Multiple sequence alignment - TraesCS2D01G215300

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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 TraesCS2D01G215300 chr2D 100.000 9228 0 0 1 9228 177865866 177856639 0.000000e+00 17042.0
1 TraesCS2D01G215300 chr2D 89.773 176 16 2 136 309 516708484 516708309 3.350000e-54 224.0
2 TraesCS2D01G215300 chr2B 95.918 8722 246 50 309 8982 234640916 234632257 0.000000e+00 14033.0
3 TraesCS2D01G215300 chr2A 97.219 6904 132 24 303 7174 192512760 192505885 0.000000e+00 11631.0
4 TraesCS2D01G215300 chr2A 97.637 1989 30 8 7173 9156 192505761 192503785 0.000000e+00 3397.0
5 TraesCS2D01G215300 chr3A 95.137 473 17 4 503 972 589604053 589603584 0.000000e+00 741.0
6 TraesCS2D01G215300 chr3A 95.567 406 13 3 570 972 589603561 589603158 0.000000e+00 645.0
7 TraesCS2D01G215300 chr3A 95.332 407 14 3 508 911 589602851 589602447 7.810000e-180 641.0
8 TraesCS2D01G215300 chr3A 95.980 199 8 0 305 503 589605928 589605730 3.210000e-84 324.0
9 TraesCS2D01G215300 chr3A 94.558 147 7 1 1 146 589606072 589605926 9.320000e-55 226.0
10 TraesCS2D01G215300 chr6D 89.243 251 23 4 2580 2827 53269925 53269676 2.500000e-80 311.0
11 TraesCS2D01G215300 chr6D 93.878 49 2 1 9180 9228 433634262 433634309 1.290000e-08 73.1
12 TraesCS2D01G215300 chr5D 88.583 254 25 4 2577 2827 440489698 440489446 1.160000e-78 305.0
13 TraesCS2D01G215300 chr5D 90.173 173 15 2 144 314 368995359 368995531 3.350000e-54 224.0
14 TraesCS2D01G215300 chr5D 95.918 49 1 1 9180 9228 486282597 486282550 2.760000e-10 78.7
15 TraesCS2D01G215300 chr5D 93.878 49 2 1 9180 9228 324399277 324399230 1.290000e-08 73.1
16 TraesCS2D01G215300 chr5D 93.878 49 2 1 9180 9228 408370524 408370571 1.290000e-08 73.1
17 TraesCS2D01G215300 chr5D 93.878 49 2 1 9180 9228 555471472 555471519 1.290000e-08 73.1
18 TraesCS2D01G215300 chr7D 92.216 167 11 2 143 307 245316187 245316021 1.550000e-57 235.0
19 TraesCS2D01G215300 chr7D 91.716 169 11 3 140 306 205230479 205230646 2.000000e-56 231.0
20 TraesCS2D01G215300 chr5B 89.944 179 16 2 139 315 295174889 295174711 7.210000e-56 230.0
21 TraesCS2D01G215300 chr3B 91.124 169 12 3 140 306 37640826 37640659 9.320000e-55 226.0
22 TraesCS2D01G215300 chr1D 91.018 167 13 2 143 307 224959776 224959942 3.350000e-54 224.0
23 TraesCS2D01G215300 chr4A 88.950 181 16 4 137 314 1072169 1072348 4.340000e-53 220.0
24 TraesCS2D01G215300 chr1A 88.950 181 17 3 137 314 247344798 247344618 4.340000e-53 220.0
25 TraesCS2D01G215300 chr3D 95.918 49 1 1 9180 9228 61218458 61218505 2.760000e-10 78.7
26 TraesCS2D01G215300 chr3D 95.918 49 1 1 9180 9228 396204516 396204469 2.760000e-10 78.7
27 TraesCS2D01G215300 chr6A 92.308 52 4 0 2770 2821 305369801 305369750 3.570000e-09 75.0
28 TraesCS2D01G215300 chr4D 93.878 49 2 1 9180 9228 464684332 464684285 1.290000e-08 73.1
29 TraesCS2D01G215300 chr4D 93.878 49 2 1 9180 9228 473839865 473839912 1.290000e-08 73.1


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 TraesCS2D01G215300 chr2D 177856639 177865866 9227 True 17042.0 17042 100.0000 1 9228 1 chr2D.!!$R1 9227
1 TraesCS2D01G215300 chr2B 234632257 234640916 8659 True 14033.0 14033 95.9180 309 8982 1 chr2B.!!$R1 8673
2 TraesCS2D01G215300 chr2A 192503785 192512760 8975 True 7514.0 11631 97.4280 303 9156 2 chr2A.!!$R1 8853
3 TraesCS2D01G215300 chr3A 589602447 589606072 3625 True 515.4 741 95.3148 1 972 5 chr3A.!!$R1 971

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
24 25 0.112995 AGTTTTGGATGGCCAGCTCA 59.887 50.000 22.39 14.43 46.91 4.26 F
883 3008 0.402121 GCCAGGGTTGTTCCTTCTCT 59.598 55.000 0.00 0.00 34.31 3.10 F
1463 3588 0.331278 TGATTCCACGGCCCATTCTT 59.669 50.000 0.00 0.00 0.00 2.52 F
2634 4895 0.105964 CCGAACACCCTGAACACTCA 59.894 55.000 0.00 0.00 0.00 3.41 F
3412 5673 0.105760 AAGGTGGGTTGCACATGGAA 60.106 50.000 0.00 0.00 0.00 3.53 F
4526 7217 2.549992 GGAGTGCACAACATCTGTACCA 60.550 50.000 21.04 0.00 36.10 3.25 F
6017 8708 0.988063 AAGAGGAGTTTGAGAGGGGC 59.012 55.000 0.00 0.00 0.00 5.80 F
6227 8918 6.603201 TGTTGGGAAATTATCAGAATCCAGAC 59.397 38.462 0.00 0.00 31.63 3.51 F
7284 10103 6.391479 AGACTCTTAGTACTTCCTACCAGT 57.609 41.667 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 3588 1.020437 TTGCAATGCAACGACACAGA 58.980 45.000 17.55 0.0 43.99 3.41 R
2615 4876 0.105964 TGAGTGTTCAGGGTGTTCGG 59.894 55.000 0.00 0.0 0.00 4.30 R
3169 5430 0.247736 ACGAGGTCTGCTGTGGATTC 59.752 55.000 0.00 0.0 0.00 2.52 R
4418 7109 0.323999 ATGATGCCTGCTCAGCCAAA 60.324 50.000 0.00 0.0 0.00 3.28 R
4877 7568 1.283347 TCTTTCTCCCAGCTGCAGAT 58.717 50.000 20.43 8.9 0.00 2.90 R
6227 8918 2.693069 AGTGCTTCAATGTTCTCCTCG 58.307 47.619 0.00 0.0 0.00 4.63 R
7284 10103 0.313987 TGCAGAGACGCGAGAAAGAA 59.686 50.000 15.93 0.0 33.35 2.52 R
8071 10891 1.001764 CCCAAGGACATCAGCTGCA 60.002 57.895 9.47 0.0 0.00 4.41 R
9200 12028 0.709992 AGTGCTCCCTCTCTTCTCCT 59.290 55.000 0.00 0.0 0.00 3.69 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
19 20 3.790223 GGCAGTTTTGGATGGCCA 58.210 55.556 8.56 8.56 44.01 5.36
24 25 0.112995 AGTTTTGGATGGCCAGCTCA 59.887 50.000 22.39 14.43 46.91 4.26
89 90 4.762251 GGATAATGTTGGAGATGCCCTTAC 59.238 45.833 0.00 0.00 34.97 2.34
133 135 9.628746 TTTTTCCAGGAAAATATAGTTAAACGC 57.371 29.630 25.19 0.00 40.50 4.84
137 139 9.016438 TCCAGGAAAATATAGTTAAACGCTTTT 57.984 29.630 0.00 0.00 0.00 2.27
149 151 8.812513 AGTTAAACGCTTTTATTTATACCCCT 57.187 30.769 0.00 0.00 0.00 4.79
150 152 8.896744 AGTTAAACGCTTTTATTTATACCCCTC 58.103 33.333 0.00 0.00 0.00 4.30
151 153 6.704289 AAACGCTTTTATTTATACCCCTCC 57.296 37.500 0.00 0.00 0.00 4.30
152 154 4.383173 ACGCTTTTATTTATACCCCTCCG 58.617 43.478 0.00 0.00 0.00 4.63
153 155 4.141642 ACGCTTTTATTTATACCCCTCCGT 60.142 41.667 0.00 0.00 0.00 4.69
154 156 4.818005 CGCTTTTATTTATACCCCTCCGTT 59.182 41.667 0.00 0.00 0.00 4.44
155 157 5.297527 CGCTTTTATTTATACCCCTCCGTTT 59.702 40.000 0.00 0.00 0.00 3.60
156 158 6.183360 CGCTTTTATTTATACCCCTCCGTTTT 60.183 38.462 0.00 0.00 0.00 2.43
157 159 7.549839 GCTTTTATTTATACCCCTCCGTTTTT 58.450 34.615 0.00 0.00 0.00 1.94
158 160 8.685427 GCTTTTATTTATACCCCTCCGTTTTTA 58.315 33.333 0.00 0.00 0.00 1.52
167 169 6.921486 ACCCCTCCGTTTTTAAATATTTGT 57.079 33.333 11.05 0.00 0.00 2.83
168 170 6.927416 ACCCCTCCGTTTTTAAATATTTGTC 58.073 36.000 11.05 0.00 0.00 3.18
169 171 6.722590 ACCCCTCCGTTTTTAAATATTTGTCT 59.277 34.615 11.05 0.00 0.00 3.41
170 172 7.233962 ACCCCTCCGTTTTTAAATATTTGTCTT 59.766 33.333 11.05 0.00 0.00 3.01
171 173 8.092068 CCCCTCCGTTTTTAAATATTTGTCTTT 58.908 33.333 11.05 0.00 0.00 2.52
172 174 9.135843 CCCTCCGTTTTTAAATATTTGTCTTTC 57.864 33.333 11.05 0.00 0.00 2.62
173 175 9.908152 CCTCCGTTTTTAAATATTTGTCTTTCT 57.092 29.630 11.05 0.00 0.00 2.52
203 205 8.690203 ATTTCAAATGGATTATCACATACGGA 57.310 30.769 0.00 0.00 0.00 4.69
204 206 8.690203 TTTCAAATGGATTATCACATACGGAT 57.310 30.769 0.00 0.00 0.00 4.18
205 207 7.671495 TCAAATGGATTATCACATACGGATG 57.329 36.000 5.94 5.94 39.16 3.51
207 209 8.371699 TCAAATGGATTATCACATACGGATGTA 58.628 33.333 14.23 0.00 44.82 2.29
208 210 9.166173 CAAATGGATTATCACATACGGATGTAT 57.834 33.333 14.23 10.02 44.82 2.29
248 250 9.559958 AAAATGTAGATTTACTCATTTGCTTCG 57.440 29.630 0.00 0.00 36.94 3.79
249 251 7.849804 ATGTAGATTTACTCATTTGCTTCGT 57.150 32.000 0.00 0.00 0.00 3.85
250 252 8.942338 ATGTAGATTTACTCATTTGCTTCGTA 57.058 30.769 0.00 0.00 0.00 3.43
251 253 8.942338 TGTAGATTTACTCATTTGCTTCGTAT 57.058 30.769 0.00 0.00 0.00 3.06
252 254 8.817100 TGTAGATTTACTCATTTGCTTCGTATG 58.183 33.333 0.00 0.00 0.00 2.39
253 255 7.849804 AGATTTACTCATTTGCTTCGTATGT 57.150 32.000 0.00 0.00 0.00 2.29
254 256 8.942338 AGATTTACTCATTTGCTTCGTATGTA 57.058 30.769 0.00 0.00 0.00 2.29
255 257 9.035607 AGATTTACTCATTTGCTTCGTATGTAG 57.964 33.333 0.00 0.00 0.00 2.74
256 258 8.718102 ATTTACTCATTTGCTTCGTATGTAGT 57.282 30.769 0.00 0.00 0.00 2.73
257 259 7.751047 TTACTCATTTGCTTCGTATGTAGTC 57.249 36.000 0.00 0.00 0.00 2.59
258 260 5.720202 ACTCATTTGCTTCGTATGTAGTCA 58.280 37.500 0.00 0.00 0.00 3.41
259 261 5.577164 ACTCATTTGCTTCGTATGTAGTCAC 59.423 40.000 0.00 0.00 0.00 3.67
260 262 5.720202 TCATTTGCTTCGTATGTAGTCACT 58.280 37.500 0.00 0.00 0.00 3.41
261 263 6.163476 TCATTTGCTTCGTATGTAGTCACTT 58.837 36.000 0.00 0.00 0.00 3.16
262 264 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
263 265 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
264 266 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
265 267 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
266 268 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
267 269 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
268 270 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
269 271 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
270 272 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
271 273 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
272 274 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
273 275 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
274 276 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
275 277 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
276 278 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
277 279 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
278 280 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
279 281 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
280 282 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
281 283 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
282 284 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
283 285 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
284 286 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
301 303 9.556030 GAAAGACAAATATTTAGAAACGAAGGG 57.444 33.333 0.00 0.00 0.00 3.95
416 421 2.550639 GGGTAGTAGAGTCCTAGAGGCG 60.551 59.091 0.00 0.00 34.44 5.52
537 2223 6.056884 TCTCTCTCCTAGTCGGAACTAAATC 58.943 44.000 0.00 0.00 42.53 2.17
614 2300 5.728621 GCTTATTTCGTCGGTAATTCCAACC 60.729 44.000 0.00 0.00 35.57 3.77
883 3008 0.402121 GCCAGGGTTGTTCCTTCTCT 59.598 55.000 0.00 0.00 34.31 3.10
1463 3588 0.331278 TGATTCCACGGCCCATTCTT 59.669 50.000 0.00 0.00 0.00 2.52
1514 3639 2.405025 GCAAAACTGCTAATTGACGTGC 59.595 45.455 0.00 0.00 0.00 5.34
1616 3741 2.569853 TCCAACATATATACCCCTGCCG 59.430 50.000 0.00 0.00 0.00 5.69
1705 3830 2.798145 CGCCAAAAGGTTTGGTTCACTC 60.798 50.000 18.46 3.07 41.53 3.51
1775 3902 1.455849 CCATCTGTGGTGGTGGTGT 59.544 57.895 0.00 0.00 40.83 4.16
1972 4102 3.067742 CCCTATCTTTTCCAGCTTGCATG 59.932 47.826 0.00 0.00 0.00 4.06
2014 4144 5.817816 TCAGTTTCTGGTTCTTTTCTGACTC 59.182 40.000 0.00 0.00 31.51 3.36
2143 4276 9.965824 ATTCCCTGCGTAATTATTTCTTATTTG 57.034 29.630 0.00 0.00 0.00 2.32
2200 4333 5.297776 GCAGTCAATATTTGCTGGATGTACT 59.702 40.000 14.37 0.00 36.21 2.73
2446 4581 3.129502 CATCCCACGCCACAGCAG 61.130 66.667 0.00 0.00 39.83 4.24
2604 4865 0.539051 ACGAGGAAGGATGCTCTTGG 59.461 55.000 0.00 0.00 41.51 3.61
2608 4869 0.915364 GGAAGGATGCTCTTGGTCCT 59.085 55.000 0.00 0.00 44.04 3.85
2609 4870 2.119495 GGAAGGATGCTCTTGGTCCTA 58.881 52.381 0.00 0.00 41.40 2.94
2610 4871 2.103941 GGAAGGATGCTCTTGGTCCTAG 59.896 54.545 0.00 0.00 41.40 3.02
2611 4872 2.559381 AGGATGCTCTTGGTCCTAGT 57.441 50.000 0.00 0.00 40.49 2.57
2612 4873 2.393646 AGGATGCTCTTGGTCCTAGTC 58.606 52.381 0.00 0.00 40.49 2.59
2613 4874 2.111384 GGATGCTCTTGGTCCTAGTCA 58.889 52.381 0.00 1.24 0.00 3.41
2614 4875 2.501723 GGATGCTCTTGGTCCTAGTCAA 59.498 50.000 0.00 0.00 0.00 3.18
2615 4876 3.526534 GATGCTCTTGGTCCTAGTCAAC 58.473 50.000 0.00 0.00 0.00 3.18
2616 4877 1.623811 TGCTCTTGGTCCTAGTCAACC 59.376 52.381 0.00 0.00 36.03 3.77
2617 4878 1.404315 GCTCTTGGTCCTAGTCAACCG 60.404 57.143 0.00 0.00 38.45 4.44
2618 4879 2.168496 CTCTTGGTCCTAGTCAACCGA 58.832 52.381 0.00 0.00 38.45 4.69
2619 4880 2.561419 CTCTTGGTCCTAGTCAACCGAA 59.439 50.000 0.00 0.00 38.45 4.30
2620 4881 2.298163 TCTTGGTCCTAGTCAACCGAAC 59.702 50.000 0.00 0.00 38.45 3.95
2621 4882 1.707106 TGGTCCTAGTCAACCGAACA 58.293 50.000 0.00 0.00 38.45 3.18
2622 4883 1.342174 TGGTCCTAGTCAACCGAACAC 59.658 52.381 0.00 0.00 38.45 3.32
2623 4884 1.337541 GGTCCTAGTCAACCGAACACC 60.338 57.143 0.00 0.00 0.00 4.16
2624 4885 0.971386 TCCTAGTCAACCGAACACCC 59.029 55.000 0.00 0.00 0.00 4.61
2625 4886 0.974383 CCTAGTCAACCGAACACCCT 59.026 55.000 0.00 0.00 0.00 4.34
2626 4887 1.337823 CCTAGTCAACCGAACACCCTG 60.338 57.143 0.00 0.00 0.00 4.45
2627 4888 1.616865 CTAGTCAACCGAACACCCTGA 59.383 52.381 0.00 0.00 0.00 3.86
2628 4889 0.834612 AGTCAACCGAACACCCTGAA 59.165 50.000 0.00 0.00 0.00 3.02
2629 4890 0.942252 GTCAACCGAACACCCTGAAC 59.058 55.000 0.00 0.00 0.00 3.18
2630 4891 0.542333 TCAACCGAACACCCTGAACA 59.458 50.000 0.00 0.00 0.00 3.18
2631 4892 0.661020 CAACCGAACACCCTGAACAC 59.339 55.000 0.00 0.00 0.00 3.32
2632 4893 0.544697 AACCGAACACCCTGAACACT 59.455 50.000 0.00 0.00 0.00 3.55
2633 4894 0.106149 ACCGAACACCCTGAACACTC 59.894 55.000 0.00 0.00 0.00 3.51
2634 4895 0.105964 CCGAACACCCTGAACACTCA 59.894 55.000 0.00 0.00 0.00 3.41
2635 4896 1.270839 CCGAACACCCTGAACACTCAT 60.271 52.381 0.00 0.00 0.00 2.90
2636 4897 1.800586 CGAACACCCTGAACACTCATG 59.199 52.381 0.00 0.00 0.00 3.07
2637 4898 2.806745 CGAACACCCTGAACACTCATGT 60.807 50.000 0.00 0.00 42.46 3.21
2725 4986 0.879090 CTGTTCAACCTTTACCGGGC 59.121 55.000 6.32 0.00 0.00 6.13
2926 5187 5.231702 CAAATGATGCATCAAGGACAAACA 58.768 37.500 31.79 6.66 40.69 2.83
3124 5385 2.039746 ACCTAATGTAGCAGCACAACCA 59.960 45.455 0.00 0.00 30.84 3.67
3169 5430 7.042925 GCAACTCAACCTATGGTTTACTATACG 60.043 40.741 0.00 0.00 44.33 3.06
3192 5453 2.298610 TCCACAGCAGACCTCGTATAG 58.701 52.381 0.00 0.00 0.00 1.31
3238 5499 0.751277 CTGCTGGTGTTGTTCCCACA 60.751 55.000 0.00 0.00 34.46 4.17
3289 5550 3.128242 CCACTCAAGCTGGTCAATCAATC 59.872 47.826 0.00 0.00 0.00 2.67
3412 5673 0.105760 AAGGTGGGTTGCACATGGAA 60.106 50.000 0.00 0.00 0.00 3.53
3513 5774 6.455646 GCTGTACAACATCGACAAAAGGATAG 60.456 42.308 0.00 0.00 0.00 2.08
3619 5880 3.411446 CAAGGAAAGTACAGCACCATCA 58.589 45.455 0.00 0.00 0.00 3.07
3620 5881 3.788227 AGGAAAGTACAGCACCATCAA 57.212 42.857 0.00 0.00 0.00 2.57
3665 5926 3.000727 GTGACTCAACCCTTACCGATTG 58.999 50.000 0.00 0.00 0.00 2.67
4081 6772 4.394300 ACATCAGCAACATCTGAAAGTAGC 59.606 41.667 0.00 0.00 45.17 3.58
4114 6805 7.337942 CCTATTCTTGGTAAAAGTGAAGCTGAT 59.662 37.037 0.00 0.00 0.00 2.90
4265 6956 2.555325 CTCTGCAAAATTGTCCTCTGCA 59.445 45.455 0.00 0.00 40.54 4.41
4490 7181 4.037446 GCAACATCTTTTGTAACTGACCCA 59.963 41.667 0.00 0.00 37.68 4.51
4526 7217 2.549992 GGAGTGCACAACATCTGTACCA 60.550 50.000 21.04 0.00 36.10 3.25
4877 7568 1.877443 GCAGAGCTTACCCGAACAAAA 59.123 47.619 0.00 0.00 0.00 2.44
4985 7676 2.975489 AGGACCACAAGAACAGTCTGAT 59.025 45.455 6.91 0.00 33.05 2.90
5816 8507 6.377146 AGCTTTTTGAACAAGTGAAAGAGGTA 59.623 34.615 11.76 0.00 30.83 3.08
6017 8708 0.988063 AAGAGGAGTTTGAGAGGGGC 59.012 55.000 0.00 0.00 0.00 5.80
6227 8918 6.603201 TGTTGGGAAATTATCAGAATCCAGAC 59.397 38.462 0.00 0.00 31.63 3.51
7284 10103 6.391479 AGACTCTTAGTACTTCCTACCAGT 57.609 41.667 0.00 0.00 0.00 4.00
7404 10223 6.574350 ACACCTTAGAATCAGAAAGGATACG 58.426 40.000 13.59 0.00 42.01 3.06
8484 11306 3.305335 CCCCACCTTTTTGATCGAAACAG 60.305 47.826 7.67 8.59 0.00 3.16
8516 11338 1.142465 CCCATCAGATGCTTGCTAGGT 59.858 52.381 4.68 0.00 0.00 3.08
8770 11595 4.562963 GGAACACTAGGGTTCGACTTGATT 60.563 45.833 27.32 0.00 46.34 2.57
8803 11628 3.017048 TCTGGCCAATATCCTTTGTGG 57.983 47.619 7.01 0.00 37.10 4.17
8986 11813 6.098982 TCTCAACTGTCCTCTCTTTTCTCTTT 59.901 38.462 0.00 0.00 0.00 2.52
9003 11830 7.488187 TTCTCTTTCTTTCTTCTCACATGTG 57.512 36.000 20.18 20.18 0.00 3.21
9004 11831 6.820335 TCTCTTTCTTTCTTCTCACATGTGA 58.180 36.000 26.33 26.33 38.06 3.58
9005 11832 7.275183 TCTCTTTCTTTCTTCTCACATGTGAA 58.725 34.615 27.63 14.32 39.39 3.18
9006 11833 7.935755 TCTCTTTCTTTCTTCTCACATGTGAAT 59.064 33.333 27.63 0.00 39.39 2.57
9007 11834 7.868775 TCTTTCTTTCTTCTCACATGTGAATG 58.131 34.615 27.63 17.79 39.39 2.67
9008 11835 7.500227 TCTTTCTTTCTTCTCACATGTGAATGT 59.500 33.333 27.63 0.00 39.39 2.71
9129 11957 9.783256 GTTATTATTGACCCATTGTTGTTCTAC 57.217 33.333 0.00 0.00 0.00 2.59
9138 11966 7.182060 ACCCATTGTTGTTCTACCAATCTTAT 58.818 34.615 0.00 0.00 0.00 1.73
9140 11968 8.840321 CCCATTGTTGTTCTACCAATCTTATAG 58.160 37.037 0.00 0.00 0.00 1.31
9156 11984 9.590451 CAATCTTATAGACAAAAACATGCCATT 57.410 29.630 0.00 0.00 0.00 3.16
9158 11986 9.807649 ATCTTATAGACAAAAACATGCCATTTC 57.192 29.630 0.00 0.00 0.00 2.17
9159 11987 8.801299 TCTTATAGACAAAAACATGCCATTTCA 58.199 29.630 0.00 0.00 0.00 2.69
9160 11988 9.421806 CTTATAGACAAAAACATGCCATTTCAA 57.578 29.630 0.00 0.00 0.00 2.69
9161 11989 9.941325 TTATAGACAAAAACATGCCATTTCAAT 57.059 25.926 0.00 0.00 0.00 2.57
9162 11990 6.790285 AGACAAAAACATGCCATTTCAATC 57.210 33.333 0.00 0.00 0.00 2.67
9163 11991 6.527423 AGACAAAAACATGCCATTTCAATCT 58.473 32.000 0.00 0.00 0.00 2.40
9164 11992 6.647895 AGACAAAAACATGCCATTTCAATCTC 59.352 34.615 0.00 0.00 0.00 2.75
9165 11993 6.289834 ACAAAAACATGCCATTTCAATCTCA 58.710 32.000 0.00 0.00 0.00 3.27
9166 11994 6.766944 ACAAAAACATGCCATTTCAATCTCAA 59.233 30.769 0.00 0.00 0.00 3.02
9167 11995 7.282675 ACAAAAACATGCCATTTCAATCTCAAA 59.717 29.630 0.00 0.00 0.00 2.69
9168 11996 6.790285 AAACATGCCATTTCAATCTCAAAC 57.210 33.333 0.00 0.00 0.00 2.93
9169 11997 5.471556 ACATGCCATTTCAATCTCAAACA 57.528 34.783 0.00 0.00 0.00 2.83
9170 11998 5.232463 ACATGCCATTTCAATCTCAAACAC 58.768 37.500 0.00 0.00 0.00 3.32
9171 11999 3.899734 TGCCATTTCAATCTCAAACACG 58.100 40.909 0.00 0.00 0.00 4.49
9172 12000 3.317711 TGCCATTTCAATCTCAAACACGT 59.682 39.130 0.00 0.00 0.00 4.49
9173 12001 4.202101 TGCCATTTCAATCTCAAACACGTT 60.202 37.500 0.00 0.00 0.00 3.99
9174 12002 5.009110 TGCCATTTCAATCTCAAACACGTTA 59.991 36.000 0.00 0.00 0.00 3.18
9175 12003 6.092748 GCCATTTCAATCTCAAACACGTTAT 58.907 36.000 0.00 0.00 0.00 1.89
9176 12004 6.251376 GCCATTTCAATCTCAAACACGTTATC 59.749 38.462 0.00 0.00 0.00 1.75
9177 12005 7.304735 CCATTTCAATCTCAAACACGTTATCA 58.695 34.615 0.00 0.00 0.00 2.15
9178 12006 7.271223 CCATTTCAATCTCAAACACGTTATCAC 59.729 37.037 0.00 0.00 0.00 3.06
9191 12019 3.867665 CGTTATCACGCACAAAGAAACA 58.132 40.909 0.00 0.00 40.18 2.83
9192 12020 4.275662 CGTTATCACGCACAAAGAAACAA 58.724 39.130 0.00 0.00 40.18 2.83
9193 12021 4.144051 CGTTATCACGCACAAAGAAACAAC 59.856 41.667 0.00 0.00 40.18 3.32
9194 12022 3.773860 ATCACGCACAAAGAAACAACA 57.226 38.095 0.00 0.00 0.00 3.33
9195 12023 3.773860 TCACGCACAAAGAAACAACAT 57.226 38.095 0.00 0.00 0.00 2.71
9196 12024 4.884458 TCACGCACAAAGAAACAACATA 57.116 36.364 0.00 0.00 0.00 2.29
9197 12025 4.843147 TCACGCACAAAGAAACAACATAG 58.157 39.130 0.00 0.00 0.00 2.23
9198 12026 4.572795 TCACGCACAAAGAAACAACATAGA 59.427 37.500 0.00 0.00 0.00 1.98
9199 12027 5.065346 TCACGCACAAAGAAACAACATAGAA 59.935 36.000 0.00 0.00 0.00 2.10
9200 12028 5.741510 CACGCACAAAGAAACAACATAGAAA 59.258 36.000 0.00 0.00 0.00 2.52
9201 12029 5.971202 ACGCACAAAGAAACAACATAGAAAG 59.029 36.000 0.00 0.00 0.00 2.62
9202 12030 5.399301 CGCACAAAGAAACAACATAGAAAGG 59.601 40.000 0.00 0.00 0.00 3.11
9203 12031 6.503524 GCACAAAGAAACAACATAGAAAGGA 58.496 36.000 0.00 0.00 0.00 3.36
9204 12032 6.638468 GCACAAAGAAACAACATAGAAAGGAG 59.362 38.462 0.00 0.00 0.00 3.69
9205 12033 7.468631 GCACAAAGAAACAACATAGAAAGGAGA 60.469 37.037 0.00 0.00 0.00 3.71
9206 12034 8.405531 CACAAAGAAACAACATAGAAAGGAGAA 58.594 33.333 0.00 0.00 0.00 2.87
9207 12035 8.624776 ACAAAGAAACAACATAGAAAGGAGAAG 58.375 33.333 0.00 0.00 0.00 2.85
9208 12036 8.840321 CAAAGAAACAACATAGAAAGGAGAAGA 58.160 33.333 0.00 0.00 0.00 2.87
9209 12037 8.614469 AAGAAACAACATAGAAAGGAGAAGAG 57.386 34.615 0.00 0.00 0.00 2.85
9210 12038 7.967908 AGAAACAACATAGAAAGGAGAAGAGA 58.032 34.615 0.00 0.00 0.00 3.10
9211 12039 8.093927 AGAAACAACATAGAAAGGAGAAGAGAG 58.906 37.037 0.00 0.00 0.00 3.20
9212 12040 6.293004 ACAACATAGAAAGGAGAAGAGAGG 57.707 41.667 0.00 0.00 0.00 3.69
9213 12041 5.188751 ACAACATAGAAAGGAGAAGAGAGGG 59.811 44.000 0.00 0.00 0.00 4.30
9214 12042 5.213868 ACATAGAAAGGAGAAGAGAGGGA 57.786 43.478 0.00 0.00 0.00 4.20
9215 12043 5.208121 ACATAGAAAGGAGAAGAGAGGGAG 58.792 45.833 0.00 0.00 0.00 4.30
9216 12044 2.466846 AGAAAGGAGAAGAGAGGGAGC 58.533 52.381 0.00 0.00 0.00 4.70
9217 12045 2.183679 GAAAGGAGAAGAGAGGGAGCA 58.816 52.381 0.00 0.00 0.00 4.26
9218 12046 1.567357 AAGGAGAAGAGAGGGAGCAC 58.433 55.000 0.00 0.00 0.00 4.40
9219 12047 0.709992 AGGAGAAGAGAGGGAGCACT 59.290 55.000 0.00 0.00 0.00 4.40
9220 12048 1.111277 GGAGAAGAGAGGGAGCACTC 58.889 60.000 0.00 0.00 37.77 3.51
9221 12049 0.738389 GAGAAGAGAGGGAGCACTCG 59.262 60.000 0.00 0.00 42.31 4.18
9222 12050 1.140804 GAAGAGAGGGAGCACTCGC 59.859 63.158 6.61 6.61 42.31 5.03
9223 12051 2.291457 GAAGAGAGGGAGCACTCGCC 62.291 65.000 10.75 4.40 42.72 5.54
9224 12052 4.200283 GAGAGGGAGCACTCGCCG 62.200 72.222 10.75 0.00 42.72 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.728069 CACTGATGCATGAGCTGGC 59.272 57.895 13.53 0.00 42.74 4.85
143 145 7.889600 AGACAAATATTTAAAAACGGAGGGGTA 59.110 33.333 0.00 0.00 0.00 3.69
144 146 6.722590 AGACAAATATTTAAAAACGGAGGGGT 59.277 34.615 0.00 0.00 0.00 4.95
145 147 7.165460 AGACAAATATTTAAAAACGGAGGGG 57.835 36.000 0.00 0.00 0.00 4.79
146 148 9.135843 GAAAGACAAATATTTAAAAACGGAGGG 57.864 33.333 0.00 0.00 0.00 4.30
147 149 9.908152 AGAAAGACAAATATTTAAAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
177 179 9.785982 TCCGTATGTGATAATCCATTTGAAATA 57.214 29.630 0.00 0.00 0.00 1.40
178 180 8.690203 TCCGTATGTGATAATCCATTTGAAAT 57.310 30.769 0.00 0.00 0.00 2.17
179 181 8.567104 CATCCGTATGTGATAATCCATTTGAAA 58.433 33.333 0.00 0.00 0.00 2.69
180 182 7.719193 ACATCCGTATGTGATAATCCATTTGAA 59.281 33.333 0.00 0.00 44.79 2.69
181 183 7.223584 ACATCCGTATGTGATAATCCATTTGA 58.776 34.615 0.00 0.00 44.79 2.69
182 184 7.439157 ACATCCGTATGTGATAATCCATTTG 57.561 36.000 0.00 0.00 44.79 2.32
222 224 9.559958 CGAAGCAAATGAGTAAATCTACATTTT 57.440 29.630 0.00 0.00 39.74 1.82
223 225 8.730680 ACGAAGCAAATGAGTAAATCTACATTT 58.269 29.630 0.00 0.00 41.53 2.32
224 226 8.268850 ACGAAGCAAATGAGTAAATCTACATT 57.731 30.769 0.00 0.00 34.99 2.71
225 227 7.849804 ACGAAGCAAATGAGTAAATCTACAT 57.150 32.000 0.00 0.00 0.00 2.29
226 228 8.817100 CATACGAAGCAAATGAGTAAATCTACA 58.183 33.333 0.00 0.00 0.00 2.74
227 229 8.818057 ACATACGAAGCAAATGAGTAAATCTAC 58.182 33.333 0.00 0.00 0.00 2.59
228 230 8.942338 ACATACGAAGCAAATGAGTAAATCTA 57.058 30.769 0.00 0.00 0.00 1.98
229 231 7.849804 ACATACGAAGCAAATGAGTAAATCT 57.150 32.000 0.00 0.00 0.00 2.40
230 232 8.818057 ACTACATACGAAGCAAATGAGTAAATC 58.182 33.333 0.00 0.00 0.00 2.17
231 233 8.718102 ACTACATACGAAGCAAATGAGTAAAT 57.282 30.769 0.00 0.00 0.00 1.40
232 234 7.815549 TGACTACATACGAAGCAAATGAGTAAA 59.184 33.333 0.00 0.00 0.00 2.01
233 235 7.274904 GTGACTACATACGAAGCAAATGAGTAA 59.725 37.037 0.00 0.00 0.00 2.24
234 236 6.750501 GTGACTACATACGAAGCAAATGAGTA 59.249 38.462 0.00 0.00 0.00 2.59
235 237 5.577164 GTGACTACATACGAAGCAAATGAGT 59.423 40.000 0.00 0.00 0.00 3.41
236 238 5.807520 AGTGACTACATACGAAGCAAATGAG 59.192 40.000 0.00 0.00 0.00 2.90
237 239 5.720202 AGTGACTACATACGAAGCAAATGA 58.280 37.500 0.00 0.00 0.00 2.57
238 240 6.128553 ACAAGTGACTACATACGAAGCAAATG 60.129 38.462 0.00 0.00 0.00 2.32
239 241 5.932303 ACAAGTGACTACATACGAAGCAAAT 59.068 36.000 0.00 0.00 0.00 2.32
240 242 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
241 243 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
242 244 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
243 245 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
244 246 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
245 247 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
246 248 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
247 249 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
248 250 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
250 252 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
251 253 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
252 254 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
253 255 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
254 256 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
255 257 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
256 258 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
257 259 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
258 260 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
275 277 9.556030 CCCTTCGTTTCTAAATATTTGTCTTTC 57.444 33.333 11.05 0.00 0.00 2.62
276 278 9.292195 TCCCTTCGTTTCTAAATATTTGTCTTT 57.708 29.630 11.05 0.00 0.00 2.52
277 279 8.857694 TCCCTTCGTTTCTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
278 280 8.101419 ACTCCCTTCGTTTCTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
279 281 8.265165 ACTCCCTTCGTTTCTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
280 282 9.159364 GTACTCCCTTCGTTTCTAAATATTTGT 57.841 33.333 11.05 0.00 0.00 2.83
281 283 9.158233 TGTACTCCCTTCGTTTCTAAATATTTG 57.842 33.333 11.05 1.65 0.00 2.32
282 284 9.729281 TTGTACTCCCTTCGTTTCTAAATATTT 57.271 29.630 5.89 5.89 0.00 1.40
283 285 9.159364 GTTGTACTCCCTTCGTTTCTAAATATT 57.841 33.333 0.00 0.00 0.00 1.28
284 286 7.490402 CGTTGTACTCCCTTCGTTTCTAAATAT 59.510 37.037 0.00 0.00 0.00 1.28
285 287 6.808212 CGTTGTACTCCCTTCGTTTCTAAATA 59.192 38.462 0.00 0.00 0.00 1.40
286 288 5.636543 CGTTGTACTCCCTTCGTTTCTAAAT 59.363 40.000 0.00 0.00 0.00 1.40
287 289 4.984161 CGTTGTACTCCCTTCGTTTCTAAA 59.016 41.667 0.00 0.00 0.00 1.85
288 290 4.037923 ACGTTGTACTCCCTTCGTTTCTAA 59.962 41.667 0.00 0.00 0.00 2.10
289 291 3.569701 ACGTTGTACTCCCTTCGTTTCTA 59.430 43.478 0.00 0.00 0.00 2.10
290 292 2.363359 ACGTTGTACTCCCTTCGTTTCT 59.637 45.455 0.00 0.00 0.00 2.52
291 293 2.747436 ACGTTGTACTCCCTTCGTTTC 58.253 47.619 0.00 0.00 0.00 2.78
292 294 2.896745 ACGTTGTACTCCCTTCGTTT 57.103 45.000 0.00 0.00 0.00 3.60
293 295 3.552890 GGTTACGTTGTACTCCCTTCGTT 60.553 47.826 0.00 0.00 33.70 3.85
294 296 2.029918 GGTTACGTTGTACTCCCTTCGT 60.030 50.000 0.00 0.00 35.73 3.85
295 297 2.030007 TGGTTACGTTGTACTCCCTTCG 60.030 50.000 0.00 0.00 0.00 3.79
296 298 3.665745 TGGTTACGTTGTACTCCCTTC 57.334 47.619 0.00 0.00 0.00 3.46
297 299 5.337813 CCTTATGGTTACGTTGTACTCCCTT 60.338 44.000 0.00 0.00 0.00 3.95
298 300 4.161001 CCTTATGGTTACGTTGTACTCCCT 59.839 45.833 0.00 0.00 0.00 4.20
299 301 4.160252 TCCTTATGGTTACGTTGTACTCCC 59.840 45.833 0.00 0.00 34.23 4.30
300 302 5.329035 TCCTTATGGTTACGTTGTACTCC 57.671 43.478 0.00 0.00 34.23 3.85
301 303 4.802563 GCTCCTTATGGTTACGTTGTACTC 59.197 45.833 0.00 0.00 34.23 2.59
397 399 3.749665 TCGCCTCTAGGACTCTACTAC 57.250 52.381 0.00 0.00 37.39 2.73
416 421 3.028366 GCTTTGGTCGCTCGCCTTC 62.028 63.158 4.86 0.00 0.00 3.46
614 2300 1.959226 CAAATCGGGGGCGATACGG 60.959 63.158 0.00 0.00 0.00 4.02
883 3008 1.651730 CCGCGCACGAAAACGAAAA 60.652 52.632 8.75 0.00 43.93 2.29
1463 3588 1.020437 TTGCAATGCAACGACACAGA 58.980 45.000 17.55 0.00 43.99 3.41
1514 3639 4.539509 ACATGCATGCAAACAACAAAAG 57.460 36.364 26.68 6.94 0.00 2.27
1616 3741 2.772287 CCAGCCCGAGGAATATTCTTC 58.228 52.381 15.72 15.72 0.00 2.87
1705 3830 6.515832 ACAATTTCTAAAGTGCAAAAGGAGG 58.484 36.000 3.01 0.00 37.49 4.30
1972 4102 5.674933 ACTGAAGAAATTTGAACCTCGAC 57.325 39.130 0.00 0.00 0.00 4.20
2200 4333 8.296713 GGAACAAAGATAATTTTCTACAGCACA 58.703 33.333 0.00 0.00 0.00 4.57
2447 4582 4.435970 TGGGGGATGCTGCTGCTG 62.436 66.667 17.00 0.77 40.48 4.41
2448 4583 4.437587 GTGGGGGATGCTGCTGCT 62.438 66.667 17.00 2.26 40.48 4.24
2604 4865 1.337541 GGGTGTTCGGTTGACTAGGAC 60.338 57.143 0.00 0.00 0.00 3.85
2608 4869 1.707106 TCAGGGTGTTCGGTTGACTA 58.293 50.000 0.00 0.00 0.00 2.59
2609 4870 0.834612 TTCAGGGTGTTCGGTTGACT 59.165 50.000 0.00 0.00 0.00 3.41
2610 4871 0.942252 GTTCAGGGTGTTCGGTTGAC 59.058 55.000 0.00 0.00 0.00 3.18
2611 4872 0.542333 TGTTCAGGGTGTTCGGTTGA 59.458 50.000 0.00 0.00 0.00 3.18
2612 4873 0.661020 GTGTTCAGGGTGTTCGGTTG 59.339 55.000 0.00 0.00 0.00 3.77
2613 4874 0.544697 AGTGTTCAGGGTGTTCGGTT 59.455 50.000 0.00 0.00 0.00 4.44
2614 4875 0.106149 GAGTGTTCAGGGTGTTCGGT 59.894 55.000 0.00 0.00 0.00 4.69
2615 4876 0.105964 TGAGTGTTCAGGGTGTTCGG 59.894 55.000 0.00 0.00 0.00 4.30
2616 4877 1.800586 CATGAGTGTTCAGGGTGTTCG 59.199 52.381 0.00 0.00 36.61 3.95
2617 4878 2.851195 ACATGAGTGTTCAGGGTGTTC 58.149 47.619 0.00 0.00 39.36 3.18
2618 4879 3.297134 AACATGAGTGTTCAGGGTGTT 57.703 42.857 0.00 0.00 45.14 3.32
2636 4897 3.261897 TCTCTCTTCACTTGGGATGGAAC 59.738 47.826 0.00 0.00 0.00 3.62
2637 4898 3.520696 TCTCTCTTCACTTGGGATGGAA 58.479 45.455 0.00 0.00 0.00 3.53
2638 4899 3.190383 TCTCTCTTCACTTGGGATGGA 57.810 47.619 0.00 0.00 0.00 3.41
2639 4900 3.199508 ACATCTCTCTTCACTTGGGATGG 59.800 47.826 6.95 0.00 35.02 3.51
2640 4901 4.190001 CACATCTCTCTTCACTTGGGATG 58.810 47.826 0.00 0.00 36.27 3.51
2926 5187 4.122776 GAGCAACAGACGGATACATCATT 58.877 43.478 0.00 0.00 0.00 2.57
3073 5334 2.481795 CCCAAGCACCACTTCTTTGTTG 60.482 50.000 0.00 0.00 36.04 3.33
3124 5385 1.382522 CAACACCACTGACTTGCTGT 58.617 50.000 0.00 0.00 0.00 4.40
3169 5430 0.247736 ACGAGGTCTGCTGTGGATTC 59.752 55.000 0.00 0.00 0.00 2.52
3192 5453 3.243334 GGAGTAATACGTACCTGACTGGC 60.243 52.174 0.00 0.00 40.22 4.85
3238 5499 1.561542 CTAAACCTGCCCTGTGATCCT 59.438 52.381 0.00 0.00 0.00 3.24
3289 5550 4.733165 ACATAGATGGGTTCATGAATGGG 58.267 43.478 12.12 0.00 32.98 4.00
3412 5673 0.841289 TGACCGAGGGAACAGGTTTT 59.159 50.000 0.00 0.00 42.52 2.43
3490 5751 6.367695 CACTATCCTTTTGTCGATGTTGTACA 59.632 38.462 0.00 0.00 0.00 2.90
3513 5774 5.648092 ACCATAGCACCAGAAATAACTTCAC 59.352 40.000 0.00 0.00 36.40 3.18
3619 5880 1.299976 GGGATGCTTCTCCACGGTT 59.700 57.895 0.00 0.00 37.01 4.44
3620 5881 1.918293 TGGGATGCTTCTCCACGGT 60.918 57.895 0.00 0.00 37.01 4.83
3665 5926 1.339291 AGTTTCTGGCTTTGCAGCTTC 59.661 47.619 0.00 0.00 46.44 3.86
4081 6772 9.231297 TCACTTTTACCAAGAATAGGAGAAATG 57.769 33.333 0.00 0.00 0.00 2.32
4114 6805 5.527214 GTGCATACCATTTACTGATGTGCTA 59.473 40.000 0.00 0.00 0.00 3.49
4168 6859 5.862924 TCGAAAAGAGACACAATTCATCC 57.137 39.130 0.00 0.00 0.00 3.51
4418 7109 0.323999 ATGATGCCTGCTCAGCCAAA 60.324 50.000 0.00 0.00 0.00 3.28
4490 7181 1.625818 CACTCCTTGGGTAGCTCTTGT 59.374 52.381 0.00 0.00 0.00 3.16
4526 7217 3.777106 TTCATCAAACTGTGCTCCTCT 57.223 42.857 0.00 0.00 0.00 3.69
4835 7526 6.252995 TGCAGTAGGTTTTTCCCTTGATAAT 58.747 36.000 0.00 0.00 35.97 1.28
4877 7568 1.283347 TCTTTCTCCCAGCTGCAGAT 58.717 50.000 20.43 8.90 0.00 2.90
5690 8381 4.130857 TGCCGACAACATACTTTTTCTCA 58.869 39.130 0.00 0.00 0.00 3.27
6017 8708 3.062763 TGCTTCAGCTTCTTCTCTTTCG 58.937 45.455 0.00 0.00 42.66 3.46
6227 8918 2.693069 AGTGCTTCAATGTTCTCCTCG 58.307 47.619 0.00 0.00 0.00 4.63
7074 9767 2.016318 CAAGTCAGGTGTGTGCTGAAA 58.984 47.619 0.00 0.00 0.00 2.69
7127 9820 7.862675 AGACCTTAAATAGTAAGACAGGCAAT 58.137 34.615 0.00 0.00 0.00 3.56
7128 9821 7.253905 AGACCTTAAATAGTAAGACAGGCAA 57.746 36.000 0.00 0.00 0.00 4.52
7284 10103 0.313987 TGCAGAGACGCGAGAAAGAA 59.686 50.000 15.93 0.00 33.35 2.52
7527 10346 4.694339 AGAGACCACTACTCAACAACAAC 58.306 43.478 0.00 0.00 36.91 3.32
8071 10891 1.001764 CCCAAGGACATCAGCTGCA 60.002 57.895 9.47 0.00 0.00 4.41
8484 11306 4.380233 GCATCTGATGGGTATATTTGCAGC 60.380 45.833 18.60 0.00 0.00 5.25
8516 11338 2.158957 GGCTCCTCGAATACAATGGTCA 60.159 50.000 0.00 0.00 0.00 4.02
8770 11595 3.003173 CCAGAAGCCACGGGAGGA 61.003 66.667 0.00 0.00 0.00 3.71
8803 11628 8.645487 CAAGTTAACCGAGTATTAAAGTCTGAC 58.355 37.037 0.88 0.00 0.00 3.51
8973 11800 8.260818 TGTGAGAAGAAAGAAAGAGAAAAGAGA 58.739 33.333 0.00 0.00 0.00 3.10
9003 11830 6.354039 TCGCATATATGATGCATCACATTC 57.646 37.500 30.92 16.82 44.75 2.67
9004 11831 6.937436 ATCGCATATATGATGCATCACATT 57.063 33.333 30.92 18.10 44.75 2.71
9005 11832 6.937436 AATCGCATATATGATGCATCACAT 57.063 33.333 30.92 26.79 44.75 3.21
9006 11833 7.846644 TTAATCGCATATATGATGCATCACA 57.153 32.000 30.92 21.60 44.75 3.58
9007 11834 9.558648 TTTTTAATCGCATATATGATGCATCAC 57.441 29.630 30.92 16.05 44.75 3.06
9041 11868 7.757097 AGTTCTTATGTGTCTTTATAGTGCG 57.243 36.000 0.00 0.00 0.00 5.34
9129 11957 7.546358 TGGCATGTTTTTGTCTATAAGATTGG 58.454 34.615 0.00 0.00 0.00 3.16
9138 11966 7.669427 AGATTGAAATGGCATGTTTTTGTCTA 58.331 30.769 0.00 0.00 0.00 2.59
9140 11968 6.424509 TGAGATTGAAATGGCATGTTTTTGTC 59.575 34.615 0.00 0.00 0.00 3.18
9142 11970 6.788684 TGAGATTGAAATGGCATGTTTTTG 57.211 33.333 0.00 0.00 0.00 2.44
9143 11971 7.282675 TGTTTGAGATTGAAATGGCATGTTTTT 59.717 29.630 0.00 0.00 0.00 1.94
9147 11975 5.232463 GTGTTTGAGATTGAAATGGCATGT 58.768 37.500 0.00 0.00 0.00 3.21
9148 11976 4.325204 CGTGTTTGAGATTGAAATGGCATG 59.675 41.667 0.00 0.00 0.00 4.06
9149 11977 4.022068 ACGTGTTTGAGATTGAAATGGCAT 60.022 37.500 0.00 0.00 0.00 4.40
9150 11978 3.317711 ACGTGTTTGAGATTGAAATGGCA 59.682 39.130 0.00 0.00 0.00 4.92
9151 11979 3.900941 ACGTGTTTGAGATTGAAATGGC 58.099 40.909 0.00 0.00 0.00 4.40
9156 11984 5.613795 GCGTGATAACGTGTTTGAGATTGAA 60.614 40.000 4.14 0.00 35.26 2.69
9157 11985 4.143200 GCGTGATAACGTGTTTGAGATTGA 60.143 41.667 4.14 0.00 35.26 2.57
9158 11986 4.081761 GCGTGATAACGTGTTTGAGATTG 58.918 43.478 4.14 0.00 35.26 2.67
9159 11987 3.743911 TGCGTGATAACGTGTTTGAGATT 59.256 39.130 4.14 0.00 35.26 2.40
9160 11988 3.122948 GTGCGTGATAACGTGTTTGAGAT 59.877 43.478 4.14 0.00 35.26 2.75
9161 11989 2.473609 GTGCGTGATAACGTGTTTGAGA 59.526 45.455 4.14 0.00 35.26 3.27
9162 11990 2.219903 TGTGCGTGATAACGTGTTTGAG 59.780 45.455 4.14 0.00 35.26 3.02
9163 11991 2.202566 TGTGCGTGATAACGTGTTTGA 58.797 42.857 4.14 0.00 35.26 2.69
9164 11992 2.654426 TGTGCGTGATAACGTGTTTG 57.346 45.000 4.14 0.00 35.26 2.93
9165 11993 3.310227 TCTTTGTGCGTGATAACGTGTTT 59.690 39.130 4.14 0.00 35.26 2.83
9166 11994 2.867368 TCTTTGTGCGTGATAACGTGTT 59.133 40.909 4.14 0.00 35.26 3.32
9167 11995 2.475818 TCTTTGTGCGTGATAACGTGT 58.524 42.857 4.14 0.00 35.26 4.49
9168 11996 3.513462 TTCTTTGTGCGTGATAACGTG 57.487 42.857 4.14 0.00 35.26 4.49
9169 11997 3.310227 TGTTTCTTTGTGCGTGATAACGT 59.690 39.130 4.14 0.00 35.26 3.99
9170 11998 3.867665 TGTTTCTTTGTGCGTGATAACG 58.132 40.909 0.00 0.00 0.00 3.18
9171 11999 5.031578 TGTTGTTTCTTTGTGCGTGATAAC 58.968 37.500 0.00 0.00 0.00 1.89
9172 12000 5.236655 TGTTGTTTCTTTGTGCGTGATAA 57.763 34.783 0.00 0.00 0.00 1.75
9173 12001 4.884458 TGTTGTTTCTTTGTGCGTGATA 57.116 36.364 0.00 0.00 0.00 2.15
9174 12002 3.773860 TGTTGTTTCTTTGTGCGTGAT 57.226 38.095 0.00 0.00 0.00 3.06
9175 12003 3.773860 ATGTTGTTTCTTTGTGCGTGA 57.226 38.095 0.00 0.00 0.00 4.35
9176 12004 4.843147 TCTATGTTGTTTCTTTGTGCGTG 58.157 39.130 0.00 0.00 0.00 5.34
9177 12005 5.493133 TTCTATGTTGTTTCTTTGTGCGT 57.507 34.783 0.00 0.00 0.00 5.24
9178 12006 5.399301 CCTTTCTATGTTGTTTCTTTGTGCG 59.601 40.000 0.00 0.00 0.00 5.34
9179 12007 6.503524 TCCTTTCTATGTTGTTTCTTTGTGC 58.496 36.000 0.00 0.00 0.00 4.57
9180 12008 7.930217 TCTCCTTTCTATGTTGTTTCTTTGTG 58.070 34.615 0.00 0.00 0.00 3.33
9181 12009 8.519799 TTCTCCTTTCTATGTTGTTTCTTTGT 57.480 30.769 0.00 0.00 0.00 2.83
9182 12010 8.840321 TCTTCTCCTTTCTATGTTGTTTCTTTG 58.160 33.333 0.00 0.00 0.00 2.77
9183 12011 8.980481 TCTTCTCCTTTCTATGTTGTTTCTTT 57.020 30.769 0.00 0.00 0.00 2.52
9184 12012 8.432805 TCTCTTCTCCTTTCTATGTTGTTTCTT 58.567 33.333 0.00 0.00 0.00 2.52
9185 12013 7.967908 TCTCTTCTCCTTTCTATGTTGTTTCT 58.032 34.615 0.00 0.00 0.00 2.52
9186 12014 7.333174 CCTCTCTTCTCCTTTCTATGTTGTTTC 59.667 40.741 0.00 0.00 0.00 2.78
9187 12015 7.164803 CCTCTCTTCTCCTTTCTATGTTGTTT 58.835 38.462 0.00 0.00 0.00 2.83
9188 12016 6.296145 CCCTCTCTTCTCCTTTCTATGTTGTT 60.296 42.308 0.00 0.00 0.00 2.83
9189 12017 5.188751 CCCTCTCTTCTCCTTTCTATGTTGT 59.811 44.000 0.00 0.00 0.00 3.32
9190 12018 5.423610 TCCCTCTCTTCTCCTTTCTATGTTG 59.576 44.000 0.00 0.00 0.00 3.33
9191 12019 5.594777 TCCCTCTCTTCTCCTTTCTATGTT 58.405 41.667 0.00 0.00 0.00 2.71
9192 12020 5.208121 CTCCCTCTCTTCTCCTTTCTATGT 58.792 45.833 0.00 0.00 0.00 2.29
9193 12021 4.039124 GCTCCCTCTCTTCTCCTTTCTATG 59.961 50.000 0.00 0.00 0.00 2.23
9194 12022 4.223144 GCTCCCTCTCTTCTCCTTTCTAT 58.777 47.826 0.00 0.00 0.00 1.98
9195 12023 3.011821 TGCTCCCTCTCTTCTCCTTTCTA 59.988 47.826 0.00 0.00 0.00 2.10
9196 12024 2.225496 TGCTCCCTCTCTTCTCCTTTCT 60.225 50.000 0.00 0.00 0.00 2.52
9197 12025 2.093711 GTGCTCCCTCTCTTCTCCTTTC 60.094 54.545 0.00 0.00 0.00 2.62
9198 12026 1.905894 GTGCTCCCTCTCTTCTCCTTT 59.094 52.381 0.00 0.00 0.00 3.11
9199 12027 1.078656 AGTGCTCCCTCTCTTCTCCTT 59.921 52.381 0.00 0.00 0.00 3.36
9200 12028 0.709992 AGTGCTCCCTCTCTTCTCCT 59.290 55.000 0.00 0.00 0.00 3.69
9201 12029 1.111277 GAGTGCTCCCTCTCTTCTCC 58.889 60.000 0.00 0.00 0.00 3.71
9202 12030 0.738389 CGAGTGCTCCCTCTCTTCTC 59.262 60.000 0.00 0.00 31.14 2.87
9203 12031 1.319614 GCGAGTGCTCCCTCTCTTCT 61.320 60.000 0.00 0.00 38.39 2.85
9204 12032 1.140804 GCGAGTGCTCCCTCTCTTC 59.859 63.158 0.00 0.00 38.39 2.87
9205 12033 2.355193 GGCGAGTGCTCCCTCTCTT 61.355 63.158 0.00 0.00 42.25 2.85
9206 12034 2.757917 GGCGAGTGCTCCCTCTCT 60.758 66.667 0.00 0.00 42.25 3.10
9207 12035 4.200283 CGGCGAGTGCTCCCTCTC 62.200 72.222 0.00 0.00 42.25 3.20


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

AutoCloner maintained by Alex Coulton.