Multiple sequence alignment - TraesCS4B01G155200

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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 TraesCS4B01G155200 chr4B 100.000 7394 0 0 1 7394 276957829 276965222 0.000000e+00 13655.0
1 TraesCS4B01G155200 chr4B 95.000 120 6 0 188 307 21371845 21371964 9.790000e-44 189.0
2 TraesCS4B01G155200 chr4D 97.155 2882 65 8 4521 7394 286394894 286392022 0.000000e+00 4852.0
3 TraesCS4B01G155200 chr4D 92.935 1826 33 24 303 2095 286397683 286395921 0.000000e+00 2569.0
4 TraesCS4B01G155200 chr4D 98.577 984 14 0 3538 4521 286395934 286394951 0.000000e+00 1740.0
5 TraesCS4B01G155200 chr4D 93.299 194 13 0 1 194 286397870 286397677 3.380000e-73 287.0
6 TraesCS4B01G155200 chr4D 86.842 76 6 3 3469 3543 12583393 12583465 1.710000e-11 82.4
7 TraesCS4B01G155200 chr4D 100.000 28 0 0 6016 6043 286393282 286393255 1.300000e-02 52.8
8 TraesCS4B01G155200 chr4A 94.764 2884 70 15 4521 7394 207980148 207977336 0.000000e+00 4414.0
9 TraesCS4B01G155200 chr4A 93.269 1857 35 19 303 2095 207983002 207981172 0.000000e+00 2654.0
10 TraesCS4B01G155200 chr4A 97.154 984 25 1 3538 4521 207981185 207980205 0.000000e+00 1659.0
11 TraesCS4B01G155200 chr4A 90.840 131 11 1 176 306 658949242 658949113 2.740000e-39 174.0
12 TraesCS4B01G155200 chr4A 93.443 61 3 1 3481 3540 465771168 465771228 1.020000e-13 89.8
13 TraesCS4B01G155200 chr4A 100.000 28 0 0 6016 6043 207978554 207978527 1.300000e-02 52.8
14 TraesCS4B01G155200 chr1B 89.345 1267 134 1 2099 3365 59967235 59968500 0.000000e+00 1591.0
15 TraesCS4B01G155200 chr1B 84.171 1472 187 28 2099 3539 112343200 112341744 0.000000e+00 1386.0
16 TraesCS4B01G155200 chr7B 86.395 1470 168 16 2097 3538 66874423 66875888 0.000000e+00 1578.0
17 TraesCS4B01G155200 chr7B 86.024 1245 171 3 2099 3342 329336799 329338041 0.000000e+00 1332.0
18 TraesCS4B01G155200 chr7B 83.260 681 102 8 4521 5197 575152815 575153487 3.790000e-172 616.0
19 TraesCS4B01G155200 chr7B 95.000 120 6 0 188 307 670232436 670232555 9.790000e-44 189.0
20 TraesCS4B01G155200 chr7B 93.388 121 8 0 187 307 141814556 141814436 5.890000e-41 180.0
21 TraesCS4B01G155200 chr3B 85.947 1473 175 20 2097 3539 413485662 413487132 0.000000e+00 1544.0
22 TraesCS4B01G155200 chr3B 86.706 1369 140 22 2208 3542 829398782 829397422 0.000000e+00 1482.0
23 TraesCS4B01G155200 chr3B 93.220 59 4 0 3482 3540 618180566 618180508 3.680000e-13 87.9
24 TraesCS4B01G155200 chr5B 84.970 1477 188 12 2097 3540 596712272 596713747 0.000000e+00 1467.0
25 TraesCS4B01G155200 chr5B 82.430 461 48 20 3105 3534 377896930 377897388 9.060000e-99 372.0
26 TraesCS4B01G155200 chr5B 95.041 121 6 0 187 307 233441441 233441561 2.720000e-44 191.0
27 TraesCS4B01G155200 chr5B 89.706 68 6 1 3482 3548 341092247 341092314 1.320000e-12 86.1
28 TraesCS4B01G155200 chr2B 88.307 1146 128 3 2097 3241 634084357 634083217 0.000000e+00 1369.0
29 TraesCS4B01G155200 chr2B 98.291 117 2 0 188 304 680227297 680227413 9.720000e-49 206.0
30 TraesCS4B01G155200 chr3D 81.806 1473 222 30 2099 3539 98534079 98535537 0.000000e+00 1194.0
31 TraesCS4B01G155200 chr3D 93.548 124 7 1 181 304 292034739 292034861 4.560000e-42 183.0
32 TraesCS4B01G155200 chr7A 85.377 677 81 8 4521 5193 613776586 613777248 0.000000e+00 686.0
33 TraesCS4B01G155200 chr7A 83.310 707 98 14 4502 5199 613778386 613779081 1.050000e-177 634.0
34 TraesCS4B01G155200 chr7A 83.235 680 99 11 4521 5198 614442269 614442935 1.760000e-170 610.0
35 TraesCS4B01G155200 chr7D 84.218 678 89 12 4523 5198 534072147 534072808 1.740000e-180 643.0
36 TraesCS4B01G155200 chr7D 84.172 676 94 9 4523 5197 534171446 534172109 1.740000e-180 643.0
37 TraesCS4B01G155200 chr7D 83.552 687 95 11 4521 5199 534194084 534194760 1.750000e-175 627.0
38 TraesCS4B01G155200 chr2A 77.332 922 161 29 2648 3537 518912100 518911195 1.110000e-137 501.0
39 TraesCS4B01G155200 chr6D 93.388 121 8 0 186 306 108860767 108860647 5.890000e-41 180.0
40 TraesCS4B01G155200 chr6D 93.388 121 8 0 186 306 302751993 302751873 5.890000e-41 180.0
41 TraesCS4B01G155200 chr6D 89.552 67 6 1 3476 3541 97015959 97016025 4.750000e-12 84.2


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 TraesCS4B01G155200 chr4B 276957829 276965222 7393 False 13655.00 13655 100.00000 1 7394 1 chr4B.!!$F2 7393
1 TraesCS4B01G155200 chr4D 286392022 286397870 5848 True 1900.16 4852 96.39320 1 7394 5 chr4D.!!$R1 7393
2 TraesCS4B01G155200 chr4A 207977336 207983002 5666 True 2194.95 4414 96.29675 303 7394 4 chr4A.!!$R2 7091
3 TraesCS4B01G155200 chr1B 59967235 59968500 1265 False 1591.00 1591 89.34500 2099 3365 1 chr1B.!!$F1 1266
4 TraesCS4B01G155200 chr1B 112341744 112343200 1456 True 1386.00 1386 84.17100 2099 3539 1 chr1B.!!$R1 1440
5 TraesCS4B01G155200 chr7B 66874423 66875888 1465 False 1578.00 1578 86.39500 2097 3538 1 chr7B.!!$F1 1441
6 TraesCS4B01G155200 chr7B 329336799 329338041 1242 False 1332.00 1332 86.02400 2099 3342 1 chr7B.!!$F2 1243
7 TraesCS4B01G155200 chr7B 575152815 575153487 672 False 616.00 616 83.26000 4521 5197 1 chr7B.!!$F3 676
8 TraesCS4B01G155200 chr3B 413485662 413487132 1470 False 1544.00 1544 85.94700 2097 3539 1 chr3B.!!$F1 1442
9 TraesCS4B01G155200 chr3B 829397422 829398782 1360 True 1482.00 1482 86.70600 2208 3542 1 chr3B.!!$R2 1334
10 TraesCS4B01G155200 chr5B 596712272 596713747 1475 False 1467.00 1467 84.97000 2097 3540 1 chr5B.!!$F4 1443
11 TraesCS4B01G155200 chr2B 634083217 634084357 1140 True 1369.00 1369 88.30700 2097 3241 1 chr2B.!!$R1 1144
12 TraesCS4B01G155200 chr3D 98534079 98535537 1458 False 1194.00 1194 81.80600 2099 3539 1 chr3D.!!$F1 1440
13 TraesCS4B01G155200 chr7A 613776586 613779081 2495 False 660.00 686 84.34350 4502 5199 2 chr7A.!!$F2 697
14 TraesCS4B01G155200 chr7A 614442269 614442935 666 False 610.00 610 83.23500 4521 5198 1 chr7A.!!$F1 677
15 TraesCS4B01G155200 chr7D 534072147 534072808 661 False 643.00 643 84.21800 4523 5198 1 chr7D.!!$F1 675
16 TraesCS4B01G155200 chr7D 534171446 534172109 663 False 643.00 643 84.17200 4523 5197 1 chr7D.!!$F2 674
17 TraesCS4B01G155200 chr7D 534194084 534194760 676 False 627.00 627 83.55200 4521 5199 1 chr7D.!!$F3 678
18 TraesCS4B01G155200 chr2A 518911195 518912100 905 True 501.00 501 77.33200 2648 3537 1 chr2A.!!$R1 889

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
205 206 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.00 44.66 3.13 F
207 208 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.00 44.66 1.40 F
300 301 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
518 519 0.104304 ATGAACCTACGGCGTGGATC 59.896 55.0 25.47 23.47 0.00 3.36 F
623 642 0.107897 AGCGTTCTCAACACACCACA 60.108 50.0 0.00 0.00 0.00 4.17 F
707 726 0.543410 TTCCTGCTTACCCGTCTCCA 60.543 55.0 0.00 0.00 0.00 3.86 F
1499 1561 0.592637 TGCAGTGCTTGTGAATTCGG 59.407 50.0 17.60 0.00 0.00 4.30 F
2422 2491 0.611714 TTTCCCTCTTACCAGTCCGC 59.388 55.0 0.00 0.00 0.00 5.54 F
2781 2852 0.790814 CTTCAGGTCGCTTTTCGGTC 59.209 55.0 0.00 0.00 39.05 4.79 F
3371 3482 0.958822 ATGGTGTTTTGCGTTCCCTC 59.041 50.0 0.00 0.00 0.00 4.30 F
4211 4326 0.250467 TCAGCCTGGTGAGCAAGTTC 60.250 55.0 0.00 0.00 0.00 3.01 F
5958 6143 0.776810 TGAAGGGGAAGCCATGTGAA 59.223 50.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2158 0.963962 CAGAGCCACTTTGCATTGGT 59.036 50.000 10.36 0.0 35.09 3.67 R
2182 2250 1.001406 CCCTCTCTGTTTGTCGAAGCT 59.999 52.381 0.00 0.0 0.00 3.74 R
2196 2264 5.450550 CGAATTCCAATAAAAAGCCCCTCTC 60.451 44.000 0.00 0.0 0.00 3.20 R
2301 2370 5.626543 GCATTTATTCATGATAGCGGTGTTG 59.373 40.000 0.00 0.0 0.00 3.33 R
2606 2676 1.625315 CAGCAATGGAGATATCCGGGA 59.375 52.381 0.00 0.0 0.00 5.14 R
2734 2804 2.343758 CCACACCACCGAGTCCAG 59.656 66.667 0.00 0.0 0.00 3.86 R
3120 3200 0.040204 CTCCAAGCCCAACCCAGAAT 59.960 55.000 0.00 0.0 0.00 2.40 R
3365 3476 1.229529 AGGCCGGAAAGAGAGGGAA 60.230 57.895 5.05 0.0 0.00 3.97 R
3785 3900 1.799181 CGTTCATCGTCTGTGGCTAGG 60.799 57.143 0.00 0.0 34.52 3.02 R
5070 5254 2.271497 GGCTGCTCTGAGTGCCAT 59.729 61.111 26.85 0.0 44.34 4.40 R
6204 6389 2.121291 TATCATGTTTTCCGGCAGCA 57.879 45.000 0.00 0.0 0.00 4.41 R
7019 7219 3.482147 CAGGCTGTGCACATGGATA 57.518 52.632 22.00 0.0 0.00 2.59 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
37 38 1.135373 CGACTGTCCGATAAGCAGTGT 60.135 52.381 1.55 0.00 42.71 3.55
68 69 3.944233 GCGGGTGCGACAAACGTT 61.944 61.111 0.00 0.00 44.60 3.99
72 73 0.110373 GGGTGCGACAAACGTTCATC 60.110 55.000 0.00 1.08 44.60 2.92
85 86 3.267483 ACGTTCATCCTTTTACATCCGG 58.733 45.455 0.00 0.00 0.00 5.14
110 111 4.397417 GCAACAGATCTTGGCATTAGTCTT 59.603 41.667 0.00 0.00 0.00 3.01
116 117 3.334691 TCTTGGCATTAGTCTTGAACCG 58.665 45.455 0.00 0.00 0.00 4.44
120 121 4.693283 TGGCATTAGTCTTGAACCGATAG 58.307 43.478 0.00 0.00 0.00 2.08
126 127 7.759886 GCATTAGTCTTGAACCGATAGCATATA 59.240 37.037 0.00 0.00 0.00 0.86
135 136 8.066612 TGAACCGATAGCATATATCTCATGAA 57.933 34.615 0.00 0.00 0.00 2.57
150 151 6.455360 TCTCATGAATAATGCAAAAGACCC 57.545 37.500 0.00 0.00 36.11 4.46
187 188 1.076777 CCGCCCACCCATCTTTCAT 60.077 57.895 0.00 0.00 0.00 2.57
188 189 0.182537 CCGCCCACCCATCTTTCATA 59.817 55.000 0.00 0.00 0.00 2.15
189 190 1.308998 CGCCCACCCATCTTTCATAC 58.691 55.000 0.00 0.00 0.00 2.39
190 191 1.134098 CGCCCACCCATCTTTCATACT 60.134 52.381 0.00 0.00 0.00 2.12
191 192 2.576615 GCCCACCCATCTTTCATACTC 58.423 52.381 0.00 0.00 0.00 2.59
192 193 2.749800 GCCCACCCATCTTTCATACTCC 60.750 54.545 0.00 0.00 0.00 3.85
193 194 2.158608 CCCACCCATCTTTCATACTCCC 60.159 54.545 0.00 0.00 0.00 4.30
194 195 2.780010 CCACCCATCTTTCATACTCCCT 59.220 50.000 0.00 0.00 0.00 4.20
195 196 3.181450 CCACCCATCTTTCATACTCCCTC 60.181 52.174 0.00 0.00 0.00 4.30
196 197 3.049344 ACCCATCTTTCATACTCCCTCC 58.951 50.000 0.00 0.00 0.00 4.30
197 198 2.037772 CCCATCTTTCATACTCCCTCCG 59.962 54.545 0.00 0.00 0.00 4.63
198 199 2.700897 CCATCTTTCATACTCCCTCCGT 59.299 50.000 0.00 0.00 0.00 4.69
199 200 3.243907 CCATCTTTCATACTCCCTCCGTC 60.244 52.174 0.00 0.00 0.00 4.79
200 201 2.385803 TCTTTCATACTCCCTCCGTCC 58.614 52.381 0.00 0.00 0.00 4.79
201 202 1.067212 CTTTCATACTCCCTCCGTCCG 59.933 57.143 0.00 0.00 0.00 4.79
202 203 0.754217 TTCATACTCCCTCCGTCCGG 60.754 60.000 0.00 0.00 0.00 5.14
203 204 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
204 205 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
205 206 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
206 207 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
207 208 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
208 209 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
209 210 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
210 211 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
211 212 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
212 213 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
213 214 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
214 215 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
215 216 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
216 217 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
217 218 2.848302 CGTCCGGAAATACTTGTCGTAC 59.152 50.000 5.23 0.00 0.00 3.67
218 219 3.182182 GTCCGGAAATACTTGTCGTACC 58.818 50.000 5.23 0.00 0.00 3.34
219 220 2.824936 TCCGGAAATACTTGTCGTACCA 59.175 45.455 0.00 0.00 0.00 3.25
220 221 3.257873 TCCGGAAATACTTGTCGTACCAA 59.742 43.478 0.00 0.00 0.00 3.67
221 222 4.081531 TCCGGAAATACTTGTCGTACCAAT 60.082 41.667 0.00 0.00 0.00 3.16
222 223 4.033587 CCGGAAATACTTGTCGTACCAATG 59.966 45.833 0.00 0.00 0.00 2.82
223 224 4.865925 CGGAAATACTTGTCGTACCAATGA 59.134 41.667 0.00 0.00 0.00 2.57
224 225 5.349270 CGGAAATACTTGTCGTACCAATGAA 59.651 40.000 0.00 0.00 0.00 2.57
225 226 6.036735 CGGAAATACTTGTCGTACCAATGAAT 59.963 38.462 0.00 0.00 0.00 2.57
226 227 7.223193 CGGAAATACTTGTCGTACCAATGAATA 59.777 37.037 0.00 0.00 0.00 1.75
227 228 8.885722 GGAAATACTTGTCGTACCAATGAATAA 58.114 33.333 0.00 0.00 0.00 1.40
232 233 8.964420 ACTTGTCGTACCAATGAATAAAATTG 57.036 30.769 0.00 0.00 35.26 2.32
276 277 6.837471 ACGTCTAGATACATCTATTTCCCC 57.163 41.667 0.00 0.00 38.60 4.81
277 278 5.415077 ACGTCTAGATACATCTATTTCCCCG 59.585 44.000 0.00 0.00 38.60 5.73
278 279 5.646793 CGTCTAGATACATCTATTTCCCCGA 59.353 44.000 0.00 0.00 38.60 5.14
279 280 6.403418 CGTCTAGATACATCTATTTCCCCGAC 60.403 46.154 0.00 2.21 38.60 4.79
280 281 6.433404 GTCTAGATACATCTATTTCCCCGACA 59.567 42.308 0.00 0.00 38.60 4.35
281 282 7.008332 TCTAGATACATCTATTTCCCCGACAA 58.992 38.462 0.00 0.00 38.60 3.18
282 283 6.102897 AGATACATCTATTTCCCCGACAAG 57.897 41.667 0.00 0.00 34.85 3.16
283 284 5.602978 AGATACATCTATTTCCCCGACAAGT 59.397 40.000 0.00 0.00 34.85 3.16
284 285 6.781014 AGATACATCTATTTCCCCGACAAGTA 59.219 38.462 0.00 0.00 34.85 2.24
285 286 5.888982 ACATCTATTTCCCCGACAAGTAT 57.111 39.130 0.00 0.00 0.00 2.12
286 287 6.248569 ACATCTATTTCCCCGACAAGTATT 57.751 37.500 0.00 0.00 0.00 1.89
287 288 6.659824 ACATCTATTTCCCCGACAAGTATTT 58.340 36.000 0.00 0.00 0.00 1.40
288 289 6.766467 ACATCTATTTCCCCGACAAGTATTTC 59.234 38.462 0.00 0.00 0.00 2.17
289 290 5.677567 TCTATTTCCCCGACAAGTATTTCC 58.322 41.667 0.00 0.00 0.00 3.13
290 291 2.389962 TTCCCCGACAAGTATTTCCG 57.610 50.000 0.00 0.00 0.00 4.30
291 292 0.538118 TCCCCGACAAGTATTTCCGG 59.462 55.000 0.00 0.00 39.85 5.14
292 293 0.538118 CCCCGACAAGTATTTCCGGA 59.462 55.000 0.00 0.00 42.49 5.14
293 294 1.648504 CCCGACAAGTATTTCCGGAC 58.351 55.000 1.83 0.00 42.49 4.79
294 295 1.274596 CCGACAAGTATTTCCGGACG 58.725 55.000 1.83 0.00 42.49 4.79
295 296 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
296 297 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
297 298 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
298 299 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
299 300 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
300 301 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
301 302 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
362 363 7.933577 TCAAACCCTGAATGTATATCTCATGAC 59.066 37.037 0.00 0.00 0.00 3.06
378 379 6.117488 TCTCATGACTAATGTAGGACGTGTA 58.883 40.000 0.00 0.00 37.56 2.90
518 519 0.104304 ATGAACCTACGGCGTGGATC 59.896 55.000 25.47 23.47 0.00 3.36
519 520 1.227176 GAACCTACGGCGTGGATCC 60.227 63.158 25.47 4.20 0.00 3.36
520 521 1.952102 GAACCTACGGCGTGGATCCA 61.952 60.000 25.47 11.44 0.00 3.41
521 522 1.546589 AACCTACGGCGTGGATCCAA 61.547 55.000 25.47 0.00 0.00 3.53
623 642 0.107897 AGCGTTCTCAACACACCACA 60.108 50.000 0.00 0.00 0.00 4.17
638 657 3.181454 ACACCACAAATTTCTCTCTCCGT 60.181 43.478 0.00 0.00 0.00 4.69
645 664 3.601443 ATTTCTCTCTCCGTCCTTGTG 57.399 47.619 0.00 0.00 0.00 3.33
707 726 0.543410 TTCCTGCTTACCCGTCTCCA 60.543 55.000 0.00 0.00 0.00 3.86
1333 1371 1.228657 GGTTGTCCGTGACTTGCTCC 61.229 60.000 5.77 0.00 33.15 4.70
1336 1374 1.733399 GTCCGTGACTTGCTCCGAC 60.733 63.158 0.00 0.00 0.00 4.79
1455 1517 5.578727 ACTCGATTTGCTATGTTTGACTCTC 59.421 40.000 0.00 0.00 0.00 3.20
1499 1561 0.592637 TGCAGTGCTTGTGAATTCGG 59.407 50.000 17.60 0.00 0.00 4.30
1568 1630 4.498345 GGTGCAGTGTTTAATTCGGACAAA 60.498 41.667 0.00 0.00 0.00 2.83
1587 1649 5.555017 ACAAATGATTATCTGGGAGATCCG 58.445 41.667 0.00 0.00 36.20 4.18
2081 2149 3.119531 CGCCATTTTGTTTCATGCTCCTA 60.120 43.478 0.00 0.00 0.00 2.94
2082 2150 4.617995 CGCCATTTTGTTTCATGCTCCTAA 60.618 41.667 0.00 0.00 0.00 2.69
2083 2151 5.237048 GCCATTTTGTTTCATGCTCCTAAA 58.763 37.500 0.00 0.00 0.00 1.85
2084 2152 5.876460 GCCATTTTGTTTCATGCTCCTAAAT 59.124 36.000 0.00 0.00 0.00 1.40
2085 2153 6.183360 GCCATTTTGTTTCATGCTCCTAAATG 60.183 38.462 13.10 13.10 33.67 2.32
2086 2154 6.183360 CCATTTTGTTTCATGCTCCTAAATGC 60.183 38.462 13.91 0.00 32.95 3.56
2087 2155 5.465532 TTTGTTTCATGCTCCTAAATGCA 57.534 34.783 0.00 0.00 43.67 3.96
2088 2156 4.439305 TGTTTCATGCTCCTAAATGCAC 57.561 40.909 0.00 0.00 42.26 4.57
2089 2157 3.825585 TGTTTCATGCTCCTAAATGCACA 59.174 39.130 0.00 0.00 42.26 4.57
2090 2158 4.280425 TGTTTCATGCTCCTAAATGCACAA 59.720 37.500 0.00 0.00 42.26 3.33
2091 2159 4.439305 TTCATGCTCCTAAATGCACAAC 57.561 40.909 0.00 0.00 42.26 3.32
2092 2160 2.754552 TCATGCTCCTAAATGCACAACC 59.245 45.455 0.00 0.00 42.26 3.77
2093 2161 2.284754 TGCTCCTAAATGCACAACCA 57.715 45.000 0.00 0.00 33.94 3.67
2094 2162 2.591923 TGCTCCTAAATGCACAACCAA 58.408 42.857 0.00 0.00 33.94 3.67
2095 2163 3.164268 TGCTCCTAAATGCACAACCAAT 58.836 40.909 0.00 0.00 33.94 3.16
2115 2183 1.881973 TGCAAAGTGGCTCTGATCAAC 59.118 47.619 0.00 0.00 34.04 3.18
2139 2207 1.722271 TGCCTATCCTCCCTGCCTATA 59.278 52.381 0.00 0.00 0.00 1.31
2196 2264 1.205064 CGCCAGCTTCGACAAACAG 59.795 57.895 0.00 0.00 0.00 3.16
2422 2491 0.611714 TTTCCCTCTTACCAGTCCGC 59.388 55.000 0.00 0.00 0.00 5.54
2460 2529 1.478105 GGCGGCTCTCAATTTTGGAAT 59.522 47.619 0.00 0.00 0.00 3.01
2462 2531 2.736400 GCGGCTCTCAATTTTGGAATGG 60.736 50.000 0.00 0.00 0.00 3.16
2467 2536 4.152938 GCTCTCAATTTTGGAATGGTTTGC 59.847 41.667 0.00 0.00 0.00 3.68
2605 2675 3.445096 CACCCTTTTCTCTTATTGCCCTG 59.555 47.826 0.00 0.00 0.00 4.45
2606 2676 3.076032 ACCCTTTTCTCTTATTGCCCTGT 59.924 43.478 0.00 0.00 0.00 4.00
2734 2804 1.134340 TCCCTACGCTCTCAGAGACTC 60.134 57.143 5.62 0.00 0.00 3.36
2766 2837 1.150536 GTGGCCCCACACTTCTTCA 59.849 57.895 12.42 0.00 45.53 3.02
2781 2852 0.790814 CTTCAGGTCGCTTTTCGGTC 59.209 55.000 0.00 0.00 39.05 4.79
2796 2867 4.985538 TTCGGTCAAGTCTCTCTATTCC 57.014 45.455 0.00 0.00 0.00 3.01
2877 2948 5.716703 TCCCCTGAAAATCAAAATCTTCCTC 59.283 40.000 0.00 0.00 0.00 3.71
2934 3011 2.483013 CCAGATTCGTAAGCGGAATGGA 60.483 50.000 1.10 0.00 38.23 3.41
3071 3151 3.140144 TCATGGGACCCTTCTTCTTTTGT 59.860 43.478 13.00 0.00 0.00 2.83
3099 3179 1.754226 CAGACCCTGGCTAAGTCTCTC 59.246 57.143 0.96 0.00 38.80 3.20
3221 3302 2.638480 AAACCTGCTGACTGCTTGTA 57.362 45.000 5.87 0.00 43.37 2.41
3228 3309 4.025396 CCTGCTGACTGCTTGTATAAATCG 60.025 45.833 5.87 0.00 43.37 3.34
3361 3444 3.005791 GCAGGTTGCTTAGATGGTGTTTT 59.994 43.478 0.00 0.00 40.96 2.43
3365 3476 2.226330 TGCTTAGATGGTGTTTTGCGT 58.774 42.857 0.00 0.00 0.00 5.24
3371 3482 0.958822 ATGGTGTTTTGCGTTCCCTC 59.041 50.000 0.00 0.00 0.00 4.30
3398 3509 2.411290 CCTGCGTGCCGTTTGTTT 59.589 55.556 0.00 0.00 0.00 2.83
3399 3510 1.657181 CCTGCGTGCCGTTTGTTTC 60.657 57.895 0.00 0.00 0.00 2.78
3453 3568 2.345876 GCCACTTTGTGTTTGCTTGTT 58.654 42.857 0.00 0.00 0.00 2.83
3458 3573 4.922692 CACTTTGTGTTTGCTTGTTCTTGA 59.077 37.500 0.00 0.00 0.00 3.02
3665 3780 6.514012 TTTCTTCTATATTGGCAGATGGGA 57.486 37.500 0.00 0.00 0.00 4.37
3785 3900 0.251787 ACCAGGCAGAAATCCCCAAC 60.252 55.000 0.00 0.00 0.00 3.77
3939 4054 9.220767 ACAAGAAGGAAGATATTACAAGTGAAC 57.779 33.333 0.00 0.00 0.00 3.18
3940 4055 9.442047 CAAGAAGGAAGATATTACAAGTGAACT 57.558 33.333 0.00 0.00 0.00 3.01
4211 4326 0.250467 TCAGCCTGGTGAGCAAGTTC 60.250 55.000 0.00 0.00 0.00 3.01
4243 4358 1.002868 CTGTTGGGGAGGTGCTCTG 60.003 63.158 0.00 0.00 0.00 3.35
4492 4607 5.240121 ACTGAAATGGTGCAAAATGAATCC 58.760 37.500 0.00 0.00 0.00 3.01
4577 4749 5.916883 GCAAATATGTTGCCTGCTGTAATAG 59.083 40.000 9.95 0.00 39.38 1.73
4958 5137 6.071391 ACACCTAAAGGCATAAATTGTTCCAG 60.071 38.462 0.00 0.00 39.32 3.86
5023 5207 7.324388 TCCAGGAGAAGTAAGGTGAAATTAA 57.676 36.000 0.00 0.00 0.00 1.40
5024 5208 7.751646 TCCAGGAGAAGTAAGGTGAAATTAAA 58.248 34.615 0.00 0.00 0.00 1.52
5025 5209 8.390921 TCCAGGAGAAGTAAGGTGAAATTAAAT 58.609 33.333 0.00 0.00 0.00 1.40
5026 5210 8.462016 CCAGGAGAAGTAAGGTGAAATTAAATG 58.538 37.037 0.00 0.00 0.00 2.32
5027 5211 9.231297 CAGGAGAAGTAAGGTGAAATTAAATGA 57.769 33.333 0.00 0.00 0.00 2.57
5070 5254 1.172180 CCCGTTTGCTTGCAAGAGGA 61.172 55.000 30.39 11.42 0.00 3.71
5226 5411 1.455383 AAAAAGTGGCAGCAGACCCG 61.455 55.000 0.00 0.00 0.00 5.28
5489 5674 3.840666 AGTTCCTCTCAGGAGCAACATAA 59.159 43.478 8.89 0.00 46.66 1.90
5551 5736 2.668457 GTGACAGCTCCTGTTAATGACG 59.332 50.000 0.00 0.00 45.44 4.35
5958 6143 0.776810 TGAAGGGGAAGCCATGTGAA 59.223 50.000 0.00 0.00 0.00 3.18
6110 6295 5.337009 GGACTTTGCCAGACAATCATGATTT 60.337 40.000 18.41 10.05 38.31 2.17
6159 6344 6.009589 TGTGGTGAATACAAATGAGGACAAT 58.990 36.000 0.00 0.00 0.00 2.71
6204 6389 6.051717 CGAGATAGTTCCTGATGTTTTGGAT 58.948 40.000 0.00 0.00 0.00 3.41
6207 6392 3.771216 AGTTCCTGATGTTTTGGATGCT 58.229 40.909 0.00 0.00 0.00 3.79
6223 6408 2.121291 TGCTGCCGGAAAACATGATA 57.879 45.000 5.05 0.00 0.00 2.15
6349 6534 2.335712 GGGGACGCAAGAAGCTTGG 61.336 63.158 2.10 0.00 42.61 3.61
6407 6592 3.947612 AGATTGAATGTGGGCATCTCT 57.052 42.857 0.00 0.00 33.50 3.10
6613 6805 1.667154 CCATCCGAAGCTGTCCTCGA 61.667 60.000 7.10 0.00 0.00 4.04
6659 6851 4.074259 CTGTTCCCTCATCATGTTCACAA 58.926 43.478 0.00 0.00 0.00 3.33
7152 7352 3.443976 CCAACAAAAACTGGTGTACTGC 58.556 45.455 0.00 0.00 41.63 4.40
7171 7371 7.666804 TGTACTGCATAATAGTATTACCTCCGA 59.333 37.037 4.71 0.00 33.60 4.55
7179 7379 4.104383 AGTATTACCTCCGACCCGAATA 57.896 45.455 0.00 0.00 0.00 1.75
7352 8589 5.548056 TGGAGGGACAGAGAGAAAAGTTAAT 59.452 40.000 0.00 0.00 0.00 1.40
7384 8621 1.289231 TGGTCAGTAGGGAGCAGATCT 59.711 52.381 0.00 0.00 40.11 2.75
7385 8622 2.514160 TGGTCAGTAGGGAGCAGATCTA 59.486 50.000 0.00 0.00 40.11 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.086094 TCGTACACTGCTTATCGGACA 58.914 47.619 0.00 0.00 0.00 4.02
37 38 0.899720 ACCCGCAAGAAAGGATCGTA 59.100 50.000 0.00 0.00 43.02 3.43
68 69 2.026729 TGCACCGGATGTAAAAGGATGA 60.027 45.455 9.46 0.00 0.00 2.92
72 73 1.883275 TGTTGCACCGGATGTAAAAGG 59.117 47.619 9.46 0.00 34.39 3.11
85 86 3.441572 ACTAATGCCAAGATCTGTTGCAC 59.558 43.478 14.19 0.00 0.00 4.57
110 111 7.645058 TCATGAGATATATGCTATCGGTTCA 57.355 36.000 0.00 0.00 0.00 3.18
126 127 6.837568 AGGGTCTTTTGCATTATTCATGAGAT 59.162 34.615 0.00 0.00 34.31 2.75
135 136 8.189119 TGAAAAAGTAGGGTCTTTTGCATTAT 57.811 30.769 8.07 0.00 43.69 1.28
149 150 2.683362 GGCGAATCCCTGAAAAAGTAGG 59.317 50.000 0.00 0.00 0.00 3.18
150 151 2.351726 CGGCGAATCCCTGAAAAAGTAG 59.648 50.000 0.00 0.00 0.00 2.57
187 188 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
188 189 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
189 190 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
190 191 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
191 192 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
192 193 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
193 194 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
194 195 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
195 196 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
196 197 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
197 198 3.182182 GGTACGACAAGTATTTCCGGAC 58.818 50.000 1.83 0.00 37.69 4.79
198 199 2.824936 TGGTACGACAAGTATTTCCGGA 59.175 45.455 0.00 0.00 37.69 5.14
199 200 3.235157 TGGTACGACAAGTATTTCCGG 57.765 47.619 0.00 0.00 37.69 5.14
200 201 4.865925 TCATTGGTACGACAAGTATTTCCG 59.134 41.667 0.00 0.00 37.69 4.30
201 202 6.730960 TTCATTGGTACGACAAGTATTTCC 57.269 37.500 0.00 0.00 37.69 3.13
207 208 8.026607 CCAATTTTATTCATTGGTACGACAAGT 58.973 33.333 3.85 0.00 44.04 3.16
208 209 8.393395 CCAATTTTATTCATTGGTACGACAAG 57.607 34.615 3.85 0.00 44.04 3.16
250 251 8.968969 GGGGAAATAGATGTATCTAGACGTATT 58.031 37.037 0.00 0.00 42.20 1.89
251 252 7.282675 CGGGGAAATAGATGTATCTAGACGTAT 59.717 40.741 0.00 0.00 42.20 3.06
252 253 6.596888 CGGGGAAATAGATGTATCTAGACGTA 59.403 42.308 0.00 0.00 42.20 3.57
253 254 5.415077 CGGGGAAATAGATGTATCTAGACGT 59.585 44.000 0.00 0.00 42.20 4.34
254 255 5.646793 TCGGGGAAATAGATGTATCTAGACG 59.353 44.000 0.00 5.87 42.20 4.18
255 256 6.433404 TGTCGGGGAAATAGATGTATCTAGAC 59.567 42.308 0.00 7.60 42.20 2.59
256 257 6.549242 TGTCGGGGAAATAGATGTATCTAGA 58.451 40.000 7.57 0.00 42.20 2.43
257 258 6.835819 TGTCGGGGAAATAGATGTATCTAG 57.164 41.667 7.57 0.00 42.20 2.43
258 259 6.781014 ACTTGTCGGGGAAATAGATGTATCTA 59.219 38.462 4.22 4.22 43.00 1.98
259 260 5.602978 ACTTGTCGGGGAAATAGATGTATCT 59.397 40.000 0.00 0.00 40.86 1.98
260 261 5.855045 ACTTGTCGGGGAAATAGATGTATC 58.145 41.667 0.00 0.00 0.00 2.24
261 262 5.888982 ACTTGTCGGGGAAATAGATGTAT 57.111 39.130 0.00 0.00 0.00 2.29
262 263 6.989155 ATACTTGTCGGGGAAATAGATGTA 57.011 37.500 0.00 0.00 0.00 2.29
263 264 5.888982 ATACTTGTCGGGGAAATAGATGT 57.111 39.130 0.00 0.00 0.00 3.06
264 265 6.204882 GGAAATACTTGTCGGGGAAATAGATG 59.795 42.308 0.00 0.00 0.00 2.90
265 266 6.296803 GGAAATACTTGTCGGGGAAATAGAT 58.703 40.000 0.00 0.00 0.00 1.98
266 267 5.677567 GGAAATACTTGTCGGGGAAATAGA 58.322 41.667 0.00 0.00 0.00 1.98
267 268 4.510340 CGGAAATACTTGTCGGGGAAATAG 59.490 45.833 0.00 0.00 0.00 1.73
268 269 4.444536 CGGAAATACTTGTCGGGGAAATA 58.555 43.478 0.00 0.00 0.00 1.40
269 270 3.275999 CGGAAATACTTGTCGGGGAAAT 58.724 45.455 0.00 0.00 0.00 2.17
270 271 2.616001 CCGGAAATACTTGTCGGGGAAA 60.616 50.000 0.00 0.00 37.35 3.13
271 272 1.065998 CCGGAAATACTTGTCGGGGAA 60.066 52.381 0.00 0.00 37.35 3.97
272 273 0.538118 CCGGAAATACTTGTCGGGGA 59.462 55.000 0.00 0.00 37.35 4.81
273 274 0.538118 TCCGGAAATACTTGTCGGGG 59.462 55.000 0.00 0.00 40.92 5.73
274 275 1.648504 GTCCGGAAATACTTGTCGGG 58.351 55.000 5.23 0.00 40.92 5.14
275 276 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
276 277 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
277 278 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
278 279 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
279 280 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
280 281 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
281 282 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
282 283 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
283 284 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
284 285 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
285 286 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
286 287 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
287 288 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
288 289 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
289 290 1.382692 GGAAGTACTCCCTCCGTCCG 61.383 65.000 0.00 0.00 38.44 4.79
290 291 1.382692 CGGAAGTACTCCCTCCGTCC 61.383 65.000 21.34 10.92 41.87 4.79
291 292 0.393537 TCGGAAGTACTCCCTCCGTC 60.394 60.000 26.02 7.07 41.87 4.79
292 293 0.258194 ATCGGAAGTACTCCCTCCGT 59.742 55.000 26.02 15.19 41.87 4.69
293 294 1.337387 GAATCGGAAGTACTCCCTCCG 59.663 57.143 22.94 22.94 41.87 4.63
294 295 2.385803 TGAATCGGAAGTACTCCCTCC 58.614 52.381 0.00 0.00 41.87 4.30
295 296 3.734293 CGTTGAATCGGAAGTACTCCCTC 60.734 52.174 0.00 0.00 41.87 4.30
296 297 2.165845 CGTTGAATCGGAAGTACTCCCT 59.834 50.000 0.00 0.00 41.87 4.20
297 298 2.537401 CGTTGAATCGGAAGTACTCCC 58.463 52.381 0.00 0.00 41.87 4.30
444 445 1.458445 GTAAGAACCGTTTCTGTCGCC 59.542 52.381 0.00 0.00 41.56 5.54
518 519 1.047002 TTGGATGCCACTTTGGTTGG 58.953 50.000 0.00 0.00 40.46 3.77
519 520 1.602668 CGTTGGATGCCACTTTGGTTG 60.603 52.381 0.00 0.00 40.46 3.77
520 521 0.673437 CGTTGGATGCCACTTTGGTT 59.327 50.000 0.00 0.00 40.46 3.67
521 522 1.178534 CCGTTGGATGCCACTTTGGT 61.179 55.000 0.00 0.00 40.46 3.67
623 642 4.319177 CACAAGGACGGAGAGAGAAATTT 58.681 43.478 0.00 0.00 0.00 1.82
638 657 1.181741 ACGAGAGAGCAGCACAAGGA 61.182 55.000 0.00 0.00 0.00 3.36
645 664 2.926838 CCTTTAAAGACGAGAGAGCAGC 59.073 50.000 16.98 0.00 0.00 5.25
707 726 4.095400 AGGGGTGGAGGCGGAGAT 62.095 66.667 0.00 0.00 0.00 2.75
1336 1374 1.455217 ATCAGGTAGGACGACGGGG 60.455 63.158 0.00 0.00 0.00 5.73
1455 1517 2.019984 GGAGCAAGCCTACAAATCTGG 58.980 52.381 0.00 0.00 0.00 3.86
1568 1630 5.028802 ACATCGGATCTCCCAGATAATCAT 58.971 41.667 0.00 0.00 34.53 2.45
1587 1649 7.041780 ACAAGTAAAACTCTGTCATGACACATC 60.042 37.037 24.56 9.06 36.21 3.06
2036 2104 6.036470 CGCTCTGTATGAATAAGTGAAGTGA 58.964 40.000 0.00 0.00 0.00 3.41
2037 2105 5.276584 GCGCTCTGTATGAATAAGTGAAGTG 60.277 44.000 0.00 0.00 0.00 3.16
2038 2106 4.806247 GCGCTCTGTATGAATAAGTGAAGT 59.194 41.667 0.00 0.00 0.00 3.01
2039 2107 4.210120 GGCGCTCTGTATGAATAAGTGAAG 59.790 45.833 7.64 0.00 0.00 3.02
2040 2108 4.119862 GGCGCTCTGTATGAATAAGTGAA 58.880 43.478 7.64 0.00 0.00 3.18
2085 2153 1.219646 CCACTTTGCATTGGTTGTGC 58.780 50.000 0.00 0.00 42.81 4.57
2086 2154 1.202557 AGCCACTTTGCATTGGTTGTG 60.203 47.619 10.36 3.72 35.09 3.33
2087 2155 1.069049 GAGCCACTTTGCATTGGTTGT 59.931 47.619 10.36 0.00 35.09 3.32
2088 2156 1.342174 AGAGCCACTTTGCATTGGTTG 59.658 47.619 10.36 0.00 35.09 3.77
2089 2157 1.342174 CAGAGCCACTTTGCATTGGTT 59.658 47.619 10.36 5.23 35.09 3.67
2090 2158 0.963962 CAGAGCCACTTTGCATTGGT 59.036 50.000 10.36 0.00 35.09 3.67
2091 2159 1.250328 TCAGAGCCACTTTGCATTGG 58.750 50.000 5.35 5.35 35.81 3.16
2092 2160 2.490509 TGATCAGAGCCACTTTGCATTG 59.509 45.455 0.00 0.00 0.00 2.82
2093 2161 2.799017 TGATCAGAGCCACTTTGCATT 58.201 42.857 0.00 0.00 0.00 3.56
2094 2162 2.490903 GTTGATCAGAGCCACTTTGCAT 59.509 45.455 0.00 0.00 0.00 3.96
2095 2163 1.881973 GTTGATCAGAGCCACTTTGCA 59.118 47.619 0.00 0.00 0.00 4.08
2115 2183 1.070445 CAGGGAGGATAGGCAAGCG 59.930 63.158 0.00 0.00 0.00 4.68
2139 2207 9.088987 GAGAGAGAGTAGAATCCCATAAGAAAT 57.911 37.037 0.00 0.00 0.00 2.17
2181 2249 2.064762 CCTCTCTGTTTGTCGAAGCTG 58.935 52.381 0.00 0.00 0.00 4.24
2182 2250 1.001406 CCCTCTCTGTTTGTCGAAGCT 59.999 52.381 0.00 0.00 0.00 3.74
2196 2264 5.450550 CGAATTCCAATAAAAAGCCCCTCTC 60.451 44.000 0.00 0.00 0.00 3.20
2301 2370 5.626543 GCATTTATTCATGATAGCGGTGTTG 59.373 40.000 0.00 0.00 0.00 3.33
2460 2529 5.763204 CAGAGGTCTAACTTTAAGCAAACCA 59.237 40.000 8.42 0.00 0.00 3.67
2462 2531 6.862711 ACAGAGGTCTAACTTTAAGCAAAC 57.137 37.500 0.00 0.00 0.00 2.93
2467 2536 7.442656 TCCAGAAACAGAGGTCTAACTTTAAG 58.557 38.462 0.00 0.00 0.00 1.85
2605 2675 1.625818 AGCAATGGAGATATCCGGGAC 59.374 52.381 0.00 0.00 0.00 4.46
2606 2676 1.625315 CAGCAATGGAGATATCCGGGA 59.375 52.381 0.00 0.00 0.00 5.14
2734 2804 2.343758 CCACACCACCGAGTCCAG 59.656 66.667 0.00 0.00 0.00 3.86
2766 2837 0.106149 ACTTGACCGAAAAGCGACCT 59.894 50.000 0.00 0.00 44.57 3.85
2781 2852 4.081198 ACAAGCCTGGAATAGAGAGACTTG 60.081 45.833 0.00 0.00 38.31 3.16
2796 2867 0.460987 GAGATCCACCGACAAGCCTG 60.461 60.000 0.00 0.00 0.00 4.85
2877 2948 1.163554 GACCTCTGAAAGCTTGCCAG 58.836 55.000 18.14 18.14 0.00 4.85
3120 3200 0.040204 CTCCAAGCCCAACCCAGAAT 59.960 55.000 0.00 0.00 0.00 2.40
3141 3221 4.503910 TCGTCCACAAAGACCAATAGATG 58.496 43.478 0.00 0.00 32.91 2.90
3146 3226 4.019681 TCCTAATCGTCCACAAAGACCAAT 60.020 41.667 0.00 0.00 32.91 3.16
3221 3302 5.817296 TGCTGCAAGAAGATACACGATTTAT 59.183 36.000 0.00 0.00 34.07 1.40
3228 3309 2.417933 CCACTGCTGCAAGAAGATACAC 59.582 50.000 3.02 0.00 45.09 2.90
3342 3423 3.317150 GCAAAACACCATCTAAGCAACC 58.683 45.455 0.00 0.00 0.00 3.77
3361 3444 1.292223 CGGAAAGAGAGGGAACGCA 59.708 57.895 0.00 0.00 0.00 5.24
3365 3476 1.229529 AGGCCGGAAAGAGAGGGAA 60.230 57.895 5.05 0.00 0.00 3.97
3371 3482 3.121030 CACGCAGGCCGGAAAGAG 61.121 66.667 5.05 0.00 42.52 2.85
3453 3568 4.141287 CTGTAACAACCAACCCATCAAGA 58.859 43.478 0.00 0.00 0.00 3.02
3458 3573 2.364002 GCAACTGTAACAACCAACCCAT 59.636 45.455 0.00 0.00 0.00 4.00
3649 3764 5.104151 TGAAGTGTTCCCATCTGCCAATATA 60.104 40.000 0.00 0.00 0.00 0.86
3656 3771 2.191128 ACTGAAGTGTTCCCATCTGC 57.809 50.000 0.00 0.00 0.00 4.26
3785 3900 1.799181 CGTTCATCGTCTGTGGCTAGG 60.799 57.143 0.00 0.00 34.52 3.02
3939 4054 6.268617 TGAGGATCCAGATATGTCCAGTTAAG 59.731 42.308 15.82 0.00 33.12 1.85
3940 4055 6.143206 TGAGGATCCAGATATGTCCAGTTAA 58.857 40.000 15.82 0.00 33.12 2.01
4211 4326 2.636830 CCAACAGTCTTGCTCCCTATG 58.363 52.381 0.00 0.00 0.00 2.23
4243 4358 8.688151 CATTATAGAACCTCCCATAGTAGTAGC 58.312 40.741 0.00 0.00 0.00 3.58
4449 4564 7.733773 TCAGTATCCCTTGTGAAAGAGATTA 57.266 36.000 0.00 0.00 0.00 1.75
4577 4749 3.375782 AATTTGGCTGTTCTCTTGTGC 57.624 42.857 0.00 0.00 0.00 4.57
4958 5137 4.582656 TGACTATCTCTTCTCTAGCAAGCC 59.417 45.833 0.00 0.00 0.00 4.35
5023 5207 4.154942 ACAGCTTCCCAAAACAGATCATT 58.845 39.130 0.00 0.00 0.00 2.57
5024 5208 3.771216 ACAGCTTCCCAAAACAGATCAT 58.229 40.909 0.00 0.00 0.00 2.45
5025 5209 3.228188 ACAGCTTCCCAAAACAGATCA 57.772 42.857 0.00 0.00 0.00 2.92
5026 5210 4.301628 CAAACAGCTTCCCAAAACAGATC 58.698 43.478 0.00 0.00 0.00 2.75
5027 5211 3.070015 CCAAACAGCTTCCCAAAACAGAT 59.930 43.478 0.00 0.00 0.00 2.90
5070 5254 2.271497 GGCTGCTCTGAGTGCCAT 59.729 61.111 26.85 0.00 44.34 4.40
5226 5411 4.941263 TCTGTCTCTAGCTGAAGAAGAGTC 59.059 45.833 9.70 5.76 38.32 3.36
5489 5674 5.045651 TGGTCATCTGACAAGTTACCATCAT 60.046 40.000 12.10 0.00 46.47 2.45
5551 5736 6.575162 ACTGTAAACTGATCCCATTTCAAC 57.425 37.500 0.00 0.00 0.00 3.18
5958 6143 3.589988 CTTCGCAACCTCTGTTATCTGT 58.410 45.455 0.00 0.00 32.09 3.41
5984 6169 3.395669 GCGATCTGCCGTTGGTAC 58.604 61.111 0.00 0.00 37.76 3.34
6110 6295 9.467258 CAGTTAGATCTTCATTTTTCTGCAAAA 57.533 29.630 0.00 0.00 38.76 2.44
6159 6344 5.239351 TCGTTATTCGAAATGGAAGGTGAA 58.761 37.500 0.00 0.00 45.98 3.18
6204 6389 2.121291 TATCATGTTTTCCGGCAGCA 57.879 45.000 0.00 0.00 0.00 4.41
6207 6392 5.189928 ACAGTTATATCATGTTTTCCGGCA 58.810 37.500 0.00 0.00 0.00 5.69
6390 6575 4.716784 ACTAGTAGAGATGCCCACATTCAA 59.283 41.667 3.59 0.00 36.35 2.69
6613 6805 2.579860 AGCTCCTCCACAAGAAATGGAT 59.420 45.455 0.00 0.00 45.27 3.41
6659 6851 0.828022 CCAATCACCAATGCCTGCAT 59.172 50.000 0.00 0.00 38.46 3.96
7019 7219 3.482147 CAGGCTGTGCACATGGATA 57.518 52.632 22.00 0.00 0.00 2.59
7152 7352 5.649395 TCGGGTCGGAGGTAATACTATTATG 59.351 44.000 0.00 0.00 0.00 1.90
7171 7371 5.067273 TGTGACAAGACAATTTATTCGGGT 58.933 37.500 0.00 0.00 0.00 5.28
7179 7379 7.710475 CCCAAATTACTTGTGACAAGACAATTT 59.290 33.333 30.03 29.04 35.32 1.82


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

AutoCloner maintained by Alex Coulton.