Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008186.1 Hibiscus syriacus cultivar Beakdansim tig00110793_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: 806808
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 3
Found at i:10092 original size:14 final size:14
Alignment explanation
Indices: 10073--10101 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10063 TCCTTCTTCT
10073 TAGCTTTTATTTCA
1 TAGCTTTTATTTCA
10087 TAGCTTTTATTTCA
1 TAGCTTTTATTTCA
10101 T
1 T
10102 TGAGAAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (14 bp):
TAGCTTTTATTTCA
Found at i:13853 original size:29 final size:31
Alignment explanation
Indices: 13802--13864 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
13792 GTTGAACTTT
* *
13802 ATTTTTTATTATTTCACTTATTATATTTTT-A
1 ATTTTTTATAATTTCACTCATTAT-TTTTTGA
13833 ATTTTTT-TAATTT-ACTCATTATTTTTTGA
1 ATTTTTTATAATTTCACTCATTATTTTTTGA
13862 ATT
1 ATT
13865 GTTCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 12 0.41
30 5 0.17
31 7 0.24
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (31 bp):
ATTTTTTATAATTTCACTCATTATTTTTTGA
Found at i:13947 original size:16 final size:16
Alignment explanation
Indices: 13928--13960 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13918 TATTTTTATT
*
13928 ATTTAATATAAAAATA
1 ATTTAAAATAAAAATA
13944 ATTTAAAATAAAAATA
1 ATTTAAAATAAAAATA
13960 A
1 A
13961 AATGATGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTTAAAATAAAAATA
Found at i:21544 original size:19 final size:20
Alignment explanation
Indices: 21520--21559 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21510 AAATTATAAA
21520 TTTTAA-TATAATTTAATTT
1 TTTTAATTATAATTTAATTT
*
21539 TTTTAATTATAATTTACTTT
1 TTTTAATTATAATTTAATTT
21559 T
1 T
21560 AAACTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATTATAATTTAATTT
Found at i:29990 original size:71 final size:73
Alignment explanation
Indices: 29873--30019 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 73
29863 ATCATTAAAA
* * * * *
29873 TAGAACCCCACTAAATTACTATATTTTCAAGTTTTTTAAATAAAAAA-TAATGTTT-AATTTTTT
1 TAGAACCCCACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAAGT-ATGTTTAAAATATTT
29936 TTTAATTAT
65 TTTAATTAT
29945 TAGAA-CCCACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAAGTATGTTTAAAAATATTT
1 TAGAACCCCACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAAGTATGTTT-AAAATATTT
30009 TTTAATTAT
65 TTTAATTAT
30018 TA
1 TA
30020 AACTTAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
71 44 0.66
72 6 0.09
73 17 0.25
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (73 bp):
TAGAACCCCACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAAGTATGTTTAAAATATTTT
TTAATTAT
Found at i:31838 original size:9 final size:9
Alignment explanation
Indices: 31826--31882 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
31816 ATGGTTCACC
31826 CCGGTTTTA
1 CCGGTTTTA
31835 CCGGTTTTCA
1 CCGGTTTT-A
*
31845 GCCGGTTCTA
1 -CCGGTTTTA
*
31855 CTGGTTTTCA
1 CCGGTTTT-A
31865 GCCGGTTTTA
1 -CCGGTTTTA
*
31875 CTGGTTTT
1 CCGGTTTT
31883 CAGCCGGTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 21 0.54
10 4 0.10
11 14 0.36
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (9 bp):
CCGGTTTTA
Found at i:31851 original size:20 final size:20
Alignment explanation
Indices: 31826--31891 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
31816 ATGGTTCACC
*
31826 CCGGTTTTACCGGTTTTCAG
1 CCGGTTTTACTGGTTTTCAG
*
31846 CCGGTTCTACTGGTTTTCAG
1 CCGGTTTTACTGGTTTTCAG
31866 CCGGTTTTACTGGTTTTCAG
1 CCGGTTTTACTGGTTTTCAG
31886 CCGGTT
1 CCGGTT
31892 CATTGCCAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.09, C:0.24, G:0.26, T:0.41
Consensus pattern (20 bp):
CCGGTTTTACTGGTTTTCAG
Found at i:32120 original size:30 final size:30
Alignment explanation
Indices: 32086--32143 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
32076 GTGCTAAAAA
* *
32086 CCGGTTTTGCAGGGTTTCAGCCGGTTCACC
1 CCGGTTCTACAGGGTTTCAGCCGGTTCACC
* *
32116 CCGGTTCTACCGGTTTTCAGCCGGTTCA
1 CCGGTTCTACAGGGTTTCAGCCGGTTCA
32144 TTACCATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.10, C:0.31, G:0.28, T:0.31
Consensus pattern (30 bp):
CCGGTTCTACAGGGTTTCAGCCGGTTCACC
Found at i:35710 original size:27 final size:27
Alignment explanation
Indices: 35671--35722 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
35661 TTAACAGAAG
* *
35671 CTCAACCGCTTCCTAACTGCCTAACCT
1 CTCAACAGCTTCCTAACCGCCTAACCT
*
35698 CTCAACAGTTTCCTAACCGCCTAAC
1 CTCAACAGCTTCCTAACCGCCTAAC
35723 TTCCTCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25
Consensus pattern (27 bp):
CTCAACAGCTTCCTAACCGCCTAACCT
Found at i:40307 original size:27 final size:27
Alignment explanation
Indices: 40268--40319 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40258 TTAACAGAAG
* *
40268 CTCAACCGCTTCCTAACTGCCTAACCT
1 CTCAACAGCTTCCTAACCGCCTAACCT
*
40295 CTCAACAGTTTCCTAACCGCCTAAC
1 CTCAACAGCTTCCTAACCGCCTAAC
40320 TTCCTCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25
Consensus pattern (27 bp):
CTCAACAGCTTCCTAACCGCCTAACCT
Found at i:57862 original size:20 final size:20
Alignment explanation
Indices: 57837--57876 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
57827 AGCAACAGAA
*
57837 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
57857 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
57877 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:57904 original size:53 final size:52
Alignment explanation
Indices: 57833--57982 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
57823 AATTAGCAAC
57833 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
57884 AGAATAAAAGACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
1 AGAATAAAA-ACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
57937 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
57983 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 9 0.10
52 36 0.38
53 49 0.52
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:57968 original size:20 final size:20
Alignment explanation
Indices: 57943--57981 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
57933 TAATAGAATA
*
57943 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
57963 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
57982 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:59512 original size:16 final size:16
Alignment explanation
Indices: 59491--59521 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59481 TTAACTCCTC
59491 AAAACTGCCTCTCTCA
1 AAAACTGCCTCTCTCA
59507 AAAACTGCCTCTCTC
1 AAAACTGCCTCTCTC
59522 CATCTCGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.39, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAACTGCCTCTCTCA
Found at i:62554 original size:20 final size:20
Alignment explanation
Indices: 62529--62568 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
62519 AGCAATAGAA
62529 TAAAAATGAT-TCTATCTAAT
1 TAAAAATGATCT-TATCTAAT
62549 TAAAAATGATCTTATCTAAT
1 TAAAAATGATCTTATCTAAT
62569 AACTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATCTTATCTAAT
Found at i:62602 original size:53 final size:52
Alignment explanation
Indices: 62522--62674 Score: 263
Period size: 53 Copynumber: 2.9 Consensus size: 52
62512 TAAAATTAGC
*
62522 AATAGAATAAAAA-TGATTCTATCTAATTAAAAATGATCTTATCTAATAACT
1 AATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
*
62573 AATAGAATAAAAGACTGATTCTATTTAATTAAAAATGATCCTATCTAATAACT
1 AATAGAATAAAA-ACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
*
62626 AATAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
62675 TTTAATTTAG
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 12 0.12
52 36 0.38
53 48 0.50
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (52 bp):
AATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
Found at i:62660 original size:20 final size:20
Alignment explanation
Indices: 62635--62673 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62625 TAATAGAATA
*
62635 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
62655 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
62674 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:71547 original size:10 final size:10
Alignment explanation
Indices: 71532--71556 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
71522 TGTAGTTTAC
71532 TCTTTAATTT
1 TCTTTAATTT
71542 TCTTTAATTT
1 TCTTTAATTT
71552 TCTTT
1 TCTTT
71557 GGTTAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (10 bp):
TCTTTAATTT
Found at i:71654 original size:30 final size:29
Alignment explanation
Indices: 71598--71663 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
71588 ATTTTAAACT
* * * *
71598 TTAAACTTTTAATAGTTATAAGATGATGA
1 TTAAATTTTTAATAATTATAAAATGATCA
71627 TTAAATTTTTAAATAATTATAAAATGATCA
1 TTAAATTTTT-AATAATTATAAAATGATCA
71657 TTAAATT
1 TTAAATT
71664 CTATGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (29 bp):
TTAAATTTTTAATAATTATAAAATGATCA
Found at i:76947 original size:16 final size:16
Alignment explanation
Indices: 76923--76956 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
76913 TATCGCCGAC
*
76923 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
76939 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
76955 CG
1 CG
76957 TGAATAGTAA
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:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:80930 original size:10 final size:9
Alignment explanation
Indices: 80907--80948 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
80897 TATATTTTTA
80907 ATAAAAAAT
1 ATAAAAAAT
80916 ATAAAAAAT
1 ATAAAAAAT
*
80925 -TCTAAAAAT
1 AT-AAAAAAT
80934 ATAAAAAAT
1 ATAAAAAAT
80943 -TAAAAA
1 ATAAAAA
80949 TTTCAAGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 7 0.24
9 21 0.72
10 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:87974 original size:2 final size:2
Alignment explanation
Indices: 87967--88011 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
87957 GTTATTTTAA
87967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88008 AT AT
1 AT AT
88012 TCTACTCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:88207 original size:18 final size:17
Alignment explanation
Indices: 88186--88219 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
88176 TTTTATAAGT
88186 AGTGTTGTGATTATTTAA
1 AGTGTT-TGATTATTTAA
*
88204 AGTGTTTTATTATTTA
1 AGTGTTTGATTATTTA
88220 TTTTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (17 bp):
AGTGTTTGATTATTTAA
Found at i:95219 original size:16 final size:16
Alignment explanation
Indices: 95198--95239 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
95188 TAAATAAACG
95198 AACATAAACGAACACA
1 AACATAAACGAACACA
* *
95214 AACATAAATGAACACG
1 AACATAAACGAACACA
95230 AACATAAACG
1 AACATAAACG
95240 TTGGAGACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.60, C:0.21, G:0.10, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:109573 original size:82 final size:84
Alignment explanation
Indices: 109428--109584 Score: 246
Period size: 82 Copynumber: 1.9 Consensus size: 84
109418 TGACTGAGAT
109428 TTTAAAAATTATAATGTACCTAAAAAATATATATATGTATGAACTAAATAAATTCGTAAGCAATG
1 TTTAAAAATTATAATGTACCTAAAAAATATATATATG--TGAACTAAATAAATTCGTAAGCAATG
*
109493 ATGTTAATGCATCTCTTTGAC
64 ATGTAAATGCATCTCTTTGAC
* * *
109514 TTTAAAAATTATAATGTACCTAAACAATATATGT-TG-GAACTAAATGAATTCGTAAGCAATGAT
1 TTTAAAAATTATAATGTACCTAAAAAATATATATATGTGAACTAAATAAATTCGTAAGCAATGAT
109577 GTAAATGC
66 GTAAATGC
109585 CGCTCTGGCA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
82 33 0.49
85 2 0.03
86 32 0.48
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (84 bp):
TTTAAAAATTATAATGTACCTAAAAAATATATATATGTGAACTAAATAAATTCGTAAGCAATGAT
GTAAATGCATCTCTTTGAC
Found at i:113550 original size:27 final size:27
Alignment explanation
Indices: 113520--113576 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
113510 CTTCTTATGG
113520 AATAAGAACTATTAACTAAATAAACTT
1 AATAAGAACTATTAACTAAATAAACTT
113547 AATAAGAACTATTAACTAAATAAACTT
1 AATAAGAACTATTAACTAAATAAACTT
113574 AAT
1 AAT
113577 TAACAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.30
Consensus pattern (27 bp):
AATAAGAACTATTAACTAAATAAACTT
Found at i:122573 original size:140 final size:140
Alignment explanation
Indices: 122321--122598 Score: 511
Period size: 140 Copynumber: 2.0 Consensus size: 140
122311 ACCAACCAGA
* *
122321 AAAACATGAAATAAGCATGCCAGAGCTTGTCTCTGCAGAAGAAAAGCAGCTTCATGGTGAAATAT
1 AAAACATGAAATAAGCATGCCAAAGCTTGTCTCTACAGAAGAAAAGCAGCTTCATGGTGAAATAT
122386 TTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCGAGTAAAAATGCAGA
66 TTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCGAGTAAAAATGCAGA
122451 TAAGTCCTTT
131 TAAGTCCTTT
* *
122461 AAAACATGATATAAGCATGCCAAAGCTTGTCTCTATAGAAGAAAAGCAGCTTCATGGTGAAATAT
1 AAAACATGAAATAAGCATGCCAAAGCTTGTCTCTACAGAAGAAAAGCAGCTTCATGGTGAAATAT
*
122526 TTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCTAGTAAAAATGCAGA
66 TTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCGAGTAAAAATGCAGA
122591 TAAGTCCT
131 TAAGTCCT
122599 AGAAGAAACA
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 133 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (140 bp):
AAAACATGAAATAAGCATGCCAAAGCTTGTCTCTACAGAAGAAAAGCAGCTTCATGGTGAAATAT
TTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCGAGTAAAAATGCAGA
TAAGTCCTTT
Found at i:132808 original size:87 final size:87
Alignment explanation
Indices: 132657--132838 Score: 267
Period size: 87 Copynumber: 2.1 Consensus size: 87
132647 GTTTTTCTTT
* * * *
132657 TTCGATTGTGTTTATTTGTTTGATGATAATCATCATTCCGAATTTATATCAATATTCAATCGAGA
1 TTCGATCGTGTTTATTTGTTTGATGATAATCATCATTACGAATTTATAACAATATTCAACCGAGA
*
132722 AAAAATTACATGTGATATGTGG
66 AAAAATTACATGTGATACGTGG
* *
132744 TTCGATCGTGTTTATTTGTTT-ACTGATAATCATCATTATGATTTTATAACAATATTCAACCGAG
1 TTCGATCGTGTTTATTTGTTTGA-TGATAATCATCATTACGAATTTATAACAATATTCAACCGAG
* *
132808 AAAAATTTACATGTGATACGTTG
65 AAAAAATTACATGTGATACGTGG
132831 TTCGATCG
1 TTCGATCG
132839 AAATATACAC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.01
87 84 0.99
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (87 bp):
TTCGATCGTGTTTATTTGTTTGATGATAATCATCATTACGAATTTATAACAATATTCAACCGAGA
AAAAATTACATGTGATACGTGG
Found at i:140568 original size:19 final size:20
Alignment explanation
Indices: 140544--140586 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
140534 GCGATTTTGA
140544 AAAATGTGTTGCGATAGT-T
1 AAAATGTGTTGCGATAGTGT
140563 AAAATGTGTTGCGATAGTGT
1 AAAATGTGTTGCGATAGTGT
140583 AAAA
1 AAAA
140587 GATTCCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (20 bp):
AAAATGTGTTGCGATAGTGT
Found at i:140922 original size:20 final size:20
Alignment explanation
Indices: 140830--140922 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
140820 GAAACTGGAG
*
140830 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* *
140850 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* * **
140870 TTCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGATAGTC-AAA
***
140891 ATCGCAACGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
140911 ATCGCGTTGCGA
1 ATCGCGTTGCGA
140923 ATCTGAAAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.70
21 16 0.28
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:140961 original size:40 final size:39
Alignment explanation
Indices: 140911--141042 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 39
140901 GATAGTCAAA
*
140911 ATCGCGTTGCGAATCTGAAAACTGATTTGCAATACTGGAG
1 ATCGCATTGCGAATCTG-AAACTGATTTGCAATACTGGAG
* * ** * ** *
140951 ATCGCATTGCGATAGTCAGAATC-GCGTTGCAAT-TTACAT
1 ATCGCATTGCGA-A-TCTGAAACTGATTTGCAATACTGGAG
*
140990 ATTCGCATTGCGAATCTGGAAACTGATTTGCGATACTGGAG
1 A-TCGCATTGCGAATCT-GAAACTGATTTGCAATACTGGAG
141031 ATCGCATTGCGA
1 ATCGCATTGCGA
141043 TTTTGTTGGT
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
38 2 0.03
39 8 0.12
40 48 0.71
41 7 0.10
42 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (39 bp):
ATCGCATTGCGAATCTGAAACTGATTTGCAATACTGGAG
Found at i:152542 original size:2 final size:2
Alignment explanation
Indices: 152535--152563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
152525 ATTCTTGATC
152535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
152564 AACAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162561 original size:12 final size:12
Alignment explanation
Indices: 162546--162571 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
162536 ACAACTAGGT
162546 GAACCTCAACAA
1 GAACCTCAACAA
162558 GAACCTCAACAA
1 GAACCTCAACAA
162570 GA
1 GA
162572 GCTTGAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.31, G:0.12, T:0.08
Consensus pattern (12 bp):
GAACCTCAACAA
Found at i:164380 original size:33 final size:34
Alignment explanation
Indices: 164337--164402 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
164327 AAACTAATTT
*
164337 GATGTCATTGCTTACAT-AAATTTGTTAGGTGAA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
*
164370 GATGTTATTGCTTACATCAAATTAGTTAGGTGA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
164403 GAGTTAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (34 bp):
GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
Found at i:177840 original size:20 final size:20
Alignment explanation
Indices: 177794--177844 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
177784 CAACGCGAAT
*
177794 TTAAAATTCGCAACACAAAA
1 TTAAAATTCACAACACAAAA
* * * *
177814 GTCAAATTCACAATACACAA
1 TTAAAATTCACAACACAAAA
177834 TTAAAATTCAC
1 TTAAAATTCAC
177845 GTTACGAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (20 bp):
TTAAAATTCACAACACAAAA
Found at i:178778 original size:22 final size:21
Alignment explanation
Indices: 178753--178840 Score: 81
Period size: 22 Copynumber: 4.1 Consensus size: 21
178743 TGAGTTACGA
178753 AATTTGTGAAATTCGCGTTGCG
1 AATTTG-GAAATTCGCGTTGCG
*
178775 AATTTGGAAAATCGCGTTGCGG
1 AATTTGGAAATTCGCGTTGC-G
** *
178797 AA--AAGAAATTCGAGTTGCG
1 AATTTGGAAATTCGCGTTGCG
* *
178816 AATCTGGGAAATTCGTGTTGCG
1 AAT-TTGGAAATTCGCGTTGCG
178838 AAT
1 AAT
178841 CTAGAAACTG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.06
20 12 0.22
21 13 0.24
22 26 0.48
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
AATTTGGAAATTCGCGTTGCG
Found at i:178789 original size:21 final size:22
Alignment explanation
Indices: 178753--178795 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
178743 TGAGTTACGA
*
178753 AATTTGTGAAATTCGCGTTGCG
1 AATTTGTGAAAATCGCGTTGCG
178775 AATTTG-GAAAATCGCGTTGCG
1 AATTTGTGAAAATCGCGTTGCG
178796 GAAAAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (22 bp):
AATTTGTGAAAATCGCGTTGCG
Found at i:178855 original size:20 final size:22
Alignment explanation
Indices: 178800--178855 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
178790 GTTGCGGAAA
* *
178800 AGAAATTCGAGTTGCGAATCTG
1 AGAAACTCGTGTTGCGAATCTG
* *
178822 GGAAATTCGTGTTGCGAATCT-
1 AGAAACTCGTGTTGCGAATCTG
178843 AGAAACT-GTGTTG
1 AGAAACTCGTGTTG
178856 TAAAATTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 6 0.20
21 5 0.17
22 19 0.63
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (22 bp):
AGAAACTCGTGTTGCGAATCTG
Found at i:178984 original size:2 final size:2
Alignment explanation
Indices: 178972--179003 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
178962 CTCTTTTCTT
178972 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
179004 TGTTGATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:197562 original size:59 final size:59
Alignment explanation
Indices: 197441--197575 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 59
197431 TACCATTCTA
* * * * ** *
197441 TAACTTCTAATAGTCGAGGGACTCAACAAAACAACACTATAGAGTTGAGGATCATTTTG
1 TAACTTTTAATAATCGAGGGACTCAACAAAACAACACTATAAAATAAAGGATCAGTTTG
* * *
197500 TAACTTTTAATAATCG-GTGACTCAACAAAATAACACTATATAAATAAAGTATCAGTTTG
1 TAACTTTTAATAATCGAGGGACTCAACAAAACAACACTATA-AAATAAAGGATCAGTTTG
*
197559 TAACTTTTAATACTCGA
1 TAACTTTTAATAATCGA
197576 ACAAAATAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 22 0.35
59 41 0.65
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (59 bp):
TAACTTTTAATAATCGAGGGACTCAACAAAACAACACTATAAAATAAAGGATCAGTTTG
Found at i:209610 original size:3 final size:3
Alignment explanation
Indices: 209602--209626 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
209592 CTCCTCACTC
209602 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
209627 GAGCAACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:209909 original size:21 final size:21
Alignment explanation
Indices: 209884--209939 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
209874 AAACCCTATG
209884 GCGGTGGCATCTAAACCAGCT
1 GCGGTGGCATCTAAACCAGCT
* * * *
209905 GCGGTGGCATATGACCCTGCT
1 GCGGTGGCATCTAAACCAGCT
*
209926 GTGGTGGCATCTAA
1 GCGGTGGCATCTAA
209940 CTCGACTACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (21 bp):
GCGGTGGCATCTAAACCAGCT
Found at i:211573 original size:27 final size:27
Alignment explanation
Indices: 211523--211574 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
211513 TAATTTAATA
* *
211523 AATACTATACAAATTAAAATATAAACT
1 AATACTATAAAAATTAAAAAATAAACT
211550 AATACTA-AAAAATTAAATAAATAAA
1 AATACTATAAAAATTAAA-AAATAAA
211575 ACATTCGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (27 bp):
AATACTATAAAAATTAAAAAATAAACT
Found at i:219225 original size:6 final size:6
Alignment explanation
Indices: 219214--219339 Score: 196
Period size: 6 Copynumber: 22.3 Consensus size: 6
219204 GACACGTATT
219214 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
219262 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
219308 A-CACG A-CACG A-CACG A-CACG A-CACG A-CACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
219340 ACGGCGGCGG
Statistics
Matches: 119, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 40 0.34
6 79 0.66
ACGTcount: A:0.36, C:0.47, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:219842 original size:6 final size:6
Alignment explanation
Indices: 219821--219853 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
219811 GTTTGTATCG
*
219821 GGTCG- GGTCGT TGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
219854 ATACGTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:219963 original size:19 final size:19
Alignment explanation
Indices: 219936--219997 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 19
219926 ACCAGTCGTT
*
219936 ACGATTTTGGACTATCGCA
1 ACGAATTTGGACTATCGCA
* *
219955 ACGAATTTGGAATAAATCACA
1 ACGAATTTGGACT--ATCGCA
*
219976 ACGCGAACTTGGACTATCGCA
1 A--CGAATTTGGACTATCGCA
219997 A
1 A
219998 TGCGATAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 11 0.33
21 12 0.36
23 10 0.30
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (19 bp):
ACGAATTTGGACTATCGCA
Found at i:220014 original size:21 final size:21
Alignment explanation
Indices: 219987--220191 Score: 147
Period size: 21 Copynumber: 9.8 Consensus size: 21
219977 CGCGAACTTG
*
219987 GACTATCGCAATGCGATAGTC
1 GACTATCGCATTGCGATAGTC
* * * *
220008 GATTATCGCAATGCGA-ACTTG
1 GACTATCGCATTGCGATA-GTC
*
220029 GACTATCGCAATGCGATAGTC
1 GACTATCGCATTGCGATAGTC
* * *
220050 GATTATCGCAATGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
220071 GACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATAGTC
*
220089 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCATTGCGATAGTC
* *
220112 AAAGT-TCGCATTGCGATAGTC
1 -GACTATCGCATTGCGATAGTC
* *
220133 AAAGT-TCGCATTGCGATAGTCC
1 -GACTATCGCATTGCGATAGT-C
* *
220155 AAGT-TCGCATTGCGATAGTC
1 GACTATCGCATTGCGATAGTC
220175 GACTATCGCATTGCGAT
1 GACTATCGCATTGCGAT
220192 TTACATATTC
Statistics
Matches: 157, Mismatches: 15, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.01
19 3 0.02
20 17 0.11
21 130 0.83
22 3 0.02
23 1 0.01
24 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:220024 original size:42 final size:42
Alignment explanation
Indices: 219978--220087 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
219968 AAATCACAAC
219978 GCGAACTTGGACTATCGCAATGCGATAGTCGATTATCGCAAT
1 GCGAACTTGGACTATCGCAATGCGATAGTCGATTATCGCAAT
220020 GCGAACTTGGACTATCGCAATGCGATAGTCGATTATCGCAAT
1 GCGAACTTGGACTATCGCAATGCGATAGTCGATTATCGCAAT
* *
220062 GCGAACTTCGACTATCGCATTGCGAT
1 GCGAACTTGGACTATCGCAATGCGAT
220088 TTACATATTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (42 bp):
GCGAACTTGGACTATCGCAATGCGATAGTCGATTATCGCAAT
Found at i:220163 original size:83 final size:83
Alignment explanation
Indices: 220096--220257 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
220086 ATTTACATAT
*
220096 TCGCATTGCGATAGT-CAAAGTTCGCATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAGTT
1 TCGCATTGCGAT-GTACAAA-TTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAGTT
220160 CGCATTGCGATAGTCGACTA
64 CGCATTGCGATAGTCGACTA
* * * * * *
220180 TCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGTATTGTGATAGTCTAAGTTCG
1 TCGCATTGCGATGTACAAATTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAGTTCG
220245 CATTGCGATAGTC
66 CATTGCGATAGTC
220258 AAAGTTCGCG
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
83 55 0.79
84 15 0.21
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (83 bp):
TCGCATTGCGATGTACAAATTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAGTTCG
CATTGCGATAGTCGACTA
Found at i:220177 original size:104 final size:104
Alignment explanation
Indices: 220069--220273 Score: 347
Period size: 104 Copynumber: 2.0 Consensus size: 104
220059 AATGCGAACT
*
220069 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAAGTTCGCATTGCGATAGTCA
1 TCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCA
*
220134 AAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
66 AAGTTCGCATTGCGATAGTCAAAGTTCGCATTGCGATAG
* * * *
220173 TCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGTATTGTGATAGTCT
1 TCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCA
*
220238 AAGTTCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
66 AAGTTCGCATTGCGATAGTCAAAGTTCGCATTGCGA
220274 ATCTGAAAAC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (104 bp):
TCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCAAAGTTCGCATTGCGATAGTCA
AAGTTCGCATTGCGATAGTCAAAGTTCGCATTGCGATAG
Found at i:220233 original size:21 final size:21
Alignment explanation
Indices: 220095--220273 Score: 220
Period size: 21 Copynumber: 8.6 Consensus size: 21
220085 GATTTACATA
220095 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
220116 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
*
220137 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCAAAG
* *
220158 TTCGCATTGCGATAGTC-GAC
1 TTCGCATTGCGATAGTCAAAG
* *
220178 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CAAAG
* *
220199 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCAAAG
* * *
220220 TTCGTATTGTGATAGTCTAAG
1 TTCGCATTGCGATAGTCAAAG
220241 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
*
220262 TTCGCGTTGCGA
1 TTCGCATTGCGA
220274 ATCTGAAAAC
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
20 16 0.12
21 119 0.88
22 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCAAAG
Found at i:230153 original size:2 final size:2
Alignment explanation
Indices: 230146--230174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
230136 TAATTAAAAT
230146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
230175 TTTAAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:234286 original size:31 final size:31
Alignment explanation
Indices: 234206--234286 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
234196 AGATGAATTT
* *
234206 TTAATTTGACCCTTAAACTTTAGATAAAATA
1 TTAATTTGACCCCTAAATTTTAGATAAAATA
* * * * * *
234237 -TCATTTTAACTCTAAATTTTAGATATATTA
1 TTAATTTGACCCCTAAATTTTAGATAAAATA
234267 TTAATTTGACCCCTAAATTT
1 TTAATTTGACCCCTAAATTT
234287 ATCAAAATCT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (31 bp):
TTAATTTGACCCCTAAATTTTAGATAAAATA
Found at i:239183 original size:18 final size:18
Alignment explanation
Indices: 239160--239200 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
239150 GAGCCAGAGC
* *
239160 TGTTGCTGCTGATGTTGT
1 TGTTGCTGATGATGATGT
239178 TGTTGCTGATGATGATGT
1 TGTTGCTGATGATGATGT
239196 TGTTG
1 TGTTG
239201 AAAGTGCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.49
Consensus pattern (18 bp):
TGTTGCTGATGATGATGT
Found at i:240793 original size:18 final size:18
Alignment explanation
Indices: 240770--240807 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
240760 GAAATTGGTG
*
240770 AATCCGTTAATGGTAGAA
1 AATCCGTTAATGATAGAA
240788 AATCCGTTAATGATAGAA
1 AATCCGTTAATGATAGAA
240806 AA
1 AA
240808 CACTATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (18 bp):
AATCCGTTAATGATAGAA
Found at i:244413 original size:17 final size:18
Alignment explanation
Indices: 244391--244425 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
244381 GATAAATGTA
244391 ATAC-AAAAAGATATATT
1 ATACAAAAAAGATATATT
244408 ATACAAAAAAGATATATT
1 ATACAAAAAAGATATATT
244426 GTGGTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
ATACAAAAAAGATATATT
Found at i:246759 original size:29 final size:29
Alignment explanation
Indices: 246717--246777 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
246707 TTGGTCTCCT
246717 TTTACAAACAAGGCTAAATATTGAACCAC
1 TTTACAAACAAGGCTAAATATTGAACCAC
246746 TTTACAAACAAGGCTAAATATTGAACCAC
1 TTTACAAACAAGGCTAAATATTGAACCAC
246775 TTT
1 TTT
246778 GACATTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (29 bp):
TTTACAAACAAGGCTAAATATTGAACCAC
Found at i:257986 original size:21 final size:21
Alignment explanation
Indices: 257961--258003 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
257951 TTCATCGTCA
257961 TCCGTCACTTGTCATCCTCCG
1 TCCGTCACTTGTCATCCTCCG
* *
257982 TCCGTCGCTTGTCGTCCTCCG
1 TCCGTCACTTGTCATCCTCCG
258003 T
1 T
258004 ACTCCGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.42, G:0.19, T:0.35
Consensus pattern (21 bp):
TCCGTCACTTGTCATCCTCCG
Found at i:262458 original size:23 final size:23
Alignment explanation
Indices: 262368--262450 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
262358 ATATTTTATA
* *
262368 TGGCACTTCGGTGCATTTTTACG
1 TGGCACTTCGGTGCAATTCTACG
* * * *
262391 CGACACTTAGGTGCAATTCTGCG
1 TGGCACTTCGGTGCAATTCTACG
* *
262414 T-GTATTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
262436 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
262451 TTTATACGAG
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
22 17 0.38
23 28 0.62
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:263110 original size:14 final size:14
Alignment explanation
Indices: 263091--263120 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
263081 GTGTTTGAAC
263091 ATATATTACATTGT
1 ATATATTACATTGT
263105 ATATATTACATTGT
1 ATATATTACATTGT
263119 AT
1 AT
263121 TTACCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
ATATATTACATTGT
Found at i:265763 original size:17 final size:17
Alignment explanation
Indices: 265720--265773 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
265710 ACTACAGTAG
*
265720 AAATTCTTTAAATTAAT
1 AAATTCTATAAATTAAT
*
265737 --ATTCAATAAATTAAT
1 AAATTCTATAAATTAAT
* *
265752 AAATTCTCTAAAATAAT
1 AAATTCTATAAATTAAT
265769 AAATT
1 AAATT
265774 TGTCCGGTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTCTATAAATTAAT
Found at i:275474 original size:19 final size:21
Alignment explanation
Indices: 275450--275488 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
275440 AAATTTAGTT
275450 TGTAAA-AT-ATAAGATTATC
1 TGTAAAGATAATAAGATTATC
*
275469 TGTAAAGTTAATAAGATTAT
1 TGTAAAGATAATAAGATTAT
275489 TATAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTAAAGATAATAAGATTATC
Found at i:281003 original size:2 final size:2
Alignment explanation
Indices: 280996--281023 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
280986 TAATTATTAA
280996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281024 GTCATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283218 original size:31 final size:31
Alignment explanation
Indices: 283176--283245 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
283166 ATTATTTTTG
*
283176 ACACGTGACATATGTT-ATATCATAACTTTAT
1 ACACGTAACATAT-TTCATATCATAACTTTAT
* * *
283207 ATACGTAACATATTTCATATTATTACTTTAT
1 ACACGTAACATATTTCATATCATAACTTTAT
283238 ACACGTAA
1 ACACGTAA
283246 AATTTATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (31 bp):
ACACGTAACATATTTCATATCATAACTTTAT
Found at i:283592 original size:21 final size:21
Alignment explanation
Indices: 283563--283607 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
283553 ATTCTGACTA
283563 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
283584 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
283605 TCG
1 TCG
283608 TAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:283672 original size:20 final size:20
Alignment explanation
Indices: 283609--283672 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
283599 CCTAATTCGT
*
283609 AATGCGAATACGTAAATCGC
1 AATGCGATTACGTAAATCGC
* ** *
283629 AACGCGAATTTGGAAAATCGC
1 AATGCG-ATTACGTAAATCGC
283650 AATGCGATTACGTAAATCGC
1 AATGCGATTACGTAAATCGC
283670 AAT
1 AAT
283673 ACGAATCTGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (20 bp):
AATGCGATTACGTAAATCGC
Found at i:283678 original size:41 final size:40
Alignment explanation
Indices: 283609--283698 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
283599 CCTAATTCGT
* * *
283609 AATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGC
1 AATGCGATTACGTAAATCGCAACACGAATCT-GAAAATCGC
* **
283650 AATGCGATTACGTAAATCGCAATACGAATCTGACTATCGC
1 AATGCGATTACGTAAATCGCAACACGAATCTGAAAATCGC
283690 AATGCGATT
1 AATGCGATT
283699 TACATAGCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 16 0.37
41 27 0.63
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
AATGCGATTACGTAAATCGCAACACGAATCTGAAAATCGC
Found at i:284298 original size:20 final size:20
Alignment explanation
Indices: 284269--284315 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
284259 ACGAGTGAAT
284269 CGCAACGCGAAAATGACTAC
1 CGCAACGCGAAAATGACTAC
* ** *
284289 CGCAATGCGAATTTGACTAT
1 CGCAACGCGAAAATGACTAC
284309 CGCAACG
1 CGCAACG
284316 AGAGAATCGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAC
Found at i:284369 original size:20 final size:20
Alignment explanation
Indices: 284344--284412 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
284334 TTTCATTTCA
284344 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
284364 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
284384 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
284404 TGTTGCGAT
1 CGTTGCGAT
284413 TTTCATTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:284409 original size:40 final size:40
Alignment explanation
Indices: 284345--284432 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
284335 TTCATTTCAC
284345 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGT
** * ** **
284385 GTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGT
284425 GTTGCGAT
1 GTTGCGAT
284433 TTAAAGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGT
Found at i:284418 original size:20 final size:20
Alignment explanation
Indices: 284380--284434 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
284370 GATAGTCAAA
**
284380 TTCGTGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
284400 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
284420 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
284435 AAAGTTTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:284442 original size:20 final size:20
Alignment explanation
Indices: 284399--284442 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
284389 CGATAGTCAT
** *
284399 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
284419 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
284439 TTTC
1 TTTC
284443 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:288338 original size:14 final size:14
Alignment explanation
Indices: 288319--288354 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
288309 ATTGTTTAAT
288319 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
288333 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
288347 TGATTTGT
1 TGATTTGT
288355 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:288516 original size:33 final size:34
Alignment explanation
Indices: 288456--288551 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
288446 AAAACAGACT
* * **
288456 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
288490 ATCGCAATGCGAAAA-GAAAGTCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
288523 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
288552 CGAAACTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:288605 original size:19 final size:20
Alignment explanation
Indices: 288568--288611 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
288558 TAATTTTGCG
288568 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCATTTTCGCA
288588 TTGCGATTTTCA-TTTCGCA
1 TTGCGATTTTCATTTTCGCA
288607 TTGCG
1 TTGCG
288612 CTTCTCTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCA
Found at i:288648 original size:20 final size:20
Alignment explanation
Indices: 288619--288712 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
288609 GCGCTTCTCT
288619 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
288639 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
288659 CATTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
288679 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
288699 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
288713 AATGAATGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:291162 original size:24 final size:24
Alignment explanation
Indices: 291128--291181 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
291118 CTGAAAAATC
*
291128 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGAACAAG
* *
291152 ATCAAAGTCCGGGTATTGAACAAG
1 ATCAAAATCCGAGTATTGAACAAG
291176 ATCAAA
1 ATCAAA
291182 TTTCGAATAC
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:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGAACAAG
Found at i:292065 original size:20 final size:20
Alignment explanation
Indices: 292042--292128 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
292032 CAGAATCTCG
292042 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
292062 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
292082 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
292103 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
292123 TTGCGA
1 TTGCGA
292129 ATTAGGGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 39 0.71
21 15 0.27
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:292107 original size:41 final size:40
Alignment explanation
Indices: 292042--292128 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 40
292032 CAGAATCTCG
*
292042 TTGCGATTTACAGATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACAAATTCGCATTGCGATTTACGTAATCGCA
* * *
292082 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA-TTTACAAATTCGCATTGCGATTTACGTAATCGCA
292123 TTGCGA
1 TTGCGA
292129 ATTAGGGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 6 0.14
41 36 0.86
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
TTGCGATTTACAAATTCGCATTGCGATTTACGTAATCGCA
Found at i:297030 original size:6 final size:6
Alignment explanation
Indices: 297019--297045 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
297009 ATAAGTTTAC
297019 GGGATT GGGATT GGGATT GGGATT GGG
1 GGGATT GGGATT GGGATT GGGATT GGG
297046 GCACGATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.30
Consensus pattern (6 bp):
GGGATT
Found at i:297865 original size:16 final size:16
Alignment explanation
Indices: 297844--297877 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
297834 GATTTCATTG
297844 TTTGGGAAGGTTATGA
1 TTTGGGAAGGTTATGA
297860 TTTGGGAAGGTTATGA
1 TTTGGGAAGGTTATGA
297876 TT
1 TT
297878 AGAAATTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (16 bp):
TTTGGGAAGGTTATGA
Found at i:308013 original size:15 final size:14
Alignment explanation
Indices: 307989--308022 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
307979 TATCATGTGT
*
307989 TGATAATGATTATG
1 TGATAATGATAATG
308003 TGATGAATGATAATG
1 TGAT-AATGATAATG
308018 TGATA
1 TGATA
308023 CATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (14 bp):
TGATAATGATAATG
Found at i:312585 original size:17 final size:17
Alignment explanation
Indices: 312563--312598 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
312553 CGGTGGAGGC
312563 AGAGGCAGCTAGGGATT
1 AGAGGCAGCTAGGGATT
*
312580 AGAGGCGGCTAGGGATT
1 AGAGGCAGCTAGGGATT
312597 AG
1 AG
312599 GGTTAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.44, T:0.17
Consensus pattern (17 bp):
AGAGGCAGCTAGGGATT
Found at i:312693 original size:12 final size:12
Alignment explanation
Indices: 312671--312712 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
312661 AATTGGTTTG
312671 TATTTTT-TTAT
1 TATTTTTATTAT
312682 TATTTTTATTAT
1 TATTTTTATTAT
*
312694 TATTTATATATAT
1 TATTTTTAT-TAT
312707 ATATTT
1 -TATTT
312713 AATATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 12 0.44
13 3 0.11
14 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:312724 original size:3 final size:3
Alignment explanation
Indices: 312712--312791 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
312702 TATATATATT
* * *
312712 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
312759 TAA TTA TAA TTA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
312792 ATAAATTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:316344 original size:34 final size:36
Alignment explanation
Indices: 316262--316340 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
316252 CTAACTAATG
*
316262 GCATGAACAAGCTAAAAAAAATTCTATCCTTAAATA
1 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
316298 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
1 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
316334 GCATGAA
1 GCATGAA
316341 AGCTCTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (36 bp):
GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
Found at i:317580 original size:24 final size:21
Alignment explanation
Indices: 317548--317601 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
317538 ATTAAAAACA
317548 ATAAATATCTAAAGAAATATTATT
1 ATAAATATCT--AGAAATATTA-T
*
317572 ATAAATATCTTGAAATATTAT
1 ATAAATATCTAGAAATATTAT
317593 ATGAAATAT
1 AT-AAATAT
317602 TATAGTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.11
22 15 0.54
24 10 0.36
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (21 bp):
ATAAATATCTAGAAATATTAT
Found at i:317605 original size:12 final size:12
Alignment explanation
Indices: 317561--317605 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
317551 AATATCTAAA
317561 GAAATATTATTAT
1 GAAATATTA-TAT
*
317574 -AAATA-TCT-T
1 GAAATATTATAT
317583 GAAATATTATAT
1 GAAATATTATAT
317595 GAAATATTATA
1 GAAATATTATA
317606 GTAGTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
9 1 0.04
10 6 0.22
11 3 0.11
12 17 0.63
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (12 bp):
GAAATATTATAT
Found at i:323268 original size:34 final size:34
Alignment explanation
Indices: 323225--323335 Score: 111
Period size: 36 Copynumber: 3.2 Consensus size: 34
323215 GGTAAGAAAT
*
323225 TTATTTTTATATTAATATCTTT-T-TAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
323258 TTATATTTTATATTAATATATTTATGTAAATATTA
1 TTAT-TTTTATATTAATATATTTATGTAAATATTA
* * *
323293 TT-TTTTTTTATTAAAATAATATTTATATAATTATTA
1 TTATTTTTATATT--AAT-ATATTTATGTAAATATTA
323329 TTTATTT
1 -TTATTT
323336 AAAATTATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
33 12 0.18
34 18 0.27
35 9 0.14
36 22 0.33
37 2 0.03
38 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:323279 original size:15 final size:15
Alignment explanation
Indices: 323229--323280 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
323219 AGAAATTTAT
*
323229 TTTTATATTAATATCT
1 TTTTATATTAATAT-A
*
323245 TTTTAAATAGTTATTATA
1 TTTT--ATA-TTAATATA
323263 TTTTATATTAATATA
1 TTTTATATTAATATA
323278 TTT
1 TTT
323281 ATGTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 10 0.33
16 7 0.23
18 7 0.23
19 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTATATTAATATA
Found at i:325818 original size:15 final size:15
Alignment explanation
Indices: 325798--325847 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
325788 ATACTACGGA
325798 TGTTTTTTT-TGTTGT
1 TGTTTTTTTAT-TTGT
*
325813 TGTTTTTTTACCTT-T
1 TGTTTTTTTA-TTTGT
325828 TGTTTTTTTATTTGT
1 TGTTTTTTTATTTGT
325843 TGTTT
1 TGTTT
325848 AGGGGCTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.04, C:0.04, G:0.14, T:0.78
Consensus pattern (15 bp):
TGTTTTTTTATTTGT
Found at i:335524 original size:25 final size:26
Alignment explanation
Indices: 335478--335530 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
335468 TAAATATTTT
* *
335478 TTCATTATTTTTAAAAACTTTATAAA
1 TTCATCATTTTTAAAAACTTTACAAA
*
335504 TTCATCATTTTTTAAAA-TTTACAAA
1 TTCATCATTTTTAAAAACTTTACAAA
335529 TT
1 TT
335531 TAAGCCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (26 bp):
TTCATCATTTTTAAAAACTTTACAAA
Found at i:337409 original size:33 final size:33
Alignment explanation
Indices: 337362--337433 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
337352 GTTGCCGCCG
*
337362 CCACCGCTGTCATCATCGTCGTCGCCACCATCA
1 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
337395 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
1 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
337428 CCACCG
1 CCACCG
337434 ATATCATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.18, C:0.49, G:0.15, T:0.18
Consensus pattern (33 bp):
CCACCGCTGCCATCATCGTCGTCGCCACCATCA
Found at i:337425 original size:18 final size:18
Alignment explanation
Indices: 337372--337427 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
337362 CCACCGCTGT
337372 CATCATCGTCGTCGCCAC
1 CATCATCGTCGTCGCCAC
** **
337390 CATCA-C--CACCGCTGC
1 CATCATCGTCGTCGCCAC
337405 CATCATCGTCGTCGCCAC
1 CATCATCGTCGTCGCCAC
337423 CATCA
1 CATCA
337428 CCACCGATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
15 10 0.37
16 1 0.04
17 1 0.04
18 15 0.56
ACGTcount: A:0.20, C:0.46, G:0.14, T:0.20
Consensus pattern (18 bp):
CATCATCGTCGTCGCCAC
Found at i:344771 original size:209 final size:212
Alignment explanation
Indices: 344376--344773 Score: 518
Period size: 209 Copynumber: 1.9 Consensus size: 212
344366 AACACATCCA
**
344376 ATACAAGAAATATCAGATGAAGCCATGAACAAATAGTGCTAACCAAATGCTCTTATTAATTTCTA
1 ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTGCTAACCAAATGCTC-T-TTAATTTCTA
* *
344441 GTTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCTTTCTGTCTACAATGGCA
64 GTTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGTCTACAATGACA
* * * *
344506 TACGTCTTAGCACACGGACTAGATACATCGATAATCTGACTGATATATTTAACCAGAAACTTTGC
129 AACGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAACTTTGC
344571 TACATTGATAATCTGATTG
194 TACATTGATAATCTGATTG
*
344590 ATACAAGAAATATCAGACAAAG-CATGAACAAATAG-GACTAACCAAATGCTC-TTACTTT-TAG
1 ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTG-CTAACCAAATGCTCTTTAATTTCTAG
** * * ** *
344651 TTTTTTAAATGAAAACTTGGTTATTTTGTATGTTGTCCTCTGCCTCCTTCTGTGCTACAATGACA
65 TTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGT-CTACAATGACA
* * * * * **
344716 AATGACTTAGCACATGGTCTTGATACATTAATAATCTGGTTGATAT-TTCAACCAGAAA
129 AACGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAA
344774 GTTAGGTTCT
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
209 59 0.37
210 52 0.33
212 1 0.01
213 27 0.17
214 20 0.13
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (212 bp):
ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTGCTAACCAAATGCTCTTTAATTTCTAGT
TTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGTCTACAATGACAAA
CGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAACTTTGCTA
CATTGATAATCTGATTG
Found at i:348649 original size:183 final size:183
Alignment explanation
Indices: 348333--348662 Score: 545
Period size: 183 Copynumber: 1.8 Consensus size: 183
348323 CTGATGCGCA
* *
348333 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGTGGATAAGCAACAGGTAGGGCACTACC
1 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGAGGATAAGCAACAGGTACGGCACTACC
* * *
348398 TGTACTTGCTCCCACGGAACTCAAACCATCCTGCCTGTTATGTCCAGAGAAGCTATTTTGTATGG
66 TGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATGG
348463 AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
131 AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
348516 CCAGACAAATGCATATTACTCAATTGATGGTCCAAA-GAAGGATAAGCAACAGGTACGGCACTAC
1 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACG-AGGATAAGCAACAGGTACGGCACTAC
* * ** * *
348580 CTGTACTTGCTCCTAAGGAATTCATGCTATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTCTG
65 CTGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATG
348645 GAGTGGAGCTCAGAATTA
130 GAGTGGAGCTCAGAATTA
348663 CTTTCAGGAG
Statistics
Matches: 135, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
182 1 0.01
183 134 0.99
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (183 bp):
CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGAGGATAAGCAACAGGTACGGCACTACC
TGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATGG
AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
Found at i:351588 original size:30 final size:32
Alignment explanation
Indices: 351552--351624 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
351542 ATAGTTTTTA
351552 TATTTTTTATT-AAT-ATAATTATATAAATAT
1 TATTTTTTATTAAATAATAATTATATAAATAT
* *
351582 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTATT-AAATAATAATTATATAAATAT
351615 TATTTATTTA
1 TATTT-TTTA
351625 AATTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.30
32 3 0.08
33 19 0.51
34 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTTTATTAAATAATAATTATATAAATAT
Found at i:351608 original size:27 final size:30
Alignment explanation
Indices: 351552--351649 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
351542 ATAGTTTTTA
*
351552 TATTTTTTATTAATATAATTATATAAATAT
1 TATTTTTTATTAAAATAATTATATAAATAT
* *
351582 TATTTTTTATTAAAATAA-TATTTATATAAT
1 TATTTTTTATTAAAATAATTATATAAAT-AT
* * *
351612 TATTATTTATTTAAAT--TTAT-TAATTAAT
1 TATTTTTTATTAAAATAATTATATAAAT-AT
351640 TATTTTTTAT
1 TATTTTTTAT
351650 GTTAATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 15 0.26
29 10 0.17
30 33 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTTATTAAAATAATTATATAAATAT
Found at i:351631 original size:25 final size:24
Alignment explanation
Indices: 351601--351648 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
351591 TTAAAATAAT
351601 ATTTATATAATT-ATTATTTATTTAA
1 ATTTAT-TAATTAATTATTT-TTTAA
351626 ATTTATTAATTAATTATTTTTTA
1 ATTTATTAATTAATTATTTTTTA
351649 TGTTAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATTAATTAATTATTTTTTAA
Found at i:351657 original size:24 final size:24
Alignment explanation
Indices: 351608--351657 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
351598 AATATTTATA
*
351608 TAATTATTATTTATTTAAATTTAT
1 TAATTATTATTTATTTAAATTAAT
**
351632 TAATTAATTATTT-TTTATGTTAAT
1 TAATT-ATTATTTATTTAAATTAAT
351656 TA
1 TA
351658 TATTTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATTATTATTTATTTAAATTAAT
Found at i:351760 original size:21 final size:24
Alignment explanation
Indices: 351730--351774 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
351720 TCTCCAGACA
351730 TTTTAGTAA-T-ATGGTAATATTT
1 TTTTAGTAATTAATGGTAATATTT
*
351752 TTTTA-TAATTAATGTTAATATTT
1 TTTTAGTAATTAATGGTAATATTT
351775 ATTATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 6 0.30
23 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (24 bp):
TTTTAGTAATTAATGGTAATATTT
Found at i:351804 original size:17 final size:18
Alignment explanation
Indices: 351784--351831 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
351774 TATTATTATT
351784 TTTAATT-TAAATTTAAA
1 TTTAATTATAAATTTAAA
* *
351801 TTT-ATTATGAATTTATA
1 TTTAATTATAAATTTAAA
351818 -TTAATTATAAATTT
1 TTTAATTATAAATTT
351832 TTATAATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAATTATAAATTTAAA
Found at i:353470 original size:21 final size:21
Alignment explanation
Indices: 353444--353504 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
353434 ATCTTCGCAG
*
353444 GGTTACATTCCTAGCCC-TCA
1 GGTTACATTCCTAGCCCGCCA
353464 TGGTTACATTCCTAGCCCGCCA
1 -GGTTACATTCCTAGCCCGCCA
*
353486 GGTTACATGCCTAGCCCGC
1 GGTTACATTCCTAGCCCGC
353505 AGAGTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCCA
Found at i:353993 original size:57 final size:58
Alignment explanation
Indices: 353921--354061 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 58
353911 TTTATCCATA
*
353921 CGTAAAAA-ATGTCGATGCTCATTCCATTAAAACC-A-ACTTATCACTTCATATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATT-AAACCGAGACTTATCACTTCACATTTATT
**
353977 CGTAAAAACATGTCGATGCTCATT---TTAGTCCTGAGTACTTATCACTTCACATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATTAAACC-GAG-ACTTATCACTTCACATTTATT
* * *
354034 CGTAAAAACATATCGATGTTTATTCCAT
1 CGTAAAAACATGTCGATGCTCATTCCAT
354062 ACAATTTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
53 3 0.04
54 2 0.03
55 1 0.01
56 8 0.11
57 56 0.79
60 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (58 bp):
CGTAAAAACATGTCGATGCTCATTCCATTAAACCGAGACTTATCACTTCACATTTATT
Found at i:354186 original size:63 final size:63
Alignment explanation
Indices: 354078--354198 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 63
354068 TCAATGTCAC
* *
354078 AACCAACTTATCACTTCACATTTATTCAATTTATCTATAACATTTTATCCAATTTATTTAAAT
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTTAAAT
* *
354141 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAATATTTTATCTAATTTATT
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATT
354199 CAAACTTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.45
Consensus pattern (63 bp):
AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTTAAAT
Found at i:354637 original size:128 final size:128
Alignment explanation
Indices: 354332--354924 Score: 760
Period size: 127 Copynumber: 4.8 Consensus size: 128
354322 CCATCCATCT
*
354332 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT-GACAAAATAA
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATAA
* *
354396 TGGAAGGCGCACCCCCAGGAACGAGCCTTCA-AGTCCCCTCAGAAATAATAGGTACTGACATGA
65 TGGAAGGCGCGCCCCCAGGAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
* * *
354459 ATAATTTCCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
**
354524 GGAAGGCGCGCCCCTGGGAACGCGCCTTCACTA-TCCCCTCAGAAATAATAGGTACTGACATGA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCAC-AGTCCCCTCAGAAATAATAGGTACTGACATGA
354587 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * * * *
354652 GGAAGGCGCG-TCCCTGAGAACGCGCCTTCA-AGTCCCCTAAGAAATATTAAGTACTGACATGA
66 GGAAGGCGCGCCCCCAG-GAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
*
354714 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * * *
354779 TGAAGGCGCGCCCAC-GAAACGCGCCTTCACCA-T----T------T--TGGGTACTGACATGA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCA-CAGTCCCCTCAGAAATAATAGGTACTGACATGA
* * * *
354829 ATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCT-GACAAAATA
1 ATAGT-TCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATA
* * *
354893 ATGAAAGGTGC-CCCCCAGGAACGCGCTTTCAC
64 ATGGAAGGCGCGCCCCCAGGAACGCGCCTTCAC
354925 GTGAATAGTG
Statistics
Matches: 421, Mismatches: 34, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
115 23 0.05
116 72 0.17
117 2 0.00
123 1 0.00
126 14 0.03
127 190 0.45
128 118 0.28
129 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (128 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
GGAAGGCGCGCCCCCAGGAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
Found at i:354916 original size:116 final size:115
Alignment explanation
Indices: 354702--354924 Score: 317
Period size: 116 Copynumber: 1.9 Consensus size: 115
354692 GAAATATTAA
* * *
354702 GTACTGACATGAATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTT
1 GTACTGACATGAATAGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTCT
*
354767 ACACAAAATAATTGAAGGCGCGCCCACGAAACGCGCCTTCACCATTTTGG
66 ACACAAAATAATTGAAGGCGCCCCCACGAAACGCGCCTTCACCATTTTGG
354817 GTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTAT
1 GTACTGACATGAATAGT-CCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATT-T
* * * *
354882 CT-GACAAAATAA-TGAAAGGTGCCCCC-CAGGAACGCGCTTTCAC
64 CTACACAAAATAATTG-AAGGCGCCCCCAC-GAAACGCGCCTTCAC
354925 GTGAATAGTG
Statistics
Matches: 96, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
115 20 0.21
116 74 0.77
117 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (115 bp):
GTACTGACATGAATAGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTCT
ACACAAAATAATTGAAGGCGCCCCCACGAAACGCGCCTTCACCATTTTGG
Found at i:355690 original size:23 final size:23
Alignment explanation
Indices: 355664--355711 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
355654 ACCGAAATGT
355664 CACGTAGAATTGCACCGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
*
355687 CACGTAGAATTGCACTGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
355710 CA
1 CA
355712 TATAATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CACGTAGAATTGCACCGTAGTGC
Found at i:357370 original size:21 final size:21
Alignment explanation
Indices: 357344--357385 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
357334 TTTTTATTCG
* *
357344 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
357365 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
357386 ATAGCCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:359548 original size:23 final size:23
Alignment explanation
Indices: 359522--359572 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
359512 CTATACTTCA
*
359522 ACTTCTCCACATATAACTAAACC
1 ACTTCTCCACATAGAACTAAACC
359545 ACTTCTCCACATAGAACTAAACC
1 ACTTCTCCACATAGAACTAAACC
359568 ACTTC
1 ACTTC
359573 ATCTAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.25
Consensus pattern (23 bp):
ACTTCTCCACATAGAACTAAACC
Found at i:360784 original size:23 final size:23
Alignment explanation
Indices: 360750--360810 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
360740 CTCATATAAA
* *
360750 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
**
360773 TGCACCGTAGTGCCGTGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
360796 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
360811 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:362511 original size:21 final size:21
Alignment explanation
Indices: 362485--362528 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
362475 TTTTTATTCG
* *
362485 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
362506 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
362527 CT
1 CT
362529 AGCCCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:372324 original size:24 final size:24
Alignment explanation
Indices: 372291--372345 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
372281 GGAAACAATG
372291 AAAT-AAGTAAATAAG-ATAGATTAA
1 AAATAAAGTAAATAAGTA-AGA-TAA
372315 AAA-AAAGTAAATAAGTAAGATAA
1 AAATAAAGTAAATAAGTAAGATAA
372338 AAATAAAG
1 AAATAAAG
372346 GAAGGGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.21
24 21 0.75
25 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (24 bp):
AAATAAAGTAAATAAGTAAGATAA
Found at i:375199 original size:9 final size:9
Alignment explanation
Indices: 375185--375232 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
375175 ATTATCAAAC
375185 ATATTTAAA
1 ATATTTAAA
375194 ATATTTAAA
1 ATATTTAAA
*
375203 ATA-TCAAA
1 ATATTTAAA
375211 CATATTTAAA
1 -ATATTTAAA
375221 ATATTTAAA
1 ATATTTAAA
375230 ATA
1 ATA
375233 ATTATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 4 0.11
9 27 0.77
10 4 0.11
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATTTAAA
Found at i:375200 original size:27 final size:27
Alignment explanation
Indices: 375170--375232 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
375160 TAGTTTTCAT
*
375170 TTTAAATTATCAAACATATTTAAAATA
1 TTTAAAATATCAAACATATTTAAAATA
375197 TTTAAAATATCAAACATATTTAAAATA
1 TTTAAAATATCAAACATATTTAAAATA
375224 TTTAAAATA
1 TTTAAAATA
375233 ATTATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTAAAATATCAAACATATTTAAAATA
Found at i:377717 original size:105 final size:105
Alignment explanation
Indices: 377535--377749 Score: 385
Period size: 105 Copynumber: 2.0 Consensus size: 105
377525 GGTGGTGAGG
* *
377535 AAGCTATATTAAGAAACGATAATGCAGTTTCTGAGGAGGGTTATTCTGCAACTCCAATTGGGGAT
1 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
* *
377600 GAGGACCATTTTGAGTCTGTTTCTTTAGAAAATCAAGATA
66 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
*
377640 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCTATTGGGGAG
1 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
377705 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
66 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
377745 AAGCT
1 AAGCT
377750 TCTGAAGAGT
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (105 bp):
AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
Found at i:399922 original size:45 final size:45
Alignment explanation
Indices: 399858--399946 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
399848 CTCCATAACG
399858 TAGTTAAACATCCTAAATGGTTTAGGACCCAATTAACTTCGCAAC
1 TAGTTAAACATCCTAAATGGTTTAGGACCCAATTAACTTCGCAAC
399903 TAGTTAAACATCCTAAATGGTTTAGGACCCAATTAACTTCGCAA
1 TAGTTAAACATCCTAAATGGTTTAGGACCCAATTAACTTCGCAA
399947 TTCTCCAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (45 bp):
TAGTTAAACATCCTAAATGGTTTAGGACCCAATTAACTTCGCAAC
Found at i:403384 original size:17 final size:17
Alignment explanation
Indices: 403362--403395 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
403352 CAAACCGGAT
*
403362 AAAAAACCGGTTTTTTA
1 AAAAAACCGGATTTTTA
*
403379 AAAAAACTGGATTTTTA
1 AAAAAACCGGATTTTTA
403396 TCCGAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (17 bp):
AAAAAACCGGATTTTTA
Found at i:407793 original size:20 final size:19
Alignment explanation
Indices: 407761--407804 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
407751 TTGTTTGTAA
407761 ATTTTTTATTCTCATTAAT
1 ATTTTTTATTCTCATTAAT
*
407780 -TTTTTTATACTCTCGTTAAT
1 ATTTTTTAT--TCTCATTAAT
407800 ATTTT
1 ATTTT
407805 AACTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTCTCATTAAT
Found at i:407917 original size:2 final size:2
Alignment explanation
Indices: 407910--407943 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
407900 GAATACAAAG
407910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
407944 TATGGTTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.