:0.53
Consensus pattern (24 bp):
TAATATGTTAGTTTGATGTATTTG
Found at i:575573 original size:24 final size:24
Alignment explanation
Indices: 575503--575574 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
575493 GATTCTAATA
*
575503 TGTTAGATTGATGTATTTGTGGAT
1 TGTTAGTTTGATGTATTTGTGGAT
* *
575527 TGTTACTTT-A-G---TTGT-AAT
1 TGTTAGTTTGATGTATTTGTGGAT
575545 ATGTTAGTTTGATGTATTTGTGGAT
1 -TGTTAGTTTGATGTATTTGTGGAT
575570 TGTTA
1 TGTTA
575575 CTTTAGTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
18 2 0.06
19 12 0.33
20 1 0.03
21 1 0.03
22 1 0.03
23 1 0.03
24 16 0.44
25 2 0.06
ACGTcount: A:0.21, C:0.01, G:0.25, T:0.53
Consensus pattern (24 bp):
TGTTAGTTTGATGTATTTGTGGAT
Found at i:575821 original size:27 final size:27
Alignment explanation
Indices: 575763--575826 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
575753 TTAGCAAACT
*
575763 TAACGAG-CAAAGAAATTTTTTAACAAG
1 TAACGAGTC-AAGAAAATTTTTAACAAG
* *
575790 T-ACGAGTCAAGAAAATTTTTATCGAG
1 TAACGAGTCAAGAAAATTTTTAACAAG
*
575816 TAACGAATCAA
1 TAACGAGTCAA
575827 ATAGTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (27 bp):
TAACGAGTCAAGAAAATTTTTAACAAG
Found at i:577752 original size:21 final size:21
Alignment explanation
Indices: 577722--577788 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
577712 GGGGCTAAGA
*
577722 GTATCGATACCTATTCATAGG
1 GTATCAATACCTATTCATAGG
* * *
577743 GTATCAATA-CTATCCTTAGC
1 GTATCAATACCTATTCATAGG
* * *
577763 ATATAAATACCTGTTCATAGG
1 GTATCAATACCTATTCATAGG
577784 GTATC
1 GTATC
577789 GATATTATCC
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCAATACCTATTCATAGG
Found at i:577813 original size:41 final size:41
Alignment explanation
Indices: 577719--577813 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
577709 TTTGGGGCTA
* *
577719 AGAGTATCGATACCTATTCATAGGGTATCAATACTATCCTT
1 AGAGTATCAATACCTATTCATAGGGTATCAATACTATCCTG
* * * *
577760 AGCA-TATAAATACCTGTTCATAGGGTATCGATATTATCCTG
1 AG-AGTATCAATACCTATTCATAGGGTATCAATACTATCCTG
577801 AGAGTATCAATAC
1 AGAGTATCAATAC
577814 TTGATGAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 43 0.96
42 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (41 bp):
AGAGTATCAATACCTATTCATAGGGTATCAATACTATCCTG
Found at i:591159 original size:112 final size:112
Alignment explanation
Indices: 590957--591173 Score: 328
Period size: 112 Copynumber: 1.9 Consensus size: 112
590947 TCATTTCAAA
* * * * *
590957 ATACTTTGTGTATGATAGTATCGATCGATTTTGTTTAATGCATAACAATGTATTTTTCGGCATAA
1 ATACTTCGTGTATGAAAGTATCGATCGATTTTGCTTAATGCATAACAATGCATTTTTCAGCATAA
*
591022 AAGGTGCCACCCACGGTATTTATAATGAGGTGAATTACCAACTCGAC
66 AAGGTGCCACCCACGGTATTCATAATGAGGTGAATTACCAACTCGAC
* *
591069 ATACTTCGTGTATGAAAGTTATCGATTGATTTTGCTTAATGCATAACAGTGCA-TTTTCAGCATA
1 ATACTTCGTGTATGAAAG-TATCGATCGATTTTGCTTAATGCATAACAATGCATTTTTCAGCATA
* *
591133 AAAGGTGCCACCCATGGTATTCATAATGAGTTGAATTACCA
65 AAAGGTGCCACCCACGGTATTCATAATGAGGTGAATTACCA
591174 TTTCGGCAGT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 64 0.68
113 30 0.32
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (112 bp):
ATACTTCGTGTATGAAAGTATCGATCGATTTTGCTTAATGCATAACAATGCATTTTTCAGCATAA
AAGGTGCCACCCACGGTATTCATAATGAGGTGAATTACCAACTCGAC
Found at i:598727 original size:54 final size:55
Alignment explanation
Indices: 598621--598728 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 55
598611 ATTCAAGCAT
*
598621 TAAACATGACCAATTCACCCACGGTCCATGTTTACTCTTTGGCATCAAAGGTCAC
1 TAAACATGACCAATTCACCCACGATCCATGTTTACTCTTTGGCATCAAAGGTCAC
* *
598676 TAAACA-GATCCAATTCACCTAC-ATCCAATG-TTACTCTTTGGTATCAAAGGTCA
1 TAAACATGA-CCAATTCACCCACGATCC-ATGTTTACTCTTTGGCATCAAAGGTCA
598729 ACCACTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
54 27 0.56
55 21 0.44
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (55 bp):
TAAACATGACCAATTCACCCACGATCCATGTTTACTCTTTGGCATCAAAGGTCAC
Found at i:605080 original size:95 final size:96
Alignment explanation
Indices: 604944--605162 Score: 264
Period size: 95 Copynumber: 2.3 Consensus size: 96
604934 AATAAGGTAA
* * * *
604944 TATCGATACCATGGTGAGGGTATCGATA-CTAGGTAACATCGAATCTAATTTTTGTATTGATACC
1 TATCGATACCATGGTGAGGGTATCGATACCAAGGTAACATCGAAGCTAATTTTGGTATCGATACC
* * *
605008 GGAAGGGGGTATCGGTACCCTAGCACACTAG
66 GGAAGGGGATATCGATACCATAGCACACTAG
* *
605039 TATCGATACCATGGTGAGGGTATCGATACCAAGG-CATATCGAAGCTAATTTTGGTATCGATACC
1 TATCGATACCATGGTGAGGGTATCGATACCAAGGTAACATCGAAGCTAATTTTGGTATCGATACC
* * * **
605103 TGAAGGGGATATCGATATCATAGTACGGTAG
66 GGAAGGGGATATCGATACCATAGCACACTAG
* *
605134 TATTGATACCATGGT-ATAGGTATCGATAC
1 TATCGATACCATGGTGA-GGGTATCGATAC
605163 TGAAGGGCCA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 101 0.95
96 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (96 bp):
TATCGATACCATGGTGAGGGTATCGATACCAAGGTAACATCGAAGCTAATTTTGGTATCGATACC
GGAAGGGGATATCGATACCATAGCACACTAG
Found at i:605892 original size:54 final size:54
Alignment explanation
Indices: 605487--605877 Score: 541
Period size: 54 Copynumber: 7.2 Consensus size: 54
605477 ACCTAATAGG
* * * *
605487 CACTAAATGTGCCTTTCACGGAATTCATCCTATGTGGATGAATAACCTTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* *
605541 CACTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
605595 CACTAAGTGTGCATTTCACAGAATTTATCATATGTGGATGAATAACCATTCCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
605649 CACTAAGTGTGTATTTCATGGAATTCATCCTATATGGATGAATAACCGTTTCAA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
605703 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATAAATAATTC-TTCCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA-CCGTTTCGA
*
605757 CACTACGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
605811 CACTAAGCGTGCATTTCACGAAATTCATCCTATGTGGATAAATAATCGTTTTGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
605865 CACTAAGTGTGCA
1 CACTAAGTGTGCA
605878 AAGCACGAAA
Statistics
Matches: 295, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 293 0.99
55 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:612156 original size:94 final size:95
Alignment explanation
Indices: 611938--612160 Score: 263
Period size: 95 Copynumber: 2.4 Consensus size: 95
611928 GTGCTGATTA
* * *
611938 GGTAGTATCAATACCATGGTTAGGGTATCGATTCCAGGTAACATCGAACCTAATTTTAGTATCGA
1 GGTAGTATCGATACCATGGTTAGGGTATCAATACCAGGTAACATCGAACCTAATTTTAGTATCGA
* * * *
612003 TACCAGAAGGGGGTATTGATACCCTAGCAT
66 TAACAGAAGGGGGTATCGATACCATAGCAG
* * * * * *
612033 AGTAGTATTGATACCATGGTGAGGGTATCAATACCAAGG-CACATCGAAGCTAATTTTGGTATCG
1 GGTAGTATCGATACCATGGTTAGGGTATCAATACC-AGGTAACATCGAACCTAATTTTAGTATCG
* *
612097 ATAACGGAA-GGGGTATCGATACCATAGTAG
65 ATAACAGAAGGGGGTATCGATACCATAGCAG
*
612127 GGTAGTATCGATACCAT-GTTATAGGTATCAATAC
1 GGTAGTATCGATACCATGGTTA-GGGTATCAATAC
612161 TGAAGGGCCA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
93 3 0.03
94 43 0.40
95 58 0.54
96 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTTAGGGTATCAATACCAGGTAACATCGAACCTAATTTTAGTATCGA
TAACAGAAGGGGGTATCGATACCATAGCAG
Found at i:612559 original size:54 final size:54
Alignment explanation
Indices: 612489--612878 Score: 534
Period size: 54 Copynumber: 7.2 Consensus size: 54
612479 ACCTAATAGG
* *
612489 CACTAAATGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* ** * * *
612543 CACTAAGTGTGAATTTCTTGGAATTCATCATATGTGCATGAATAACTGTTTC-A
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* *
612596 GCACTAAGTGTGCAATTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 -CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* *
612651 CACTAAGTGTGCATTTCACGAAATTCATCCTATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * * *
612705 CACTAAGCGTTCTTTTTACAGAATTCATCCTATGTGGATGAATAACCGTTACGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
*
612759 CACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAAT-ACCTGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACC-GTTTCGA
* * *
612813 CACTGAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTAGGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT-CGA
612868 -ACTAAGTGTGC
1 CACTAAGTGTGC
612879 TAATCACGTA
Statistics
Matches: 291, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
53 4 0.01
54 282 0.97
55 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:613585 original size:20 final size:23
Alignment explanation
Indices: 613534--613589 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
613524 ACACTTAATC
*
613534 TGGTATCGATA-CTACAATACTA
1 TGGTATCGATACCTACAACACTA
*
613556 TGGTACCGATACCTA-AACA-T-
1 TGGTATCGATACCTACAACACTA
613576 TGGTATCGATACCT
1 TGGTATCGATACCT
613590 CATGAAGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 13 0.43
23 3 0.10
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (23 bp):
TGGTATCGATACCTACAACACTA
Found at i:619173 original size:89 final size:90
Alignment explanation
Indices: 619011--619187 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 90
619001 TAATCCCAAA
* * * *
619011 TATTTAATTTCAATTGATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
619076 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
619101 TATTAAATTCCAATTAATTAAATATAGATTTAATTAA-TTGAAATAATAAAAACCTTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
619165 TAGGGTAACTTGGATATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
619188 GTGTATTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 48 0.59
90 34 0.41
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:625977 original size:89 final size:89
Alignment explanation
Indices: 625816--625989 Score: 278
Period size: 89 Copynumber: 2.0 Consensus size: 89
625806 TCTCGAATAT
* * * *
625816 TTAATTTCAATTGATTAAATATATATTTAATTAATTTGAAATAATAAAATCGCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACGCTAATATGATTAG
*
625881 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTAGATATAAAAGGATTA
*
625905 TTAAATTCTAATTAATTAAATATAGATTTAATTAA-TTGAAATAATAAAAACTCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACGCTAATATGATTA
625969 GGGTAACTTAGATATAAAAGG
65 GGGTAACTTAGATATAAAAGG
625990 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 54 0.69
90 24 0.31
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACGCTAATATGATTAG
GGTAACTTAGATATAAAAGGATTA
Found at i:628037 original size:18 final size:18
Alignment explanation
Indices: 628006--628061 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
627996 GCACTTAAAA
*
628006 TTTATCCCGCAGGACCAC
1 TTTATCCCGAAGGACCAC
*
628024 TTTGTCCCGAAGGACCAC
1 TTTATCCCGAAGGACCAC
*
628042 TATATCCCGAAGGACCAC
1 TTTATCCCGAAGGACCAC
628060 TT
1 TT
628062 ATAACCCTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (18 bp):
TTTATCCCGAAGGACCAC
Found at i:634093 original size:4 final size:4
Alignment explanation
Indices: 634084--634114 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
634074 AAGTGTTGAA
634084 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
634115 ATAACAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:643557 original size:23 final size:23
Alignment explanation
Indices: 643510--643557 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
643500 CGTGTTTGAG
* * **
643510 ATACACCATCATCACCATCTTCC
1 ATACAACATCAACACCATCAACC
643533 ATACAACATCAACACCATCAACC
1 ATACAACATCAACACCATCAACC
643556 AT
1 AT
643558 CTTTCATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (23 bp):
ATACAACATCAACACCATCAACC
Found at i:643565 original size:23 final size:22
Alignment explanation
Indices: 643539--643582 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
643529 TTCCATACAA
* *
643539 CATCAACACCATCAACCATCTTT
1 CATCAAAACCACCAA-CATCTTT
643562 CATCAAAACCACCAACATCTT
1 CATCAAAACCACCAACATCTT
643583 AATTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (22 bp):
CATCAAAACCACCAACATCTTT
Found at i:648035 original size:23 final size:23
Alignment explanation
Indices: 648003--648050 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
647993 CGTGTTTGAG
* * *
648003 ATACACCATCATCATCATCTTCC
1 ATACAACATCAACACCATCTTCC
648026 ATACAACATCAACACCATCTTCC
1 ATACAACATCAACACCATCTTCC
648049 AT
1 AT
648051 CAAGACCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (23 bp):
ATACAACATCAACACCATCTTCC
Found at i:649563 original size:8 final size:8
Alignment explanation
Indices: 649550--649589 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
649540 ATTTTTTTTT
649550 CAAAAAAA
1 CAAAAAAA
649558 CAAAAAAA
1 CAAAAAAA
*
649566 CAAAAAAGG
1 CAAAAAA-A
649575 CAAAAAAA
1 CAAAAAAA
649583 -AAAAAAA
1 CAAAAAAA
649590 AAAGAGCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:649592 original size:22 final size:24
Alignment explanation
Indices: 649552--649602 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
649542 TTTTTTTTCA
*
649552 AAAAAACAAAAAAACAAAAAAGGC
1 AAAAAACAAAAAAACAAAAAAGCC
*
649576 AAAAAA-AAAAAAA-AAAAGAGCC
1 AAAAAACAAAAAAACAAAAAAGCC
649598 AAAAA
1 AAAAA
649603 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 7 0.28
24 6 0.24
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (24 bp):
AAAAAACAAAAAAACAAAAAAGCC
Found at i:649602 original size:20 final size:20
Alignment explanation
Indices: 649554--649593 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
649544 TTTTTTCAAA
649554 AAAACAAAAAAACAAAAAAGGC
1 AAAA-AAAAAAA-AAAAAAGGC
649576 AAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAG
649594 AGCCAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAGGC
Found at i:649602 original size:30 final size:28
Alignment explanation
Indices: 649551--649609 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
649541 TTTTTTTTTC
* *
649551 AAAAAAACAAAAAAACAAAAAAGGCAAA
1 AAAAAAAAAAAAAAACAAAAAAGCCAAA
*
649579 AAAAAAAAAAAAAAGAGCCAAAAAGCCAAA
1 AAAAAAAAAAAAAA-A-CAAAAAAGCCAAA
649609 A
1 A
649610 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 1 0.04
30 12 0.46
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAAAAAAACAAAAAAGCCAAA
Found at i:655429 original size:15 final size:16
Alignment explanation
Indices: 655405--655447 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
655395 CAAAAACGTC
655405 TTTTAA-AAAAA-CAA
1 TTTTAAGAAAAATCAA
*
655419 TTTTAAGAAAAATCAT
1 TTTTAAGAAAAATCAA
655435 TTTTAAGACAAAA
1 TTTTAAGA-AAAA
655448 ACTGATCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (16 bp):
TTTTAAGAAAAATCAA
Found at i:656081 original size:16 final size:16
Alignment explanation
Indices: 656060--656093 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
656050 GCATAAATGA
656060 ATATATATACATATAT
1 ATATATATACATATAT
*
656076 ATATATATACATGTAT
1 ATATATATACATATAT
656092 AT
1 AT
656094 GTTGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
ATATATATACATATAT
Found at i:657959 original size:3 final size:3
Alignment explanation
Indices: 657937--657976 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
657927 TGCACAAATG
* *
657937 TAA TAA TAC TAT TAA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
657977 TTTAAAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:661165 original size:21 final size:21
Alignment explanation
Indices: 661132--661181 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
661122 ACAATGAAGG
*
661132 GATCGATCCTTTCTTTCAAGA
1 GATCGATCATTTCTTTCAAGA
* *
661153 GATTGATCATTTCTTTCAAGG
1 GATCGATCATTTCTTTCAAGA
661174 GATCGATC
1 GATCGATC
661182 CCTTTGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
GATCGATCATTTCTTTCAAGA
Found at i:668101 original size:66 final size:65
Alignment explanation
Indices: 667996--668157 Score: 207
Period size: 66 Copynumber: 2.4 Consensus size: 65
667986 CAACAGAAGT
* * * * *
667996 TATCTCAAGTGAGATGAAACTTTGTTTAAAGTGAAACAATTTCAAAATTTGTGTTTTAAGGGAAA
1 TATCTCAAGCGAGA--AAAATTTGTTTTAAGTGAAACAATTTCAAAATTTATGTTTCAAGGGAAA
668061 AC
64 AC
* *
668063 TATCTCAAGCGAGACAAAATTTGTTTTAAGTTAAACAATTTCAAAATTTATGTTTCGAGGGAAAA
1 TATCTCAAGCGAGA-AAAATTTGTTTTAAGTGAAACAATTTCAAAATTTATGTTTCAAGGGAAAA
668128 C
65 C
*
668129 TGTCTCAAGCGAGAAGAAATTTAGTTTTA
1 TATCTCAAGCGAGAA-AAATTT-GTTTTA
668158 GGAAAACAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 64 0.76
67 19 0.23
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (65 bp):
TATCTCAAGCGAGAAAAATTTGTTTTAAGTGAAACAATTTCAAAATTTATGTTTCAAGGGAAAAC
Done.