Multiple sequence alignment - TraesCS2D01G006000

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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 TraesCS2D01G006000 chr2D 100.000 3521 0 0 1 3521 2949595 2946075 0.000000e+00 6503.0
1 TraesCS2D01G006000 chr2D 95.082 122 5 1 196 316 7396590 7396469 1.290000e-44 191.0
2 TraesCS2D01G006000 chr2D 95.041 121 6 0 196 316 138294511 138294391 1.290000e-44 191.0
3 TraesCS2D01G006000 chr2B 93.465 2173 100 26 315 2478 7836882 7839021 0.000000e+00 3188.0
4 TraesCS2D01G006000 chr2B 90.314 1941 158 21 557 2481 8071874 8069948 0.000000e+00 2516.0
5 TraesCS2D01G006000 chr2B 90.309 1940 159 20 557 2481 8227628 8225703 0.000000e+00 2514.0
6 TraesCS2D01G006000 chr2B 89.892 1949 156 25 549 2482 7902663 7900741 0.000000e+00 2470.0
7 TraesCS2D01G006000 chr2B 92.701 1466 70 23 315 1774 7761659 7763093 0.000000e+00 2080.0
8 TraesCS2D01G006000 chr2B 94.910 668 31 3 1814 2478 7763090 7763757 0.000000e+00 1042.0
9 TraesCS2D01G006000 chr2B 90.114 263 25 1 2478 2740 7849985 7850246 1.210000e-89 340.0
10 TraesCS2D01G006000 chr2B 88.848 269 28 2 2472 2740 7845803 7846069 2.620000e-86 329.0
11 TraesCS2D01G006000 chr2B 82.152 381 50 8 3155 3518 303847 304226 9.490000e-81 311.0
12 TraesCS2D01G006000 chr2B 93.564 202 12 1 1 201 7761459 7761660 2.050000e-77 300.0
13 TraesCS2D01G006000 chr2B 85.448 268 39 0 3254 3521 7847303 7847570 2.680000e-71 279.0
14 TraesCS2D01G006000 chr2B 91.089 202 17 1 1 201 7836682 7836883 4.480000e-69 272.0
15 TraesCS2D01G006000 chr2B 95.868 121 4 1 200 320 766070366 766070247 9.970000e-46 195.0
16 TraesCS2D01G006000 chr2A 95.820 1938 65 5 549 2480 2725773 2727700 0.000000e+00 3116.0
17 TraesCS2D01G006000 chr2A 90.503 1074 67 14 2472 3521 2729681 2730743 0.000000e+00 1386.0
18 TraesCS2D01G006000 chr2A 83.073 384 47 8 3155 3521 1778224 1777842 2.030000e-87 333.0
19 TraesCS2D01G006000 chr2A 82.199 382 50 8 3155 3519 1783783 1784163 2.640000e-81 313.0
20 TraesCS2D01G006000 chr2A 94.554 202 10 1 1 201 2725039 2725240 9.490000e-81 311.0
21 TraesCS2D01G006000 chr2A 95.536 112 5 0 315 426 2725239 2725350 2.790000e-41 180.0
22 TraesCS2D01G006000 chr3D 79.658 1519 236 39 963 2461 606940935 606942400 0.000000e+00 1026.0
23 TraesCS2D01G006000 chr3D 82.857 70 11 1 2602 2670 523751762 523751831 1.060000e-05 62.1
24 TraesCS2D01G006000 chr5D 78.331 1246 227 25 1122 2350 371862258 371863477 0.000000e+00 765.0
25 TraesCS2D01G006000 chr5A 77.769 1246 234 26 1122 2350 475294991 475296210 0.000000e+00 726.0
26 TraesCS2D01G006000 chr7A 82.609 552 76 7 2988 3521 65165213 65164664 1.480000e-128 470.0
27 TraesCS2D01G006000 chr7A 75.000 516 123 5 1185 1696 517581845 517581332 2.110000e-57 233.0
28 TraesCS2D01G006000 chr7A 95.161 124 4 2 200 323 632588268 632588147 9.970000e-46 195.0
29 TraesCS2D01G006000 chr7D 81.346 520 73 7 3026 3521 61236979 61236460 5.470000e-108 401.0
30 TraesCS2D01G006000 chr7D 75.086 582 123 19 1117 1687 477855753 477856323 5.830000e-63 252.0
31 TraesCS2D01G006000 chr4D 82.984 382 49 9 3133 3498 494878707 494878326 7.290000e-87 331.0
32 TraesCS2D01G006000 chr4B 82.768 383 48 10 3133 3498 634459304 634459685 3.390000e-85 326.0
33 TraesCS2D01G006000 chr3B 97.436 117 3 0 200 316 564169701 564169817 2.140000e-47 200.0
34 TraesCS2D01G006000 chr4A 95.833 120 5 0 200 319 732350163 732350282 9.970000e-46 195.0
35 TraesCS2D01G006000 chr6D 94.400 125 7 0 192 316 305136403 305136527 3.590000e-45 193.0
36 TraesCS2D01G006000 chr3A 95.798 119 5 0 198 316 671258201 671258083 3.590000e-45 193.0
37 TraesCS2D01G006000 chr1D 95.000 120 6 0 200 319 344598781 344598662 4.640000e-44 189.0
38 TraesCS2D01G006000 chr1D 86.792 53 7 0 2618 2670 351041634 351041686 3.800000e-05 60.2
39 TraesCS2D01G006000 chr6B 85.714 70 9 1 2602 2670 320192151 320192220 4.880000e-09 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 TraesCS2D01G006000 chr2D 2946075 2949595 3520 True 6503.000000 6503 100.000000 1 3521 1 chr2D.!!$R1 3520
1 TraesCS2D01G006000 chr2B 8069948 8071874 1926 True 2516.000000 2516 90.314000 557 2481 1 chr2B.!!$R2 1924
2 TraesCS2D01G006000 chr2B 8225703 8227628 1925 True 2514.000000 2514 90.309000 557 2481 1 chr2B.!!$R3 1924
3 TraesCS2D01G006000 chr2B 7900741 7902663 1922 True 2470.000000 2470 89.892000 549 2482 1 chr2B.!!$R1 1933
4 TraesCS2D01G006000 chr2B 7836682 7839021 2339 False 1730.000000 3188 92.277000 1 2478 2 chr2B.!!$F3 2477
5 TraesCS2D01G006000 chr2B 7761459 7763757 2298 False 1140.666667 2080 93.725000 1 2478 3 chr2B.!!$F2 2477
6 TraesCS2D01G006000 chr2B 7845803 7850246 4443 False 316.000000 340 88.136667 2472 3521 3 chr2B.!!$F4 1049
7 TraesCS2D01G006000 chr2A 2725039 2730743 5704 False 1248.250000 3116 94.103250 1 3521 4 chr2A.!!$F2 3520
8 TraesCS2D01G006000 chr3D 606940935 606942400 1465 False 1026.000000 1026 79.658000 963 2461 1 chr3D.!!$F2 1498
9 TraesCS2D01G006000 chr5D 371862258 371863477 1219 False 765.000000 765 78.331000 1122 2350 1 chr5D.!!$F1 1228
10 TraesCS2D01G006000 chr5A 475294991 475296210 1219 False 726.000000 726 77.769000 1122 2350 1 chr5A.!!$F1 1228
11 TraesCS2D01G006000 chr7A 65164664 65165213 549 True 470.000000 470 82.609000 2988 3521 1 chr7A.!!$R1 533
12 TraesCS2D01G006000 chr7A 517581332 517581845 513 True 233.000000 233 75.000000 1185 1696 1 chr7A.!!$R2 511
13 TraesCS2D01G006000 chr7D 61236460 61236979 519 True 401.000000 401 81.346000 3026 3521 1 chr7D.!!$R1 495
14 TraesCS2D01G006000 chr7D 477855753 477856323 570 False 252.000000 252 75.086000 1117 1687 1 chr7D.!!$F1 570

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
312 314 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
314 316 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.00 46.06 3.85 F
503 835 0.179004 TGCCATAAAATCCGCCGGAT 60.179 50.0 14.09 14.09 45.46 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2039 0.038159 CTGTTGGACACCGAGACCTC 60.038 60.000 0.0 0.0 32.90 3.85 R
2502 4871 7.582435 TCTCTTCTACTTCAATGTAAAAGCG 57.418 36.000 0.0 0.0 0.00 4.68 R
2571 4940 1.276138 CCCTCCAAAAGTCAAATGGGC 59.724 52.381 0.0 0.0 34.89 5.36 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
88 89 6.970043 TGCGCATTAAACTAAATACCAATGAC 59.030 34.615 5.66 0.00 0.00 3.06
97 98 8.579850 AACTAAATACCAATGACATGATGTGT 57.420 30.769 1.23 0.00 45.83 3.72
103 104 2.391616 ATGACATGATGTGTGTCGCT 57.608 45.000 1.23 0.00 46.89 4.93
107 109 1.001293 ACATGATGTGTGTCGCTCTGT 59.999 47.619 0.00 0.00 40.28 3.41
138 140 4.083484 GGTTGTTAGCGCAGTTCAAATACT 60.083 41.667 11.47 0.00 0.00 2.12
202 204 9.520515 AAAATTTGGTGTGACATCTTATCTACT 57.479 29.630 0.00 0.00 0.00 2.57
203 205 8.723942 AATTTGGTGTGACATCTTATCTACTC 57.276 34.615 0.00 0.00 0.00 2.59
204 206 5.854010 TGGTGTGACATCTTATCTACTCC 57.146 43.478 0.00 0.00 0.00 3.85
205 207 4.649674 TGGTGTGACATCTTATCTACTCCC 59.350 45.833 0.00 0.00 0.00 4.30
206 208 4.896482 GGTGTGACATCTTATCTACTCCCT 59.104 45.833 0.00 0.00 0.00 4.20
207 209 5.364157 GGTGTGACATCTTATCTACTCCCTT 59.636 44.000 0.00 0.00 0.00 3.95
208 210 6.461788 GGTGTGACATCTTATCTACTCCCTTC 60.462 46.154 0.00 0.00 0.00 3.46
209 211 5.299531 TGTGACATCTTATCTACTCCCTTCG 59.700 44.000 0.00 0.00 0.00 3.79
210 212 5.299782 GTGACATCTTATCTACTCCCTTCGT 59.700 44.000 0.00 0.00 0.00 3.85
211 213 5.531659 TGACATCTTATCTACTCCCTTCGTC 59.468 44.000 0.00 0.00 0.00 4.20
212 214 4.828387 ACATCTTATCTACTCCCTTCGTCC 59.172 45.833 0.00 0.00 0.00 4.79
213 215 3.830121 TCTTATCTACTCCCTTCGTCCC 58.170 50.000 0.00 0.00 0.00 4.46
214 216 2.267174 TATCTACTCCCTTCGTCCCG 57.733 55.000 0.00 0.00 0.00 5.14
215 217 0.549950 ATCTACTCCCTTCGTCCCGA 59.450 55.000 0.00 0.00 0.00 5.14
216 218 0.329261 TCTACTCCCTTCGTCCCGAA 59.671 55.000 0.00 0.00 43.75 4.30
217 219 1.180029 CTACTCCCTTCGTCCCGAAA 58.820 55.000 0.47 0.00 45.23 3.46
218 220 1.755380 CTACTCCCTTCGTCCCGAAAT 59.245 52.381 0.47 0.00 45.23 2.17
219 221 1.856629 ACTCCCTTCGTCCCGAAATA 58.143 50.000 0.47 0.00 45.23 1.40
220 222 1.479730 ACTCCCTTCGTCCCGAAATAC 59.520 52.381 0.47 0.00 45.23 1.89
221 223 1.755380 CTCCCTTCGTCCCGAAATACT 59.245 52.381 0.47 0.00 45.23 2.12
222 224 2.167900 CTCCCTTCGTCCCGAAATACTT 59.832 50.000 0.47 0.00 45.23 2.24
223 225 2.093869 TCCCTTCGTCCCGAAATACTTG 60.094 50.000 0.47 0.00 45.23 3.16
224 226 2.354403 CCCTTCGTCCCGAAATACTTGT 60.354 50.000 0.47 0.00 45.23 3.16
225 227 2.671396 CCTTCGTCCCGAAATACTTGTG 59.329 50.000 0.47 0.00 45.23 3.33
226 228 2.373540 TCGTCCCGAAATACTTGTGG 57.626 50.000 0.00 0.00 31.06 4.17
227 229 1.066716 TCGTCCCGAAATACTTGTGGG 60.067 52.381 0.00 0.00 41.43 4.61
228 230 1.066716 CGTCCCGAAATACTTGTGGGA 60.067 52.381 0.00 0.00 46.47 4.37
230 232 2.542550 TCCCGAAATACTTGTGGGAGA 58.457 47.619 0.00 0.00 43.85 3.71
231 233 2.907696 TCCCGAAATACTTGTGGGAGAA 59.092 45.455 0.00 0.00 43.85 2.87
232 234 3.328343 TCCCGAAATACTTGTGGGAGAAA 59.672 43.478 0.00 0.00 43.85 2.52
233 235 4.018779 TCCCGAAATACTTGTGGGAGAAAT 60.019 41.667 0.00 0.00 43.85 2.17
234 236 4.096382 CCCGAAATACTTGTGGGAGAAATG 59.904 45.833 0.00 0.00 42.77 2.32
235 237 4.096382 CCGAAATACTTGTGGGAGAAATGG 59.904 45.833 0.00 0.00 0.00 3.16
236 238 4.941263 CGAAATACTTGTGGGAGAAATGGA 59.059 41.667 0.00 0.00 0.00 3.41
237 239 5.590259 CGAAATACTTGTGGGAGAAATGGAT 59.410 40.000 0.00 0.00 0.00 3.41
238 240 6.765989 CGAAATACTTGTGGGAGAAATGGATA 59.234 38.462 0.00 0.00 0.00 2.59
239 241 7.282224 CGAAATACTTGTGGGAGAAATGGATAA 59.718 37.037 0.00 0.00 0.00 1.75
240 242 8.893563 AAATACTTGTGGGAGAAATGGATAAA 57.106 30.769 0.00 0.00 0.00 1.40
241 243 8.893563 AATACTTGTGGGAGAAATGGATAAAA 57.106 30.769 0.00 0.00 0.00 1.52
242 244 9.492730 AATACTTGTGGGAGAAATGGATAAAAT 57.507 29.630 0.00 0.00 0.00 1.82
243 245 7.174107 ACTTGTGGGAGAAATGGATAAAATG 57.826 36.000 0.00 0.00 0.00 2.32
244 246 6.155049 ACTTGTGGGAGAAATGGATAAAATGG 59.845 38.462 0.00 0.00 0.00 3.16
245 247 4.961730 TGTGGGAGAAATGGATAAAATGGG 59.038 41.667 0.00 0.00 0.00 4.00
246 248 5.208121 GTGGGAGAAATGGATAAAATGGGA 58.792 41.667 0.00 0.00 0.00 4.37
247 249 5.840693 GTGGGAGAAATGGATAAAATGGGAT 59.159 40.000 0.00 0.00 0.00 3.85
248 250 5.840149 TGGGAGAAATGGATAAAATGGGATG 59.160 40.000 0.00 0.00 0.00 3.51
249 251 5.840693 GGGAGAAATGGATAAAATGGGATGT 59.159 40.000 0.00 0.00 0.00 3.06
250 252 7.010160 GGGAGAAATGGATAAAATGGGATGTA 58.990 38.462 0.00 0.00 0.00 2.29
251 253 7.675619 GGGAGAAATGGATAAAATGGGATGTAT 59.324 37.037 0.00 0.00 0.00 2.29
252 254 8.743714 GGAGAAATGGATAAAATGGGATGTATC 58.256 37.037 0.00 0.00 0.00 2.24
253 255 9.525826 GAGAAATGGATAAAATGGGATGTATCT 57.474 33.333 0.00 0.00 0.00 1.98
286 288 9.838339 AAAATACGTCTAGATTCATCCATTTCT 57.162 29.630 0.00 0.00 0.00 2.52
287 289 9.482627 AAATACGTCTAGATTCATCCATTTCTC 57.517 33.333 0.00 0.00 0.00 2.87
288 290 5.848406 ACGTCTAGATTCATCCATTTCTCC 58.152 41.667 0.00 0.00 0.00 3.71
289 291 4.920340 CGTCTAGATTCATCCATTTCTCCG 59.080 45.833 0.00 0.00 0.00 4.63
290 292 5.278512 CGTCTAGATTCATCCATTTCTCCGA 60.279 44.000 0.00 0.00 0.00 4.55
291 293 5.923684 GTCTAGATTCATCCATTTCTCCGAC 59.076 44.000 0.00 0.00 0.00 4.79
292 294 4.760530 AGATTCATCCATTTCTCCGACA 57.239 40.909 0.00 0.00 0.00 4.35
293 295 5.102953 AGATTCATCCATTTCTCCGACAA 57.897 39.130 0.00 0.00 0.00 3.18
294 296 5.121811 AGATTCATCCATTTCTCCGACAAG 58.878 41.667 0.00 0.00 0.00 3.16
295 297 3.981071 TCATCCATTTCTCCGACAAGT 57.019 42.857 0.00 0.00 0.00 3.16
296 298 5.414789 TTCATCCATTTCTCCGACAAGTA 57.585 39.130 0.00 0.00 0.00 2.24
297 299 5.614324 TCATCCATTTCTCCGACAAGTAT 57.386 39.130 0.00 0.00 0.00 2.12
298 300 5.989477 TCATCCATTTCTCCGACAAGTATT 58.011 37.500 0.00 0.00 0.00 1.89
299 301 6.414732 TCATCCATTTCTCCGACAAGTATTT 58.585 36.000 0.00 0.00 0.00 1.40
300 302 6.538742 TCATCCATTTCTCCGACAAGTATTTC 59.461 38.462 0.00 0.00 0.00 2.17
301 303 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
302 304 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
303 305 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
304 306 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
305 307 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
306 308 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
307 309 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
308 310 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
309 311 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
310 312 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
311 313 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
312 314 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
313 315 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
314 316 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
315 317 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
327 329 6.150034 ACGGAGGGAGTAGTATATACCAAT 57.850 41.667 9.32 0.00 0.00 3.16
363 365 4.828072 AGAGGTAGAACCAAACCATCTC 57.172 45.455 0.00 0.00 41.95 2.75
366 368 2.027469 GGTAGAACCAAACCATCTCGGT 60.027 50.000 0.00 0.00 44.65 4.69
426 428 6.035542 CCAATGTTGAACACCAAACACTTTAC 59.964 38.462 0.00 0.00 36.36 2.01
443 775 7.209471 CACTTTACAGTGCTAAAATTACCCA 57.791 36.000 0.00 0.00 44.16 4.51
478 810 9.316730 ACTTGTTATAAACACGTTTAGACTCAA 57.683 29.630 8.25 9.72 40.47 3.02
503 835 0.179004 TGCCATAAAATCCGCCGGAT 60.179 50.000 14.09 14.09 45.46 4.18
505 837 1.467342 GCCATAAAATCCGCCGGATAC 59.533 52.381 20.72 0.00 42.27 2.24
507 839 3.000727 CCATAAAATCCGCCGGATACTC 58.999 50.000 20.72 0.00 42.27 2.59
508 840 3.556213 CCATAAAATCCGCCGGATACTCA 60.556 47.826 20.72 5.59 42.27 3.41
509 841 2.702592 AAAATCCGCCGGATACTCAA 57.297 45.000 20.72 0.00 42.27 3.02
532 864 9.013229 TCAATATCCTACCAATTATCAACATGC 57.987 33.333 0.00 0.00 0.00 4.06
533 865 8.795513 CAATATCCTACCAATTATCAACATGCA 58.204 33.333 0.00 0.00 0.00 3.96
534 866 8.938801 ATATCCTACCAATTATCAACATGCAA 57.061 30.769 0.00 0.00 0.00 4.08
535 867 7.844493 ATCCTACCAATTATCAACATGCAAT 57.156 32.000 0.00 0.00 0.00 3.56
536 868 7.658525 TCCTACCAATTATCAACATGCAATT 57.341 32.000 0.00 0.00 0.00 2.32
537 869 8.076910 TCCTACCAATTATCAACATGCAATTT 57.923 30.769 0.00 0.00 0.00 1.82
538 870 8.538701 TCCTACCAATTATCAACATGCAATTTT 58.461 29.630 0.00 0.00 0.00 1.82
539 871 9.165035 CCTACCAATTATCAACATGCAATTTTT 57.835 29.630 0.00 0.00 0.00 1.94
797 1130 9.023962 TGCCATCCCATACATTTTCTTAATATC 57.976 33.333 0.00 0.00 0.00 1.63
929 1264 2.293955 GGGAGGAGTAGTAGCAACGATC 59.706 54.545 0.00 0.00 0.00 3.69
988 1325 4.134563 GCTCACCTTAACCTTCTTGTTCA 58.865 43.478 0.00 0.00 0.00 3.18
1292 1635 3.777910 GTACCGGTCCGTGGGCAT 61.778 66.667 12.40 0.00 0.00 4.40
1361 1704 2.333938 CAACCAGACGTCGACGGT 59.666 61.111 37.89 24.54 44.95 4.83
1410 1753 4.442052 GGCGAGCTCTATTATGCCATATCA 60.442 45.833 19.47 0.00 42.03 2.15
1955 2310 2.092753 AGTCCATGGCCTACATCAACAG 60.093 50.000 6.96 0.00 37.84 3.16
2146 2513 1.361668 CGGGAAGATGAGCAACGTGG 61.362 60.000 0.00 0.00 0.00 4.94
2474 2855 1.270550 CCTGCCAAAACGAGCATCTTT 59.729 47.619 0.00 0.00 38.56 2.52
2523 4892 6.673316 GCTCCGCTTTTACATTGAAGTAGAAG 60.673 42.308 0.00 0.00 38.51 2.85
2527 4896 7.278868 CCGCTTTTACATTGAAGTAGAAGAGAT 59.721 37.037 8.13 0.00 37.84 2.75
2537 4906 8.516811 TTGAAGTAGAAGAGATGTTTTACGAC 57.483 34.615 0.00 0.00 0.00 4.34
2551 4920 5.508573 TGTTTTACGACACACAATCAAAACG 59.491 36.000 0.00 0.00 37.26 3.60
2576 4945 1.994885 ATTTCCCGACCGATGCCCAT 61.995 55.000 0.00 0.00 0.00 4.00
2578 4947 2.124320 CCCGACCGATGCCCATTT 60.124 61.111 0.00 0.00 0.00 2.32
2624 4993 5.604565 TCACATGATTGTTGCGAGAGATAT 58.395 37.500 0.00 0.00 32.34 1.63
2670 5039 8.097038 TGAACTACACTTGCTTCTTGATAGATT 58.903 33.333 0.00 0.00 0.00 2.40
2676 5045 7.392673 ACACTTGCTTCTTGATAGATTGATTGT 59.607 33.333 0.00 0.00 0.00 2.71
2686 5055 6.594744 TGATAGATTGATTGTGCCACATAGT 58.405 36.000 0.00 0.00 0.00 2.12
2698 5067 3.054434 TGCCACATAGTCATAGTTGCCTT 60.054 43.478 0.00 0.00 0.00 4.35
2740 5109 5.240013 ACAGCTCTCCTTCATCTTTTTCT 57.760 39.130 0.00 0.00 0.00 2.52
2743 5112 5.704515 CAGCTCTCCTTCATCTTTTTCTTCA 59.295 40.000 0.00 0.00 0.00 3.02
2744 5113 6.374894 CAGCTCTCCTTCATCTTTTTCTTCAT 59.625 38.462 0.00 0.00 0.00 2.57
2747 5116 7.309073 GCTCTCCTTCATCTTTTTCTTCATGTT 60.309 37.037 0.00 0.00 0.00 2.71
2778 5262 7.094634 GCACTCCATATAATACAACAGGGAATG 60.095 40.741 0.00 0.00 0.00 2.67
2790 5274 6.165577 ACAACAGGGAATGCAATATGAAAAC 58.834 36.000 0.00 0.00 0.00 2.43
2828 5553 2.315176 CCCACATGTCAAACCTTGGAA 58.685 47.619 0.00 0.00 0.00 3.53
2831 5556 3.573538 CCACATGTCAAACCTTGGAATCA 59.426 43.478 0.00 0.00 0.00 2.57
2832 5557 4.321452 CCACATGTCAAACCTTGGAATCAG 60.321 45.833 0.00 0.00 0.00 2.90
2846 5571 0.602638 AATCAGTTCCGCTTGCGACA 60.603 50.000 16.99 0.00 0.00 4.35
2920 5645 2.281761 CCGGTTTCTGCTGTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
2966 5691 1.205893 CACCTCCTTCTTCCTTCTCCG 59.794 57.143 0.00 0.00 0.00 4.63
3000 5730 9.072294 CGACTAATCCCAAAAATACAAATTCAC 57.928 33.333 0.00 0.00 0.00 3.18
3032 6163 6.616947 ACAAATAGCTGCTGCGTTTTATTAA 58.383 32.000 13.43 0.00 45.42 1.40
3033 6164 7.257722 ACAAATAGCTGCTGCGTTTTATTAAT 58.742 30.769 13.43 0.00 45.42 1.40
3034 6165 8.402472 ACAAATAGCTGCTGCGTTTTATTAATA 58.598 29.630 13.43 0.00 45.42 0.98
3039 6170 7.576236 AGCTGCTGCGTTTTATTAATATACAG 58.424 34.615 10.14 2.13 45.42 2.74
3044 6177 8.629986 GCTGCGTTTTATTAATATACAGCATTG 58.370 33.333 19.82 13.52 45.50 2.82
3062 6195 0.660488 TGCACCGTTTGTAAGCACAG 59.340 50.000 0.00 0.00 35.67 3.66
3135 6280 5.104562 TGTACGTGTCTGCTATATGCTAC 57.895 43.478 0.00 0.00 43.37 3.58
3152 6297 2.791613 TACCTAGCCCTGCACGTCCA 62.792 60.000 0.00 0.00 0.00 4.02
3300 6461 3.706373 GCCACTTCCCTGCCGAGA 61.706 66.667 0.00 0.00 0.00 4.04
3313 6474 1.381872 CCGAGACAGGTCCTGGGAT 60.382 63.158 23.06 8.09 35.51 3.85
3315 6476 0.396417 CGAGACAGGTCCTGGGATCT 60.396 60.000 23.06 15.99 35.71 2.75
3329 6490 0.651031 GGATCTGCGTTAAAGGCGAC 59.349 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.877097 TACTACGTACTGTGTGGGGA 57.123 50.000 0.00 0.00 0.00 4.81
83 84 2.674852 GAGCGACACACATCATGTCATT 59.325 45.455 6.01 0.00 45.64 2.57
88 89 1.657594 GACAGAGCGACACACATCATG 59.342 52.381 0.00 0.00 0.00 3.07
97 98 0.888619 CCCTACTTGACAGAGCGACA 59.111 55.000 0.00 0.00 0.00 4.35
103 104 3.305813 CGCTAACAACCCTACTTGACAGA 60.306 47.826 0.00 0.00 0.00 3.41
107 109 1.345089 TGCGCTAACAACCCTACTTGA 59.655 47.619 9.73 0.00 0.00 3.02
209 211 2.235402 TCTCCCACAAGTATTTCGGGAC 59.765 50.000 0.00 0.00 41.08 4.46
210 212 2.542550 TCTCCCACAAGTATTTCGGGA 58.457 47.619 4.98 4.98 43.77 5.14
211 213 3.343941 TTCTCCCACAAGTATTTCGGG 57.656 47.619 0.00 0.00 38.34 5.14
212 214 4.096382 CCATTTCTCCCACAAGTATTTCGG 59.904 45.833 0.00 0.00 0.00 4.30
213 215 4.941263 TCCATTTCTCCCACAAGTATTTCG 59.059 41.667 0.00 0.00 0.00 3.46
214 216 8.519799 TTATCCATTTCTCCCACAAGTATTTC 57.480 34.615 0.00 0.00 0.00 2.17
215 217 8.893563 TTTATCCATTTCTCCCACAAGTATTT 57.106 30.769 0.00 0.00 0.00 1.40
216 218 8.893563 TTTTATCCATTTCTCCCACAAGTATT 57.106 30.769 0.00 0.00 0.00 1.89
217 219 8.917088 CATTTTATCCATTTCTCCCACAAGTAT 58.083 33.333 0.00 0.00 0.00 2.12
218 220 7.341769 CCATTTTATCCATTTCTCCCACAAGTA 59.658 37.037 0.00 0.00 0.00 2.24
219 221 6.155049 CCATTTTATCCATTTCTCCCACAAGT 59.845 38.462 0.00 0.00 0.00 3.16
220 222 6.407299 CCCATTTTATCCATTTCTCCCACAAG 60.407 42.308 0.00 0.00 0.00 3.16
221 223 5.424895 CCCATTTTATCCATTTCTCCCACAA 59.575 40.000 0.00 0.00 0.00 3.33
222 224 4.961730 CCCATTTTATCCATTTCTCCCACA 59.038 41.667 0.00 0.00 0.00 4.17
223 225 5.208121 TCCCATTTTATCCATTTCTCCCAC 58.792 41.667 0.00 0.00 0.00 4.61
224 226 5.480058 TCCCATTTTATCCATTTCTCCCA 57.520 39.130 0.00 0.00 0.00 4.37
225 227 5.840693 ACATCCCATTTTATCCATTTCTCCC 59.159 40.000 0.00 0.00 0.00 4.30
226 228 6.983906 ACATCCCATTTTATCCATTTCTCC 57.016 37.500 0.00 0.00 0.00 3.71
227 229 9.525826 AGATACATCCCATTTTATCCATTTCTC 57.474 33.333 0.00 0.00 0.00 2.87
260 262 9.838339 AGAAATGGATGAATCTAGACGTATTTT 57.162 29.630 0.00 0.00 0.00 1.82
261 263 9.482627 GAGAAATGGATGAATCTAGACGTATTT 57.517 33.333 0.00 0.00 0.00 1.40
262 264 8.091449 GGAGAAATGGATGAATCTAGACGTATT 58.909 37.037 0.00 0.00 0.00 1.89
263 265 7.575909 CGGAGAAATGGATGAATCTAGACGTAT 60.576 40.741 0.00 0.00 0.00 3.06
264 266 6.294010 CGGAGAAATGGATGAATCTAGACGTA 60.294 42.308 0.00 0.00 0.00 3.57
265 267 5.508153 CGGAGAAATGGATGAATCTAGACGT 60.508 44.000 0.00 0.00 0.00 4.34
266 268 4.920340 CGGAGAAATGGATGAATCTAGACG 59.080 45.833 0.00 0.00 0.00 4.18
267 269 5.923684 GTCGGAGAAATGGATGAATCTAGAC 59.076 44.000 0.00 0.00 39.69 2.59
268 270 5.598417 TGTCGGAGAAATGGATGAATCTAGA 59.402 40.000 0.00 0.00 39.69 2.43
269 271 5.847304 TGTCGGAGAAATGGATGAATCTAG 58.153 41.667 0.00 0.00 39.69 2.43
270 272 5.869649 TGTCGGAGAAATGGATGAATCTA 57.130 39.130 0.00 0.00 39.69 1.98
271 273 4.760530 TGTCGGAGAAATGGATGAATCT 57.239 40.909 0.00 0.00 39.69 2.40
272 274 4.878397 ACTTGTCGGAGAAATGGATGAATC 59.122 41.667 0.00 0.00 39.69 2.52
273 275 4.848357 ACTTGTCGGAGAAATGGATGAAT 58.152 39.130 0.00 0.00 39.69 2.57
274 276 4.286297 ACTTGTCGGAGAAATGGATGAA 57.714 40.909 0.00 0.00 39.69 2.57
275 277 3.981071 ACTTGTCGGAGAAATGGATGA 57.019 42.857 0.00 0.00 39.69 2.92
276 278 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
277 279 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
278 280 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
279 281 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
280 282 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
281 283 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
282 284 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
283 285 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
284 286 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
285 287 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
286 288 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
287 289 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
288 290 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
289 291 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
290 292 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
291 293 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
292 294 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
293 295 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
294 296 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
295 297 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
296 298 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
297 299 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
298 300 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
299 301 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
300 302 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
301 303 2.847327 TATACTACTCCCTCCGTCCG 57.153 55.000 0.00 0.00 0.00 4.79
302 304 4.018960 TGGTATATACTACTCCCTCCGTCC 60.019 50.000 12.54 0.00 0.00 4.79
303 305 5.171339 TGGTATATACTACTCCCTCCGTC 57.829 47.826 12.54 0.00 0.00 4.79
304 306 5.589367 TTGGTATATACTACTCCCTCCGT 57.411 43.478 12.54 0.00 0.00 4.69
305 307 9.857656 TTATATTGGTATATACTACTCCCTCCG 57.142 37.037 12.54 0.00 30.68 4.63
327 329 8.931568 GGTTCTACCTCTATGGGTCTTTTTATA 58.068 37.037 0.00 0.00 40.48 0.98
363 365 1.393539 GACCACGTGATTTGATGACCG 59.606 52.381 19.30 0.00 0.00 4.79
366 368 4.801330 ACTAGACCACGTGATTTGATGA 57.199 40.909 19.30 0.00 0.00 2.92
426 428 5.163754 GCAGTAGTGGGTAATTTTAGCACTG 60.164 44.000 0.00 10.79 35.92 3.66
443 775 5.407387 CGTGTTTATAACAAGTGGCAGTAGT 59.593 40.000 0.00 0.00 44.16 2.73
478 810 2.297033 GGCGGATTTTATGGCATGACAT 59.703 45.455 20.10 20.10 34.90 3.06
507 839 8.795513 TGCATGTTGATAATTGGTAGGATATTG 58.204 33.333 0.00 0.00 0.00 1.90
508 840 8.938801 TGCATGTTGATAATTGGTAGGATATT 57.061 30.769 0.00 0.00 0.00 1.28
509 841 8.938801 TTGCATGTTGATAATTGGTAGGATAT 57.061 30.769 0.00 0.00 0.00 1.63
537 869 8.359875 TGCATGTAGATAATTTCCCTCAAAAA 57.640 30.769 0.00 0.00 0.00 1.94
538 870 7.953005 TGCATGTAGATAATTTCCCTCAAAA 57.047 32.000 0.00 0.00 0.00 2.44
539 871 7.953005 TTGCATGTAGATAATTTCCCTCAAA 57.047 32.000 0.00 0.00 0.00 2.69
540 872 8.537728 AATTGCATGTAGATAATTTCCCTCAA 57.462 30.769 0.00 0.00 0.00 3.02
541 873 9.639563 TTAATTGCATGTAGATAATTTCCCTCA 57.360 29.630 0.00 0.00 0.00 3.86
555 887 8.029782 AGTAGGTAGGACATTAATTGCATGTA 57.970 34.615 5.35 0.00 34.89 2.29
660 992 7.222872 AGATATCTTAGATTTGGTGCCAAGAG 58.777 38.462 0.00 0.46 37.24 2.85
702 1034 7.839680 AAACAATCCTCAGTTAATGTCCTTT 57.160 32.000 0.00 0.00 0.00 3.11
1410 1753 0.954452 CAAGAAGGTTGCTCGCCTTT 59.046 50.000 8.09 0.00 45.51 3.11
1521 1864 2.221055 GGCATCAATGACGTTATCGACC 59.779 50.000 0.00 0.00 40.62 4.79
1635 1978 2.661537 CACTTCAGCACGACGCCA 60.662 61.111 0.00 0.00 44.04 5.69
1696 2039 0.038159 CTGTTGGACACCGAGACCTC 60.038 60.000 0.00 0.00 32.90 3.85
2502 4871 7.582435 TCTCTTCTACTTCAATGTAAAAGCG 57.418 36.000 0.00 0.00 0.00 4.68
2523 4892 6.223138 TGATTGTGTGTCGTAAAACATCTC 57.777 37.500 0.00 0.00 0.00 2.75
2527 4896 5.508573 CGTTTTGATTGTGTGTCGTAAAACA 59.491 36.000 0.00 0.00 36.73 2.83
2533 4902 2.286833 CCTCGTTTTGATTGTGTGTCGT 59.713 45.455 0.00 0.00 0.00 4.34
2537 4906 6.074356 GGAAATTTCCTCGTTTTGATTGTGTG 60.074 38.462 26.94 0.00 44.11 3.82
2551 4920 1.940613 CATCGGTCGGGAAATTTCCTC 59.059 52.381 31.23 21.56 46.72 3.71
2571 4940 1.276138 CCCTCCAAAAGTCAAATGGGC 59.724 52.381 0.00 0.00 34.89 5.36
2576 4945 9.131791 GAAATATATAGCCCTCCAAAAGTCAAA 57.868 33.333 0.00 0.00 0.00 2.69
2578 4947 7.719633 GTGAAATATATAGCCCTCCAAAAGTCA 59.280 37.037 0.00 0.00 0.00 3.41
2670 5039 5.357742 ACTATGACTATGTGGCACAATCA 57.642 39.130 25.95 25.55 44.16 2.57
2676 5045 2.917933 GGCAACTATGACTATGTGGCA 58.082 47.619 0.00 0.00 38.56 4.92
2707 5076 2.968574 AGGAGAGCTGTTGAGACTTGAA 59.031 45.455 0.00 0.00 0.00 2.69
2719 5088 5.704515 TGAAGAAAAAGATGAAGGAGAGCTG 59.295 40.000 0.00 0.00 0.00 4.24
2720 5089 5.874093 TGAAGAAAAAGATGAAGGAGAGCT 58.126 37.500 0.00 0.00 0.00 4.09
2744 5113 9.489084 GTTGTATTATATGGAGTGCAGATAACA 57.511 33.333 13.09 6.75 0.00 2.41
2747 5116 8.314021 CCTGTTGTATTATATGGAGTGCAGATA 58.686 37.037 0.00 0.00 0.00 1.98
2778 5262 0.104120 GGGGCGGGTTTTCATATTGC 59.896 55.000 0.00 0.00 0.00 3.56
2806 5531 1.703411 CAAGGTTTGACATGTGGGGT 58.297 50.000 1.15 0.00 0.00 4.95
2828 5553 1.005037 TGTCGCAAGCGGAACTGAT 60.005 52.632 14.98 0.00 40.25 2.90
2831 5556 3.044305 GCTGTCGCAAGCGGAACT 61.044 61.111 14.98 0.00 40.25 3.01
2846 5571 2.582436 CGACCCATAACCCACGCT 59.418 61.111 0.00 0.00 0.00 5.07
2920 5645 0.842030 AGCACCAAGGTGGAGATGGA 60.842 55.000 20.02 0.00 45.49 3.41
2966 5691 9.665264 GTATTTTTGGGATTAGTCGATTTCATC 57.335 33.333 0.00 0.00 0.00 2.92
3000 5730 3.485877 GCAGCAGCTATTTGTAAGTTCCG 60.486 47.826 0.00 0.00 37.91 4.30
3032 6163 3.694072 ACAAACGGTGCAATGCTGTATAT 59.306 39.130 6.82 0.00 0.00 0.86
3033 6164 3.078097 ACAAACGGTGCAATGCTGTATA 58.922 40.909 6.82 0.00 0.00 1.47
3034 6165 1.885887 ACAAACGGTGCAATGCTGTAT 59.114 42.857 6.82 0.00 0.00 2.29
3039 6170 1.059942 GCTTACAAACGGTGCAATGC 58.940 50.000 0.00 0.00 0.00 3.56
3044 6177 0.941542 TCTGTGCTTACAAACGGTGC 59.058 50.000 0.00 0.00 0.00 5.01
3062 6195 0.179179 GAGCTTGCGAAAGTGGCATC 60.179 55.000 4.74 0.00 40.62 3.91
3135 6280 2.735772 ATGGACGTGCAGGGCTAGG 61.736 63.158 16.77 0.00 0.00 3.02
3152 6297 2.169352 CCATGAAGAGGAGGAACGTCAT 59.831 50.000 0.00 0.00 36.15 3.06
3292 6453 2.575993 CAGGACCTGTCTCGGCAG 59.424 66.667 13.84 0.00 36.31 4.85
3300 6461 2.362369 CGCAGATCCCAGGACCTGT 61.362 63.158 20.24 1.36 38.04 4.00
3313 6474 0.318869 TTCGTCGCCTTTAACGCAGA 60.319 50.000 0.00 0.00 38.72 4.26
3315 6476 0.598158 AGTTCGTCGCCTTTAACGCA 60.598 50.000 0.00 0.00 38.72 5.24
3329 6490 0.982673 CGAGCCGTCTTACAAGTTCG 59.017 55.000 0.00 0.00 0.00 3.95
3413 6574 2.111878 GGAGGATGGATGGCGTGG 59.888 66.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.