Multiple sequence alignment - TraesCS4A01G052900

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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 TraesCS4A01G052900 chr4A 100.000 4515 0 0 1 4515 44652806 44657320 0.000000e+00 8338.0
1 TraesCS4A01G052900 chr4A 95.667 3831 107 10 1 3792 44306861 44310671 0.000000e+00 6100.0
2 TraesCS4A01G052900 chr4A 96.343 3063 83 6 750 3792 44271704 44274757 0.000000e+00 5009.0
3 TraesCS4A01G052900 chr4A 97.750 2133 42 3 1664 3792 44785971 44788101 0.000000e+00 3668.0
4 TraesCS4A01G052900 chr4A 96.456 1665 25 11 1 1664 44784302 44785933 0.000000e+00 2717.0
5 TraesCS4A01G052900 chr4A 94.834 1142 42 6 1 1140 45017081 45018207 0.000000e+00 1766.0
6 TraesCS4A01G052900 chr4A 94.851 1107 40 9 1833 2938 45018248 45019338 0.000000e+00 1712.0
7 TraesCS4A01G052900 chr4A 94.332 741 18 2 3798 4515 44274913 44275652 0.000000e+00 1114.0
8 TraesCS4A01G052900 chr4A 93.927 741 20 3 3798 4515 44310827 44311565 0.000000e+00 1096.0
9 TraesCS4A01G052900 chr4A 92.162 740 15 9 3798 4515 44788257 44788975 0.000000e+00 1005.0
10 TraesCS4A01G052900 chr4A 89.047 703 39 13 3101 3792 45031715 45032390 0.000000e+00 837.0
11 TraesCS4A01G052900 chr4A 92.678 519 29 8 3988 4502 45032650 45033163 0.000000e+00 739.0
12 TraesCS4A01G052900 chr4A 95.035 141 7 0 2965 3105 45019335 45019475 5.880000e-54 222.0
13 TraesCS4A01G052900 chr4D 94.367 2308 77 18 121 2391 419986053 419983762 0.000000e+00 3493.0
14 TraesCS4A01G052900 chr4D 91.795 1170 58 19 2412 3548 419983778 419982614 0.000000e+00 1594.0
15 TraesCS4A01G052900 chr4D 95.055 182 6 3 1 181 419986220 419986041 2.660000e-72 283.0
16 TraesCS4A01G052900 chr3A 93.132 1325 55 15 886 2191 686680115 686681422 0.000000e+00 1910.0
17 TraesCS4A01G052900 chr3A 88.251 1132 78 21 2305 3409 686681429 686682532 0.000000e+00 1303.0
18 TraesCS4A01G052900 chr3A 85.818 1241 101 30 2340 3548 619504655 619503458 0.000000e+00 1247.0
19 TraesCS4A01G052900 chr3A 92.254 426 29 3 888 1311 619505734 619505311 6.460000e-168 601.0
20 TraesCS4A01G052900 chr3A 95.000 100 4 1 3449 3548 686682536 686682634 6.050000e-34 156.0
21 TraesCS4A01G052900 chr1A 88.057 1323 107 18 886 2178 496825139 496823838 0.000000e+00 1520.0
22 TraesCS4A01G052900 chr1A 90.456 241 22 1 2174 2413 496823163 496822923 2.620000e-82 316.0
23 TraesCS4A01G052900 chr5B 91.590 1094 76 9 1131 2217 99475481 99476565 0.000000e+00 1496.0
24 TraesCS4A01G052900 chr5B 92.750 400 27 2 3 401 646624310 646624708 1.090000e-160 577.0
25 TraesCS4A01G052900 chr5B 90.766 444 23 5 393 835 646624976 646625402 1.090000e-160 577.0
26 TraesCS4A01G052900 chr3B 87.155 1339 107 15 2254 3548 728798068 728799385 0.000000e+00 1459.0
27 TraesCS4A01G052900 chr3B 88.245 1208 95 18 1987 3191 633519277 633518114 0.000000e+00 1400.0
28 TraesCS4A01G052900 chr3B 91.473 903 56 12 1 887 129529013 129528116 0.000000e+00 1221.0
29 TraesCS4A01G052900 chr3B 90.169 356 32 3 3194 3548 633517810 633517457 1.140000e-125 460.0
30 TraesCS4A01G052900 chr3B 97.266 256 6 1 1375 1630 728796932 728797186 2.490000e-117 433.0
31 TraesCS4A01G052900 chr3B 90.840 262 18 4 886 1145 728796280 728796537 3.340000e-91 346.0
32 TraesCS4A01G052900 chr3B 78.182 275 38 10 4205 4470 743104946 743104685 6.050000e-34 156.0
33 TraesCS4A01G052900 chr3D 88.306 1240 88 19 2343 3548 549230438 549231654 0.000000e+00 1434.0
34 TraesCS4A01G052900 chr3D 87.971 981 70 18 1209 2178 542810040 542809097 0.000000e+00 1114.0
35 TraesCS4A01G052900 chr3D 95.257 506 21 3 1862 2365 549229922 549230426 0.000000e+00 798.0
36 TraesCS4A01G052900 chr3D 96.681 452 15 0 1131 1582 549229475 549229926 0.000000e+00 752.0
37 TraesCS4A01G052900 chr3D 94.656 262 12 2 886 1145 549229190 549229451 5.440000e-109 405.0
38 TraesCS4A01G052900 chr3D 81.717 361 52 11 3966 4318 431447695 431448049 5.710000e-74 289.0
39 TraesCS4A01G052900 chr3D 78.571 294 36 14 4199 4470 559606057 559605769 7.770000e-38 169.0
40 TraesCS4A01G052900 chr1B 87.231 1300 109 21 914 2178 537470311 537469034 0.000000e+00 1428.0
41 TraesCS4A01G052900 chr2B 92.575 431 23 3 408 832 107084489 107084916 1.070000e-170 610.0
42 TraesCS4A01G052900 chr2B 89.712 243 20 3 1 240 107082134 107082374 5.670000e-79 305.0
43 TraesCS4A01G052900 chr2B 95.706 163 7 0 248 410 107082451 107082613 3.460000e-66 263.0
44 TraesCS4A01G052900 chr1D 92.116 241 18 1 2174 2413 400389451 400389211 5.590000e-89 339.0
45 TraesCS4A01G052900 chr1D 88.168 262 29 2 886 1145 380607930 380608191 1.220000e-80 311.0
46 TraesCS4A01G052900 chr7A 77.342 587 94 31 3944 4515 60637088 60636526 1.220000e-80 311.0
47 TraesCS4A01G052900 chr6D 81.633 392 46 20 3945 4319 310874245 310874627 7.340000e-78 302.0
48 TraesCS4A01G052900 chr6D 88.272 162 16 3 222 380 467802277 467802438 1.660000e-44 191.0
49 TraesCS4A01G052900 chr6D 87.730 163 18 2 215 375 446478328 446478166 5.960000e-44 189.0
50 TraesCS4A01G052900 chr2D 78.308 461 66 21 3974 4410 424168877 424169327 2.680000e-67 267.0
51 TraesCS4A01G052900 chr7D 79.018 448 49 21 3958 4367 161462064 161462504 9.630000e-67 265.0
52 TraesCS4A01G052900 chr7D 86.517 89 10 2 3798 3886 399450557 399450471 3.720000e-16 97.1
53 TraesCS4A01G052900 chr7B 91.111 90 8 0 3798 3887 403419913 403419824 6.130000e-24 122.0


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 TraesCS4A01G052900 chr4A 44652806 44657320 4514 False 8338.000000 8338 100.000000 1 4515 1 chr4A.!!$F1 4514
1 TraesCS4A01G052900 chr4A 44306861 44311565 4704 False 3598.000000 6100 94.797000 1 4515 2 chr4A.!!$F3 4514
2 TraesCS4A01G052900 chr4A 44271704 44275652 3948 False 3061.500000 5009 95.337500 750 4515 2 chr4A.!!$F2 3765
3 TraesCS4A01G052900 chr4A 44784302 44788975 4673 False 2463.333333 3668 95.456000 1 4515 3 chr4A.!!$F4 4514
4 TraesCS4A01G052900 chr4A 45017081 45019475 2394 False 1233.333333 1766 94.906667 1 3105 3 chr4A.!!$F5 3104
5 TraesCS4A01G052900 chr4A 45031715 45033163 1448 False 788.000000 837 90.862500 3101 4502 2 chr4A.!!$F6 1401
6 TraesCS4A01G052900 chr4D 419982614 419986220 3606 True 1790.000000 3493 93.739000 1 3548 3 chr4D.!!$R1 3547
7 TraesCS4A01G052900 chr3A 686680115 686682634 2519 False 1123.000000 1910 92.127667 886 3548 3 chr3A.!!$F1 2662
8 TraesCS4A01G052900 chr3A 619503458 619505734 2276 True 924.000000 1247 89.036000 888 3548 2 chr3A.!!$R1 2660
9 TraesCS4A01G052900 chr1A 496822923 496825139 2216 True 918.000000 1520 89.256500 886 2413 2 chr1A.!!$R1 1527
10 TraesCS4A01G052900 chr5B 99475481 99476565 1084 False 1496.000000 1496 91.590000 1131 2217 1 chr5B.!!$F1 1086
11 TraesCS4A01G052900 chr5B 646624310 646625402 1092 False 577.000000 577 91.758000 3 835 2 chr5B.!!$F2 832
12 TraesCS4A01G052900 chr3B 129528116 129529013 897 True 1221.000000 1221 91.473000 1 887 1 chr3B.!!$R1 886
13 TraesCS4A01G052900 chr3B 633517457 633519277 1820 True 930.000000 1400 89.207000 1987 3548 2 chr3B.!!$R3 1561
14 TraesCS4A01G052900 chr3B 728796280 728799385 3105 False 746.000000 1459 91.753667 886 3548 3 chr3B.!!$F1 2662
15 TraesCS4A01G052900 chr3D 542809097 542810040 943 True 1114.000000 1114 87.971000 1209 2178 1 chr3D.!!$R1 969
16 TraesCS4A01G052900 chr3D 549229190 549231654 2464 False 847.250000 1434 93.725000 886 3548 4 chr3D.!!$F2 2662
17 TraesCS4A01G052900 chr1B 537469034 537470311 1277 True 1428.000000 1428 87.231000 914 2178 1 chr1B.!!$R1 1264
18 TraesCS4A01G052900 chr2B 107082134 107084916 2782 False 392.666667 610 92.664333 1 832 3 chr2B.!!$F1 831
19 TraesCS4A01G052900 chr7A 60636526 60637088 562 True 311.000000 311 77.342000 3944 4515 1 chr7A.!!$R1 571

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
745 3042 1.209504 TCCAGCCCATGTAGTGCTTAC 59.790 52.381 0.0 0.0 31.77 2.34 F
1073 3377 0.536260 AGAGAAGCGAGCAGAGCAAT 59.464 50.000 0.0 0.0 37.01 3.56 F
2130 5522 0.878416 TGAATTTCGGGCAAGGAACG 59.122 50.000 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 6688 1.681327 AGTTCGGGCCTTCTCGCTA 60.681 57.895 0.84 0.0 0.00 4.26 R
2837 7006 2.599408 TTACTCGGAGACTGGAGGTT 57.401 50.000 12.86 0.0 34.58 3.50 R
3895 8559 0.035458 CAGACACGAGGCTTCCCTTT 59.965 55.000 0.00 0.0 43.12 3.11 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
434 2724 2.026641 GCTTTGCTAATGGCCTGATCA 58.973 47.619 3.32 0.00 40.92 2.92
461 2751 1.224592 GCCATGACACGAAGGGGAT 59.775 57.895 0.00 0.00 0.00 3.85
640 2931 3.983044 ATTAGGAAAGCGAACAGGAGT 57.017 42.857 0.00 0.00 0.00 3.85
745 3042 1.209504 TCCAGCCCATGTAGTGCTTAC 59.790 52.381 0.00 0.00 31.77 2.34
924 3227 3.429141 CGCAAGGAGCAGCAGGTG 61.429 66.667 0.00 0.00 46.13 4.00
969 3272 4.643387 GTCCAGCACGGGCCACTT 62.643 66.667 5.73 0.00 42.56 3.16
1045 3349 2.033757 CAGAAGCCAGGCAGCTGT 59.966 61.111 15.80 0.00 44.11 4.40
1073 3377 0.536260 AGAGAAGCGAGCAGAGCAAT 59.464 50.000 0.00 0.00 37.01 3.56
1152 3501 4.535781 TCTCTCTCTCTCTCTGGATTTGG 58.464 47.826 0.00 0.00 0.00 3.28
2130 5522 0.878416 TGAATTTCGGGCAAGGAACG 59.122 50.000 0.00 0.00 0.00 3.95
2540 6688 1.529244 GGGGCGCCAATTGCTAGAT 60.529 57.895 30.85 0.00 38.05 1.98
2625 6773 4.265073 ACCTTCTGCTTACTGGCATTTAG 58.735 43.478 0.00 0.00 41.63 1.85
2808 6977 6.767456 TGCCAGGAATTATTGTTGAAAATGT 58.233 32.000 0.00 0.00 0.00 2.71
2814 6983 8.859090 AGGAATTATTGTTGAAAATGTGAGACA 58.141 29.630 0.00 0.00 0.00 3.41
2837 7006 4.093011 CTGGGGATTCCAACCAAAACATA 58.907 43.478 4.80 0.00 46.51 2.29
2852 7021 2.526888 ACATAACCTCCAGTCTCCGA 57.473 50.000 0.00 0.00 0.00 4.55
2854 7023 2.291670 ACATAACCTCCAGTCTCCGAGT 60.292 50.000 0.00 0.00 0.00 4.18
2953 7122 2.034221 GAAGCGTGAGGGCCCTTT 59.966 61.111 29.39 16.65 0.00 3.11
2963 7132 2.418083 GGGCCCTTTGATTGCCGAG 61.418 63.158 17.04 0.00 46.31 4.63
3084 7257 4.759183 GCTCTTTCTTTGTCCTTCTGTGAT 59.241 41.667 0.00 0.00 0.00 3.06
3117 7290 2.480555 CGTCTCGCCATGTTTGCC 59.519 61.111 0.00 0.00 0.00 4.52
3418 7895 0.543410 TTCCTGAGAACCGCCCACTA 60.543 55.000 0.00 0.00 0.00 2.74
3516 8026 4.713946 CCATGTGTGGCGTTAGGT 57.286 55.556 0.00 0.00 39.01 3.08
3792 8306 7.286316 ACAGAAACAAGAGATCTGGTGAAAAAT 59.714 33.333 0.00 0.00 43.79 1.82
3793 8307 7.594015 CAGAAACAAGAGATCTGGTGAAAAATG 59.406 37.037 0.00 0.00 37.51 2.32
3794 8308 6.966534 AACAAGAGATCTGGTGAAAAATGT 57.033 33.333 0.00 0.00 28.76 2.71
3795 8309 8.463930 AAACAAGAGATCTGGTGAAAAATGTA 57.536 30.769 0.00 0.00 28.76 2.29
3796 8310 8.641498 AACAAGAGATCTGGTGAAAAATGTAT 57.359 30.769 0.00 0.00 28.76 2.29
3915 8579 0.832135 AAGGGAAGCCTCGTGTCTGA 60.832 55.000 0.00 0.00 0.00 3.27
3942 8606 7.076175 AGGAGCCCCAGATAGATAGATATACAT 59.924 40.741 0.00 0.00 33.88 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 220 8.791675 TCTTTGCACATATTCAACTTATGTTCA 58.208 29.630 0.00 0.00 38.02 3.18
640 2931 1.100510 ACGTACTAGCCTCGAATGCA 58.899 50.000 9.05 0.00 0.00 3.96
711 3002 0.721718 GCTGGACACGCAGATGTAAC 59.278 55.000 0.00 0.00 31.24 2.50
745 3042 7.571059 CGCATTATTTTGTTTTGGAAAAGGAGG 60.571 37.037 0.00 0.00 0.00 4.30
923 3226 1.988539 TAAAGCCCTACCATTCCCCA 58.011 50.000 0.00 0.00 0.00 4.96
924 3227 2.716969 AGATAAAGCCCTACCATTCCCC 59.283 50.000 0.00 0.00 0.00 4.81
969 3272 3.309121 CCCTGGCTTCCCTTCATCTTTTA 60.309 47.826 0.00 0.00 0.00 1.52
1045 3349 1.670087 GCTCGCTTCTCTGCACTTACA 60.670 52.381 0.00 0.00 0.00 2.41
1152 3501 6.655062 TCAACAACACGAGTCAATTCATAAC 58.345 36.000 0.00 0.00 0.00 1.89
1886 5276 8.849168 ACAATTTTGATAGAAACATGTGAGACA 58.151 29.630 0.00 0.00 0.00 3.41
2039 5430 4.523083 ACCAGAACACAAAAGAGTTGCTA 58.477 39.130 0.00 0.00 0.00 3.49
2130 5522 5.002464 ACAGAAGATGCATAAACAATGGC 57.998 39.130 0.00 0.00 35.99 4.40
2540 6688 1.681327 AGTTCGGGCCTTCTCGCTA 60.681 57.895 0.84 0.00 0.00 4.26
2697 6846 4.175787 AGCTAAGACAACGACGAATCTT 57.824 40.909 0.00 9.73 35.60 2.40
2808 6977 3.492686 TGGAATCCCCAGTGTCTCA 57.507 52.632 0.00 0.00 40.82 3.27
2837 7006 2.599408 TTACTCGGAGACTGGAGGTT 57.401 50.000 12.86 0.00 34.58 3.50
2852 7021 5.413833 CACTCTCTCATTTTGCACCATTACT 59.586 40.000 0.00 0.00 0.00 2.24
2854 7023 4.701651 CCACTCTCTCATTTTGCACCATTA 59.298 41.667 0.00 0.00 0.00 1.90
3063 7236 5.528690 CACATCACAGAAGGACAAAGAAAGA 59.471 40.000 0.00 0.00 0.00 2.52
3084 7257 0.380378 GACGCCAGACAAAAAGCACA 59.620 50.000 0.00 0.00 0.00 4.57
3117 7290 5.055812 ACCTGCAACAATTAACCACAATTG 58.944 37.500 3.24 3.24 46.66 2.32
3418 7895 5.008712 GTCCTTGACTTCAAAGAAATCCGTT 59.991 40.000 0.00 0.00 35.15 4.44
3792 8306 2.506231 TCAGGCCGACCCATTTTATACA 59.494 45.455 0.00 0.00 36.11 2.29
3793 8307 3.202829 TCAGGCCGACCCATTTTATAC 57.797 47.619 0.00 0.00 36.11 1.47
3794 8308 4.141367 TGAATCAGGCCGACCCATTTTATA 60.141 41.667 0.00 0.00 36.11 0.98
3795 8309 3.222603 GAATCAGGCCGACCCATTTTAT 58.777 45.455 0.00 0.00 36.11 1.40
3796 8310 2.025793 TGAATCAGGCCGACCCATTTTA 60.026 45.455 0.00 0.00 36.11 1.52
3895 8559 0.035458 CAGACACGAGGCTTCCCTTT 59.965 55.000 0.00 0.00 43.12 3.11
3915 8579 4.708420 ATCTATCTATCTGGGGCTCCTT 57.292 45.455 3.07 0.00 0.00 3.36
4307 8995 8.751335 ACACGTTCAACATTGTCAATATTTTTC 58.249 29.630 0.00 0.00 0.00 2.29
4308 8996 8.641499 ACACGTTCAACATTGTCAATATTTTT 57.359 26.923 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.