Multiple sequence alignment - TraesCS7A01G008100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G008100 chr7A 100.000 2973 0 0 1 2973 3633857 3630885 0.000000e+00 5491
1 TraesCS7A01G008100 chr7A 88.796 1312 129 12 692 1997 1998060 1996761 0.000000e+00 1592
2 TraesCS7A01G008100 chr7A 87.323 1412 149 16 733 2136 3311057 3312446 0.000000e+00 1589
3 TraesCS7A01G008100 chr7A 88.768 1291 126 13 692 1977 3209568 3208292 0.000000e+00 1563
4 TraesCS7A01G008100 chr7A 92.349 745 55 1 2229 2973 3208034 3207292 0.000000e+00 1059
5 TraesCS7A01G008100 chr7A 87.678 211 25 1 263 473 3211518 3211309 8.230000e-61 244
6 TraesCS7A01G008100 chr7A 87.204 211 23 3 263 473 2000247 2000041 1.380000e-58 237
7 TraesCS7A01G008100 chr7A 85.714 119 12 3 369 485 94784875 94784760 1.450000e-23 121
8 TraesCS7A01G008100 chr4A 90.251 1313 115 6 773 2081 739650503 739651806 0.000000e+00 1703
9 TraesCS7A01G008100 chr4A 88.897 1387 119 14 773 2155 741485751 741484396 0.000000e+00 1676
10 TraesCS7A01G008100 chr4A 89.794 1313 121 6 773 2081 742055782 742057085 0.000000e+00 1670
11 TraesCS7A01G008100 chr4A 90.464 1206 101 6 952 2153 740456801 740455606 0.000000e+00 1578
12 TraesCS7A01G008100 chr4A 92.549 765 53 4 2210 2973 739652023 739652784 0.000000e+00 1094
13 TraesCS7A01G008100 chr4A 92.418 765 54 4 2210 2973 742057302 742058063 0.000000e+00 1088
14 TraesCS7A01G008100 chr4A 92.573 754 53 3 2222 2973 740270886 740271638 0.000000e+00 1079
15 TraesCS7A01G008100 chr4A 92.440 754 54 3 2222 2973 740348292 740349044 0.000000e+00 1074
16 TraesCS7A01G008100 chr4A 92.308 754 55 3 2222 2973 740305038 740305790 0.000000e+00 1068
17 TraesCS7A01G008100 chr4A 91.512 754 64 0 2220 2973 741815646 741814893 0.000000e+00 1038
18 TraesCS7A01G008100 chr4A 86.957 207 26 1 263 469 740929353 740929558 6.410000e-57 231
19 TraesCS7A01G008100 chr7D 90.484 1240 102 8 922 2155 2611280 2610051 0.000000e+00 1622
20 TraesCS7A01G008100 chr7D 89.992 1229 105 11 773 1997 2359173 2357959 0.000000e+00 1572
21 TraesCS7A01G008100 chr7D 92.553 752 56 0 2220 2971 3787003 3786252 0.000000e+00 1079
22 TraesCS7A01G008100 chr7D 92.215 745 58 0 2229 2973 3633199 3632455 0.000000e+00 1055
23 TraesCS7A01G008100 chr7D 91.379 754 65 0 2220 2973 2609945 2609192 0.000000e+00 1033
24 TraesCS7A01G008100 chr7D 91.989 699 56 0 2275 2973 2357659 2356961 0.000000e+00 981
25 TraesCS7A01G008100 chr7D 89.249 772 63 10 2217 2973 2566116 2565350 0.000000e+00 948
26 TraesCS7A01G008100 chr7D 89.933 745 62 7 2229 2973 3906951 3907682 0.000000e+00 948
27 TraesCS7A01G008100 chr7D 79.230 727 125 14 2258 2962 10505189 10505911 1.600000e-132 483
28 TraesCS7A01G008100 chr7D 88.889 216 23 1 263 478 3903282 3903496 6.320000e-67 265
29 TraesCS7A01G008100 chr7D 85.526 228 25 7 21 243 396452204 396452428 6.410000e-57 231
30 TraesCS7A01G008100 chr7D 87.097 186 21 2 303 486 2568865 2568681 1.080000e-49 207
31 TraesCS7A01G008100 chr4B 82.663 646 106 6 2271 2911 660134949 660135593 4.300000e-158 568
32 TraesCS7A01G008100 chr6A 85.463 227 28 5 21 243 514705116 514704891 6.410000e-57 231
33 TraesCS7A01G008100 chr6A 85.366 123 14 3 376 495 538097836 538097715 1.120000e-24 124
34 TraesCS7A01G008100 chr2D 85.202 223 31 2 23 243 566250507 566250729 8.290000e-56 228
35 TraesCS7A01G008100 chr4D 84.545 220 32 2 26 243 255811228 255811447 1.790000e-52 217
36 TraesCS7A01G008100 chr7B 84.141 227 31 5 21 243 313691030 313690805 6.450000e-52 215
37 TraesCS7A01G008100 chr7B 84.305 223 30 5 24 243 40342898 40342678 2.320000e-51 213
38 TraesCS7A01G008100 chr7B 86.441 118 13 2 380 495 437669566 437669682 3.110000e-25 126
39 TraesCS7A01G008100 chr3B 84.234 222 33 2 24 243 682655380 682655601 6.450000e-52 215
40 TraesCS7A01G008100 chr6D 82.996 247 29 10 24 264 340467965 340467726 8.350000e-51 211
41 TraesCS7A01G008100 chr6D 86.179 123 13 3 376 495 392273231 392273110 2.400000e-26 130
42 TraesCS7A01G008100 chr1A 82.258 248 34 9 21 264 520561475 520561234 3.880000e-49 206
43 TraesCS7A01G008100 chr1A 85.950 121 14 2 377 495 459273228 459273347 3.110000e-25 126
44 TraesCS7A01G008100 chr1D 84.034 119 15 4 369 485 7349693 7349809 8.710000e-21 111
45 TraesCS7A01G008100 chr6B 83.898 118 13 5 380 495 519402957 519402844 1.130000e-19 108
46 TraesCS7A01G008100 chr5A 81.538 130 16 8 370 495 358486302 358486427 1.890000e-17 100


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G008100 chr7A 3630885 3633857 2972 True 5491.000000 5491 100.000000 1 2973 1 chr7A.!!$R1 2972
1 TraesCS7A01G008100 chr7A 3311057 3312446 1389 False 1589.000000 1589 87.323000 733 2136 1 chr7A.!!$F1 1403
2 TraesCS7A01G008100 chr7A 3207292 3211518 4226 True 955.333333 1563 89.598333 263 2973 3 chr7A.!!$R4 2710
3 TraesCS7A01G008100 chr7A 1996761 2000247 3486 True 914.500000 1592 88.000000 263 1997 2 chr7A.!!$R3 1734
4 TraesCS7A01G008100 chr4A 741484396 741485751 1355 True 1676.000000 1676 88.897000 773 2155 1 chr4A.!!$R2 1382
5 TraesCS7A01G008100 chr4A 740455606 740456801 1195 True 1578.000000 1578 90.464000 952 2153 1 chr4A.!!$R1 1201
6 TraesCS7A01G008100 chr4A 739650503 739652784 2281 False 1398.500000 1703 91.400000 773 2973 2 chr4A.!!$F5 2200
7 TraesCS7A01G008100 chr4A 742055782 742058063 2281 False 1379.000000 1670 91.106000 773 2973 2 chr4A.!!$F6 2200
8 TraesCS7A01G008100 chr4A 740270886 740271638 752 False 1079.000000 1079 92.573000 2222 2973 1 chr4A.!!$F1 751
9 TraesCS7A01G008100 chr4A 740348292 740349044 752 False 1074.000000 1074 92.440000 2222 2973 1 chr4A.!!$F3 751
10 TraesCS7A01G008100 chr4A 740305038 740305790 752 False 1068.000000 1068 92.308000 2222 2973 1 chr4A.!!$F2 751
11 TraesCS7A01G008100 chr4A 741814893 741815646 753 True 1038.000000 1038 91.512000 2220 2973 1 chr4A.!!$R3 753
12 TraesCS7A01G008100 chr7D 2609192 2611280 2088 True 1327.500000 1622 90.931500 922 2973 2 chr7D.!!$R5 2051
13 TraesCS7A01G008100 chr7D 2356961 2359173 2212 True 1276.500000 1572 90.990500 773 2973 2 chr7D.!!$R3 2200
14 TraesCS7A01G008100 chr7D 3786252 3787003 751 True 1079.000000 1079 92.553000 2220 2971 1 chr7D.!!$R2 751
15 TraesCS7A01G008100 chr7D 3632455 3633199 744 True 1055.000000 1055 92.215000 2229 2973 1 chr7D.!!$R1 744
16 TraesCS7A01G008100 chr7D 3903282 3907682 4400 False 606.500000 948 89.411000 263 2973 2 chr7D.!!$F3 2710
17 TraesCS7A01G008100 chr7D 2565350 2568865 3515 True 577.500000 948 88.173000 303 2973 2 chr7D.!!$R4 2670
18 TraesCS7A01G008100 chr7D 10505189 10505911 722 False 483.000000 483 79.230000 2258 2962 1 chr7D.!!$F1 704
19 TraesCS7A01G008100 chr4B 660134949 660135593 644 False 568.000000 568 82.663000 2271 2911 1 chr4B.!!$F1 640

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
706 2508 0.955428 TCTTCATGCAGACAACGGGC 60.955 55.0 0.0 0.0 0.0 6.13 F
1136 2948 0.250338 GGGGTCAATGATAGGTCGCC 60.250 60.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 3385 0.183492 GGCATCATAGGCCCAACAGA 59.817 55.000 0.0 0.0 45.87 3.41 R
2309 4295 1.598962 CCCATGCTGCTGTATCCCG 60.599 63.158 0.0 0.0 0.00 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.562454 AAATATCAAACCAATACTACCACCG 57.438 36.000 0.00 0.00 0.00 4.94
34 35 4.563140 ATCAAACCAATACTACCACCGT 57.437 40.909 0.00 0.00 0.00 4.83
35 36 3.929094 TCAAACCAATACTACCACCGTC 58.071 45.455 0.00 0.00 0.00 4.79
36 37 3.004862 CAAACCAATACTACCACCGTCC 58.995 50.000 0.00 0.00 0.00 4.79
37 38 2.242882 ACCAATACTACCACCGTCCT 57.757 50.000 0.00 0.00 0.00 3.85
38 39 1.829222 ACCAATACTACCACCGTCCTG 59.171 52.381 0.00 0.00 0.00 3.86
39 40 1.138266 CCAATACTACCACCGTCCTGG 59.862 57.143 0.00 0.00 46.41 4.45
50 51 1.746470 CCGTCCTGGTTTATTGGTCC 58.254 55.000 0.00 0.00 0.00 4.46
51 52 1.680860 CCGTCCTGGTTTATTGGTCCC 60.681 57.143 0.00 0.00 0.00 4.46
52 53 1.680860 CGTCCTGGTTTATTGGTCCCC 60.681 57.143 0.00 0.00 0.00 4.81
53 54 1.639108 GTCCTGGTTTATTGGTCCCCT 59.361 52.381 0.00 0.00 0.00 4.79
54 55 2.042569 GTCCTGGTTTATTGGTCCCCTT 59.957 50.000 0.00 0.00 0.00 3.95
55 56 2.310647 TCCTGGTTTATTGGTCCCCTTC 59.689 50.000 0.00 0.00 0.00 3.46
56 57 2.365582 CTGGTTTATTGGTCCCCTTCG 58.634 52.381 0.00 0.00 0.00 3.79
57 58 1.706305 TGGTTTATTGGTCCCCTTCGT 59.294 47.619 0.00 0.00 0.00 3.85
58 59 2.911636 TGGTTTATTGGTCCCCTTCGTA 59.088 45.455 0.00 0.00 0.00 3.43
59 60 3.524380 TGGTTTATTGGTCCCCTTCGTAT 59.476 43.478 0.00 0.00 0.00 3.06
60 61 4.018233 TGGTTTATTGGTCCCCTTCGTATT 60.018 41.667 0.00 0.00 0.00 1.89
61 62 4.951715 GGTTTATTGGTCCCCTTCGTATTT 59.048 41.667 0.00 0.00 0.00 1.40
62 63 5.419788 GGTTTATTGGTCCCCTTCGTATTTT 59.580 40.000 0.00 0.00 0.00 1.82
63 64 6.327154 GTTTATTGGTCCCCTTCGTATTTTG 58.673 40.000 0.00 0.00 0.00 2.44
64 65 3.512219 TTGGTCCCCTTCGTATTTTGT 57.488 42.857 0.00 0.00 0.00 2.83
65 66 2.785562 TGGTCCCCTTCGTATTTTGTG 58.214 47.619 0.00 0.00 0.00 3.33
66 67 1.471287 GGTCCCCTTCGTATTTTGTGC 59.529 52.381 0.00 0.00 0.00 4.57
67 68 2.433436 GTCCCCTTCGTATTTTGTGCT 58.567 47.619 0.00 0.00 0.00 4.40
68 69 3.602483 GTCCCCTTCGTATTTTGTGCTA 58.398 45.455 0.00 0.00 0.00 3.49
69 70 4.004982 GTCCCCTTCGTATTTTGTGCTAA 58.995 43.478 0.00 0.00 0.00 3.09
70 71 4.456566 GTCCCCTTCGTATTTTGTGCTAAA 59.543 41.667 0.00 0.00 0.00 1.85
71 72 5.124936 GTCCCCTTCGTATTTTGTGCTAAAT 59.875 40.000 0.00 0.00 0.00 1.40
72 73 5.712917 TCCCCTTCGTATTTTGTGCTAAATT 59.287 36.000 0.00 0.00 0.00 1.82
73 74 6.209788 TCCCCTTCGTATTTTGTGCTAAATTT 59.790 34.615 0.00 0.00 0.00 1.82
74 75 6.871492 CCCCTTCGTATTTTGTGCTAAATTTT 59.129 34.615 0.00 0.00 0.00 1.82
75 76 8.030106 CCCCTTCGTATTTTGTGCTAAATTTTA 58.970 33.333 0.00 0.00 0.00 1.52
76 77 9.413048 CCCTTCGTATTTTGTGCTAAATTTTAA 57.587 29.630 0.00 0.00 0.00 1.52
79 80 9.745880 TTCGTATTTTGTGCTAAATTTTAACCA 57.254 25.926 0.00 0.00 0.00 3.67
80 81 9.915629 TCGTATTTTGTGCTAAATTTTAACCAT 57.084 25.926 0.00 0.00 0.00 3.55
113 114 8.783833 ACTATGAGATAATAATGCATGTCACC 57.216 34.615 0.00 0.00 28.43 4.02
114 115 8.377799 ACTATGAGATAATAATGCATGTCACCA 58.622 33.333 0.00 0.00 28.43 4.17
115 116 9.223099 CTATGAGATAATAATGCATGTCACCAA 57.777 33.333 0.00 0.00 28.43 3.67
116 117 7.878547 TGAGATAATAATGCATGTCACCAAA 57.121 32.000 0.00 0.00 0.00 3.28
117 118 8.291191 TGAGATAATAATGCATGTCACCAAAA 57.709 30.769 0.00 0.00 0.00 2.44
118 119 8.747471 TGAGATAATAATGCATGTCACCAAAAA 58.253 29.630 0.00 0.00 0.00 1.94
119 120 9.754382 GAGATAATAATGCATGTCACCAAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
126 127 8.578308 AATGCATGTCACCAAAAATTATATCG 57.422 30.769 0.00 0.00 0.00 2.92
127 128 7.094508 TGCATGTCACCAAAAATTATATCGT 57.905 32.000 0.00 0.00 0.00 3.73
128 129 7.542890 TGCATGTCACCAAAAATTATATCGTT 58.457 30.769 0.00 0.00 0.00 3.85
129 130 7.487509 TGCATGTCACCAAAAATTATATCGTTG 59.512 33.333 0.00 0.00 0.00 4.10
130 131 7.700234 GCATGTCACCAAAAATTATATCGTTGA 59.300 33.333 0.00 0.00 0.00 3.18
131 132 9.566530 CATGTCACCAAAAATTATATCGTTGAA 57.433 29.630 0.00 0.00 0.00 2.69
149 150 8.317891 TCGTTGAATTTGTATGTGAACATAGT 57.682 30.769 3.38 0.00 39.29 2.12
150 151 8.779303 TCGTTGAATTTGTATGTGAACATAGTT 58.221 29.630 3.38 0.00 39.29 2.24
151 152 9.393249 CGTTGAATTTGTATGTGAACATAGTTT 57.607 29.630 3.38 0.00 39.29 2.66
153 154 9.906660 TTGAATTTGTATGTGAACATAGTTTCC 57.093 29.630 3.38 0.00 39.29 3.13
154 155 8.519526 TGAATTTGTATGTGAACATAGTTTCCC 58.480 33.333 3.38 0.00 39.29 3.97
155 156 6.489127 TTTGTATGTGAACATAGTTTCCCG 57.511 37.500 3.38 0.00 39.29 5.14
156 157 5.155278 TGTATGTGAACATAGTTTCCCGT 57.845 39.130 3.38 0.00 39.29 5.28
157 158 4.932799 TGTATGTGAACATAGTTTCCCGTG 59.067 41.667 3.38 0.00 39.29 4.94
158 159 3.755112 TGTGAACATAGTTTCCCGTGA 57.245 42.857 0.00 0.00 0.00 4.35
159 160 4.280436 TGTGAACATAGTTTCCCGTGAT 57.720 40.909 0.00 0.00 0.00 3.06
160 161 5.408880 TGTGAACATAGTTTCCCGTGATA 57.591 39.130 0.00 0.00 0.00 2.15
161 162 5.984725 TGTGAACATAGTTTCCCGTGATAT 58.015 37.500 0.00 0.00 0.00 1.63
162 163 6.411376 TGTGAACATAGTTTCCCGTGATATT 58.589 36.000 0.00 0.00 0.00 1.28
163 164 7.557724 TGTGAACATAGTTTCCCGTGATATTA 58.442 34.615 0.00 0.00 0.00 0.98
164 165 8.208224 TGTGAACATAGTTTCCCGTGATATTAT 58.792 33.333 0.00 0.00 0.00 1.28
165 166 9.052759 GTGAACATAGTTTCCCGTGATATTATT 57.947 33.333 0.00 0.00 0.00 1.40
166 167 9.621629 TGAACATAGTTTCCCGTGATATTATTT 57.378 29.630 0.00 0.00 0.00 1.40
169 170 8.846211 ACATAGTTTCCCGTGATATTATTTTGG 58.154 33.333 0.00 0.00 0.00 3.28
170 171 6.709018 AGTTTCCCGTGATATTATTTTGGG 57.291 37.500 0.00 0.00 36.48 4.12
171 172 5.596772 AGTTTCCCGTGATATTATTTTGGGG 59.403 40.000 7.71 0.00 35.82 4.96
172 173 4.799715 TCCCGTGATATTATTTTGGGGT 57.200 40.909 7.71 0.00 35.82 4.95
173 174 5.908562 TCCCGTGATATTATTTTGGGGTA 57.091 39.130 7.71 0.00 35.82 3.69
174 175 5.623169 TCCCGTGATATTATTTTGGGGTAC 58.377 41.667 7.71 0.00 35.82 3.34
175 176 5.132312 TCCCGTGATATTATTTTGGGGTACA 59.868 40.000 0.00 0.00 35.82 2.90
176 177 6.007703 CCCGTGATATTATTTTGGGGTACAT 58.992 40.000 0.00 0.00 0.00 2.29
177 178 6.072175 CCCGTGATATTATTTTGGGGTACATG 60.072 42.308 0.00 0.00 0.00 3.21
178 179 6.378582 CGTGATATTATTTTGGGGTACATGC 58.621 40.000 0.00 0.00 0.00 4.06
179 180 6.016693 CGTGATATTATTTTGGGGTACATGCA 60.017 38.462 0.00 0.00 0.00 3.96
180 181 7.309133 CGTGATATTATTTTGGGGTACATGCAT 60.309 37.037 0.00 0.00 0.00 3.96
181 182 8.367156 GTGATATTATTTTGGGGTACATGCATT 58.633 33.333 0.00 0.00 0.00 3.56
182 183 9.593565 TGATATTATTTTGGGGTACATGCATTA 57.406 29.630 0.00 0.00 0.00 1.90
185 186 7.482169 TTATTTTGGGGTACATGCATTAACA 57.518 32.000 0.00 0.00 0.00 2.41
186 187 6.558488 ATTTTGGGGTACATGCATTAACAT 57.442 33.333 0.00 0.00 0.00 2.71
187 188 6.365970 TTTTGGGGTACATGCATTAACATT 57.634 33.333 0.00 0.00 0.00 2.71
188 189 6.365970 TTTGGGGTACATGCATTAACATTT 57.634 33.333 0.00 0.00 0.00 2.32
189 190 6.365970 TTGGGGTACATGCATTAACATTTT 57.634 33.333 0.00 0.00 0.00 1.82
190 191 5.728471 TGGGGTACATGCATTAACATTTTG 58.272 37.500 0.00 0.00 0.00 2.44
191 192 5.247110 TGGGGTACATGCATTAACATTTTGT 59.753 36.000 0.00 0.00 0.00 2.83
192 193 6.169800 GGGGTACATGCATTAACATTTTGTT 58.830 36.000 0.00 0.00 43.88 2.83
193 194 6.091986 GGGGTACATGCATTAACATTTTGTTG 59.908 38.462 0.00 0.00 41.30 3.33
194 195 6.870965 GGGTACATGCATTAACATTTTGTTGA 59.129 34.615 0.00 0.00 41.30 3.18
195 196 7.548780 GGGTACATGCATTAACATTTTGTTGAT 59.451 33.333 0.00 0.00 41.30 2.57
232 233 9.787532 ATCAAATTAGACACAAAATACGAATGG 57.212 29.630 0.00 0.00 0.00 3.16
233 234 8.240682 TCAAATTAGACACAAAATACGAATGGG 58.759 33.333 0.00 0.00 0.00 4.00
234 235 7.931578 AATTAGACACAAAATACGAATGGGA 57.068 32.000 0.00 0.00 0.00 4.37
235 236 6.730960 TTAGACACAAAATACGAATGGGAC 57.269 37.500 0.00 0.00 0.00 4.46
236 237 4.007659 AGACACAAAATACGAATGGGACC 58.992 43.478 0.00 0.00 0.00 4.46
237 238 3.754323 GACACAAAATACGAATGGGACCA 59.246 43.478 0.00 0.00 0.00 4.02
238 239 4.145807 ACACAAAATACGAATGGGACCAA 58.854 39.130 0.00 0.00 0.00 3.67
239 240 4.770010 ACACAAAATACGAATGGGACCAAT 59.230 37.500 0.00 0.00 0.00 3.16
240 241 5.946972 ACACAAAATACGAATGGGACCAATA 59.053 36.000 0.00 0.00 0.00 1.90
241 242 6.434652 ACACAAAATACGAATGGGACCAATAA 59.565 34.615 0.00 0.00 0.00 1.40
242 243 7.039644 ACACAAAATACGAATGGGACCAATAAA 60.040 33.333 0.00 0.00 0.00 1.40
243 244 7.978975 CACAAAATACGAATGGGACCAATAAAT 59.021 33.333 0.00 0.00 0.00 1.40
244 245 9.191479 ACAAAATACGAATGGGACCAATAAATA 57.809 29.630 0.00 0.00 0.00 1.40
249 250 7.889873 ACGAATGGGACCAATAAATAAATCA 57.110 32.000 0.00 0.00 0.00 2.57
250 251 7.712797 ACGAATGGGACCAATAAATAAATCAC 58.287 34.615 0.00 0.00 0.00 3.06
251 252 6.855914 CGAATGGGACCAATAAATAAATCACG 59.144 38.462 0.00 0.00 0.00 4.35
252 253 7.254966 CGAATGGGACCAATAAATAAATCACGA 60.255 37.037 0.00 0.00 0.00 4.35
253 254 8.477419 AATGGGACCAATAAATAAATCACGAT 57.523 30.769 0.00 0.00 0.00 3.73
254 255 7.270757 TGGGACCAATAAATAAATCACGATG 57.729 36.000 0.00 0.00 0.00 3.84
255 256 6.264292 TGGGACCAATAAATAAATCACGATGG 59.736 38.462 0.00 0.00 0.00 3.51
256 257 6.488683 GGGACCAATAAATAAATCACGATGGA 59.511 38.462 0.00 0.00 0.00 3.41
257 258 7.308589 GGGACCAATAAATAAATCACGATGGAG 60.309 40.741 0.00 0.00 0.00 3.86
258 259 7.308589 GGACCAATAAATAAATCACGATGGAGG 60.309 40.741 0.00 0.00 0.00 4.30
259 260 7.060421 ACCAATAAATAAATCACGATGGAGGT 58.940 34.615 0.00 0.00 0.00 3.85
260 261 8.215050 ACCAATAAATAAATCACGATGGAGGTA 58.785 33.333 0.00 0.00 0.00 3.08
261 262 8.721478 CCAATAAATAAATCACGATGGAGGTAG 58.279 37.037 0.00 0.00 0.00 3.18
274 275 8.173130 CACGATGGAGGTAGTAATTAACAAAAC 58.827 37.037 0.00 0.00 0.00 2.43
275 276 8.098912 ACGATGGAGGTAGTAATTAACAAAACT 58.901 33.333 0.00 0.00 0.00 2.66
277 278 7.894376 TGGAGGTAGTAATTAACAAAACTCG 57.106 36.000 0.00 0.00 33.17 4.18
367 368 1.423541 AGTAGATTTGTGGTGGTGGCA 59.576 47.619 0.00 0.00 0.00 4.92
369 370 2.014010 AGATTTGTGGTGGTGGCATT 57.986 45.000 0.00 0.00 0.00 3.56
396 397 9.104965 TGTTTTAAATACTCCATCCGTTCATAG 57.895 33.333 0.00 0.00 0.00 2.23
451 452 7.093354 ACACTACATACAGACTGAAATGAGTG 58.907 38.462 26.26 26.26 34.30 3.51
469 470 6.993786 TGAGTGAACAAACACACTAAATCA 57.006 33.333 0.00 0.00 45.54 2.57
482 483 6.432936 CACACTAAATCATGTGTATGCATCC 58.567 40.000 0.19 0.00 44.43 3.51
532 2281 6.757897 TGTGAAAACAAGTTCAAGTCATCT 57.242 33.333 0.00 0.00 39.18 2.90
539 2288 6.919775 ACAAGTTCAAGTCATCTAGTACCT 57.080 37.500 0.00 0.00 0.00 3.08
540 2289 6.692486 ACAAGTTCAAGTCATCTAGTACCTG 58.308 40.000 0.00 0.00 0.00 4.00
543 2292 6.010850 AGTTCAAGTCATCTAGTACCTGACA 58.989 40.000 14.26 0.00 41.34 3.58
549 2298 7.062749 AGTCATCTAGTACCTGACAAAAACA 57.937 36.000 14.26 0.00 41.34 2.83
600 2349 4.500887 CCGGTCGGACACAAGATTACATAT 60.501 45.833 10.76 0.00 37.50 1.78
601 2350 5.278610 CCGGTCGGACACAAGATTACATATA 60.279 44.000 10.76 0.00 37.50 0.86
603 2352 7.362315 CCGGTCGGACACAAGATTACATATATA 60.362 40.741 10.76 0.00 37.50 0.86
604 2353 7.696872 CGGTCGGACACAAGATTACATATATAG 59.303 40.741 10.76 0.00 0.00 1.31
605 2354 7.488471 GGTCGGACACAAGATTACATATATAGC 59.512 40.741 10.76 0.00 0.00 2.97
610 2370 8.079211 ACACAAGATTACATATATAGCCCGAT 57.921 34.615 0.00 0.00 0.00 4.18
616 2376 8.938883 AGATTACATATATAGCCCGATTGGATT 58.061 33.333 0.00 0.00 37.49 3.01
629 2389 2.300956 TTGGATTGCCAGCCAAACTA 57.699 45.000 4.81 0.00 46.91 2.24
631 2391 1.106285 GGATTGCCAGCCAAACTAGG 58.894 55.000 0.00 0.00 36.92 3.02
634 2394 1.178534 TTGCCAGCCAAACTAGGTGC 61.179 55.000 0.00 0.00 0.00 5.01
641 2401 3.758554 CAGCCAAACTAGGTGCATAAACT 59.241 43.478 0.00 0.00 0.00 2.66
645 2405 4.335594 CCAAACTAGGTGCATAAACTAGGC 59.664 45.833 16.70 0.00 38.75 3.93
646 2406 4.837093 AACTAGGTGCATAAACTAGGCA 57.163 40.909 16.70 0.00 43.88 4.75
650 2410 2.840651 AGGTGCATAAACTAGGCAGAGT 59.159 45.455 0.00 0.00 46.91 3.24
651 2411 3.118592 AGGTGCATAAACTAGGCAGAGTC 60.119 47.826 0.00 0.00 46.91 3.36
654 2414 3.769300 TGCATAAACTAGGCAGAGTCTCA 59.231 43.478 1.94 0.00 40.93 3.27
667 2427 5.580297 GGCAGAGTCTCAGTCTTTTATGAAG 59.420 44.000 1.94 0.00 0.00 3.02
686 2446 3.281727 AGTTTCTCTTTGCCTGTGTGA 57.718 42.857 0.00 0.00 0.00 3.58
706 2508 0.955428 TCTTCATGCAGACAACGGGC 60.955 55.000 0.00 0.00 0.00 6.13
714 2516 4.012895 GACAACGGGCGTGTGCTG 62.013 66.667 0.00 0.00 42.25 4.41
718 2520 2.325082 AACGGGCGTGTGCTGATTC 61.325 57.895 0.00 0.00 42.25 2.52
721 2523 1.672356 GGGCGTGTGCTGATTCTGT 60.672 57.895 0.00 0.00 42.25 3.41
725 2527 1.678360 CGTGTGCTGATTCTGTTTGC 58.322 50.000 0.00 0.00 0.00 3.68
730 2532 3.189910 TGTGCTGATTCTGTTTGCATCTC 59.810 43.478 0.00 0.00 36.04 2.75
731 2533 3.439476 GTGCTGATTCTGTTTGCATCTCT 59.561 43.478 0.00 0.00 36.04 3.10
739 2541 3.439129 TCTGTTTGCATCTCTGATGCTTG 59.561 43.478 26.10 14.76 44.79 4.01
744 2546 6.151480 TGTTTGCATCTCTGATGCTTGATTTA 59.849 34.615 26.10 7.88 44.79 1.40
755 2558 9.412460 TCTGATGCTTGATTTAGGTCAATAAAT 57.588 29.630 0.00 0.00 37.47 1.40
756 2559 9.674824 CTGATGCTTGATTTAGGTCAATAAATC 57.325 33.333 10.75 10.75 45.90 2.17
758 2561 7.953005 TGCTTGATTTAGGTCAATAAATCCA 57.047 32.000 13.71 5.28 45.45 3.41
759 2562 7.771183 TGCTTGATTTAGGTCAATAAATCCAC 58.229 34.615 13.71 6.54 45.45 4.02
761 2564 7.654022 TTGATTTAGGTCAATAAATCCACCC 57.346 36.000 13.71 0.00 45.45 4.61
762 2565 6.980577 TGATTTAGGTCAATAAATCCACCCT 58.019 36.000 13.71 0.00 45.45 4.34
765 2568 9.416284 GATTTAGGTCAATAAATCCACCCTTTA 57.584 33.333 7.62 0.00 42.48 1.85
766 2569 9.951866 ATTTAGGTCAATAAATCCACCCTTTAT 57.048 29.630 0.00 0.00 31.21 1.40
767 2570 8.990163 TTAGGTCAATAAATCCACCCTTTATC 57.010 34.615 0.00 0.00 30.43 1.75
770 2576 7.561356 AGGTCAATAAATCCACCCTTTATCAAG 59.439 37.037 0.00 0.00 30.43 3.02
781 2587 7.610305 TCCACCCTTTATCAAGAAAATGTCTAC 59.390 37.037 0.00 0.00 34.56 2.59
785 2591 9.231297 CCCTTTATCAAGAAAATGTCTACAAGA 57.769 33.333 0.00 0.00 34.56 3.02
822 2628 5.295950 TGCAATTTAAATGTGTTGGTGGAG 58.704 37.500 0.39 0.00 0.00 3.86
840 2646 5.347342 GTGGAGATGATGAGTGAAGTACAG 58.653 45.833 0.00 0.00 0.00 2.74
910 2716 7.275779 GTGAATAGAAATAGAAGCGAGTGTGAA 59.724 37.037 0.00 0.00 0.00 3.18
917 2724 3.903360 AGAAGCGAGTGTGAAAGTACTC 58.097 45.455 0.00 0.00 39.86 2.59
932 2739 9.913451 GTGAAAGTACTCGTAGTTAGTATGTAG 57.087 37.037 0.00 0.00 32.34 2.74
1009 2821 3.689347 TCAGATGTTTCAATGGGAGGTG 58.311 45.455 0.00 0.00 0.00 4.00
1010 2822 3.074390 TCAGATGTTTCAATGGGAGGTGT 59.926 43.478 0.00 0.00 0.00 4.16
1012 2824 5.009631 CAGATGTTTCAATGGGAGGTGTAA 58.990 41.667 0.00 0.00 0.00 2.41
1116 2928 1.546923 CATGGATGCAAGCTGACCAAA 59.453 47.619 0.00 0.00 34.28 3.28
1136 2948 0.250338 GGGGTCAATGATAGGTCGCC 60.250 60.000 0.00 0.00 0.00 5.54
1139 2951 0.529773 GTCAATGATAGGTCGCCGCA 60.530 55.000 0.00 0.00 0.00 5.69
1309 3124 3.632604 CGAGTCTCCTGGCTACAAATCTA 59.367 47.826 0.00 0.00 0.00 1.98
1310 3125 4.279671 CGAGTCTCCTGGCTACAAATCTAT 59.720 45.833 0.00 0.00 0.00 1.98
1331 3146 7.720442 TCTATCCACAAGATGACTCATGTTAG 58.280 38.462 1.25 0.53 36.33 2.34
1340 3155 5.610132 AGATGACTCATGTTAGGATTCCCAT 59.390 40.000 0.00 0.00 33.88 4.00
1347 3162 3.664320 TGTTAGGATTCCCATGAGGCTA 58.336 45.455 0.00 0.00 34.51 3.93
1402 3217 4.769688 TGATGTGTCAGGACATGTTATCC 58.230 43.478 5.29 0.00 43.97 2.59
1415 3230 6.098124 GGACATGTTATCCCCAAAATCATTCA 59.902 38.462 0.00 0.00 0.00 2.57
1437 3252 2.076100 GTTGATGTCATTCGTGCTCCA 58.924 47.619 0.00 0.00 0.00 3.86
1479 3294 3.941483 AGCAGATGGTTGAAAAGGTATCG 59.059 43.478 0.00 0.00 0.00 2.92
1509 3324 0.639943 TCTATGCCCAGGAGGTGGTA 59.360 55.000 0.00 0.00 46.37 3.25
1510 3325 1.051812 CTATGCCCAGGAGGTGGTAG 58.948 60.000 0.00 0.00 46.37 3.18
1537 3352 1.640917 TGAGAGGTACCAACTCCACC 58.359 55.000 25.64 10.71 35.58 4.61
1550 3365 1.705186 ACTCCACCATTGTAGCACCTT 59.295 47.619 0.00 0.00 0.00 3.50
1552 3367 1.702401 TCCACCATTGTAGCACCTTGA 59.298 47.619 0.00 0.00 0.00 3.02
1557 3372 1.064505 CATTGTAGCACCTTGATGGCG 59.935 52.381 0.00 0.00 40.22 5.69
1570 3385 0.928229 GATGGCGCGTAGATTTTCGT 59.072 50.000 8.43 0.00 0.00 3.85
1572 3387 0.108992 TGGCGCGTAGATTTTCGTCT 60.109 50.000 8.43 0.00 0.00 4.18
1573 3388 0.297820 GGCGCGTAGATTTTCGTCTG 59.702 55.000 8.43 0.00 0.00 3.51
1619 3434 3.031013 CACCCCCTTGTGAGAAAACTTT 58.969 45.455 0.00 0.00 38.55 2.66
1620 3435 3.031013 ACCCCCTTGTGAGAAAACTTTG 58.969 45.455 0.00 0.00 0.00 2.77
1642 3457 2.775384 TCCGGCCTAGTAATTGATGGTT 59.225 45.455 0.00 0.00 0.00 3.67
1716 3531 0.902531 AGGTGGTGTCTATTCACGGG 59.097 55.000 0.00 0.00 39.00 5.28
1782 3597 6.179040 CAATAAAATTGGGAGGCAATTCCAA 58.821 36.000 3.53 3.53 43.62 3.53
1948 3763 5.950544 TTGTCTACATGGCAATAGGTACT 57.049 39.130 0.00 0.00 37.72 2.73
2002 3853 9.557338 GTACTAGTTGTATAGCATAGTATGCAC 57.443 37.037 31.44 22.45 44.87 4.57
2041 3898 3.993081 GGTCCAGAATCGCATCTAGATTG 59.007 47.826 1.33 0.00 38.32 2.67
2045 3902 6.426328 GTCCAGAATCGCATCTAGATTGAATT 59.574 38.462 1.33 2.95 38.32 2.17
2073 3931 4.928615 CAGGTTGCTCTTTTGTTTTTCACA 59.071 37.500 0.00 0.00 0.00 3.58
2074 3932 4.929211 AGGTTGCTCTTTTGTTTTTCACAC 59.071 37.500 0.00 0.00 33.98 3.82
2075 3933 4.688413 GGTTGCTCTTTTGTTTTTCACACA 59.312 37.500 0.00 0.00 33.98 3.72
2076 3934 5.389411 GGTTGCTCTTTTGTTTTTCACACAC 60.389 40.000 0.00 0.00 33.98 3.82
2077 3935 4.876125 TGCTCTTTTGTTTTTCACACACA 58.124 34.783 0.00 0.00 33.98 3.72
2128 3986 8.137437 GTCAATTTCTGGAAAGATGTTTCTCAA 58.863 33.333 14.34 3.40 41.72 3.02
2174 4126 3.594134 AGTCAGCACTAACTTGATGCTC 58.406 45.455 0.00 0.00 46.68 4.26
2214 4168 9.213777 ACTTCAGGTTAATATCATAAGTCCTGA 57.786 33.333 6.49 6.49 45.24 3.86
2215 4169 9.482627 CTTCAGGTTAATATCATAAGTCCTGAC 57.517 37.037 9.61 0.00 46.12 3.51
2290 4276 4.337555 GCATTCTTGACATGCAGGTATCTT 59.662 41.667 2.88 0.00 45.50 2.40
2389 4375 8.726988 GGAAGCAGAATAATAACAACTACACAA 58.273 33.333 0.00 0.00 0.00 3.33
2680 4684 6.201517 AGTGTCTTGTTTGTCATCAAATTCG 58.798 36.000 0.00 0.00 43.92 3.34
2707 4711 7.977853 ACTTCAGAAAGAACGAAACAAGTACTA 59.022 33.333 0.00 0.00 36.30 1.82
2713 4717 6.839820 AGAACGAAACAAGTACTAAACCTG 57.160 37.500 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.612633 ACGGTGGTAGTATTGGTTTGATATTTT 59.387 33.333 0.00 0.00 0.00 1.82
11 12 6.243216 ACGGTGGTAGTATTGGTTTGATAT 57.757 37.500 0.00 0.00 0.00 1.63
12 13 5.395546 GGACGGTGGTAGTATTGGTTTGATA 60.396 44.000 0.00 0.00 0.00 2.15
14 15 3.306919 GGACGGTGGTAGTATTGGTTTGA 60.307 47.826 0.00 0.00 0.00 2.69
15 16 3.004862 GGACGGTGGTAGTATTGGTTTG 58.995 50.000 0.00 0.00 0.00 2.93
16 17 2.908351 AGGACGGTGGTAGTATTGGTTT 59.092 45.455 0.00 0.00 0.00 3.27
17 18 2.235402 CAGGACGGTGGTAGTATTGGTT 59.765 50.000 0.00 0.00 0.00 3.67
18 19 1.829222 CAGGACGGTGGTAGTATTGGT 59.171 52.381 0.00 0.00 0.00 3.67
19 20 1.138266 CCAGGACGGTGGTAGTATTGG 59.862 57.143 0.00 0.00 32.32 3.16
20 21 2.596904 CCAGGACGGTGGTAGTATTG 57.403 55.000 0.00 0.00 32.32 1.90
31 32 1.680860 GGGACCAATAAACCAGGACGG 60.681 57.143 0.00 0.00 42.50 4.79
32 33 1.746470 GGGACCAATAAACCAGGACG 58.254 55.000 0.00 0.00 0.00 4.79
47 48 2.433436 AGCACAAAATACGAAGGGGAC 58.567 47.619 0.00 0.00 0.00 4.46
48 49 2.871096 AGCACAAAATACGAAGGGGA 57.129 45.000 0.00 0.00 0.00 4.81
49 50 5.576447 ATTTAGCACAAAATACGAAGGGG 57.424 39.130 0.00 0.00 0.00 4.79
50 51 7.883229 AAAATTTAGCACAAAATACGAAGGG 57.117 32.000 0.00 0.00 0.00 3.95
53 54 9.745880 TGGTTAAAATTTAGCACAAAATACGAA 57.254 25.926 2.25 0.00 0.00 3.85
54 55 9.915629 ATGGTTAAAATTTAGCACAAAATACGA 57.084 25.926 2.25 0.00 0.00 3.43
87 88 9.224267 GGTGACATGCATTATTATCTCATAGTT 57.776 33.333 0.00 0.00 0.00 2.24
88 89 8.377799 TGGTGACATGCATTATTATCTCATAGT 58.622 33.333 0.00 0.00 33.40 2.12
89 90 8.782339 TGGTGACATGCATTATTATCTCATAG 57.218 34.615 0.00 0.00 33.40 2.23
90 91 9.571816 TTTGGTGACATGCATTATTATCTCATA 57.428 29.630 0.00 0.00 42.32 2.15
91 92 8.467963 TTTGGTGACATGCATTATTATCTCAT 57.532 30.769 0.00 0.00 42.32 2.90
92 93 7.878547 TTTGGTGACATGCATTATTATCTCA 57.121 32.000 0.00 0.00 42.32 3.27
93 94 9.754382 ATTTTTGGTGACATGCATTATTATCTC 57.246 29.630 0.00 0.00 42.32 2.75
100 101 9.676195 CGATATAATTTTTGGTGACATGCATTA 57.324 29.630 0.00 0.00 42.32 1.90
101 102 8.196771 ACGATATAATTTTTGGTGACATGCATT 58.803 29.630 0.00 0.00 42.32 3.56
102 103 7.715657 ACGATATAATTTTTGGTGACATGCAT 58.284 30.769 0.00 0.00 42.32 3.96
103 104 7.094508 ACGATATAATTTTTGGTGACATGCA 57.905 32.000 0.00 0.00 42.32 3.96
104 105 7.700234 TCAACGATATAATTTTTGGTGACATGC 59.300 33.333 0.00 0.00 42.32 4.06
105 106 9.566530 TTCAACGATATAATTTTTGGTGACATG 57.433 29.630 0.00 0.00 42.32 3.21
123 124 8.946085 ACTATGTTCACATACAAATTCAACGAT 58.054 29.630 0.00 0.00 37.76 3.73
124 125 8.317891 ACTATGTTCACATACAAATTCAACGA 57.682 30.769 0.00 0.00 37.76 3.85
125 126 8.948853 AACTATGTTCACATACAAATTCAACG 57.051 30.769 0.00 0.00 37.76 4.10
127 128 9.906660 GGAAACTATGTTCACATACAAATTCAA 57.093 29.630 0.00 0.00 37.76 2.69
128 129 8.519526 GGGAAACTATGTTCACATACAAATTCA 58.480 33.333 0.00 0.00 37.76 2.57
129 130 7.696453 CGGGAAACTATGTTCACATACAAATTC 59.304 37.037 0.00 0.17 37.76 2.17
130 131 7.175990 ACGGGAAACTATGTTCACATACAAATT 59.824 33.333 0.00 0.00 37.76 1.82
131 132 6.657541 ACGGGAAACTATGTTCACATACAAAT 59.342 34.615 0.00 0.00 37.76 2.32
132 133 5.998981 ACGGGAAACTATGTTCACATACAAA 59.001 36.000 0.00 0.00 37.76 2.83
133 134 5.410132 CACGGGAAACTATGTTCACATACAA 59.590 40.000 0.00 0.00 37.76 2.41
134 135 4.932799 CACGGGAAACTATGTTCACATACA 59.067 41.667 0.00 0.00 37.76 2.29
135 136 5.172934 TCACGGGAAACTATGTTCACATAC 58.827 41.667 0.00 0.00 37.76 2.39
136 137 5.408880 TCACGGGAAACTATGTTCACATA 57.591 39.130 0.00 0.00 37.76 2.29
137 138 4.280436 TCACGGGAAACTATGTTCACAT 57.720 40.909 0.00 0.00 40.22 3.21
138 139 3.755112 TCACGGGAAACTATGTTCACA 57.245 42.857 0.00 0.00 29.67 3.58
139 140 6.920569 AATATCACGGGAAACTATGTTCAC 57.079 37.500 0.00 0.00 0.00 3.18
140 141 9.621629 AAATAATATCACGGGAAACTATGTTCA 57.378 29.630 0.00 0.00 0.00 3.18
143 144 8.846211 CCAAAATAATATCACGGGAAACTATGT 58.154 33.333 0.00 0.00 0.00 2.29
144 145 8.296713 CCCAAAATAATATCACGGGAAACTATG 58.703 37.037 0.00 0.00 33.83 2.23
145 146 7.450323 CCCCAAAATAATATCACGGGAAACTAT 59.550 37.037 0.00 0.00 33.83 2.12
146 147 6.773685 CCCCAAAATAATATCACGGGAAACTA 59.226 38.462 0.00 0.00 33.83 2.24
147 148 5.596772 CCCCAAAATAATATCACGGGAAACT 59.403 40.000 0.00 0.00 33.83 2.66
148 149 5.361571 ACCCCAAAATAATATCACGGGAAAC 59.638 40.000 0.00 0.00 33.83 2.78
149 150 5.520751 ACCCCAAAATAATATCACGGGAAA 58.479 37.500 0.00 0.00 33.83 3.13
150 151 5.132043 ACCCCAAAATAATATCACGGGAA 57.868 39.130 0.00 0.00 33.83 3.97
151 152 4.799715 ACCCCAAAATAATATCACGGGA 57.200 40.909 0.00 0.00 33.83 5.14
152 153 5.378332 TGTACCCCAAAATAATATCACGGG 58.622 41.667 0.00 0.00 35.30 5.28
153 154 6.569610 GCATGTACCCCAAAATAATATCACGG 60.570 42.308 0.00 0.00 0.00 4.94
154 155 6.016693 TGCATGTACCCCAAAATAATATCACG 60.017 38.462 0.00 0.00 0.00 4.35
155 156 7.283625 TGCATGTACCCCAAAATAATATCAC 57.716 36.000 0.00 0.00 0.00 3.06
156 157 8.489676 AATGCATGTACCCCAAAATAATATCA 57.510 30.769 0.00 0.00 0.00 2.15
159 160 9.201989 TGTTAATGCATGTACCCCAAAATAATA 57.798 29.630 0.00 0.00 0.00 0.98
160 161 8.083828 TGTTAATGCATGTACCCCAAAATAAT 57.916 30.769 0.00 0.00 0.00 1.28
161 162 7.482169 TGTTAATGCATGTACCCCAAAATAA 57.518 32.000 0.00 0.00 0.00 1.40
162 163 7.667575 ATGTTAATGCATGTACCCCAAAATA 57.332 32.000 0.00 0.00 0.00 1.40
163 164 6.558488 ATGTTAATGCATGTACCCCAAAAT 57.442 33.333 0.00 0.00 0.00 1.82
164 165 6.365970 AATGTTAATGCATGTACCCCAAAA 57.634 33.333 0.00 0.00 0.00 2.44
165 166 6.365970 AAATGTTAATGCATGTACCCCAAA 57.634 33.333 0.00 0.00 0.00 3.28
166 167 6.169094 CAAAATGTTAATGCATGTACCCCAA 58.831 36.000 0.00 0.00 0.00 4.12
167 168 5.247110 ACAAAATGTTAATGCATGTACCCCA 59.753 36.000 0.00 0.00 0.00 4.96
168 169 5.729510 ACAAAATGTTAATGCATGTACCCC 58.270 37.500 0.00 0.00 0.00 4.95
169 170 6.870965 TCAACAAAATGTTAATGCATGTACCC 59.129 34.615 0.00 0.00 38.77 3.69
170 171 7.881643 TCAACAAAATGTTAATGCATGTACC 57.118 32.000 0.00 0.00 38.77 3.34
171 172 9.138062 TCATCAACAAAATGTTAATGCATGTAC 57.862 29.630 0.00 1.88 38.77 2.90
172 173 9.702494 TTCATCAACAAAATGTTAATGCATGTA 57.298 25.926 0.00 0.00 38.77 2.29
173 174 8.604640 TTCATCAACAAAATGTTAATGCATGT 57.395 26.923 0.00 0.00 38.77 3.21
176 177 9.491675 AGATTTCATCAACAAAATGTTAATGCA 57.508 25.926 2.16 0.00 38.77 3.96
206 207 9.787532 CCATTCGTATTTTGTGTCTAATTTGAT 57.212 29.630 0.00 0.00 0.00 2.57
207 208 8.240682 CCCATTCGTATTTTGTGTCTAATTTGA 58.759 33.333 0.00 0.00 0.00 2.69
208 209 8.240682 TCCCATTCGTATTTTGTGTCTAATTTG 58.759 33.333 0.00 0.00 0.00 2.32
209 210 8.241367 GTCCCATTCGTATTTTGTGTCTAATTT 58.759 33.333 0.00 0.00 0.00 1.82
210 211 7.148137 GGTCCCATTCGTATTTTGTGTCTAATT 60.148 37.037 0.00 0.00 0.00 1.40
211 212 6.317893 GGTCCCATTCGTATTTTGTGTCTAAT 59.682 38.462 0.00 0.00 0.00 1.73
212 213 5.644636 GGTCCCATTCGTATTTTGTGTCTAA 59.355 40.000 0.00 0.00 0.00 2.10
213 214 5.180271 GGTCCCATTCGTATTTTGTGTCTA 58.820 41.667 0.00 0.00 0.00 2.59
214 215 4.007659 GGTCCCATTCGTATTTTGTGTCT 58.992 43.478 0.00 0.00 0.00 3.41
215 216 3.754323 TGGTCCCATTCGTATTTTGTGTC 59.246 43.478 0.00 0.00 0.00 3.67
216 217 3.757270 TGGTCCCATTCGTATTTTGTGT 58.243 40.909 0.00 0.00 0.00 3.72
217 218 4.775058 TTGGTCCCATTCGTATTTTGTG 57.225 40.909 0.00 0.00 0.00 3.33
218 219 7.469537 TTTATTGGTCCCATTCGTATTTTGT 57.530 32.000 0.00 0.00 0.00 2.83
223 224 9.581289 TGATTTATTTATTGGTCCCATTCGTAT 57.419 29.630 0.00 0.00 0.00 3.06
224 225 8.842280 GTGATTTATTTATTGGTCCCATTCGTA 58.158 33.333 0.00 0.00 0.00 3.43
225 226 7.468084 CGTGATTTATTTATTGGTCCCATTCGT 60.468 37.037 0.00 0.00 0.00 3.85
226 227 6.855914 CGTGATTTATTTATTGGTCCCATTCG 59.144 38.462 0.00 0.00 0.00 3.34
227 228 7.936584 TCGTGATTTATTTATTGGTCCCATTC 58.063 34.615 0.00 0.00 0.00 2.67
228 229 7.889873 TCGTGATTTATTTATTGGTCCCATT 57.110 32.000 0.00 0.00 0.00 3.16
229 230 7.039784 CCATCGTGATTTATTTATTGGTCCCAT 60.040 37.037 0.00 0.00 0.00 4.00
230 231 6.264292 CCATCGTGATTTATTTATTGGTCCCA 59.736 38.462 0.00 0.00 0.00 4.37
231 232 6.488683 TCCATCGTGATTTATTTATTGGTCCC 59.511 38.462 0.00 0.00 0.00 4.46
232 233 7.308589 CCTCCATCGTGATTTATTTATTGGTCC 60.309 40.741 0.00 0.00 0.00 4.46
233 234 7.228706 ACCTCCATCGTGATTTATTTATTGGTC 59.771 37.037 0.00 0.00 0.00 4.02
234 235 7.060421 ACCTCCATCGTGATTTATTTATTGGT 58.940 34.615 0.00 0.00 0.00 3.67
235 236 7.510549 ACCTCCATCGTGATTTATTTATTGG 57.489 36.000 0.00 0.00 0.00 3.16
236 237 9.273016 ACTACCTCCATCGTGATTTATTTATTG 57.727 33.333 0.00 0.00 0.00 1.90
240 241 9.847224 AATTACTACCTCCATCGTGATTTATTT 57.153 29.630 0.00 0.00 0.00 1.40
243 244 9.754382 GTTAATTACTACCTCCATCGTGATTTA 57.246 33.333 0.00 0.00 0.00 1.40
244 245 8.262227 TGTTAATTACTACCTCCATCGTGATTT 58.738 33.333 0.00 0.00 0.00 2.17
245 246 7.788026 TGTTAATTACTACCTCCATCGTGATT 58.212 34.615 0.00 0.00 0.00 2.57
246 247 7.356089 TGTTAATTACTACCTCCATCGTGAT 57.644 36.000 0.00 0.00 0.00 3.06
247 248 6.778834 TGTTAATTACTACCTCCATCGTGA 57.221 37.500 0.00 0.00 0.00 4.35
248 249 7.837202 TTTGTTAATTACTACCTCCATCGTG 57.163 36.000 0.00 0.00 0.00 4.35
249 250 8.098912 AGTTTTGTTAATTACTACCTCCATCGT 58.901 33.333 0.00 0.00 0.00 3.73
250 251 8.488651 AGTTTTGTTAATTACTACCTCCATCG 57.511 34.615 0.00 0.00 0.00 3.84
251 252 8.601476 CGAGTTTTGTTAATTACTACCTCCATC 58.399 37.037 0.00 0.00 0.00 3.51
252 253 8.098912 ACGAGTTTTGTTAATTACTACCTCCAT 58.901 33.333 0.00 0.00 0.00 3.41
253 254 7.444299 ACGAGTTTTGTTAATTACTACCTCCA 58.556 34.615 0.00 0.00 0.00 3.86
254 255 7.895975 ACGAGTTTTGTTAATTACTACCTCC 57.104 36.000 0.00 0.00 0.00 4.30
255 256 9.080915 CCTACGAGTTTTGTTAATTACTACCTC 57.919 37.037 0.00 0.00 0.00 3.85
256 257 8.806146 TCCTACGAGTTTTGTTAATTACTACCT 58.194 33.333 0.00 0.00 0.00 3.08
257 258 8.986477 TCCTACGAGTTTTGTTAATTACTACC 57.014 34.615 0.00 0.00 0.00 3.18
310 311 1.468520 CGATTTGTTCATGCGGAAGGT 59.531 47.619 0.00 0.00 35.82 3.50
317 318 2.634982 TCCAAGCGATTTGTTCATGC 57.365 45.000 0.00 0.00 34.87 4.06
367 368 8.798402 TGAACGGATGGAGTATTTAAAACAAAT 58.202 29.630 0.00 0.00 0.00 2.32
369 370 7.747155 TGAACGGATGGAGTATTTAAAACAA 57.253 32.000 0.00 0.00 0.00 2.83
427 428 7.315890 TCACTCATTTCAGTCTGTATGTAGTG 58.684 38.462 22.59 22.59 33.03 2.74
478 479 0.880441 TGGTTTGTGTGCATCGGATG 59.120 50.000 13.63 13.63 0.00 3.51
481 482 2.437200 AATTGGTTTGTGTGCATCGG 57.563 45.000 0.00 0.00 0.00 4.18
482 483 6.464895 AATAAAATTGGTTTGTGTGCATCG 57.535 33.333 0.00 0.00 0.00 3.84
509 2258 6.757897 AGATGACTTGAACTTGTTTTCACA 57.242 33.333 0.00 0.00 35.18 3.58
510 2259 7.920738 ACTAGATGACTTGAACTTGTTTTCAC 58.079 34.615 0.00 0.00 35.18 3.18
575 2324 0.037605 AATCTTGTGTCCGACCGGTC 60.038 55.000 25.28 25.28 36.47 4.79
600 2349 1.702401 TGGCAATCCAATCGGGCTATA 59.298 47.619 0.00 0.00 39.99 1.31
601 2350 0.478072 TGGCAATCCAATCGGGCTAT 59.522 50.000 0.00 0.00 39.99 2.97
603 2352 1.454479 CTGGCAATCCAATCGGGCT 60.454 57.895 0.00 0.00 42.91 5.19
604 2353 3.122850 CTGGCAATCCAATCGGGC 58.877 61.111 0.00 0.00 42.91 6.13
605 2354 2.492773 GGCTGGCAATCCAATCGGG 61.493 63.158 0.00 0.00 42.91 5.14
610 2370 2.170166 CTAGTTTGGCTGGCAATCCAA 58.830 47.619 17.75 14.63 42.91 3.53
616 2376 1.603455 GCACCTAGTTTGGCTGGCA 60.603 57.895 0.00 0.00 0.00 4.92
629 2389 2.840651 ACTCTGCCTAGTTTATGCACCT 59.159 45.455 0.00 0.00 0.00 4.00
631 2391 4.116238 GAGACTCTGCCTAGTTTATGCAC 58.884 47.826 0.00 0.00 0.00 4.57
634 2394 5.359576 AGACTGAGACTCTGCCTAGTTTATG 59.640 44.000 9.11 0.00 0.00 1.90
641 2401 5.952347 TCATAAAAGACTGAGACTCTGCCTA 59.048 40.000 9.11 0.00 0.00 3.93
645 2405 8.600449 AAACTTCATAAAAGACTGAGACTCTG 57.400 34.615 7.74 7.74 0.00 3.35
646 2406 8.646900 AGAAACTTCATAAAAGACTGAGACTCT 58.353 33.333 3.68 0.00 0.00 3.24
650 2410 9.838339 AAAGAGAAACTTCATAAAAGACTGAGA 57.162 29.630 0.00 0.00 37.93 3.27
651 2411 9.875675 CAAAGAGAAACTTCATAAAAGACTGAG 57.124 33.333 0.00 0.00 37.93 3.35
654 2414 7.503902 AGGCAAAGAGAAACTTCATAAAAGACT 59.496 33.333 0.00 0.00 37.93 3.24
667 2427 3.817647 AGATCACACAGGCAAAGAGAAAC 59.182 43.478 0.00 0.00 0.00 2.78
686 2446 1.742761 CCCGTTGTCTGCATGAAGAT 58.257 50.000 6.69 0.00 0.00 2.40
706 2508 1.002576 TGCAAACAGAATCAGCACACG 60.003 47.619 0.00 0.00 0.00 4.49
714 2516 4.335874 AGCATCAGAGATGCAAACAGAATC 59.664 41.667 27.64 1.44 46.77 2.52
718 2520 3.439129 TCAAGCATCAGAGATGCAAACAG 59.561 43.478 27.64 15.06 46.77 3.16
721 2523 5.654603 AAATCAAGCATCAGAGATGCAAA 57.345 34.783 27.64 15.75 46.77 3.68
725 2527 6.053650 TGACCTAAATCAAGCATCAGAGATG 58.946 40.000 2.71 2.71 0.00 2.90
730 2532 9.674824 GATTTATTGACCTAAATCAAGCATCAG 57.325 33.333 10.26 0.00 43.17 2.90
731 2533 8.632679 GGATTTATTGACCTAAATCAAGCATCA 58.367 33.333 14.90 0.00 44.47 3.07
739 2541 7.898014 AAGGGTGGATTTATTGACCTAAATC 57.102 36.000 7.66 7.66 43.04 2.17
744 2546 6.980577 TGATAAAGGGTGGATTTATTGACCT 58.019 36.000 0.00 0.00 33.94 3.85
755 2558 6.552008 AGACATTTTCTTGATAAAGGGTGGA 58.448 36.000 0.00 0.00 0.00 4.02
756 2559 6.840780 AGACATTTTCTTGATAAAGGGTGG 57.159 37.500 0.00 0.00 0.00 4.61
758 2561 8.934023 TTGTAGACATTTTCTTGATAAAGGGT 57.066 30.769 0.00 0.00 35.55 4.34
759 2562 9.231297 TCTTGTAGACATTTTCTTGATAAAGGG 57.769 33.333 0.00 0.00 35.55 3.95
792 2598 8.901793 ACCAACACATTTAAATTGCAGAAAAAT 58.098 25.926 0.00 0.00 0.00 1.82
822 2628 7.089770 TGTACTCTGTACTTCACTCATCATC 57.910 40.000 8.94 0.00 0.00 2.92
878 2684 9.249457 CTCGCTTCTATTTCTATTCACATAACA 57.751 33.333 0.00 0.00 0.00 2.41
917 2724 7.911727 TGTTGCATGTACTACATACTAACTACG 59.088 37.037 15.87 0.00 36.53 3.51
932 2739 2.742053 ACAGAACGGATGTTGCATGTAC 59.258 45.455 0.00 0.00 38.78 2.90
978 2788 7.658575 CCCATTGAAACATCTGAAAAGAAACAT 59.341 33.333 0.00 0.00 0.00 2.71
984 2794 5.244626 ACCTCCCATTGAAACATCTGAAAAG 59.755 40.000 0.00 0.00 0.00 2.27
1009 2821 2.103771 TGGCATCCATCTCTCTGCTTAC 59.896 50.000 0.00 0.00 35.03 2.34
1010 2822 2.367894 CTGGCATCCATCTCTCTGCTTA 59.632 50.000 0.00 0.00 35.03 3.09
1012 2824 0.759959 CTGGCATCCATCTCTCTGCT 59.240 55.000 0.00 0.00 35.03 4.24
1116 2928 0.759346 GCGACCTATCATTGACCCCT 59.241 55.000 0.00 0.00 0.00 4.79
1136 2948 3.264947 TCAAGATCATCTTTGAGGTGCG 58.735 45.455 0.00 0.00 33.78 5.34
1139 2951 9.393512 CTATTTCTTCAAGATCATCTTTGAGGT 57.606 33.333 0.00 0.00 33.78 3.85
1287 3099 2.428890 AGATTTGTAGCCAGGAGACTCG 59.571 50.000 0.00 0.00 40.21 4.18
1295 3110 5.674525 TCTTGTGGATAGATTTGTAGCCAG 58.325 41.667 0.00 0.00 39.14 4.85
1309 3124 5.426509 TCCTAACATGAGTCATCTTGTGGAT 59.573 40.000 1.56 0.00 41.55 3.41
1310 3125 4.777366 TCCTAACATGAGTCATCTTGTGGA 59.223 41.667 1.56 7.89 41.55 4.02
1331 3146 3.217626 CACTTTAGCCTCATGGGAATCC 58.782 50.000 0.00 0.00 37.23 3.01
1340 3155 2.158682 TGTTTCTGCCACTTTAGCCTCA 60.159 45.455 0.00 0.00 0.00 3.86
1347 3162 5.796424 ATTCAATCTGTTTCTGCCACTTT 57.204 34.783 0.00 0.00 0.00 2.66
1402 3217 6.399743 TGACATCAACATGAATGATTTTGGG 58.600 36.000 13.61 7.22 35.38 4.12
1415 3230 2.679837 GGAGCACGAATGACATCAACAT 59.320 45.455 0.00 0.00 0.00 2.71
1437 3252 0.984995 GGTACCACTTGAGCCTCCTT 59.015 55.000 7.15 0.00 0.00 3.36
1479 3294 3.560882 CCTGGGCATAGATCCTGAATTCC 60.561 52.174 2.27 0.00 0.00 3.01
1509 3324 1.567649 TGGTACCTCTCATACCGTCCT 59.432 52.381 14.36 0.00 44.46 3.85
1510 3325 2.062971 TGGTACCTCTCATACCGTCC 57.937 55.000 14.36 0.00 44.46 4.79
1537 3352 1.064505 CGCCATCAAGGTGCTACAATG 59.935 52.381 0.00 0.00 41.83 2.82
1550 3365 0.927537 CGAAAATCTACGCGCCATCA 59.072 50.000 5.73 0.00 0.00 3.07
1552 3367 0.928229 GACGAAAATCTACGCGCCAT 59.072 50.000 5.73 0.00 0.00 4.40
1557 3372 2.093783 CCCAACAGACGAAAATCTACGC 59.906 50.000 0.00 0.00 0.00 4.42
1570 3385 0.183492 GGCATCATAGGCCCAACAGA 59.817 55.000 0.00 0.00 45.87 3.41
1602 3417 3.243068 CGGACAAAGTTTTCTCACAAGGG 60.243 47.826 0.00 0.00 0.00 3.95
1619 3434 2.104111 CCATCAATTACTAGGCCGGACA 59.896 50.000 11.69 0.00 0.00 4.02
1620 3435 2.104281 ACCATCAATTACTAGGCCGGAC 59.896 50.000 5.05 0.00 0.00 4.79
1642 3457 4.943705 GGAGTTGATAAACTTGCTCATCCA 59.056 41.667 0.00 0.00 32.22 3.41
1716 3531 6.381801 CATTGTTTTACCAAGACATCCAGAC 58.618 40.000 0.00 0.00 0.00 3.51
1782 3597 1.153168 CCGGATGAAAGCCCGACAT 60.153 57.895 0.00 0.00 41.45 3.06
1941 3756 8.322828 TGCATGTGGAAAATAAGTAAGTACCTA 58.677 33.333 0.00 0.00 0.00 3.08
2000 3851 5.476599 TGGACCATGTGGAAAATAAGAAGTG 59.523 40.000 5.96 0.00 38.94 3.16
2002 3853 5.945784 TCTGGACCATGTGGAAAATAAGAAG 59.054 40.000 5.96 0.00 38.94 2.85
2003 3854 5.886609 TCTGGACCATGTGGAAAATAAGAA 58.113 37.500 5.96 0.00 38.94 2.52
2004 3855 5.512942 TCTGGACCATGTGGAAAATAAGA 57.487 39.130 5.96 0.00 38.94 2.10
2041 3898 5.241728 ACAAAAGAGCAACCTGTAGGAATTC 59.758 40.000 4.64 0.00 38.94 2.17
2045 3902 3.857157 ACAAAAGAGCAACCTGTAGGA 57.143 42.857 4.64 0.00 38.94 2.94
2128 3986 3.808728 TCAGCTCACTGTAAAGCTTGTT 58.191 40.909 12.62 0.00 46.49 2.83
2174 4126 5.607119 ACCTGAAGTTAAATGTTACTGCG 57.393 39.130 0.00 0.00 0.00 5.18
2202 4154 6.490381 AGTTAGATATGCGTCAGGACTTATGA 59.510 38.462 0.00 0.00 0.00 2.15
2214 4168 6.395629 ACAGTAACAACAGTTAGATATGCGT 58.604 36.000 0.00 0.00 0.00 5.24
2215 4169 6.887376 ACAGTAACAACAGTTAGATATGCG 57.113 37.500 0.00 0.00 0.00 4.73
2290 4276 7.873719 ATCCCGTAAATCATCAACAACAATA 57.126 32.000 0.00 0.00 0.00 1.90
2309 4295 1.598962 CCCATGCTGCTGTATCCCG 60.599 63.158 0.00 0.00 0.00 5.14
2618 4622 5.825151 TGTGTGTCAACAAATCCACTGATAA 59.175 36.000 4.07 0.00 38.27 1.75
2680 4684 6.108097 ACTTGTTTCGTTCTTTCTGAAGTC 57.892 37.500 0.00 0.00 35.01 3.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.