Multiple sequence alignment - TraesCS5A01G043200

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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 TraesCS5A01G043200 chr5A 100.000 4507 0 0 1 4507 39245504 39240998 0.000000e+00 8323.0
1 TraesCS5A01G043200 chr5A 89.545 220 16 5 4174 4386 708833768 708833549 5.740000e-69 272.0
2 TraesCS5A01G043200 chr5A 87.121 132 12 3 4000 4126 490149654 490149785 1.310000e-30 145.0
3 TraesCS5A01G043200 chr5A 78.469 209 35 7 2060 2266 36365651 36365451 1.320000e-25 128.0
4 TraesCS5A01G043200 chr5A 95.238 63 3 0 4441 4503 551344177 551344115 2.870000e-17 100.0
5 TraesCS5A01G043200 chr5D 97.061 4526 85 19 1 4507 50201534 50197038 0.000000e+00 7577.0
6 TraesCS5A01G043200 chr5D 96.047 4554 84 26 1 4507 49764877 49760373 0.000000e+00 7324.0
7 TraesCS5A01G043200 chr5D 97.280 3272 58 15 1242 4507 50039183 50035937 0.000000e+00 5520.0
8 TraesCS5A01G043200 chr5D 96.207 580 21 1 1 579 50040440 50039861 0.000000e+00 948.0
9 TraesCS5A01G043200 chr5D 87.204 211 19 7 3922 4127 171681120 171681327 2.710000e-57 233.0
10 TraesCS5A01G043200 chr5D 95.652 138 4 2 3177 3314 282707991 282707856 2.110000e-53 220.0
11 TraesCS5A01G043200 chr5D 89.231 65 6 1 2117 2180 45487978 45487914 3.740000e-11 80.5
12 TraesCS5A01G043200 chr5D 100.000 31 0 0 4138 4168 171681409 171681439 1.750000e-04 58.4
13 TraesCS5A01G043200 chr5B 95.191 3057 76 30 904 3926 52649891 52646872 0.000000e+00 4765.0
14 TraesCS5A01G043200 chr5B 95.079 3028 78 30 904 3897 52915053 52918043 0.000000e+00 4700.0
15 TraesCS5A01G043200 chr5B 96.460 565 11 5 3948 4507 52646698 52646138 0.000000e+00 924.0
16 TraesCS5A01G043200 chr5B 92.466 438 32 1 270 707 52913112 52913548 3.830000e-175 625.0
17 TraesCS5A01G043200 chr5B 91.011 445 36 4 270 714 52651833 52651393 8.350000e-167 597.0
18 TraesCS5A01G043200 chr5B 80.423 189 26 8 2060 2246 45538274 45538095 2.830000e-27 134.0
19 TraesCS5A01G043200 chrUn 96.694 1815 40 5 2087 3897 371433358 371431560 0.000000e+00 3001.0
20 TraesCS5A01G043200 chrUn 91.961 933 27 11 918 1820 460220116 460221030 0.000000e+00 1264.0
21 TraesCS5A01G043200 chr4A 87.336 608 67 5 34 639 37772262 37771663 0.000000e+00 688.0
22 TraesCS5A01G043200 chr4A 89.732 224 21 1 4165 4386 261150484 261150707 7.380000e-73 285.0
23 TraesCS5A01G043200 chr4A 92.537 67 5 0 4441 4507 629586414 629586480 3.710000e-16 97.1
24 TraesCS5A01G043200 chr4A 91.525 59 5 0 4449 4507 446464142 446464084 1.040000e-11 82.4
25 TraesCS5A01G043200 chr2B 88.530 558 57 6 85 638 91033229 91033783 0.000000e+00 669.0
26 TraesCS5A01G043200 chr1B 90.093 323 30 2 34 354 554692032 554692354 6.970000e-113 418.0
27 TraesCS5A01G043200 chr1B 86.192 239 29 3 376 614 554692345 554692579 5.790000e-64 255.0
28 TraesCS5A01G043200 chr6A 92.093 215 15 1 4174 4386 15380607 15380821 7.330000e-78 302.0
29 TraesCS5A01G043200 chr6A 88.710 124 9 4 3922 4043 15379790 15379910 3.630000e-31 147.0
30 TraesCS5A01G043200 chr6D 89.286 224 21 2 4165 4386 14025586 14025808 1.230000e-70 278.0
31 TraesCS5A01G043200 chr6D 86.730 211 18 8 3922 4126 14025263 14025469 4.540000e-55 226.0
32 TraesCS5A01G043200 chr6D 90.588 85 5 2 2927 3008 90111901 90111817 4.770000e-20 110.0
33 TraesCS5A01G043200 chr6D 100.000 29 0 0 4138 4166 14025530 14025558 2.000000e-03 54.7
34 TraesCS5A01G043200 chr2D 95.652 138 5 1 3177 3314 592468110 592467974 2.110000e-53 220.0
35 TraesCS5A01G043200 chr2D 89.571 163 16 1 34 195 647525440 647525602 5.910000e-49 206.0
36 TraesCS5A01G043200 chr2D 90.698 86 4 2 2926 3008 425742653 425742569 1.330000e-20 111.0
37 TraesCS5A01G043200 chr1A 95.652 138 5 1 3177 3314 388684886 388685022 2.110000e-53 220.0
38 TraesCS5A01G043200 chr2A 90.184 163 15 1 34 195 772955261 772955099 1.270000e-50 211.0
39 TraesCS5A01G043200 chr2A 97.297 74 2 0 4434 4507 527320832 527320905 4.730000e-25 126.0
40 TraesCS5A01G043200 chr2A 100.000 30 0 0 4138 4167 720953846 720953875 6.300000e-04 56.5
41 TraesCS5A01G043200 chr3B 89.231 130 9 3 4000 4126 458277560 458277433 1.680000e-34 158.0
42 TraesCS5A01G043200 chr7A 86.029 136 14 3 3996 4126 454755053 454755188 1.690000e-29 141.0
43 TraesCS5A01G043200 chr7A 89.189 111 12 0 4397 4507 422041561 422041671 6.080000e-29 139.0
44 TraesCS5A01G043200 chr7A 100.000 28 0 0 4140 4167 454755272 454755299 8.000000e-03 52.8
45 TraesCS5A01G043200 chr3A 88.636 88 7 2 2924 3008 491189513 491189426 2.220000e-18 104.0


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 TraesCS5A01G043200 chr5A 39240998 39245504 4506 True 8323.000000 8323 100.000000 1 4507 1 chr5A.!!$R2 4506
1 TraesCS5A01G043200 chr5D 50197038 50201534 4496 True 7577.000000 7577 97.061000 1 4507 1 chr5D.!!$R3 4506
2 TraesCS5A01G043200 chr5D 49760373 49764877 4504 True 7324.000000 7324 96.047000 1 4507 1 chr5D.!!$R2 4506
3 TraesCS5A01G043200 chr5D 50035937 50040440 4503 True 3234.000000 5520 96.743500 1 4507 2 chr5D.!!$R5 4506
4 TraesCS5A01G043200 chr5B 52913112 52918043 4931 False 2662.500000 4700 93.772500 270 3897 2 chr5B.!!$F1 3627
5 TraesCS5A01G043200 chr5B 52646138 52651833 5695 True 2095.333333 4765 94.220667 270 4507 3 chr5B.!!$R2 4237
6 TraesCS5A01G043200 chrUn 371431560 371433358 1798 True 3001.000000 3001 96.694000 2087 3897 1 chrUn.!!$R1 1810
7 TraesCS5A01G043200 chrUn 460220116 460221030 914 False 1264.000000 1264 91.961000 918 1820 1 chrUn.!!$F1 902
8 TraesCS5A01G043200 chr4A 37771663 37772262 599 True 688.000000 688 87.336000 34 639 1 chr4A.!!$R1 605
9 TraesCS5A01G043200 chr2B 91033229 91033783 554 False 669.000000 669 88.530000 85 638 1 chr2B.!!$F1 553
10 TraesCS5A01G043200 chr1B 554692032 554692579 547 False 336.500000 418 88.142500 34 614 2 chr1B.!!$F1 580
11 TraesCS5A01G043200 chr6A 15379790 15380821 1031 False 224.500000 302 90.401500 3922 4386 2 chr6A.!!$F1 464

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
141 143 0.467384 TAGTAGGTCGTAGCTCCGCT 59.533 55.000 0.0 0.00 43.41 5.52 F
866 1472 0.532115 CTGGCCCATAAACAACAGGC 59.468 55.000 0.0 0.00 43.09 4.85 F
1276 2660 0.745845 CAGATTTCAGGCCTCCCGTG 60.746 60.000 0.0 0.00 35.76 4.94 F
1448 2836 1.225691 GACGAAGACGACGAGGACG 60.226 63.158 0.0 4.85 42.66 4.79 F
2111 3500 2.288213 GGCAAAACCAGCACCTTAGAAC 60.288 50.000 0.0 0.00 38.86 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 2822 1.224069 TTCGTCGTCCTCGTCGTCTT 61.224 55.000 7.05 0.0 45.27 3.01 R
2790 4179 5.438761 AAGCATTTGACAAGACAAGGTAC 57.561 39.130 0.00 0.0 0.00 3.34 R
2965 4355 5.862924 ATAGGACGTTTTTGACAGTCATG 57.137 39.130 3.45 0.0 35.16 3.07 R
3476 4868 4.269183 TGTCAGAACAAAGAACACCATGT 58.731 39.130 0.00 0.0 30.70 3.21 R
3791 5183 1.067142 GCACTCTCGGACAACATACCA 60.067 52.381 0.00 0.0 0.00 3.25 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
72 73 8.298854 GCATAATGTATGTAGCAAAATCCATCA 58.701 33.333 0.00 0.00 38.43 3.07
141 143 0.467384 TAGTAGGTCGTAGCTCCGCT 59.533 55.000 0.00 0.00 43.41 5.52
354 357 2.441348 TATGCTCCTCGTCGGCCA 60.441 61.111 2.24 0.00 0.00 5.36
382 416 1.005037 AGTTGCAACATCTCGCCGA 60.005 52.632 30.11 0.00 0.00 5.54
572 607 2.671396 GCGAGACGATTGTTTACATGGT 59.329 45.455 0.00 0.00 0.00 3.55
633 668 1.377725 CGGACTGCTGGCTCCAAAT 60.378 57.895 0.00 0.00 0.00 2.32
709 744 3.071167 GGGGTGCGAGGTATCTTCTTTAT 59.929 47.826 0.00 0.00 0.00 1.40
866 1472 0.532115 CTGGCCCATAAACAACAGGC 59.468 55.000 0.00 0.00 43.09 4.85
959 2317 2.432444 CCATTCGCAACTAGAAACCCA 58.568 47.619 0.00 0.00 0.00 4.51
1100 2458 1.001887 AGTCGTCGCCTCTTCCTCT 60.002 57.895 0.00 0.00 0.00 3.69
1121 2479 2.261671 CCTGACCGACCTGTTCCG 59.738 66.667 0.00 0.00 0.00 4.30
1274 2658 1.153086 CCAGATTTCAGGCCTCCCG 60.153 63.158 0.00 0.00 35.76 5.14
1276 2660 0.745845 CAGATTTCAGGCCTCCCGTG 60.746 60.000 0.00 0.00 35.76 4.94
1277 2661 2.044946 ATTTCAGGCCTCCCGTGC 60.045 61.111 0.00 0.00 35.76 5.34
1279 2663 2.826777 ATTTCAGGCCTCCCGTGCTG 62.827 60.000 0.00 0.00 35.76 4.41
1353 2741 7.662083 TCCTTAGGATATATTCTCCCTGCATA 58.338 38.462 0.00 0.00 32.89 3.14
1438 2826 4.741570 GACGAGGACGACGAAGAC 57.258 61.111 0.00 0.00 42.66 3.01
1447 2835 4.741570 GACGAAGACGACGAGGAC 57.258 61.111 0.00 0.00 42.66 3.85
1448 2836 1.225691 GACGAAGACGACGAGGACG 60.226 63.158 0.00 4.85 42.66 4.79
2111 3500 2.288213 GGCAAAACCAGCACCTTAGAAC 60.288 50.000 0.00 0.00 38.86 3.01
2790 4179 9.577110 AAAATATGAACTTAGTTGTCATGCATG 57.423 29.630 21.07 21.07 0.00 4.06
3476 4868 3.621268 GCTTCATGTGTGAAACCGCTATA 59.379 43.478 0.00 0.00 43.39 1.31
3479 4871 4.765273 TCATGTGTGAAACCGCTATACAT 58.235 39.130 0.00 0.00 34.36 2.29
3659 5051 8.962679 GGATTTGTAACTATGGTGGATGTTAAA 58.037 33.333 0.00 0.00 0.00 1.52
3755 5147 1.485294 ATGTGGTACTGGGTTGCCGA 61.485 55.000 0.00 0.00 0.00 5.54
3791 5183 4.689345 GCTGTTCCTACGTTTCATACTGTT 59.311 41.667 0.00 0.00 0.00 3.16
3923 5316 4.225267 TGGTGTTGGGGTGTTTTTGTTTAT 59.775 37.500 0.00 0.00 0.00 1.40
4109 6153 3.788227 TCAACCTAGGCACATTGACTT 57.212 42.857 9.30 0.00 36.80 3.01
4172 6296 0.107214 CGACTTGCACCCCCATGTAT 60.107 55.000 0.00 0.00 0.00 2.29
4256 6382 2.961536 TCACCATCCCCTTCCTCTTA 57.038 50.000 0.00 0.00 0.00 2.10
4257 6383 3.214694 TCACCATCCCCTTCCTCTTAA 57.785 47.619 0.00 0.00 0.00 1.85
4401 6530 9.688091 ACAATAGAACTCAGACTTATCTAGACA 57.312 33.333 0.00 0.00 32.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.548993 TGGATTTTGCTACATACATTATGCCA 59.451 34.615 0.00 0.00 39.79 4.92
72 73 3.072768 TGTTGGATTTTGGTACTACCGGT 59.927 43.478 13.98 13.98 42.58 5.28
113 115 0.314302 ACGACCTACTATGGCGATGC 59.686 55.000 0.00 0.00 33.32 3.91
116 118 1.202734 AGCTACGACCTACTATGGCGA 60.203 52.381 0.00 0.00 33.32 5.54
141 143 2.221169 GGATTTGCTACATCCATCGCA 58.779 47.619 4.92 0.00 40.21 5.10
354 357 5.163703 CGAGATGTTGCAACTCTACTCTACT 60.164 44.000 28.61 13.99 32.30 2.57
382 416 2.273908 ACGAAGTGCTACCATCGGT 58.726 52.632 0.00 0.00 42.51 4.69
477 511 1.074566 CTCTTTCTTCAACCCCCAGCT 59.925 52.381 0.00 0.00 0.00 4.24
715 1309 7.329588 TCGCTTTTTACTCTTTTCCTTTTCT 57.670 32.000 0.00 0.00 0.00 2.52
716 1310 7.980742 TTCGCTTTTTACTCTTTTCCTTTTC 57.019 32.000 0.00 0.00 0.00 2.29
765 1363 0.893727 GCTTCCGGCTCTTTTTCCCA 60.894 55.000 0.00 0.00 38.06 4.37
766 1364 1.883732 GCTTCCGGCTCTTTTTCCC 59.116 57.895 0.00 0.00 38.06 3.97
829 1435 1.601759 GCCCAGTGAGCTTCTGCAA 60.602 57.895 12.47 0.00 42.74 4.08
959 2317 4.115199 GGCGTGGGGAGATGGCTT 62.115 66.667 0.00 0.00 0.00 4.35
1032 2390 2.637025 CCTTTGTCGCCGGTTGTG 59.363 61.111 1.90 0.00 0.00 3.33
1100 2458 2.430382 GAACAGGTCGGTCAGGCGAA 62.430 60.000 0.00 0.00 0.00 4.70
1121 2479 3.194005 TCTTGTCCAGACCAAAGTGTC 57.806 47.619 0.00 0.00 35.43 3.67
1274 2658 3.318017 ACGAATTATAGCGATCCAGCAC 58.682 45.455 0.00 0.00 40.15 4.40
1276 2660 5.232414 GGATTACGAATTATAGCGATCCAGC 59.768 44.000 0.00 0.00 33.56 4.85
1277 2661 5.749109 GGGATTACGAATTATAGCGATCCAG 59.251 44.000 0.00 0.00 34.45 3.86
1279 2663 4.738740 CGGGATTACGAATTATAGCGATCC 59.261 45.833 0.00 0.00 32.96 3.36
1349 2737 6.814506 AGCACTCATTTCCTGAATATATGC 57.185 37.500 0.00 0.00 32.14 3.14
1353 2741 6.115446 TCGAAAGCACTCATTTCCTGAATAT 58.885 36.000 0.00 0.00 33.92 1.28
1434 2822 1.224069 TTCGTCGTCCTCGTCGTCTT 61.224 55.000 7.05 0.00 45.27 3.01
1435 2823 1.624865 CTTCGTCGTCCTCGTCGTCT 61.625 60.000 7.05 0.00 45.27 4.18
1436 2824 1.225691 CTTCGTCGTCCTCGTCGTC 60.226 63.158 7.05 0.00 45.27 4.20
1437 2825 1.665916 TCTTCGTCGTCCTCGTCGT 60.666 57.895 7.05 0.00 45.27 4.34
1438 2826 1.225691 GTCTTCGTCGTCCTCGTCG 60.226 63.158 0.00 1.62 46.06 5.12
1439 2827 1.225691 CGTCTTCGTCGTCCTCGTC 60.226 63.158 0.00 0.00 38.33 4.20
1440 2828 1.665916 TCGTCTTCGTCGTCCTCGT 60.666 57.895 0.00 0.00 38.33 4.18
1441 2829 1.225691 GTCGTCTTCGTCGTCCTCG 60.226 63.158 0.00 0.00 38.33 4.63
1442 2830 1.225691 CGTCGTCTTCGTCGTCCTC 60.226 63.158 0.00 0.00 41.73 3.71
1443 2831 1.624865 CTCGTCGTCTTCGTCGTCCT 61.625 60.000 7.05 0.00 45.27 3.85
1444 2832 1.225691 CTCGTCGTCTTCGTCGTCC 60.226 63.158 7.05 0.00 45.27 4.79
1445 2833 1.225691 CCTCGTCGTCTTCGTCGTC 60.226 63.158 7.05 0.00 45.27 4.20
1446 2834 2.675056 CCCTCGTCGTCTTCGTCGT 61.675 63.158 7.05 0.00 45.27 4.34
1447 2835 2.097918 CCCTCGTCGTCTTCGTCG 59.902 66.667 0.00 1.62 46.06 5.12
1448 2836 2.202453 GCCCTCGTCGTCTTCGTC 60.202 66.667 0.00 0.00 38.33 4.20
2111 3500 8.461222 TCAATAAAAGGATGTTAATGACAGCAG 58.539 33.333 0.00 0.00 46.35 4.24
2790 4179 5.438761 AAGCATTTGACAAGACAAGGTAC 57.561 39.130 0.00 0.00 0.00 3.34
2965 4355 5.862924 ATAGGACGTTTTTGACAGTCATG 57.137 39.130 3.45 0.00 35.16 3.07
3476 4868 4.269183 TGTCAGAACAAAGAACACCATGT 58.731 39.130 0.00 0.00 30.70 3.21
3479 4871 3.278574 CCTGTCAGAACAAAGAACACCA 58.721 45.455 0.00 0.00 34.24 4.17
3659 5051 8.239314 TCACGATTTACTGATAGAACGTTAACT 58.761 33.333 0.00 0.00 0.00 2.24
3677 5069 1.155889 TCAGCACGCATTCACGATTT 58.844 45.000 0.00 0.00 36.70 2.17
3678 5070 1.155889 TTCAGCACGCATTCACGATT 58.844 45.000 0.00 0.00 36.70 3.34
3773 5165 4.877378 ACCAACAGTATGAAACGTAGGA 57.123 40.909 0.00 0.00 39.69 2.94
3791 5183 1.067142 GCACTCTCGGACAACATACCA 60.067 52.381 0.00 0.00 0.00 3.25
4172 6296 4.263435 CGGTAAGTGGCCCAAAATAGTTA 58.737 43.478 0.00 0.00 0.00 2.24
4256 6382 4.832266 TGATGCTAACTGGAAAATGGTGTT 59.168 37.500 0.00 0.00 0.00 3.32
4257 6383 4.406456 TGATGCTAACTGGAAAATGGTGT 58.594 39.130 0.00 0.00 0.00 4.16
4400 6529 0.264359 AGAGATGAGAGGGAGGGGTG 59.736 60.000 0.00 0.00 0.00 4.61
4401 6530 0.264359 CAGAGATGAGAGGGAGGGGT 59.736 60.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.