Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1927
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: 302399
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:131358 original size:19 final size:19
Alignment explanation
Indices: 131315--131364 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
131305 TCTTTTGGTA
131315 ATAAA-AATT-TAATTATT
1 ATAAATAATTATAATTATT
** *
131332 ATTTATAATTATAATTGTT
1 ATAAATAATTATAATTATT
131351 ATAAATAAATTATA
1 ATAAAT-AATTATA
131365 TATATAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 3 0.12
18 4 0.16
19 11 0.44
20 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAAATAATTATAATTATT
Found at i:132071 original size:5 final size:5
Alignment explanation
Indices: 132055--132105 Score: 70
Period size: 5 Copynumber: 10.4 Consensus size: 5
132045 TTAAATTTTA
*
132055 AATTT AAATTT AATTT AATTT AATTT AATTT AATTT TATTT -ATTT -ATTT
1 AATTT -AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
132104 AA
1 AA
132106 ATTTTAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
4 8 0.19
5 30 0.70
6 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
AATTT
Found at i:132109 original size:6 final size:6
Alignment explanation
Indices: 132044--132092 Score: 52
Period size: 5 Copynumber: 8.7 Consensus size: 6
132034 TTTAAAATTT
*
132044 TTTAAA TTTTAAA TTTAAA TTT-AA TTT-AA TTT-AA TTT-AA TTTAAT
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
132089 TTTA
1 TTTA
132093 TTTATTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
5 20 0.50
6 14 0.35
7 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:132143 original size:6 final size:6
Alignment explanation
Indices: 132134--132173 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
132124 TTTATTAAAA
* *
132134 TTATTT TTATAT TAATAT TTATATT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATA-T TTATAT TTATAT TTA
132174 AATAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:132148 original size:17 final size:19
Alignment explanation
Indices: 132126--132165 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
132116 TCATATATTT
132126 TATTAA-AATTAT-TTTTA
1 TATTAATAATTATATTTTA
*
132143 TATTAATATTTATATTTTA
1 TATTAATAATTATATTTTA
132162 TATT
1 TATT
132166 TATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTAATAATTATATTTTA
Found at i:132162 original size:19 final size:18
Alignment explanation
Indices: 132134--132173 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
132124 TTTATTAAAA
132134 TTATTTTTATATTAATAT
1 TTATTTTTATATTAATAT
*
132152 TTATATTTTATATTTATAT
1 TTAT-TTTTATATTAATAT
132171 TTA
1 TTA
132174 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTTATATTAATAT
Found at i:132166 original size:13 final size:13
Alignment explanation
Indices: 132134--132172 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
132124 TTTATTAAAA
*
132134 TTATTTTTATA-T
1 TTATATTTATATT
*
132146 TAATATTTATATT
1 TTATATTTATATT
132159 TTATATTTATATT
1 TTATATTTATATT
132172 T
1 T
132173 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATTTATATT
Found at i:133894 original size:92 final size:92
Alignment explanation
Indices: 133737--133923 Score: 320
Period size: 92 Copynumber: 2.0 Consensus size: 92
133727 GAAATTATAT
* * *
133737 AAACACCCCTATATGATTTGGAAATGCATGAAAATGACTTTAGAATGTGTCGAAACGTGCCTAAA
1 AAACACCCCTATATGATTTGGAAAGGCATGAAAATGACTTTAGAATATGTCGAAACATGCCTAAA
133802 ACCTAAGGCACATCAATTTCTAAGAGA
66 ACCTAAGGCACATCAATTTCTAAGAGA
**
133829 AAACACCTTTATATGATTTGGAAAGGCATGAAAATGACTTTAGAATATGTCGAAACATGCCTAAA
1 AAACACCCCTATATGATTTGGAAAGGCATGAAAATGACTTTAGAATATGTCGAAACATGCCTAAA
*
133894 ACCTAAGGCACATCAATTTCTAGGAGA
66 ACCTAAGGCACATCAATTTCTAAGAGA
133921 AAA
1 AAA
133924 AATATGTTTG
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (92 bp):
AAACACCCCTATATGATTTGGAAAGGCATGAAAATGACTTTAGAATATGTCGAAACATGCCTAAA
ACCTAAGGCACATCAATTTCTAAGAGA
Found at i:134082 original size:9 final size:9
Alignment explanation
Indices: 134068--134097 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
134058 GAAATTTATC
134068 TTTTTAAAA
1 TTTTTAAAA
134077 TTTTTAAAA
1 TTTTTAAAA
134086 TTTTTAAAA
1 TTTTTAAAA
134095 TTT
1 TTT
134098 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:136515 original size:19 final size:19
Alignment explanation
Indices: 136491--136545 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
136481 TGTATCGATA
*
136491 CATTGTATCGATATATGCT
1 CATTGTATCGATATATACT
*
136510 CATTGTATCGATACATACT
1 CATTGTATCGATATATACT
136529 CAATTGTATCGATATAT
1 C-ATTGTATCGATATAT
136546 CAAACTGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATATATACT
Found at i:136603 original size:20 final size:20
Alignment explanation
Indices: 136578--136627 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
136568 AGTGAAATGC
*
136578 ATCGATACATG-GGACATTGT
1 ATCGATACATGAAGA-ATTGT
136598 ATCGATACATGAAGAATTGT
1 ATCGATACATGAAGAATTGT
136618 ATCGATACAT
1 ATCGATACAT
136628 TAAGCCCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (20 bp):
ATCGATACATGAAGAATTGT
Found at i:137544 original size:14 final size:14
Alignment explanation
Indices: 137463--137545 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 14
137453 TTATTTTTAA
*
137463 ATATT-TATAGTAT
1 ATATTATATAATAT
137476 AATATTATAT-ATAT
1 -ATATTATATAATAT
* * *
137490 ATTTTTAGATGATAT
1 A-TATTATATAATAT
* **
137505 AAATTGCATAATAT
1 ATATTATATAATAT
*
137519 ATATAAATATAATAT
1 ATAT-TATATAATAT
137534 ATATTATATAAT
1 ATATTATATAAT
137546 TGAAAAAGAG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
13 1 0.02
14 32 0.62
15 19 0.37
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (14 bp):
ATATTATATAATAT
Found at i:138672 original size:5 final size:5
Alignment explanation
Indices: 138659--138710 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
138649 TCCTTTTTAA
* * *
138659 TTTTT TTTTC TTTTC TTTTC TTTTC CTTTC GGTGTTC ATTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC --TTTTC -TTTTC TTTTC
138707 TTTT
1 TTTT
138711 TTCAATAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 32 0.82
6 4 0.10
7 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:139321 original size:11 final size:12
Alignment explanation
Indices: 139305--139337 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
139295 GATTCACCTA
139305 TTATAAATTTT-
1 TTATAAATTTTG
139316 TTATAAATTTTG
1 TTATAAATTTTG
*
139328 TTAAAAATTT
1 TTATAAATTT
139338 AATTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TTATAAATTTTG
Found at i:139360 original size:19 final size:18
Alignment explanation
Indices: 139332--139367 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
139322 ATTTTGTTAA
139332 AAATTTAATTTTATATTT
1 AAATTTAATTTTATATTT
*
139350 AAATATTAATTTTTTATT
1 AAAT-TTAATTTTATATT
139368 CAATCAATTC
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAATTTAATTTTATATTT
Found at i:139679 original size:28 final size:28
Alignment explanation
Indices: 139641--139737 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 28
139631 ATATAATATT
*
139641 TAAATA-A-AAATA-ATTTAAATATGATA
1 TAAATATATAAATATATTAAAAT-TGATA
*
139667 TAAATATATAAATATATTAAAATTTATA
1 TAAATATATAAATATATTAAAATTGATA
* *
139695 TAATATATATTATTAATATTTTAAAATTTATA
1 TAA-ATATA-TA--AATATATTAAAATTGATA
*
139727 AAAATATATAA
1 TAAATATATAA
139738 TACTTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 6 0.10
27 1 0.02
28 13 0.22
29 12 0.20
30 4 0.07
31 5 0.08
32 19 0.32
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TAAATATATAAATATATTAAAATTGATA
Found at i:139750 original size:32 final size:31
Alignment explanation
Indices: 139650--139751 Score: 81
Period size: 32 Copynumber: 3.3 Consensus size: 31
139640 TTAAATAAAA
*
139650 ATAATTT-AAATATGATATAAATATATAA-A-T
1 ATAATTTAAAAT-TTATA-AAATATATAATATT
* *
139680 AT-A-TTAAAATTTATATAATATATATTATT
1 ATAATTTAAAATTTATAAAATATATAATATT
*
139709 AATATTTTAAAATTTATAAAAATATATAATACTT
1 -ATAATTTAAAATTTAT-AAAATATATAATA-TT
139743 -TAATTTAAA
1 ATAATTTAAA
139752 TTACAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
27 8 0.14
28 7 0.12
29 6 0.11
30 4 0.07
32 19 0.33
33 11 0.19
34 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
ATAATTTAAAATTTATAAAATATATAATATT
Found at i:140106 original size:18 final size:18
Alignment explanation
Indices: 140077--140126 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
140067 AAATCTATTT
140077 ATAAAT-AATAAATAAAA
1 ATAAATAAATAAATAAAA
** **
140094 ATATTTAAATAAATTTAA
1 ATAAATAAATAAATAAAA
140112 ATAAATAAATAAATA
1 ATAAATAAATAAATA
140127 TGTTTATTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAATAAATAAAA
Found at i:140114 original size:31 final size:30
Alignment explanation
Indices: 140078--140149 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
140068 AATCTATTTA
140078 TAAATAATAAATAAAAATATTTAAATAAATT
1 TAAATAATAAATAAAAATATTT-AATAAATT
* * * *
140109 TAAATAAATAAATAAATATGTTTATTAATTT
1 TAAAT-AATAAATAAAAATATTTAATAAATT
140140 TAAAT-ATAAA
1 TAAATAATAAA
140150 ATAATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.14
31 16 0.44
32 15 0.42
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TAAATAATAAATAAAAATATTTAATAAATT
Found at i:147376 original size:33 final size:33
Alignment explanation
Indices: 147338--147404 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
147328 TGGCAGCTGT
147338 GTCCAACACTCCAATTTGCAATATAACTAGCAA
1 GTCCAACACTCCAATTTGCAATATAACTAGCAA
* * *
147371 GTCCAACATTCTAATTTGCAATATGACTAGCAA
1 GTCCAACACTCCAATTTGCAATATAACTAGCAA
147404 G
1 G
147405 ATTCACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (33 bp):
GTCCAACACTCCAATTTGCAATATAACTAGCAA
Found at i:149157 original size:92 final size:89
Alignment explanation
Indices: 149000--149180 Score: 326
Period size: 92 Copynumber: 2.0 Consensus size: 89
148990 GCTACTTCAC
149000 ATTCCCTTTCTTGTCGACTTTTGGGTGCTTAATTAATATCATAAGATAATTACCAAAAAAAAAAA
1 ATTCCCTTTCTTGTCGACTTTTGGGTGCTTAATTAATATCATAAGATAATTACC--AAAAAAAAA
*
149065 AAAAGTTCAAATCAAACCAACTTTAAG
64 AAAA-TGCAAATCAAACCAACTTTAAG
149092 ATTCCCTTTCTTGTCGACTTTTGGGTGCTTAATTAATATCATAAGATAATTACCAAAAAAAAAAA
1 ATTCCCTTTCTTGTCGACTTTTGGGTGCTTAATTAATATCATAAGATAATTACCAAAAAAAAAAA
149157 AATGCAAATCAAACCAACTTTAAG
66 AATGCAAATCAAACCAACTTTAAG
149181 CTTTAAAAGT
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
89 21 0.24
90 13 0.15
92 54 0.61
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (89 bp):
ATTCCCTTTCTTGTCGACTTTTGGGTGCTTAATTAATATCATAAGATAATTACCAAAAAAAAAAA
AATGCAAATCAAACCAACTTTAAG
Found at i:151077 original size:48 final size:47
Alignment explanation
Indices: 151025--151127 Score: 136
Period size: 48 Copynumber: 2.2 Consensus size: 47
151015 AAACAAATTA
*
151025 ATAAAATAAGTCAAATTCAAGCTATTATTAAATATAAAATAATAAAAT
1 ATAAAATAA-TCAAATTCAAGCTATTATTAAATATAAAATAATAAAAC
* * * *
151073 ATAAATATTATTAAATTTAAGTTATTATTAAATATAAAATAATAAAAC
1 ATAAA-ATAATCAAATTCAAGCTATTATTAAATATAAAATAATAAAAC
151121 A-AAAATA
1 ATAAAATA
151128 TTATTAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 2 0.04
47 3 0.06
48 40 0.83
49 3 0.06
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (47 bp):
ATAAAATAATCAAATTCAAGCTATTATTAAATATAAAATAATAAAAC
Found at i:151128 original size:48 final size:48
Alignment explanation
Indices: 151037--151134 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
151027 AAAATAAGTC
* *
151037 AAATTCAAGCTATTATTAAATATAAAATAATAAAATATAAATATTATT
1 AAATTCAAGCTATTATTAAATATAAAATAATAAAACAAAAATATTATT
* *
151085 AAATTTAAGTTATTATTAAATATAAAATAATAAAACAAAAATATTATT
1 AAATTCAAGCTATTATTAAATATAAAATAATAAAACAAAAATATTATT
151133 AA
1 AA
151135 TTATGTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (48 bp):
AAATTCAAGCTATTATTAAATATAAAATAATAAAACAAAAATATTATT
Found at i:151153 original size:36 final size:35
Alignment explanation
Indices: 151109--151187 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 35
151099 ATTAAATATA
*
151109 AAAT-AATAAAACAAAAATATTATTAATTATGTTAT
1 AAATAAATAAAA-AAAAATATTACTAATTATGTTAT
* *
151144 AAATAAAT---AAAAGATTTTACTAATTATGTTAT
1 AAATAAATAAAAAAAAATATTACTAATTATGTTAT
*
151176 AACTAAATAAAA
1 AAATAAATAAAA
151188 GATTATCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
32 27 0.75
33 1 0.03
35 5 0.14
36 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (35 bp):
AAATAAATAAAAAAAAATATTACTAATTATGTTAT
Found at i:151503 original size:52 final size:52
Alignment explanation
Indices: 151253--151503 Score: 221
Period size: 52 Copynumber: 4.9 Consensus size: 52
151243 GCTCGCAAAT
* *
151253 TATAATAGAGGGATCTCGCTTATGTCATAGAGATCA-A-A--AGCTTGCAGGC
1 TATAATAGAGAGATCTCG-TTATGTCATAGAGATCATAGATTAGCTTACAGGC
* * * * * *
151302 TACATTAGAAAGATCTCATTATGTCGA-AGAGATTATAGATTAG-TTCACTGGC
1 TATAATAGAGAGATCTCGTTATGTC-ATAGAGATCATAGATTAGCTT-ACAGGC
* * * * *
151354 TATACTAGAGAGATCTCGTTATGTCATAGAGATCGTAGATTAACTTATAGGT
1 TATAATAGAGAGATCTCGTTATGTCATAGAGATCATAGATTAGCTTACAGGC
* * * *
151406 TATAATAGA-AGTATCTTTC-TTATGTCACAAAAATCATAGATTAGCTTAAAGGC
1 TATAATAGAGAG-ATC--TCGTTATGTCATAGAGATCATAGATTAGCTTACAGGC
* *
151459 TATATTAGAGAGATCTCGTTATGTCGTAGAGATCATAGATTAGCT
1 TATAATAGAGAGATCTCGTTATGTCATAGAGATCATAGATTAGCT
151504 CATAAGGTTT
Statistics
Matches: 158, Mismatches: 31, Indels: 23
0.75 0.15 0.11
Matches are distributed among these distances:
48 14 0.09
49 15 0.09
50 1 0.01
51 7 0.04
52 77 0.49
53 40 0.25
54 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (52 bp):
TATAATAGAGAGATCTCGTTATGTCATAGAGATCATAGATTAGCTTACAGGC
Found at i:152366 original size:58 final size:58
Alignment explanation
Indices: 152258--152472 Score: 208
Period size: 58 Copynumber: 3.7 Consensus size: 58
152248 CCTATGTGTT
* *
152258 TTGAAGTCATTTTAGGTCATTTTTTATGATCT-AGGAACTTTAATGTAATTTTATGAAT-
1 TTGATGTCA-TTTAGGTCATTTTTTATGATCTAAGG-ACTTTTATGTAATTTTATGAATG
* **
152316 TTCGAT-TCCATTCT-GGTCATTTTTCATGATCTAAGGACTTTTATAAAATTTTATGAATG
1 TT-GATGT-CATT-TAGGTCATTTTTTATGATCTAAGGACTTTTATGTAATTTTATGAATG
* *** *
152375 TTGATGTCATTTAGGTCATTTTTTATGAT-TAAGGGATTTTTATGTAATTTTACCTATA
1 TTGATGTCATTTAGGTCATTTTTTATGATCTAA-GGACTTTTATGTAATTTTATGAATG
** * *
152433 TTGGGGTCATTTAGGTCATTTTTCATGATCTAGGGA-TTTT
1 TTGATGTCATTTAGGTCATTTTTTATGATCTAAGGACTTTT
152473 CATGCAAATG
Statistics
Matches: 131, Mismatches: 17, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
57 8 0.06
58 110 0.84
59 13 0.10
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (58 bp):
TTGATGTCATTTAGGTCATTTTTTATGATCTAAGGACTTTTATGTAATTTTATGAATG
Found at i:156498 original size:88 final size:88
Alignment explanation
Indices: 156393--156729 Score: 306
Period size: 88 Copynumber: 3.8 Consensus size: 88
156383 CAAATCTTTT
* * * * *
156393 CATTGAAGACTTGTTAAAAACTTTTTAAATGCTTTAGATTCCCCTATCAAAAACTTTTTAAAAAC
1 CATTAAAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTCCCCTATCAAAGACTTGTTAAAAAC
*
156458 TTCTTAAATGTTTCGAATTCCTC
66 TTCTTAAATGTTTCAAATTCCTC
* * ** ** * *** *
156481 TACTTAAAG-CTTGTTAAAAACTTCTTAAATTCTTTGGATTCCTTTGT-TTTGGCTTGTTAAAAA
1 CA-TTAAAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTCCCCTATCAAAGACTTGTTAAAAA
156544 CTTCTTAAATGTTTCAAATTCCTC
65 CTTCTTAAATGTTTCAAATTCCTC
* * ** * * *
156568 CAATGAAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTTATCC-ATCAGAGACGTGTTAAAAT
1 CATTAAAGACTTGTTAAAAACTTCTTAAATGCTTCAGA-TTCCCCTATCAAAGACTTGTTAAAAA
* * *
156632 CTTATTAAATGCTTCAAAATT-TTC
65 CTTCTTAAATGTTTC-AAATTCCTC
* * * * * *
156656 GATCAAAGACTTGTTGAAAACTTCTTAAATGCTTCAAATTTCCCTA-CGAAAGACTTATTAAAAA
1 CATTAAAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTCCCCTATC-AAAGACTTGTTAAAAA
156720 CTTCTTAAAT
65 CTTCTTAAAT
156730 ACTTTAGATT
Statistics
Matches: 194, Mismatches: 48, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
86 4 0.02
87 66 0.34
88 114 0.59
89 10 0.05
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (88 bp):
CATTAAAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTCCCCTATCAAAGACTTGTTAAAAAC
TTCTTAAATGTTTCAAATTCCTC
Found at i:156756 original size:44 final size:43
Alignment explanation
Indices: 156398--156743 Score: 252
Period size: 44 Copynumber: 7.9 Consensus size: 43
156388 CTTTTCATTG
* *
156398 AAGACTTGTTAAAAACTTTTTAAATGCTTTAGATTCCCCTATCA
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAGATTCCTCTAT-A
* * *
156442 AAAACTTTTTAAAAACTTCTTAAATG-TTTCGAATTCCTCTACTTA
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAG-ATTCCTCTA--TA
* * * * *
156487 AAG-CTTGTTAAAAACTTCTTAAATTCTTTGGATTCCTTTGTT
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAGATTCCTCTATA
** * * * *
156529 TTGGCTTGTTAAAAACTTCTTAAATG-TTTCAAATTCCTCCAATG
1 AAGACTTGTTAAAAACTTCTTAAATGCTTT-AGATTCCT-CTATA
* ** *
156573 AAGACTTGTTAAAAACTTCTTAAATGCTTCAGATTTATCCATCA
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAGATTCCTCTAT-A
* * * * * * * *
156617 GAGACGTGTTAAAATCTTATTAAATGCTTCAAAATT-TTCGATCA
1 AAGACTTGTTAAAAACTTCTTAAATGCTT-TAGATTCCTCTAT-A
* * * *
156661 AAGACTTGTTGAAAACTTCTTAAATGCTTCAAATTTCC-CTACGA
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAGA-TTCCTCTA-TA
* *
156705 AAGACTTATTAAAAACTTCTTAAATACTTTAGATTCCTC
1 AAGACTTGTTAAAAACTTCTTAAATGCTTTAGATTCCTC
156744 AACTAAAAAC
Statistics
Matches: 236, Mismatches: 52, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
42 5 0.02
43 41 0.17
44 176 0.75
45 13 0.06
46 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (43 bp):
AAGACTTGTTAAAAACTTCTTAAATGCTTTAGATTCCTCTATA
Found at i:159669 original size:148 final size:148
Alignment explanation
Indices: 159496--159791 Score: 425
Period size: 148 Copynumber: 2.0 Consensus size: 148
159486 AGATAATAAA
* ** * *
159496 TTTATTTAATTTTTAATTTTTGAAAAATTCATTTTGTACTTTAATGGAGAACTGAAAAGATATGA
1 TTTATTTAATTTTAAATTTTTGAAAAATTCATTTAATACCTTAATGGAGAACTGAAAAGATACGA
* * * * *
159561 CAAGTTTTGAA-GATTTTTATACTCCTATGAAAAACCAT-AGAAATATTATAAATCTTGAAAAAT
66 AAAGTTTT-AAGGATTTTTATACCCCTACGAAAAACCATAAG-AATATTAGAAATCTTAAAAAAT
* *
159624 TAAGATAATAATTTTTATTT
129 TAAGATAATAAATCTTATTT
* *
159644 TTTATTTAATTTTAAATTTTTGAAAAATTTATTTAATACCTTAATGGAGAATTGAAAAGATACGA
1 TTTATTTAATTTTAAATTTTTGAAAAATTCATTTAATACCTTAATGGAGAACTGAAAAGATACGA
*
159709 AAAGTTTTAAGGATTTTTATACCCCTACGAAAAACCATAAGAATATTAGAAATCTTAAAAAATTC
66 AAAGTTTTAAGGATTTTTATACCCCTACGAAAAACCATAAGAATATTAGAAATCTTAAAAAATTA
159774 AGATAATAAATCTTATTT
131 AGATAATAAATCTTATTT
159792 AGTGATAAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
147 2 0.02
148 127 0.97
149 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (148 bp):
TTTATTTAATTTTAAATTTTTGAAAAATTCATTTAATACCTTAATGGAGAACTGAAAAGATACGA
AAAGTTTTAAGGATTTTTATACCCCTACGAAAAACCATAAGAATATTAGAAATCTTAAAAAATTA
AGATAATAAATCTTATTT
Found at i:163729 original size:18 final size:18
Alignment explanation
Indices: 163706--163740 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
163696 CCATTATCAT
163706 GTTTTTCGAAGACATTTG
1 GTTTTTCGAAGACATTTG
*
163724 GTTTTTGGAAGACATTT
1 GTTTTTCGAAGACATTT
163741 TATCTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (18 bp):
GTTTTTCGAAGACATTTG
Found at i:163748 original size:19 final size:18
Alignment explanation
Indices: 163707--163758 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
163697 CATTATCATG
*
163707 TTTTTCGAAGACATTTGG
1 TTTTTCGAAGACATTTGA
* *
163725 TTTTTGGAAGACATTTTA
1 TTTTTCGAAGACATTTGA
*
163743 TCTTTTC-AAAACATTT
1 T-TTTTCGAAGACATTT
163759 AAAATATGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (18 bp):
TTTTTCGAAGACATTTGA
Found at i:166354 original size:28 final size:28
Alignment explanation
Indices: 166335--166406 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
166325 GTTGACTTGG
166335 AGCAAGTTGAGTAGAGTGGTTAACCTGA
1 AGCAAGTTGAGTAGAGTGGTTAACCTGA
* *
166363 AGCAAGTTGAGTAGAGTGGTCAATCTGA
1 AGCAAGTTGAGTAGAGTGGTTAACCTGA
* *
166391 AGCATGTTGGGTAGAG
1 AGCAAGTTGAGTAGAG
166407 CAATCAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.10, G:0.35, T:0.25
Consensus pattern (28 bp):
AGCAAGTTGAGTAGAGTGGTTAACCTGA
Found at i:167672 original size:33 final size:32
Alignment explanation
Indices: 167625--167692 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
167615 CGTTACAAGC
*
167625 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCAATACATCTT-GT-ATGTATCGATA
167658 CAATGTATCAATACATCTTGTATGTATCGATA
1 CAATGTATCAATACATCTTGTATGTATCGATA
167690 CAA
1 CAA
167693 ACAGTTAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATCTTGTATGTATCGATA
Found at i:167779 original size:13 final size:13
Alignment explanation
Indices: 167761--167785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
167751 TACAGTGGTC
167761 ATGTATCGATACA
1 ATGTATCGATACA
167774 ATGTATCGATAC
1 ATGTATCGATAC
167786 TGTGCATTAT
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:167803 original size:33 final size:32
Alignment explanation
Indices: 167744--167806 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
167734 ATCTTTGCAA
*
167744 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
167776 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
167807 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:168417 original size:43 final size:43
Alignment explanation
Indices: 168368--168503 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
168358 ATAAAAAAAA
*
168368 TTCTCCCCCTTAATAAGGCAATTTCCTTTAATCACATGTTTCC
1 TTCTCCCCCTTAATAAGGAAATTTCCTTTAATCACATGTTTCC
* * * * **
168411 TTCTCCCCCTTAATCA-TAAATTT-ATTT-A-CAGA-AATT-C
1 TTCTCCCCCTTAATAAGGAAATTTCCTTTAATCACATGTTTCC
*
168448 -TCTCCCCCTTAATAAGGTAATTTCCTTTAATCACATGTTTCC
1 TTCTCCCCCTTAATAAGGAAATTTCCTTTAATCACATGTTTCC
168490 TTCTCCCCCTTAAT
1 TTCTCCCCCTTAAT
168504 CATAAATTTA
Statistics
Matches: 72, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
36 14 0.19
37 6 0.08
38 5 0.07
39 4 0.06
40 4 0.06
41 5 0.07
42 6 0.08
43 28 0.39
ACGTcount: A:0.25, C:0.29, G:0.05, T:0.40
Consensus pattern (43 bp):
TTCTCCCCCTTAATAAGGAAATTTCCTTTAATCACATGTTTCC
Found at i:168456 original size:36 final size:36
Alignment explanation
Indices: 168412--168530 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 36
168402 CATGTTTCCT
168412 TCTCCCCCTTAATCATAAATTTATTTACAGAAATTC
1 TCTCCCCCTTAATCATAAATTTATTTACAGAAATTC
* * * **
168448 TCTCCCCCTTAATAAGGT-AATTTCCTTTAATCACATGTTTCC
1 TCTCCCCCTTAATCA--TAAATTT-ATTT-A-CAGA-AATT-C
168490 TTCTCCCCCTTAATCATAAATTTATTTACAGAAATTC
1 -TCTCCCCCTTAATCATAAATTTATTTACAGAAATTC
168527 TCTC
1 TCTC
168531 ATCCTTTTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
36 18 0.28
37 6 0.09
38 6 0.09
39 4 0.06
40 4 0.06
41 6 0.09
42 6 0.09
43 14 0.22
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (36 bp):
TCTCCCCCTTAATCATAAATTTATTTACAGAAATTC
Found at i:168460 original size:79 final size:79
Alignment explanation
Indices: 168369--168530 Score: 315
Period size: 79 Copynumber: 2.1 Consensus size: 79
168359 TAAAAAAAAT
168369 TCTCCCCCTTAATAAGGCAATTTCCTTTAATCACATGTTTCCTTCTCCCCCTTAATCATAAATTT
1 TCTCCCCCTTAATAAGGCAATTTCCTTTAATCACATGTTTCCTTCTCCCCCTTAATCATAAATTT
168434 ATTTACAGAAATTC
66 ATTTACAGAAATTC
*
168448 TCTCCCCCTTAATAAGGTAATTTCCTTTAATCACATGTTTCCTTCTCCCCCTTAATCATAAATTT
1 TCTCCCCCTTAATAAGGCAATTTCCTTTAATCACATGTTTCCTTCTCCCCCTTAATCATAAATTT
168513 ATTTACAGAAATTC
66 ATTTACAGAAATTC
168527 TCTC
1 TCTC
168531 ATCCTTTTTG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.27, C:0.28, G:0.05, T:0.40
Consensus pattern (79 bp):
TCTCCCCCTTAATAAGGCAATTTCCTTTAATCACATGTTTCCTTCTCCCCCTTAATCATAAATTT
ATTTACAGAAATTC
Found at i:170344 original size:13 final size:13
Alignment explanation
Indices: 170322--170359 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
170312 ATAAACCCTT
170322 TGTATCGATA-AA
1 TGTATCGATACAA
*
170334 CTGTATTGATACAA
1 -TGTATCGATACAA
170348 TGTATCGATACA
1 TGTATCGATACA
170360 GAGAATGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:173938 original size:79 final size:79
Alignment explanation
Indices: 173800--174301 Score: 691
Period size: 79 Copynumber: 6.3 Consensus size: 79
173790 TCCGGGTTAA
* * * ***
173800 AGTATCCCCAATTATAAAAAAAATTGATGCTTTAGAAATAAGGGCCGGGGTTGGAGTATCCCCGT
1 AGTATCCCCGATTAT--GAAAAATTGATGTTTTAGAAATAA-AATCGGGGTTGGAGTATCCCC-T
**
173865 -GAAAATAACAAGGTTGG
62 CGAAAATAACGGGGTTGG
* * * * ** *
173882 AGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAGCTAAAATCGGAGTTGGAGTATCCCCTCGAA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
173947 AATAACGGGGTTGG
66 AATAACGGGGTTGG
* *
173961 AGTATTCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
*
174026 AATAACGGGGTTTG
66 AATAACGGGGTTGG
* *
174040 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAATCGGGGTTGGAGTATCCCCTCGGA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
*
174105 AATAACGGGGTTAG
66 AATAACGGGGTTGG
* * * *
174119 AGTATCCCTGATTACGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTTGAGTATCCCCTCGAA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
*
174184 AATAACGGGGTTAG
66 AATAACGGGGTTGG
* * *
174198 AGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCTCTCGGA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
174263 AATAACGGGGTTGG
66 AATAACGGGGTTGG
*
174277 AGTATCCCCGATTGTGAAAAATTGA
1 AGTATCCCCGATTATGAAAAATTGA
174302 GAAAATTAAA
Statistics
Matches: 373, Mismatches: 46, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
78 1 0.00
79 342 0.92
80 17 0.05
82 13 0.03
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
AATAACGGGGTTGG
Found at i:175734 original size:21 final size:21
Alignment explanation
Indices: 175710--175761 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
175700 TATGCCCATC
*
175710 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
175731 ATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
175752 ATTCCATGCC
1 ATTCCATGCC
175762 CATCATTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (21 bp):
ATTCCATGCCTCCATTTTTAT
Found at i:175770 original size:35 final size:35
Alignment explanation
Indices: 175731--175964 Score: 414
Period size: 35 Copynumber: 6.7 Consensus size: 35
175721 TCATTTTTAT
*
175731 ATTCCATGCCTCCATTTTTATATTCCATGCCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
* * *
175766 ATTCCTTGACTTCATTTTTATATTCCATGGCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
175801 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
*
175836 ATTCCATGCCTCCATTTTTATATTCCATGCCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
*
175871 ATTCCATGCCTTCTTTTTTATATTCCATGCCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
175906 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
1 ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
175941 ATTCCATGCCTTCATTTTTATATT
1 ATTCCATGCCTTCATTTTTATATT
175965 TTTTTTTGAA
Statistics
Matches: 188, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 188 1.00
ACGTcount: A:0.20, C:0.30, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTCCATGCCTTCATTTTTATATTCCATGCCCATC
Found at i:176473 original size:40 final size:41
Alignment explanation
Indices: 176427--176530 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 41
176417 TCCCACTTTT
*
176427 TTGAGGACAAAGAAAAAGAG-AATGAAATAG-GTCCTGCTCC
1 TTGAGGACAAAGAAAAAGAGAAAAGAAA-AGTGTCCTGCTCC
* *
176467 TTGAGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCCTGCTTC
1 TTGAGGACAAAGAAAAAG-AGAAAAGAAAAGTGTCCTGCTCC
176509 TTGAGGACAAAGTGAAAAAGAG
1 TTGAGGACAAA--GAAAAAGAG
176531 TACGTCTCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 17 0.31
41 4 0.07
42 26 0.47
43 2 0.04
44 6 0.11
ACGTcount: A:0.45, C:0.12, G:0.27, T:0.16
Consensus pattern (41 bp):
TTGAGGACAAAGAAAAAGAGAAAAGAAAAGTGTCCTGCTCC
Found at i:176636 original size:119 final size:117
Alignment explanation
Indices: 176423--176638 Score: 262
Period size: 119 Copynumber: 1.8 Consensus size: 117
176413 GGTGTCCCAC
* * * *
176423 TTTTTTGAGGACAAAGAAAAAGAGAATGAAATAGGTCCTGCTCCTTGAGGACAAAGGAAAAGAAG
1 TTTTTCGAGGACAAAGAAAAAGAGAACGAAATACGTCCTGCTCCTTAAGGACAAAGGAAAAGAAG
176488 AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCTCA
66 AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCTCA
* *
176540 TTTTTCGAGGACAAAGGAAAAAAGGGAAACGAAATACTTCCTGCT-CTCTAAGGACAAA-GAAAA
1 TTTTTCGAGGACAAA-G-AAAAAGAG-AACGAAATACGTCCTGCTCCT-TAAGGACAAAGGAAAA
* *
176603 -AGGAAAA-TAAAGTGCGTCCTGC-TCTTTGAGGACAAA
62 GAAGAAAAGAAAAGT--GTCCTGCTTC-TTGAGGACAAA
176639 AGAGAAAAGA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
117 19 0.23
118 9 0.11
119 32 0.38
120 24 0.29
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (117 bp):
TTTTTCGAGGACAAAGAAAAAGAGAACGAAATACGTCCTGCTCCTTAAGGACAAAGGAAAAGAAG
AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCTCA
Found at i:176648 original size:119 final size:117
Alignment explanation
Indices: 176423--176646 Score: 260
Period size: 120 Copynumber: 1.9 Consensus size: 117
176413 GGTGTCCCAC
* * * *
176423 TTTTTTGAGGACAAAGAAAAAGAGAATGAAATAGGTCCTGCTCCTTGAGGACAAAGGAAAAGAAG
1 TTTTTCGAGGACAAAGAAAAAGAGAACGAAATACGTCCTGCTCCTTAAGGACAAAGGAAAAGAAG
*
176488 AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCTCA
66 AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGAGAAAAAGAGTACGTCTCA
* *
176540 TTTTTCGAGGACAAAGGAAAAAAGGGAAACGAAATACTTCCTGCT-CTCTAAGGACAAA-GAAAA
1 TTTTTCGAGGACAAA-G-AAAAAGAG-AACGAAATACGTCCTGCTCCT-TAAGGACAAAGGAAAA
* *
176603 -AGGAAAA-TAAAGTGCGTCCTGC-TCTTTGAGGACAAAAGAGAAAA
62 GAAGAAAAGAAAAGT--GTCCTGCTTC-TTGAGGAC-AAAGAGAAAA
176647 GAAGGGAAAG
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
117 19 0.21
118 9 0.10
119 29 0.32
120 33 0.37
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (117 bp):
TTTTTCGAGGACAAAGAAAAAGAGAACGAAATACGTCCTGCTCCTTAAGGACAAAGGAAAAGAAG
AAAAGAAAAGTGTCCTGCTTCTTGAGGACAAAGAGAAAAAGAGTACGTCTCA
Found at i:176765 original size:61 final size:60
Alignment explanation
Indices: 176664--176806 Score: 198
Period size: 61 Copynumber: 2.4 Consensus size: 60
176654 AAGAAGTGTG
*
176664 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGTCTTTGCAAAA-AGAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTT--AAAAGAGAAAGCA
* * * *
176725 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTAAAA-GAGAAAGCA
*
176786 TCCTGCTCTTTGAGGATTGAA
1 TCCTGCTCTTTGAGGACTGAA
176807 GGTGAAAGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.05
61 69 0.95
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGAGAAAGCA
Found at i:177023 original size:61 final size:60
Alignment explanation
Indices: 176811--177082 Score: 314
Period size: 55 Copynumber: 4.6 Consensus size: 60
176801 ATTGAAGGTG
* *
176811 AAAGGAGAGAGCGTCCTGCTCTTTGAGGACT-AGGAAGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAAAG-GCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTA
* * * *
176872 AAAGG--A---GTCCTGCTCTCTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGATTT-
1 AAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA
*
176926 ----GAAAGGCGTCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA
* * * * *
176982 AAAGGATAAGGCGTCGTGCTCTTTGAGGACTGAAAAATGCCACTAGCTTGTGTGGGCTTTG
1 AAAGGA-AAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA
177043 AAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTG
1 AAAGG-AAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTG
177083 GAAGAAGAAG
Statistics
Matches: 179, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
50 1 0.01
52 1 0.01
55 84 0.47
56 1 0.01
59 1 0.01
60 2 0.01
61 81 0.45
62 8 0.04
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (60 bp):
AAAGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA
Found at i:190622 original size:79 final size:79
Alignment explanation
Indices: 190461--191523 Score: 1468
Period size: 79 Copynumber: 13.4 Consensus size: 79
190451 AAAATAAAAT
** * * ***
190461 CGGGGTTAAAGTATCCCCGATTATAAAAAAAATTGATGCTTTAGAAATAAGGGCCGGGGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTAT--GAAAAATTGATGTTTTAGAAATAA-AATCGGGGTTGGAG
*
190526 TATCCCCGT-GAAAATAA
63 TATCCCC-TCGGAAATAA
* * * * * * ** *
190543 CAGGGTTGAAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAGCTAAAATCGGAGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
* *
190608 CCTCTTGGAAATAA
66 CCCCTCGGAAATAA
* *
190622 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
**
190687 CCCCTCAAAAATAA
66 CCCCTCGGAAATAA
* *
190701 CGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
*
190766 -CCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * * *
190779 TGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
*
190844 CCCCTCAGAAATAA
66 CCCCTCGGAAATAA
** * *
190858 CGGGGTTGGAGTATCCCCGATTACAAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
190923 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * *
190937 CGGGGTTGGAGTATCCCCGATTATGAAAAACTAATGTTTTAGAGATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
**
191002 CCCCTCAAAAATAA
66 CCCCTCGGAAATAA
*
191016 CGGGGTTGGAGTATCCCCGATTACGAAAAATTGATGTTTTAGAAATAAAA-CTGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATC-GGGGTTGGAGTA
191080 TCCCCTCGGAAATAA
65 TCCCCTCGGAAATAA
* *
191095 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
* * *
191160 CCCTTCAGAAAAAA
66 CCCCTCGGAAATAA
* * * *
191174 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAGATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
*
191239 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * * * * *
191253 CGGGTTTAGAGTATCCCCGATTATGAGAAATTAATTTTTTAGAAATAAAATCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
191318 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * *
191332 CGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTA-AAGATAAAATCGGGTTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAA-ATAAAATCGGGGTTGGAGTA
191396 TCCCCTCGGAAATAA
65 TCCCCTCGGAAATAA
*
191411 CGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
*
191476 CCTCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
191490 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTGA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGA
191524 GAAAATTAAA
Statistics
Matches: 881, Mismatches: 94, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
78 77 0.09
79 763 0.87
80 20 0.02
82 21 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:192943 original size:14 final size:14
Alignment explanation
Indices: 192924--192956 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
192914 TTCATTTTTT
192924 ATGCCCATCATTCC
1 ATGCCCATCATTCC
192938 ATGCCCATCATTCC
1 ATGCCCATCATTCC
192952 ATGCC
1 ATGCC
192957 TCCATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.09, T:0.27
Consensus pattern (14 bp):
ATGCCCATCATTCC
Found at i:192973 original size:21 final size:21
Alignment explanation
Indices: 192947--193047 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 21
192937 CATGCCCATC
192947 ATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
*
192968 ATTCCATG-C-CCA----T-C
1 ATTCCATGCCTCCATTTTTAT
*
192982 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
*
193003 ATTCCATG-C-CCA----T-C
1 ATTCCATGCCTCCATTTTTAT
193017 ATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
193038 ATTCCATGCC
1 ATTCCATGCC
193048 CGTCATGCCA
Statistics
Matches: 60, Mismatches: 6, Indels: 28
0.64 0.06 0.30
Matches are distributed among these distances:
14 16 0.27
15 4 0.07
16 5 0.08
19 5 0.08
20 4 0.07
21 26 0.43
ACGTcount: A:0.20, C:0.33, G:0.06, T:0.42
Consensus pattern (21 bp):
ATTCCATGCCTCCATTTTTAT
Found at i:192979 original size:35 final size:35
Alignment explanation
Indices: 192933--193108 Score: 316
Period size: 35 Copynumber: 5.0 Consensus size: 35
192923 TATGCCCATC
*
192933 ATTCCATGCCCATCATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
192968 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
*
193003 ATTCCATGCCCATCATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
* *
193038 ATTCCATGCCCGTCATGCCATGCCTTCATTTTTAT
1 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
193073 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
193108 A
1 A
193109 ATTTTTTTTT
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 134 1.00
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.41
Consensus pattern (35 bp):
ATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
Found at i:196952 original size:13 final size:13
Alignment explanation
Indices: 196934--196959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
196924 ACATTTGGTC
196934 ATGTATCGATACA
1 ATGTATCGATACA
196947 ATGTATCGATACA
1 ATGTATCGATACA
196960 TCTTGTATGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:196954 original size:33 final size:32
Alignment explanation
Indices: 196912--196979 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
196902 CGTTACAAGC
*
196912 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCAATA
196945 CAATGTATCGATACATCTTGTATGTATCAATA
1 CAATGTATCGATACATCTTGTATGTATCAATA
196977 CAA
1 CAA
196980 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCAATA
Found at i:199579 original size:13 final size:13
Alignment explanation
Indices: 199561--199586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199551 TACACAAAGT
199561 ATGTATCGATACA
1 ATGTATCGATACA
199574 ATGTATCGATACA
1 ATGTATCGATACA
199587 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:199584 original size:32 final size:33
Alignment explanation
Indices: 199543--199606 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
199533 TAGCCAAACT
**
199543 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
199575 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
199607 TTGGCCTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:211733 original size:38 final size:37
Alignment explanation
Indices: 211689--211764 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
211679 TATAATATAA
*
211689 ATATAATATCAAAATTAATAAAAAATATATAAAATATT
1 ATATAATATAAAAATTAATAAAAAATATA-AAAATATT
* *
211727 ATATAATATAAAAATTAATATAAAATATAAATATATT
1 ATATAATATAAAAATTAATAAAAAATATAAAAATATT
211764 A
1 A
211765 AAATTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 8 0.23
38 27 0.77
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
ATATAATATAAAAATTAATAAAAAATATAAAAATATT
Found at i:211734 original size:19 final size:19
Alignment explanation
Indices: 211712--211764 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
211702 ATTAATAAAA
211712 AATATATAAAATATTATAT
1 AATATATAAAATATTATAT
*
211731 AATATA-AAAAT-TAATAT
1 AATATATAAAATATTATAT
*
211748 AAAATATAAATATATTA
1 AATATATAAA-ATATTA
211765 AAATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.36
18 8 0.29
19 8 0.29
20 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATATAAAATATTATAT
Found at i:211737 original size:17 final size:18
Alignment explanation
Indices: 211682--211765 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 18
211672 ATTTAAATAT
*
211682 AATATAAATATAATATCAA
1 AATATTAATATAATAT-AA
* * *
211701 AATTAATAAAAAATATATAA
1 AA-TATTAATATA-ATATAA
211721 AATATT-ATATAATATAA
1 AATATTAATATAATATAA
211738 AA-ATTAATATAAAATATAA
1 AATATTAATAT--AATATAA
211757 ATATATTAA
1 A-ATATTAA
211766 AATTTATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.06
17 12 0.24
18 3 0.06
19 13 0.25
20 11 0.22
21 9 0.18
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATTAATATAATATAA
Found at i:211745 original size:12 final size:12
Alignment explanation
Indices: 211676--211775 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 12
211666 GGTAGTATTT
211676 AAATATAATATAA
1 AAAT-TAATATAA
* *
211689 ATA-TAATATCA
1 AAATTAATATAA
211700 AAATTAATA-AA
1 AAATTAATATAA
211711 AAA-T-ATATAAA
1 AAATTAATAT-AA
211722 ATATTATATAATATAA
1 A-A--AT-TAATATAA
211738 AAATTAATATAA
1 AAATTAATATAA
*
211750 AATATAAATATATTA
1 AA-ATTAATATA--A
*
211765 AAATTTATATA
1 AAATTAATATA
211776 TTAATAATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 23
0.69 0.07 0.23
Matches are distributed among these distances:
9 3 0.04
10 1 0.01
11 16 0.24
12 16 0.24
13 12 0.18
14 8 0.12
15 4 0.06
16 4 0.06
17 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:211762 original size:27 final size:28
Alignment explanation
Indices: 211706--211775 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
211696 ATCAAAATTA
* *
211706 ATAAAAAATATATAAAATATTATATAAT
1 ATAAAAATTATATAAAATATTAAATAAT
211734 ATAAAAATTAATATAAAATA-TAAAT-AT
1 ATAAAAATT-ATATAAAATATTAAATAAT
*
211761 ATTAAAATTTATATA
1 A-TAAAAATTATATA
211776 TTAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 19 0.51
29 10 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATAAAAATTATATAAAATATTAAATAAT
Found at i:212270 original size:3 final size:3
Alignment explanation
Indices: 212262--212290 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
212252 TAAACTGCAA
212262 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
212291 AGAGACAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:212579 original size:20 final size:21
Alignment explanation
Indices: 212538--212601 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
212528 TATATATCTA
*
212538 TATAAATATTAATATAAAATT
1 TATAAATAATAATATAAAATT
*
212559 TTTAAATAATAATAT-AAATT
1 TATAAATAATAATATAAAATT
* *
212579 TATAAATAAAAAAATTAAAATT
1 TATAAATAATAATA-TAAAATT
212601 T
1 T
212602 TCGAATGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.44
21 14 0.39
22 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAAATAATAATATAAAATT
Found at i:218348 original size:13 final size:13
Alignment explanation
Indices: 218330--218354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218320 TACTATGAAC
218330 ATGTATCGATACA
1 ATGTATCGATACA
218343 ATGTATCGATAC
1 ATGTATCGATAC
218355 TAAGCAATAT
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:218353 original size:32 final size:33
Alignment explanation
Indices: 218312--218375 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
218302 CTTTTCAAGG
*
218312 TGTATCGATACTATG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
218344 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
218376 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:221289 original size:23 final size:23
Alignment explanation
Indices: 221241--221294 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
221231 CAACATATTT
*
221241 CAACATCAAATTCATCAACAATA
1 CAACATCAAAATCATCAACAATA
221264 CAACATCAATAATCA-CAA-AATCA
1 CAACATCAA-AATCATCAACAAT-A
*
221287 CAAGATCA
1 CAACATCA
221295 TTCAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.19
Consensus pattern (23 bp):
CAACATCAAAATCATCAACAATA
Found at i:225174 original size:52 final size:52
Alignment explanation
Indices: 225103--225223 Score: 208
Period size: 52 Copynumber: 2.3 Consensus size: 52
225093 GAAAATTTAT
*
225103 CTGCATGTATCGATCCATTTAAT-AGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAAG-GTATCGATACATCTGGGCAAATTTGC
*
225155 CTGCATGTATCGATACATTTTATAAGGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAAGGTATCGATACATCTGGGCAAATTTGC
225207 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
225224 AAGATCGGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 64 0.97
53 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAAGGTATCGATACATCTGGGCAAATTTGC
Found at i:225237 original size:52 final size:53
Alignment explanation
Indices: 225103--225243 Score: 182
Period size: 52 Copynumber: 2.7 Consensus size: 53
225093 GAAAATTTAT
* *
225103 CTGCATGTATCGATCCATTTA-AT-AGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAAGTGTATCGATACATCTGGGCAAATTTGC
***
225155 CTGCATGTATCGATACATTTTATAAG-GTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAAGTGTATCGATACATCTGGGCAAATTTGC
**
225207 CTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGATAAGTGTATCGATACA
225244 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
51 5 0.06
52 72 0.91
53 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (53 bp):
CTGCATGTATCGATACATAAGATAAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:225250 original size:13 final size:13
Alignment explanation
Indices: 225232--225256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225222 CAAAGATCGG
225232 TGTATCGATACAA
1 TGTATCGATACAA
225245 TGTATCGATACA
1 TGTATCGATACA
225257 TTTGAGTAAT
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:225338 original size:13 final size:13
Alignment explanation
Indices: 225320--225344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225310 CAAAAAAATA
225320 TGTATCGATACAT
1 TGTATCGATACAT
225333 TGTATCGATACA
1 TGTATCGATACA
225345 ACATTTTATG
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:225344 original size:33 final size:33
Alignment explanation
Indices: 225302--225364 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
225292 GCTTAAATTA
225302 TATCGATACAAAAAAATATGTATCGATACATTG
1 TATCGATACAAAAAAATATGTATCGATACATTG
* ***
225335 TATCGATACAACATTTTATGTATCGATACA
1 TATCGATACAAAAAAATATGTATCGATACA
225365 AATCATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (33 bp):
TATCGATACAAAAAAATATGTATCGATACATTG
Found at i:229452 original size:49 final size:49
Alignment explanation
Indices: 229256--229764 Score: 554
Period size: 49 Copynumber: 10.2 Consensus size: 49
229246 GGATGAATTG
* * *
229256 GCACCTTGGCACCTTAACCATCTTTAAGACCGATGTCGTTGGCCTTGAATCA
1 GCACATTGGCACCTT---CATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
*
229308 GCACATTGGCACCTTAACCATCTTTAAGTTCGATATCGTTGGCCTTGAATCA
1 GCACATTGGCACCTT---CATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
229360 GCACATTGGCACCTTAACCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
1 GCACATTGGCACCTT---CATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* * * * *
229412 GCACATTGTCATCTTCATCTTTAAGTTCGATATCGCTGGCCTTGAATTA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* * * * *
229461 GCATATTGGTACCTTCATCTTTAAGACCAATATCGCTGGCCTTGAATCA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* *** *
229510 GCACATTGGCATCTTCATCTTTAAGTCCGATATCACCGGCCTTGAATTA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* * * * ** * *
229559 GCATATTGGCACCTTTATCTTTAAGTCCAATGTC-ACGGCCTTCAACCA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* * * * *
229607 GCACATTGGAATCTTTATCCTTAAGTCCAATATCGTTGGCCTTGAATCA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* * * * *
229656 GCATATTGGCACCTTTATCTTTAAGACCAATGTCGTTGGCCTTGAATCA
1 GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
* *
229705 GCACATTGACACCCGT-ATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
1 GCACATTGGCA-CCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
*
229754 GCATATTGGCA
1 GCACATTGGCA
229765 TCTTTAACAT
Statistics
Matches: 397, Mismatches: 58, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
48 39 0.10
49 243 0.61
50 3 0.01
52 112 0.28
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
GCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCA
Found at i:229523 original size:98 final size:98
Alignment explanation
Indices: 229274--229814 Score: 618
Period size: 98 Copynumber: 5.4 Consensus size: 98
229264 GCACCTTAAC
* * *
229274 CATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTTC
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTT---CATCTTTAAGTCC
*
229339 GATATCGTTGGCCTTGAATCAGCACATTGGCACCTT
63 GATATCGTTGGCCTTGAATCAGCATATTGGCACCTT
* * * * *
229375 AACCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCACATTGTCATCTTCATCTTTAAGTTC
1 ---CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCC
* * *
229440 GATATCGCTGGCCTTGAATTAGCATATTGGTACCTT
63 GATATCGTTGGCCTTGAATCAGCATATTGGCACCTT
* *
229476 CATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGAT
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGAT
*** *
229541 ATCACCGGCCTTGAATTAGCATATTGGCACCTT
66 ATCGTTGGCCTTGAATCAGCATATTGGCACCTT
* * ** * * * * * *
229574 TATCTTTAAGTCCAATGTC-ACGGCCTTCAACCAGCACATTGGAATCTTTATCCTTAAGTCCAAT
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGAT
229638 ATCGTTGGCCTTGAATCAGCATATTGGCACCTT
66 ATCGTTGGCCTTGAATCAGCATATTGGCACCTT
* * * *
229671 TATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGACACCCGT-ATCTTTAAGTCCGA
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-TCTTCATCTTTAAGTCCGA
*
229735 TATCGTTGGCCTTGAATCAGCATATTGGCATCTT
65 TATCGTTGGCCTTGAATCAGCATATTGGCACCTT
* * * * * **
229769 TAACATTCCTAAGCCCAATGTCGCTGCCCTTGTCTCAGCACATTGG
1 CATC-TT--TAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGG
229815 TATTCTTCTT
Statistics
Matches: 382, Mismatches: 50, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
97 84 0.22
98 173 0.45
99 4 0.01
101 76 0.20
104 45 0.12
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (98 bp):
CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGAT
ATCGTTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:229679 original size:195 final size:196
Alignment explanation
Indices: 229274--229770 Score: 647
Period size: 195 Copynumber: 2.5 Consensus size: 196
229264 GCACCTTAAC
* *
229274 CATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTTC
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCC
* * * **
229339 GATATCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCGATATCGTTGGCC
63 GATATCGTTGGCCTTGAATCAGCATATTGGCACCTT---TATCTTTAAGTCCAATATCGACGGCC
* * ** * * * *
229404 TTGAATCAGCACATTGTCATCTTCATCTTTAAGTTCGATATCGCTGGCCTTGAATTAGCATATTG
125 TTCAACCAGCACATTGGAATCTTCATCCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
229469 GTACCTT
190 GCACCTT
* * *
229476 CATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGAT
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGAT
*** * *
229541 ATCACCGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC-ACGGCCTTCAAC
66 ATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATCGACGGCCTTCAAC
* *
229605 CAGCACATTGGAATCTTTATCCTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCT
131 CAGCACATTGGAATCTTCATCCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
229670 T
196 T
* * *
229671 TATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGACACCCGT-ATCTTTAAGTCCGA
1 CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTTTAAGTCCGA
*
229735 TATCGTTGGCCTTGAATCAGCATATTGGCATCTTTA
65 TATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
229771 ACATTCCTAA
Statistics
Matches: 257, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
195 151 0.59
196 18 0.07
199 43 0.17
202 45 0.18
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (196 bp):
CATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGAT
ATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATCGACGGCCTTCAAC
CAGCACATTGGAATCTTCATCCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
T
Found at i:230673 original size:13 final size:13
Alignment explanation
Indices: 230639--230679 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
230629 ACAAACAGTA
230639 AATGTATCGATAC
1 AATGTATCGATAC
**
230652 TGTTGTATCGATAC
1 -AATGTATCGATAC
230666 AATGTATCGATAC
1 AATGTATCGATAC
230679 A
1 A
230680 GAGCTACCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:230745 original size:13 final size:13
Alignment explanation
Indices: 230727--230754 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
230717 CATTATTCAA
230727 TGTATCGATACAT
1 TGTATCGATACAT
230740 TGTATCGATACAT
1 TGTATCGATACAT
230753 TG
1 TG
230755 ATTTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:230749 original size:33 final size:33
Alignment explanation
Indices: 230707--230772 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
230697 GCCAAGCAAA
230707 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGATT-AATGTATCGATACAT
**
230740 TGTATCGATACATTGATTTTTGTATCGATACAT
1 TGTATCGATACATTGATTAATGTATCGATACAT
230773 CTGGAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATTAATGTATCGATACAT
Found at i:234557 original size:19 final size:20
Alignment explanation
Indices: 234534--234577 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
234524 TTTTTTTTCG
234534 ATTTTTCATTT-TTTC-ATA
1 ATTTTTCATTTATTTCTATA
*
234552 ACTTTTTCTTTTATTTCTATA
1 A-TTTTTCATTTATTTCTATA
234573 ATTTT
1 ATTTT
234578 AAAACTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 8 0.36
21 4 0.18
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTCATTTATTTCTATA
Found at i:235435 original size:28 final size:28
Alignment explanation
Indices: 235284--236174 Score: 422
Period size: 28 Copynumber: 30.6 Consensus size: 28
235274 TACTAACTCA
* **
235284 TGTGGGCTTTGAAAAGAGTTGCCACCAACTT
1 TGTGGGCTTT-AAAA-AGATGCCACTGAC-T
* *
235315 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTAAAAAGATGCCACTGACT
* *
235344 TGTAGGCTTTGAAAAATGAGTTGCCACCGACTT
1 TGTGGGCTTT-AAAAA-GA--TGCCACTGAC-T
* * * *
235377 GTGTGGGCTTTGAAAGGGTGCCACCGACT
1 -TGTGGGCTTTAAAAAGATGCCACTGACT
*
235406 TGT-AGCTTTTAAAAAGATGCCACTGACT
1 TGTGGGC-TTTAAAAAGATGCCACTGACT
* * * *
235434 TGTGGGTTTTTCAAAGGATGCTACTGACT
1 TGTGGG-CTTTAAAAAGATGCCACTGACT
* *
235463 TGTGGGCTTTGAAAAGATGCCACTGTCT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * * * *
235491 TATGGGCTTTGAAAAGGTGCCGCTCACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
235519 TCTGGGCTTTGAAAAGGATGCCACTCACT
1 TGTGGGCTTT-AAAAAGATGCCACTGACT
* * * *
235548 TATAGGCTTTGAAAAGATGCCACTGTCT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
235576 TGTGGGCTTTGAAAAGGTGCCACTCACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* *
235604 TCTGGGCTTTGAAAAAGATGCCACTCACT
1 TGTGGGCTTT-AAAAAGATGCCACTGACT
* * * *
235633 TATGGGCTTTGAAAAGATGCCATTGTCT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* *
235661 TGTGGGCTTTAAAAAGGTGCCACCGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* ** **
235689 TGTGTGCTTTGAAAGGGTATGCGTCTGACT
1 TGTGGGCTTT-AAAAAG-ATGCCACTGACT
** * * *
235719 TGTGGGCTTTGGAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
** * * ** *
235747 TGTGGGCTTTGGAAGGGTGCCACCAATTTT
1 TGTGGGCTTTAAAAAGATGCCACTGA--CT
* * *
235777 TGTGGGCTTTGAAAAGAGTTGCCACCGAGT
1 TGTGGGCTTT-AAAA-AGATGCCACTGACT
* *
235807 TGTGTGGACTTTGAAAAGAGTTGCCACTGATT
1 TGTG-GG-CTTT-AAAA-AGATGCCACTGACT
* * *
235839 TATGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
** * * * * *
235867 TGTGAACTTTAGAAGGGTGCCACCGATTT
1 TGTGGGCTTTAAAAAGATGCCACTGA-CT
* *
235896 GTGTGGGCGTTAAAAAGAGTTGCCACTAACTT
1 -TGTGGGCTTTAAAAAGA--TGCCACTGAC-T
* * * *
235928 ATGTGGACTTTGAAAAGAGTTACCACTAACT
1 -TGTGGGCTTT-AAAA-AGATGCCACTGACT
* * *
235959 TGTGGGCTTCAAAAATGGTGCCATTGACT
1 TGTGGGCTTTAAAAA-GATGCCACTGACT
** *
235988 TGTGGGCTTTGAAAGTGTATGCCATTGACT
1 TGTGGGCTTT-AAAAAG-ATGCCACTGACT
** * * * *
236018 TGTAAGCTTTGAAACGGTGCCA-TTATCT
1 TGTGGGCTTTAAAAAGATGCCACTGA-CT
** * * ** *
236046 TGTGGGCTTTGGAAGGTTGCCACCAATT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
236074 TATGGGCTTTGAAGAG-TGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
236101 TCT-GGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * * * *
236128 TGTGGGCTTTGAAAGGGTGCCACCGATTT
1 TGTGGGCTTTAAAAAGATGCCACTGA-CT
*
236157 GTGTGGGCTTTGAAAAGA
1 -TGTGGGCTTTAAAAAGA
236175 GTTACCACCA
Statistics
Matches: 671, Mismatches: 153, Indels: 72
0.75 0.17 0.08
Matches are distributed among these distances:
26 9 0.01
27 27 0.04
28 295 0.44
29 118 0.18
30 113 0.17
31 11 0.02
32 79 0.12
33 8 0.01
34 11 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTAAAAAGATGCCACTGACT
Found at i:235479 original size:57 final size:56
Alignment explanation
Indices: 235265--236174 Score: 459
Period size: 57 Copynumber: 15.6 Consensus size: 56
235255 GGCTTTAACA
* * ** *
235265 AAAAGGTGCTACTAACTCATGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGTGCCACTGACT--TGTGGGCTTTGAAAAGA--TGCCACTGACTTGTG-GGCCTTT
* * *
235326 AAAAGGGTGCCACTGACTTGTAGGCTTTGAAAAATGAGTTGCCACCGACTTGTGTGGGCTTT
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG-AAAA-GA--TGCCACTGACTTGTG-GGCCTTT
* * * * **
235388 GAAAGGGTGCCACCGACTTGT-AGCTTTTAAAAAGATGCCACTGACTTGTGGGTTTTT
1 -AAAAGGTGCCACTGACTTGTGGGC-TTTGAAAAGATGCCACTGACTTGTGGGCCTTT
* * * *
235445 CAAAGGATGCTACTGACTTGTGGGCTTTGAAAAGATGCCACTGTCTTATGGG-CTTT
1 AAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCCTTT
* * * * * *
235501 GAAAAGGTGCCGCTCACTTCTGGGCTTTGAAAAGGATGCCACTCACTTATAGG-CTTT
1 -AAAAGGTGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCCTTT
* * * * *
235558 GAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTCACTTCTGGG-CTTT
1 -AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCCTTT
* * * * *
235614 GAAAAAGATGCCACTCACTTATGGGCTTTGAAAAGATGCCATTGTCTTGTGGG-CTTT
1 --AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCCTTT
* * * **
235671 AAAAAGGTGCCACCGACTTGTGTGCTTTGAAAGGGTATGCGTCTGACTTGTGGG-CTTT
1 -AAAAGGTGCCACTGACTTGTGGGCTTTGAAA-AG-ATGCCACTGACTTGTGGGCCTTT
* * * * * * ** *
235729 GGAAGGGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCAATTTTTGTGGG-CTTT
1 -AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGA--CTTGTGGGCCTTT
* * * *
235787 GAAAAGAGTTGCCACCGAGTTGTGTGGACTTTGAAAAGAGTTGCCACTGATTTATGGG-CTTT
1 -AAAAG-G-TGCCACTGACTTGTG-GG-CTTTGAAAAGA--TGCCACTGACTTGTGGGCCTTT
** * * * * * *
235849 AAAAGGGTGCCACTGACTTGTGAACTTT-AGAAGGGTGCCACCGATTTGTGTGGGCGTTA
1 AAAA-GGTGCCACTGACTTGTGGGCTTTGA-AAAGATGCCACTGA-CT-TGTGGGCCTTT
* * * * *
235908 AAAAGAGTTGCCACTAACTTATGTGGACTTTGAAAAGAGTTACCACTAACTTGTGGG-CTTCA
1 AAAAG-G-TGCCACTGAC-T-TGTGGGCTTTGAAAAGA--TGCCACTGACTTGTGGGCCTT-T
* * * **
235970 AAAATGGTGCCATTGACTTGTGGGCTTTGAAAGTGTATGCCATTGACTTGTAAG-CTTT
1 AAAA-GGTGCCACTGACTTGTGGGCTTTGAAA-AG-ATGCCACTGACTTGTGGGCCTTT
* * * * * ** * *
236028 GAAACGGTGCCA-TTATCTTGTGGGCTTTGGAAGGTTGCCACCAATTTATGGG-CTTT
1 -AAAAGGTGCCACTGA-CTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCCTTT
* * *
236084 -GAAGAGTGCCACTGACTTCT-GGCTTT-AAAAGGGTGCCACTGACTTGTGGG-CTTT
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCCTTT
* * *
236138 GAAAGGGTGCCACCGATTTGTGTGGGCTTTGAAAAGA
1 -AAAAGGTGCCACTGA-CT-TGTGGGCTTTGAAAAGA
236175 GTTACCACCA
Statistics
Matches: 665, Mismatches: 137, Indels: 97
0.74 0.15 0.11
Matches are distributed among these distances:
53 2 0.00
54 26 0.04
55 19 0.03
56 108 0.16
57 152 0.23
58 116 0.17
59 43 0.06
60 48 0.07
61 33 0.05
62 99 0.15
63 6 0.01
64 13 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (56 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCCTTT
Found at i:235506 original size:85 final size:85
Alignment explanation
Indices: 235284--236174 Score: 609
Period size: 85 Copynumber: 10.2 Consensus size: 85
235274 TACTAACTCA
*** *
235284 TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTA
1 TGTGGGCTTTGAAAAGA--TGCCACTGTC-T-TGTGGGCTTTGAAAA-GGTGCCACTGACTTGTG
* *
235348 GGCTTTGAAAAATGAGTTGCCACCGACTT
61 GGCTTTG-AAAA-G-GATGCCACTGAC-T
* * * * * * * *
235377 GTGTGGGCTTTGAAAGGGTGCCACCGACTTGT-AGCTTTTAAAAAGATGCCACTGACTTGTGGGT
1 -TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGC-TTTGAAAAGGTGCCACTGACTTGTGGGC
** *
235441 TTTTCAAAGGATGCTACTGACT
64 TTTGAAAAGGATGCCACTGACT
* * * *
235463 TGTGGGCTTTGAAAAGATGCCACTGTCTTATGGGCTTTGAAAAGGTGCCGCTCACTTCTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
*
235528 TGAAAAGGATGCCACTCACT
66 TGAAAAGGATGCCACTGACT
* * * *
235548 TATAGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTCACTTCTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
* *
235613 TGAAAAAGATGCCACTCACT
66 TGAAAAGGATGCCACTGACT
* * * * *
235633 TATGGGCTTTGAAAAGATGCCATTGTCTTGTGGGCTTTAAAAAGGTGCCACCGACTTGTGTGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
* **
235698 TGAAAGGGTATGCGTCTGACT
66 TGAAAAGG-ATGCCACTGACT
* * * ** * * ** *
235719 TGTGGGCTTTGGAAGGGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCAATTTTTGTGGGC
1 TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGA--CTTGTGGGC
* * *
235784 TTTGAAAAGAGTTGCCACCGAGT
64 TTTGAAAAG-GATGCCACTGACT
*
235807 TGTGTGGACTTTGAAAAGAGTTGCCACTGAT-TTATGGGCTTT-AAAAGGGTGCCACTGACTTGT
1 TGTG-GG-CTTTGAAAAGA--TGCCACTG-TCTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGT
** * * * *
235870 GAACTTT-AGAAGGGTGCCACCGATTT
60 GGGCTTTGAAAAGGATGCCACTGA-CT
* * ** * * *
235896 GTGTGGGCGTTAAAAAGAGTTGCCACTAACTTATGTGGACTTTGAAAAGAGTTACCACTAACTTG
1 -TGTGGGCTTTGAAAAGA--TGCCACTGTC-T-TGTGGGCTTTGAAAAG-G-TGCCACTGACTTG
** *
235961 TGGGCTTCAAAAATGG-TGCCATTGACT
59 TGGGCTTTGAAAA-GGATGCCACTGACT
* * * ** * *
235988 TGTGGGCTTTGAAAGTGTATGCCATTGACTTGTAAGCTTTGAAACGGTGCCA-TTATCTTGTGGG
1 TGTGGGCTTTGAAA-AG-ATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGA-CTTGTGGG
* * ** *
236052 CTTTG-GAAGGTTGCCACCAATT
63 CTTTGAAAAGGATGCCACTGACT
* * * *
236074 TATGGGCTTTGAAGAG-TGCCACTGACTTCT-GGCTTT-AAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCT
* * *
236136 TTG-AAAGGGTGCCACCGATTT
65 TTGAAAAGGATGCCACTGA-CT
236157 GTGTGGGCTTTGAAAAGA
1 -TGTGGGCTTTGAAAAGA
236175 GTTACCACCA
Statistics
Matches: 639, Mismatches: 126, Indels: 73
0.76 0.15 0.09
Matches are distributed among these distances:
81 3 0.00
82 37 0.06
83 16 0.03
84 14 0.02
85 213 0.33
86 78 0.12
87 24 0.04
88 56 0.09
89 28 0.04
90 57 0.09
91 32 0.05
92 53 0.08
93 11 0.02
94 17 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGATGCCACTGTCTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
TGAAAAGGATGCCACTGACT
Found at i:235855 original size:120 final size:118
Alignment explanation
Indices: 235284--236182 Score: 478
Period size: 120 Copynumber: 7.7 Consensus size: 118
235274 TACTAACTCA
* * * * *
235284 TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTT-AAAAG-GGTGCCACTGACTTGT
1 TGTGGGCTTTG-AAAG-GATGCCACC-ATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGT
* * * *
235347 -AGGCTTTGAAAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGGTGCCAC-CGACT
63 GTGGCTTTG-AAAA-GAGTTGCCACTGAC-T-TATGGGCTTTAAAAGGGTGCCACTC-ACT
* * * ** * ** * * *
235406 TGT-AGCTTTTAAAAAGATGCCA-C-TGACTTGTGGGTTTTTCAAAG-GATGCTACTGACTTGTG
1 TGTGGGC-TTTGAAAGGATGCCACCAT-TTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTG
* *
235467 -GGCTTTGAAAAGA--TGCCACTGTCTTATGGGCTTTGAAAA-GGTGCCGCTCACT
64 TGGCTTTGAAAAGAGTTGCCACTGACTTATGGGCTTT-AAAAGGGTGCCACTCACT
* * * * * *
235519 TCTGGGCTTTGAAAAGGATGCCACTCA--CTTATAGGCTTTGAAAAGA--TGCCACTGTCTTGTG
1 TGTGGGCTTTG-AAAGGATGCCAC-CATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTG
* * * *
235580 -GGCTTTGAAAAG-G-TGCCACTCACTTCTGGGCTTTGAAAAAGATGCCACTCACT
64 TGGCTTTGAAAAGAGTTGCCACTGACTTATGGGCTTT-AAAAGGGTGCCACTCACT
* * *
235633 TATGGGCTTTGAAAAGATG---CCATTGTCTTGTGGGCTTT-AAAA-AGGTGCCACCGACTTGTG
1 TGTGGGCTTTGAAAGGATGCCACCATT-T-TTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTG
* ** * ** *
235693 T-GCTTTG-AAAGGGTATGCGTCTGACTTGTGGGCTTTGGAAGGGTGCCACTAACT
64 TGGCTTTGAAAAGAGT-TGCCACTGACTTATGGGCTTTAAAAGGGTGCCACTCACT
* * *
235747 TGTGGGCTTTGGAAGGGTGCCACCAATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGAGTTGTGT
1 TGTGGGCTTTGAAAGGATGCCACC-ATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT
* *
235812 GGACTTTGAAAAGAGTTGCCACTGATTTATGGGCTTTAAAAGGGTGCCACTGACT
65 GG-CTTTGAAAAGAGTTGCCACTGACTTATGGGCTTTAAAAGGGTGCCACTCACT
** * * * * ** *
235867 TGTGAACTTT-AGAAGGGTGCCACCGATTTGTGTGGGCGTTAAAAAGAGTTGCCACTAACTTATG
1 TGTGGGCTTTGA-AAGGATGCCACC-ATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTG
* * * * * * *
235931 TGGACTTTGAAAAGAGTTACCACTAACTTGTGGGCTTCAAAAATGGTGCCATTGACT
64 TGG-CTTTGAAAAGAGTTGCCACTGACTTATGGGCTT-TAAAAGGGTGCCACTCACT
* ** * **
235988 TGTGGGCTTTGAAAGTGTATG---CCATTGACTTGTAAGCTTTGAAACG-G-TGCCA-TTATCTT
1 TGTGGGCTTTGAAAG-G-ATGCCACCATT--TTTGTGGGCTTTGAAAAGAGTTGCCACCGA-CTT
* ** * * * *
236047 GTG-GGCTTTG-GAAG-GTTGCCACCAATTTATGGGCTTT-GAAGAGTGCCACTGACT
61 GTGTGGCTTTGAAAAGAGTTGCCACTGACTTATGGGCTTTAAAAGGGTGCCACTCACT
* * * ** * *
236101 TCT-GGCTTTAAAAGGGTGCCA-C-TGACTTGTGGGCTTTG-AAAG-GGTGCCACCGATTTGTGT
1 TGTGGGCTTTGAAAGGATGCCACCAT-TTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT
*
236161 GGGCTTTGAAAAGAGTTACCAC
65 -GGCTTTGAAAAGAGTTGCCAC
236183 CAACTAGTGT
Statistics
Matches: 611, Mismatches: 115, Indels: 110
0.73 0.14 0.13
Matches are distributed among these distances:
109 6 0.01
110 24 0.04
111 4 0.01
112 26 0.04
113 126 0.21
114 86 0.14
115 43 0.07
116 15 0.02
117 14 0.02
118 37 0.06
119 40 0.07
120 131 0.21
121 49 0.08
122 8 0.01
123 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (118 bp):
TGTGGGCTTTGAAAGGATGCCACCATTTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTG
GCTTTGAAAAGAGTTGCCACTGACTTATGGGCTTTAAAAGGGTGCCACTCACT
Found at i:236439 original size:28 final size:27
Alignment explanation
Indices: 236380--236442 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
236370 TATACAGCAA
236380 GTGCCACTGATTGTGAACTTCAAAAAG
1 GTGCCACTGATTGTGAACTTCAAAAAG
* * * * *
236407 ATGCCATTGATTTGTGGACTTCGAAGAG
1 GTGCCACTGA-TTGTGAACTTCAAAAAG
236435 GTGCCACT
1 GTGCCACT
236443 AACTAATGGG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (27 bp):
GTGCCACTGATTGTGAACTTCAAAAAG
Found at i:236516 original size:13 final size:13
Alignment explanation
Indices: 236472--236544 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
236462 GGGATTTGTG
*
236472 TTGACAAACATTTC
1 TTGACAAA-AGTTC
* *
236486 TTGAC-GAAGTTT
1 TTGACAAAAGTTC
* *
236498 TTGACACACGTTC
1 TTGACAAAAGTTC
236511 TTGACAAAAGTTC
1 TTGACAAAAGTTC
* *
236524 TTGGCAAAAATTTC
1 TTGAC-AAAAGTTC
236538 TTGACAA
1 TTGACAA
236545 CAATTTTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
12 8 0.17
13 22 0.48
14 16 0.35
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (13 bp):
TTGACAAAAGTTC
Found at i:236538 original size:14 final size:14
Alignment explanation
Indices: 236508--236550 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
236498 TTGACACACG
*
236508 TTCTTGAC-AAAAG
1 TTCTTGACAAAAAT
*
236521 TTCTTGGCAAAAAT
1 TTCTTGACAAAAAT
*
236535 TTCTTGACAACAAT
1 TTCTTGACAAAAAT
236549 TT
1 TT
236551 TGCTGACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (14 bp):
TTCTTGACAAAAAT
Found at i:236821 original size:28 final size:28
Alignment explanation
Indices: 236770--236827 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
236760 TTTTTTTTTC
*
236770 TTGCAATTTATCCCGACTCTACTAAGGA
1 TTGCAATTTATCCCGACTCCACTAAGGA
*
236798 TTGCAATTTATCCC-AGTTCCACTAAGGA
1 TTGCAATTTATCCCGA-CTCCACTAAGGA
236826 TT
1 TT
236828 AGGACCTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (28 bp):
TTGCAATTTATCCCGACTCCACTAAGGA
Found at i:237775 original size:27 final size:26
Alignment explanation
Indices: 237745--237795 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
237735 TTCTTCCCCC
*
237745 TTTTCTTGTTTGTTGTTTTTTTATGTT
1 TTTTCTTGTTT-TTATTTTTTTATGTT
*
237772 TTTTTTTGTTTTTATTTTTTTATG
1 TTTTCTTGTTTTTATTTTTTTATG
237796 AAGGACGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.06, C:0.02, G:0.12, T:0.80
Consensus pattern (26 bp):
TTTTCTTGTTTTTATTTTTTTATGTT
Found at i:250347 original size:155 final size:154
Alignment explanation
Indices: 250171--250659 Score: 474
Period size: 155 Copynumber: 3.2 Consensus size: 154
250161 AATATTTTGA
* *
250171 TAACCTTAAAGGACTAAAAAATGATCATAGAAAGGTGAACCTATCCTAAATGCACACTTTTAGCG
1 TAACCCTAAAGGACTAAAAAATGATCATA-AAAGGTGAACCTATCCTAAATGCACACTTTTAGCA
* *
250236 TAAAAGCATCTCGATGACTACAT-TAGACTTAGTTCTAATAAAATTACCAAAATACCCTTAAGAG
65 TAAAAGCATCTCGATGACTATATCGA-ACTTAGTTCTAA-AAAATTACCAAAATACCCTTAAGAG
* * *
250300 -CTACCTTCGTCTTGAAAGCATCTCGG
128 TATACCTTCGTCATGAAAGTATCTCGG
* * * * * *
250326 TGACCCTAAAGGACTCAAAAATGATCATAAAAAGGTGAACATATCCTAAATGCACACCTTTGGAA
1 TAACCCTAAAGGACTAAAAAATGATCAT-AAAAGGTGAACCTATCCTAAATGCACACTTTTAGCA
* * *
250391 TAAAAGCATACTAG-TGACTATATCGAACTCTAGTTCTAGGAATATTACCAAAA-AGCCCTTAAG
65 TAAAAGCAT-CTCGATGACTATATCGAACT-TAGTTCTA-AAAAATTACCAAAATA-CCCTTAAG
* * *
250454 -GTATATCTTCGAT-ATGAAAGTATCCCAG
126 AGTATACCTTCG-TCATGAAAGTATCTCGG
* * * * * * *
250482 TAACCCTAAAAGACTAAAAAATAATAATAAATA-ATGAACCGATCCTTAATGCACACTTTTAACA
1 TAACCCTAAAGGACTAAAAAATGATCATAAA-AGGTGAACCTATCCTAAATGCACACTTTTAGCA
* * * * *
250546 TAAAAACA-CCCTGATGACTATATCGAACTCAGTTCTAAAAAATTACCAAAATGCCATT-AGAGT
65 TAAAAGCATCTC-GATGACTATATCGAACTTAGTTCTAAAAAATTACCAAAATACCCTTAAGAGT
* ** * *
250609 ATACTTTCAACGTGAAAGTATCTTGG
129 ATACCTTCGTCATGAAAGTATCTCGG
**
250635 TAACCCTAAAGGACTCTAAAATGAT
1 TAACCCTAAAGGACTAAAAAATGAT
250660 AGAAAAAATA
Statistics
Matches: 268, Mismatches: 52, Indels: 30
0.77 0.15 0.09
Matches are distributed among these distances:
152 2 0.01
153 57 0.21
154 8 0.03
155 125 0.47
156 75 0.28
157 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (154 bp):
TAACCCTAAAGGACTAAAAAATGATCATAAAAGGTGAACCTATCCTAAATGCACACTTTTAGCAT
AAAAGCATCTCGATGACTATATCGAACTTAGTTCTAAAAAATTACCAAAATACCCTTAAGAGTAT
ACCTTCGTCATGAAAGTATCTCGG
Found at i:250669 original size:155 final size:153
Alignment explanation
Indices: 250120--250671 Score: 415
Period size: 155 Copynumber: 3.6 Consensus size: 153
250110 GTTCTAATGC
* * * * * * * *
250120 AAAATTACCAAAAAG-ACTTTGAGGTATACTTTTGACATGACAA-TATTTTGATAACCTTAAAGG
1 AAAATTACCAAAATGCCCTTAGA-GTATACTTTCGACATGA-AAGTATCTCGGTAACCCTAAAGG
* * * ** * * *
250183 ACTAAAAAATGATCATAGAAA-GGTGAACCTATCCTAAATGCACACTTTTAGCGTAAAAGCATCT
64 ACTCAAAAATGAT-AAAAAAATAATGAACCTATCCTAAATGCACACTTTTAACATAAAAGCAACT
* * *
250247 CGATGACTACAT-TAGACTTAGTTCTAA
128 -GATGACTATATCGA-ACTCAGTTCTAA
* * * * * * *
250274 TAAAATTACCAAAATACCCTTAAGAG-CTACCTTCGTCTTGAAAGCATCTCGGTGACCCTAAAGG
1 -AAAATTACCAAAATGCCCTT-AGAGTATACTTTCGACATGAAAGTATCTCGGTAACCCTAAAGG
* ** * **
250338 ACTCAAAAATGATCATAAAAA-GGTGAACATATCCTAAATGCACACCTTTGGA-ATAAAAGCATA
64 ACTCAAAAATGAT-AAAAAAATAATGAACCTATCCTAAATGCACA-CTTTTAACATAAAAGCA-A
*
250401 CT-AGTGACTATATCGAACTCTAGTTCTAGG
126 CTGA-TGACTATATCGAACTC-AGTTCTA-A
* * * * * *
250431 AATATTACCAAAAAGCCCTTA-AGGTATA-TCTTCGATATGAAAGTATCCCAGTAACCCTAAAAG
1 AAAATTACCAAAATGCCCTTAGA-GTATACT-TTCGACATGAAAGTATCTCGGTAACCCTAAAGG
* * * * * * *
250494 ACTAAAAAATAAT-AATAAATAATGAACCGATCCTTAATGCACACTTTTAACATAAAAACACCCT
64 ACTCAAAAATGATAAAAAAATAATGAACCTATCCTAAATGCACACTTTTAACATAAAAGCA-ACT
250558 GATGACTATATCGAACTCAGTTCTAA
128 GATGACTATATCGAACTCAGTTCTAA
* * * *
250584 AAAATTACCAAAATGCCATTAGAGTATACTTTCAACGTGAAAGTATCTTGGTAACCCTAAAGGAC
1 AAAATTACCAAAATGCCCTTAGAGTATACTTTCGACATGAAAGTATCTCGGTAACCCTAAAGGAC
*
250649 TCTAAAATGATAGAAAAAATAAT
66 TCAAAAATGATA-AAAAAATAAT
250672 CATTTCACCC
Statistics
Matches: 309, Mismatches: 69, Indels: 38
0.74 0.17 0.09
Matches are distributed among these distances:
153 59 0.19
154 22 0.07
155 152 0.49
156 74 0.24
157 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (153 bp):
AAAATTACCAAAATGCCCTTAGAGTATACTTTCGACATGAAAGTATCTCGGTAACCCTAAAGGAC
TCAAAAATGATAAAAAAATAATGAACCTATCCTAAATGCACACTTTTAACATAAAAGCAACTGAT
GACTATATCGAACTCAGTTCTAA
Found at i:253900 original size:35 final size:35
Alignment explanation
Indices: 253854--253923 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
253844 CTTAACTTAG
*
253854 ATTTGTTTCAAGGGTTTTGGAAACTTGATCTTGAA
1 ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
* *
253889 ATTTGCTTCAAGGGTTTTTGAGACTTGATCTTGAA
1 ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
253924 TTAATAGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.43
Consensus pattern (35 bp):
ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
Found at i:254036 original size:35 final size:35
Alignment explanation
Indices: 253996--254067 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
253986 CTTGATCATG
*
253996 AATCTTGCTTTAAGGGTCATT-AAACTTCATCTTGA
1 AATCTTGCTTCAAGGGTC-TTCAAACTTCATCTTGA
*
254031 AATCTTGCTTCAAGGGTCTTCAAACTTGATCTTGA
1 AATCTTGCTTCAAGGGTCTTCAAACTTCATCTTGA
254066 AA
1 AA
254068 AACAAAGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (35 bp):
AATCTTGCTTCAAGGGTCTTCAAACTTCATCTTGA
Found at i:254508 original size:41 final size:41
Alignment explanation
Indices: 254463--254600 Score: 127
Period size: 46 Copynumber: 3.3 Consensus size: 41
254453 AAATTAATTT
* *
254463 TTAATTTAATTAAAGATAAAACTCTTTTATTTATCCTTTGA
1 TTAATTTAATTAAAGATAAAATTCTTTTATTTATCCTTTAA
* * *
254504 TTAATTTAATTGAATCAGAGATAAAATTCTTTGATTCATCTTTTAA
1 TTAATTTAATT--A--A-AGATAAAATTCTTTTATTTATCCTTTAA
* * *
254550 TTAATTTAATTAGAGAT-AAATTATTTTATTTAT-GTCTTAA
1 TTAATTTAATTAAAGATAAAATTCTTTTATTTATCCT-TTAA
*
254590 TTAATATAATT
1 TTAATTTAATT
254601 TAATTAGAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
39 1 0.01
40 27 0.34
41 15 0.19
43 1 0.01
44 1 0.01
45 1 0.01
46 34 0.43
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (41 bp):
TTAATTTAATTAAAGATAAAATTCTTTTATTTATCCTTTAA
Found at i:254590 original size:40 final size:41
Alignment explanation
Indices: 254504--254600 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 41
254494 TATCCTTTGA
* * * *
254504 TTAATTTAATTGAATCAGAGATAAAATTCTTTGATTCATCTT
1 TTAA-TTAATTTAATTAGAGATAAAATTATTTGATTCATCTC
* * *
254546 TTAATTAATTTAATTAGAGAT-AAATTATTTTATTTATGTC
1 TTAATTAATTTAATTAGAGATAAAATTATTTGATTCATCTC
*
254586 TTAATTAATATAATT
1 TTAATTAATTTAATT
254601 TAATTAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 28 0.60
41 15 0.32
42 4 0.09
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (41 bp):
TTAATTAATTTAATTAGAGATAAAATTATTTGATTCATCTC
Found at i:255412 original size:78 final size:78
Alignment explanation
Indices: 255251--255507 Score: 274
Period size: 78 Copynumber: 3.3 Consensus size: 78
255241 TTTGAGTAGG
* * **
255251 CAGTTTAAGCTCGTGCTTAGGAG-TATCATAATAGTTTAAGCTTTTGTTTAGGAGCA-ACA--AC
1 CAGTTTAAGCTCATGCTTAGGAGCAAT-ATAATAGTTTAAGCTCGTGTTTAGGAGCATA-ATTA-
*
255312 TTTT-TTTTTTGGAGGAA
63 TTTTGTTTTTTTGA--AA
* *
255329 CAGTTTGAGCTCATGCTTAGGAGCAATATAACAGTTTAAGCTCGTGTTTAGGAGCATAATTATTT
1 CAGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTT
255394 TGTTTTTTTGAAA
66 TGTTTTTTTGAAA
* * * * * ** *
255407 TAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGTTTAGGAGTGTCATTATTT
1 CAGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTT
255472 TG-TTTTTTGAAA
66 TGTTTTTTTGAAA
* *
255484 CAGTTTAAGCTTATGTTTAGGAGC
1 CAGTTTAAGCTCATGCTTAGGAGC
255508 TTAATCATAT
Statistics
Matches: 154, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
77 31 0.20
78 107 0.69
79 7 0.05
80 9 0.06
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (78 bp):
CAGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTT
TGTTTTTTTGAAA
Found at i:255591 original size:119 final size:119
Alignment explanation
Indices: 255398--255625 Score: 314
Period size: 119 Copynumber: 1.9 Consensus size: 119
255388 TTATTTTGTT
* * * **
255398 TTTTTGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGTTTAGGAGTG
1 TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGCTTAAGAGCA
* * *
255463 TCATTATTTTGTTTTTTGAAACAGTTTAAGCTTATGTTTAGGAGCTTAATCATA
66 TCATCATTTTGTTTTTTGAAACAATTTAAGCTCATGTTTAGGAGCTTAATCATA
* * **
255517 TTTTAGAAATAGTTTAAGCTCGTGTTTAGGAGTGATATAGTAGTTTGAGCAT-GTGCTTAAGAGC
1 TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGC-TCGTGCTTAAGAGC
* *
255581 ATCATCATTTTTTTTTTTGAAATAATTTAAGCTCATGTTTAGGAG
65 ATCATCATTTTGTTTTTTGAAACAATTTAAGCTCATGTTTAGGAG
255626 GATATAACAA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
119 93 0.99
120 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (119 bp):
TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGCTTAAGAGCA
TCATCATTTTGTTTTTTGAAACAATTTAAGCTCATGTTTAGGAGCTTAATCATA
Found at i:256166 original size:109 final size:109
Alignment explanation
Indices: 255975--256180 Score: 385
Period size: 109 Copynumber: 1.9 Consensus size: 109
255965 TAAAGAAAAA
*
255975 GATTGGCTTTATTCCCTTAGAGATCCACCATTATACTTATGCTTTGAGCTAGAATAATAAGATTA
1 GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
256040 AAAGAGTCAAATTTTATGGTTCTATTGAACTGATTAGATTGCAT
66 AAAGAGTCAAATTTTATGGTTCTATTGAACTGATTAGATTGCAT
* *
256084 GATTGGCTTTATTTCCTTAGAGATCCACCATCGTACTTATGCTTTGAGCTAGAATAATAAGATTA
1 GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
256149 AAAGAGTCAAATTTTATGGTTCTATTGAACTG
66 AAAGAGTCAAATTTTATGGTTCTATTGAACTG
256181 TGTGAGCTCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 94 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (109 bp):
GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
AAAGAGTCAAATTTTATGGTTCTATTGAACTGATTAGATTGCAT
Found at i:256997 original size:13 final size:13
Alignment explanation
Indices: 256979--257004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256969 CTATTTATGA
256979 TGTATCGATACAC
1 TGTATCGATACAC
256992 TGTATCGATACAC
1 TGTATCGATACAC
257005 ACAAATATGT
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:257149 original size:22 final size:22
Alignment explanation
Indices: 257094--257149 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
257084 ATAGTGACCT
257094 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
257116 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
257137 ATGAACAGTGATG
1 ATGAACAGTGATG
257150 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:257156 original size:10 final size:10
Alignment explanation
Indices: 257137--257167 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
257127 GTATCGATAC
257137 ATGAACAGTG
1 ATGAACAGTG
*
257147 ATGAATAGTG
1 ATGAACAGTG
257157 ATGAACAGTG
1 ATGAACAGTG
257167 A
1 A
257168 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:257255 original size:53 final size:53
Alignment explanation
Indices: 257191--257327 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
257181 CTACTTCCAA
*
257191 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
257244 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
257297 TGTATCGATACATATTTGTCTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
257328 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:257433 original size:21 final size:21
Alignment explanation
Indices: 257407--257447 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
257397 GTCAACCTTG
257407 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
257428 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
257448 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:260579 original size:14 final size:14
Alignment explanation
Indices: 260558--260591 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
260548 TGGGGCAAAT
260558 AAGATACCCTTGGA
1 AAGATACCCTTGGA
*
260572 AGGATACCCTTGGA
1 AAGATACCCTTGGA
260586 AAGATA
1 AAGATA
260592 TTTTGACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (14 bp):
AAGATACCCTTGGA
Found at i:263995 original size:97 final size:96
Alignment explanation
Indices: 263836--264082 Score: 316
Period size: 97 Copynumber: 2.5 Consensus size: 96
263826 AATTTTATTT
* * * *
263836 ATCGGGGATACTCCAACCCTATTCCTCTAATGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1 ATCGGGGACACTTCAACCC-ATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
* *
263901 GTTTAAATCTTATTCTTAGTTAAATTGCCACC
65 GTTTAAATCTTATTCTCACTTAAATTGCCACC
**
263933 ATCGGGGACACTTCAACTCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAAGGCATCAAA
1 ATCGGGGACACTTCAAC-CCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
* * *
263998 GTTTAAATTTTATTCTCACTTAAATTGTCATC
65 GTTTAAATCTTATTCTCACTTAAATTGCCACC
* * * *
264030 ATCGAGGACA-TTCCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGTTTTT
1 ATCGGGGACACTT-CAA-CCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTT
264083 CAATCAAAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
96 2 0.02
97 127 0.96
98 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (96 bp):
ATCGGGGACACTTCAACCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAG
TTTAAATCTTATTCTCACTTAAATTGCCACC
Found at i:264832 original size:13 final size:13
Alignment explanation
Indices: 264814--264838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
264804 CATAAAATGT
264814 TGTATCGATACAA
1 TGTATCGATACAA
264827 TGTATCGATACA
1 TGTATCGATACA
264839 TATTTTTTTT
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:264923 original size:13 final size:13
Alignment explanation
Indices: 264905--264929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
264895 ATTACTCACA
264905 TGTATCGATACAT
1 TGTATCGATACAT
264918 TGTATCGATACA
1 TGTATCGATACA
264930 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:264994 original size:52 final size:52
Alignment explanation
Indices: 264938--265062 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
264928 CACTGATCTT
*
264938 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
264990 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
265042 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
265063 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:278544 original size:37 final size:36
Alignment explanation
Indices: 278503--278577 Score: 82
Period size: 37 Copynumber: 2.0 Consensus size: 36
278493 AAAAAATGTC
*
278503 AAAA-GCAAAAGTACAAAATATGAAAA-GAAAAACAAAA
1 AAAAGGCAAAAG--CAAAATA-AAAAAGGAAAAACAAAA
*
278540 AAAAGTGCAAAAGCAAAATAAAAAAGGAACAACAAAA
1 AAAAG-GCAAAAGCAAAATAAAAAAGGAAAAACAAAA
278577 A
1 A
278578 TCCAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
36 4 0.12
37 22 0.67
39 7 0.21
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (36 bp):
AAAAGGCAAAAGCAAAATAAAAAAGGAAAAACAAAA
Found at i:278584 original size:45 final size:46
Alignment explanation
Indices: 278489--278589 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 46
278479 CATCATAATG
* *
278489 ACAAAAAAAA-TGTCAAAAGCAAAAGTACAAAATATGAAAAGAAAA
1 ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAA
278534 ACAAAAAAAAGTG-CAAAAGCAAAA-TA-AAAA-AGGAACAACAAAA
1 ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAA-AACAAAA
278577 ATCCAAAAAAAAG
1 A--CAAAAAAAAG
278590 ACATGAATGC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
42 4 0.08
43 11 0.22
44 2 0.04
45 31 0.62
46 2 0.04
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.08
Consensus pattern (46 bp):
ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAA
Found at i:279887 original size:27 final size:27
Alignment explanation
Indices: 279854--280126 Score: 377
Period size: 27 Copynumber: 10.0 Consensus size: 27
279844 TTTCTTTTCA
279854 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
279881 AAGTCCACAACTCCGTGGTATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
279908 AAAGTCTACAACTTCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
279936 AAAGTCCACAACTCCGTGGCATCTTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
279964 AAGTCCACAACTCCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
279991 AAGTCCACAACTCCGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
280018 AAGTCCACAACTCCGTGGCACCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* *
280046 AAGTCCACAACTCTGTGGCGTTCCTTTT
1 AAGTCCACAACTCCGTGGC-ATCCTTTT
*
280074 AAG-CCACAACTCCTTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
280100 AAGTCCACAACTTCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
280127 TATGCCCACA
Statistics
Matches: 220, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
26 10 0.05
27 134 0.61
28 74 0.34
29 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:280081 original size:109 final size:109
Alignment explanation
Indices: 279854--280125 Score: 402
Period size: 109 Copynumber: 2.5 Consensus size: 109
279844 TTTCTTTTCA
* * *
279854 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGTATCCTTTTAAAGTCTACAA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTAAAGTCCACAA
* * *
279919 CTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTT
65 CTCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGCATCCTTTT
*
279964 AAGTCCACAACTCCGTGGCATCTTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAAC
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAAC
* * *
280029 TCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTTT
66 TCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGC-ATCCTTTT
* * *
280074 AAG-CCACAACTCCTTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
280126 TTATGCCCAC
Statistics
Matches: 147, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
109 93 0.63
110 54 0.37
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (109 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAAC
TCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:280136 original size:55 final size:55
Alignment explanation
Indices: 279854--280192 Score: 375
Period size: 55 Copynumber: 6.2 Consensus size: 55
279844 TTTCTTTTCA
* *
279854 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGTATCCTTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTT
* * *
279909 AAGTCTACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCAT-CTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTTT
* * *
279964 AAGTCCACAACTCCGTGGCATCTTTTTAAGTCCACAACTCCGTGGCA-CCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTT
* * * *
280018 AAGTCCACAACTCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCC-TTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGC-ATCCTTTTT
* *
280074 AAG-CCACAACTCCTTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTT
* * * * ** ** *
280128 ATGCCCACAAGTCAGTGGCA-CCTATCCAAAGTCCACAACT-TTTGGCATCTTTTTT
1 AAGTCCACAACTCCGTGGCATCCT-T-TTAAGTCCACAACTCCGTGGCATCCTTTTT
*
280183 AAGCCCACAA
1 AAGTCCACAA
280193 GTCAATGGCA
Statistics
Matches: 242, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
53 3 0.01
54 74 0.31
55 125 0.52
56 38 0.16
57 2 0.01
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.30
Consensus pattern (55 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTT
Found at i:280145 original size:28 final size:28
Alignment explanation
Indices: 279835--280743 Score: 631
Period size: 28 Copynumber: 31.9 Consensus size: 28
279825 AGTTCACGAT
* * *
279835 TCAGTGGCATTTCTTTTCAAAGTCCACAAC
1 TCAGTGGCA--TCCTTTCAAAGCCCACAAG
* * * *
279865 TCCGTGGCATCCTTT-TAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * * * *
279892 TCCGTGGTATCCTTTTAAAGTCTACAACT
1 TCAGTGGCATCCTTTCAAAGCCCACAA-G
* * * *
279921 TC-GTGGCACCCTTTTAAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* ** * *
279948 TCCGTGGCAT-CTTTTTAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* ** * *
279975 TCCGTGGCAT-CTTTTTAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
280002 TCCGTGGCACCCTTT-AAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
280029 TCCGTGGCACCCGTTTC-AAGTCCACAAC
1 TCAGTGGCATCC-TTTCAAAGCCCACAAG
* * * *
280057 TCTGTGGCGTTCCTTT-TAAG-CCACAAC
1 TCAGTGGC-ATCCTTTCAAAGCCCACAAG
** * * *
280084 TCCTTGGCATCCTTT-TAAGTCCACAACT
1 TCAGTGGCATCCTTTCAAAGCCCACAA-G
** *
280112 TC-GTGGCATCCTTTTTATGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
280139 TCAGTGGCA-CCTATCCAAAGTCCACAAC
1 TCAGTGGCATCCT-TTCAAAGCCCACAAG
** * **
280167 T-TTTGGCATCTTTTTTAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
280194 TCAATGGCACCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * ** *
280222 TTAGTGGCACCCCTTTTTAAGCCCATAAG
1 TCAGTGGCA-TCCTTTCAAAGCCCACAAG
**
280251 TCAGTGGCATTATTTCAAAGCCCACACAAG
1 TCAGTGGCATCCTTTCAAAG-CC-CACAAG
** * *
280281 TTGGTGGCAACTCATTTGAAAGCCGACACAAG
1 TCAGTGGC-A-TCCTTTCAAAGCC--CACAAG
*
280313 TCAGTGGCAACCTATTTCAAAGCCCACATAAG
1 TCAGTGGCATCC--TTTCAAAGCCCAC--AAG
*
280345 TC-GTTGGCAACCCATTTCAAAGCCCACAAG
1 TCAG-TGGC-ATCC-TTTCAAAGCCCACAAG
*
280375 TCAATGGCATCCTTCTCAAAGCCCACAAG
1 TCAGTGGCATCCTT-TCAAAGCCCACAAG
*
280404 TTAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
280432 TTAGTGGCATCCTTCTCAAAGCCCACACAAA
1 TCAGTGGCATCCTT-TCAAAG-CC-CACAAG
* *
280463 TCAGTGACATCTTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
280491 TCAGTGGTATCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
280519 TCTGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
280547 TTAGTGGCATCCTTTTAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
280575 TTAGTGGCATCCTTCTCAAAGCTCACACAAA
1 TCAGTGGCATCCTT-TCAAAGC-C-CACAAG
* * *
280606 T-TGATGGCATCTTTTCAAAGCCCATAAG
1 TCAG-TGGCATCCTTTCAAAGCCCACAAG
* *
280634 TCAATGGCATCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
**
280662 TCAGTGGCATCCTTTTGAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
280690 TCAGTGGCATCCTTTCGAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
280718 TCAGTGGCATCCTTTCAAAGCCCACA
1 TCAGTGGCATCCTTTCAAAGCCCACA
280744 CAAGTCAATG
Statistics
Matches: 740, Mismatches: 102, Indels: 76
0.81 0.11 0.08
Matches are distributed among these distances:
26 10 0.01
27 153 0.21
28 360 0.49
29 75 0.10
30 49 0.07
31 36 0.05
32 54 0.07
33 3 0.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (28 bp):
TCAGTGGCATCCTTTCAAAGCCCACAAG
Found at i:280176 original size:82 final size:82
Alignment explanation
Indices: 279854--280167 Score: 375
Period size: 82 Copynumber: 3.8 Consensus size: 82
279844 TTTCTTTTCA
* *
279854 AAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGTATCCTTTTAAAGTCTACA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACA
*
279918 ACTTCGTGGCACCCTTTT
65 ACTCCGTGGCACCCTTTT
* *
279936 AAAGTCCACAACTCCGTGGCAT-CTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAGTCCACA
1 -AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACA
*
280000 ACTCCGTGGCACCCTTTA
65 ACTCCGTGGCACCCTTTT
* * * * *
280018 AAGTCCACAACTCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTTT-AAG-CCAC
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGC--ACCTTTTAAAGTCCAC
* *
280081 AACTCCTTGGCATCCTTTT
64 AACTCCGTGGCACCCTTTT
* * * * * **
280100 AAGTCCACAACTTCGTGGCATCCTTTTTATGCCCACAAGTCAGTGGCACCTATCCAAAGTCCACA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACCT-TTTAAAGTCCACA
280165 ACT
65 ACT
280168 TTTGGCATCT
Statistics
Matches: 198, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.02
81 21 0.11
82 114 0.58
83 55 0.28
84 5 0.03
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (82 bp):
AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAA
CTCCGTGGCACCCTTTT
Found at i:280190 original size:27 final size:28
Alignment explanation
Indices: 279858--280192 Score: 170
Period size: 27 Copynumber: 12.2 Consensus size: 28
279848 TTTTCAAAGT
* * *
279858 CCACAACTCCGTGGCATC-CTTTTAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* * * * *
279885 CCACAACTCCGTGGTATCCTTTTAAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* * * * *
279913 CTACAACT-TCGTGGCACCCTTTTAAAGT
1 CCACAACTCT-GTGGCATCTTTTTTAAGC
* *
279941 CCACAACTCCGTGGCATC-TTTTTAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* *
279968 CCACAACTCCGTGGCATC-TTTTTAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* ** * *
279995 CCACAACTCCGTGGCA-CCCTTTAAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* * ** * *
280022 CCACAACTCCGTGGCACCCGTTTCAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
* *
280050 CCACAACTCTGTGGCGT-TCCTTTTAAG-
1 CCACAACTCTGTGGCATCT-TTTTTAAGC
* *
280077 CCACAACTCCT-TGGCATC-CTTTTAAGT
1 CCACAACT-CTGTGGCATCTTTTTTAAGC
* *
280104 CCACAACT-TCGTGGCATCCTTTTTATGC
1 CCACAACTCT-GTGGCATCTTTTTTAAGC
* * * * *** *
280132 CCACAAGTCAGTGGCACCTATCCAAAGT
1 CCACAACTCTGTGGCATCTTTTTTAAGC
*
280160 CCACAACT-TTTGGCATCTTTTTTAAGC
1 CCACAACTCTGTGGCATCTTTTTTAAGC
280187 CCACAA
1 CCACAA
280193 GTCAATGGCA
Statistics
Matches: 251, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.00
26 9 0.04
27 136 0.54
28 105 0.42
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.30
Consensus pattern (28 bp):
CCACAACTCTGTGGCATCTTTTTTAAGC
Found at i:280536 original size:115 final size:112
Alignment explanation
Indices: 279849--280741 Score: 555
Period size: 115 Copynumber: 7.9 Consensus size: 112
279839 TGGCATTTCT
* * ** * * * *
279849 TTTCAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGTATCCTTTT-AAAG
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAG
* * * * * * * * *
279912 TCTACAACTTC-GTGGCACCCTTTTAAAGTCCACAACTCCGTGGCAT-C
65 CCCACAA-GTCAGTGGCATCCTTTCAAAGCCCATAAGTCTGTGGCATCC
** * * ** * * * * * * *
279959 TTTTTAAGTCCACAACTCCGTGGCAT-CTTTTTAAGTCCACAACTCCGTGGCACCCTTT-AAAGT
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
* * * * * * *
280022 CCACAACTCCGTGGCACCCGTTTC-AAGTCCACAACTCTGTGGCGTTCC
66 CCACAAGTCAGTGGCATCC-TTTCAAAGCCCATAAGTCTGTGGC-ATCC
* * *** * * * *
280070 TTT-TAAG-CCACAACTCCTTGGCATCCTTTT-AAGTCCACAACTTC-GTGGCATCCTTTT-TAT
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAA-GTCAGTGGCAT-CTTTTCAAA
* * * * * *
280130 GCCCACAAGTCAGTGGCA-CCTATCCAAAGTCCACAACT-TTTGGCATCT
64 GCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCATAAGTCTGTGGCATCC
** * * * * * * * *
280178 TTTTTAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCATAAGTTAGTGGCACCCCTTTT-TAA
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCA--TCTTTTCAAA
* ** * *
280242 GCCCATAAGTCAGTGGCATTATTTCAAAGCCCACACAAGT-TGGTGGCAACTCA
64 GCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CATAAGTCT-GTGGC-A-TCC
* * * * *
280295 TTTGAAAGCCGACACAAGTCAGTGGCAACCTATTTCAAAGCCCACATAAGTC-GTTGGCAACCCA
1 TTTCAAAGCC--CACAAGTTAGTGGCATCCT-TTT-AAAGCCCAC--AAGTCAG-TGGC-A-TCT
* *
280359 TTTCAAAGCCCACAAGTCAATGGCATCCTTCTCAAAGCCCACAAGT-TAGTGGCATCC
57 TTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCATAAGTCT-GTGGCATCC
* * *
280416 TTTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACACAAATCAGTGACATCTTTTCAA
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTT-TTAAAG-CC-CACAAGTCAGTGGCATCTTTTCAA
*
280481 AGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCATAAGTCTGTGGCATCC
63 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCTGTGGCATCC
* *
280531 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAG
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAG
* * * **
280596 CTCACACAAAT-TGATGGCATCTTTTCAAAGCCCATAAGTCAATGGCATCC
65 C-C-CACAAGTCAG-TGGCATCCTTTCAAAGCCCATAAGTCTGTGGCATCC
* * * * *
280646 TTTCAAAGCCCATAAGTCAGTGGCATCCTTTTGAAGCCCACAAGTCAGTGGCATCCTTTCGAAGC
1 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
280711 CCACAAGTCAGTGGCATCCTTTCAAAGCCCA
66 CCACAAGTCAGTGGCATCCTTTCAAAGCCCA
280742 CACAAGTCAA
Statistics
Matches: 652, Mismatches: 89, Indels: 82
0.79 0.11 0.10
Matches are distributed among these distances:
108 8 0.01
109 91 0.14
110 109 0.17
111 18 0.03
112 68 0.10
113 16 0.02
114 22 0.03
115 145 0.22
116 31 0.05
117 11 0.02
118 12 0.02
119 38 0.06
120 5 0.01
121 19 0.03
122 2 0.00
123 27 0.04
124 24 0.04
125 6 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (112 bp):
TTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
CCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCTGTGGCATCC
Found at i:280559 original size:143 final size:142
Alignment explanation
Indices: 280088--280746 Score: 702
Period size: 143 Copynumber: 4.6 Consensus size: 142
280078 CACAACTCCT
* * * * ** * *
280088 TGGCATCCTTT-TAAGTCCACAACTTCGTGGCATCCTTTTTATGCCCACAAGTCAGTGGCA-CCT
1 TGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
* * ** **
280151 ATC-CAAAG-TC-CACAACTTTTGGCATCTTTTTTAAGCCCACAAGTCAATGGCACCCTTTCAAA
66 -TCTCAAAGCCCACACAAATAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAA
*
280213 GCCCATAAGTTAG
130 GCCCATAAGTCAG
* ** * * ** *
280226 TGGCACCCCTTTTTAAGCCCATAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAA
1 TGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAG-CC-CACAAGTTAGTGGC-A
* * * * * **
280291 CTCATT-TGAAAGCCGACACAAGTCAGTGGCAACCTATTTCAAAGCCCACATAAGTCGTTGGCAA
62 -TCCTTCTCAAAGCCCACACAAAT-AGTGGC-ATCT-TTTCAAAGCCCAC--AAGTCAATGGC-A
* *
280355 CCCATTTCAAAGCCCACAAGTCAA
120 CCC-TTTCAAAGCCCATAAGTCAG
280379 TGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
1 TGGCATCCTT-TCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
280444 TTCTCAAAGCCCACACAAATCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGTATCCTTTCAA
65 TTCTCAAAGCCCACACAAAT-AGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAA
*
280509 AGCCCATAAGTCTG
129 AGCCCATAAGTCAG
*
280523 TGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTTAGTGGCATCCT
1 TGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
* * * *
280588 TCTCAAAGCTCACACAAATTGATGGCATCTTTTCAAAGCCCATAAGTCAATGGCATCCTTTCAAA
66 TCTCAAAGCCCACACAAATAG-TGGCATCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAA
280653 GCCCATAAGTCAG
130 GCCCATAAGTCAG
** * * *
280666 TGGCATCCTTTTGAAGCCCACAAGTCAGTGGCATCCTTTCGAAGCCCACAAGTCAGTGGCATCCT
1 TGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
280731 T-TCAAAGCCCACACAA
66 TCTCAAAGCCCACACAA
280747 GTCAATGGCT
Statistics
Matches: 437, Mismatches: 64, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
138 5 0.01
139 5 0.01
140 22 0.05
141 2 0.00
142 27 0.06
143 184 0.42
144 32 0.07
145 5 0.01
146 14 0.03
147 4 0.01
148 16 0.04
149 18 0.04
150 21 0.05
151 22 0.05
152 10 0.02
153 50 0.11
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (142 bp):
TGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
TCTCAAAGCCCACACAAATAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAG
CCCATAAGTCAG
Found at i:283502 original size:97 final size:97
Alignment explanation
Indices: 283398--283637 Score: 329
Period size: 97 Copynumber: 2.5 Consensus size: 97
283388 AATTTTAATT
*
283398 ATCGGGGATACTCTAACCCTATTCCTCCAAGGGGATACTCCAACCCAGCTTTTAAACACATCAAA
1 ATCGGGGATACTCTAACCCTATTCCTCCGAGGGGATACTCCAACCCAGCTTTTAAACACATCAAA
* *
283463 TTTTAAATCTTATTCTCACTTAAATTGTCACC
66 GTTTAAATCTTATTCTAACTTAAATTGTCACC
* * *
283495 ATCGGGGATACT-TCAACCCTATTCCTCTGAGGGGATACTCCAACCCTGCTTTTAAACGCATCAA
1 ATCGGGGATACTCT-AACCCTATTCCTCCGAGGGGATACTCCAACCCAGCTTTTAAACACATCAA
* *
283559 AGTTTAAATTTTATTCTAACTTAAATTGTCATC
65 AGTTTAAATCTTATTCTAACTTAAATTGTCACC
* * * * * * *
283592 ATCGAGGACACTCCAACCCCATTCTTTCGAGAGGATACTCCAACCC
1 ATCGGGGATACTCTAACCCTATTCCTCCGAGGGGATACTCCAACCC
283638 CATTTTTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 1 0.01
97 124 0.99
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (97 bp):
ATCGGGGATACTCTAACCCTATTCCTCCGAGGGGATACTCCAACCCAGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTAACTTAAATTGTCACC
Found at i:283631 original size:27 final size:26
Alignment explanation
Indices: 283595--283645 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
283585 TGTCATCATC
283595 GAGGACACTCCAACCCCATTCTTTCGA
1 GAGGACACTCCAACCCCATT-TTTCGA
*
283622 GAGGATACTCCAACCCCATTTTTC
1 GAGGACACTCCAACCCCATTTTTC
283646 AATCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.25
Consensus pattern (26 bp):
GAGGACACTCCAACCCCATTTTTCGA
Found at i:289087 original size:15 final size:15
Alignment explanation
Indices: 289045--289092 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
289035 GCAGTGTATC
289045 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
289060 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
289075 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
289090 GAT
1 GAT
289093 TTGGCAAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GATGATTTTGTGGTG
Found at i:293786 original size:28 final size:28
Alignment explanation
Indices: 293752--293833 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
293742 TTTTGGAGAT
*
293752 AATAACGAGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
* *
293780 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
293808 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
293834 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 40 0.87
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:293976 original size:51 final size:50
Alignment explanation
Indices: 293816--293986 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 50
293806 GAAATAACGA
* * * *
293816 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATGA-TA-TTTTGAAAATAAAATCGG
** * * * * * *
293868 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGA-AAAATGATATTTTGAAAATAAAATCGG
*
293921 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAT-GATATTTTGAAAATAAAATCGG
293972 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
293987 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.37
52 16 0.17
53 32 0.34
54 3 0.03
55 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATGATATTTTGAAAATAAAATCGG
Done.