Multiple sequence alignment - TraesCS1D01G448400

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 TraesCS1D01G448400 chr1D 100.000 2585 0 0 1 2585 490881210 490883794 0.000000e+00 4774.0
1 TraesCS1D01G448400 chr1D 92.582 2184 127 23 424 2585 424634905 424637075 0.000000e+00 3103.0
2 TraesCS1D01G448400 chr1D 90.967 2192 146 30 424 2578 254795376 254797552 0.000000e+00 2904.0
3 TraesCS1D01G448400 chr1D 91.209 455 32 4 2139 2585 236097094 236096640 1.700000e-171 612.0
4 TraesCS1D01G448400 chr2D 92.272 2174 130 17 424 2570 7031492 7033654 0.000000e+00 3049.0
5 TraesCS1D01G448400 chr2D 93.698 1809 94 15 789 2580 644015123 644013318 0.000000e+00 2691.0
6 TraesCS1D01G448400 chr7D 92.022 2181 132 20 430 2578 207197774 207199944 0.000000e+00 3025.0
7 TraesCS1D01G448400 chr3D 91.636 2200 137 24 423 2585 429783968 429786157 0.000000e+00 3000.0
8 TraesCS1D01G448400 chr3D 93.022 1906 113 15 420 2311 382523092 382521193 0.000000e+00 2765.0
9 TraesCS1D01G448400 chr3D 93.982 1346 61 11 1254 2585 515977138 515975799 0.000000e+00 2019.0
10 TraesCS1D01G448400 chr5D 92.552 1893 120 17 422 2304 495796216 495794335 0.000000e+00 2695.0
11 TraesCS1D01G448400 chr5D 92.051 1887 121 20 430 2304 179972950 179971081 0.000000e+00 2627.0
12 TraesCS1D01G448400 chr6B 89.223 2162 144 37 461 2585 636474273 636476382 0.000000e+00 2619.0
13 TraesCS1D01G448400 chr6B 92.476 319 21 2 2267 2585 227279697 227280012 1.090000e-123 453.0
14 TraesCS1D01G448400 chr6D 91.483 1902 142 14 423 2311 430885510 430883616 0.000000e+00 2597.0
15 TraesCS1D01G448400 chr6D 92.857 252 16 2 4 255 427969252 427969003 5.260000e-97 364.0
16 TraesCS1D01G448400 chr4D 91.560 936 51 9 1674 2585 419417895 419418826 0.000000e+00 1266.0
17 TraesCS1D01G448400 chr4A 87.242 533 54 11 422 948 62460242 62460766 1.710000e-166 595.0
18 TraesCS1D01G448400 chr2A 87.451 510 53 9 430 934 603689306 603689809 6.200000e-161 577.0
19 TraesCS1D01G448400 chr6A 86.220 254 34 1 2 255 23245388 23245640 9.110000e-70 274.0
20 TraesCS1D01G448400 chr6A 89.655 174 16 2 252 423 23248899 23249072 1.200000e-53 220.0
21 TraesCS1D01G448400 chr6A 100.000 28 0 0 2 29 535421969 535421996 5.000000e-03 52.8
22 TraesCS1D01G448400 chr1B 87.283 173 20 2 253 423 534256181 534256353 2.030000e-46 196.0
23 TraesCS1D01G448400 chr1B 81.143 175 13 10 251 423 534249420 534249576 3.490000e-24 122.0
24 TraesCS1D01G448400 chr1B 80.460 174 16 7 251 423 534254015 534254171 1.630000e-22 117.0
25 TraesCS1D01G448400 chr1B 100.000 28 0 0 2 29 443488971 443488998 5.000000e-03 52.8
26 TraesCS1D01G448400 chr7A 89.333 75 3 3 2 72 48766888 48766961 3.540000e-14 89.8
27 TraesCS1D01G448400 chr3A 89.333 75 3 3 2 72 434799117 434799044 3.540000e-14 89.8
28 TraesCS1D01G448400 chr5B 100.000 28 0 0 2 29 524221830 524221857 5.000000e-03 52.8


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 TraesCS1D01G448400 chr1D 490881210 490883794 2584 False 4774 4774 100.0000 1 2585 1 chr1D.!!$F3 2584
1 TraesCS1D01G448400 chr1D 424634905 424637075 2170 False 3103 3103 92.5820 424 2585 1 chr1D.!!$F2 2161
2 TraesCS1D01G448400 chr1D 254795376 254797552 2176 False 2904 2904 90.9670 424 2578 1 chr1D.!!$F1 2154
3 TraesCS1D01G448400 chr2D 7031492 7033654 2162 False 3049 3049 92.2720 424 2570 1 chr2D.!!$F1 2146
4 TraesCS1D01G448400 chr2D 644013318 644015123 1805 True 2691 2691 93.6980 789 2580 1 chr2D.!!$R1 1791
5 TraesCS1D01G448400 chr7D 207197774 207199944 2170 False 3025 3025 92.0220 430 2578 1 chr7D.!!$F1 2148
6 TraesCS1D01G448400 chr3D 429783968 429786157 2189 False 3000 3000 91.6360 423 2585 1 chr3D.!!$F1 2162
7 TraesCS1D01G448400 chr3D 382521193 382523092 1899 True 2765 2765 93.0220 420 2311 1 chr3D.!!$R1 1891
8 TraesCS1D01G448400 chr3D 515975799 515977138 1339 True 2019 2019 93.9820 1254 2585 1 chr3D.!!$R2 1331
9 TraesCS1D01G448400 chr5D 495794335 495796216 1881 True 2695 2695 92.5520 422 2304 1 chr5D.!!$R2 1882
10 TraesCS1D01G448400 chr5D 179971081 179972950 1869 True 2627 2627 92.0510 430 2304 1 chr5D.!!$R1 1874
11 TraesCS1D01G448400 chr6B 636474273 636476382 2109 False 2619 2619 89.2230 461 2585 1 chr6B.!!$F2 2124
12 TraesCS1D01G448400 chr6D 430883616 430885510 1894 True 2597 2597 91.4830 423 2311 1 chr6D.!!$R2 1888
13 TraesCS1D01G448400 chr4D 419417895 419418826 931 False 1266 1266 91.5600 1674 2585 1 chr4D.!!$F1 911
14 TraesCS1D01G448400 chr4A 62460242 62460766 524 False 595 595 87.2420 422 948 1 chr4A.!!$F1 526
15 TraesCS1D01G448400 chr2A 603689306 603689809 503 False 577 577 87.4510 430 934 1 chr2A.!!$F1 504
16 TraesCS1D01G448400 chr6A 23245388 23249072 3684 False 247 274 87.9375 2 423 2 chr6A.!!$F2 421

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
386 3650 0.033991 AGCTAGAACTCGAGGCTCCA 60.034 55.0 18.41 1.08 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 4971 0.044092 TGCTTCCTCCCCCTGTATGA 59.956 55.0 0.0 0.0 0.0 2.15 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
34 35 1.225376 TTTAGCACGGCGTTCAGTGG 61.225 55.000 11.19 0.00 38.68 4.00
35 36 4.235762 AGCACGGCGTTCAGTGGT 62.236 61.111 11.19 0.47 43.23 4.16
39 40 1.740296 ACGGCGTTCAGTGGTATGC 60.740 57.895 6.77 0.00 0.00 3.14
57 58 1.354506 CGTATCGTGGACGTCCTCC 59.645 63.158 33.39 22.50 40.80 4.30
70 71 1.205655 CGTCCTCCAGCTTTGAGATCA 59.794 52.381 10.89 0.00 31.26 2.92
73 74 3.055530 GTCCTCCAGCTTTGAGATCAAGA 60.056 47.826 10.89 0.00 37.15 3.02
78 79 4.999950 TCCAGCTTTGAGATCAAGAAGAAC 59.000 41.667 0.00 0.00 37.15 3.01
85 86 4.887748 TGAGATCAAGAAGAACCACTGAC 58.112 43.478 0.00 0.00 0.00 3.51
94 95 1.552337 AGAACCACTGACGCATCTGAT 59.448 47.619 0.00 0.00 0.00 2.90
95 96 1.662629 GAACCACTGACGCATCTGATG 59.337 52.381 13.26 13.26 0.00 3.07
115 116 2.268298 GCGCGAAGACTTTTAGGATCA 58.732 47.619 12.10 0.00 0.00 2.92
119 120 5.862323 GCGCGAAGACTTTTAGGATCATATA 59.138 40.000 12.10 0.00 0.00 0.86
126 127 7.841956 AGACTTTTAGGATCATATATCCACCG 58.158 38.462 6.79 0.00 40.61 4.94
138 139 7.158697 TCATATATCCACCGTATGAAACCTTG 58.841 38.462 0.00 0.00 33.29 3.61
139 140 3.713826 ATCCACCGTATGAAACCTTGT 57.286 42.857 0.00 0.00 0.00 3.16
140 141 3.495434 TCCACCGTATGAAACCTTGTT 57.505 42.857 0.00 0.00 0.00 2.83
150 151 4.300189 TGAAACCTTGTTGTGTACATGC 57.700 40.909 0.00 0.00 36.44 4.06
163 164 0.899019 TACATGCACCGGCTCAGTTA 59.101 50.000 0.00 0.00 41.91 2.24
164 165 0.253044 ACATGCACCGGCTCAGTTAT 59.747 50.000 0.00 0.00 41.91 1.89
186 187 1.231197 TCCCCTCCCTCCTCCCTTA 60.231 63.158 0.00 0.00 0.00 2.69
190 191 1.051556 CCTCCCTCCTCCCTTAGCAC 61.052 65.000 0.00 0.00 0.00 4.40
194 195 1.118838 CCTCCTCCCTTAGCACTCAG 58.881 60.000 0.00 0.00 0.00 3.35
195 196 1.342474 CCTCCTCCCTTAGCACTCAGA 60.342 57.143 0.00 0.00 0.00 3.27
198 199 2.183679 CCTCCCTTAGCACTCAGAAGT 58.816 52.381 0.00 0.00 35.60 3.01
206 207 5.337089 CCTTAGCACTCAGAAGTTGATCTCA 60.337 44.000 0.00 0.00 34.68 3.27
220 221 6.970484 AGTTGATCTCATGTTTTTGTACCAC 58.030 36.000 0.00 0.00 0.00 4.16
221 222 6.772716 AGTTGATCTCATGTTTTTGTACCACT 59.227 34.615 0.00 0.00 0.00 4.00
227 228 4.578516 TCATGTTTTTGTACCACTGGACAG 59.421 41.667 0.71 0.00 0.00 3.51
230 231 2.719531 TTTGTACCACTGGACAGCAA 57.280 45.000 0.71 0.00 0.00 3.91
231 232 2.719531 TTGTACCACTGGACAGCAAA 57.280 45.000 0.71 0.00 0.00 3.68
232 233 2.254546 TGTACCACTGGACAGCAAAG 57.745 50.000 0.71 0.00 0.00 2.77
233 234 1.488812 TGTACCACTGGACAGCAAAGT 59.511 47.619 0.71 0.00 0.00 2.66
236 237 3.100545 CACTGGACAGCAAAGTGGT 57.899 52.632 0.00 0.00 38.10 4.16
267 3530 1.302271 TGAACAGCCAGCTCAGCAG 60.302 57.895 0.00 2.35 0.00 4.24
268 3531 1.004080 GAACAGCCAGCTCAGCAGA 60.004 57.895 0.00 0.00 0.00 4.26
270 3533 1.478526 AACAGCCAGCTCAGCAGAGA 61.479 55.000 10.77 0.00 44.98 3.10
305 3569 0.961019 ACACATGGCTTGCATTTCGT 59.039 45.000 0.00 0.00 0.00 3.85
307 3571 0.168788 ACATGGCTTGCATTTCGTCG 59.831 50.000 0.00 0.00 0.00 5.12
315 3579 1.876714 GCATTTCGTCGCGCTCCTA 60.877 57.895 5.56 0.00 0.00 2.94
321 3585 3.224324 GTCGCGCTCCTATCCCCA 61.224 66.667 5.56 0.00 0.00 4.96
342 3606 4.925054 CCATGCTTGACATCGTTTTCAAAT 59.075 37.500 0.22 0.00 36.64 2.32
346 3610 6.038985 TGCTTGACATCGTTTTCAAATGAAA 58.961 32.000 4.52 4.52 41.77 2.69
350 3614 7.856492 TGACATCGTTTTCAAATGAAATCAG 57.144 32.000 9.23 4.89 42.83 2.90
354 3618 5.460646 TCGTTTTCAAATGAAATCAGCCTC 58.539 37.500 9.23 0.00 42.83 4.70
355 3619 5.241506 TCGTTTTCAAATGAAATCAGCCTCT 59.758 36.000 9.23 0.00 42.83 3.69
356 3620 6.429692 TCGTTTTCAAATGAAATCAGCCTCTA 59.570 34.615 9.23 0.00 42.83 2.43
357 3621 7.121168 TCGTTTTCAAATGAAATCAGCCTCTAT 59.879 33.333 9.23 0.00 42.83 1.98
358 3622 8.397906 CGTTTTCAAATGAAATCAGCCTCTATA 58.602 33.333 9.23 0.00 42.83 1.31
365 3629 9.844257 AAATGAAATCAGCCTCTATATATAGCC 57.156 33.333 14.03 5.99 0.00 3.93
366 3630 7.366847 TGAAATCAGCCTCTATATATAGCCC 57.633 40.000 14.03 5.69 0.00 5.19
367 3631 6.902974 TGAAATCAGCCTCTATATATAGCCCA 59.097 38.462 14.03 0.00 0.00 5.36
368 3632 6.992664 AATCAGCCTCTATATATAGCCCAG 57.007 41.667 14.03 7.28 0.00 4.45
369 3633 4.219115 TCAGCCTCTATATATAGCCCAGC 58.781 47.826 14.03 12.74 0.00 4.85
370 3634 4.078922 TCAGCCTCTATATATAGCCCAGCT 60.079 45.833 14.03 14.39 43.41 4.24
371 3635 5.134509 TCAGCCTCTATATATAGCCCAGCTA 59.865 44.000 14.03 0.00 45.55 3.32
372 3636 5.476599 CAGCCTCTATATATAGCCCAGCTAG 59.523 48.000 14.03 5.41 44.66 3.42
373 3637 5.374154 AGCCTCTATATATAGCCCAGCTAGA 59.626 44.000 14.03 0.00 44.66 2.43
374 3638 6.071984 GCCTCTATATATAGCCCAGCTAGAA 58.928 44.000 14.03 0.00 44.66 2.10
375 3639 6.015772 GCCTCTATATATAGCCCAGCTAGAAC 60.016 46.154 14.03 0.00 44.66 3.01
376 3640 7.294584 CCTCTATATATAGCCCAGCTAGAACT 58.705 42.308 14.03 0.00 44.66 3.01
377 3641 7.447238 CCTCTATATATAGCCCAGCTAGAACTC 59.553 44.444 14.03 0.00 44.66 3.01
378 3642 6.993308 TCTATATATAGCCCAGCTAGAACTCG 59.007 42.308 14.03 0.00 44.66 4.18
379 3643 2.366640 ATAGCCCAGCTAGAACTCGA 57.633 50.000 2.41 0.00 44.66 4.04
380 3644 1.681538 TAGCCCAGCTAGAACTCGAG 58.318 55.000 11.84 11.84 40.44 4.04
381 3645 1.040339 AGCCCAGCTAGAACTCGAGG 61.040 60.000 18.41 0.00 36.99 4.63
382 3646 1.439644 CCCAGCTAGAACTCGAGGC 59.560 63.158 18.41 9.98 0.00 4.70
383 3647 1.040339 CCCAGCTAGAACTCGAGGCT 61.040 60.000 18.41 15.58 0.00 4.58
384 3648 0.383949 CCAGCTAGAACTCGAGGCTC 59.616 60.000 18.41 12.74 0.00 4.70
385 3649 0.383949 CAGCTAGAACTCGAGGCTCC 59.616 60.000 18.41 8.37 0.00 4.70
386 3650 0.033991 AGCTAGAACTCGAGGCTCCA 60.034 55.000 18.41 1.08 0.00 3.86
387 3651 1.036707 GCTAGAACTCGAGGCTCCAT 58.963 55.000 18.41 1.00 0.00 3.41
388 3652 1.410882 GCTAGAACTCGAGGCTCCATT 59.589 52.381 18.41 0.00 0.00 3.16
389 3653 2.544903 GCTAGAACTCGAGGCTCCATTC 60.545 54.545 18.41 10.07 0.00 2.67
390 3654 1.561643 AGAACTCGAGGCTCCATTCA 58.438 50.000 18.41 0.00 0.00 2.57
391 3655 2.114616 AGAACTCGAGGCTCCATTCAT 58.885 47.619 18.41 0.00 0.00 2.57
392 3656 3.300388 AGAACTCGAGGCTCCATTCATA 58.700 45.455 18.41 0.00 0.00 2.15
393 3657 3.068873 AGAACTCGAGGCTCCATTCATAC 59.931 47.826 18.41 0.00 0.00 2.39
394 3658 2.672098 ACTCGAGGCTCCATTCATACT 58.328 47.619 18.41 0.00 0.00 2.12
395 3659 2.625790 ACTCGAGGCTCCATTCATACTC 59.374 50.000 18.41 0.00 0.00 2.59
396 3660 2.625314 CTCGAGGCTCCATTCATACTCA 59.375 50.000 9.32 0.00 0.00 3.41
397 3661 3.031013 TCGAGGCTCCATTCATACTCAA 58.969 45.455 9.32 0.00 0.00 3.02
398 3662 3.450817 TCGAGGCTCCATTCATACTCAAA 59.549 43.478 9.32 0.00 0.00 2.69
399 3663 4.101585 TCGAGGCTCCATTCATACTCAAAT 59.898 41.667 9.32 0.00 0.00 2.32
400 3664 4.818546 CGAGGCTCCATTCATACTCAAATT 59.181 41.667 9.32 0.00 0.00 1.82
401 3665 5.297776 CGAGGCTCCATTCATACTCAAATTT 59.702 40.000 9.32 0.00 0.00 1.82
402 3666 6.183360 CGAGGCTCCATTCATACTCAAATTTT 60.183 38.462 9.32 0.00 0.00 1.82
403 3667 7.486407 AGGCTCCATTCATACTCAAATTTTT 57.514 32.000 0.00 0.00 0.00 1.94
404 3668 8.593945 AGGCTCCATTCATACTCAAATTTTTA 57.406 30.769 0.00 0.00 0.00 1.52
405 3669 8.470002 AGGCTCCATTCATACTCAAATTTTTAC 58.530 33.333 0.00 0.00 0.00 2.01
406 3670 8.250332 GGCTCCATTCATACTCAAATTTTTACA 58.750 33.333 0.00 0.00 0.00 2.41
407 3671 9.638239 GCTCCATTCATACTCAAATTTTTACAA 57.362 29.630 0.00 0.00 0.00 2.41
418 3682 8.888716 ACTCAAATTTTTACAAATTGGTGGAAC 58.111 29.630 0.46 0.00 41.02 3.62
419 3683 8.792830 TCAAATTTTTACAAATTGGTGGAACA 57.207 26.923 0.46 0.00 41.02 3.18
420 3684 8.887717 TCAAATTTTTACAAATTGGTGGAACAG 58.112 29.630 0.46 0.00 41.02 3.16
427 3691 4.148838 CAAATTGGTGGAACAGTTAGGGA 58.851 43.478 0.00 0.00 41.80 4.20
428 3692 4.463050 AATTGGTGGAACAGTTAGGGAA 57.537 40.909 0.00 0.00 41.80 3.97
450 3714 0.537143 TTTGGTTGCCTGCATCGAGT 60.537 50.000 0.00 0.00 0.00 4.18
491 3755 1.217942 AGGAAGAGGCCTGTTTGGTTT 59.782 47.619 17.52 0.00 36.76 3.27
518 3782 1.303888 CACTGTTGGGCCTGCATCT 60.304 57.895 4.53 0.00 0.00 2.90
570 3834 0.530650 GCTGGAAATGCTCGGATCGA 60.531 55.000 0.00 0.00 0.00 3.59
660 3925 0.557729 ATGGCGGGAGATGGGAAATT 59.442 50.000 0.00 0.00 0.00 1.82
690 3955 0.742990 TCCCGTTGCCAAATCTAGCG 60.743 55.000 0.00 0.00 0.00 4.26
720 3987 3.491104 CCTTTCTACTCGCTCACCCATAC 60.491 52.174 0.00 0.00 0.00 2.39
722 3989 2.298610 TCTACTCGCTCACCCATACTG 58.701 52.381 0.00 0.00 0.00 2.74
723 3990 0.744874 TACTCGCTCACCCATACTGC 59.255 55.000 0.00 0.00 0.00 4.40
724 3991 1.227380 CTCGCTCACCCATACTGCC 60.227 63.158 0.00 0.00 0.00 4.85
725 3992 1.680522 CTCGCTCACCCATACTGCCT 61.681 60.000 0.00 0.00 0.00 4.75
726 3993 1.227380 CGCTCACCCATACTGCCTC 60.227 63.158 0.00 0.00 0.00 4.70
727 3994 1.907739 GCTCACCCATACTGCCTCA 59.092 57.895 0.00 0.00 0.00 3.86
728 3995 0.462759 GCTCACCCATACTGCCTCAC 60.463 60.000 0.00 0.00 0.00 3.51
729 3996 0.179000 CTCACCCATACTGCCTCACC 59.821 60.000 0.00 0.00 0.00 4.02
730 3997 0.546507 TCACCCATACTGCCTCACCA 60.547 55.000 0.00 0.00 0.00 4.17
731 3998 0.392998 CACCCATACTGCCTCACCAC 60.393 60.000 0.00 0.00 0.00 4.16
732 3999 1.153369 CCCATACTGCCTCACCACG 60.153 63.158 0.00 0.00 0.00 4.94
754 4029 2.569404 ACTTTCTTCCCTACTGCCTCAG 59.431 50.000 0.00 0.00 37.52 3.35
787 4062 1.329906 CTGTGATTTCAGATCTGCGCC 59.670 52.381 18.36 7.44 37.61 6.53
981 4280 3.670625 TCGATTTCCCATTGAACGAACT 58.329 40.909 0.00 0.00 31.07 3.01
982 4281 4.069304 TCGATTTCCCATTGAACGAACTT 58.931 39.130 0.00 0.00 31.07 2.66
1016 4320 1.540363 GGTTATGGACGCACGGATGAT 60.540 52.381 0.00 0.00 0.00 2.45
1063 4369 2.592102 AAGTGTGATTCAGGCATGGT 57.408 45.000 0.00 0.00 0.00 3.55
1097 4403 0.039978 CAGAGAGCTGTTCGTCGTGT 60.040 55.000 0.00 0.00 37.37 4.49
1134 4441 4.787551 TCCGCTATGGTCCAATGTTTATT 58.212 39.130 0.00 0.00 39.52 1.40
1376 4685 2.283298 CACGTTCAGGAGATCAATGGG 58.717 52.381 0.00 0.00 0.00 4.00
1443 4752 5.316167 GAGCTTAGAGGAGAGATGATCAGA 58.684 45.833 0.09 0.00 0.00 3.27
1559 4870 5.973565 GGCTTGATATGCTTGTATTGTTCAC 59.026 40.000 0.00 0.00 0.00 3.18
1566 4877 3.249799 TGCTTGTATTGTTCACGTTGAGG 59.750 43.478 0.00 0.00 0.00 3.86
1568 4879 4.154195 GCTTGTATTGTTCACGTTGAGGAT 59.846 41.667 0.00 0.00 0.00 3.24
1659 4971 2.234908 GTTCCTAGGTCACAGTCTGCAT 59.765 50.000 9.08 0.00 0.00 3.96
1825 5142 0.179009 ATCAACATCCCCGATGGCAG 60.179 55.000 6.58 0.00 43.60 4.85
1864 5181 2.421314 CTATGCATGTCGGCCGGA 59.579 61.111 27.83 13.31 0.00 5.14
1903 5220 3.264450 AGGAAAACCAGGTACCATCTCAG 59.736 47.826 15.94 0.00 0.00 3.35
1941 5258 2.035632 ACTATCCTAGGACTGCACAGC 58.964 52.381 15.42 0.00 0.00 4.40
2058 5377 1.361197 TCCACCCATACTCCACTCAGA 59.639 52.381 0.00 0.00 0.00 3.27
2115 5434 0.332972 GATCCTCCAGTGGGGCTTTT 59.667 55.000 9.92 0.00 36.21 2.27
2117 5436 1.681229 TCCTCCAGTGGGGCTTTTAT 58.319 50.000 9.92 0.00 36.21 1.40
2162 5484 2.695359 GGTTGAGCCTGACGATGTTAA 58.305 47.619 0.00 0.00 0.00 2.01
2173 5495 1.065709 ACGATGTTAACTCCGGCCATT 60.066 47.619 18.98 0.00 0.00 3.16
2192 5514 1.608055 TGTGTGGAGGCATTTGACAG 58.392 50.000 0.00 0.00 0.00 3.51
2196 5518 2.229792 GTGGAGGCATTTGACAGTGAA 58.770 47.619 0.00 0.00 0.00 3.18
2213 5535 5.127682 ACAGTGAAGCTTGGAAGAACAAAAT 59.872 36.000 2.10 0.00 0.00 1.82
2315 5683 4.352009 AGCAGAAGAAGAGGAAGATCTGA 58.648 43.478 0.00 0.00 37.14 3.27
2342 5710 2.201732 CAACACCGATGAACTATCCCG 58.798 52.381 0.00 0.00 31.82 5.14
2455 5823 4.682787 TCAGATTATGTGTGGTAAGCTCG 58.317 43.478 0.00 0.00 0.00 5.03
2480 5848 4.680110 CACTAGTTAGAAGTGGTGACAACG 59.320 45.833 7.61 0.00 46.06 4.10
2537 5905 2.730094 GCCTAATGCAATGCGGGG 59.270 61.111 0.00 1.06 40.77 5.73
2560 5929 2.102757 ACCAAACGCCGGGTTAAAAATT 59.897 40.909 2.18 0.00 38.08 1.82
2580 5949 6.882610 AATTGTTGTCTCATGCAACTAAGA 57.117 33.333 13.56 0.00 44.54 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.392756 GACGTCCACGATACGCATAC 58.607 55.000 3.51 0.00 44.04 2.39
35 36 0.308684 GGACGTCCACGATACGCATA 59.691 55.000 29.75 0.00 44.04 3.14
39 40 1.354506 GGAGGACGTCCACGATACG 59.645 63.158 35.00 0.00 46.10 3.06
57 58 4.758674 TGGTTCTTCTTGATCTCAAAGCTG 59.241 41.667 0.00 0.00 35.15 4.24
70 71 2.037772 AGATGCGTCAGTGGTTCTTCTT 59.962 45.455 8.99 0.00 0.00 2.52
73 74 1.344438 TCAGATGCGTCAGTGGTTCTT 59.656 47.619 8.99 0.00 0.00 2.52
94 95 2.268298 GATCCTAAAAGTCTTCGCGCA 58.732 47.619 8.75 0.00 0.00 6.09
95 96 2.268298 TGATCCTAAAAGTCTTCGCGC 58.732 47.619 0.00 0.00 0.00 6.86
97 98 8.035394 TGGATATATGATCCTAAAAGTCTTCGC 58.965 37.037 9.27 0.00 38.95 4.70
98 99 9.360093 GTGGATATATGATCCTAAAAGTCTTCG 57.640 37.037 9.27 0.00 38.95 3.79
115 116 7.074653 ACAAGGTTTCATACGGTGGATATAT 57.925 36.000 0.00 0.00 0.00 0.86
119 120 3.713826 ACAAGGTTTCATACGGTGGAT 57.286 42.857 0.00 0.00 0.00 3.41
126 127 5.856455 GCATGTACACAACAAGGTTTCATAC 59.144 40.000 0.00 0.00 42.70 2.39
138 139 1.209127 GCCGGTGCATGTACACAAC 59.791 57.895 16.11 0.00 42.55 3.32
139 140 0.953471 GAGCCGGTGCATGTACACAA 60.953 55.000 16.11 0.00 42.55 3.33
140 141 1.375396 GAGCCGGTGCATGTACACA 60.375 57.895 16.11 0.00 42.55 3.72
150 151 1.067821 GGAGAGATAACTGAGCCGGTG 59.932 57.143 1.90 0.00 0.00 4.94
163 164 1.376249 GGAGGAGGGAGGGGAGAGAT 61.376 65.000 0.00 0.00 0.00 2.75
164 165 2.015726 GGAGGAGGGAGGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
186 187 4.020396 ACATGAGATCAACTTCTGAGTGCT 60.020 41.667 0.00 0.00 37.52 4.40
190 191 7.646314 ACAAAAACATGAGATCAACTTCTGAG 58.354 34.615 0.00 0.00 37.52 3.35
194 195 7.591426 GTGGTACAAAAACATGAGATCAACTTC 59.409 37.037 0.00 0.00 44.16 3.01
195 196 7.285401 AGTGGTACAAAAACATGAGATCAACTT 59.715 33.333 0.00 0.00 44.16 2.66
198 199 6.016360 CCAGTGGTACAAAAACATGAGATCAA 60.016 38.462 0.00 0.00 44.16 2.57
206 207 3.317993 GCTGTCCAGTGGTACAAAAACAT 59.682 43.478 9.54 0.00 44.16 2.71
220 221 1.972872 AGAACCACTTTGCTGTCCAG 58.027 50.000 0.00 0.00 0.00 3.86
221 222 2.023673 CAAGAACCACTTTGCTGTCCA 58.976 47.619 0.00 0.00 36.61 4.02
227 228 1.404035 ACCGAACAAGAACCACTTTGC 59.596 47.619 0.00 0.00 36.61 3.68
230 231 2.014128 CACACCGAACAAGAACCACTT 58.986 47.619 0.00 0.00 39.70 3.16
231 232 1.208535 TCACACCGAACAAGAACCACT 59.791 47.619 0.00 0.00 0.00 4.00
232 233 1.658994 TCACACCGAACAAGAACCAC 58.341 50.000 0.00 0.00 0.00 4.16
233 234 2.404923 TTCACACCGAACAAGAACCA 57.595 45.000 0.00 0.00 0.00 3.67
267 3530 1.066502 GTCCTCCCAAGACAAGCTCTC 60.067 57.143 0.00 0.00 34.27 3.20
268 3531 0.980423 GTCCTCCCAAGACAAGCTCT 59.020 55.000 0.00 0.00 34.27 4.09
270 3533 0.398318 GTGTCCTCCCAAGACAAGCT 59.602 55.000 0.00 0.00 45.37 3.74
305 3569 2.203640 ATGGGGATAGGAGCGCGA 60.204 61.111 12.10 0.00 0.00 5.87
307 3571 2.359230 GCATGGGGATAGGAGCGC 60.359 66.667 0.00 0.00 0.00 5.92
315 3579 0.548031 ACGATGTCAAGCATGGGGAT 59.452 50.000 0.00 0.00 38.06 3.85
321 3585 5.771469 TCATTTGAAAACGATGTCAAGCAT 58.229 33.333 0.00 0.00 41.24 3.79
342 3606 6.902974 TGGGCTATATATAGAGGCTGATTTCA 59.097 38.462 24.86 13.65 39.67 2.69
346 3610 4.837860 GCTGGGCTATATATAGAGGCTGAT 59.162 45.833 24.86 0.00 39.67 2.90
350 3614 5.636123 TCTAGCTGGGCTATATATAGAGGC 58.364 45.833 21.65 19.72 40.54 4.70
354 3618 6.993308 TCGAGTTCTAGCTGGGCTATATATAG 59.007 42.308 14.45 14.45 40.54 1.31
355 3619 6.896883 TCGAGTTCTAGCTGGGCTATATATA 58.103 40.000 0.00 0.00 40.54 0.86
356 3620 5.756918 TCGAGTTCTAGCTGGGCTATATAT 58.243 41.667 0.00 0.00 40.54 0.86
357 3621 5.175388 TCGAGTTCTAGCTGGGCTATATA 57.825 43.478 0.00 0.00 40.54 0.86
358 3622 4.013728 CTCGAGTTCTAGCTGGGCTATAT 58.986 47.826 3.62 0.00 40.54 0.86
359 3623 3.413327 CTCGAGTTCTAGCTGGGCTATA 58.587 50.000 3.62 0.00 40.54 1.31
360 3624 2.235016 CTCGAGTTCTAGCTGGGCTAT 58.765 52.381 3.62 0.00 40.54 2.97
361 3625 1.681538 CTCGAGTTCTAGCTGGGCTA 58.318 55.000 3.62 0.00 40.44 3.93
362 3626 1.040339 CCTCGAGTTCTAGCTGGGCT 61.040 60.000 12.31 0.00 43.41 5.19
363 3627 1.439644 CCTCGAGTTCTAGCTGGGC 59.560 63.158 12.31 0.00 0.00 5.36
364 3628 1.040339 AGCCTCGAGTTCTAGCTGGG 61.040 60.000 12.31 0.00 31.23 4.45
365 3629 0.383949 GAGCCTCGAGTTCTAGCTGG 59.616 60.000 16.39 0.00 32.97 4.85
366 3630 0.383949 GGAGCCTCGAGTTCTAGCTG 59.616 60.000 16.39 0.00 32.97 4.24
367 3631 0.033991 TGGAGCCTCGAGTTCTAGCT 60.034 55.000 12.31 12.23 36.25 3.32
368 3632 1.036707 ATGGAGCCTCGAGTTCTAGC 58.963 55.000 12.31 7.10 0.00 3.42
369 3633 2.690497 TGAATGGAGCCTCGAGTTCTAG 59.310 50.000 12.31 0.00 0.00 2.43
370 3634 2.735151 TGAATGGAGCCTCGAGTTCTA 58.265 47.619 12.31 7.17 0.00 2.10
371 3635 1.561643 TGAATGGAGCCTCGAGTTCT 58.438 50.000 12.31 7.93 0.00 3.01
372 3636 2.611225 ATGAATGGAGCCTCGAGTTC 57.389 50.000 12.31 8.57 0.00 3.01
373 3637 3.034635 AGTATGAATGGAGCCTCGAGTT 58.965 45.455 12.31 0.00 0.00 3.01
374 3638 2.625790 GAGTATGAATGGAGCCTCGAGT 59.374 50.000 12.31 0.00 0.00 4.18
375 3639 2.625314 TGAGTATGAATGGAGCCTCGAG 59.375 50.000 5.13 5.13 0.00 4.04
376 3640 2.666317 TGAGTATGAATGGAGCCTCGA 58.334 47.619 0.00 0.00 0.00 4.04
377 3641 3.459232 TTGAGTATGAATGGAGCCTCG 57.541 47.619 0.00 0.00 0.00 4.63
378 3642 6.705863 AAATTTGAGTATGAATGGAGCCTC 57.294 37.500 0.00 0.00 0.00 4.70
379 3643 7.486407 AAAAATTTGAGTATGAATGGAGCCT 57.514 32.000 0.00 0.00 0.00 4.58
380 3644 8.250332 TGTAAAAATTTGAGTATGAATGGAGCC 58.750 33.333 0.00 0.00 0.00 4.70
381 3645 9.638239 TTGTAAAAATTTGAGTATGAATGGAGC 57.362 29.630 0.00 0.00 0.00 4.70
392 3656 8.888716 GTTCCACCAATTTGTAAAAATTTGAGT 58.111 29.630 8.74 1.98 30.51 3.41
393 3657 8.887717 TGTTCCACCAATTTGTAAAAATTTGAG 58.112 29.630 8.74 2.00 30.51 3.02
394 3658 8.792830 TGTTCCACCAATTTGTAAAAATTTGA 57.207 26.923 8.74 0.00 30.51 2.69
395 3659 8.672815 ACTGTTCCACCAATTTGTAAAAATTTG 58.327 29.630 0.53 1.09 30.51 2.32
396 3660 8.800370 ACTGTTCCACCAATTTGTAAAAATTT 57.200 26.923 0.53 0.00 30.51 1.82
397 3661 8.800370 AACTGTTCCACCAATTTGTAAAAATT 57.200 26.923 0.00 0.00 32.97 1.82
398 3662 9.541143 CTAACTGTTCCACCAATTTGTAAAAAT 57.459 29.630 0.00 0.00 0.00 1.82
399 3663 7.982354 CCTAACTGTTCCACCAATTTGTAAAAA 59.018 33.333 0.00 0.00 0.00 1.94
400 3664 7.418025 CCCTAACTGTTCCACCAATTTGTAAAA 60.418 37.037 0.00 0.00 0.00 1.52
401 3665 6.041069 CCCTAACTGTTCCACCAATTTGTAAA 59.959 38.462 0.00 0.00 0.00 2.01
402 3666 5.536916 CCCTAACTGTTCCACCAATTTGTAA 59.463 40.000 0.00 0.00 0.00 2.41
403 3667 5.074115 CCCTAACTGTTCCACCAATTTGTA 58.926 41.667 0.00 0.00 0.00 2.41
404 3668 3.895041 CCCTAACTGTTCCACCAATTTGT 59.105 43.478 0.00 0.00 0.00 2.83
405 3669 4.148838 TCCCTAACTGTTCCACCAATTTG 58.851 43.478 0.00 0.00 0.00 2.32
406 3670 4.463050 TCCCTAACTGTTCCACCAATTT 57.537 40.909 0.00 0.00 0.00 1.82
407 3671 4.463050 TTCCCTAACTGTTCCACCAATT 57.537 40.909 0.00 0.00 0.00 2.32
408 3672 4.202673 ACATTCCCTAACTGTTCCACCAAT 60.203 41.667 0.00 0.00 0.00 3.16
409 3673 3.139397 ACATTCCCTAACTGTTCCACCAA 59.861 43.478 0.00 0.00 0.00 3.67
410 3674 2.714250 ACATTCCCTAACTGTTCCACCA 59.286 45.455 0.00 0.00 0.00 4.17
411 3675 3.434940 ACATTCCCTAACTGTTCCACC 57.565 47.619 0.00 0.00 0.00 4.61
412 3676 4.022329 CCAAACATTCCCTAACTGTTCCAC 60.022 45.833 0.00 0.00 32.18 4.02
413 3677 4.148838 CCAAACATTCCCTAACTGTTCCA 58.851 43.478 0.00 0.00 32.18 3.53
414 3678 4.149598 ACCAAACATTCCCTAACTGTTCC 58.850 43.478 0.00 0.00 32.18 3.62
415 3679 5.528870 CAACCAAACATTCCCTAACTGTTC 58.471 41.667 0.00 0.00 32.18 3.18
416 3680 4.202212 GCAACCAAACATTCCCTAACTGTT 60.202 41.667 0.00 0.00 34.71 3.16
417 3681 3.320826 GCAACCAAACATTCCCTAACTGT 59.679 43.478 0.00 0.00 0.00 3.55
418 3682 3.306019 GGCAACCAAACATTCCCTAACTG 60.306 47.826 0.00 0.00 0.00 3.16
419 3683 2.897326 GGCAACCAAACATTCCCTAACT 59.103 45.455 0.00 0.00 0.00 2.24
420 3684 2.897326 AGGCAACCAAACATTCCCTAAC 59.103 45.455 0.00 0.00 37.17 2.34
427 3691 1.337074 CGATGCAGGCAACCAAACATT 60.337 47.619 0.00 0.00 37.17 2.71
428 3692 0.244450 CGATGCAGGCAACCAAACAT 59.756 50.000 0.00 0.00 37.17 2.71
491 3755 0.467290 GCCCAACAGTGAAACCAGGA 60.467 55.000 0.00 0.00 37.80 3.86
570 3834 1.373497 CTGGCTCGCGAGAAACTGT 60.373 57.895 38.74 0.00 41.32 3.55
676 3941 1.448985 GGTGACGCTAGATTTGGCAA 58.551 50.000 0.00 0.00 0.00 4.52
677 3942 0.392461 GGGTGACGCTAGATTTGGCA 60.392 55.000 0.00 0.00 0.00 4.92
720 3987 0.034059 AGAAAGTCGTGGTGAGGCAG 59.966 55.000 0.00 0.00 0.00 4.85
722 3989 1.149148 GAAGAAAGTCGTGGTGAGGC 58.851 55.000 0.00 0.00 0.00 4.70
723 3990 1.608283 GGGAAGAAAGTCGTGGTGAGG 60.608 57.143 0.00 0.00 0.00 3.86
724 3991 1.344763 AGGGAAGAAAGTCGTGGTGAG 59.655 52.381 0.00 0.00 0.00 3.51
725 3992 1.420430 AGGGAAGAAAGTCGTGGTGA 58.580 50.000 0.00 0.00 0.00 4.02
726 3993 2.299297 AGTAGGGAAGAAAGTCGTGGTG 59.701 50.000 0.00 0.00 0.00 4.17
727 3994 2.299297 CAGTAGGGAAGAAAGTCGTGGT 59.701 50.000 0.00 0.00 0.00 4.16
728 3995 2.931320 GCAGTAGGGAAGAAAGTCGTGG 60.931 54.545 0.00 0.00 0.00 4.94
729 3996 2.338500 GCAGTAGGGAAGAAAGTCGTG 58.662 52.381 0.00 0.00 0.00 4.35
730 3997 1.275573 GGCAGTAGGGAAGAAAGTCGT 59.724 52.381 0.00 0.00 0.00 4.34
731 3998 1.550976 AGGCAGTAGGGAAGAAAGTCG 59.449 52.381 0.00 0.00 0.00 4.18
732 3999 2.567615 TGAGGCAGTAGGGAAGAAAGTC 59.432 50.000 0.00 0.00 0.00 3.01
820 4116 4.619320 TGGCCAACAGCAAGGGGG 62.619 66.667 0.61 0.00 46.50 5.40
1063 4369 3.340928 CTCTCTGGTGCATGAACATGAA 58.659 45.455 17.40 5.20 41.20 2.57
1097 4403 1.956629 GCGGATCGAAGGTCTCCCAA 61.957 60.000 0.00 0.00 0.00 4.12
1109 4415 1.270305 ACATTGGACCATAGCGGATCG 60.270 52.381 0.00 0.00 38.63 3.69
1134 4441 0.397254 GGATCCTCTCCTGTTCCCGA 60.397 60.000 3.84 0.00 41.29 5.14
1229 4537 1.768275 TGAAGGTCTCAACAAGCCTGA 59.232 47.619 0.00 0.00 33.46 3.86
1376 4685 4.202172 GCTTGAAGTACCTAGAGATGGTCC 60.202 50.000 0.00 0.00 38.88 4.46
1457 4766 1.676014 CGTGAATCTTGGGTGGAGTCC 60.676 57.143 0.73 0.73 0.00 3.85
1559 4870 2.699954 AGCCTGTGTTAATCCTCAACG 58.300 47.619 0.00 0.00 0.00 4.10
1659 4971 0.044092 TGCTTCCTCCCCCTGTATGA 59.956 55.000 0.00 0.00 0.00 2.15
1825 5142 2.420687 CCAGCATCTCCAAGGTAGAACC 60.421 54.545 0.00 0.00 38.99 3.62
1864 5181 2.348472 TCCTGAAGGGTGGAAGAACAT 58.652 47.619 0.00 0.00 36.25 2.71
1941 5258 4.629200 GGAGTGTCTGAGATTAAACAGCTG 59.371 45.833 13.48 13.48 34.57 4.24
2095 5414 0.846427 AAAGCCCCACTGGAGGATCA 60.846 55.000 0.00 0.00 36.25 2.92
2115 5434 1.621317 TCCTCAGGCACGTGTTCAATA 59.379 47.619 18.38 0.00 0.00 1.90
2117 5436 0.249868 CTCCTCAGGCACGTGTTCAA 60.250 55.000 18.38 0.01 0.00 2.69
2162 5484 2.034066 CCACACAATGGCCGGAGT 59.966 61.111 5.05 0.00 43.24 3.85
2173 5495 1.133823 ACTGTCAAATGCCTCCACACA 60.134 47.619 0.00 0.00 0.00 3.72
2192 5514 5.351458 ACATTTTGTTCTTCCAAGCTTCAC 58.649 37.500 0.00 0.00 0.00 3.18
2196 5518 4.405358 TCCAACATTTTGTTCTTCCAAGCT 59.595 37.500 0.00 0.00 38.77 3.74
2213 5535 3.160585 CCTCTGCCCACTCCAACA 58.839 61.111 0.00 0.00 0.00 3.33
2315 5683 2.009774 GTTCATCGGTGTTGCTGCTAT 58.990 47.619 0.00 0.00 0.00 2.97
2537 5905 0.667453 TTTAACCCGGCGTTTGGTTC 59.333 50.000 19.83 0.00 43.63 3.62


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

AutoCloner maintained by Alex Coulton.