Multiple sequence alignment - TraesCS1D01G033900

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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 TraesCS1D01G033900 chr1D 100.000 3250 0 0 1 3250 13854226 13850977 0.000000e+00 6002.0
1 TraesCS1D01G033900 chr1D 96.945 1375 27 7 1876 3250 13970056 13968697 0.000000e+00 2292.0
2 TraesCS1D01G033900 chr1D 96.145 1375 24 2 1876 3250 14001355 14000010 0.000000e+00 2218.0
3 TraesCS1D01G033900 chr1D 90.452 1372 99 12 907 2273 14188339 14186995 0.000000e+00 1779.0
4 TraesCS1D01G033900 chr1D 94.387 1069 38 5 1 1047 14002420 14001352 0.000000e+00 1622.0
5 TraesCS1D01G033900 chr1D 93.920 1069 43 1 1 1047 13971121 13970053 0.000000e+00 1594.0
6 TraesCS1D01G033900 chr1B 92.070 2875 173 23 380 3209 20292351 20295215 0.000000e+00 3995.0
7 TraesCS1D01G033900 chr1B 94.348 1840 89 7 631 2462 20061452 20059620 0.000000e+00 2808.0
8 TraesCS1D01G033900 chr1B 89.428 927 82 10 907 1828 20127543 20126628 0.000000e+00 1155.0
9 TraesCS1D01G033900 chr1B 90.262 534 38 8 2462 2988 20059291 20058765 0.000000e+00 686.0
10 TraesCS1D01G033900 chr1B 90.500 400 34 3 1881 2276 20102635 20102236 2.870000e-145 525.0
11 TraesCS1D01G033900 chr1B 89.349 169 18 0 241 409 20048488 20048320 2.540000e-51 213.0
12 TraesCS1D01G033900 chr1B 92.405 79 6 0 165 243 20292152 20292230 2.650000e-21 113.0
13 TraesCS1D01G033900 chr1A 91.508 2885 183 29 407 3250 14801094 14798231 0.000000e+00 3914.0
14 TraesCS1D01G033900 chr1A 87.052 1730 144 40 605 2298 14858676 14856991 0.000000e+00 1881.0
15 TraesCS1D01G033900 chr1A 81.017 295 37 8 133 409 14841019 14840726 1.960000e-52 217.0
16 TraesCS1D01G033900 chr7A 92.308 39 3 0 1892 1930 574129332 574129370 4.530000e-04 56.5


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 TraesCS1D01G033900 chr1D 13850977 13854226 3249 True 6002 6002 100.0000 1 3250 1 chr1D.!!$R1 3249
1 TraesCS1D01G033900 chr1D 13968697 13971121 2424 True 1943 2292 95.4325 1 3250 2 chr1D.!!$R3 3249
2 TraesCS1D01G033900 chr1D 14000010 14002420 2410 True 1920 2218 95.2660 1 3250 2 chr1D.!!$R4 3249
3 TraesCS1D01G033900 chr1D 14186995 14188339 1344 True 1779 1779 90.4520 907 2273 1 chr1D.!!$R2 1366
4 TraesCS1D01G033900 chr1B 20292152 20295215 3063 False 2054 3995 92.2375 165 3209 2 chr1B.!!$F1 3044
5 TraesCS1D01G033900 chr1B 20058765 20061452 2687 True 1747 2808 92.3050 631 2988 2 chr1B.!!$R4 2357
6 TraesCS1D01G033900 chr1B 20126628 20127543 915 True 1155 1155 89.4280 907 1828 1 chr1B.!!$R3 921
7 TraesCS1D01G033900 chr1A 14798231 14801094 2863 True 3914 3914 91.5080 407 3250 1 chr1A.!!$R1 2843
8 TraesCS1D01G033900 chr1A 14856991 14858676 1685 True 1881 1881 87.0520 605 2298 1 chr1A.!!$R3 1693

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
260 283 1.134068 GCCTCCCAAATGACCTCCTAC 60.134 57.143 0.0 0.0 0.0 3.18 F
281 304 1.226831 GGCAACCCACAACACAACG 60.227 57.895 0.0 0.0 0.0 4.10 F
1091 1151 0.247736 TTTTGCCACACCTTTGCGTT 59.752 45.000 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1091 1151 0.320683 CAGTGCCATGGACTTGACGA 60.321 55.000 18.4 0.0 0.0 4.20 R
1614 1698 1.259142 TTATCCCGGCGAACACCTCA 61.259 55.000 9.3 0.0 0.0 3.86 R
2697 3156 2.149578 GGCGATTGATGCAGAGCTAAT 58.850 47.619 0.0 0.0 0.0 1.73 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
24 25 1.758440 GAGGGGCATACATCAGGCGA 61.758 60.000 0.00 0.00 33.74 5.54
218 219 4.092968 GCTCGAAACACACTCCGAATAAAT 59.907 41.667 0.00 0.00 0.00 1.40
221 222 7.622672 GCTCGAAACACACTCCGAATAAATAAA 60.623 37.037 0.00 0.00 0.00 1.40
247 270 3.089838 CCAATCACCAGCCTCCCA 58.910 61.111 0.00 0.00 0.00 4.37
260 283 1.134068 GCCTCCCAAATGACCTCCTAC 60.134 57.143 0.00 0.00 0.00 3.18
270 293 1.911702 GACCTCCTACCTGGCAACCC 61.912 65.000 0.00 0.00 35.26 4.11
281 304 1.226831 GGCAACCCACAACACAACG 60.227 57.895 0.00 0.00 0.00 4.10
286 318 1.358759 CCCACAACACAACGAAGGC 59.641 57.895 0.00 0.00 0.00 4.35
339 371 2.663826 AGATCTGCCGACTCTTTGTC 57.336 50.000 0.00 0.00 42.06 3.18
354 386 3.582647 TCTTTGTCAGATGGAACTAGGCA 59.417 43.478 0.00 0.00 0.00 4.75
359 391 3.125316 GTCAGATGGAACTAGGCAAAACG 59.875 47.826 0.00 0.00 0.00 3.60
542 574 6.870971 AAATATATTATGTTCCGCGTGGTT 57.129 33.333 16.01 1.44 36.30 3.67
584 616 6.532657 GCATGAATTTTGAGGTCCTAATGTTG 59.467 38.462 0.00 0.00 0.00 3.33
641 676 9.645059 CGATATTATCTTTTAGAGAATGCTCCA 57.355 33.333 0.00 0.00 42.30 3.86
658 693 4.454504 TGCTCCAACTTAAGATTTTCCGTC 59.545 41.667 10.09 0.00 0.00 4.79
915 972 6.070656 CCTCATAATTTGCCCCTCTTATGAA 58.929 40.000 0.00 0.00 39.07 2.57
1091 1151 0.247736 TTTTGCCACACCTTTGCGTT 59.752 45.000 0.00 0.00 0.00 4.84
1137 1197 1.059369 CGTGAAGCTTGGAATCGCG 59.941 57.895 2.10 3.37 40.15 5.87
1450 1534 4.341783 GGCTGCACCAGTGGCTCT 62.342 66.667 9.78 0.00 38.86 4.09
1522 1606 2.260434 GGAGCTTGTACGGCGTCA 59.740 61.111 19.21 12.17 34.52 4.35
1614 1698 0.534877 TTGCTGTCCGTGAATGCAGT 60.535 50.000 0.00 0.00 35.02 4.40
1740 1824 2.432510 GGAACTCCCACAGGTGATAGAG 59.567 54.545 0.00 6.74 34.14 2.43
1775 1859 1.024271 GGCACAGTTGAGCTTGTTGA 58.976 50.000 1.78 0.00 0.00 3.18
2334 2457 6.943146 TGTGGGTGATGCTTAAAGTTTGTATA 59.057 34.615 0.00 0.00 0.00 1.47
2697 3156 3.944650 TGTTGTTAACAGCTGCTTCTTCA 59.055 39.130 21.06 3.24 36.25 3.02
2985 3458 1.975680 GGGATTGCCCGATACCTTCTA 59.024 52.381 0.00 0.00 46.48 2.10
2990 3463 2.404559 TGCCCGATACCTTCTACCAAT 58.595 47.619 0.00 0.00 0.00 3.16
3113 3586 8.114331 ACAAATCTGCTTGATTGTATTCTCAA 57.886 30.769 6.35 0.00 43.99 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.306502 CGGGTACGGCCTGTATTAATGAT 60.307 47.826 0.00 0.00 38.84 2.45
65 66 1.138859 TGCTTGCTATGTACATCGCCT 59.861 47.619 24.72 0.64 0.00 5.52
239 262 0.551131 AGGAGGTCATTTGGGAGGCT 60.551 55.000 0.00 0.00 0.00 4.58
247 270 1.668826 TGCCAGGTAGGAGGTCATTT 58.331 50.000 0.00 0.00 41.22 2.32
260 283 1.326213 TTGTGTTGTGGGTTGCCAGG 61.326 55.000 0.00 0.00 0.00 4.45
270 293 0.732571 AGTGCCTTCGTTGTGTTGTG 59.267 50.000 0.00 0.00 0.00 3.33
281 304 0.938008 GCGGTATGCTAAGTGCCTTC 59.062 55.000 0.00 0.00 42.00 3.46
286 318 1.636340 GCACGCGGTATGCTAAGTG 59.364 57.895 12.47 0.00 43.27 3.16
295 327 3.291101 GAGTTCCTGGCACGCGGTA 62.291 63.158 12.47 0.00 0.00 4.02
339 371 3.334691 TCGTTTTGCCTAGTTCCATCTG 58.665 45.455 0.00 0.00 0.00 2.90
354 386 1.659794 GTGTGGCATGCCTCGTTTT 59.340 52.632 35.53 0.00 36.94 2.43
359 391 3.434319 CCACGTGTGGCATGCCTC 61.434 66.667 35.53 31.63 44.73 4.70
534 566 7.561556 CCTTAATATTTTCTACTAACCACGCG 58.438 38.462 3.53 3.53 0.00 6.01
536 568 8.428186 TGCCTTAATATTTTCTACTAACCACG 57.572 34.615 0.00 0.00 0.00 4.94
634 669 5.010282 ACGGAAAATCTTAAGTTGGAGCAT 58.990 37.500 1.63 0.00 0.00 3.79
639 674 5.941948 ACAGACGGAAAATCTTAAGTTGG 57.058 39.130 1.63 0.00 0.00 3.77
915 972 0.246635 GGACTGATAGCACCACACGT 59.753 55.000 0.00 0.00 0.00 4.49
1091 1151 0.320683 CAGTGCCATGGACTTGACGA 60.321 55.000 18.40 0.00 0.00 4.20
1450 1534 1.380515 CTCCCTCCTCCTCGCTCAA 60.381 63.158 0.00 0.00 0.00 3.02
1522 1606 1.262640 AATTCGGGGTCACGGCTACT 61.263 55.000 0.00 0.00 0.00 2.57
1614 1698 1.259142 TTATCCCGGCGAACACCTCA 61.259 55.000 9.30 0.00 0.00 3.86
1740 1824 4.787871 CCATCAGGCGAGATTCCC 57.212 61.111 0.00 0.00 0.00 3.97
1775 1859 3.760151 CACAAACTCCATCATGTCACCAT 59.240 43.478 0.00 0.00 0.00 3.55
2697 3156 2.149578 GGCGATTGATGCAGAGCTAAT 58.850 47.619 0.00 0.00 0.00 1.73
3083 3556 3.438087 ACAATCAAGCAGATTTGTCGAGG 59.562 43.478 2.06 0.00 44.48 4.63


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

AutoCloner maintained by Alex Coulton.