Multiple sequence alignment - TraesCS5A01G464800

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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 TraesCS5A01G464800 chr5A 100.000 3601 0 0 1 3601 644102826 644099226 0.000000e+00 6650
1 TraesCS5A01G464800 chr7B 94.861 3269 114 24 1 3225 732134279 732131021 0.000000e+00 5057
2 TraesCS5A01G464800 chr7B 94.648 3270 119 26 1 3225 732183157 732179899 0.000000e+00 5018
3 TraesCS5A01G464800 chr7B 96.511 1605 45 2 1631 3225 237928164 237926561 0.000000e+00 2643
4 TraesCS5A01G464800 chr7B 92.950 383 24 1 3213 3595 732179835 732179456 4.060000e-154 555
5 TraesCS5A01G464800 chr7A 94.708 3269 127 14 1 3225 712344480 712341214 0.000000e+00 5036
6 TraesCS5A01G464800 chr7A 84.599 2279 278 55 1 2237 681694242 681691995 0.000000e+00 2196
7 TraesCS5A01G464800 chr7A 93.995 383 23 0 3213 3595 712341141 712340759 6.700000e-162 580
8 TraesCS5A01G464800 chr3B 94.589 3271 118 23 1 3225 23791523 23788266 0.000000e+00 5005
9 TraesCS5A01G464800 chr3B 96.108 2749 84 12 477 3213 444139726 444142463 0.000000e+00 4462
10 TraesCS5A01G464800 chr3B 95.687 1136 37 3 2100 3225 20815401 20816534 0.000000e+00 1816
11 TraesCS5A01G464800 chr3B 93.473 383 22 1 3213 3595 23788193 23787814 1.880000e-157 566
12 TraesCS5A01G464800 chr3B 94.475 362 17 1 3213 3574 20816607 20816965 4.060000e-154 555
13 TraesCS5A01G464800 chr3B 92.950 383 24 1 3213 3595 444142547 444142926 4.060000e-154 555
14 TraesCS5A01G464800 chr4D 94.407 3272 113 19 1 3225 8878542 8875294 0.000000e+00 4964
15 TraesCS5A01G464800 chr4D 93.963 381 20 1 3215 3595 8875219 8874842 1.120000e-159 573
16 TraesCS5A01G464800 chr6D 93.501 3308 127 28 1 3225 452939851 452943153 0.000000e+00 4837
17 TraesCS5A01G464800 chr6D 90.838 513 42 4 12 523 39081855 39082363 0.000000e+00 682
18 TraesCS5A01G464800 chr7D 93.639 3270 117 24 1 3225 528810214 528806991 0.000000e+00 4802
19 TraesCS5A01G464800 chr7D 95.467 2603 97 9 638 3225 614686742 614689338 0.000000e+00 4133
20 TraesCS5A01G464800 chr7D 90.244 697 33 23 1 664 156195209 156195903 0.000000e+00 878
21 TraesCS5A01G464800 chr7D 88.617 694 42 12 4 664 614917129 614916440 0.000000e+00 809
22 TraesCS5A01G464800 chr7D 93.995 383 20 1 3213 3595 528806918 528806539 8.670000e-161 577
23 TraesCS5A01G464800 chr1D 84.366 1388 163 35 2 1365 451281120 451282477 0.000000e+00 1312
24 TraesCS5A01G464800 chrUn 95.368 734 23 2 2502 3225 402351672 402350940 0.000000e+00 1157
25 TraesCS5A01G464800 chr5B 91.250 560 33 10 1 558 668202762 668203307 0.000000e+00 749
26 TraesCS5A01G464800 chr4A 90.329 517 46 4 2 515 620745270 620744755 0.000000e+00 675
27 TraesCS5A01G464800 chr6B 89.423 520 50 4 1 515 134391037 134390518 0.000000e+00 651
28 TraesCS5A01G464800 chr6B 93.995 383 20 2 3213 3595 703250361 703249982 8.670000e-161 577
29 TraesCS5A01G464800 chr1B 93.211 383 22 2 3213 3595 58495670 58495292 8.730000e-156 560


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 TraesCS5A01G464800 chr5A 644099226 644102826 3600 True 6650.0 6650 100.0000 1 3601 1 chr5A.!!$R1 3600
1 TraesCS5A01G464800 chr7B 732131021 732134279 3258 True 5057.0 5057 94.8610 1 3225 1 chr7B.!!$R2 3224
2 TraesCS5A01G464800 chr7B 732179456 732183157 3701 True 2786.5 5018 93.7990 1 3595 2 chr7B.!!$R3 3594
3 TraesCS5A01G464800 chr7B 237926561 237928164 1603 True 2643.0 2643 96.5110 1631 3225 1 chr7B.!!$R1 1594
4 TraesCS5A01G464800 chr7A 712340759 712344480 3721 True 2808.0 5036 94.3515 1 3595 2 chr7A.!!$R2 3594
5 TraesCS5A01G464800 chr7A 681691995 681694242 2247 True 2196.0 2196 84.5990 1 2237 1 chr7A.!!$R1 2236
6 TraesCS5A01G464800 chr3B 23787814 23791523 3709 True 2785.5 5005 94.0310 1 3595 2 chr3B.!!$R1 3594
7 TraesCS5A01G464800 chr3B 444139726 444142926 3200 False 2508.5 4462 94.5290 477 3595 2 chr3B.!!$F2 3118
8 TraesCS5A01G464800 chr3B 20815401 20816965 1564 False 1185.5 1816 95.0810 2100 3574 2 chr3B.!!$F1 1474
9 TraesCS5A01G464800 chr4D 8874842 8878542 3700 True 2768.5 4964 94.1850 1 3595 2 chr4D.!!$R1 3594
10 TraesCS5A01G464800 chr6D 452939851 452943153 3302 False 4837.0 4837 93.5010 1 3225 1 chr6D.!!$F2 3224
11 TraesCS5A01G464800 chr6D 39081855 39082363 508 False 682.0 682 90.8380 12 523 1 chr6D.!!$F1 511
12 TraesCS5A01G464800 chr7D 614686742 614689338 2596 False 4133.0 4133 95.4670 638 3225 1 chr7D.!!$F2 2587
13 TraesCS5A01G464800 chr7D 528806539 528810214 3675 True 2689.5 4802 93.8170 1 3595 2 chr7D.!!$R2 3594
14 TraesCS5A01G464800 chr7D 156195209 156195903 694 False 878.0 878 90.2440 1 664 1 chr7D.!!$F1 663
15 TraesCS5A01G464800 chr7D 614916440 614917129 689 True 809.0 809 88.6170 4 664 1 chr7D.!!$R1 660
16 TraesCS5A01G464800 chr1D 451281120 451282477 1357 False 1312.0 1312 84.3660 2 1365 1 chr1D.!!$F1 1363
17 TraesCS5A01G464800 chrUn 402350940 402351672 732 True 1157.0 1157 95.3680 2502 3225 1 chrUn.!!$R1 723
18 TraesCS5A01G464800 chr5B 668202762 668203307 545 False 749.0 749 91.2500 1 558 1 chr5B.!!$F1 557
19 TraesCS5A01G464800 chr4A 620744755 620745270 515 True 675.0 675 90.3290 2 515 1 chr4A.!!$R1 513
20 TraesCS5A01G464800 chr6B 134390518 134391037 519 True 651.0 651 89.4230 1 515 1 chr6B.!!$R1 514

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
19 20 0.035439 AACCCTACTGCCAATGTCCG 60.035 55.0 0.0 0.0 0.0 4.79 F
211 218 0.107703 TTTGCGGATCGAGATGGCTT 60.108 50.0 0.0 0.0 0.0 4.35 F
1884 2023 0.836400 AAGGTCTTCTCGGGCAAGGA 60.836 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2023 1.165270 GGCCTTGTACATCGCACTTT 58.835 50.000 14.55 0.0 0.00 2.66 R
2020 2161 1.754803 CCCAAGCTCTATCGTGGTACA 59.245 52.381 0.00 0.0 34.42 2.90 R
2755 2912 0.773644 AGCTTGTTGTCACCCTCCAT 59.226 50.000 0.00 0.0 0.00 3.41 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
19 20 0.035439 AACCCTACTGCCAATGTCCG 60.035 55.000 0.00 0.00 0.00 4.79
41 43 3.866356 GGTAAGTGCCGAACGGTC 58.134 61.111 14.63 7.73 37.65 4.79
211 218 0.107703 TTTGCGGATCGAGATGGCTT 60.108 50.000 0.00 0.00 0.00 4.35
275 284 8.553696 TCGTTTTAGTTAAGAAGCTTTCGATTT 58.446 29.630 0.00 0.00 34.02 2.17
312 322 5.127682 GGCACAAGATGAACCCTATTTCATT 59.872 40.000 0.15 0.00 44.59 2.57
584 634 2.104451 AGATGAGGTGATGAGGTGATGC 59.896 50.000 0.00 0.00 0.00 3.91
857 976 2.548057 CCGGCGATTGCACTAATTACAT 59.452 45.455 9.30 0.00 45.35 2.29
1066 1186 1.608109 TGAACTACGACAACCGCTACA 59.392 47.619 0.00 0.00 43.32 2.74
1289 1409 1.557371 TCTCATTGGGTGCGTGGATAA 59.443 47.619 0.00 0.00 0.00 1.75
1516 1637 2.102588 GACAACGCCCTATGGATGTACT 59.897 50.000 0.00 0.00 0.00 2.73
1587 1708 2.079158 CTCGTGTACCTCTACCGTTCA 58.921 52.381 0.00 0.00 0.00 3.18
1884 2023 0.836400 AAGGTCTTCTCGGGCAAGGA 60.836 55.000 0.00 0.00 0.00 3.36
1997 2138 7.675962 ATACTTTCACGGTTGCTAAACAATA 57.324 32.000 0.00 0.00 41.27 1.90
2020 2161 5.508280 TTTGTATAGGTTAACTGGTGGCT 57.492 39.130 5.42 0.00 0.00 4.75
2180 2321 1.678627 GTATTGCAACACACACCACCA 59.321 47.619 0.00 0.00 0.00 4.17
2317 2464 0.548031 CCCCTATGCAGGAAGAGCAA 59.452 55.000 0.00 0.00 45.91 3.91
2318 2465 1.144503 CCCCTATGCAGGAAGAGCAAT 59.855 52.381 0.00 0.00 45.91 3.56
2482 2629 0.874390 GGCATCAAGTTTCGTCTGCA 59.126 50.000 0.00 0.00 0.00 4.41
2709 2866 0.745845 AGGCCGCAGAGCTAAACATG 60.746 55.000 0.00 0.00 0.00 3.21
2736 2893 3.188786 GACGGCTCGAATGCGCTT 61.189 61.111 9.73 0.00 37.46 4.68
2755 2912 2.409064 TAGTTCTGACCCTGGAACCA 57.591 50.000 0.00 0.00 41.69 3.67
2867 3024 5.801947 GCCACATGTTCTTACTTATTTGCAG 59.198 40.000 0.00 0.00 0.00 4.41
3197 3354 1.135139 CGACGATGATGGACCTCAACT 59.865 52.381 0.00 0.00 0.00 3.16
3214 3371 1.673665 CTGACTCAGCCAACCCAGC 60.674 63.158 0.00 0.00 0.00 4.85
3241 3482 1.959226 GGCCGCTCGAAGACAAACA 60.959 57.895 0.00 0.00 0.00 2.83
3242 3483 1.503818 GGCCGCTCGAAGACAAACAA 61.504 55.000 0.00 0.00 0.00 2.83
3243 3484 0.110644 GCCGCTCGAAGACAAACAAG 60.111 55.000 0.00 0.00 0.00 3.16
3482 3726 5.922053 TGCTGTGCTTATCTATCTGTGATT 58.078 37.500 0.00 0.00 0.00 2.57
3528 3772 1.035139 AGCAAGCAACTGAACTTGGG 58.965 50.000 5.04 0.00 42.82 4.12
3547 3791 4.810345 TGGGAAAATAAAACACAGGACCT 58.190 39.130 0.00 0.00 0.00 3.85
3551 3795 6.265876 GGGAAAATAAAACACAGGACCTTACA 59.734 38.462 0.00 0.00 0.00 2.41
3559 3803 1.229082 AGGACCTTACAGCCACGGA 60.229 57.895 0.00 0.00 0.00 4.69
3575 3819 4.814294 GACGCTGGCGGTAGGGTG 62.814 72.222 18.99 0.00 42.96 4.61
3578 3822 3.391382 GCTGGCGGTAGGGTGTCT 61.391 66.667 0.00 0.00 0.00 3.41
3581 3825 1.305802 TGGCGGTAGGGTGTCTCAT 60.306 57.895 0.00 0.00 0.00 2.90
3582 3826 1.144057 GGCGGTAGGGTGTCTCATG 59.856 63.158 0.00 0.00 0.00 3.07
3595 3839 1.221840 CTCATGCTACCGCCAACCT 59.778 57.895 0.00 0.00 34.43 3.50
3596 3840 0.464036 CTCATGCTACCGCCAACCTA 59.536 55.000 0.00 0.00 34.43 3.08
3597 3841 1.070758 CTCATGCTACCGCCAACCTAT 59.929 52.381 0.00 0.00 34.43 2.57
3598 3842 1.070134 TCATGCTACCGCCAACCTATC 59.930 52.381 0.00 0.00 34.43 2.08
3599 3843 0.033504 ATGCTACCGCCAACCTATCG 59.966 55.000 0.00 0.00 34.43 2.92
3600 3844 1.954651 GCTACCGCCAACCTATCGC 60.955 63.158 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 4.832608 CCCTGCGGGCTTACGACC 62.833 72.222 5.85 0.00 35.35 4.79
211 218 4.868067 AGAGCTTACTTTTCTCGTTTCGA 58.132 39.130 0.00 0.00 32.42 3.71
275 284 2.816672 TCTTGTGCCAAATAATGCGTCA 59.183 40.909 0.00 0.00 0.00 4.35
482 532 5.315348 TCACCACATCAACTCATCAATCAA 58.685 37.500 0.00 0.00 0.00 2.57
584 634 3.073678 TCATCTTCAAACCACATCACCG 58.926 45.455 0.00 0.00 0.00 4.94
810 925 2.840753 GGGGGCCTCCTGAAACACA 61.841 63.158 17.08 0.00 35.33 3.72
1066 1186 2.037772 CGGCTCTCCTGTAATATGGCTT 59.962 50.000 0.00 0.00 0.00 4.35
1130 1250 2.280797 GAGCCGTGTGGACAAGCA 60.281 61.111 5.99 0.00 37.49 3.91
1182 1302 2.915604 ACATGGGAGATGGAAAGAGTGT 59.084 45.455 0.00 0.00 0.00 3.55
1289 1409 1.674057 CTGTCCGGCCAGTTCTTCT 59.326 57.895 3.79 0.00 0.00 2.85
1444 1564 6.043938 TCTGTGAAAAGAAACCATAGGTAGGT 59.956 38.462 0.00 0.00 42.34 3.08
1462 1582 2.104792 CAGGAAAGACCACCTCTGTGAA 59.895 50.000 0.00 0.00 45.76 3.18
1516 1637 1.841556 AGTCGGCCAGGAAGTCCAA 60.842 57.895 2.24 0.00 38.89 3.53
1571 1692 4.697352 GTCTTACTGAACGGTAGAGGTACA 59.303 45.833 0.00 0.00 0.00 2.90
1587 1708 5.194432 AGGTGAGATGTATGACGTCTTACT 58.806 41.667 30.33 20.61 44.99 2.24
1884 2023 1.165270 GGCCTTGTACATCGCACTTT 58.835 50.000 14.55 0.00 0.00 2.66
1997 2138 5.885912 CAGCCACCAGTTAACCTATACAAAT 59.114 40.000 0.88 0.00 0.00 2.32
2020 2161 1.754803 CCCAAGCTCTATCGTGGTACA 59.245 52.381 0.00 0.00 34.42 2.90
2180 2321 4.643387 GTGTCGTGGGGCCTTGCT 62.643 66.667 0.84 0.00 0.00 3.91
2317 2464 7.450014 AGTCCAATATCGACTGAGAATACTGAT 59.550 37.037 4.94 0.00 39.14 2.90
2318 2465 6.773200 AGTCCAATATCGACTGAGAATACTGA 59.227 38.462 4.94 0.00 39.14 3.41
2482 2629 1.826024 GTCCATCGTGGCCTCAGAT 59.174 57.895 3.32 5.33 37.47 2.90
2506 2653 1.340308 CCTGAAGTGATGCCATGTCCA 60.340 52.381 0.00 0.00 0.00 4.02
2736 2893 2.409064 TGGTTCCAGGGTCAGAACTA 57.591 50.000 3.22 0.00 41.69 2.24
2755 2912 0.773644 AGCTTGTTGTCACCCTCCAT 59.226 50.000 0.00 0.00 0.00 3.41
2867 3024 2.026262 TGACTTGGATCAGGTTTAGGGC 60.026 50.000 0.00 0.00 0.00 5.19
2961 3118 2.616330 ATGCACGTCAACCAAGGCG 61.616 57.895 0.00 0.00 0.00 5.52
3197 3354 2.431683 GCTGGGTTGGCTGAGTCA 59.568 61.111 0.00 0.00 0.00 3.41
3241 3482 4.496336 GGCGGCATGCTCCTCCTT 62.496 66.667 18.92 0.00 45.43 3.36
3243 3484 4.802051 TTGGCGGCATGCTCCTCC 62.802 66.667 18.92 13.43 45.43 4.30
3331 3575 2.910319 AGGTAGCAATAACAGGACACCA 59.090 45.455 0.00 0.00 0.00 4.17
3461 3705 7.714377 AGGAAAATCACAGATAGATAAGCACAG 59.286 37.037 0.00 0.00 0.00 3.66
3528 3772 6.861572 GCTGTAAGGTCCTGTGTTTTATTTTC 59.138 38.462 0.00 0.00 0.00 2.29
3582 3826 1.954651 GCGATAGGTTGGCGGTAGC 60.955 63.158 0.00 0.00 44.18 3.58


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

AutoCloner maintained by Alex Coulton.