Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold213
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: 483536
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 2 of 4
Found at i:153784 original size:44 final size:44
Alignment explanation
Indices: 153721--153811 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
153711 TCGATGATAA
*
153721 TTAATGTTACTATAATAAGTAGAGTTTGTTCGTGTCTAATTTTC
1 TTAATGTTACTATAATAAGTAGAGTTTGTTCATGTCTAATTTTC
153765 TTAATGTTACTATAATAAGTAGAGTTTGTTCATGTCTAATTTTC
1 TTAATGTTACTATAATAAGTAGAGTTTGTTCATGTCTAATTTTC
153809 TTA
1 TTA
153812 GAACAGTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (44 bp):
TTAATGTTACTATAATAAGTAGAGTTTGTTCATGTCTAATTTTC
Found at i:153886 original size:20 final size:20
Alignment explanation
Indices: 153848--153886 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
153838 TATTATTTTT
*
153848 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
153868 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
153887 TTTTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:153945 original size:11 final size:11
Alignment explanation
Indices: 153925--153963 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
153915 TATATATTCG
153925 TATATTTATAT
1 TATATTTATAT
*
153936 TATCTTTATAT
1 TATATTTATAT
153947 TA-ATTTATAT
1 TATATTTATAT
153957 TATATTT
1 TATATTT
153964 TAATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:153969 original size:11 final size:11
Alignment explanation
Indices: 153929--153979 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
153919 TATTCGTATA
*
153929 TTTATATTATC
1 TTTATATTATT
*
153940 TTTATATTA-A
1 TTTATATTATT
153950 TTTATATTATAT
1 TTTATATTAT-T
153962 TTTA-ATTATT
1 TTTATATTATT
153972 TTTCATAT
1 TTT-ATAT
153980 ATCGTATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 13 0.38
11 15 0.44
12 6 0.18
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATATTATT
Found at i:154158 original size:17 final size:17
Alignment explanation
Indices: 154133--154179 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
154123 ATAAATTTTT
* *
154133 TTAAAAAATTAATTTAA
1 TTAATAAATTAATATAA
* *
154150 TTATTAAATAAATATAA
1 TTAATAAATTAATATAA
154167 TTAAT-AATTAATA
1 TTAATAAATTAATA
154180 AAAATATGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATAAATTAATATAA
Found at i:154170 original size:21 final size:21
Alignment explanation
Indices: 154133--154181 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
154123 ATAAATTTTT
*
154133 TTAAA-AAATTAATTTAATTA
1 TTAAATAAATTAATTTAATAA
154153 TTAAATAAATATAA-TTAATAA
1 TTAAATAAAT-TAATTTAATAA
154174 TT-AATAAA
1 TTAAATAAA
154182 AATATGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 11 0.42
21 12 0.46
22 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAATAAATTAATTTAATAA
Found at i:154367 original size:34 final size:34
Alignment explanation
Indices: 154306--154370 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
154296 AATTAAATTA
*
154306 ATTTTTATTAATTTCATAAAAATTTAATTTTAAT
1 ATTTTTATTAAATTCATAAAAATTTAATTTTAAT
154340 ATTTTTATTAAATT-A-AAAAATTATTAATTTT
1 ATTTTTATTAAATTCATAAAAA-T-TTAATTTT
154371 CAATTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 5 0.18
33 2 0.07
34 21 0.75
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (34 bp):
ATTTTTATTAAATTCATAAAAATTTAATTTTAAT
Found at i:154663 original size:125 final size:125
Alignment explanation
Indices: 154434--154682 Score: 363
Period size: 125 Copynumber: 2.0 Consensus size: 125
154424 AAAAAGGGAT
** * * *
154434 ATATTACTTGGAAATTAGCATTAAGTCTGACATGAATAAATGAATGAGGATTCTCTTTCAAATGA
1 ATATTACTTGGAAACAAGCATTAAGTCTGACATGAATAAATGAATGAAGAATCTCTTCCAAATGA
* * *
154499 ACAAAACATTTATTCTGCAACTTTCACCAATACTGTTTCTCTGTAATGATCCACTTAGTC
66 ACAAAACATTTATTCTACAACTTCCACCAATACTATTTCTCTGTAATGATCCACTTAGTC
** * *
154559 ATATTACTTGGAAACAAGCATTGCGTCTGACATGAATAAATGAATGAAGAATGTCTTCCATATGA
1 ATATTACTTGGAAACAAGCATTAAGTCTGACATGAATAAATGAATGAAGAATCTCTTCCAAATGA
* * *
154624 GCAAAACATTTATTCTACAACTTCCACCAATATTATTTCTCTGTAATGATTCACTTAGT
66 ACAAAACATTTATTCTACAACTTCCACCAATACTATTTCTCTGTAATGATCCACTTAGT
154683 AAAAAATTAC
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (125 bp):
ATATTACTTGGAAACAAGCATTAAGTCTGACATGAATAAATGAATGAAGAATCTCTTCCAAATGA
ACAAAACATTTATTCTACAACTTCCACCAATACTATTTCTCTGTAATGATCCACTTAGTC
Found at i:155178 original size:21 final size:20
Alignment explanation
Indices: 155144--155184 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
155134 AAATTTTATT
155144 TAAATTTAATTATAAAGTATA
1 TAAATTTAATTATAAA-TATA
155165 TAAATATTAA-TATAAATATA
1 TAAAT-TTAATTATAAATATA
155185 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATTTAATTATAAATATA
Found at i:156625 original size:12 final size:13
Alignment explanation
Indices: 156599--156624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
156589 TTTTGGAAAT
156599 ATAAATTAAAAAA
1 ATAAATTAAAAAA
156612 ATAAATTAAAAAA
1 ATAAATTAAAAAA
156625 TGCGAAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATTAAAAAA
Found at i:156766 original size:35 final size:35
Alignment explanation
Indices: 156720--156808 Score: 169
Period size: 35 Copynumber: 2.5 Consensus size: 35
156710 TGCAGCAGCG
156720 GAAACCGATGCAGCGAATGTCGATCAGGAATGTTT
1 GAAACCGATGCAGCGAATGTCGATCAGGAATGTTT
*
156755 GAAACCGATGCAGCGAACGTCGATCAGGAATGTTT
1 GAAACCGATGCAGCGAATGTCGATCAGGAATGTTT
156790 GAAACCGATGCAGCGAATG
1 GAAACCGATGCAGCGAATG
156809 CAGCAGCGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (35 bp):
GAAACCGATGCAGCGAATGTCGATCAGGAATGTTT
Found at i:158106 original size:51 final size:49
Alignment explanation
Indices: 157989--158106 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 49
157979 TAAATATTTA
*
157989 TAATAATATTTTATTTCAAATTTATTTATAAATAATATTAAAAATAATAT
1 TAAT-ATATTATATTTCAAATTTATTTATAAATAATATTAAAAATAATAT
* * *
158039 AAATAT-TTAATCTATTTCAAATTTATTTATAAATAATGTTAAAGATAATATT
1 TAATATATT-A--TATTTCAAATTTATTTATAAATAATATTAAAAATAATA-T
158091 GTAATATATTATATTT
1 -TAATATATTATATTT
158107 AAAAATAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
48 2 0.04
49 2 0.04
50 3 0.05
51 41 0.72
52 1 0.02
53 6 0.11
54 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (49 bp):
TAATATATTATATTTCAAATTTATTTATAAATAATATTAAAAATAATAT
Found at i:158183 original size:19 final size:20
Alignment explanation
Indices: 158159--158198 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
158149 AAATTTATTT
* *
158159 TAATAT-TTACATTTAAAAA
1 TAATATATTAAATATAAAAA
158178 TAATATATTAAATATAAAAA
1 TAATATATTAAATATAAAAA
158198 T
1 T
158199 GTTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATATATTAAATATAAAAA
Found at i:161013 original size:13 final size:13
Alignment explanation
Indices: 160995--161020 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160985 ATGAGGAAAC
160995 TTATTAGCATTAT
1 TTATTAGCATTAT
161008 TTATTAGCATTAT
1 TTATTAGCATTAT
161021 AGCATTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TTATTAGCATTAT
Found at i:163233 original size:32 final size:32
Alignment explanation
Indices: 163192--163296 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 32
163182 AAAAGTCAAC
*
163192 AACCCGAATCCGAAATGACTTGAACCCAAAAT
1 AACCCGAATCTGAAATGACTTGAACCCAAAAT
* ** *
163224 AACCCGAATCTAAAATGACCCGAACCCGAAAT
1 AACCCGAATCTGAAATGACTTGAACCCAAAAT
* * * *
163256 AACTCGAATTTGAAAT-AATCTGAACCTAAAAT
1 AACCCGAATCTGAAATGACT-TGAACCCAAAAT
163288 AACCCGAAT
1 AACCCGAAT
163297 AATTAACCTG
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 1 0.02
32 57 0.98
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (32 bp):
AACCCGAATCTGAAATGACTTGAACCCAAAAT
Found at i:163238 original size:16 final size:16
Alignment explanation
Indices: 163219--163296 Score: 66
Period size: 16 Copynumber: 4.9 Consensus size: 16
163209 ACTTGAACCC
163219 AAAATAACCCGAATCT
1 AAAATAACCCGAATCT
* * *
163235 AAAATGACCCGAACCC
1 AAAATAACCCGAATCT
* * *
163251 GAAATAACTCGAATTT
1 AAAATAACCCGAATCT
* * * *
163267 GAAATAATCTGAACCT
1 AAAATAACCCGAATCT
163283 AAAATAACCCGAAT
1 AAAATAACCCGAAT
163297 AATTAACCTG
Statistics
Matches: 44, Mismatches: 18, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAATAACCCGAATCT
Found at i:163310 original size:23 final size:25
Alignment explanation
Indices: 163269--163318 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
163259 TCGAATTTGA
163269 AATAATCTGAACCTAAAATAACCCG
1 AATAATCTGAACCTAAAATAACCCG
* *
163294 AATAAT-T-AACCTGAAATGACCCG
1 AATAATCTGAACCTAAAATAACCCG
163317 AA
1 AA
163319 CTTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 1 0.04
25 6 0.26
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.20
Consensus pattern (25 bp):
AATAATCTGAACCTAAAATAACCCG
Found at i:163835 original size:33 final size:33
Alignment explanation
Indices: 163798--163864 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
163788 TTCAACGATC
163798 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
163831 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
163864 T
1 T
163865 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:163836 original size:13 final size:13
Alignment explanation
Indices: 163818--163842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163808 CATAAAATGT
163818 TGTATCGATACAA
1 TGTATCGATACAA
163831 TGTATCGATACA
1 TGTATCGATACA
163843 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:163926 original size:13 final size:13
Alignment explanation
Indices: 163908--163932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163898 ATTACTCATA
163908 TGTATCGATACAT
1 TGTATCGATACAT
163921 TGTATCGATACA
1 TGTATCGATACA
163933 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:164069 original size:52 final size:52
Alignment explanation
Indices: 163941--164061 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
163931 CACTGATCTT
*
163941 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
163993 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
164045 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
164062 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:169627 original size:19 final size:17
Alignment explanation
Indices: 169581--169626 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
169571 TCCTAAATTG
169581 ATGAGAATTTTCTATAT
1 ATGAGAATTTTCTATAT
169598 ATGAGAATTTTCTATAT
1 ATGAGAATTTTCTATAT
*
169615 ATAGAGCATTTT
1 AT-GAGAATTTT
169627 TGTGCAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (17 bp):
ATGAGAATTTTCTATAT
Found at i:170771 original size:29 final size:30
Alignment explanation
Indices: 170704--170779 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
170694 ATAGCTCTCA
*
170704 TTTGGCACAGATACTTCTAGCACATGTACC
1 TTTGGCACACATACTTCTAGCACATGTACC
170734 TTTGGCACACATACTT-TGACGCA-A-GTACC
1 TTTGGCACACATACTTCT-A-GCACATGTACC
*
170763 TTTGGCACACGTACTTC
1 TTTGGCACACATACTTC
170780 GGCATAGGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 21 0.51
30 17 0.41
31 3 0.07
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (30 bp):
TTTGGCACACATACTTCTAGCACATGTACC
Found at i:170825 original size:14 final size:14
Alignment explanation
Indices: 170806--170881 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
170796 CACAGGTATT
*
170806 TTTGACACACGTAC
1 TTTGACACAAGTAC
* *
170820 TTTGACATAAGTATT
1 TTTGACACAAGTA-C
*
170835 TTTGGCACATA-TAC
1 TTTGACACA-AGTAC
170849 TTTGACACAAGTAC
1 TTTGACACAAGTAC
* *
170863 TTTTAGCACATGTAC
1 TTTGA-CACAAGTAC
170878 TTTG
1 TTTG
170882 GCATAGGTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 1 0.02
14 26 0.54
15 20 0.42
16 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (14 bp):
TTTGACACAAGTAC
Found at i:170834 original size:29 final size:29
Alignment explanation
Indices: 170801--170886 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
170791 TTTAGCACAG
*
170801 GTATTTTTGACACACGTACTTTGACATAA
1 GTATTTTTGACACATGTACTTTGACATAA
* * *
170830 GTATTTTTGGCACATATACTTTGACACAA
1 GTATTTTTGACACATGTACTTTGACATAA
* *
170859 GTACTTTT-AGCACATGTACTTTGGCATA
1 GTATTTTTGA-CACATGTACTTTGACATA
170887 GGTACCTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (29 bp):
GTATTTTTGACACATGTACTTTGACATAA
Found at i:173149 original size:36 final size:37
Alignment explanation
Indices: 173077--173173 Score: 142
Period size: 36 Copynumber: 2.6 Consensus size: 37
173067 ATGTGAATAC
* *
173077 TATTAGTCATGCACCAAATGATGACCCCCACTCTTTT
1 TATTAATCATGTACCAAATGATGACCCCCACTCTTTT
* *
173114 TATTAATCATGTTCCAAATGATGA-CCCCATTCTTTT
1 TATTAATCATGTACCAAATGATGACCCCCACTCTTTT
*
173150 TATTAATCATGTACCCAATGATGA
1 TATTAATCATGTACCAAATGATGA
173174 TCTTACTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
36 33 0.61
37 21 0.39
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (37 bp):
TATTAATCATGTACCAAATGATGACCCCCACTCTTTT
Found at i:174406 original size:69 final size:69
Alignment explanation
Indices: 174330--174463 Score: 216
Period size: 69 Copynumber: 1.9 Consensus size: 69
174320 AGAATAAAAT
*
174330 ACTACATTAATTAAGCTTT-TATAGAAGTATAAGGATATGTTTGCCTGGACCTATGAAGAAATGC
1 ACTACATTAATTAAG-TTTATATAGAAGTAAAAGGATATGTTTGCCTGGACCTATGAAGAAATGC
174394 CTAAG
65 CTAAG
* * *
174399 ACTACATTAATTAAGTTTATATGGGAGTAAAAGGATGTGTTTGCCTGGACCTATGAAGAAATGCC
1 ACTACATTAATTAAGTTTATATAGAAGTAAAAGGATATGTTTGCCTGGACCTATGAAGAAATGCC
174464 CGGGTTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 3 0.05
69 57 0.95
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (69 bp):
ACTACATTAATTAAGTTTATATAGAAGTAAAAGGATATGTTTGCCTGGACCTATGAAGAAATGCC
TAAG
Found at i:182315 original size:14 final size:13
Alignment explanation
Indices: 182297--182321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182287 CACGACTTAA
182297 AAAAAATTTATGC
1 AAAAAATTTATGC
182310 AAAAAATTTATG
1 AAAAAATTTATG
182322 ACATTCACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAAAAATTTATGC
Found at i:185266 original size:16 final size:16
Alignment explanation
Indices: 185242--185282 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
185232 AGCAGTAGTT
* *
185242 GCTGACAACACCTGTC
1 GCTGGCAACAACTGTC
*
185258 GCTGGCAACAACTGTT
1 GCTGGCAACAACTGTC
185274 GCTGGCAAC
1 GCTGGCAAC
185283 TTTTGCTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (16 bp):
GCTGGCAACAACTGTC
Found at i:186239 original size:2 final size:2
Alignment explanation
Indices: 186232--186260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
186222 TATATTTCTT
186232 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
186261 CTAATAATTA
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:186530 original size:15 final size:15
Alignment explanation
Indices: 186490--186530 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
186480 TTCGACGCAA
*
186490 GTACCTTTGGTACAG
1 GTACCTTTGGCACAG
*
186505 GTA-CATTGGCACAG
1 GTACCTTTGGCACAG
186519 GTACCTTTGGCA
1 GTACCTTTGGCA
186531 TACATGCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (15 bp):
GTACCTTTGGCACAG
Found at i:187800 original size:13 final size:13
Alignment explanation
Indices: 187784--187809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187774 ATTTTTTTAA
187784 AATATTTATATTT
1 AATATTTATATTT
187797 AATATTTATATTT
1 AATATTTATATTT
187810 TTTTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:187805 original size:30 final size:31
Alignment explanation
Indices: 187762--187819 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
187752 TGATTTATAT
* *
187762 TATTTATTTTTTAT-TTTTTTAAAATATTTA
1 TATTTAATATTTATATTTTTTAAAATATTTA
*
187792 TATTTAATATTTATATTTTTTTAAATAT
1 TATTTAATATTTATATTTTTTAAAATAT
187820 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TATTTAATATTTATATTTTTTAAAATATTTA
Found at i:192716 original size:26 final size:26
Alignment explanation
Indices: 192664--192736 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
192654 GTTAATCTTA
* *
192664 ATAATATTAAATATAATTATATA-AAT
1 ATAATA-TAAAAATAATTAAATATAAT
192690 ATAATATAAAAATAATTAAATATAAT
1 ATAATATAAAAATAATTAAATATAAT
192716 ATAATATAAAAAT-A-TAAATAT
1 ATAATATAAAAATAATTAAATAT
192737 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.16
25 15 0.34
26 22 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATATAAAAATAATTAAATATAAT
Found at i:192767 original size:31 final size:31
Alignment explanation
Indices: 192721--192812 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 31
192711 ATAATATAAT
*
192721 ATAAAAATATAAATATTTTAAAATTTATATA
1 ATAAAAATATAAATATATTAAAATTTATATA
* * *
192752 ATAAAATTATTAATATATTAAATTTTATATAA
1 ATAAAAATATAAATATATTAAAATTTATAT-A
192784 ATATAAAATATTTTAAATATAATTAAAAT
1 ATA-AAAATA---TAAATAT-ATTAAAAT
192813 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
31 26 0.54
32 4 0.08
33 5 0.10
36 6 0.12
37 7 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
ATAAAAATATAAATATATTAAAATTTATATA
Found at i:192796 original size:20 final size:20
Alignment explanation
Indices: 192773--192814 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
192763 AATATATTAA
*
192773 ATTTTATATA-AATATAAAAT
1 ATTTTAAATATAAT-TAAAAT
192793 ATTTTAAATATAATTAAAAT
1 ATTTTAAATATAATTAAAAT
192813 AT
1 AT
192815 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAAATATAATTAAAAT
Found at i:192818 original size:16 final size:16
Alignment explanation
Indices: 192682--192818 Score: 61
Period size: 16 Copynumber: 8.2 Consensus size: 16
192672 AAATATAATT
* *
192682 ATATAAATATAATATAA
1 ATATAATTAAAATAT-A
*
192699 AAATAATT-AAATATA
1 ATATAATTAAAATATA
192714 ATATAATATAAAAATATA
1 ATATAAT-T-AAAATATA
* *
192732 A-ATATTTTAAAAT-TT
1 ATATA-ATTAAAATATA
192747 ATATAA-TAAAATTATTA
1 ATATAATTAAAA-TA-TA
* *
192764 ATAT-ATT-AAATTTT
1 ATATAATTAAAATATA
192778 ATATAAATATAAAATATTTTAA
1 ATAT-AAT-TAAAATA---T-A
192800 ATATAATTAAAATATA
1 ATATAATTAAAATATA
192816 ATA
1 ATA
192819 AAAATTTATA
Statistics
Matches: 91, Mismatches: 12, Indels: 35
0.66 0.09 0.25
Matches are distributed among these distances:
14 10 0.11
15 11 0.12
16 24 0.26
17 18 0.20
18 13 0.14
20 7 0.08
21 4 0.04
22 4 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATTAAAATATA
Found at i:193656 original size:20 final size:19
Alignment explanation
Indices: 193612--193670 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
193602 TACTATATAA
*
193612 ATTTTAATATATTTA-TATT
1 ATTTTAAT-TATTTATTTTT
193631 ATTTTTAATTATTTAATTTTT
1 A-TTTTAATTATTT-ATTTTT
*
193652 ATTTT-ATAATTTTATTTTT
1 ATTTTAATTA-TTTATTTTT
193671 TTCATATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 15 0.44
20 15 0.44
21 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTAATTATTTATTTTT
Found at i:193671 original size:20 final size:21
Alignment explanation
Indices: 193613--193662 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
193603 ACTATATAAA
*
193613 TTTTAATATATTT-A-TATTAT
1 TTTTAAT-TATTTAATTTTTAT
193633 TTTTAATTATTTAATTTTTAT
1 TTTTAATTATTTAATTTTTAT
193654 TTTATAATT
1 TTT-TAATT
193663 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 8 0.31
22 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAATTATTTAATTTTTAT
Found at i:193873 original size:20 final size:22
Alignment explanation
Indices: 193848--193890 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
193838 ACATTAATTT
*
193848 AATT-AATAAAAT-TATTAAAA
1 AATTAAATAAAATATAATAAAA
193868 AATTAAATAAAATATAATAAAA
1 AATTAAATAAAATATAATAAAA
193890 A
1 A
193891 TATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTAAATAAAATATAATAAAA
Found at i:194111 original size:21 final size:21
Alignment explanation
Indices: 194064--194113 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
194054 TAGCAAATTG
* *
194064 TAATATATACATACATATTAT
1 TAATATATACATACATATAAA
* * *
194085 TTATATATATATATATATAAA
1 TAATATATACATACATATAAA
194106 TAATATAT
1 TAATATAT
194114 GTGAACGGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATATATACATACATATAAA
Found at i:194559 original size:35 final size:32
Alignment explanation
Indices: 194473--194568 Score: 85
Period size: 35 Copynumber: 2.9 Consensus size: 32
194463 TAAAAATAAA
*
194473 AATATA-TTAATATTTATATAATATAAATTATT
1 AATATATTTAA-AATTATATAATATAAATTATT
194505 AATATATTTAAAATTTATATAGATATAATATT-TT
1 AATATATTTAAAA-TTATATA-ATATAA-ATTATT
194539 AAATATAATTATAAAA-TATATAA-A-AAATTA
1 -AATAT-ATT-TAAAATTATATAATATAAATTA
194569 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
31 3 0.05
32 9 0.16
33 12 0.22
34 9 0.16
35 14 0.25
36 3 0.05
37 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
AATATATTTAAAATTATATAATATAAATTATT
Found at i:195753 original size:2 final size:2
Alignment explanation
Indices: 195746--195787 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
195736 ATTCATTTTC
* * *
195746 TA TA TA TA TA TA TA TA T- TA TG TA TA TA TA AA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
195787 T
1 T
195788 GTACACTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196774 original size:25 final size:25
Alignment explanation
Indices: 196720--196774 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
196710 ATTTTTTATT
*
196720 TGAAAAAAATAAATTTATATAATAA
1 TGAAAAAAATAAATTTAAATAATAA
* *
196745 T-AAAAAATTTAAATTTAAAT-TTAA
1 TGAAAAAA-ATAAATTTAAATAATAA
196769 TGAAAA
1 TGAAAA
196775 TTATGAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TGAAAAAAATAAATTTAAATAATAA
Found at i:197311 original size:2 final size:2
Alignment explanation
Indices: 197304--197339 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
197294 AATTATATTG
* *
197304 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
197340 ATCATGAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:197339 original size:14 final size:14
Alignment explanation
Indices: 197297--197330 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
197287 GACAAGAAAT
197297 TATAT-TGTATATA
1 TATATATGTATATA
197310 TATATATGTATATA
1 TATATATGTATATA
197324 TATATAT
1 TATATAT
197331 ATATGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:201258 original size:24 final size:21
Alignment explanation
Indices: 201216--201258 Score: 50
Period size: 24 Copynumber: 1.9 Consensus size: 21
201206 ATTAATAAAA
*
201216 AATTAAAAAATTTTTAAATTT
1 AATTAAAAAATTTTAAAATTT
201237 AATTATAAAAATAATTTAAAAT
1 AATTA-AAAAAT--TTTAAAAT
201259 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
24 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAAAAAATTTTAAAATTT
Found at i:201797 original size:21 final size:22
Alignment explanation
Indices: 201762--201823 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
201752 AAATATTTTT
* *
201762 AAATTTTTATTATTTTTATATA
1 AAATATTTATAATTTTTATATA
* *
201784 ATA-ATTTATAA-TTTAATATA
1 AAATATTTATAATTTTTATATA
201804 AAATATTTCATAATTTTTAT
1 AAATATTT-ATAATTTTTAT
201824 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 10 0.32
21 10 0.32
22 6 0.19
23 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATTTATAATTTTTATATA
Found at i:201808 original size:22 final size:22
Alignment explanation
Indices: 201778--201819 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
201768 TTATTATTTT
*
201778 TATATAATAATTT-ATAATTTAA
1 TATAAAAT-ATTTCATAATTTAA
201800 TATAAAATATTTCATAATTT
1 TATAAAATATTTCATAATTT
201820 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATAAAATATTTCATAATTTAA
Found at i:202559 original size:235 final size:231
Alignment explanation
Indices: 201993--202822 Score: 926
Period size: 235 Copynumber: 3.6 Consensus size: 231
201983 CACCAGCTTT
* * * *
201993 TTTTTAATTTTATAATTTAAAAAAAACTTTCTTTTTATTTAATTTTTTTTCAAACTCATA----A
1 TTTTT-ATTTTACAATTTTAAAAAAA---TCTTTTTATCTAA-TTTTCTTCAAACTCATAGTTCA
* * * * *
202054 TTTATTTT-TTT-TAGTCAAATTATTGCTACTTAAAGATTTTAAATATTTGAATG-GAACTATTA
61 TTT-TTTTCTTTGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAG-ACTATTA
** * *
202116 TTTGTGGTGAAAAAGAGAAACCTTTTTAA--TTTT----TT--T---AAATCAATTGAGTTCTGT
124 TTTACGG-GAAAAAGAGAAA-CTTTTAAATTTTTTGAAGTTGATAGCAAATCAATTGAGTTTTGT
** *
202170 AAATTATATTTGAAACCAACCCTTTACACCAAC-TTTTTTATTTC
187 AGGTTATATTTGAAACCAACCCTTTACATCAACTTTTTTTATTTC
202214 TTTTTATTTTACAATTTTAAAAAAATCTTTTTATCTAATTTTCTTCAAACTCATAGTTCATTTTT
1 TTTTTATTTTACAATTTTAAAAAAATCTTTTTATCTAATTTTCTTCAAACTCATAGTTCATTTTT
* *
202279 TTCTTTGTAGTTAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTGCGG
66 TTCTTTGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTACGG
* * *
202344 GAAAAAAAGAAACTTTTAAATTTTATTTAGGTTGATAGCAAATCAATTGAGTTTTGTAGGTTATA
131 GAAAAAGAGAAACTTTTAAATTTT-TTGAAGTTGATAGCAAATCAATTGAGTTTTGTAGGTTATA
** *
202409 TTTGAAATTAACCCTTTACATCAGCTATTTTTTATTTC
195 TTTGAAACCAACCCTTTACATCAACT-TTTTTTATTTC
* * * *
202447 TTTTTATTTTACAATTTAAGAAAAAATCCTTTTTATTTAATCTTCTTCAAACTTATAGTTCATTT
1 TTTTTATTTTACAATTTTA-AAAAAAT-CTTTTTATCTAATTTTCTTCAAACTCATAGTTCATTT
*
202512 TTTTCTTCGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTAC
64 TTTTCTTTGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTAC
* *
202577 GAGGAAAAAGAGAAAATTTTAAATTTTTTGAAGTTGATAGCAAATCAATTAAG-TTTGTAGGTTA
129 G-GGAAAAAGAGAAACTTTTAAATTTTTTGAAGTTGATAGCAAATCAATTGAGTTTTGTAGGTTA
* *
202641 TATTTGAAACCAACCCCTTATATCAACTTTTTTTA----
193 TATTTGAAACCAACCCTTTACATCAACTTTTTTTATTTC
* * * **
202676 -TTTTA---TA-ATTTTTAAAAATATTCTTTTTATCTAATTTTTTTCAAACTCATAGTTTGTTTT
1 TTTTTATTTTACAATTTTAAAAA-AATCTTTTTATCTAATTTTCTTCAAACTCATAGTTCATTTT
* * *
202736 TTTCTTTGTTGTCAAATTATTACTACTCAAAGATCTTAAATATTCAAGTGGGACTATTATTTATC
65 TTTCTTTGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTA-C
* *
202801 GAGAAAAAGAGAAACCTTTAAA
129 GGGAAAAAGAGAAACTTTTAAA
202823 AACCAACCCT
Statistics
Matches: 530, Mismatches: 53, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
216 16 0.03
217 12 0.02
219 11 0.02
220 36 0.07
221 56 0.11
222 3 0.01
223 113 0.21
224 9 0.02
225 2 0.00
226 2 0.00
228 6 0.01
231 44 0.08
233 36 0.07
234 41 0.08
235 120 0.23
236 23 0.04
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (231 bp):
TTTTTATTTTACAATTTTAAAAAAATCTTTTTATCTAATTTTCTTCAAACTCATAGTTCATTTTT
TTCTTTGTAGTCAAATTATTACTACTCAAAGATCTTAAATATTCGAGTGAGACTATTATTTACGG
GAAAAAGAGAAACTTTTAAATTTTTTGAAGTTGATAGCAAATCAATTGAGTTTTGTAGGTTATAT
TTGAAACCAACCCTTTACATCAACTTTTTTTATTTC
Found at i:203782 original size:27 final size:28
Alignment explanation
Indices: 203750--203821 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 28
203740 TAAAATTTAT
203750 TTAATATTAATTATAAAAATA-TTAAAA
1 TTAATATTAATTATAAAAATATTTAAAA
* *
203777 TTAATA-TAAATAT-AAAATATTTTAAA
1 TTAATATTAATTATAAAAATATTTAAAA
*
203803 TATAATATAAATATATAAA
1 T-TAATATTAAT-TATAAA
203822 CTACATTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 6 0.17
26 12 0.33
27 11 0.31
28 2 0.06
29 3 0.08
30 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAATATTAATTATAAAAATATTTAAAA
Found at i:204959 original size:128 final size:127
Alignment explanation
Indices: 204804--205133 Score: 369
Period size: 128 Copynumber: 2.6 Consensus size: 127
204794 AGGTTGATAG
* * * **
204804 CAAATCAATTAAGTTCTATATATGGATACTTAAGTGGAATGAGATACATTTTTTTTTAAATTTTT
1 CAAATCAATTGAGTTCTATATGTGGATACTTAACTGGAATGAGATGTA-TTTTTTTTAAATTTTT
204869 ATCATATAAGTTATTATTCAGAGAGAAAAAA-AGAGAAATCTCT-AAATATTTTGAAATTAATAA
65 ATCATATAAGTTATTATTCAGAG-GAAAAAACA-AGAAATCTCTGAAATATTTTGAAATTAATAA
* * * * *
204932 CAAATTAATTGAGTTCTATACGTGGATACTTAACTAGAATAAGATGTACTATTTTTT-AATTCTT
1 CAAATCAATTGAGTTCTATATGTGGATACTTAACTGGAATGAGATGTA-TTTTTTTTAAATT-TT
* * * * * ** * *
204996 TATCATATAAGTTATTATTCGGAGGAAAAAACAAGATATCTTTGAATTTTTTTGAGGTTGATAG
64 TATCATATAAGTTATTATTCAGAGGAAAAAACAAGAAATCTCTGAAATATTTTGAAATTAATAA
* * * * *
205060 CAAATCAATTGAGTTCTATATGTAGATACTTGACTGAAATGAGCTGTACTTTTTTTAAATTTTTT
1 CAAATCAATTGAGTTCTATATGTGGATACTTAACTGGAATGAGATGTATTTTTTTTAAA-TTTTT
205125 ATCATATAA
65 ATCATATAA
205134 ATGATTTTTT
Statistics
Matches: 167, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
127 25 0.15
128 140 0.84
129 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (127 bp):
CAAATCAATTGAGTTCTATATGTGGATACTTAACTGGAATGAGATGTATTTTTTTTAAATTTTTA
TCATATAAGTTATTATTCAGAGGAAAAAACAAGAAATCTCTGAAATATTTTGAAATTAATAA
Found at i:205610 original size:124 final size:126
Alignment explanation
Indices: 205443--205789 Score: 450
Period size: 128 Copynumber: 2.7 Consensus size: 126
205433 TCTTTAAATC
* * * * *
205443 TTTTGAGGCTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATTGAAATGATATGCA-T
1 TTTTGAGGTTGATAGCAAATTAATTGAGTTCTATATGT-GATACTTAATTGAAATGAAATGCACT
* * *
205507 TTTTTTAAATTTTTTATCATATAAGTTATTATTC-AGG-GAAAAAAA-AGAAATCTCTGAATT
65 TTTTTTTAATTCTTTATCATATAAGTTATTATTCAAGGAAAAAAAAAGAGAAATCTCTGAA-T
* *
205567 TTTTGAGGTTAATAGCAAATTAATTGAGTTCTATATGTAGATACTTAATTGAAATAAAATGCACT
1 TTTTGAGGTTGATAGCAAATTAATTGAGTTCTATATGT-GATACTTAATTGAAATGAAATGCACT
* *
205632 TTTTTTTAATTCTTTATCATATAAGTTATTATTCTAAGGAAAAAAAAAGAGAAATTTTTGAAT
65 TTTTTTTAATTCTTTATCATATAAGTTATTATTC-AAGGAAAAAAAAAGAGAAATCTCTGAAT
* * * * * * *
205695 TTTTGAGCTTGATAGTAAATTAATTGAGTTTTATACGTGAAAACTTAACTGAAATGAGATGCACT
1 TTTTGAGGTTGATAGCAAATTAATTGAGTTCTATATGTG-ATACTTAATTGAAATGAAATGCACT
205760 TTTTTTTAATTCTTTATCATATAAGTTATT
65 TTTTTTTAATTCTTTATCATATAAGTTATT
205790 TTTTAGGTTT
Statistics
Matches: 195, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
124 55 0.28
125 33 0.17
127 4 0.02
128 92 0.47
129 11 0.06
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (126 bp):
TTTTGAGGTTGATAGCAAATTAATTGAGTTCTATATGTGATACTTAATTGAAATGAAATGCACTT
TTTTTTAATTCTTTATCATATAAGTTATTATTCAAGGAAAAAAAAAGAGAAATCTCTGAAT
Found at i:205650 original size:650 final size:647
Alignment explanation
Indices: 204714--206675 Score: 2624
Period size: 650 Copynumber: 3.0 Consensus size: 647
204704 CTTCATAATC
* *** *
204714 AAATTATTACTACTCAAAGACCTTAAATATTAGAGTGAGACTATTATTTGTGGAAAAAAAAAATC
1 AAATTATTGCTACTCAAAGACCTTAAATATTAGAGTGAGACTATTATTTAAAGAAAAAAAAATTC
* *
204779 TTTGAATTTTTTTTGAGGTTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAAGTGGAAT
66 TTT-AA-ATTTTTTGAGGTTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATTGGAAT
* *
204844 GAGATACATTTTTTTTTAAA-TTTTTATCATATAAGTTATTATTCAGAGAGAAAAAAAGAGAAAT
129 GATATGCA--TTTTTTTAAATTTTTTATCATATAAGTTATTATTCAG-G-GAAAAAAAGAGAAAT
* * * *
204908 CTCTAAATATTTTGAAATTAATAACAAATTAATTGAGTTCTATACGTGGATACTTAACTAGAATA
190 CTCTGAATTTTTTGAAGTTAATAACAAATTAATTGAGTTCTATATGTGGATACTTAACTA-AATA
* * * * *
204973 AGATGTACTATTTTTTAATTCTTTATCATATAAGTTATTATTCGGAGGAAAAAACA-AGATATCT
254 AAATGCACTTTTTTTTAATTCTTTATCATATAAGTTATTATTCGGAGGAAAAAA-AGAGAAATTT
* * * *
205037 TTGAATTTTTTTGAGGTTGATAGCAAATCAATTGAGTTCTATATGTAGATACTTGACTGAAATGA
318 TTGAATTTTTTTGAGATTGATAGTAAATCAATTGAGTTTTATATGT-GATACTTAACTGAAATGA
* * * * *
205102 GCTGTACTTTTTTTAAATTTTTTATCATATAAATGATTTTTTACATTTGATGGTAATTTTATTGA
382 GATGTACTTTTTTTAAATTTTTTATCATATAAGTTATTTTTTACGTTTGATGGTAATTTTAATGA
*
205167 TGATTAATTTTTATCTTTTCTCCATTTTTAAAGTAAATTAATATTATTTTTTTCTAATAATTTTC
447 TGATTAATTTTTATCTTTTCTCCATTTTTAAGGTAAATTAATATTATTTTTTTCTAATAATTTTC
*
205232 CTGTAAGTTTCTAAATGAACTGATAGAAGATGTTCTTTTGCTTTATCAATGAAAAGGTTTGAATT
512 CTGTAAGTTTCTAAATGAACTGATAGAGGATGTTCTTTTGC-TTATCAATGAAAAGGTTTGAATT
* * * *
205297 TAATACTAGTTTGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGTACGTGCAAACA
576 GAATA-TTGTTTGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGCATGTGCAAACA
205362 AGACAAAA
640 AGACAAAA
* * * *
205370 TAAATTATTGTTACTCAAAGACCTTAAATATTATAGTGAGACTATTA-TTCACGAAAAAAAAATT
1 -AAATTATTGCTACTCAAAGACCTTAAATATTAGAGTGAGACTATTATTTAAAGAAAAAAAAATT
* * *
205434 CTTTAAATCTTTTGAGGCTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATTGAAATG
65 CTTTAAATTTTTTGAGGTTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATTGGAATG
205499 ATATGCATTTTTTTAAATTTTTTATCATATAAGTTATTATTCAGGGAAAAAAA-AGAAATCTCTG
130 ATATGCATTTTTTTAAATTTTTTATCATATAAGTTATTATTCAGGGAAAAAAAGAGAAATCTCTG
* * * *
205563 AATTTTTTGAGGTTAATAGCAAATTAATTGAGTTCTATATGTAGATACTTAATTGAAATAAAATG
195 AATTTTTTGAAGTTAATAACAAATTAATTGAGTTCTATATGTGGATACTTAACT-AAATAAAATG
**
205628 CACTTTTTTTTAATTCTTTATCATATAAGTTATTATTCTAAGGAAAAAAAAAGAGAAATTTTTGA
259 CACTTTTTTTTAATTCTTTATCATATAAGTTATTATTCGGAGG--AAAAAAAGAGAAATTTTTGA
* * * *
205693 A--TTTTTGAGCTTGATAGTAAATTAATTGAGTTTTATACGTGAAAACTTAACTGAAATGAGATG
322 ATTTTTTTGAGATTGATAGTAAATCAATTGAGTTTTATATGTG-ATACTTAACTGAAATGAGATG
* * * * *
205756 CACTTTTTTTTAATTCTTTATCATATAAGTTATTTTTTAGGTTTGATAGTAATTTTAATGATGAT
386 TACTTTTTTTAAATTTTTTATCATATAAGTTATTTTTTACGTTTGATGGTAATTTTAATGATGAT
*
205821 TACA-TTTTATCTTTCCTCCATTTTTAAGGTAAATTAATATTATTTTCTTT-TAATAATTTTCCT
451 TA-ATTTTTATCTTTTCTCCATTTTTAAGGTAAATTAATATTATTTT-TTTCTAATAATTTTCCT
* * * * *
205884 ATAATTTTCTAAATGAACTAATGGAGGATGTTCTTTTGC---T--ATGAAGAGGTTTGAATTGAA
514 GTAAGTTTCTAAATGAACTGATAGAGGATGTTCTTTTGCTTATCAATGAAAAGGTTTGAATTGAA
* *
205944 TATTGTTTGAGGCTTTGTTCAAACGGGAGAA-AAGAAGATGAATAAAAGCATGTGCAAACAAGAC
579 TATTGTTTGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGCATGTGCAAACAAGAC
206008 GAAAAA
644 --AAAA
* * * * *
206014 CAAATTATTGCTACTAAAAAATCTCAAATATTAGAGTGAGACTATTATTTGTAAAAAAAGAAAGA
1 -AAATTATTGCTACTCAAAGACCTTAAATATTAGAGTGAGACTATTA-TT-T-AAAGAA-AAA-A
* * * *
206079 GAAATT-TTTGAATTTTTTAAGATTGATAGCAAATCAATTAAGTTTTATATATGGATACTTAATT
60 -AAATTCTTTAAATTTTTTGAGGTTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATT
* * * *
206143 GGAATGATATGTATTTTTTT-TATTTTTTATCAGATAAGTTATTATTTAGGGAAAAAAAGAGAAA
124 GGAATGATATGCATTTTTTTAAATTTTTTATCATATAAGTTATTATTCAGGGAAAAAAAGAGAAA
* *
206207 TCTCTGAATTTTTTGAAGTTAATAATAAATTAATTGAATTCTATATGTGGATACTTAACTAAAAT
189 TCTCTGAATTTTTTGAAGTTAATAACAAATTAATTGAGTTCTATATGTGGATACTTAACT-AAAT
* * * *
206272 AAAATACATTCTTTTTTTAATTTTTTATCATATAAGTTATTATTCGGAAGAAAAAAAGAGAAATT
253 AAAATGCACT-TTTTTTTAATTCTTTATCATATAAGTTATTATTCGGAGGAAAAAAAGAGAAATT
** * * *
206337 TTTGAATTTTTTAAATATTGACAGTAAATCAATTGAGTTTTATATGTGGATACTTAACTAAAATG
317 TTTGAATTTTTTTGAGATTGATAGTAAATCAATTGAGTTTTATATGT-GATACTTAACTGAAATG
* * * *
206402 ATATATATTTTTTTTAAAAATTTTTTATCATATAAGTTATTTTTTATGTTTGATGGTAATTTTAA
381 AGATGTACTTTTTTT--AAATTTTTTATCATATAAGTTATTTTTTACGTTTGATGGTAATTTTAA
* * * *
206467 TGATGATTACTTTTTATCTTTTTTCTATTTTTAAGGTAAATTAATATTATTTTCTTCTAATAATT
444 TGATGATTAATTTTTATCTTTTCTCCATTTTTAAGGTAAATTAATATTATTTTTTTCTAATAATT
* * * *
206532 TTCTTGCAAGTTTCTAAATGAATTGATAGAGGATATTCTTTTGCTCTATCAATGAAAAGGTTTGA
509 TTCCTGTAAGTTTCTAAATGAACTGATAGAGGATGTTCTTTTGCT-TATCAATGAAAAGGTTTGA
206597 ATTGAATATTGTTTGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGCATGTGCAAA
573 ATTGAATATTGTTTGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGCATGTGCAAA
206662 CAAGACAAAA
638 CAAGACAAAA
206672 AAAT
1 AAAT
206676 AAACTCGTAA
Statistics
Matches: 1145, Mismatches: 127, Indels: 66
0.86 0.09 0.05
Matches are distributed among these distances:
642 31 0.03
643 26 0.02
644 64 0.06
646 2 0.00
647 1 0.00
648 3 0.00
649 60 0.05
650 443 0.39
651 111 0.10
652 31 0.03
653 162 0.14
654 59 0.05
655 2 0.00
656 17 0.01
657 48 0.04
658 4 0.00
659 48 0.04
660 33 0.03
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (647 bp):
AAATTATTGCTACTCAAAGACCTTAAATATTAGAGTGAGACTATTATTTAAAGAAAAAAAAATTC
TTTAAATTTTTTGAGGTTGATAGCAAATCAATTAAGTTCTATATATGGATACTTAATTGGAATGA
TATGCATTTTTTTAAATTTTTTATCATATAAGTTATTATTCAGGGAAAAAAAGAGAAATCTCTGA
ATTTTTTGAAGTTAATAACAAATTAATTGAGTTCTATATGTGGATACTTAACTAAATAAAATGCA
CTTTTTTTTAATTCTTTATCATATAAGTTATTATTCGGAGGAAAAAAAGAGAAATTTTTGAATTT
TTTTGAGATTGATAGTAAATCAATTGAGTTTTATATGTGATACTTAACTGAAATGAGATGTACTT
TTTTTAAATTTTTTATCATATAAGTTATTTTTTACGTTTGATGGTAATTTTAATGATGATTAATT
TTTATCTTTTCTCCATTTTTAAGGTAAATTAATATTATTTTTTTCTAATAATTTTCCTGTAAGTT
TCTAAATGAACTGATAGAGGATGTTCTTTTGCTTATCAATGAAAAGGTTTGAATTGAATATTGTT
TGAGGCTTTGATCAAATGGGAGAAGAAGAAGATGAATAAAAGCATGTGCAAACAAGACAAAA
Found at i:206391 original size:129 final size:125
Alignment explanation
Indices: 206069--206447 Score: 440
Period size: 124 Copynumber: 3.0 Consensus size: 125
206059 TATTTGTAAA
* * *
206069 AAAAGAAAGAGAAATTTTTGAATTTTTTAAGATTGATAGCAAATCAATTAAGTTTTATATATGGA
1 AAAA-AAAGAGAAATTTTTGAATTTTTTAA-ATTGATAGTAAATCAATTGAGTTTTATATGTGGA
* ** * *
206134 TACTTAATTGGAATGATATGTA-TTTTTTTT-ATTTTTTATCAGATAAGTTATTATTTAGGG
64 TACTTAACTAAAATGATATATATTTTTTTTTAATTTTTTATCATATAAGTTATTATTTAGGG
* * * * * * * *
206194 AAAAAAAGAGAAATCTCTGAATTTTTTGAAGTTAATAATAAATTAATTGAATTCTATATGTGGAT
1 AAAAAAAGAGAAATTTTTGAATTTTTT-AAATTGATAGTAAATCAATTGAGTTTTATATGTGGAT
* * * *
206259 ACTTAACTAAAATAAAATACATTCTTTTTTTAATTTTTTATCATATAAGTTATTA-TTCGGAAG
65 ACTTAACTAAAATGATATATATT-TTTTTTTAATTTTTTATCATATAAGTTATTATTTAGG--G
*
206322 AAAAAAAGAGAAATTTTTGAATTTTTTAAATATTGACAGTAAATCAATTGAGTTTTATATGTGGA
1 AAAAAAAGAGAAATTTTTGAATTTTTT-AA-ATTGATAGTAAATCAATTGAGTTTTATATGTGGA
* *
206387 TACTTAACTAAAATGATATATATTTTTTTTAAAAATTTTTTATCATATAAGTTATTTTTTA
64 TACTTAACTAAAATGATATATATTTTTTTT--TAATTTTTTATCATATAAGTTATTATTTA
206448 TGTTTGATGG
Statistics
Matches: 208, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
124 61 0.29
125 7 0.03
126 11 0.05
127 22 0.11
128 34 0.16
129 48 0.23
130 23 0.11
131 2 0.01
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (125 bp):
AAAAAAAGAGAAATTTTTGAATTTTTTAAATTGATAGTAAATCAATTGAGTTTTATATGTGGATA
CTTAACTAAAATGATATATATTTTTTTTTAATTTTTTATCATATAAGTTATTATTTAGGG
Found at i:207035 original size:5 final size:5
Alignment explanation
Indices: 207025--207071 Score: 69
Period size: 5 Copynumber: 9.2 Consensus size: 5
207015 ATTAAGTATG
207025 AATAT AATAT -ATAT ATATAT AATAT AATAT AATAT AATAT AAGTAT A
1 AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AA-TAT A
207072 TATTTTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.10
5 26 0.67
6 9 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:208297 original size:22 final size:21
Alignment explanation
Indices: 208272--208319 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
208262 TATATTATTA
208272 TTATATTTAAAATATAATATAT
1 TTATA-TTAAAATATAATATAT
* *
208294 TTATA-TAAATTTTAATATAT
1 TTATATTAAAATATAATATAT
208314 TTATAT
1 TTATAT
208320 ATTTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 18 0.78
22 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATATTAAAATATAATATAT
Found at i:208302 original size:20 final size:20
Alignment explanation
Indices: 208279--208320 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
208269 TTATTATATT
208279 TAAAATATAATATATTTATA
1 TAAAATATAATATATTTATA
* *
208299 TAAATTTTAATATATTTATA
1 TAAAATATAATATATTTATA
208319 TA
1 TA
208321 TTTATATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATATAATATATTTATA
Found at i:208315 original size:10 final size:9
Alignment explanation
Indices: 208254--208324 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
208244 AAGTATTAAT
*
208254 ATATATTTT
1 ATATATTTA
208263 ATAT-TATTA
1 ATATAT-TTA
*
208272 TTATATTTA
1 ATATATTTA
*
208281 A-A-ATATA
1 ATATATTTA
208288 ATATATTTA
1 ATATATTTA
*
208297 TATAAATTTTA
1 -ATATA-TTTA
208308 ATATATTT-
1 ATATATTTA
208316 ATATATTTA
1 ATATATTTA
208325 TATTACTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 5 0.10
8 11 0.23
9 19 0.40
10 9 0.19
11 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATTTA
Found at i:208910 original size:21 final size:21
Alignment explanation
Indices: 208884--208925 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
208874 ATTTTAATTT
208884 TAAAAATATATAATATTAATA
1 TAAAAATATATAATATTAATA
208905 TAAAAATATATAATATTAATA
1 TAAAAATATATAATATTAATA
208926 AGATCAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAATATATAATATTAATA
Found at i:210156 original size:14 final size:14
Alignment explanation
Indices: 210133--210167 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
210123 ACATTTAAAA
*
210133 AAAATGTAAATATT
1 AAAATTTAAATATT
210147 AAAATTTAAATATT
1 AAAATTTAAATATT
210161 -AAATTTA
1 AAAATTTA
210168 TTAGATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:213130 original size:26 final size:26
Alignment explanation
Indices: 213094--213145 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
213084 ATAAAATCAA
*
213094 AAACACCTCTGCAACTACAGGTGAGG
1 AAACACCTCTGCAACCACAGGTGAGG
*
213120 AAACACGTCTGCAACCACAGGTGAGG
1 AAACACCTCTGCAACCACAGGTGAGG
213146 GATCATGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (26 bp):
AAACACCTCTGCAACCACAGGTGAGG
Found at i:214742 original size:18 final size:18
Alignment explanation
Indices: 214703--214741 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
214693 TTCAAAAGTT
214703 TAAAAT-ATT-AAATAAA
1 TAAAATAATTAAAATAAA
214719 TAAAATAATTAAAATATAA
1 TAAAATAATTAAAATA-AA
214738 TAAA
1 TAAA
214742 TTATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 5 0.25
19 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATAATTAAAATAAA
Found at i:214906 original size:22 final size:22
Alignment explanation
Indices: 214871--214912 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
214861 TATGTTAGGT
*
214871 AGTGTGTTAAGTAAACATATTA
1 AGTGTGCTAAGTAAACATATTA
*
214893 AGTGTGCTAGGTAAACATAT
1 AGTGTGCTAAGTAAACATAT
214913 CTTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGTGCTAAGTAAACATATTA
Found at i:220937 original size:163 final size:155
Alignment explanation
Indices: 220746--221126 Score: 505
Period size: 163 Copynumber: 2.4 Consensus size: 155
220736 AAAGATCAAT
* * *
220746 AAAAAAAATGAAATAA-TCCTTTTAAAAGAGGATCTATTTTTATTAATGATGAAAAATTAAATTA
1 AAAAGAAATGAAGTAATTCTTTTTAAAAGAGGATCTATTTTTATTAATGATGAAAAATTAAATTA
*
220810 AATCAATTTAATCAAAAATTATTAAATTATGTAATTCGATATACTATTCAATCGATTAGACCAAT
66 AATCAATTTAATCAAAAATTATTAAATTATGCAATTCGATATACTATTCAATCGATTAGACCAAT
220875 GATCAATTTCTTTGAACATCGTAGC
131 GATCAATTTCTTTGAACATCGTAGC
* * *
220900 AAAAGAAATGAAGAAATGAAGTAATTTTTTTTAAAAGATGATCTATTTTTATTAATGATAAAAAA
1 ------AA--AAGAAATGAAGTAATTCTTTTTAAAAGAGGATCTATTTTTATTAATGATGAAAAA
* * ** * * *
220965 TCAAATTAAATCAATTTAATCAAGAATTATTAGGTTATGCAATTTGATATACTATTTAATCTATT
58 TTAAATTAAATCAATTTAATCAAAAATTATTAAATTATGCAATTCGATATACTATTCAATCGATT
* *
221030 AGACCAATGATCAATTTCTTTTAACATTGTAGC
123 AGACCAATGATCAATTTCTTTGAACATCGTAGC
* *
221063 AAAAGAAATGAAGTAATTCTTTTTAAAAGAGGATCTATCTTTATT-CTGGATGAAAAATTAAATT
1 AAAAGAAATGAAGTAATTCTTTTTAAAAGAGGATCTATTTTTATTAAT-GATGAAAAATTAAATT
221127 GAATTATTGA
Statistics
Matches: 195, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
154 1 0.01
155 54 0.28
157 2 0.01
160 2 0.01
162 12 0.06
163 124 0.64
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (155 bp):
AAAAGAAATGAAGTAATTCTTTTTAAAAGAGGATCTATTTTTATTAATGATGAAAAATTAAATTA
AATCAATTTAATCAAAAATTATTAAATTATGCAATTCGATATACTATTCAATCGATTAGACCAAT
GATCAATTTCTTTGAACATCGTAGC
Found at i:221291 original size:17 final size:15
Alignment explanation
Indices: 221242--221279 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
221232 GTCAAGACTA
* *
221242 AATTTTATATATTTT
1 AATTTTTTAGATTTT
221257 AATTTTTTAGATTTT
1 AATTTTTTAGATTTT
221272 AATTTTTT
1 AATTTTTT
221280 TGAACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
AATTTTTTAGATTTT
Found at i:227649 original size:15 final size:15
Alignment explanation
Indices: 227627--227689 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
227617 GGTGTTATAA
227627 AAAT-TTATTTTATT
1 AAATATTATTTTATT
** *
227641 ATTTATTATATTATT
1 AAATATTATTTTATT
227656 AAATATTATTTTTATAT
1 AAATATTA-TTTTAT-T
227673 AAATATATATTTT-TT
1 AAATAT-TATTTTATT
227688 AA
1 AA
227690 TTAGATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
14 2 0.05
15 18 0.46
16 6 0.15
17 11 0.28
18 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATATTATTTTATT
Found at i:227677 original size:17 final size:17
Alignment explanation
Indices: 227651--227686 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
227641 ATTTATTATA
227651 TTATTAAATAT-TATTT
1 TTATTAAATATATATTT
227667 TTATATAAATATATATTT
1 TTAT-TAAATATATATTT
227685 TT
1 TT
227687 TAATTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 7 0.39
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAATATATATTT
Found at i:227682 original size:21 final size:21
Alignment explanation
Indices: 227637--227687 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
227627 AAATTTATTT
* *
227637 TATTATTTATTATATTATTAAA
1 TATTATTT-TTATATAAATAAA
*
227659 TATTATTTTTATATAAATATA
1 TATTATTTTTATATAAATAAA
227680 TATT-TTTT
1 TATTATTTT
227688 AATTAGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTTTTATATAAATAAA
Found at i:227816 original size:2 final size:2
Alignment explanation
Indices: 227809--227845 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
227799 TAAATTTTAA
*
227809 AT AT AT AT AT AT AT AT AT AT AT AA 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 A
227846 AATTTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:228412 original size:23 final size:20
Alignment explanation
Indices: 228348--228398 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
228338 AATTATTTTA
*
228348 ATTTTTTACGTTGTTCGATATT
1 ATTTTTTA--TTGTTTGATATT
228370 ATTTTTTATTGTTTGATATT
1 ATTTTTTATTGTTTGATATT
228390 ATTTTTTAT
1 ATTTTTTAT
228399 ATTTTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 20 0.71
22 8 0.29
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.67
Consensus pattern (20 bp):
ATTTTTTATTGTTTGATATT
Found at i:229162 original size:29 final size:30
Alignment explanation
Indices: 229081--229162 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
229071 GTATATTTTG
*
229081 AAAAATAATATGTACATATTGAAAATTTAAAT
1 AAAAATAATATATACATATT-AAAA-TTAAAT
** *
229113 TCAAATAATTATATA-AAATTAAAA-TAAAT
1 AAAAATAA-TATATACATATTAAAATTAAAT
229142 AAAAATAATATATACATATTA
1 AAAAATAATATATACATATTA
229163 GGAATAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
28 6 0.15
29 16 0.39
31 4 0.10
32 10 0.24
33 5 0.12
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAATAATATATACATATTAAAATTAAAT
Found at i:230188 original size:17 final size:16
Alignment explanation
Indices: 230154--230247 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 16
230144 TGAATTATTA
230154 TTTATTTTATTAAAAT
1 TTTATTTTATTAAAAT
*
230170 TTTATTTTAATTAATAT
1 TTTATTTT-ATTAAAAT
* *
230187 TTATATATT-TTATAAT
1 TT-TATTTTATTAAAAT
** * *
230203 TAAATTTAATCAAAAT
1 TTTATTTTATTAAAAT
230219 ATATTATTTTAACTTAAAAT
1 -T-TTATTTT-A-TTAAAAT
230239 TATTATTTT
1 T-TTATTTT
230248 TAGTTAAATC
Statistics
Matches: 57, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
15 3 0.05
16 19 0.33
17 10 0.18
18 9 0.16
19 10 0.18
20 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATTTTATTAAAAT
Found at i:230336 original size:33 final size:33
Alignment explanation
Indices: 230293--230360 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
230283 GAGACTCAAA
*
230293 ACCCGTCTCAATTGGATCAAGCCTGCCGGGCAG
1 ACCCGACTCAATTGGATCAAGCCTGCCGGGCAG
230326 ACCCGACTCAATTGGATCAAGCCTGCCGGGCAG
1 ACCCGACTCAATTGGATCAAGCCTGCCGGGCAG
230359 AC
1 AC
230361 AGGCTGCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (33 bp):
ACCCGACTCAATTGGATCAAGCCTGCCGGGCAG
Found at i:230581 original size:2 final size:2
Alignment explanation
Indices: 230574--230599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
230564 TAGTTTACCC
230574 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
230600 GAACTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:232073 original size:17 final size:17
Alignment explanation
Indices: 232048--232082 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
232038 AAAACCAACA
*
232048 CCGGCTTTCTTCCTTTT
1 CCGGCTTTCTACCTTTT
*
232065 CCGGGTTTCTACCTTTT
1 CCGGCTTTCTACCTTTT
232082 C
1 C
232083 AGGGATGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.34, G:0.14, T:0.49
Consensus pattern (17 bp):
CCGGCTTTCTACCTTTT
Found at i:236391 original size:19 final size:21
Alignment explanation
Indices: 236343--236397 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
236333 AATTCCAATA
*
236343 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
236364 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
236384 -TTTGTATCGATACA
1 ATTTGTATCGATACA
236398 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:236448 original size:21 final size:21
Alignment explanation
Indices: 236422--236463 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
236412 AGCTACTGCC
236422 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
236443 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
236464 GTATCAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:238902 original size:51 final size:51
Alignment explanation
Indices: 238845--239114 Score: 239
Period size: 51 Copynumber: 5.3 Consensus size: 51
238835 ATTTTTCATC
*
238845 TCGGGGATACTCCAA-TCCCGGTTTCATTTTCAAAACATCAATTTTTCCTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTTCAAAACATCAATTTTTCCTAA
* * * * ** *
238896 TCGGGGATACTCCAACTCCGATTTTA-TTTCTAAAGCCTCGATTTACCCCAA
1 TCGGGGATACTCCAACTCCGATTTCATTTTC-AAAACATCAATTTTTCCTAA
* * * * *
238947 CCGGGGATACTTCAA-TCCCGATTTCATCTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTTCAAAACATCAATTTTTCCTAA
* * * *
238998 TCAGGGATACTCCAACTCCGATTTTA-TTTCTAAAACACCCA-TTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTCATTTTC-AAAACATCAATTTTTCC-TAA
* * * *
239049 TCGGGGATACTCCAACTCCGATTT-ATTTCCAAAACACCGACTTTTCAC-AA
1 TCGGGGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTTTTC-CTAA
*
239099 TTGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
239115 CCCGTTATTT
Statistics
Matches: 176, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
50 39 0.22
51 132 0.75
52 5 0.03
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTTTTCCTAA
Found at i:239022 original size:102 final size:102
Alignment explanation
Indices: 238846--239084 Score: 322
Period size: 102 Copynumber: 2.4 Consensus size: 102
238836 TTTTTCATCT
* * * *
238846 CGGGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCCTAATCGGGGATACTCCAA
1 CGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCCTAATCAGGGATACTCCAA
238911 CTCCGATTTTATTTCTAAAGCCTCGATTTACCCCAAC
66 CTCCGATTTTATTTCTAAAGCCTCGATTTACCCCAAC
* *
238948 CGGGGATACTTCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCAGGGATACTCCAA
1 CGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCCTAATCAGGGATACTCCAA
* * * ** *
239013 CTCCGATTTTATTTCTAAAACAC-CCATTTTCCATAAT
66 CTCCGATTTTATTTCTAAAGC-CTCGATTTACCCCAAC
*
239050 CGGGGATACTCCAA-CTCCGATTT-ATTTCCAAAACA
1 CGGGGATACTCCAATC-CCGATTTCATCTCCAAAACA
239085 CCGACTTTTC
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
101 12 0.10
102 108 0.89
103 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (102 bp):
CGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCCTAATCAGGGATACTCCAA
CTCCGATTTTATTTCTAAAGCCTCGATTTACCCCAAC
Found at i:239245 original size:79 final size:78
Alignment explanation
Indices: 239052--239350 Score: 363
Period size: 79 Copynumber: 3.8 Consensus size: 78
239042 TCCATAATCG
* * * *
239052 GGGATACTCCAACTCC-GATTTATTTCCAAAACACCGACTTT-TCACAATTGGGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACC-AATTTCTCACAATCGGGGATACTCCAAC
239115 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * * * * * *
239129 GGGACACTCCAACCCTGTTTTTATTTCTAAAATATCAATTTCTCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAACC
239194 CCGTTA-TTTCGGA
66 CCGTTATTTTC-GA
* * * *
239207 GGAGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGAGATACTCCAAC
1 GG-GATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
*
239272 CTCGTTATTTTCGA
65 CCCGTTATTTTCGA
* *
239286 GGGGATACGCCAACCCCGGTTTTATTTCTAAAACACCAA-TTCTCCACAATCGGGGATACTCCAA
1 -GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTCT-CACAATCGGGGATACTCCAA
239350 C
64 C
239351 TCCGATTTTA
Statistics
Matches: 190, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
77 21 0.11
78 48 0.25
79 115 0.61
80 6 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (78 bp):
GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:239362 original size:51 final size:51
Alignment explanation
Indices: 239286--239405 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
239276 TTATTTTCGA
* *
239286 GGGGATACGCCAACCCCGGTTTTA-TTTCTAAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTCTCCACAATC
* * * *
239337 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATC
*
239388 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
239406 TTATTTCATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 56 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATC
Found at i:239408 original size:209 final size:209
Alignment explanation
Indices: 239165--239559 Score: 549
Period size: 209 Copynumber: 1.9 Consensus size: 209
239155 CTAAAATATC
* * *
239165 AATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCGGAGGAGATACTCCAACCCCGGTTTT
1 AATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCAGAGGAGATACTCCAACCCCGGCTTT
* * *
239230 ATTTCCAAAACATCAATTTTTCATAATCGGAGATACTCCAACCTCGTTATTTTCGA-GGGGATAC
66 ATTTCCAAAACATCAATTTCTCATAATCGGAGATACTCCAACCCCATTATTTTC-ACGGGGATAC
* *
239294 GCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAACTCCGATTT
130 GCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTCCAACTCCGATTT
239359 TATTTTCAAAACACT
195 TATTTTCAAAACACT
* * ** *
239374 AATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTCATCGGGGATACTCCAACCCCGGCTTT
1 AATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCAGAGGAGATACTCCAACCCCGGCTTT
* ** * * * *
239439 ATTTCCAAAATATTGATTTCTCATAATTGGGGATACTTCAACCCCATTATTTTCACGGGGATACT
66 ATTTCCAAAACATCAATTTCTCATAATCGGAGATACTCCAACCCCATTATTTTCACGGGGATACG
* * * * *
239504 CCAATCCCGATTTTATTTTTAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
131 CCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTCCAAC
239560 CCTGTTATTT
Statistics
Matches: 160, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
208 1 0.01
209 159 0.99
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (209 bp):
AATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCAGAGGAGATACTCCAACCCCGGCTTT
ATTTCCAAAACATCAATTTCTCATAATCGGAGATACTCCAACCCCATTATTTTCACGGGGATACG
CCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTCCAACTCCGATTTT
ATTTTCAAAACACT
Found at i:239417 original size:79 final size:80
Alignment explanation
Indices: 239334--239645 Score: 351
Period size: 79 Copynumber: 3.9 Consensus size: 80
239324 ATTCTCCACA
* * * * *
239334 ATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCT
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCC
239399 AACCCCGTTA-TTTC
66 AACCCCGTTATTTTC
** * *** * * *
239413 ATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATTGGGGATACTTC
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCC
*
239478 AACCCCATTATTTTC
66 AACCCCGTTATTTTC
* ** *
239493 A-CGGGGATACTCCAATCCCGATTTTATTTTTAAAACACCAA-TTTTCTATAATCAGGGATACTC
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ATAATCGGGGATACTC
*
239556 CAACCCTGTTATTTTC
65 CAACCCCGTTATTTTC
*** * * *
239572 CGAGGGGATACTCCAACCCCGATTTTACTTCCAAAACACCGATTTTCCATAATCGGGGATACTCC
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCC
*
239637 AGCCCCGTT
66 AACCCCGTT
239646 GTTATCTCCA
Statistics
Matches: 190, Mismatches: 39, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
78 4 0.02
79 120 0.63
80 62 0.33
81 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCC
AACCCCGTTATTTTC
Found at i:239475 original size:130 final size:129
Alignment explanation
Indices: 239210--239448 Score: 338
Period size: 130 Copynumber: 1.8 Consensus size: 129
239200 TTTCGGAGGA
* * *
239210 GATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGAGATACTCCAACCTC
1 GATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCCC
* *
239275 GTTATTTTCGAGGGGATACGCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGG
66 GTTATTTTC-AGGGGATACGCCAACCCCGGCTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* * * *
239340 GATACTCCAACTCCGATTTTATTTTCAAAACA-CTAATTTTTCACAATCGGGGATACTCTAACCC
1 GATACTCCAACCCCGATTTTATTTCCAAAACATC-AATTTTTCACAATCGGAGATACTCCAACCC
*
239404 CGTTA-TTTCATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAA
65 CGTTATTTTCA--GGGGATACGCCAACCCCGGCTTTATTTCCAAAA
239449 TATTGATTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 1 0.01
129 5 0.05
130 90 0.94
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (129 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCCC
GTTATTTTCAGGGGATACGCCAACCCCGGCTTTATTTCCAAAACACCAATTCTCCACAATCGGG
Found at i:239551 original size:158 final size:159
Alignment explanation
Indices: 239336--239634 Score: 399
Period size: 158 Copynumber: 1.9 Consensus size: 159
239326 TCTCCACAAT
* * *
239336 CGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCTAA
1 CGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCAGGGATACTCCAA
** * * * **
239401 CCCCGTTA-TTTCATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATA
66 CCCCGTTATTTTCAGAGGGGATACTCCAACCCCGACTTTACTTCCAAAACACCGATTTTC-CATA
*
239464 ATTGGGGATACTTCAACCCCATTATTTTCA
130 ATCGGGGATACTTCAACCCCATTATTTTCA
* *
239494 CGGGGATACTCCAA-TCCCGATTTTATTTTTAAAACACCAA-TTTTCTATAATCAGGGATACTCC
1 CGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTTTC-ACAATCAGGGATACTCC
* * *
239557 AACCCTGTTATTTTCCGAGGGGATACTCCAACCCCGATTTTACTTCCAAAACACCGATTTTCCAT
64 AACCCCGTTATTTTCAGAGGGGATACTCCAACCCCGACTTTACTTCCAAAACACCGATTTTCCAT
239622 AATCGGGGATACT
129 AATCGGGGATACT
239635 CCAGCCCCGT
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
157 6 0.05
158 59 0.49
159 52 0.43
160 4 0.03
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (159 bp):
CGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCAGGGATACTCCAA
CCCCGTTATTTTCAGAGGGGATACTCCAACCCCGACTTTACTTCCAAAACACCGATTTTCCATAA
TCGGGGATACTTCAACCCCATTATTTTCA
Found at i:240888 original size:20 final size:21
Alignment explanation
Indices: 240850--240890 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
240840 TAAAAAATTA
240850 TAAAATATTTATATTTTAAAT
1 TAAAATATTTATATTTTAAAT
*
240871 TAAAATTTTTAT-TTTTAAAT
1 TAAAATATTTATATTTTAAAT
240891 ATATTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAATATTTATATTTTAAAT
Found at i:244272 original size:20 final size:20
Alignment explanation
Indices: 244247--244286 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
244237 TTAACAATAG
244247 GCGAATGGGGTAATCTTGTT
1 GCGAATGGGGTAATCTTGTT
244267 GCGAATGGGGTAATCTTGTT
1 GCGAATGGGGTAATCTTGTT
244287 AAACCCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (20 bp):
GCGAATGGGGTAATCTTGTT
Found at i:245346 original size:17 final size:18
Alignment explanation
Indices: 245321--245366 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
245311 TTCATGTGCT
*
245321 TTTTATTTTTTTTTGAAA
1 TTTTATTTTTTTTCGAAA
245339 TTTT-TTTTTTTTCGAAA
1 TTTTATTTTTTTTCGAAA
*
245356 TATTATGTTTT
1 TTTTAT-TTTT
245367 CTACTTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.62
18 5 0.21
19 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTTTTCGAAA
Found at i:245515 original size:165 final size:163
Alignment explanation
Indices: 245237--245602 Score: 411
Period size: 165 Copynumber: 2.2 Consensus size: 163
245227 TTTTTTTTAG
* *
245237 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTGATAATAATTTAATTTTCAAAAATT
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAATTTTCAAAAATT
* * * * ** *
245302 CATTTCATTTTCATGTGCTTTTTATTTTTTTTTGAAATTTT-TTTTTTTTCG-AAATATTATGTT
66 CAATTCATTTCCAGGAGCTTTTTATTTTTCCTTGAAATTTTCTTTTTTTTCGAAAACATTA--TT
*
245365 TTCTACTTCGTAAATTTTTTCGAGAGGA-TTTTCTTGA
129 TTCTACTTCGT-AATTTTTT-AAG-GGATTTTTCTTGA
* * * * * * * * *
245402 TTTTCAATTTTCAAAATTCATCAAACATCATTATTTTTTTAATATTAATTCAGTTTTTAAAAATT
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAATTTTCAAAAATT
*
245467 -AATTCATTTCCAGGAG-TTTTTAAATTTTCTCCTTGAAA-TTTCTTTTTTTTTGAAAAACATTA
66 CAATTCATTTCCAGGAGCTTTTT--ATTTT-TCCTTGAAATTTTCTTTTTTTTCG-AAAACATTA
245529 TTTTCTACTTCGTAATTTTTTAAGGGATTTTTCTTGA
127 TTTTCTACTTCGTAATTTTTTAAGGGATTTTTCTTGA
* *
245566 TTTTTATTTTTTTAAATTTATCAAATATTATTATTTA
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTA
245603 ACTCATACTA
Statistics
Matches: 166, Mismatches: 28, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
163 8 0.05
164 52 0.31
165 70 0.42
166 29 0.17
168 7 0.04
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (163 bp):
TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAATTTTCAAAAATT
CAATTCATTTCCAGGAGCTTTTTATTTTTCCTTGAAATTTTCTTTTTTTTCGAAAACATTATTTT
CTACTTCGTAATTTTTTAAGGGATTTTTCTTGA
Found at i:245679 original size:164 final size:163
Alignment explanation
Indices: 245237--245694 Score: 430
Period size: 164 Copynumber: 2.8 Consensus size: 163
245227 TTTTTTTTAG
* * *
245237 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTGATAATAATTTAATTTTCAAAAATT
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAGTTTT-AAAAA-T
* * * * * *
245302 CATTTCATTTTCATGTGCTTTTTATTTTTT-TTTGAAATTTTTTTTTTTTCG--AAATATTATGT
64 CAATTCATTTTCAT-AGATTTTAATTTTTTCTTTGAAATTCTTTTTTTTT-GAAAAACATTA-GT
*
245364 TTTCTACTTCGTAAATTTTTTCGAGAGGATTTTCTTGA
126 TTTCTACTTCGTAAATTTTTTCAAGAGGATTTTCTTGA
* * * * * * * *
245402 TTTTCAATTTTCAAAATTCATCAAACATCATTATTTTTTTAATATTAATTCAGTTTTTAAAAATT
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAG-TTTTAAAAATC
* * * * *
245467 AATTCATTTCCAGGAGTTTTTAAATTTTCTCCTTGAAATTTCTTTTTTTTTGAAAAACATTA-TT
65 AATTCATTTTCA-TAGATTTT-AATTTTTTCTTTGAAA-TTCTTTTTTTTTGAAAAACATTAGTT
245531 TTCTACTTCGT-AATTTTTT-AAG-GGATTTTTCTTGA
127 TTCTACTTCGTAAATTTTTTCAAGAGGA-TTTTCTTGA
* * ** * * *
245566 TTTTTATTTTTTTAAATTTATCAAATATTATTATTTAACTCATACTAAATCAGTTTTAAAATATC
1 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAGTTTTAAAA-ATC
* * * *
245631 AATTCATTTTTATAAATTTTGGATTTTTTCTTTGAAA-TCTCTTTTTTTTGAAAAAC-TGAGTTT
65 AATTCATTTTCATAGATTTT-AATTTTTTCTTTGAAATTCT-TTTTTTTTGAAAAACATTAGTTT
245694 T
128 T
245695 TTAATCCATA
Statistics
Matches: 236, Mismatches: 46, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
161 5 0.02
162 19 0.08
163 29 0.12
164 79 0.33
165 62 0.26
166 24 0.10
167 11 0.05
168 7 0.03
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (163 bp):
TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTAATAATAATTCAGTTTTAAAAATCA
ATTCATTTTCATAGATTTTAATTTTTTCTTTGAAATTCTTTTTTTTTGAAAAACATTAGTTTTCT
ACTTCGTAAATTTTTTCAAGAGGATTTTCTTGA
Found at i:248334 original size:153 final size:153
Alignment explanation
Indices: 248137--248611 Score: 702
Period size: 153 Copynumber: 3.1 Consensus size: 153
248127 TGTCTACTAA
** * * * * * *
248137 GGGTATCAGGTGTTTTCACGTCAAAGGTATCTCTTGGAGGTATTTTTATAATTTTTTAAAATCGA
1 GGGTATCAGGTACTTTCACGTCGAAGGTATCCCTTAG-GGTATTTTTGTAATTTCTTAGAATCGA
*
248202 GTCTTAGGTTGTCACCGGGTACGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCA-CCCAT
65 GTCTTAGGTTGTCACCGGGTCCGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCCCAT
248266 CCACATCCTTTTTAAGTCTTTTAG
130 CCACATCCTTTTTAAGTCTTTTAG
*
248290 GGGTATCAGATACTTTCACGTCGAAGGTATCCCTTAAGGGTATTTTTGTAATTTCTTAGAATCGA
1 GGGTATCAGGTACTTTCACGTCGAAGGTATCCCTT-AGGGTATTTTTGTAATTTCTTAGAATCGA
* * *
248355 GTCCTAGGTTGTCACCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGG-TCACCCCAT
65 GTCTTAGGTTGTCACCGGGTCCGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCCCAT
* * *
248419 ACACATCCTTTTTAAGTCCTTTAA
130 CCACATCCTTTTTAAGTCTTTTAG
* * *
248443 GGCTATCAGGTACTTTTACGTCGAAGGTATCCCTTAGGGTAATTTTCGTAATTTCTTAGAATCGA
1 GGGTATCAGGTACTTTCACGTCGAAGGTATCCCTTAGGGT-ATTTTTGTAATTTCTTAGAATCGA
* *
248508 GTCTTAGGTTGTCACCGGGTCCGTTTTTATGTCGAAGGTGGGCATTTAGGATAGGTTCACCCCGT
65 GTCTTAGGTTGTCACCGGGTCCGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCCCAT
248573 CCACATCCTTTTTAAGTCTTTTAG
130 CCACATCCTTTTTAAGTCTTTTAG
**
248597 AAGTATCAGGTACTT
1 GGGTATCAGGTACTT
248612 GTACGTCTAA
Statistics
Matches: 287, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
152 8 0.03
153 237 0.83
154 42 0.15
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (153 bp):
GGGTATCAGGTACTTTCACGTCGAAGGTATCCCTTAGGGTATTTTTGTAATTTCTTAGAATCGAG
TCTTAGGTTGTCACCGGGTCCGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCCCATC
CACATCCTTTTTAAGTCTTTTAG
Found at i:248703 original size:306 final size:306
Alignment explanation
Indices: 248134--248706 Score: 712
Period size: 306 Copynumber: 1.9 Consensus size: 306
248124 TAATGTCTAC
* * * * * *
248134 TAAGGGTATCAGGTGTTTTCACGTCAAAGGTATCTCTTGGAGGTATTTTTATAATTTTTTAAAAT
1 TAAGGCTATCAGGTCTTTTCACGTCAAAGGTATCCCTTAGAGGTATTTTCATAATTTCTTAAAAT
248199 CGAGTCTTAGGTTGTCACCGGGTACGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCC
66 CGAGTCTTAGGTTGTCACCGGGTACGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCC
** * *
248264 ATCCACATCCTTTTTAAGTCTTTTAGGGGTATCAGATACTTTCACGTCGAAGGTATCCCTTAAGG
131 ATCCACATCCTTTTTAAGTCTTTTAGAAGTATCAGATACTTTCACGTCGAAGGCATCCCTTAAAG
** * * * * * * * *
248329 GTATTTTTGTAATTTCTTAGAATCGAGTCCTAGGTTGTCACCGGATCCGCTTTTATGCCGAAGGT
196 ACATTTTCGTAATTTCTTAAAATCAACTCCTAGGCTGCCACCGGATCCGCTTGTACGCCGAAGGT
248394 GGGCATTTAGGATAGGTCACCCCATACACATCCTTTTTAAGTCCTT
261 GGGCATTTAGGATAGGTCACCCCATACACATCCTTTTTAAGTCCTT
* * *
248440 TAAGGCTATCAGGTACTTTT-ACGTCGAAGGTATCCCTTAG-GGTAATTTTCGTAATTTCTTAGA
1 TAAGGCTATCAGGT-CTTTTCACGTCAAAGGTATCCCTTAGAGGT-ATTTTCATAATTTCTTAAA
* *
248503 ATCGAGTCTTAGGTTGTCACCGGGTCCGTTTTTATGTCGAAGGTGGGCATTTAGGATAGGTTCAC
64 ATCGAGTCTTAGGTTGTCACCGGGTACGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCA-
* * *
248568 CCCGTCCACATCCTTTTTAAGTCTTTTAGAAGTATCAGGTACTTGT-ACGTCTAAGGCATCTCC-
128 CCCATCCACATCCTTTTTAAGTCTTTTAGAAGTATCAGATACTT-TCACGTCGAAGGCATC-CCT
* * **
248631 TAAAGACATTTTCGT-TTATTC-TAAAA-CTAACTCTTAGGCTGCCACC-GAGTTTGCTTGTACG
191 TAAAGACATTTTCGTAAT-TTCTTAAAATC-AACTCCTAGGCTGCCACCGGA-TCCGCTTGTACG
* *
248692 CTGAGGGTGGGCATT
253 CCGAAGGTGGGCATT
248707 AAGAGCAGGT
Statistics
Matches: 225, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
305 6 0.03
306 146 0.65
307 70 0.31
308 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (306 bp):
TAAGGCTATCAGGTCTTTTCACGTCAAAGGTATCCCTTAGAGGTATTTTCATAATTTCTTAAAAT
CGAGTCTTAGGTTGTCACCGGGTACGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCACCC
ATCCACATCCTTTTTAAGTCTTTTAGAAGTATCAGATACTTTCACGTCGAAGGCATCCCTTAAAG
ACATTTTCGTAATTTCTTAAAATCAACTCCTAGGCTGCCACCGGATCCGCTTGTACGCCGAAGGT
GGGCATTTAGGATAGGTCACCCCATACACATCCTTTTTAAGTCCTT
Found at i:250387 original size:18 final size:18
Alignment explanation
Indices: 250343--250384 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
250333 ATATAAATTT
*
250343 TATAATTTTA-GATATAA
1 TATAATTATACGATATAA
*
250360 TCTAATTATACGATATAAA
1 TATAATTATACGATAT-AA
250379 TATAAT
1 TATAAT
250385 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
TATAATTATACGATATAA
Found at i:252018 original size:15 final size:14
Alignment explanation
Indices: 251985--252022 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
251975 TCATAAATAA
251985 TAAATTTA-ATATC
1 TAAATTTATATATC
*
251998 TAAATTTATATTATT
1 TAAATTTATA-TATC
252013 TAAATTTATA
1 TAAATTTATA
252023 AAAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATTTATATATC
Found at i:252048 original size:19 final size:19
Alignment explanation
Indices: 252026--252070 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
252016 ATTTATAAAA
252026 AATAATTAAAA-TAATATTG
1 AATAATTAAAAGTAA-ATTG
* *
252045 AATATTTAAAAGTAAATTT
1 AATAATTAAAAGTAAATTG
252064 AATAATT
1 AATAATT
252071 TTTATATCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATAATTAAAAGTAAATTG
Found at i:252113 original size:21 final size:21
Alignment explanation
Indices: 252071--252113 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
252061 TTTAATAATT
* *
252071 TTTATATCTGTTTATATTTTA
1 TTTATATATGTTTATATATTA
252092 TTTATATAT-TTTATTATATTA
1 TTTATATATGTTTA-TATATTA
252113 T
1 T
252114 AATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATATATGTTTATATATTA
Found at i:252142 original size:33 final size:31
Alignment explanation
Indices: 252105--252232 Score: 95
Period size: 35 Copynumber: 4.0 Consensus size: 31
252095 ATATATTTTA
252105 TTATATTATAATTAAATTTAAAATATTTTATA-
1 TTATATTAT-A-TAAATTTAAAATATTTTATAT
* * *
252137 TT-TA-TATA-AATTTTAATATA-TTAATAAT
1 TTATATTATATAAATTTAAAATATTTTAT-AT
*
252165 TTATATTATATAAAATTTTAAATATTTATATATTT
1 TTATATTATAT-AAATTTAAAATATTT-TATA--T
*
252200 TTATATTATATAATATTTAATAATTTTTTATAT
1 TTATATTATATAA-ATTTAA-AATATTTTATAT
252233 CGTATTTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
26 4 0.05
27 11 0.15
28 2 0.03
29 3 0.04
30 7 0.09
31 2 0.03
32 11 0.15
33 4 0.05
34 4 0.05
35 21 0.28
36 6 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTATATTATATAAATTTAAAATATTTTATAT
Found at i:252214 original size:60 final size:58
Alignment explanation
Indices: 252105--252232 Score: 156
Period size: 59 Copynumber: 2.2 Consensus size: 58
252095 ATATATTTTA
*
252105 TTATATTATAATTAAATTTAAAATATTTTATATTTATATAAATTTTAATATATTAATAAT
1 TTATATTAT-ATAAAATTTAAAATATTTTATATTTATATAAATTTTAATAT-TTAATAAT
* *
252165 TTATATTATATAAAATTTTAAATATTTATATATTT-T-TATATTATATAATATTTAATAAT
1 TTATATTATATAAAATTTAAAATATTT-TATATTTATATAAATT-T-TAATATTTAATAAT
252224 TT-T-TTATAT
1 TTATATTATAT
252233 CGTATTTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
57 6 0.10
58 6 0.10
59 28 0.45
60 22 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (58 bp):
TTATATTATATAAAATTTAAAATATTTTATATTTATATAAATTTTAATATTTAATAAT
Found at i:252232 original size:35 final size:35
Alignment explanation
Indices: 252130--252232 Score: 106
Period size: 35 Copynumber: 3.0 Consensus size: 35
252120 ATTTAAAATA
* *
252130 TTTTATATTTATATAAATTTTAATATA-TTA-ATA-
1 TTTTATA-TTATATAAAATTTAAAATATTTATATAT
* *
252163 ATTTATATTATATAAAATTTTAAATATTTATATAT
1 TTTTATATTATATAAAATTTAAAATATTTATATAT
* *
252198 TTTTATATTATATAATATTTAATAAT-TTTTTATAT
1 TTTTATATTATATAAAATTTAA-AATATTTATATAT
252233 CGTATTTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 16 0.28
33 9 0.16
34 3 0.05
35 27 0.47
36 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TTTTATATTATATAAAATTTAAAATATTTATATAT
Found at i:257718 original size:15 final size:16
Alignment explanation
Indices: 257695--257735 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
257685 AACATATTTT
257695 TATAAAATTTAT-TTA
1 TATAAAATTTATATTA
257710 T-TAATAATTTATATTA
1 TATAA-AATTTATATTA
257726 TATAAAATTT
1 TATAAAATTT
257736 TAAATACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 8 0.35
16 9 0.39
17 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAAAATTTATATTA
Found at i:257737 original size:17 final size:15
Alignment explanation
Indices: 257689--257735 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
257679 ATATTTAACA
*
257689 TATTTTTATAAAATT
1 TATTTATATAAAATT
257704 TATTTAT-TAATAATT
1 TATTTATATAA-AATT
257719 TATATTATATAAAATT
1 TAT-TTATATAAAATT
257735 T
1 T
257736 TAAATACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 13 0.46
16 9 0.32
17 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATATAAAATT
Found at i:259052 original size:14 final size:15
Alignment explanation
Indices: 259035--259078 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
259025 TTTAATTTTT
259035 TAATTAAAATTAA-A
1 TAATTAAAATTAAGA
259049 TAATTAAAA-TAAGA
1 TAATTAAAATTAAGA
*
259063 TAA--AAAATTAATA
1 TAATTAAAATTAAGA
259076 TAA
1 TAA
259079 AAATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.15
13 10 0.37
14 13 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
TAATTAAAATTAAGA
Found at i:259105 original size:26 final size:26
Alignment explanation
Indices: 259078--259127 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
259068 AATTAATATA
259078 AAAATATAATAT-ATATAAA-TATTTT
1 AAAAT-TAATATAATATAAATTATTTT
*
259103 AAAATTTATATAATATAAATTATTT
1 AAAATTAATATAATATAAATTATTT
259128 ATTTATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAATTAATATAATATAAATTATTTT
Found at i:259113 original size:29 final size:32
Alignment explanation
Indices: 259081--259147 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
259071 TAATATAAAA
*
259081 ATATAATATATA-TAAATATTT-T-AAAATTT
1 ATATAATATAAATTAAATATTTATCAAAATTT
**
259110 ATATAATATAAATTATTTATTTATCAAAATTT
1 ATATAATATAAATTAAATATTTATCAAAATTT
259142 ATATAA
1 ATATAA
259148 AAAATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.34
30 7 0.22
31 1 0.03
32 13 0.41
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (32 bp):
ATATAATATAAATTAAATATTTATCAAAATTT
Found at i:259464 original size:21 final size:22
Alignment explanation
Indices: 259400--259452 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
259390 AGGTTTTAAA
* *
259400 ATTTTATTAAATATGTTGT-ATT
1 ATTTT-TTTAATATATTGTAATT
*
259422 ATTTTTTTAATATATTTTAATT
1 ATTTTTTTAATATATTGTAATT
259444 ATTTTTTTA
1 ATTTTTTTA
259453 TTTTATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
ATTTTTTTAATATATTGTAATT
Found at i:260584 original size:14 final size:14
Alignment explanation
Indices: 260565--260603 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
260555 AATATATCAT
260565 TTAAAAATAAAAAA
1 TTAAAAATAAAAAA
*
260579 TTAAAACTAAAAAAA
1 TTAAAAAT-AAAAAA
260594 TTAAAAATAA
1 TTAAAAATAA
260604 TTAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
TTAAAAATAAAAAA
Found at i:272399 original size:19 final size:20
Alignment explanation
Indices: 272354--272405 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
272344 TTACAAGCCA
*
272354 ATGTATCGATACATTTTGTG
1 ATGTATCGATACATATTGTG
272374 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGTG
272394 -TGTATCGATACA
1 ATGTATCGATACA
272406 AATTTGGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATATTGTG
Found at i:272486 original size:20 final size:21
Alignment explanation
Indices: 272439--272491 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
272429 GCCAATGACC
*
272439 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
272460 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
272480 TGTATCGATACA
1 TGTATCGATACA
272492 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:272497 original size:13 final size:13
Alignment explanation
Indices: 272479--272503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272469 ACATTTGGTC
272479 ATGTATCGATACA
1 ATGTATCGATACA
272492 ATGTATCGATAC
1 ATGTATCGATAC
272504 TGTGCAAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:274523 original size:21 final size:20
Alignment explanation
Indices: 274483--274524 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
274473 TGGGGACTGC
* *
274483 CCGGTTGCGACCTGGGGGTG
1 CCGGTCGCGACCTGGAGGTG
274503 CCGGTCGCGACCTGGTAGGTG
1 CCGGTCGCGACCTGG-AGGTG
274524 C
1 C
274525 TGCCTAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.07, C:0.29, G:0.45, T:0.19
Consensus pattern (20 bp):
CCGGTCGCGACCTGGAGGTG
Found at i:274976 original size:13 final size:13
Alignment explanation
Indices: 274958--275045 Score: 149
Period size: 13 Copynumber: 6.8 Consensus size: 13
274948 ATAAACCCTT
*
274958 TGTATCGATACAC
1 TGTATCGATACAA
274971 TGTATCGATACAA
1 TGTATCGATACAA
*
274984 TGTATCGATACAC
1 TGTATCGATACAA
274997 TGTATCGATACAA
1 TGTATCGATACAA
*
275010 TGTATCGATACAC
1 TGTATCGATACAA
275023 TGTATCGATACAA
1 TGTATCGATACAA
275036 TGTATCGATA
1 TGTATCGATA
275046 TAGAGAATGC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:274987 original size:26 final size:26
Alignment explanation
Indices: 274958--275045 Score: 176
Period size: 26 Copynumber: 3.4 Consensus size: 26
274948 ATAAACCCTT
274958 TGTATCGATACACTGTATCGATACAA
1 TGTATCGATACACTGTATCGATACAA
274984 TGTATCGATACACTGTATCGATACAA
1 TGTATCGATACACTGTATCGATACAA
275010 TGTATCGATACACTGTATCGATACAA
1 TGTATCGATACACTGTATCGATACAA
275036 TGTATCGATA
1 TGTATCGATA
275046 TAGAGAATGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (26 bp):
TGTATCGATACACTGTATCGATACAA
Found at i:275263 original size:8 final size:8
Alignment explanation
Indices: 275250--275275 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
275240 AACATCATTC
275250 ATCACAAA
1 ATCACAAA
275258 ATCACAAA
1 ATCACAAA
275266 ATCACAAA
1 ATCACAAA
275274 AT
1 AT
275276 TGAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:281242 original size:19 final size:20
Alignment explanation
Indices: 281197--281248 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
281187 TTACAAGCCA
*
281197 ATGTATCGATACATTTTGTG
1 ATGTATCGATACATATTGTG
281217 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGTG
281237 -TGTATCGATACA
1 ATGTATCGATACA
281249 AATTTGGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATATTGTG
Found at i:281329 original size:20 final size:21
Alignment explanation
Indices: 281285--281334 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
281275 AATGACCTGA
**
281285 ATCGATACATTCTTTTCAAGT
1 ATCGATACATTCTGGTCAAGT
*
281306 ATCGATACATT-TGGTCATGT
1 ATCGATACATTCTGGTCAAGT
281326 ATCGATACA
1 ATCGATACA
281335 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (21 bp):
ATCGATACATTCTGGTCAAGT
Found at i:281340 original size:13 final size:13
Alignment explanation
Indices: 281322--281346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
281312 ACATTTGGTC
281322 ATGTATCGATACA
1 ATGTATCGATACA
281335 ATGTATCGATAC
1 ATGTATCGATAC
281347 TGTGCAAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:285554 original size:20 final size:21
Alignment explanation
Indices: 285526--285565 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
285516 TAATAGCTAT
285526 AGAAAATTAT-GATAAGATGA
1 AGAAAATTATAGATAAGATGA
* *
285546 AGAATATTATAGTTAAGATG
1 AGAAAATTATAGATAAGATG
285566 CTAACCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
AGAAAATTATAGATAAGATGA
Found at i:291774 original size:20 final size:21
Alignment explanation
Indices: 291746--291785 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
291736 TAATAGCTAT
291746 AGAAAATTAT-GATAAGATGA
1 AGAAAATTATAGATAAGATGA
* *
291766 AGAATATTATAGTTAAGATG
1 AGAAAATTATAGATAAGATG
291786 CTAACCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
AGAAAATTATAGATAAGATGA
Found at i:310333 original size:20 final size:21
Alignment explanation
Indices: 310305--310344 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
310295 TAATAGCTAT
310305 AGAAAATTAT-GATAAGATGA
1 AGAAAATTATAGATAAGATGA
* *
310325 AGAATATTATAGTTAAGATG
1 AGAAAATTATAGATAAGATG
310345 CTAACCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
AGAAAATTATAGATAAGATGA
Done.