Multiple sequence alignment - TraesCS6D01G260200

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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 TraesCS6D01G260200 chr6D 100.000 3419 0 0 1 3419 367863893 367867311 0.000000e+00 6314
1 TraesCS6D01G260200 chr6D 91.304 1219 95 9 975 2191 367875894 367877103 0.000000e+00 1653
2 TraesCS6D01G260200 chr6D 89.627 1234 124 2 1013 2243 368741027 368739795 0.000000e+00 1567
3 TraesCS6D01G260200 chr6D 89.757 1191 120 2 1016 2205 368372233 368371044 0.000000e+00 1522
4 TraesCS6D01G260200 chr6D 90.635 598 32 11 2842 3419 19734364 19733771 0.000000e+00 773
5 TraesCS6D01G260200 chr6D 86.829 205 20 3 2413 2617 367877100 367877297 4.440000e-54 222
6 TraesCS6D01G260200 chr6B 94.822 2530 99 13 314 2820 554166294 554163774 0.000000e+00 3917
7 TraesCS6D01G260200 chr6B 88.931 1328 121 16 873 2190 554123885 554122574 0.000000e+00 1615
8 TraesCS6D01G260200 chr6B 93.578 218 10 2 10 223 554166528 554166311 4.260000e-84 322
9 TraesCS6D01G260200 chr6B 86.000 200 15 6 2425 2617 554122564 554122371 5.790000e-48 202
10 TraesCS6D01G260200 chr6B 98.864 88 0 1 221 308 301580188 301580102 4.570000e-34 156
11 TraesCS6D01G260200 chr6A 94.837 2421 98 15 306 2709 508293273 508295683 0.000000e+00 3753
12 TraesCS6D01G260200 chr6A 91.583 1200 90 8 994 2191 508333649 508334839 0.000000e+00 1646
13 TraesCS6D01G260200 chr6A 89.439 1231 129 1 1013 2243 509562293 509561064 0.000000e+00 1552
14 TraesCS6D01G260200 chr6A 88.401 1207 118 10 1016 2205 509285785 509284584 0.000000e+00 1434
15 TraesCS6D01G260200 chr6A 90.148 203 10 2 31 223 508293066 508293268 4.380000e-64 255
16 TraesCS6D01G260200 chr6A 90.116 172 14 3 2413 2584 508334836 508335004 1.600000e-53 220
17 TraesCS6D01G260200 chr6A 100.000 86 0 0 222 307 374418721 374418806 3.530000e-35 159
18 TraesCS6D01G260200 chr6A 94.118 102 4 2 209 308 504351271 504351372 1.640000e-33 154
19 TraesCS6D01G260200 chr1D 92.809 598 17 7 2846 3419 463249904 463250499 0.000000e+00 843
20 TraesCS6D01G260200 chr1D 91.414 594 24 16 2843 3414 490367956 490368544 0.000000e+00 789
21 TraesCS6D01G260200 chr1D 85.167 418 58 4 994 1408 93821396 93821812 3.150000e-115 425
22 TraesCS6D01G260200 chr4D 91.980 611 24 6 2831 3419 364026909 364026302 0.000000e+00 833
23 TraesCS6D01G260200 chr3D 91.987 599 21 7 2846 3419 612020073 612019477 0.000000e+00 815
24 TraesCS6D01G260200 chr2D 91.847 601 20 5 2846 3419 493077361 493076763 0.000000e+00 811
25 TraesCS6D01G260200 chr7D 91.809 586 33 8 2846 3419 313353073 313353655 0.000000e+00 802
26 TraesCS6D01G260200 chr7D 90.620 597 28 10 2847 3419 164537632 164538224 0.000000e+00 767
27 TraesCS6D01G260200 chr7D 98.889 90 1 0 217 306 34334207 34334118 9.820000e-36 161
28 TraesCS6D01G260200 chrUn 91.404 570 37 10 2855 3419 51090196 51089634 0.000000e+00 771
29 TraesCS6D01G260200 chr4A 91.404 570 36 11 2855 3419 719421834 719422395 0.000000e+00 769
30 TraesCS6D01G260200 chr4A 94.949 99 2 3 222 317 42254273 42254371 5.910000e-33 152
31 TraesCS6D01G260200 chr4A 94.059 101 3 3 208 306 625245923 625245824 2.130000e-32 150
32 TraesCS6D01G260200 chr7B 89.708 583 46 9 2841 3419 11618847 11618275 0.000000e+00 732
33 TraesCS6D01G260200 chr2B 89.050 484 36 11 2949 3419 734043023 734043502 4.920000e-163 584
34 TraesCS6D01G260200 chr2B 100.000 86 0 0 222 307 182712416 182712501 3.530000e-35 159
35 TraesCS6D01G260200 chr2B 91.304 115 4 6 197 308 751263551 751263662 5.910000e-33 152
36 TraesCS6D01G260200 chr3A 100.000 86 0 0 222 307 51753328 51753243 3.530000e-35 159


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 TraesCS6D01G260200 chr6D 367863893 367867311 3418 False 6314.0 6314 100.0000 1 3419 1 chr6D.!!$F1 3418
1 TraesCS6D01G260200 chr6D 368739795 368741027 1232 True 1567.0 1567 89.6270 1013 2243 1 chr6D.!!$R3 1230
2 TraesCS6D01G260200 chr6D 368371044 368372233 1189 True 1522.0 1522 89.7570 1016 2205 1 chr6D.!!$R2 1189
3 TraesCS6D01G260200 chr6D 367875894 367877297 1403 False 937.5 1653 89.0665 975 2617 2 chr6D.!!$F2 1642
4 TraesCS6D01G260200 chr6D 19733771 19734364 593 True 773.0 773 90.6350 2842 3419 1 chr6D.!!$R1 577
5 TraesCS6D01G260200 chr6B 554163774 554166528 2754 True 2119.5 3917 94.2000 10 2820 2 chr6B.!!$R3 2810
6 TraesCS6D01G260200 chr6B 554122371 554123885 1514 True 908.5 1615 87.4655 873 2617 2 chr6B.!!$R2 1744
7 TraesCS6D01G260200 chr6A 508293066 508295683 2617 False 2004.0 3753 92.4925 31 2709 2 chr6A.!!$F3 2678
8 TraesCS6D01G260200 chr6A 509561064 509562293 1229 True 1552.0 1552 89.4390 1013 2243 1 chr6A.!!$R2 1230
9 TraesCS6D01G260200 chr6A 509284584 509285785 1201 True 1434.0 1434 88.4010 1016 2205 1 chr6A.!!$R1 1189
10 TraesCS6D01G260200 chr6A 508333649 508335004 1355 False 933.0 1646 90.8495 994 2584 2 chr6A.!!$F4 1590
11 TraesCS6D01G260200 chr1D 463249904 463250499 595 False 843.0 843 92.8090 2846 3419 1 chr1D.!!$F2 573
12 TraesCS6D01G260200 chr1D 490367956 490368544 588 False 789.0 789 91.4140 2843 3414 1 chr1D.!!$F3 571
13 TraesCS6D01G260200 chr4D 364026302 364026909 607 True 833.0 833 91.9800 2831 3419 1 chr4D.!!$R1 588
14 TraesCS6D01G260200 chr3D 612019477 612020073 596 True 815.0 815 91.9870 2846 3419 1 chr3D.!!$R1 573
15 TraesCS6D01G260200 chr2D 493076763 493077361 598 True 811.0 811 91.8470 2846 3419 1 chr2D.!!$R1 573
16 TraesCS6D01G260200 chr7D 313353073 313353655 582 False 802.0 802 91.8090 2846 3419 1 chr7D.!!$F2 573
17 TraesCS6D01G260200 chr7D 164537632 164538224 592 False 767.0 767 90.6200 2847 3419 1 chr7D.!!$F1 572
18 TraesCS6D01G260200 chrUn 51089634 51090196 562 True 771.0 771 91.4040 2855 3419 1 chrUn.!!$R1 564
19 TraesCS6D01G260200 chr4A 719421834 719422395 561 False 769.0 769 91.4040 2855 3419 1 chr4A.!!$F2 564
20 TraesCS6D01G260200 chr7B 11618275 11618847 572 True 732.0 732 89.7080 2841 3419 1 chr7B.!!$R1 578

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
237 252 0.251297 TCGTACTCCCTCCGTTCCAA 60.251 55.0 0.0 0.0 0.0 3.53 F
457 476 0.459585 TATGAACCAAGACTCGCCGC 60.460 55.0 0.0 0.0 0.0 6.53 F
1394 1458 0.322277 ACGCCTTCTCCGACTACTCA 60.322 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1374 0.035056 AGCCCTGCACAATCCAGTAC 60.035 55.0 0.00 0.00 0.00 2.73 R
2069 2136 0.806868 CGAACTGGTAGTACTCGCCA 59.193 55.0 15.63 15.63 0.00 5.69 R
2720 2798 0.179018 AGCACACCTTTCCTGTGGAC 60.179 55.0 1.03 0.00 39.62 4.02 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
61 63 1.673808 ATCGGAAGTCCACCTACCGC 61.674 60.000 0.00 0.00 42.73 5.68
64 66 1.218316 GAAGTCCACCTACCGCCTG 59.782 63.158 0.00 0.00 0.00 4.85
117 119 2.629137 TGGTACCTCGTTTTACTGCTGA 59.371 45.455 14.36 0.00 0.00 4.26
223 238 7.917597 TCTGACTGAATATGTCTTAGTCGTAC 58.082 38.462 0.00 0.00 40.37 3.67
225 240 7.917597 TGACTGAATATGTCTTAGTCGTACTC 58.082 38.462 0.00 0.00 40.37 2.59
227 242 6.262720 ACTGAATATGTCTTAGTCGTACTCCC 59.737 42.308 0.00 0.00 0.00 4.30
228 243 6.363065 TGAATATGTCTTAGTCGTACTCCCT 58.637 40.000 0.00 0.00 0.00 4.20
229 244 6.485984 TGAATATGTCTTAGTCGTACTCCCTC 59.514 42.308 0.00 0.00 0.00 4.30
230 245 2.996631 TGTCTTAGTCGTACTCCCTCC 58.003 52.381 0.00 0.00 0.00 4.30
231 246 1.939255 GTCTTAGTCGTACTCCCTCCG 59.061 57.143 0.00 0.00 0.00 4.63
232 247 1.556911 TCTTAGTCGTACTCCCTCCGT 59.443 52.381 0.00 0.00 0.00 4.69
233 248 2.026822 TCTTAGTCGTACTCCCTCCGTT 60.027 50.000 0.00 0.00 0.00 4.44
234 249 2.029838 TAGTCGTACTCCCTCCGTTC 57.970 55.000 0.00 0.00 0.00 3.95
235 250 0.679321 AGTCGTACTCCCTCCGTTCC 60.679 60.000 0.00 0.00 0.00 3.62
236 251 0.962356 GTCGTACTCCCTCCGTTCCA 60.962 60.000 0.00 0.00 0.00 3.53
237 252 0.251297 TCGTACTCCCTCCGTTCCAA 60.251 55.000 0.00 0.00 0.00 3.53
238 253 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
239 254 1.001181 CGTACTCCCTCCGTTCCAAAA 59.999 52.381 0.00 0.00 0.00 2.44
240 255 2.354403 CGTACTCCCTCCGTTCCAAAAT 60.354 50.000 0.00 0.00 0.00 1.82
241 256 3.119029 CGTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
242 257 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
243 258 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
244 259 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
245 260 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
246 261 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
247 262 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
248 263 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
249 264 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
250 265 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
251 266 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
252 267 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
253 268 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
254 269 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
255 270 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
256 271 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
257 272 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
258 273 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
259 274 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
260 275 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
261 276 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
262 277 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
263 278 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
264 279 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
265 280 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
266 281 7.970102 AGATGACCCAACTTTGTACTAACTTA 58.030 34.615 0.00 0.00 0.00 2.24
267 282 8.095169 AGATGACCCAACTTTGTACTAACTTAG 58.905 37.037 0.00 0.00 0.00 2.18
268 283 7.128234 TGACCCAACTTTGTACTAACTTAGT 57.872 36.000 6.68 6.68 42.68 2.24
269 284 8.248904 TGACCCAACTTTGTACTAACTTAGTA 57.751 34.615 4.76 4.76 40.14 1.82
282 297 7.128234 ACTAACTTAGTACAAAGTTGGGTCA 57.872 36.000 14.60 0.00 46.44 4.02
283 298 7.742767 ACTAACTTAGTACAAAGTTGGGTCAT 58.257 34.615 14.60 0.00 46.44 3.06
284 299 7.876582 ACTAACTTAGTACAAAGTTGGGTCATC 59.123 37.037 14.60 0.00 46.44 2.92
285 300 6.435292 ACTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 36.26 2.90
286 301 7.549147 ACTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 36.26 1.98
287 302 8.147244 ACTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 36.26 1.98
288 303 8.603304 ACTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 36.26 1.73
289 304 9.449719 CTTAGTACAAAGTTGGGTCATCTATTT 57.550 33.333 0.00 0.00 0.00 1.40
290 305 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
291 306 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
292 307 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
293 308 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
294 309 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
295 310 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
296 311 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
297 312 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
298 313 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
299 314 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
300 315 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
301 316 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
302 317 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
303 318 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
304 319 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
358 377 4.537135 TTGGCGTTCTACTTGAAGAGAT 57.463 40.909 0.00 0.00 35.01 2.75
361 380 3.368531 GGCGTTCTACTTGAAGAGATGGT 60.369 47.826 0.00 0.00 35.01 3.55
385 404 4.642429 GATGGCTTATATTTGACCGTCCT 58.358 43.478 0.00 0.00 31.47 3.85
439 458 6.887626 TCTTACTGGATATGTACATGCGTA 57.112 37.500 18.81 8.96 0.00 4.42
446 465 5.221541 TGGATATGTACATGCGTATGAACCA 60.222 40.000 20.86 12.66 37.73 3.67
447 466 5.699001 GGATATGTACATGCGTATGAACCAA 59.301 40.000 20.86 3.06 37.73 3.67
455 474 1.278238 CGTATGAACCAAGACTCGCC 58.722 55.000 0.00 0.00 0.00 5.54
457 476 0.459585 TATGAACCAAGACTCGCCGC 60.460 55.000 0.00 0.00 0.00 6.53
475 494 0.730494 GCGCACTGCCTCATTTTGAC 60.730 55.000 0.30 0.00 37.76 3.18
483 502 2.293122 TGCCTCATTTTGACCGAGTTTG 59.707 45.455 0.00 0.00 0.00 2.93
498 518 2.017049 AGTTTGTGGCGCATATCCTTC 58.983 47.619 10.83 0.00 0.00 3.46
552 581 4.053295 GTGTTTTACTGAAGTACGGCAGA 58.947 43.478 20.20 5.84 36.07 4.26
572 601 4.410492 GACGATTTGTCTGTGATTGCTT 57.590 40.909 0.00 0.00 44.58 3.91
886 926 7.227711 CAGCAGAACTAGAGTATAGTCAGCTTA 59.772 40.741 10.21 0.00 31.33 3.09
887 927 7.776030 AGCAGAACTAGAGTATAGTCAGCTTAA 59.224 37.037 10.21 0.00 30.30 1.85
1004 1047 0.613572 TCGTGCCATCTGACCACCTA 60.614 55.000 0.00 0.00 0.00 3.08
1346 1410 4.673298 TGCGTCATGACCGGCGTT 62.673 61.111 20.03 0.00 0.00 4.84
1355 1419 2.114411 ACCGGCGTTTGGGTCATT 59.886 55.556 6.01 0.00 0.00 2.57
1394 1458 0.322277 ACGCCTTCTCCGACTACTCA 60.322 55.000 0.00 0.00 0.00 3.41
1575 1639 3.911260 TCCTTACATCTACAACAACCCCA 59.089 43.478 0.00 0.00 0.00 4.96
1739 1803 4.600032 CTCAGATCTTCATCTCAGACGTG 58.400 47.826 0.00 0.00 37.25 4.49
1775 1839 1.233285 CGTTGGCTCTGCTGAAGCTT 61.233 55.000 0.00 0.00 42.66 3.74
2069 2136 4.567318 GCGATCAAGCCCATCCTT 57.433 55.556 0.00 0.00 0.00 3.36
2662 2736 5.955488 TCTCGTGACTTTATTTCTCTCTGG 58.045 41.667 0.00 0.00 0.00 3.86
2683 2757 2.641305 GAGTGGATGATTGCTTGCTCT 58.359 47.619 0.00 0.00 0.00 4.09
2684 2758 2.355132 GAGTGGATGATTGCTTGCTCTG 59.645 50.000 0.00 0.00 0.00 3.35
2709 2787 0.944311 CGACCAAGGTTGTCCACTCG 60.944 60.000 0.00 0.00 35.89 4.18
2720 2798 2.820767 GTCCACTCGGTTGGAGCTCG 62.821 65.000 7.83 0.00 46.75 5.03
2738 2817 1.507141 CGTCCACAGGAAAGGTGTGC 61.507 60.000 0.00 0.00 43.39 4.57
2777 2856 5.696822 CATATGCTGCAAATCTGTACATCC 58.303 41.667 6.36 0.00 0.00 3.51
2778 2857 3.354948 TGCTGCAAATCTGTACATCCT 57.645 42.857 0.00 0.00 0.00 3.24
2788 2868 7.629222 GCAAATCTGTACATCCTGCAAATAACT 60.629 37.037 0.00 0.00 0.00 2.24
2790 2870 4.635765 TCTGTACATCCTGCAAATAACTGC 59.364 41.667 0.00 0.00 42.95 4.40
2795 2875 2.016318 TCCTGCAAATAACTGCCGATG 58.984 47.619 0.00 0.00 41.90 3.84
2902 2982 3.133464 CGCCCACACGCATGGATT 61.133 61.111 7.11 0.00 43.02 3.01
2906 2986 0.392863 CCCACACGCATGGATTCTCA 60.393 55.000 7.11 0.00 43.02 3.27
3095 3183 4.918360 AGGGGGCTGGTGTGTGGA 62.918 66.667 0.00 0.00 0.00 4.02
3109 3217 3.805422 GTGTGTGGACGTTTATCACTTCA 59.195 43.478 12.53 9.33 33.04 3.02
3229 3361 3.455327 TGTCATGTGTTTTTGCATGGTG 58.545 40.909 0.00 0.00 41.83 4.17
3275 3407 5.633601 CACGTAAGCAGATGACAACTCTTTA 59.366 40.000 0.00 0.00 45.62 1.85
3365 3502 3.940209 TTTTGCCATGCCTTCTTGTAG 57.060 42.857 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.151817 AGGTGCTTAATCTCCTTGCTTTTAAG 59.848 38.462 0.00 0.00 34.51 1.85
3 4 4.411013 AGGTGCTTAATCTCCTTGCTTTT 58.589 39.130 0.00 0.00 0.00 2.27
5 6 3.728385 AGGTGCTTAATCTCCTTGCTT 57.272 42.857 0.00 0.00 0.00 3.91
7 8 3.772060 CAAGGTGCTTAATCTCCTTGC 57.228 47.619 20.94 1.19 45.12 4.01
19 20 0.745845 GATGCCATCGACAAGGTGCT 60.746 55.000 0.00 0.00 0.00 4.40
61 63 1.372087 GAACAGGGCGCATCTTCAGG 61.372 60.000 10.83 0.00 0.00 3.86
64 66 0.169009 GTTGAACAGGGCGCATCTTC 59.831 55.000 10.83 4.54 0.00 2.87
117 119 2.722201 GGCGACCGAGACCAAGGAT 61.722 63.158 0.00 0.00 0.00 3.24
152 164 4.135153 CTCGAGCACACCTCCCCG 62.135 72.222 0.00 0.00 37.27 5.73
223 238 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
225 240 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
227 242 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
228 243 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
229 244 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
230 245 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
231 246 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
232 247 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
233 248 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
234 249 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
235 250 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
236 251 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
237 252 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
238 253 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
239 254 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
240 255 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
241 256 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
242 257 7.876582 ACTAAGTTAGTACAAAGTTGGGTCATC 59.123 37.037 14.00 0.00 37.23 2.92
243 258 7.742767 ACTAAGTTAGTACAAAGTTGGGTCAT 58.257 34.615 14.00 0.00 37.23 3.06
244 259 7.128234 ACTAAGTTAGTACAAAGTTGGGTCA 57.872 36.000 14.00 0.00 37.23 4.02
257 272 8.248904 TGACCCAACTTTGTACTAAGTTAGTA 57.751 34.615 27.33 17.12 44.33 1.82
258 273 7.128234 TGACCCAACTTTGTACTAAGTTAGT 57.872 36.000 27.33 25.69 44.33 2.24
259 274 8.095169 AGATGACCCAACTTTGTACTAAGTTAG 58.905 37.037 27.33 23.50 44.33 2.34
260 275 7.970102 AGATGACCCAACTTTGTACTAAGTTA 58.030 34.615 27.33 16.34 44.33 2.24
261 276 6.838382 AGATGACCCAACTTTGTACTAAGTT 58.162 36.000 23.96 23.96 46.42 2.66
262 277 6.435292 AGATGACCCAACTTTGTACTAAGT 57.565 37.500 15.68 15.68 39.97 2.24
263 278 9.449719 AAATAGATGACCCAACTTTGTACTAAG 57.550 33.333 14.42 14.42 0.00 2.18
264 279 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
265 280 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
266 281 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
267 282 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
268 283 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
269 284 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
270 285 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
271 286 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
272 287 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
273 288 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
274 289 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
275 290 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
276 291 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
277 292 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
278 293 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
279 294 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
280 295 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
281 296 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
282 297 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
283 298 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
284 299 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
285 300 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
286 301 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
287 302 2.565834 CTCTACTCCCTCCGTTCCAAAA 59.434 50.000 0.00 0.00 0.00 2.44
288 303 2.176889 CTCTACTCCCTCCGTTCCAAA 58.823 52.381 0.00 0.00 0.00 3.28
289 304 1.618888 CCTCTACTCCCTCCGTTCCAA 60.619 57.143 0.00 0.00 0.00 3.53
290 305 0.033405 CCTCTACTCCCTCCGTTCCA 60.033 60.000 0.00 0.00 0.00 3.53
291 306 1.393487 GCCTCTACTCCCTCCGTTCC 61.393 65.000 0.00 0.00 0.00 3.62
292 307 1.726533 CGCCTCTACTCCCTCCGTTC 61.727 65.000 0.00 0.00 0.00 3.95
293 308 1.753463 CGCCTCTACTCCCTCCGTT 60.753 63.158 0.00 0.00 0.00 4.44
294 309 2.124236 CGCCTCTACTCCCTCCGT 60.124 66.667 0.00 0.00 0.00 4.69
295 310 2.907917 CCGCCTCTACTCCCTCCG 60.908 72.222 0.00 0.00 0.00 4.63
296 311 2.522193 CCCGCCTCTACTCCCTCC 60.522 72.222 0.00 0.00 0.00 4.30
297 312 1.529713 CTCCCGCCTCTACTCCCTC 60.530 68.421 0.00 0.00 0.00 4.30
298 313 2.002018 CTCTCCCGCCTCTACTCCCT 62.002 65.000 0.00 0.00 0.00 4.20
299 314 1.529713 CTCTCCCGCCTCTACTCCC 60.530 68.421 0.00 0.00 0.00 4.30
300 315 0.536460 CTCTCTCCCGCCTCTACTCC 60.536 65.000 0.00 0.00 0.00 3.85
301 316 0.470766 TCTCTCTCCCGCCTCTACTC 59.529 60.000 0.00 0.00 0.00 2.59
302 317 0.472471 CTCTCTCTCCCGCCTCTACT 59.528 60.000 0.00 0.00 0.00 2.57
303 318 0.470766 TCTCTCTCTCCCGCCTCTAC 59.529 60.000 0.00 0.00 0.00 2.59
304 319 0.470766 GTCTCTCTCTCCCGCCTCTA 59.529 60.000 0.00 0.00 0.00 2.43
358 377 4.385825 GGTCAAATATAAGCCATCGACCA 58.614 43.478 0.00 0.00 41.08 4.02
361 380 4.304110 GACGGTCAAATATAAGCCATCGA 58.696 43.478 2.62 0.00 0.00 3.59
385 404 4.422057 TCAAATCCTACCAGACACACCTA 58.578 43.478 0.00 0.00 0.00 3.08
439 458 1.741770 GCGGCGAGTCTTGGTTCAT 60.742 57.895 12.98 0.00 0.00 2.57
455 474 1.798725 CAAAATGAGGCAGTGCGCG 60.799 57.895 9.45 0.00 43.84 6.86
457 476 0.109597 GGTCAAAATGAGGCAGTGCG 60.110 55.000 9.45 0.00 0.00 5.34
475 494 0.304705 GATATGCGCCACAAACTCGG 59.695 55.000 4.18 0.00 0.00 4.63
483 502 1.680338 AAAGGAAGGATATGCGCCAC 58.320 50.000 4.18 0.00 0.00 5.01
498 518 3.377172 GTGACCGATCCAATGGTTAAAGG 59.623 47.826 0.00 0.03 38.99 3.11
552 581 5.237815 TCTAAGCAATCACAGACAAATCGT 58.762 37.500 0.00 0.00 0.00 3.73
570 599 1.698532 AGATCTGCCCATGCCTCTAAG 59.301 52.381 0.00 0.00 36.33 2.18
572 601 1.054231 CAGATCTGCCCATGCCTCTA 58.946 55.000 10.38 0.00 36.33 2.43
610 644 1.424240 CGCAGCTGCTTCACATGAG 59.576 57.895 34.22 13.26 39.32 2.90
611 645 2.036571 CCGCAGCTGCTTCACATGA 61.037 57.895 34.22 0.00 39.32 3.07
735 769 7.478721 TCCTCCCTTCAAAAATATTCCTTTCT 58.521 34.615 0.00 0.00 0.00 2.52
965 1008 6.420008 GCACGAACGAGGTTATAATGTATTCT 59.580 38.462 0.14 0.00 0.00 2.40
966 1009 6.346359 GGCACGAACGAGGTTATAATGTATTC 60.346 42.308 0.14 0.00 0.00 1.75
967 1010 5.464389 GGCACGAACGAGGTTATAATGTATT 59.536 40.000 0.14 0.00 0.00 1.89
968 1011 4.986659 GGCACGAACGAGGTTATAATGTAT 59.013 41.667 0.14 0.00 0.00 2.29
980 1023 1.078759 GGTCAGATGGCACGAACGAG 61.079 60.000 0.14 0.00 0.00 4.18
1310 1374 0.035056 AGCCCTGCACAATCCAGTAC 60.035 55.000 0.00 0.00 0.00 2.73
1553 1617 3.911260 TGGGGTTGTTGTAGATGTAAGGA 59.089 43.478 0.00 0.00 0.00 3.36
1575 1639 4.760047 GTGCACCAGACGGCCGAT 62.760 66.667 35.90 17.82 34.57 4.18
1775 1839 1.299316 GAACCCGAACGACGACACA 60.299 57.895 0.00 0.00 45.77 3.72
2069 2136 0.806868 CGAACTGGTAGTACTCGCCA 59.193 55.000 15.63 15.63 0.00 5.69
2618 2692 6.475076 CGAGAAAGAACATCCATCTAGACTTG 59.525 42.308 0.00 0.00 0.00 3.16
2620 2694 5.654650 ACGAGAAAGAACATCCATCTAGACT 59.345 40.000 0.00 0.00 0.00 3.24
2623 2697 5.746245 GTCACGAGAAAGAACATCCATCTAG 59.254 44.000 0.00 0.00 0.00 2.43
2662 2736 1.674962 GAGCAAGCAATCATCCACTCC 59.325 52.381 0.00 0.00 0.00 3.85
2684 2758 1.499049 GACAACCTTGGTCGACAGAC 58.501 55.000 18.91 0.00 46.34 3.51
2720 2798 0.179018 AGCACACCTTTCCTGTGGAC 60.179 55.000 1.03 0.00 39.62 4.02
2770 2849 3.242739 CGGCAGTTATTTGCAGGATGTAC 60.243 47.826 0.11 0.00 45.86 2.90
2772 2851 1.745087 CGGCAGTTATTTGCAGGATGT 59.255 47.619 0.11 0.00 45.86 3.06
2777 2856 3.544048 CGTACATCGGCAGTTATTTGCAG 60.544 47.826 0.11 0.00 45.86 4.41
2778 2857 2.350192 CGTACATCGGCAGTTATTTGCA 59.650 45.455 0.11 0.00 45.86 4.08
2834 2914 7.951030 GGCGTTAAACTTTTCGAAAAAGAAAAA 59.049 29.630 22.67 11.49 45.78 1.94
2835 2915 7.411696 GGGCGTTAAACTTTTCGAAAAAGAAAA 60.412 33.333 22.67 12.70 44.79 2.29
2836 2916 6.034790 GGGCGTTAAACTTTTCGAAAAAGAAA 59.965 34.615 22.67 12.39 38.23 2.52
2837 2917 5.515982 GGGCGTTAAACTTTTCGAAAAAGAA 59.484 36.000 22.67 11.95 0.00 2.52
2838 2918 5.036090 GGGCGTTAAACTTTTCGAAAAAGA 58.964 37.500 22.67 6.99 0.00 2.52
2839 2919 4.799428 TGGGCGTTAAACTTTTCGAAAAAG 59.201 37.500 22.67 18.01 0.00 2.27
2853 2933 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
2902 2982 3.084039 GTGCAGAATTGGTTGGATGAGA 58.916 45.455 0.00 0.00 0.00 3.27
2906 2986 2.198827 TCGTGCAGAATTGGTTGGAT 57.801 45.000 0.00 0.00 0.00 3.41
3095 3183 3.135994 GTGTGGGTGAAGTGATAAACGT 58.864 45.455 0.00 0.00 0.00 3.99
3109 3217 2.198426 CCAGCTTTGGGTGTGGGT 59.802 61.111 0.00 0.00 39.09 4.51
3210 3342 2.481854 GCACCATGCAAAAACACATGA 58.518 42.857 0.00 0.00 45.23 3.07
3247 3379 3.518634 TGTCATCTGCTTACGTGCATA 57.481 42.857 0.00 0.00 42.48 3.14
3248 3380 2.385013 TGTCATCTGCTTACGTGCAT 57.615 45.000 0.00 0.00 42.48 3.96
3316 3449 4.342951 TGTTCGGGTAAAAGAGAGAGTTGA 59.657 41.667 0.00 0.00 0.00 3.18
3364 3501 1.947678 GCAGTTGCCATGTAGCACTCT 60.948 52.381 0.00 0.00 43.97 3.24
3365 3502 0.449388 GCAGTTGCCATGTAGCACTC 59.551 55.000 0.00 0.00 43.97 3.51


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

AutoCloner maintained by Alex Coulton.