Multiple sequence alignment - TraesCS7B01G304400

Loading Multiple Alignment...

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 TraesCS7B01G304400 chr7B 100.000 2986 0 0 501 3486 544981729 544984714 0.000000e+00 5515
1 TraesCS7B01G304400 chr7B 98.122 2715 26 9 772 3486 545975504 545972815 0.000000e+00 4708
2 TraesCS7B01G304400 chr7B 95.684 1923 49 15 596 2492 544880728 544882642 0.000000e+00 3061
3 TraesCS7B01G304400 chr7B 100.000 254 0 0 1 254 544981229 544981482 1.460000e-128 470
4 TraesCS7B01G304400 chr7B 92.913 254 17 1 1 254 434927517 434927265 5.500000e-98 368
5 TraesCS7B01G304400 chr7D 93.678 1914 71 16 599 2486 513311542 513313431 0.000000e+00 2819
6 TraesCS7B01G304400 chr7D 92.968 1877 75 20 610 2478 514091991 514093818 0.000000e+00 2682
7 TraesCS7B01G304400 chr7D 94.894 1038 25 5 596 1632 515238372 515237362 0.000000e+00 1598
8 TraesCS7B01G304400 chr7D 94.701 1038 27 5 596 1632 515222166 515221156 0.000000e+00 1587
9 TraesCS7B01G304400 chr7D 95.745 752 32 0 1727 2478 515236979 515236228 0.000000e+00 1212
10 TraesCS7B01G304400 chr7D 95.479 752 34 0 1727 2478 515220773 515220022 0.000000e+00 1201
11 TraesCS7B01G304400 chr7A 92.413 1898 101 29 600 2491 586694079 586692219 0.000000e+00 2667
12 TraesCS7B01G304400 chr7A 91.241 1918 112 31 599 2476 588740868 588738967 0.000000e+00 2560
13 TraesCS7B01G304400 chr7A 92.929 1499 61 21 984 2476 587518481 587519940 0.000000e+00 2139
14 TraesCS7B01G304400 chr7A 86.353 425 24 18 596 994 588750956 588750540 1.920000e-117 433
15 TraesCS7B01G304400 chr7A 90.798 163 7 4 599 759 587518183 587518339 9.800000e-51 211
16 TraesCS7B01G304400 chr2B 92.032 251 20 0 4 254 414767437 414767187 1.540000e-93 353
17 TraesCS7B01G304400 chr2B 90.945 254 23 0 1 254 520026237 520025984 3.330000e-90 342
18 TraesCS7B01G304400 chr2B 80.000 150 29 1 3060 3209 74810054 74809906 3.680000e-20 110
19 TraesCS7B01G304400 chr6B 89.764 254 24 2 2 254 648735440 648735188 1.210000e-84 324
20 TraesCS7B01G304400 chr6B 89.412 255 26 1 1 254 213547728 213547982 1.560000e-83 320
21 TraesCS7B01G304400 chr6B 89.370 254 26 1 2 254 648741287 648741034 5.610000e-83 318
22 TraesCS7B01G304400 chr6B 87.008 254 32 1 2 254 125385795 125385542 5.690000e-73 285
23 TraesCS7B01G304400 chr5B 89.723 253 25 1 2 254 481151879 481152130 4.340000e-84 322
24 TraesCS7B01G304400 chr5B 88.976 254 28 0 1 254 149709383 149709130 7.260000e-82 315
25 TraesCS7B01G304400 chr6A 78.571 448 83 5 3036 3472 513363946 513364391 2.050000e-72 283
26 TraesCS7B01G304400 chr3A 78.293 410 78 8 3062 3465 13332494 13332090 1.610000e-63 254
27 TraesCS7B01G304400 chr3A 77.011 261 48 10 3094 3347 131918351 131918096 4.690000e-29 139
28 TraesCS7B01G304400 chr3D 78.395 324 54 7 3033 3344 124569245 124568926 2.740000e-46 196


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 TraesCS7B01G304400 chr7B 544981229 544984714 3485 False 2992.5 5515 100.0000 1 3486 2 chr7B.!!$F2 3485
1 TraesCS7B01G304400 chr7B 545972815 545975504 2689 True 4708.0 4708 98.1220 772 3486 1 chr7B.!!$R2 2714
2 TraesCS7B01G304400 chr7B 544880728 544882642 1914 False 3061.0 3061 95.6840 596 2492 1 chr7B.!!$F1 1896
3 TraesCS7B01G304400 chr7D 513311542 513313431 1889 False 2819.0 2819 93.6780 599 2486 1 chr7D.!!$F1 1887
4 TraesCS7B01G304400 chr7D 514091991 514093818 1827 False 2682.0 2682 92.9680 610 2478 1 chr7D.!!$F2 1868
5 TraesCS7B01G304400 chr7D 515236228 515238372 2144 True 1405.0 1598 95.3195 596 2478 2 chr7D.!!$R2 1882
6 TraesCS7B01G304400 chr7D 515220022 515222166 2144 True 1394.0 1587 95.0900 596 2478 2 chr7D.!!$R1 1882
7 TraesCS7B01G304400 chr7A 586692219 586694079 1860 True 2667.0 2667 92.4130 600 2491 1 chr7A.!!$R1 1891
8 TraesCS7B01G304400 chr7A 588738967 588740868 1901 True 2560.0 2560 91.2410 599 2476 1 chr7A.!!$R2 1877
9 TraesCS7B01G304400 chr7A 587518183 587519940 1757 False 1175.0 2139 91.8635 599 2476 2 chr7A.!!$F1 1877

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
216 217 0.179089 CATCCGAGTTGAGAGCCCAG 60.179 60.000 0.00 0.0 0.00 4.45 F
592 593 0.179097 GCCATCCTCTCGACCAGTTC 60.179 60.000 0.00 0.0 0.00 3.01 F
2002 2397 1.004560 CATCAGCGGTGTGACCTGT 60.005 57.895 15.22 0.0 35.66 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1272 0.321919 TACGTACCTCGGTGCAGTCT 60.322 55.0 5.07 0.0 44.69 3.24 R
2143 2538 0.325296 TCTTGGATGCTACGAGGGGT 60.325 55.0 0.00 0.0 0.00 4.95 R
3263 3658 0.391130 AATGCATGCGTCGTAGTGGT 60.391 50.0 13.95 0.0 0.00 4.16 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
20 21 3.340789 GGGACCAACACGAAGCAC 58.659 61.111 0.00 0.00 0.00 4.40
22 23 2.248431 GACCAACACGAAGCACGC 59.752 61.111 0.00 0.00 46.94 5.34
23 24 3.236618 GACCAACACGAAGCACGCC 62.237 63.158 0.00 0.00 46.94 5.68
24 25 4.368808 CCAACACGAAGCACGCCG 62.369 66.667 0.00 0.00 46.94 6.46
59 60 4.115199 GGCGCCACCCATCTTCCT 62.115 66.667 24.80 0.00 0.00 3.36
60 61 2.514824 GCGCCACCCATCTTCCTC 60.515 66.667 0.00 0.00 0.00 3.71
61 62 2.190578 CGCCACCCATCTTCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
62 63 2.669133 CGCCACCCATCTTCCTCCA 61.669 63.158 0.00 0.00 0.00 3.86
63 64 1.077429 GCCACCCATCTTCCTCCAC 60.077 63.158 0.00 0.00 0.00 4.02
64 65 1.221840 CCACCCATCTTCCTCCACG 59.778 63.158 0.00 0.00 0.00 4.94
65 66 1.221840 CACCCATCTTCCTCCACGG 59.778 63.158 0.00 0.00 0.00 4.94
66 67 1.080354 ACCCATCTTCCTCCACGGA 59.920 57.895 0.00 0.00 41.06 4.69
72 73 2.528127 TTCCTCCACGGAAGGCCA 60.528 61.111 5.01 0.00 46.80 5.36
73 74 2.592993 TTCCTCCACGGAAGGCCAG 61.593 63.158 5.01 0.00 46.80 4.85
74 75 3.003173 CCTCCACGGAAGGCCAGA 61.003 66.667 5.01 0.00 33.16 3.86
75 76 2.592993 CCTCCACGGAAGGCCAGAA 61.593 63.158 5.01 0.00 33.16 3.02
76 77 1.374947 CTCCACGGAAGGCCAGAAA 59.625 57.895 5.01 0.00 0.00 2.52
77 78 0.674895 CTCCACGGAAGGCCAGAAAG 60.675 60.000 5.01 0.00 0.00 2.62
78 79 1.675641 CCACGGAAGGCCAGAAAGG 60.676 63.158 5.01 0.00 41.84 3.11
116 117 3.777925 CGAACTTGTGCCGGCGAG 61.778 66.667 23.90 21.06 0.00 5.03
117 118 4.090057 GAACTTGTGCCGGCGAGC 62.090 66.667 23.90 15.15 0.00 5.03
180 181 4.760220 GGGGGAGAAGGGGCCTCA 62.760 72.222 4.79 0.00 32.48 3.86
181 182 3.093172 GGGGAGAAGGGGCCTCAG 61.093 72.222 4.79 0.00 32.48 3.35
182 183 2.041265 GGGAGAAGGGGCCTCAGA 59.959 66.667 4.79 0.00 32.48 3.27
183 184 1.616628 GGGAGAAGGGGCCTCAGAA 60.617 63.158 4.79 0.00 32.48 3.02
184 185 0.990818 GGGAGAAGGGGCCTCAGAAT 60.991 60.000 4.79 0.00 32.48 2.40
185 186 0.472044 GGAGAAGGGGCCTCAGAATC 59.528 60.000 4.79 0.00 32.48 2.52
186 187 0.472044 GAGAAGGGGCCTCAGAATCC 59.528 60.000 4.79 0.00 0.00 3.01
187 188 0.253347 AGAAGGGGCCTCAGAATCCA 60.253 55.000 4.79 0.00 0.00 3.41
188 189 0.625849 GAAGGGGCCTCAGAATCCAA 59.374 55.000 4.79 0.00 0.00 3.53
189 190 0.627986 AAGGGGCCTCAGAATCCAAG 59.372 55.000 4.79 0.00 0.00 3.61
190 191 1.454663 GGGGCCTCAGAATCCAAGC 60.455 63.158 0.84 0.00 0.00 4.01
191 192 1.454663 GGGCCTCAGAATCCAAGCC 60.455 63.158 0.84 0.00 39.73 4.35
192 193 1.821332 GGCCTCAGAATCCAAGCCG 60.821 63.158 0.00 0.00 0.00 5.52
193 194 1.821332 GCCTCAGAATCCAAGCCGG 60.821 63.158 0.00 0.00 0.00 6.13
201 202 2.674754 TCCAAGCCGGAACCATCC 59.325 61.111 5.05 0.00 42.52 3.51
211 212 2.301577 GGAACCATCCGAGTTGAGAG 57.698 55.000 0.00 0.00 35.59 3.20
212 213 1.646189 GAACCATCCGAGTTGAGAGC 58.354 55.000 0.00 0.00 0.00 4.09
213 214 0.250513 AACCATCCGAGTTGAGAGCC 59.749 55.000 0.00 0.00 0.00 4.70
214 215 1.144936 CCATCCGAGTTGAGAGCCC 59.855 63.158 0.00 0.00 0.00 5.19
215 216 1.617018 CCATCCGAGTTGAGAGCCCA 61.617 60.000 0.00 0.00 0.00 5.36
216 217 0.179089 CATCCGAGTTGAGAGCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
217 218 0.324738 ATCCGAGTTGAGAGCCCAGA 60.325 55.000 0.00 0.00 0.00 3.86
218 219 0.541998 TCCGAGTTGAGAGCCCAGAA 60.542 55.000 0.00 0.00 0.00 3.02
219 220 0.390472 CCGAGTTGAGAGCCCAGAAC 60.390 60.000 0.00 0.00 0.00 3.01
220 221 0.605589 CGAGTTGAGAGCCCAGAACT 59.394 55.000 0.00 0.00 0.00 3.01
221 222 1.001406 CGAGTTGAGAGCCCAGAACTT 59.999 52.381 0.00 0.00 0.00 2.66
222 223 2.231478 CGAGTTGAGAGCCCAGAACTTA 59.769 50.000 0.00 0.00 0.00 2.24
223 224 3.118956 CGAGTTGAGAGCCCAGAACTTAT 60.119 47.826 0.00 0.00 0.00 1.73
224 225 4.621747 CGAGTTGAGAGCCCAGAACTTATT 60.622 45.833 0.00 0.00 0.00 1.40
225 226 5.394224 CGAGTTGAGAGCCCAGAACTTATTA 60.394 44.000 0.00 0.00 0.00 0.98
226 227 5.983540 AGTTGAGAGCCCAGAACTTATTAG 58.016 41.667 0.00 0.00 0.00 1.73
227 228 4.408182 TGAGAGCCCAGAACTTATTAGC 57.592 45.455 0.00 0.00 0.00 3.09
228 229 3.134804 TGAGAGCCCAGAACTTATTAGCC 59.865 47.826 0.00 0.00 0.00 3.93
229 230 2.439880 AGAGCCCAGAACTTATTAGCCC 59.560 50.000 0.00 0.00 0.00 5.19
230 231 1.141053 AGCCCAGAACTTATTAGCCCG 59.859 52.381 0.00 0.00 0.00 6.13
231 232 1.814248 GCCCAGAACTTATTAGCCCGG 60.814 57.143 0.00 0.00 0.00 5.73
232 233 1.766496 CCCAGAACTTATTAGCCCGGA 59.234 52.381 0.73 0.00 0.00 5.14
233 234 2.224305 CCCAGAACTTATTAGCCCGGAG 60.224 54.545 0.73 0.00 0.00 4.63
234 235 2.698797 CCAGAACTTATTAGCCCGGAGA 59.301 50.000 0.73 0.00 0.00 3.71
235 236 3.243907 CCAGAACTTATTAGCCCGGAGAG 60.244 52.174 0.73 0.00 0.00 3.20
236 237 2.966516 AGAACTTATTAGCCCGGAGAGG 59.033 50.000 0.73 0.00 40.63 3.69
245 246 3.610669 CCGGAGAGGGGCGATGAG 61.611 72.222 0.00 0.00 35.97 2.90
246 247 3.610669 CGGAGAGGGGCGATGAGG 61.611 72.222 0.00 0.00 0.00 3.86
247 248 2.123251 GGAGAGGGGCGATGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
248 249 2.503382 GGAGAGGGGCGATGAGGAC 61.503 68.421 0.00 0.00 0.00 3.85
249 250 1.758514 GAGAGGGGCGATGAGGACA 60.759 63.158 0.00 0.00 0.00 4.02
250 251 1.743321 GAGAGGGGCGATGAGGACAG 61.743 65.000 0.00 0.00 0.00 3.51
251 252 1.758514 GAGGGGCGATGAGGACAGA 60.759 63.158 0.00 0.00 0.00 3.41
252 253 1.743321 GAGGGGCGATGAGGACAGAG 61.743 65.000 0.00 0.00 0.00 3.35
253 254 2.107953 GGGCGATGAGGACAGAGC 59.892 66.667 0.00 0.00 0.00 4.09
555 556 3.834056 CCGCTAGGGGGAGAGGGA 61.834 72.222 18.03 0.00 37.91 4.20
556 557 2.282446 CGCTAGGGGGAGAGGGAA 59.718 66.667 0.00 0.00 0.00 3.97
557 558 1.834822 CGCTAGGGGGAGAGGGAAG 60.835 68.421 0.00 0.00 0.00 3.46
558 559 1.627019 GCTAGGGGGAGAGGGAAGA 59.373 63.158 0.00 0.00 0.00 2.87
559 560 0.471022 GCTAGGGGGAGAGGGAAGAG 60.471 65.000 0.00 0.00 0.00 2.85
560 561 0.189822 CTAGGGGGAGAGGGAAGAGG 59.810 65.000 0.00 0.00 0.00 3.69
561 562 1.304936 TAGGGGGAGAGGGAAGAGGG 61.305 65.000 0.00 0.00 0.00 4.30
562 563 2.788589 GGGGAGAGGGAAGAGGGT 59.211 66.667 0.00 0.00 0.00 4.34
563 564 1.690985 GGGGAGAGGGAAGAGGGTG 60.691 68.421 0.00 0.00 0.00 4.61
564 565 1.690985 GGGAGAGGGAAGAGGGTGG 60.691 68.421 0.00 0.00 0.00 4.61
565 566 1.392534 GGAGAGGGAAGAGGGTGGA 59.607 63.158 0.00 0.00 0.00 4.02
566 567 0.689412 GGAGAGGGAAGAGGGTGGAG 60.689 65.000 0.00 0.00 0.00 3.86
567 568 0.336737 GAGAGGGAAGAGGGTGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
568 569 0.338120 AGAGGGAAGAGGGTGGAGAG 59.662 60.000 0.00 0.00 0.00 3.20
569 570 0.689412 GAGGGAAGAGGGTGGAGAGG 60.689 65.000 0.00 0.00 0.00 3.69
570 571 1.156322 AGGGAAGAGGGTGGAGAGGA 61.156 60.000 0.00 0.00 0.00 3.71
571 572 0.689412 GGGAAGAGGGTGGAGAGGAG 60.689 65.000 0.00 0.00 0.00 3.69
572 573 0.336737 GGAAGAGGGTGGAGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
573 574 1.687996 GGAAGAGGGTGGAGAGGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
574 575 0.325203 AAGAGGGTGGAGAGGAGAGC 60.325 60.000 0.00 0.00 0.00 4.09
575 576 1.760480 GAGGGTGGAGAGGAGAGCC 60.760 68.421 0.00 0.00 0.00 4.70
576 577 2.039624 GGGTGGAGAGGAGAGCCA 59.960 66.667 0.00 0.00 36.29 4.75
577 578 1.383803 GGGTGGAGAGGAGAGCCAT 60.384 63.158 0.00 0.00 36.29 4.40
578 579 1.406860 GGGTGGAGAGGAGAGCCATC 61.407 65.000 0.00 0.00 36.29 3.51
579 580 1.406860 GGTGGAGAGGAGAGCCATCC 61.407 65.000 0.00 0.00 40.78 3.51
588 589 3.941081 GAGCCATCCTCTCGACCA 58.059 61.111 0.00 0.00 37.60 4.02
589 590 1.739049 GAGCCATCCTCTCGACCAG 59.261 63.158 0.00 0.00 37.60 4.00
590 591 1.000993 AGCCATCCTCTCGACCAGT 59.999 57.895 0.00 0.00 0.00 4.00
591 592 0.616111 AGCCATCCTCTCGACCAGTT 60.616 55.000 0.00 0.00 0.00 3.16
592 593 0.179097 GCCATCCTCTCGACCAGTTC 60.179 60.000 0.00 0.00 0.00 3.01
727 744 3.454812 GGAGGTGTTGTATCCCATGTACT 59.545 47.826 0.00 0.00 0.00 2.73
728 745 4.442706 GAGGTGTTGTATCCCATGTACTG 58.557 47.826 0.00 0.00 0.00 2.74
729 746 3.844211 AGGTGTTGTATCCCATGTACTGT 59.156 43.478 0.00 0.00 0.00 3.55
730 747 5.027460 AGGTGTTGTATCCCATGTACTGTA 58.973 41.667 0.00 0.00 0.00 2.74
731 748 5.665812 AGGTGTTGTATCCCATGTACTGTAT 59.334 40.000 0.00 0.00 0.00 2.29
826 877 5.418840 CCTAAAATAACCAGTGGACAGCAAT 59.581 40.000 18.40 0.00 0.00 3.56
980 1034 3.878778 CCTGAAAAGGATCAAGGATCGT 58.121 45.455 0.00 0.00 39.72 3.73
1432 1516 1.064003 TCAAGCTGGAAGGCAACCTA 58.936 50.000 0.00 0.00 31.13 3.08
1501 1585 1.734477 GCGCGTGAAGAAGCTCTCA 60.734 57.895 8.43 0.00 0.00 3.27
1993 2388 1.229428 CACAAGTCAACATCAGCGGT 58.771 50.000 0.00 0.00 0.00 5.68
2002 2397 1.004560 CATCAGCGGTGTGACCTGT 60.005 57.895 15.22 0.00 35.66 4.00
2139 2534 1.310933 AAGTCGTACGAGGACGCCAT 61.311 55.000 20.18 0.00 42.62 4.40
2504 2899 2.092103 TGAACCATTATACCACCCTGCC 60.092 50.000 0.00 0.00 0.00 4.85
2809 3204 2.978156 AAACCCTGCCAGAATGAAGA 57.022 45.000 0.00 0.00 39.69 2.87
2907 3302 8.445275 TTTACTTGCAGATTCACTAGTCAAAA 57.555 30.769 0.00 0.00 0.00 2.44
3037 3432 4.423960 AGACTCCCCTTATGAGATAGGGAA 59.576 45.833 8.74 0.00 46.08 3.97
3214 3609 1.153881 GGGAGCGACTTGTACGACC 60.154 63.158 0.00 0.00 0.00 4.79
3242 3637 5.105797 TGCATTCACATGATAGGTTGTTTCC 60.106 40.000 0.00 0.00 31.07 3.13
3243 3638 5.126061 GCATTCACATGATAGGTTGTTTCCT 59.874 40.000 0.00 0.00 35.70 3.36
3244 3639 6.558009 CATTCACATGATAGGTTGTTTCCTG 58.442 40.000 0.00 0.00 34.34 3.86
3245 3640 4.009675 TCACATGATAGGTTGTTTCCTGC 58.990 43.478 0.00 0.00 38.41 4.85
3246 3641 3.758023 CACATGATAGGTTGTTTCCTGCA 59.242 43.478 0.00 0.00 38.41 4.41
3247 3642 3.758554 ACATGATAGGTTGTTTCCTGCAC 59.241 43.478 0.00 0.00 38.41 4.57
3248 3643 3.500448 TGATAGGTTGTTTCCTGCACA 57.500 42.857 0.00 0.00 38.41 4.57
3249 3644 3.411446 TGATAGGTTGTTTCCTGCACAG 58.589 45.455 0.00 0.00 38.41 3.66
3250 3645 3.181445 TGATAGGTTGTTTCCTGCACAGT 60.181 43.478 0.00 0.00 38.41 3.55
3251 3646 1.680338 AGGTTGTTTCCTGCACAGTC 58.320 50.000 0.00 0.00 36.35 3.51
3252 3647 0.307760 GGTTGTTTCCTGCACAGTCG 59.692 55.000 0.00 0.00 0.00 4.18
3253 3648 0.317020 GTTGTTTCCTGCACAGTCGC 60.317 55.000 0.00 0.00 0.00 5.19
3254 3649 1.771073 TTGTTTCCTGCACAGTCGCG 61.771 55.000 0.00 0.00 33.35 5.87
3255 3650 2.108157 TTTCCTGCACAGTCGCGT 59.892 55.556 5.77 0.00 33.35 6.01
3256 3651 2.243957 TTTCCTGCACAGTCGCGTG 61.244 57.895 5.77 0.00 40.00 5.34
3257 3652 4.662961 TCCTGCACAGTCGCGTGG 62.663 66.667 5.77 0.00 37.37 4.94
3259 3654 4.662961 CTGCACAGTCGCGTGGGA 62.663 66.667 5.77 0.00 37.37 4.37
3260 3655 4.961511 TGCACAGTCGCGTGGGAC 62.962 66.667 5.77 8.85 37.37 4.46
3274 3669 2.570181 GGACCCACCACTACGACG 59.430 66.667 0.00 0.00 38.79 5.12
3279 3674 2.452813 CCACCACTACGACGCATGC 61.453 63.158 7.91 7.91 0.00 4.06
3299 3694 4.980590 TGCATTATTGATTTCGTGTCACC 58.019 39.130 0.00 0.00 0.00 4.02
3366 3761 7.540745 ACCGTTATGCAAAATTGAATTAGTGTC 59.459 33.333 0.00 0.00 0.00 3.67
3367 3762 7.253288 CCGTTATGCAAAATTGAATTAGTGTCG 60.253 37.037 0.00 0.00 0.00 4.35
3418 3813 3.907788 CGTTTTCGTACACATGTAGTCGA 59.092 43.478 0.00 6.19 38.65 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.047877 CTTCGTGTTGGTCCCCGC 61.048 66.667 0.00 0.00 0.00 6.13
1 2 3.047877 GCTTCGTGTTGGTCCCCG 61.048 66.667 0.00 0.00 0.00 5.73
2 3 2.112297 TGCTTCGTGTTGGTCCCC 59.888 61.111 0.00 0.00 0.00 4.81
3 4 2.604174 CGTGCTTCGTGTTGGTCCC 61.604 63.158 0.00 0.00 34.52 4.46
4 5 2.935955 CGTGCTTCGTGTTGGTCC 59.064 61.111 0.00 0.00 34.52 4.46
5 6 2.248431 GCGTGCTTCGTGTTGGTC 59.752 61.111 4.16 0.00 42.13 4.02
6 7 3.276846 GGCGTGCTTCGTGTTGGT 61.277 61.111 4.16 0.00 42.13 3.67
7 8 4.368808 CGGCGTGCTTCGTGTTGG 62.369 66.667 0.00 0.00 42.13 3.77
42 43 4.115199 AGGAAGATGGGTGGCGCC 62.115 66.667 22.73 22.73 0.00 6.53
43 44 2.514824 GAGGAAGATGGGTGGCGC 60.515 66.667 0.00 0.00 0.00 6.53
44 45 2.190578 GGAGGAAGATGGGTGGCG 59.809 66.667 0.00 0.00 0.00 5.69
45 46 1.077429 GTGGAGGAAGATGGGTGGC 60.077 63.158 0.00 0.00 0.00 5.01
46 47 1.221840 CGTGGAGGAAGATGGGTGG 59.778 63.158 0.00 0.00 0.00 4.61
47 48 1.221840 CCGTGGAGGAAGATGGGTG 59.778 63.158 0.00 0.00 45.00 4.61
48 49 3.727387 CCGTGGAGGAAGATGGGT 58.273 61.111 0.00 0.00 45.00 4.51
57 58 2.124507 TTTCTGGCCTTCCGTGGAGG 62.125 60.000 3.32 0.00 42.97 4.30
58 59 0.674895 CTTTCTGGCCTTCCGTGGAG 60.675 60.000 3.32 0.00 34.14 3.86
59 60 1.374947 CTTTCTGGCCTTCCGTGGA 59.625 57.895 3.32 0.00 34.14 4.02
60 61 1.675641 CCTTTCTGGCCTTCCGTGG 60.676 63.158 3.32 0.00 34.14 4.94
61 62 3.987404 CCTTTCTGGCCTTCCGTG 58.013 61.111 3.32 0.00 34.14 4.94
99 100 3.777925 CTCGCCGGCACAAGTTCG 61.778 66.667 28.98 7.38 0.00 3.95
100 101 4.090057 GCTCGCCGGCACAAGTTC 62.090 66.667 28.98 4.88 0.00 3.01
163 164 4.760220 TGAGGCCCCTTCTCCCCC 62.760 72.222 0.00 0.00 0.00 5.40
164 165 3.093172 CTGAGGCCCCTTCTCCCC 61.093 72.222 0.00 0.00 0.00 4.81
165 166 0.990818 ATTCTGAGGCCCCTTCTCCC 60.991 60.000 0.00 0.00 0.00 4.30
166 167 0.472044 GATTCTGAGGCCCCTTCTCC 59.528 60.000 0.00 0.00 0.00 3.71
167 168 0.472044 GGATTCTGAGGCCCCTTCTC 59.528 60.000 0.00 0.00 0.00 2.87
168 169 0.253347 TGGATTCTGAGGCCCCTTCT 60.253 55.000 0.00 0.00 0.00 2.85
169 170 0.625849 TTGGATTCTGAGGCCCCTTC 59.374 55.000 0.00 0.00 0.00 3.46
170 171 0.627986 CTTGGATTCTGAGGCCCCTT 59.372 55.000 0.00 0.00 0.00 3.95
171 172 1.931007 GCTTGGATTCTGAGGCCCCT 61.931 60.000 0.00 0.00 0.00 4.79
172 173 1.454663 GCTTGGATTCTGAGGCCCC 60.455 63.158 0.00 0.00 0.00 5.80
173 174 1.454663 GGCTTGGATTCTGAGGCCC 60.455 63.158 0.00 0.00 34.19 5.80
174 175 1.821332 CGGCTTGGATTCTGAGGCC 60.821 63.158 0.00 0.00 36.60 5.19
175 176 1.821332 CCGGCTTGGATTCTGAGGC 60.821 63.158 0.00 4.20 42.00 4.70
176 177 1.907739 TCCGGCTTGGATTCTGAGG 59.092 57.895 0.00 0.00 43.74 3.86
192 193 1.740718 GCTCTCAACTCGGATGGTTCC 60.741 57.143 0.00 0.00 38.81 3.62
193 194 1.646189 GCTCTCAACTCGGATGGTTC 58.354 55.000 0.00 0.00 0.00 3.62
194 195 0.250513 GGCTCTCAACTCGGATGGTT 59.749 55.000 0.00 0.00 0.00 3.67
195 196 1.617947 GGGCTCTCAACTCGGATGGT 61.618 60.000 0.00 0.00 0.00 3.55
196 197 1.144936 GGGCTCTCAACTCGGATGG 59.855 63.158 0.00 0.00 0.00 3.51
197 198 0.179089 CTGGGCTCTCAACTCGGATG 60.179 60.000 0.00 0.00 0.00 3.51
198 199 0.324738 TCTGGGCTCTCAACTCGGAT 60.325 55.000 0.00 0.00 0.00 4.18
199 200 0.541998 TTCTGGGCTCTCAACTCGGA 60.542 55.000 0.00 0.00 0.00 4.55
200 201 0.390472 GTTCTGGGCTCTCAACTCGG 60.390 60.000 0.00 0.00 0.00 4.63
201 202 0.605589 AGTTCTGGGCTCTCAACTCG 59.394 55.000 0.00 0.00 0.00 4.18
202 203 2.849294 AAGTTCTGGGCTCTCAACTC 57.151 50.000 1.69 0.00 0.00 3.01
203 204 4.917906 AATAAGTTCTGGGCTCTCAACT 57.082 40.909 0.00 0.00 0.00 3.16
204 205 4.572795 GCTAATAAGTTCTGGGCTCTCAAC 59.427 45.833 0.00 0.00 0.00 3.18
205 206 4.384208 GGCTAATAAGTTCTGGGCTCTCAA 60.384 45.833 0.00 0.00 0.00 3.02
206 207 3.134804 GGCTAATAAGTTCTGGGCTCTCA 59.865 47.826 0.00 0.00 0.00 3.27
207 208 3.495276 GGGCTAATAAGTTCTGGGCTCTC 60.495 52.174 0.00 0.00 0.00 3.20
208 209 2.439880 GGGCTAATAAGTTCTGGGCTCT 59.560 50.000 0.00 0.00 0.00 4.09
209 210 2.807108 CGGGCTAATAAGTTCTGGGCTC 60.807 54.545 0.00 0.00 0.00 4.70
210 211 1.141053 CGGGCTAATAAGTTCTGGGCT 59.859 52.381 0.00 0.00 0.00 5.19
211 212 1.594331 CGGGCTAATAAGTTCTGGGC 58.406 55.000 0.00 0.00 0.00 5.36
212 213 1.766496 TCCGGGCTAATAAGTTCTGGG 59.234 52.381 0.00 0.00 0.00 4.45
213 214 2.698797 TCTCCGGGCTAATAAGTTCTGG 59.301 50.000 0.00 0.00 0.00 3.86
214 215 3.243907 CCTCTCCGGGCTAATAAGTTCTG 60.244 52.174 0.00 0.00 0.00 3.02
215 216 2.966516 CCTCTCCGGGCTAATAAGTTCT 59.033 50.000 0.00 0.00 0.00 3.01
216 217 3.388345 CCTCTCCGGGCTAATAAGTTC 57.612 52.381 0.00 0.00 0.00 3.01
228 229 3.610669 CTCATCGCCCCTCTCCGG 61.611 72.222 0.00 0.00 0.00 5.14
229 230 3.610669 CCTCATCGCCCCTCTCCG 61.611 72.222 0.00 0.00 0.00 4.63
230 231 2.123251 TCCTCATCGCCCCTCTCC 60.123 66.667 0.00 0.00 0.00 3.71
231 232 1.743321 CTGTCCTCATCGCCCCTCTC 61.743 65.000 0.00 0.00 0.00 3.20
232 233 1.760086 CTGTCCTCATCGCCCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
233 234 1.743321 CTCTGTCCTCATCGCCCCTC 61.743 65.000 0.00 0.00 0.00 4.30
234 235 1.760086 CTCTGTCCTCATCGCCCCT 60.760 63.158 0.00 0.00 0.00 4.79
235 236 2.818132 CTCTGTCCTCATCGCCCC 59.182 66.667 0.00 0.00 0.00 5.80
236 237 2.107953 GCTCTGTCCTCATCGCCC 59.892 66.667 0.00 0.00 0.00 6.13
538 539 3.390671 TTCCCTCTCCCCCTAGCGG 62.391 68.421 0.00 0.00 0.00 5.52
539 540 1.834822 CTTCCCTCTCCCCCTAGCG 60.835 68.421 0.00 0.00 0.00 4.26
540 541 0.471022 CTCTTCCCTCTCCCCCTAGC 60.471 65.000 0.00 0.00 0.00 3.42
541 542 0.189822 CCTCTTCCCTCTCCCCCTAG 59.810 65.000 0.00 0.00 0.00 3.02
542 543 1.304936 CCCTCTTCCCTCTCCCCCTA 61.305 65.000 0.00 0.00 0.00 3.53
543 544 2.652113 CCCTCTTCCCTCTCCCCCT 61.652 68.421 0.00 0.00 0.00 4.79
544 545 2.040359 CCCTCTTCCCTCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
545 546 1.690985 CACCCTCTTCCCTCTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
546 547 1.690985 CCACCCTCTTCCCTCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
547 548 0.689412 CTCCACCCTCTTCCCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
548 549 0.336737 TCTCCACCCTCTTCCCTCTC 59.663 60.000 0.00 0.00 0.00 3.20
549 550 0.338120 CTCTCCACCCTCTTCCCTCT 59.662 60.000 0.00 0.00 0.00 3.69
550 551 0.689412 CCTCTCCACCCTCTTCCCTC 60.689 65.000 0.00 0.00 0.00 4.30
551 552 1.156322 TCCTCTCCACCCTCTTCCCT 61.156 60.000 0.00 0.00 0.00 4.20
552 553 0.689412 CTCCTCTCCACCCTCTTCCC 60.689 65.000 0.00 0.00 0.00 3.97
553 554 0.336737 TCTCCTCTCCACCCTCTTCC 59.663 60.000 0.00 0.00 0.00 3.46
554 555 1.775385 CTCTCCTCTCCACCCTCTTC 58.225 60.000 0.00 0.00 0.00 2.87
555 556 0.325203 GCTCTCCTCTCCACCCTCTT 60.325 60.000 0.00 0.00 0.00 2.85
556 557 1.309688 GCTCTCCTCTCCACCCTCT 59.690 63.158 0.00 0.00 0.00 3.69
557 558 1.760480 GGCTCTCCTCTCCACCCTC 60.760 68.421 0.00 0.00 0.00 4.30
558 559 1.895886 ATGGCTCTCCTCTCCACCCT 61.896 60.000 0.00 0.00 31.94 4.34
559 560 1.383803 ATGGCTCTCCTCTCCACCC 60.384 63.158 0.00 0.00 31.94 4.61
560 561 1.406860 GGATGGCTCTCCTCTCCACC 61.407 65.000 0.12 0.00 35.92 4.61
561 562 0.398381 AGGATGGCTCTCCTCTCCAC 60.398 60.000 3.68 0.00 42.12 4.02
562 563 2.022681 AGGATGGCTCTCCTCTCCA 58.977 57.895 3.68 0.00 42.12 3.86
568 569 1.460273 GGTCGAGAGGATGGCTCTCC 61.460 65.000 0.00 0.00 43.09 3.71
569 570 0.753479 TGGTCGAGAGGATGGCTCTC 60.753 60.000 0.00 0.00 42.72 3.20
570 571 0.754957 CTGGTCGAGAGGATGGCTCT 60.755 60.000 0.00 0.00 0.00 4.09
571 572 1.040339 ACTGGTCGAGAGGATGGCTC 61.040 60.000 0.00 0.00 0.00 4.70
572 573 0.616111 AACTGGTCGAGAGGATGGCT 60.616 55.000 0.00 0.00 0.00 4.75
573 574 0.179097 GAACTGGTCGAGAGGATGGC 60.179 60.000 0.00 0.00 0.00 4.40
584 585 4.965119 ATAAAAAGGATGCGAACTGGTC 57.035 40.909 0.00 0.00 0.00 4.02
585 586 8.567948 CATATAATAAAAAGGATGCGAACTGGT 58.432 33.333 0.00 0.00 0.00 4.00
586 587 8.567948 ACATATAATAAAAAGGATGCGAACTGG 58.432 33.333 0.00 0.00 0.00 4.00
587 588 9.385902 CACATATAATAAAAAGGATGCGAACTG 57.614 33.333 0.00 0.00 0.00 3.16
588 589 9.337396 TCACATATAATAAAAAGGATGCGAACT 57.663 29.630 0.00 0.00 0.00 3.01
592 593 9.897744 ACAATCACATATAATAAAAAGGATGCG 57.102 29.630 0.00 0.00 0.00 4.73
750 767 7.334844 TGCTTTCTCGTATTATCTCTCTCAA 57.665 36.000 0.00 0.00 0.00 3.02
751 768 6.944234 TGCTTTCTCGTATTATCTCTCTCA 57.056 37.500 0.00 0.00 0.00 3.27
752 769 7.197017 TGTTGCTTTCTCGTATTATCTCTCTC 58.803 38.462 0.00 0.00 0.00 3.20
753 770 7.101652 TGTTGCTTTCTCGTATTATCTCTCT 57.898 36.000 0.00 0.00 0.00 3.10
804 853 5.417580 GGATTGCTGTCCACTGGTTATTTTA 59.582 40.000 0.00 0.00 38.20 1.52
826 877 1.302993 GGTTGCCAGCTAAACCGGA 60.303 57.895 9.46 0.00 36.75 5.14
1135 1219 3.525545 GTCGTACTCCCCGCCCTC 61.526 72.222 0.00 0.00 0.00 4.30
1136 1220 3.674050 ATGTCGTACTCCCCGCCCT 62.674 63.158 0.00 0.00 0.00 5.19
1188 1272 0.321919 TACGTACCTCGGTGCAGTCT 60.322 55.000 5.07 0.00 44.69 3.24
1432 1516 0.608640 CCAGGTCGTTGGAAGCTAGT 59.391 55.000 0.00 0.00 40.87 2.57
1501 1585 1.112315 TGTTGCCTTTGCCGGTGATT 61.112 50.000 1.90 0.00 36.33 2.57
2139 2534 1.327690 GGATGCTACGAGGGGTGACA 61.328 60.000 0.00 0.00 0.00 3.58
2143 2538 0.325296 TCTTGGATGCTACGAGGGGT 60.325 55.000 0.00 0.00 0.00 4.95
2504 2899 4.264543 CCGAGAAAAGAAATCATGTCGG 57.735 45.455 0.00 0.00 39.73 4.79
2907 3302 4.528596 ACTGCTGTATTTGAGTAGACCACT 59.471 41.667 0.00 0.00 41.47 4.00
3037 3432 6.067350 GGAAGGAGGAGCATCAAAATAGAAT 58.933 40.000 0.00 0.00 36.25 2.40
3214 3609 5.163591 ACAACCTATCATGTGAATGCATGTG 60.164 40.000 0.00 0.00 44.68 3.21
3242 3637 4.662961 TCCCACGCGACTGTGCAG 62.663 66.667 15.93 0.00 38.55 4.41
3243 3638 4.961511 GTCCCACGCGACTGTGCA 62.962 66.667 15.93 0.00 38.55 4.57
3255 3650 1.909781 GTCGTAGTGGTGGGTCCCA 60.910 63.158 6.47 6.47 34.77 4.37
3256 3651 2.976356 GTCGTAGTGGTGGGTCCC 59.024 66.667 0.00 0.00 34.77 4.46
3257 3652 2.570181 CGTCGTAGTGGTGGGTCC 59.430 66.667 0.00 0.00 0.00 4.46
3258 3653 2.126189 GCGTCGTAGTGGTGGGTC 60.126 66.667 0.00 0.00 0.00 4.46
3259 3654 2.280552 ATGCGTCGTAGTGGTGGGT 61.281 57.895 0.00 0.00 0.00 4.51
3260 3655 1.809619 CATGCGTCGTAGTGGTGGG 60.810 63.158 0.00 0.00 0.00 4.61
3261 3656 2.452813 GCATGCGTCGTAGTGGTGG 61.453 63.158 0.00 0.00 0.00 4.61
3262 3657 1.083806 ATGCATGCGTCGTAGTGGTG 61.084 55.000 14.09 0.00 0.00 4.17
3263 3658 0.391130 AATGCATGCGTCGTAGTGGT 60.391 50.000 13.95 0.00 0.00 4.16
3264 3659 1.566404 TAATGCATGCGTCGTAGTGG 58.434 50.000 13.95 0.00 0.00 4.00
3265 3660 3.245048 TCAATAATGCATGCGTCGTAGTG 59.755 43.478 13.95 12.25 0.00 2.74
3266 3661 3.453424 TCAATAATGCATGCGTCGTAGT 58.547 40.909 13.95 0.00 0.00 2.73
3274 3669 5.036090 TGACACGAAATCAATAATGCATGC 58.964 37.500 11.82 11.82 0.00 4.06
3279 3674 4.587306 CCGGTGACACGAAATCAATAATG 58.413 43.478 0.00 0.00 35.47 1.90
3299 3694 1.223187 AACTGTGTAGAAAACGGCCG 58.777 50.000 26.86 26.86 0.00 6.13
3366 3761 1.135689 GCTATGTGGAAACAACAGGCG 60.136 52.381 0.00 0.00 46.06 5.52
3367 3762 1.135689 CGCTATGTGGAAACAACAGGC 60.136 52.381 0.00 0.00 46.06 4.85
3418 3813 0.534203 ATTAATGGGCGACGGCGATT 60.534 50.000 28.86 28.86 39.47 3.34


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

AutoCloner maintained by Alex Coulton.