Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007932.1 Hibiscus syriacus cultivar Beakdansim tig00110342_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: 1116633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:21045 original size:16 final size:15
Alignment explanation
Indices: 21024--21053 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21014 ATTTTGCTTG
21024 AAGAAGAAAAGAAAAA
1 AAGAAGAAAA-AAAAA
21040 AAGAAGAAAAAAAA
1 AAGAAGAAAAAAAA
21054 GAAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAAAAAAA
Found at i:21055 original size:25 final size:23
Alignment explanation
Indices: 21027--21089 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
21017 TTGCTTGAAG
21027 AAGAAAAGAAAAAAAGAAGAAAAAA
1 AAGAAAA-AAAAAAA-AAGAAAAAA
*
21052 AAGAAATAAATAATAAAAGAAAAAA
1 AAGAAA-AAA-AAAAAAAGAAAAAA
* *
21077 AAGGAAATAAAAA
1 AAGAAAAAAAAAA
21090 GGGGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 22 0.69
26 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (23 bp):
AAGAAAAAAAAAAAAAGAAAAAA
Found at i:21069 original size:20 final size:21
Alignment explanation
Indices: 21027--21078 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
21017 TTGCTTGAAG
21027 AAGAAAAGAAAAAAAGAAGAA
1 AAGAAAAGAAAAAAAGAAGAA
* * *
21048 AA-AAAAGAAATAAATAATAA
1 AAGAAAAGAAAAAAAGAAGAA
21068 AAGAAAA-AAAA
1 AAGAAAAGAAAA
21079 GGAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (21 bp):
AAGAAAAGAAAAAAAGAAGAA
Found at i:21810 original size:13 final size:13
Alignment explanation
Indices: 21770--21798 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21760 GAAATGATCA
21770 AAAGAGAAAAAAT
1 AAAGAGAAAAAAT
21783 AAAGAGAAAAAAT
1 AAAGAGAAAAAAT
21796 AAA
1 AAA
21799 ATAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAGAGAAAAAAT
Found at i:21831 original size:15 final size:14
Alignment explanation
Indices: 21769--21831 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 14
21759 AGAAATGATC
*
21769 AAAAGAGAAAAAAT
1 AAAAAAGAAAAAAT
*
21783 -AAAGAGAAAAAAT
1 AAAAAAGAAAAAAT
*
21796 AAAATAAGAAAATAAG
1 AAAA-AAGAAAA-AAT
21812 AAAAAAGAAAAAGAT
1 AAAAAAGAAAAA-AT
21827 AAAAA
1 AAAAA
21832 CCAAAGTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 13 0.31
14 4 0.10
15 19 0.45
16 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAAAAGAAAAAAT
Found at i:24107 original size:20 final size:20
Alignment explanation
Indices: 24078--24120 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
24068 ATCCCACCAC
*
24078 ATGCAACTACATGCTTCTAA
1 ATGCAACTACATGCTCCTAA
* *
24098 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
24118 ATG
1 ATG
24121 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:34944 original size:90 final size:90
Alignment explanation
Indices: 34836--35002 Score: 291
Period size: 90 Copynumber: 1.9 Consensus size: 90
34826 ATTTAATTTT
34836 AATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGATTAGCGTAACT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAT-CCTAATATGATTAGCGTAACT
*
34900 TGGATATAAAAGGATTATTAAACTCC
65 TAGATATAAAAGGATTATTAAACTCC
*
34926 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGCGTAACTT
*
34991 AGCTATAAAAGG
66 AGATATAAAAGG
35003 GTGTGTTAGG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
90 68 0.93
91 5 0.07
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGCGTAACTT
AGATATAAAAGGATTATTAAACTCC
Found at i:37899 original size:25 final size:25
Alignment explanation
Indices: 37871--37933 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
37861 TTAAGTAATA
37871 ATTGCATGTTATTAATTCATG-TGAC
1 ATTGCATGTTATTAATTCATGTTG-C
*
37896 ATTGCATGTTATTAATTTATGTTGC
1 ATTGCATGTTATTAATTCATGTTGC
37921 ATTGCATGTTATT
1 ATTGCATGTTATT
37934 CATGTTGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 34 0.94
26 2 0.06
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTGC
Found at i:44565 original size:43 final size:43
Alignment explanation
Indices: 44446--44692 Score: 273
Period size: 43 Copynumber: 5.8 Consensus size: 43
44436 ACGCCGCAAA
* * * *
44446 ATCTATAGCAGTGTTTTTGCA-ACAAACGCCACAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
** * * *
44488 ATCTATAGCGGTATTTTTTTGATATAAATGCCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGT-ATACAAACGCCGCAAAAGGTCAT
* * *
44532 ATCTATAGTGGCGTTTTTGTATACAAACGCCGCAAAAAGTCAG
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
** *
44575 ATCTATAGCGGCGTTTTTGTATACAAACGTTGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
* ** * * *
44618 ATCTATAACAACATTTTTGGATACAAACGACGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
*
44661 ATCTATAGCAGCGTTTTT-TATACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGC
44693 TAATTTCAAT
Statistics
Matches: 170, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
42 28 0.16
43 108 0.64
44 34 0.20
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
Found at i:48485 original size:41 final size:41
Alignment explanation
Indices: 48432--48673 Score: 204
Period size: 41 Copynumber: 5.9 Consensus size: 41
48422 TTTGTAAACT
* *
48432 CAAGTGTATAGCGGCGATTGAATAAAAACGCCACTAAAGTA
1 CAAGTCTATAGCGGCGATTGTATAAAAACGCCACTAAAGTA
*
48473 -AGAGTCTTTAGCGGC-ATTTGTATAAAAACGCCACTAAAGTA
1 CA-AGTCTATAGCGGCGA-TTGTATAAAAACGCCACTAAAGTA
* * * * * *
48514 CAATTGTATAACGAC-ATTTATATAAAAAAGCCACTAAAGTA
1 CAAGTCTATAGCGGCGA-TTGTATAAAAACGCCACTAAAGTA
* * *
48555 CAATTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTA
1 CAAGTCTATAGCGGCGATTGTATAAAAACGCCACTAAAGTA
* * * * * *
48596 CGAGTCTTTTGCGCCGTTTGTATAAAAATGCCACTAAAGTA
1 CAAGTCTATAGCGGCGATTGTATAAAAACGCCACTAAAGTA
* * * * *
48637 CTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACTA
1 CAAGTCTATAGCGGCGATTGTAT--AAAAACGCCACTA
48674 TCGATGAACC
Statistics
Matches: 167, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
40 3 0.02
41 151 0.90
42 13 0.08
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (41 bp):
CAAGTCTATAGCGGCGATTGTATAAAAACGCCACTAAAGTA
Found at i:48522 original size:82 final size:81
Alignment explanation
Indices: 48432--48673 Score: 236
Period size: 82 Copynumber: 2.9 Consensus size: 81
48422 TTTGTAAACT
* * * *
48432 CAAGTGTATAGCGGCGATTGAATAAAAACGCCACTAAAGTAAGAGTCTTTAGCGGCATTTGTATA
1 CAAGTGTATAGCGACGATTGAATAAAAAAGCCACTAAAGTAA-ACTCTTTAGCGGCGTTTGTATA
48497 AAAACGCCACTAAAGTA
65 AAAACGCCACTAAAGTA
* * * * *
48514 CAATTGTATAACGAC-ATTTATATAAAAAAGCCACTAAAGTACAATTCTATAGCGGCGTTTGTAT
1 CAAGTGTATAGCGACGATTGA-ATAAAAAAGCCACTAAAGTA-AACTCTTTAGCGGCGTTTGTAT
*
48578 AAAAACACCACTAAAGTA
64 AAAAACGCCACTAAAGTA
* * * * * * * * * *
48596 CGAGTCTTTTGCGCCGTTTGTATAAAAATGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TG
1 CAAGTGTATAGCGACGATTGAATAAAAAAGCCACTAAAGTA-AACTCTTTAGCGGCGTTTGTAT-
48660 AAAAAACGCCACTA
64 -AAAAACGCCACTA
48674 TCGATGAACC
Statistics
Matches: 130, Mismatches: 25, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
81 5 0.04
82 110 0.85
83 15 0.12
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (81 bp):
CAAGTGTATAGCGACGATTGAATAAAAAAGCCACTAAAGTAAACTCTTTAGCGGCGTTTGTATAA
AAACGCCACTAAAGTA
Found at i:48690 original size:82 final size:82
Alignment explanation
Indices: 48453--48705 Score: 208
Period size: 82 Copynumber: 3.1 Consensus size: 82
48443 CGGCGATTGA
* * * * *
48453 ATAAAAACGCCACTAAAGTA-AGAGTCTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTAC-A
1 ATAAAAAAGCCACTAAAGTACA-ACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGA
** ** * *
48516 ATTGTATAACGACATTTAT
65 A-CCTATTGCGCCATTTGT
* *
48535 ATAAAAAAGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAG
1 ATAAAAAAGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAA
* * *
48600 TCTTTTGCGCCGTTTGT
66 CCTATTGCGCCATTTGT
* * * * * ** *
48617 ATAAAAATGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACTATCG-ATG
1 ATAAAAAAGCCACTAAAGTACAACTCTATAGCGGCGTTTGTAT--AAAAACACCACTAAAGTACG
* *
48680 AACCTATTGCGGCATTTTT
64 AACCTATTGCGCCATTTGT
48699 ATAAAAA
1 ATAAAAA
48706 CGATGCTAAA
Statistics
Matches: 139, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
81 1 0.01
82 123 0.88
83 15 0.11
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (82 bp):
ATAAAAAAGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAA
CCTATTGCGCCATTTGT
Found at i:54228 original size:16 final size:17
Alignment explanation
Indices: 54177--54231 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
54167 TTCATAATTC
54177 AAAATAATATTAAATAA
1 AAAATAATATTAAATAA
*
54194 AAAATACAT-GTAAATAA
1 AAAATA-ATATTAAATAA
54211 AAAATAATATTATAA-AA
1 AAAATAATATTA-AATAA
54228 AAAA
1 AAAA
54232 AAAAATATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 27 0.82
18 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAATAATATTAAATAA
Found at i:58440 original size:6 final size:6
Alignment explanation
Indices: 58429--58478 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
58419 TCCGCAGCAT
*
58429 CCGCAA CCGCAA CCGCGACA CCGCAA CCGCAACA CCGCAA CCGTAA CCGC
1 CCGCAA CCGCAA CCGC-A-A CCGCAA CCGC-A-A CCGCAA CCGCAA CCGC
58479 GACAGATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 24 0.63
7 4 0.11
8 10 0.26
ACGTcount: A:0.30, C:0.50, G:0.18, T:0.02
Consensus pattern (6 bp):
CCGCAA
Found at i:58453 original size:14 final size:14
Alignment explanation
Indices: 58434--58471 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
58424 AGCATCCGCA
*
58434 ACCGCAACCGCGAC
1 ACCGCAACCGCAAC
58448 ACCGCAACCGCAAC
1 ACCGCAACCGCAAC
58462 ACCGCAACCG
1 ACCGCAACCG
58472 TAACCGCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (14 bp):
ACCGCAACCGCAAC
Found at i:59527 original size:40 final size:41
Alignment explanation
Indices: 59472--59577 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
59462 AACTAAAACC
59472 TATTTTATTAATATTTTTATAACAT-GACATCAATTAGTAT
1 TATTTTATTAATATTTTTATAACATCGACATCAATTAGTAT
** * *
59512 TATTTTATTAATATTTTT-TATGATGCGGCATCTATTAGTAT
1 TATTTTATTAATATTTTTATAACAT-CGACATCAATTAGTAT
* *
59553 TATTTTATTAATATTGTTATTACAT
1 TATTTTATTAATATTTTTATAACAT
59578 AAAATTAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.07
40 18 0.33
41 30 0.55
42 3 0.05
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.54
Consensus pattern (41 bp):
TATTTTATTAATATTTTTATAACATCGACATCAATTAGTAT
Found at i:60414 original size:32 final size:30
Alignment explanation
Indices: 60378--60444 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
60368 AAACAAATAC
**
60378 ATTAAAATAAAAAGTAATTTAAACTTTGAGTT
1 ATTAAAATAAAAA-TAAAATAAA-TTTGAGTT
**
60410 ATTAAAATATTAATAAAATAAATTTGAGTT
1 ATTAAAATAAAAATAAAATAAATTTGAGTT
60440 ATTAA
1 ATTAA
60445 TAGATGTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 13 0.42
31 7 0.23
32 11 0.35
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.39
Consensus pattern (30 bp):
ATTAAAATAAAAATAAAATAAATTTGAGTT
Found at i:71277 original size:14 final size:16
Alignment explanation
Indices: 71249--71283 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
71239 AATATAAAAC
71249 ATAAAATATAGGATAA
1 ATAAAATATAGGATAA
71265 ATAAAA-ATA-GATAA
1 ATAAAATATAGGATAA
71279 ATAAA
1 ATAAA
71284 TGAGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
ATAAAATATAGGATAA
Found at i:71917 original size:37 final size:36
Alignment explanation
Indices: 71861--71961 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
71851 ATAGTAGAAC
71861 TCTATCCTA-TTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
71897 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
71931 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
71962 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
34 33 0.55
36 8 0.13
37 19 0.32
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:76692 original size:124 final size:124
Alignment explanation
Indices: 76505--77230 Score: 779
Period size: 124 Copynumber: 5.9 Consensus size: 124
76495 GGCATTACTG
* * * *
76505 CTGGTGGGCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCATTCGTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTG
*
76570 AGCCTTGAATTGGATA-CCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTA
66 AGCCTTGAATTGGATATCC-TTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * *
76629 CTGGTGAGAACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTAAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTG
* *
76694 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGCTG
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * * * * *
76753 CTGGTGAGCACGATTCCATTCATCGTGAAGTTGAAACTGTGAATGACCCCTTCTTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTG
* *
76818 ATCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTA
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * * * *
76877 CTGGTGAGCACGATTCCCTTCGTCATGAAGTTAAAACAGTGGACGGCCCTTTCGTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTG
*
76942 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTG
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * * * *
77001 CT-TTGAGTC-CAATAT-CCTTCGCCGTGAAGATGAAATTGGCTCTGAATGAAACTGGGAAGCCC
1 CTGGTGAG-CACGAT-TCCCTTCGTCGTGAAGTTGAAA----C-C-G--TG-GA-T--G--GCCC
** * * *
77063 CTTCGCCGTGAAGTTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTGAAATTCAAT-T----
50 CTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAG
77123 -T--A-G--A
115 ATGAATGTTA
* ** * *
77127 --GTTG-GCACGATAT-TATTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTT
1 CTGGTGAGCACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTT
* * *
77188 GAGCCTTGACTTGAATATCCTTCGTTGTGAAGTTGAAATCCAA
65 GAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
77231 GCTTGTATTG
Statistics
Matches: 516, Mismatches: 67, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
110 54 0.10
112 1 0.00
114 1 0.00
115 1 0.00
116 2 0.00
119 1 0.00
123 24 0.05
124 360 0.70
125 5 0.01
127 1 0.00
128 1 0.00
129 2 0.00
131 3 0.01
132 1 0.00
135 1 0.00
136 1 0.00
137 57 0.11
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (124 bp):
CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTG
AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
Found at i:77392 original size:244 final size:241
Alignment explanation
Indices: 76885--77611 Score: 1007
Period size: 244 Copynumber: 3.0 Consensus size: 241
76875 TACTGGTGAG
* * * *
76885 CACGAT-TCCCTTCGTCATGAAGTT-AAAACAGTGGACGGCCCTTTCGTTGTGAAGTTGAGCCTT
1 CACGATAT-CCTTCGTCGTGAAGTTGAAATCA-TGGATGGCCCATTCGTTGTGAAGTTGAGCCTT
* * * *
76948 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTT-GAGTCCA
64 GACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-----TG--TATTG-TTTCGAGTCCA
*
77012 ATATCCTTCGCCGTGAAGATGAAATTGGCTCTGAATGAAACTGGGAAGC-CCCTTCGCCGTGAAG
121 ATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCACCCTTCGCCGTGAAG
* * *
77076 TTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTGAAATTCAAT-TTAGAGTTGG
186 TTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTT-GAGTTGA
** *
77132 CACGATATTATTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
*
77197 CTTGAATATCCTTCGTTGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* * *
77262 CCATGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCAGCCCTTCGCCGTGAAGTTGATCT
131 CCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAG--CA-CCCTTCGCCGTGAAGTTGAGCT
77327 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
193 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
* * *
77376 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCATTGTCAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
77441 CTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTATTTCGAGTCCAATATTCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* * * * *
77506 TCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAACA-CATTCACCATGAAGTTGAGCTTTG
131 CCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCACCCTTCGCCGTGAAGTTGAGCTTTG
*
77570 AATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTTGAG
196 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAG
77612 AAAGTTGGTT
Statistics
Matches: 435, Mismatches: 37, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
239 3 0.01
240 117 0.27
242 5 0.01
244 218 0.50
245 2 0.00
247 84 0.19
248 6 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (241 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
CCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCACCCTTCGCCGTGAAGTTGAGCTTTG
AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
Found at i:81731 original size:7 final size:7
Alignment explanation
Indices: 81705--81746 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
81695 GAGGAATAAT
81705 AAAAATA
1 AAAAATA
81712 AAAAAGTA
1 AAAAA-TA
81720 AAAAA-A
1 AAAAATA
81726 ATAAAATA
1 A-AAAATA
81734 AAAAATA
1 AAAAATA
81741 AAAAAT
1 AAAAAT
81747 GTCAAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 2 0.06
7 21 0.66
8 9 0.28
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:91917 original size:3 final size:3
Alignment explanation
Indices: 91909--91934 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
91899 TATCCGCCCT
91909 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
91935 TTGTGGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:94064 original size:12 final size:12
Alignment explanation
Indices: 94047--94071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94037 AACTCAATCT
94047 TATAGATAGAGA
1 TATAGATAGAGA
94059 TATAGATAGAGA
1 TATAGATAGAGA
94071 T
1 T
94072 TGACATCCAC
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:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TATAGATAGAGA
Found at i:95904 original size:2 final size:2
Alignment explanation
Indices: 95897--95925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
95887 ATGTGAATTA
95897 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
95926 GATTTTTTTT
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:96848 original size:18 final size:18
Alignment explanation
Indices: 96825--96860 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
96815 CCACTATGAA
*
96825 ATGTCCCGAATGACCACT
1 ATGTCCCGAAGGACCACT
96843 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
96861 GTATATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:111319 original size:19 final size:18
Alignment explanation
Indices: 111293--111328 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
111283 ATACTATCCA
111293 TTTCTTATAAATTTATCT
1 TTTCTTATAAATTTATCT
*
111311 TTTCATTATAATTTTATC
1 TTTC-TTATAAATTTATC
111329 ATTTAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTATAAATTTATCT
Found at i:111968 original size:15 final size:15
Alignment explanation
Indices: 111948--111977 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
111938 TTGTTTATAA
111948 TTAATTATTATTATT
1 TTAATTATTATTATT
111963 TTAATTATTATTATT
1 TTAATTATTATTATT
111978 ATTTCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTATTATTATT
Found at i:111974 original size:18 final size:19
Alignment explanation
Indices: 111945--111981 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
111935 TAATTGTTTA
111945 TAATTAATTATTATTATTT
1 TAATTAATTATTATTATTT
111964 TAATT-ATTATTATTATTT
1 TAATTAATTATTATTATTT
111982 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTAATTATTATTATTT
Found at i:115067 original size:35 final size:35
Alignment explanation
Indices: 115028--115095 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
115018 TTTAATTTAA
*
115028 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTAAAGTATTTTAGAATTTGG
* * *
115063 GGTTTAGAATGTAATTGAAGTGTTTTAGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTAGAATTT
115096 TGAACATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTAGAATTTGG
Found at i:120782 original size:7 final size:7
Alignment explanation
Indices: 120766--120796 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
120756 GTCAAAGAAA
*
120766 GTCAATG
1 GTCAACG
120773 GTCAACG
1 GTCAACG
120780 GTCAACG
1 GTCAACG
120787 GTCAACG
1 GTCAACG
120794 GTC
1 GTC
120797 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:120803 original size:5 final size:5
Alignment explanation
Indices: 120793--120850 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
120783 AACGGTCAAC
* *
120793 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
120842 GGTCG GGTC
1 GGTCG GGTC
120851 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:120812 original size:22 final size:22
Alignment explanation
Indices: 120786--120850 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
120776 AACGGTCAAC
120786 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
120808 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
120830 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
120851 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:120865 original size:9 final size:9
Alignment explanation
Indices: 120847--120945 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
120837 GGTCGGGTCG
*
120847 GGTCAGACC
1 GGTCAAACC
120856 GGTCAAACC
1 GGTCAAACC
* *
120865 GATTCAGACC
1 G-GTCAAACC
120875 GGTCAAACC
1 GGTCAAACC
*
120884 GGTTCGAACC
1 GG-TCAAACC
*
120894 GGTTGAAACC
1 GG-TCAAACC
120904 GGTCAAACC
1 GGTCAAACC
120913 GGTCAGAACC
1 GGTCA-AACC
*
120923 GGTTGAAAACC
1 GG-T-CAAACC
*
120934 GGTTAAACC
1 GGTCAAACC
120943 GGT
1 GGT
120946 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:120904 original size:29 final size:31
Alignment explanation
Indices: 120872--120946 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
120862 ACCGATTCAG
120872 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
120901 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
120931 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
120947 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:120924 original size:19 final size:19
Alignment explanation
Indices: 120847--120945 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
120837 GGTCGGGTCG
120847 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
120865 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
120884 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
120904 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
120923 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
120943 GGT
1 GGT
120946 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:127157 original size:5 final size:5
Alignment explanation
Indices: 127147--127199 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
127137 AACGGTCAAC
* *
127147 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
127196 GGTC
1 GGTC
127200 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:127162 original size:17 final size:17
Alignment explanation
Indices: 127140--127200 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
127130 AACGGTCAAC
127140 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
127157 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
127179 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
127196 GGTCA
1 GGTCA
127201 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:127167 original size:7 final size:7
Alignment explanation
Indices: 127113--127150 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
127103 GTCAAAGAAA
*
127113 GTCAATG
1 GTCAACG
127120 GTCAACG
1 GTCAACG
127127 GTCAACG
1 GTCAACG
127134 GTCAACG
1 GTCAACG
127141 GTCAACG
1 GTCAACG
127148 GTC
1 GTC
127151 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:127175 original size:22 final size:22
Alignment explanation
Indices: 127133--127199 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
127123 AACGGTCAAC
*
127133 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
127157 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
127179 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
127200 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:127214 original size:9 final size:9
Alignment explanation
Indices: 127196--127294 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
127186 GGTCGGGTCG
*
127196 GGTCAGACC
1 GGTCAAACC
127205 GGTCAAACC
1 GGTCAAACC
* *
127214 GATTCAGACC
1 G-GTCAAACC
127224 GGTCAAACC
1 GGTCAAACC
*
127233 GGTTCGAACC
1 GG-TCAAACC
*
127243 GGTTGAAACC
1 GG-TCAAACC
127253 GGTCAAACC
1 GGTCAAACC
127262 GGTCAGAACC
1 GGTCA-AACC
*
127272 GGTTGAAAACC
1 GG-T-CAAACC
*
127283 GGTTAAACC
1 GGTCAAACC
127292 GGT
1 GGT
127295 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:127253 original size:29 final size:31
Alignment explanation
Indices: 127221--127295 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
127211 ACCGATTCAG
127221 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
127250 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
127280 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
127296 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:127273 original size:19 final size:19
Alignment explanation
Indices: 127196--127294 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
127186 GGTCGGGTCG
127196 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
127214 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
127233 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
127253 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
127272 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
127292 GGT
1 GGT
127295 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:130197 original size:14 final size:14
Alignment explanation
Indices: 130146--130237 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
130136 TATTTTTCCT
* *
130146 TTTAGGA-TTATGG
1 TTTAGGATTTAAGA
*
130159 TTTAGGGTTTAAGA
1 TTTAGGATTTAAGA
* * *
130173 TTTAAGTTTTAATA
1 TTTAGGATTTAAGA
130187 TTTAGGATTTAA-A
1 TTTAGGATTTAAGA
* *
130200 GTTTATGATTT-GGA
1 -TTTAGGATTTAAGA
*
130214 GTTTAGGGTTTAAGA
1 -TTTAGGATTTAAGA
*
130229 TTTTGGATT
1 TTTAGGATT
130238 GGGTAAAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
13 7 0.12
14 51 0.85
15 2 0.03
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTTAGGATTTAAGA
Found at i:130210 original size:21 final size:20
Alignment explanation
Indices: 130171--130237 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
130161 TAGGGTTTAA
*
130171 GATTT-AAGTTTTAATATTTAG
1 GATTTAAAG-TTTAAGATTT-G
*
130192 GATTTAAAGTTTATGATTTG
1 GATTTAAAGTTTAAGATTTG
**
130212 GAGTTTAGGGTTTAAGATTTTG
1 GA-TTTAAAGTTTAAGA-TTTG
130234 GATT
1 GATT
130238 GGGTAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.08
21 26 0.68
22 9 0.24
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
GATTTAAAGTTTAAGATTTG
Found at i:137640 original size:22 final size:22
Alignment explanation
Indices: 137605--137704 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
137595 TGACCATTAT
* * *
137605 GTCCCAAAGAACCACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
*
137627 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
137649 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
137671 GTCCCGAAGGATCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
137693 GTCTCGAAGGAC
1 GTCCCGAAGGAC
137705 TAATATACCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:138360 original size:64 final size:64
Alignment explanation
Indices: 138251--138414 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 64
138241 TCCCTTGACG
* * **
138251 GGTGCATCGATGCACTACCCATGCATCGGTGCA-TAAATCTTATTCGATGTT-TGTATTTTAAGC
1 GGTGCATCGATGCACT-CCTATGCATCGATGCACTAAATCGAATTCGATGTTATGTATTTTAA--
138314 A-
63 AT
* *
138315 GGTGCATCGATGCACTCCTTATGCATCGATGCACT-AATGGAATTCGATGTTCATTTATTTTAAA
1 GGTGCATCGATGCACTCC-TATGCATCGATGCACTAAATCGAATTCGATGTT-ATGTATTTTAAA
138379 T
64 T
*
138380 GAGTGCATCGATACACTCCATATGCATCGATGCAC
1 G-GTGCATCGATGCACTCC-TATGCATCGATGCAC
138415 CTTCAACAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.49
65 2 0.02
66 40 0.47
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACTCCTATGCATCGATGCACTAAATCGAATTCGATGTTATGTATTTTAAAT
Found at i:144030 original size:20 final size:20
Alignment explanation
Indices: 144001--144045 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
143991 TATTATTCAT
*
144001 AGTTTGGAAACTTCTGTAAG
1 AGTTTGGAAACTTCAGTAAG
*
144021 AGTTTTGAAACTTCAGTAAG
1 AGTTTGGAAACTTCAGTAAG
144041 AGTTT
1 AGTTT
144046 CAAAACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (20 bp):
AGTTTGGAAACTTCAGTAAG
Found at i:144051 original size:20 final size:20
Alignment explanation
Indices: 144008--144053 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
143998 CATAGTTTGG
* **
144008 AAACTTCTGTAAGAGTTTTG
1 AAACTTCAGTAAGAGTTTCA
144028 AAACTTCAGTAAGAGTTTCA
1 AAACTTCAGTAAGAGTTTCA
144048 AAACTT
1 AAACTT
144054 TGCACCCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
AAACTTCAGTAAGAGTTTCA
Found at i:145414 original size:19 final size:20
Alignment explanation
Indices: 145390--145438 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
145380 AATGATTTTC
* *
145390 TTTTGAAAATCAAAGTG-GA
1 TTTTGAAAAACAAAATGAGA
145409 TTTTGAAAAACAAAATGAGA
1 TTTTGAAAAACAAAATGAGA
145429 TTTTGAAAAA
1 TTTTGAAAAA
145439 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAGA
Found at i:147287 original size:20 final size:20
Alignment explanation
Indices: 147264--147302 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
147254 AATTAAATCA
147264 TGTTTAAAG-TGTTTAAAATG
1 TGTTTAAAGCT-TTTAAAATG
147284 TGTTTAAAGCTTTTAAAAT
1 TGTTTAAAGCTTTTAAAAT
147303 ATGAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTTTAAAGCTTTTAAAATG
Found at i:147443 original size:20 final size:20
Alignment explanation
Indices: 147378--147435 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
147368 CATAGTTTGG
* *
147378 AAACTTTTGTAAAAGTTTCC
1 AAACTTCTGTAAGAGTTTCC
147398 AAACTTCTGTAAGAGTTTCC
1 AAACTTCTGTAAGAGTTTCC
147418 AAACTTCTGTAAGAGTTT
1 AAACTTCTGTAAGAGTTT
147436 TGAAACTTTG
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:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
AAACTTCTGTAAGAGTTTCC
Found at i:147595 original size:20 final size:20
Alignment explanation
Indices: 147552--147599 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
147542 AGTGTGTTTA
147552 AAAGTTTC-GATACTTTCAC
1 AAAGTTTCAGATACTTTCAC
*
147571 AAAGTTTCAGA-ACTTTCTCC
1 AAAGTTTCAGATACTTTC-AC
147591 AAAGTTTCA
1 AAAGTTTCA
147600 AAATTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (20 bp):
AAAGTTTCAGATACTTTCAC
Found at i:147798 original size:20 final size:20
Alignment explanation
Indices: 147755--147798 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
147745 AACCACTATG
* **
147755 TCCCGAAGGACCACAGTTTG
1 TCCCGAAGGACCACAGATAA
*
147775 TCCCGAAGGACCACTGATAA
1 TCCCGAAGGACCACAGATAA
147795 TCCC
1 TCCC
147799 TCGACTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.18
Consensus pattern (20 bp):
TCCCGAAGGACCACAGATAA
Found at i:151217 original size:3 final size:3
Alignment explanation
Indices: 151209--151267 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
151199 TGTTCTCACC
151209 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
151257 ATT ATT ATT AT
1 ATT ATT ATT AT
151268 GGACAAATTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:157432 original size:11 final size:11
Alignment explanation
Indices: 157416--157461 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
157406 ATCGATTCCC
157416 CTGCTACAGTA
1 CTGCTACAGTA
157427 CTGCTACAGTA
1 CTGCTACAGTA
* *
157438 CTGTTACAGTT
1 CTGCTACAGTA
*
157449 CTACTACAGTA
1 CTGCTACAGTA
157460 CT
1 CT
157462 TCCGTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:158009 original size:21 final size:21
Alignment explanation
Indices: 157960--158023 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
157950 CATATGAAAT
*
157960 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
157981 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
158003 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
158024 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:164283 original size:22 final size:22
Alignment explanation
Indices: 164258--164303 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
164248 GTTTACAAAT
*
164258 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
164280 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
164302 AG
1 AG
164304 TACTGCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:164843 original size:22 final size:21
Alignment explanation
Indices: 164807--164880 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
164797 CACTTAGTGG
164807 CATATGAAATTTGTCCCGAAGGA
1 CATATG-AA-TTGTCCCGAAGGA
*
164830 CATGTGAATATGTCCCGAAGGA
1 CATATGAAT-TGTCCCGAAGGA
* *
164852 CCTATGAGTTGTCCCGAAGGA
1 CATATGAATTGTCCCGAAGGA
*
164873 CCTATGAA
1 CATATGAA
164881 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
21 20 0.44
22 20 0.44
23 5 0.11
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
CATATGAATTGTCCCGAAGGA
Found at i:164866 original size:21 final size:21
Alignment explanation
Indices: 164817--164880 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
164807 CATATGAAAT
* *
164817 TTGTCCCGAAGGACATGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
164838 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
164860 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
164881 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:167471 original size:6 final size:6
Alignment explanation
Indices: 167460--167494 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
167450 TTTATTTGCG
167460 AAAATT AAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAA
167495 ATTCAGTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:169128 original size:32 final size:32
Alignment explanation
Indices: 169074--169241 Score: 225
Period size: 32 Copynumber: 5.3 Consensus size: 32
169064 AGTCGATGGT
* *
169074 TTACCTATGTTCTAT-GGAACATATGGACAGAA
1 TTACCTATG-TCTTTCGGGACATATGGACAGAA
* *
169106 TTACTTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* * * *
169138 TTATCTATGTCTTTCGGGATATATGGGCAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
169170 TTACCTATGTCTTTCGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
169202 TTACCTATGTTTTTCGGGACATATGGACAG--
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
169232 TTACCTATGT
1 TTACCTATGT
169242 TCTTAAGAAC
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.08
31 4 0.03
32 108 0.89
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:169941 original size:12 final size:12
Alignment explanation
Indices: 169921--169967 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
169911 ACTGTAGTAG
169921 GGTACTGTTCAC
1 GGTACTGTTCAC
*
169933 GGTATTGTTCAC
1 GGTACTGTTCAC
* * *
169945 GATATTGTTCAT
1 GGTACTGTTCAC
169957 GGTACTGTTCA
1 GGTACTGTTCA
169968 GACCGTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (12 bp):
GGTACTGTTCAC
Found at i:170267 original size:16 final size:16
Alignment explanation
Indices: 170246--170300 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
170236 CATTTAATAA
*
170246 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
170262 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
170278 ATAAATGAACACAAAC
1 ATAAACGAACACGAAC
170294 ATAAACG
1 ATAAACG
170301 TTGGAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:171408 original size:14 final size:14
Alignment explanation
Indices: 171371--171414 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
171361 GATTGGGTTA
*
171371 AACATAAATGAATG
1 AACATAAATGAACG
171385 AACAT--A--AACG
1 AACATAAATGAACG
171395 AACATAAATGAACG
1 AACATAAATGAACG
171409 AACATA
1 AACATA
171415 GCCGAACGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 8 0.32
12 2 0.08
14 15 0.60
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:174636 original size:32 final size:32
Alignment explanation
Indices: 174580--174796 Score: 248
Period size: 32 Copynumber: 6.8 Consensus size: 32
174570 AGTCAAGGGT
* *
174580 TTACCTATGT-TCTACGGAACATATGGACAGAA
1 TTACCTATGTCT-TTCGGGACATATGGACAGAA
* * *
174612 TTACCTATATCTTTCGGGATATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
174644 TTACCTATGT-TCTAC-GGAGCATATGGACAGAA
1 TTACCTATGTCT-TTCGGGA-CATATGGACAGAA
* * *
174676 TTACCTATGTCTTTCGGGATATATAGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
174708 TTACCTATGTCTTTCGGGACATATGGACAGAG
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
174740 TTACCTATGTCTTTCGGGACATATGGAC--AA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
174770 TTACCTATGT-TCTTAGGAACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
174797 TAGGTCCTTC
Statistics
Matches: 159, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
29 1 0.01
30 24 0.15
31 4 0.03
32 125 0.79
33 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:174659 original size:64 final size:65
Alignment explanation
Indices: 174580--174796 Score: 329
Period size: 64 Copynumber: 3.4 Consensus size: 65
174570 AGTCAAGGGT
*
174580 TTACCTATGTTC-TACGGAACATATGGACAGAATTACCTATATCTTTCGGGATATATGGACAGTA
1 TTACCTATGTTCTTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGATATATGGACAGTA
* *
174644 TTACCTATGTTC-TACGGAGCATATGGACAGAATTACCTATGTCTTTCGGGATATATAGACAGTA
1 TTACCTATGTTCTTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGATATATGGACAGTA
* * * *
174708 TTACCTATG-TCTTTCGGGACATATGGACAGAGTTACCTATGTCTTTCGGGACATATGGACA--A
1 TTACCTATGTTCTTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGATATATGGACAGTA
174770 TTACCTATGTTCTTA-GGAACATATGGA
1 TTACCTATGTTCTTACGGAACATATGGA
174797 TAGGTCCTTC
Statistics
Matches: 140, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
62 21 0.15
63 6 0.04
64 113 0.81
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (65 bp):
TTACCTATGTTCTTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGATATATGGACAGTA
Found at i:175517 original size:22 final size:22
Alignment explanation
Indices: 175492--175533 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
175482 TTGTAGCAGG
175492 TTACTGTTCACGGTACTGTTTA
1 TTACTGTTCACGGTACTGTTTA
*
175514 TTACTGTTCATGGTACTGTT
1 TTACTGTTCACGGTACTGTT
175534 CATACCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (22 bp):
TTACTGTTCACGGTACTGTTTA
Found at i:175536 original size:12 final size:12
Alignment explanation
Indices: 175493--175536 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
175483 TGTAGCAGGT
*
175493 TACTGTTCACGG
1 TACTGTTCATGG
*
175505 TACTGTTTAT--
1 TACTGTTCATGG
175515 TACTGTTCATGG
1 TACTGTTCATGG
175527 TACTGTTCAT
1 TACTGTTCAT
175537 ACCGTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (12 bp):
TACTGTTCATGG
Found at i:177817 original size:47 final size:47
Alignment explanation
Indices: 177729--177827 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
177719 CTGGAGTCCG
* * * *
177729 AATTTCTTTATACTAGTTGTTTATTTTACTGAATGTACCCACCCTGT
1 AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGACCCACCCTGA
*
177776 AATTTCTTTATACTAGTTGTTCACTTTACTGAA-GGAGCCCACTCTGA
1 AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGA-CCCACCCTGA
177823 AATTT
1 AATTT
177828 TATTTATGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 2 0.04
47 44 0.96
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (47 bp):
AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGACCCACCCTGA
Found at i:183146 original size:12 final size:12
Alignment explanation
Indices: 183129--183160 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
183119 TGGTGATTTT
183129 GAAGAAGAGGAA
1 GAAGAAGAGGAA
183141 GAAGAAGAGGAA
1 GAAGAAGAGGAA
183153 GAAGAAGA
1 GAAGAAGA
183161 CGATGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
GAAGAAGAGGAA
Found at i:183177 original size:12 final size:12
Alignment explanation
Indices: 183162--183192 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
183152 AGAAGAAGAC
183162 GATGATGATGCA
1 GATGATGATGCA
183174 GATGATGATGCA
1 GATGATGATGCA
183186 GATGATG
1 GATGATG
183193 GATCTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (12 bp):
GATGATGATGCA
Found at i:185439 original size:69 final size:70
Alignment explanation
Indices: 185306--185446 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 70
185296 TTGGTATAAC
*
185306 TAAGAGTAATCAACATGGGATCTTTTCTCTCTCAAAAATTTATTGCTGAAACATAACACGTATCT
1 TAAGAGTAATCAACATGGGATCTTTTCTCTCT-AAAAATTTATTGCAGAAACATAACACGTATCT
185371 GTAGCA
65 GTAGCA
* * *
185377 TAAGAGTAATCGACATGGGATCTTTTCTCTCT-AAAATTTATTGCAGAAGCATAACATGTATCTG
1 TAAGAGTAATCAACATGGGATCTTTTCTCTCTAAAAATTTATTGCAGAAACATAACACGTATCTG
185441 TAGCA
66 TAGCA
185446 T
1 T
185447 CTGTTAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
69 35 0.53
71 31 0.47
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (70 bp):
TAAGAGTAATCAACATGGGATCTTTTCTCTCTAAAAATTTATTGCAGAAACATAACACGTATCTG
TAGCA
Found at i:196040 original size:2 final size:2
Alignment explanation
Indices: 196033--196062 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
196023 TTTTGTAAGA
196033 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
196063 GAAAAACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199235 original size:31 final size:31
Alignment explanation
Indices: 199200--199260 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
199190 TCATGCTCAT
* *
199200 TAAAAATTTTTATTGCTCAACTCGTGCTCGC
1 TAAAAAATCTTATTGCTCAACTCGTGCTCGC
* **
199231 TAAAAAATCTTGTTGCTTGACTCGTGCTCG
1 TAAAAAATCTTATTGCTCAACTCGTGCTCG
199261 TTGCTCGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (31 bp):
TAAAAAATCTTATTGCTCAACTCGTGCTCGC
Found at i:211419 original size:14 final size:15
Alignment explanation
Indices: 211391--211423 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
211381 ACACGTTCTC
*
211391 TTTTTATTTTATATT
1 TTTTTATCTTATATT
211406 TTTTTATCTT-TATT
1 TTTTTATCTTATATT
211420 TTTT
1 TTTT
211424 CGATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATCTTATATT
Found at i:211841 original size:17 final size:18
Alignment explanation
Indices: 211819--211852 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
211809 TCTTTAAGGT
211819 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
211836 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
211853 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:211863 original size:33 final size:32
Alignment explanation
Indices: 211820--211895 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 32
211810 CTTTAAGGTA
* *
211820 TATTTTATTATATTTAATATTTTGTTAGT-ATTT
1 TATTTAATTATATTTAAT-TTTT-TTAATAATTT
211853 TATTTAA-T-TATTTAATTTTTTTAATAATTT
1 TATTTAATTATATTTAATTTTTTTAATAATTT
211883 T-TTTAATTA-ATTT
1 TATTTAATTATATTT
211896 TTTACAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 9 0.24
30 14 0.37
31 8 0.21
32 1 0.03
33 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (32 bp):
TATTTAATTATATTTAATTTTTTTAATAATTT
Found at i:211877 original size:17 final size:18
Alignment explanation
Indices: 211849--211882 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
211839 TTTTGTTAGT
*
211849 ATTTTATTTAATTATTTA
1 ATTTTATTTAATAATTTA
211867 ATTTT-TTTAATAATTT
1 ATTTTATTTAATAATTT
211883 TTTTAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTATTTAATAATTTA
Found at i:211887 original size:29 final size:31
Alignment explanation
Indices: 211819--211891 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
211809 TCTTTAAGGT
211819 ATATTTTA-TT-A-TATTTAATATTTTGTTA
1 ATATTTTATTTAATTATTTAATATTTTGTTA
*
211847 GTATTTTATTTAATTATTTAAT-TTTT-TTA
1 ATATTTTATTTAATTATTTAATATTTTGTTA
211876 ATAATTTT-TTTAATTA
1 AT-ATTTTATTTAATTA
211892 ATTTTTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 7 0.18
29 14 0.36
30 10 0.26
31 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (31 bp):
ATATTTTATTTAATTATTTAATATTTTGTTA
Found at i:211899 original size:12 final size:13
Alignment explanation
Indices: 211864--211898 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
211854 ATTTAATTAT
211864 TTAATTTTTTTAA
1 TTAATTTTTTTAA
211877 -TAATTTTTTTAA
1 TTAATTTTTTTAA
211889 TTAATTTTTT
1 TTAATTTTTT
211899 ACAGTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTAATTTTTTTAA
Found at i:214261 original size:24 final size:24
Alignment explanation
Indices: 214227--214328 Score: 177
Period size: 24 Copynumber: 4.2 Consensus size: 24
214217 CCTTACAACG
*
214227 AAAGATCGAACAAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
*
214251 AAAGATTGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
214275 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
*
214299 AAAGATCGAACGAACTTCTGTATC
1 AAAGATCGAACGAACTTCTGAATC
214323 AAAGAT
1 AAAGAT
214329 AAGAGGATTG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (24 bp):
AAAGATCGAACGAACTTCTGAATC
Found at i:218033 original size:15 final size:16
Alignment explanation
Indices: 218011--218057 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
218001 AGGATAAATA
218011 TATATTTTGTAAAAAG
1 TATATTTTGTAAAAAG
*
218027 TAT-TTTTTTCAAAAA-
1 TATATTTTGT-AAAAAG
218042 TATATTTTGTAAAAAG
1 TATATTTTGTAAAAAG
218058 AGTCTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (16 bp):
TATATTTTGTAAAAAG
Found at i:218049 original size:16 final size:15
Alignment explanation
Indices: 218005--218056 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
217995 ATCGTTAGGA
*
218005 TAAATATATATTTTG
1 TAAAAATATATTTTG
*
218020 TAAAAAGTAT-TTTTT
1 TAAAAA-TATATTTTG
218035 TCAAAAATATATTTTG
1 T-AAAAATATATTTTG
218051 TAAAAA
1 TAAAAA
218057 GAGTCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.58
16 13 0.42
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (15 bp):
TAAAAATATATTTTG
Found at i:219252 original size:20 final size:20
Alignment explanation
Indices: 219205--219254 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
219195 AAAGATTTTA
* *
219205 TTCTTCATTCATTCTTCATCT
1 TTCTTCATT-TTTCTTCATCC
*
219226 TTC-TCATTTTTCTTCTTCC
1 TTCTTCATTTTTCTTCATCC
219245 TTCTTCATTT
1 TTCTTCATTT
219255 CTCAAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 11 0.44
20 11 0.44
21 3 0.12
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTCATTTTTCTTCATCC
Found at i:221353 original size:30 final size:30
Alignment explanation
Indices: 221314--221399 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 30
221304 AGTCAATATT
*
221314 GTATATAGATAATTCAAAGCAGTCAAAGTC
1 GTATTTAGATAATTCAAAGCAGTCAAAGTC
* * *
221344 GTATTTAGATAATATC-GAGTTGAGTCAAAGTT
1 GTATTTAGATAAT-TCAAAG--CAGTCAAAGTC
* *
221376 GCATTTAGATAATGCAAAGCAGTC
1 GTATTTAGATAATTCAAAGCAGTC
221400 GCAATTAGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
30 18 0.41
31 3 0.07
32 23 0.52
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (30 bp):
GTATTTAGATAATTCAAAGCAGTCAAAGTC
Found at i:231527 original size:45 final size:45
Alignment explanation
Indices: 231412--231652 Score: 340
Period size: 45 Copynumber: 5.3 Consensus size: 45
231402 GCTTATAATG
* * * *
231412 CACCATTATGCATTTTCATTTATGGAAAT-CATTCATGTCTTTTTATA
1 CACCATTATACA-TTTCATTTAT-GACATCCTTTCATG-CCTTTTATA
* * * *
231459 TACTATTATACATTTCATTTATGACATCCTTTCATGCATTTTTTA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
231504 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
*
231549 CACCATTATACATTTCATTTATGATATCCTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
* **
231594 CACCATTATACATTTCATTTATGGCATTTTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
231639 CACCATTATACATT
1 CACCATTATACATT
231653 GTTATACATC
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 151 0.85
46 17 0.10
47 9 0.05
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (45 bp):
CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
Found at i:231592 original size:22 final size:22
Alignment explanation
Indices: 231476--231592 Score: 71
Period size: 22 Copynumber: 5.2 Consensus size: 22
231466 ATACATTTCA
*
231476 TTTATGACATCCTTTCATGCAT
1 TTTATGACATCCTTTCATGCCT
* ** *
231498 TTT-TTACA-CCATTATACATTTCA
1 TTTATGACATCC-TT-T-CATGCCT
231521 TTTATGACATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGCCT
** *
231543 TTTAT-ACA-CCATTATACATTTCA
1 TTTATGACATCC-TT-T-CATGCCT
*
231566 TTTATGATATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGCCT
231588 TTTAT
1 TTTAT
231593 ACACCATTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
20 4 0.06
21 11 0.16
22 23 0.33
23 17 0.25
24 10 0.14
25 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTATGACATCCTTTCATGCCT
Found at i:231782 original size:68 final size:68
Alignment explanation
Indices: 231673--232285 Score: 852
Period size: 68 Copynumber: 9.0 Consensus size: 68
231663 TAGTCTTTTA
* * * * * * * *
231673 CTCAAAGGTATTTAACCTTTCATCTAACTGACATGATTGACACCTTTCTGTCCAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
*
231738 AGC
66 GGC
* * *
231741 CTCAAAGGCACTTAGTCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATTCAGAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
*
231806 GGT
66 GGC
* * * *
231809 CTCAAAGACATTTAGCCTTTCATTTAACTGGCATAATTGACACATTTCTTTC-AATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
231873 GGC
66 GGC
* * * *
231876 CTCAAAGGTACTTAGCCTTTCATCGAACTGGCATAATTGACATATTTATGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
*
231941 TGC
66 GGC
* *
231944 CTCAAAGGCACTTAGTCTTTCATCTAACTGGCATAATTGACACATATCTGTCAAAT-CTACAGTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC-ACAGTT
232008 AGGC
65 AGGC
* * *
232012 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTTACACCTATCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
232077 GGC
66 GGC
* * * *
232080 CTCAAAGACACTTAGCATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGTACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
232145 GGC
66 GGC
* * * * * * *
232148 CTCAAAGGAACTTAACTTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATACACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
232213 GGC
66 GGC
*
232216 CTCAAAGGCACTTAGCCTTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
232281 GGC
66 GGC
232284 CT
1 CT
232286 TTAATATTTT
Statistics
Matches: 479, Mismatches: 63, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
67 57 0.12
68 421 0.88
69 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
GGC
Found at i:232854 original size:58 final size:58
Alignment explanation
Indices: 232767--232933 Score: 223
Period size: 58 Copynumber: 2.9 Consensus size: 58
232757 ACTAACATTT
* * * *
232767 CCCAA-ATGAAAATTCATACATTTATTATGAATCTCTTAACGA-TTTGCACAC-ACAGTG
1 CCCAATATGGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTGCACACGA-AGTG
* *
232824 CCCAATATGGAAATTTATACACTTAGTATGAATTTCTCAACATTTTGCACACGAAGTG
1 CCCAATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTG
* *
232882 CCCAATACGGAAATTCATACACTTAGTATGAATTTTTTAACATTTTGCACAC
1 CCCAATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACAC
232934 TTAGTGTCAT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
57 6 0.06
58 90 0.93
59 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (58 bp):
CCCAATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTG
Found at i:237581 original size:17 final size:18
Alignment explanation
Indices: 237551--237588 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
237541 AATTTTAATT
237551 AAATTAAAAATATTA-AA
1 AAATTAAAAATATTATAA
* *
237568 AAATTTAAATTATTATAA
1 AAATTAAAAATATTATAA
237586 AAA
1 AAA
237589 ATAATAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAAAATATTATAA
Found at i:240785 original size:15 final size:15
Alignment explanation
Indices: 240765--240801 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
240755 TGAGACATTA
*
240765 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
240780 CCCGCCCCACATTCG
1 CCCGCCCCACATCCG
240795 CCCGCCC
1 CCCGCCC
240802 AGCTAAATAT
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:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:241764 original size:32 final size:32
Alignment explanation
Indices: 241728--241793 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
241718 TTGATCGAAT
* *
241728 TTCAATAG-CTAAATTAATTTTTTTTTAGAAAA
1 TTCAA-AGACTAAATTAATTTTTTTTGAAAAAA
* *
241760 TTCAAAGACTAAGTTACTTTTTTTTGAAAAAA
1 TTCAAAGACTAAATTAATTTTTTTTGAAAAAA
241792 TT
1 TT
241794 AATTTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (32 bp):
TTCAAAGACTAAATTAATTTTTTTTGAAAAAA
Found at i:241861 original size:20 final size:20
Alignment explanation
Indices: 241819--241872 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
241809 TTGTGAATTT
* **
241819 AAAAATATTCAAAAATTTTA
1 AAAAATATACAAAAATTAAA
*
241839 AAAAATATACAAATATTAAA
1 AAAAATATACAAAAATTAAA
*
241859 AAAAAAATA-AAAAA
1 AAAAATATACAAAAA
241873 AAATTACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATACAAAAATTAAA
Found at i:241948 original size:24 final size:23
Alignment explanation
Indices: 241909--241977 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 23
241899 CTAAAACACC
241909 ATTA-AAAATGAA-AAATGTTTAAA
1 ATTATAAAAT-AATAAAT-TTTAAA
241932 ATTATAAAATAATAAATTATT--A
1 ATTATAAAATAATAAATT-TTAAA
*
241954 ATTATTAAA-AATAAATATTTAAA
1 ATTATAAAATAATAAAT-TTTAAA
241977 A
1 A
241978 AAATGCTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
21 9 0.23
22 10 0.26
23 9 0.23
24 11 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
ATTATAAAATAATAAATTTTAAA
Found at i:243538 original size:18 final size:18
Alignment explanation
Indices: 243515--243567 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
243505 ACTGAATATT
243515 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
243533 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
243551 TCTCCCGAAGAACCACT
1 TGTCCCGAAGGACCACT
243568 GATAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.36, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:245153 original size:24 final size:22
Alignment explanation
Indices: 245103--245158 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 22
245093 AATAAAGGTA
245103 TGCATCGATGCATTCTACAGTG
1 TGCATCGATGCATTCTACAGTG
245125 T--ATCGATGCATTCCTTA-ACGTG
1 TGCATCGATGCATT-C-TACA-GTG
245147 TGCATCGATGCA
1 TGCATCGATGCA
245159 CTACCTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 7 0.24
24 9 0.31
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (22 bp):
TGCATCGATGCATTCTACAGTG
Found at i:246718 original size:2 final size:2
Alignment explanation
Indices: 246711--246740 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
246701 TTTGAGAATC
246711 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
246741 ATTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251411 original size:55 final size:55
Alignment explanation
Indices: 251323--251981 Score: 716
Period size: 55 Copynumber: 12.1 Consensus size: 55
251313 ATTTCGAATG
* *
251323 ACGGGTCTGCTC-CATATTCCTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAA
1 ACGGGTCTGCTCTC-TATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * * * * * * *
251378 ATGTGTCTGTTCCCTATTCGTTCAGGGAGTATA-AGACTCGAATAATCTTTAGCAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * * * *
251433 ACGGGTCCGCTCCCTATTCTTTCA-AGGAGTATA-AGACTCGGACATTCTTCAGCAA
1 ACGGGTCTGCTCTCTATTCCTTCAGA-GAGTATAGA-ACTCGAACAATCTTCAACAA
* * * *
251488 ATGAGT-TCGCTCTCTATTTCTTCAGAGAGTATAGAACTTGAACAATCTTCAACAA
1 ACGGGTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * *
251543 ACGAGT-TCGCTCTCTATTTCTTCAGAGAGTATAGAACTTGAACAATCTTTAACAA
1 ACGGGTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* *
251598 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * *
251653 ACGTGTCTACTCCCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* *
251708 ATGGGT-TCGCTCTCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCATA-AA
1 ACGGGTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAA
* * * * *
251763 ATGGGTCCGCTCTCTATTTCTTCAGAGAGTACAAAACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* *
251818 ACGGGTCCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
*
251873 ACGGGT-TCACTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
** * * *
251928 ACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAA
1 ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
251979 ACG
1 ACG
251982 AGTTTGCTTC
Statistics
Matches: 528, Mismatches: 64, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
51 15 0.03
54 2 0.00
55 507 0.96
56 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
ACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:253345 original size:21 final size:20
Alignment explanation
Indices: 253321--253480 Score: 112
Period size: 22 Copynumber: 7.4 Consensus size: 20
253311 TGAACCCTCA
253321 TTTTATTTCTTTTTCTTTTTC
1 TTTT-TTTCTTTTTCTTTTTC
253342 TTTTTTTCTTCTTTCTTCTTTC
1 TTTTTTTCTT-TTTCTT-TTTC
253364 TTCTTTCTTCTTTCTTCTTTTT-
1 TT-TTT-TTCTTT-TTCTTTTTC
*
253386 TCATTTTTCATTTTTCATTTTTC
1 T-TTTTTTC-TTTTTC-TTTTTC
* *
253409 ATTTTTTT-TTATT-TTCTTC
1 -TTTTTTTCTTTTTCTTTTTC
253428 ATTTTTTTCTTTCTTCTTTTCTC
1 -TTTTTTTCTTT-TTCTTTT-TC
*
253451 TCTTTTTT-TTTCTTATTTTCTC
1 T-TTTTTTCTTT-TTCTTTT-TC
253473 TTTTTTTC
1 TTTTTTTC
253481 ATTATTTTTC
Statistics
Matches: 116, Mismatches: 7, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
19 13 0.11
20 8 0.07
21 28 0.24
22 36 0.31
23 20 0.17
24 11 0.09
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTCTTTTTCTTTTTC
Found at i:253346 original size:7 final size:7
Alignment explanation
Indices: 253326--253499 Score: 90
Period size: 7 Copynumber: 23.9 Consensus size: 7
253316 CCTCATTTTA
253326 TTTC-TT
1 TTTCTTT
253332 TTTC-TT
1 TTTCTTT
253338 TTTCTTTT
1 TTTC-TTT
253346 TTTCTTCTT
1 TTTC-T-TT
253355 TCTTCTTT
1 T-TTCTTT
*
253363 CTTCTTT
1 TTTCTTT
*
253370 CTTCTTT
1 TTTCTTT
*
253377 CTTCTTT
1 TTTCTTT
*
253384 TTTCATT
1 TTTCTTT
*
253391 TTTCATT
1 TTTCTTT
*
253398 TTTCATT
1 TTTCTTT
253405 TTTCATTT
1 TTTC-TTT
*
253413 TTTTTTAT
1 TTTCTT-T
253421 TTTCTTCAT
1 TTTCTT--T
253430 TTT-TTT
1 TTTCTTT
253436 CTTTCTTCT
1 -TTTCTT-T
*
253445 TTTCTCTC
1 TTTCT-TT
253453 TTT-TTT
1 TTTCTTT
253459 TTTCTTAT
1 TTTCTT-T
253467 TTTCTCTT
1 TTTCT-TT
*
253475 TTT-TTC
1 TTTCTTT
* *
253481 ATT-ATT
1 TTTCTTT
253487 TTTCTTT
1 TTTCTTT
253494 TTTCTT
1 TTTCTT
253500 CAAGCGAAAT
Statistics
Matches: 139, Mismatches: 14, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
6 21 0.15
7 60 0.43
8 43 0.31
9 12 0.09
10 3 0.02
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCTTT
Found at i:253485 original size:19 final size:17
Alignment explanation
Indices: 253336--253496 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 17
253326 TTTCTTTTTC
*
253336 TTTTTCTTTTTTTCTTC
1 TTTTTCTTTTTTTCTTA
*
253353 TTTCTTCTTTCTTCTTTCTTC
1 TTT-TTC-TT-TT-TTTCTTA
253374 TTTCTTC-TTTTTTC--A
1 TTT-TTCTTTTTTTCTTA
*
253389 TTTTTCATTTTTCATTTTTCA
1 TTTTTC-TTTTT--TTCTT-A
*
253410 TTTTTTTTTATTTTCTTCA
1 TTTTTCTTT-TTTTCTT-A
253429 TTTTT-TTCTTTCTTCTT-
1 TTTTTCTT-TTT-TTCTTA
*
253446 TTCTCTCTTTTTTTTTCTTA
1 TT-T-T-TCTTTTTTTCTTA
253466 TTTTCTCTTTTTTTCATTA
1 TTTT-TCTTTTTTTC-TTA
253485 TTTTTCTTTTTT
1 TTTTTCTTTTTT
253497 CTTCAAGCGA
Statistics
Matches: 119, Mismatches: 5, Indels: 39
0.73 0.03 0.24
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 4 0.03
17 9 0.08
18 31 0.26
19 34 0.29
20 11 0.09
21 24 0.20
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTTTTTCTTA
Found at i:253489 original size:20 final size:18
Alignment explanation
Indices: 253454--253501 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
253444 TTTTCTCTCT
253454 TTTTTTTTC-TTATTTTC
1 TTTTTTTTCATTATTTTC
253471 TCTTTTTTTCATTATTTTTC
1 T-TTTTTTTCATTA-TTTTC
253491 TTTTTTCTTCA
1 TTTTTT-TTCA
253502 AGCGAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 8 0.30
20 10 0.37
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCATTATTTTC
Found at i:256996 original size:8 final size:8
Alignment explanation
Indices: 256983--257010 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
256973 AAGAGAAGAT
256983 ATATATAC
1 ATATATAC
256991 ATATATAC
1 ATATATAC
256999 ATATATAC
1 ATATATAC
257007 ATAT
1 ATAT
257011 GGGAGGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:257062 original size:8 final size:8
Alignment explanation
Indices: 257051--257075 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
257041 AAATAAATAA
257051 ATATATAC
1 ATATATAC
257059 ATATATAC
1 ATATATAC
257067 ATATATAC
1 ATATATAC
257075 A
1 A
257076 ACAAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:263177 original size:46 final size:46
Alignment explanation
Indices: 263074--263211 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
263064 CCATGCTTTG
*
263074 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
263121 TTATTC-AAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
*
263166 TTATTCAAAAAAATAAACCTAACTGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
263212 ATTTATTTGA
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
45 35 0.40
46 47 0.53
47 6 0.07
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (46 bp):
TTATTCAAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
Found at i:263786 original size:11 final size:11
Alignment explanation
Indices: 263758--263799 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
263748 AATTAAATTA
263758 AAAAATCAAAAT
1 AAAAA-CAAAAT
263770 --AAACAAAAT
1 AAAAACAAAAT
*
263779 ACAAACAAAAT
1 AAAAACAAAAT
263790 AAAAACAAAA
1 AAAAACAAAA
263800 CTTATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.22
10 3 0.11
11 18 0.67
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAACAAAAT
Found at i:268007 original size:29 final size:29
Alignment explanation
Indices: 267965--268023 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
267955 ATTTTCACCT
267965 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
267994 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
268023 A
1 A
268024 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:272686 original size:29 final size:29
Alignment explanation
Indices: 272644--272702 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
272634 ATTTTCACCT
272644 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
272673 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
272702 A
1 A
272703 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:276165 original size:22 final size:23
Alignment explanation
Indices: 276115--276170 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
276105 TTATTTTTAT
* *
276115 TTTAAATTATTATTATTATTATTA
1 TTTACATT-TTATTATTATAATTA
276139 TTTAC-TTTTATTATTACTAATTA
1 TTTACATTTTATTATTA-TAATTA
276162 -TTACATTTT
1 TTTACATTTT
276171 GTAGGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 13 0.46
23 11 0.39
24 4 0.14
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTACATTTTATTATTATAATTA
Found at i:285439 original size:17 final size:17
Alignment explanation
Indices: 285417--285456 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
285407 TATTAAAAAA
285417 TTTGGTAACCGGTAAAC
1 TTTGGTAACCGGTAAAC
* *
285434 TTTGGTTATCGGTAAAC
1 TTTGGTAACCGGTAAAC
285451 TTTGGT
1 TTTGGT
285457 TATCGGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (17 bp):
TTTGGTAACCGGTAAAC
Found at i:285457 original size:17 final size:17
Alignment explanation
Indices: 285426--285465 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
285416 ATTTGGTAAC
285426 CGGTAAACTTTGGTTAT
1 CGGTAAACTTTGGTTAT
285443 CGGTAAACTTTGGTTAT
1 CGGTAAACTTTGGTTAT
285460 CGGTAA
1 CGGTAA
285466 GTATCTATCC
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:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (17 bp):
CGGTAAACTTTGGTTAT
Found at i:285989 original size:230 final size:227
Alignment explanation
Indices: 285582--286031 Score: 783
Period size: 230 Copynumber: 2.0 Consensus size: 227
285572 GTAAATTATC
* * *
285582 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* **
285647 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTGAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
285712 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
285777 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
285811 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
285876 TTAATATTGTTAAATTGAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTGAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
285941 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
286006 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
286032 GCAGTTATAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 66 0.31
230 140 0.67
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTGAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:286120 original size:20 final size:20
Alignment explanation
Indices: 286097--286142 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
286087 CGATATACCA
*
286097 GGTAAAAATATGATAAAACC
1 GGTAAAAAAATGATAAAACC
286117 GGTAAAAAAATGATAAAACC
1 GGTAAAAAAATGATAAAACC
286137 GGTAAA
1 GGTAAA
286143 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAAAATGATAAAACC
Found at i:286287 original size:20 final size:19
Alignment explanation
Indices: 286264--286310 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
286254 CGATATAACA
286264 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
286284 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
286304 GGTAAAA
1 GGTAAAA
286311 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:286312 original size:17 final size:19
Alignment explanation
Indices: 286273--286315 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
286263 AGGTAAAAAT
286273 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
286293 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
286310 ATGATA
1 ATGATA
286316 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:288587 original size:21 final size:21
Alignment explanation
Indices: 288540--288604 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
288530 AAGACAATCA
* *
288540 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
288562 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
288582 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
288603 AG
1 AG
288605 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:288680 original size:33 final size:33
Alignment explanation
Indices: 288638--288703 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
288628 AAATAGATGG
*
288638 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
288671 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
288704 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:290514 original size:19 final size:19
Alignment explanation
Indices: 290490--290538 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
290480 AATGTAGGGT
290490 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
290509 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
290528 TATTTTTGTAT
1 TAATTTTGTAT
290539 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:291356 original size:197 final size:197
Alignment explanation
Indices: 290663--291573 Score: 1754
Period size: 197 Copynumber: 4.6 Consensus size: 197
290653 GGCCAAAAGG
290663 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
290728 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGATGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCA-C
290793 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
290858 TAAT
194 TAAT
*
290862 ATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
290927 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTACACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
290992 TAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
291055 AT
196 AT
291057 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
291122 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
291187 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
291252 AT
196 AT
291254 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
291319 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
291384 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
291449 AT
196 AT
291451 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
291516 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGG
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGG
291574 ATTAGACATG
Statistics
Matches: 704, Mismatches: 6, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
195 163 0.23
196 60 0.09
197 358 0.51
198 30 0.04
199 93 0.13
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Done.