Multiple sequence alignment - TraesCS4B01G383600

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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 TraesCS4B01G383600 chr4B 100.000 6999 0 0 1 6999 662764456 662771454 0.000000e+00 12925
1 TraesCS4B01G383600 chr4B 97.361 7011 162 14 1 6997 663802887 663795886 0.000000e+00 11900
2 TraesCS4B01G383600 chr4B 93.953 3324 177 15 1481 4786 662726537 662729854 0.000000e+00 5003
3 TraesCS4B01G383600 chr4B 92.003 1363 99 7 1 1355 662725178 662726538 0.000000e+00 1905
4 TraesCS4B01G383600 chr4B 87.046 1212 129 11 291 1476 663783822 663782613 0.000000e+00 1343
5 TraesCS4B01G383600 chr4B 92.842 475 27 4 5280 5752 662742207 662742676 0.000000e+00 682
6 TraesCS4B01G383600 chr4B 96.059 406 13 2 4789 5192 662741808 662742212 0.000000e+00 658
7 TraesCS4B01G383600 chr4B 94.911 393 18 2 6122 6512 663782062 663781670 1.290000e-171 614
8 TraesCS4B01G383600 chrUn 94.767 6421 294 25 597 6997 41984176 41977778 0.000000e+00 9958
9 TraesCS4B01G383600 chrUn 95.191 603 27 2 1 601 41986216 41985614 0.000000e+00 952
10 TraesCS4B01G383600 chrUn 95.550 382 9 6 670 1044 480593147 480592767 7.770000e-169 604
11 TraesCS4B01G383600 chrUn 78.610 374 75 4 6531 6902 41978633 41978263 7.010000e-60 243
12 TraesCS4B01G383600 chr3B 94.658 6421 305 22 597 6997 800115365 800108963 0.000000e+00 9923
13 TraesCS4B01G383600 chr3B 95.522 603 25 2 1 601 800117399 800116797 0.000000e+00 963
14 TraesCS4B01G383600 chr3B 78.075 374 77 4 6531 6902 800109818 800109448 1.520000e-56 231
15 TraesCS4B01G383600 chr5A 92.440 5040 297 40 1 5014 702723177 702718196 0.000000e+00 7119
16 TraesCS4B01G383600 chr5A 95.414 1330 53 5 5514 6842 702718145 702716823 0.000000e+00 2111
17 TraesCS4B01G383600 chr5A 73.829 363 81 10 6550 6904 702743005 702742649 1.580000e-26 132
18 TraesCS4B01G383600 chr5A 92.593 81 6 0 6917 6997 702716825 702716745 4.440000e-22 117
19 TraesCS4B01G383600 chr7D 80.161 1245 234 9 1290 2529 630489166 630487930 0.000000e+00 918
20 TraesCS4B01G383600 chr7D 87.626 396 44 5 1 394 523554652 523554260 8.280000e-124 455
21 TraesCS4B01G383600 chr7D 83.850 452 52 14 2086 2529 630486630 630486192 1.820000e-110 411
22 TraesCS4B01G383600 chr4D 77.701 870 163 27 5634 6487 506457694 506456840 2.910000e-138 503
23 TraesCS4B01G383600 chr5D 87.160 405 48 4 1 403 450144726 450144324 2.300000e-124 457
24 TraesCS4B01G383600 chr7A 82.420 529 81 9 2000 2523 734626292 734626813 1.070000e-122 451
25 TraesCS4B01G383600 chr7A 86.585 164 22 0 2198 2361 734613255 734613418 1.550000e-41 182
26 TraesCS4B01G383600 chr7A 86.806 144 14 3 2390 2529 726457609 726457467 9.400000e-34 156
27 TraesCS4B01G383600 chr2A 86.318 402 48 7 7 403 593500474 593500075 1.390000e-116 431
28 TraesCS4B01G383600 chr4A 85.468 406 54 5 1 403 714821942 714822345 1.090000e-112 418
29 TraesCS4B01G383600 chr7B 82.895 228 34 4 568 792 382612791 382612566 4.280000e-47 200
30 TraesCS4B01G383600 chr7B 74.502 251 56 6 4591 4837 91197271 91197025 1.240000e-17 102
31 TraesCS4B01G383600 chr6B 85.385 130 16 3 3986 4113 46035267 46035139 1.580000e-26 132
32 TraesCS4B01G383600 chr6D 74.060 266 63 4 4567 4829 102266257 102265995 3.450000e-18 104


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 TraesCS4B01G383600 chr4B 662764456 662771454 6998 False 12925.000000 12925 100.000000 1 6999 1 chr4B.!!$F1 6998
1 TraesCS4B01G383600 chr4B 663795886 663802887 7001 True 11900.000000 11900 97.361000 1 6997 1 chr4B.!!$R1 6996
2 TraesCS4B01G383600 chr4B 662725178 662729854 4676 False 3454.000000 5003 92.978000 1 4786 2 chr4B.!!$F2 4785
3 TraesCS4B01G383600 chr4B 663781670 663783822 2152 True 978.500000 1343 90.978500 291 6512 2 chr4B.!!$R2 6221
4 TraesCS4B01G383600 chr4B 662741808 662742676 868 False 670.000000 682 94.450500 4789 5752 2 chr4B.!!$F3 963
5 TraesCS4B01G383600 chrUn 41977778 41984176 6398 True 9958.000000 9958 94.767000 597 6997 1 chrUn.!!$R1 6400
6 TraesCS4B01G383600 chrUn 41985614 41986216 602 True 952.000000 952 95.191000 1 601 1 chrUn.!!$R3 600
7 TraesCS4B01G383600 chr3B 800108963 800115365 6402 True 9923.000000 9923 94.658000 597 6997 1 chr3B.!!$R1 6400
8 TraesCS4B01G383600 chr3B 800116797 800117399 602 True 963.000000 963 95.522000 1 601 1 chr3B.!!$R3 600
9 TraesCS4B01G383600 chr5A 702716745 702723177 6432 True 3115.666667 7119 93.482333 1 6997 3 chr5A.!!$R2 6996
10 TraesCS4B01G383600 chr7D 630486192 630489166 2974 True 664.500000 918 82.005500 1290 2529 2 chr7D.!!$R2 1239
11 TraesCS4B01G383600 chr4D 506456840 506457694 854 True 503.000000 503 77.701000 5634 6487 1 chr4D.!!$R1 853
12 TraesCS4B01G383600 chr7A 734626292 734626813 521 False 451.000000 451 82.420000 2000 2523 1 chr7A.!!$F2 523

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
496 508 1.277273 CACTGCCATCAAGAGAGACCA 59.723 52.381 0.00 0.00 0.00 4.02 F
1407 1563 1.067749 CTCGCCAGAGGAGCTCATG 59.932 63.158 17.19 10.72 40.75 3.07 F
2187 2358 0.397564 TCAGTGTTGATGCTGCCTCA 59.602 50.000 3.38 3.38 33.09 3.86 F
2421 2593 2.375146 TCTGCGCAGGTATGTCTCTTA 58.625 47.619 35.36 10.29 0.00 2.10 F
4116 5002 2.777913 TCTCTAGCCCTAGACCTCTCA 58.222 52.381 0.97 0.00 37.28 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1807 0.037882 CTCTTCGAGCAAGACAGGCA 60.038 55.000 0.00 0.0 36.08 4.75 R
3228 4105 1.064825 GGAACCCCTTTCACCTCTCA 58.935 55.000 0.00 0.0 35.70 3.27 R
4116 5002 2.548464 AAGAGGAGACCAGAGCTCAT 57.452 50.000 17.77 0.0 34.07 2.90 R
4180 5067 4.067896 TGAGATCTTTGGAGCAAGAACAC 58.932 43.478 0.00 0.0 0.00 3.32 R
6053 7072 2.305343 CAATCTCATGATCCCCTCCTCC 59.695 54.545 0.00 0.0 31.51 4.30 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
269 270 3.527507 TCAAGGGATAGGAGTAGCGAT 57.472 47.619 0.00 0.00 0.00 4.58
389 391 3.889538 CAGAGTTCGGTGGTATATCCTCA 59.110 47.826 0.00 0.00 37.07 3.86
496 508 1.277273 CACTGCCATCAAGAGAGACCA 59.723 52.381 0.00 0.00 0.00 4.02
524 536 1.303888 TCGTCCGAGCCCTAGTTGT 60.304 57.895 0.00 0.00 0.00 3.32
553 565 4.214332 CCGGCCTTCTGATTAAGATTTAGC 59.786 45.833 0.00 0.00 33.93 3.09
566 578 3.891049 AGATTTAGCCTTCCGAGCAATT 58.109 40.909 0.00 0.00 0.00 2.32
878 899 9.880157 TGCCTATTATATATCCGGTAAAAGAAC 57.120 33.333 0.00 0.00 0.00 3.01
902 923 5.438761 AAAGGTGGATATTATTGCTTCGC 57.561 39.130 0.00 0.00 0.00 4.70
1044 1072 1.998530 CATTAGGCACTCCCCACCA 59.001 57.895 0.00 0.00 41.75 4.17
1205 1233 2.406559 CAACCTCTGGATCCATCTCCT 58.593 52.381 16.63 0.00 36.20 3.69
1313 1342 1.739338 GCCCTCGACATCCGTCTCAT 61.739 60.000 0.00 0.00 40.23 2.90
1372 1528 2.287009 GCGCTTGCTAAGAAGTTGTTGT 60.287 45.455 0.00 0.00 35.07 3.32
1407 1563 1.067749 CTCGCCAGAGGAGCTCATG 59.932 63.158 17.19 10.72 40.75 3.07
1544 1700 1.299648 CGGCCAACCAGATCCTTCA 59.700 57.895 2.24 0.00 34.57 3.02
1649 1807 3.953775 CACCTGCCGTGGGGTCTT 61.954 66.667 0.00 0.00 38.96 3.01
1861 2019 7.809806 GCTTCAACAAATATTTTACTGCTGAGT 59.190 33.333 0.00 0.00 36.07 3.41
2089 2260 1.086696 AATCCGCTCAACATCGTTGG 58.913 50.000 6.99 0.11 0.00 3.77
2187 2358 0.397564 TCAGTGTTGATGCTGCCTCA 59.602 50.000 3.38 3.38 33.09 3.86
2421 2593 2.375146 TCTGCGCAGGTATGTCTCTTA 58.625 47.619 35.36 10.29 0.00 2.10
2861 3738 5.418524 TCAATAATGTTGTCCATCAAGGGTG 59.581 40.000 0.00 0.00 36.66 4.61
2987 3864 4.221924 TGTCCTCTTCCGACATGTTTATCA 59.778 41.667 0.00 0.00 35.35 2.15
3561 4441 3.543680 ACTGCCTATGCGTCTTTGTAT 57.456 42.857 0.00 0.00 41.78 2.29
3632 4512 7.015877 ACACTACAACTGAGTAAACTAATGGGA 59.984 37.037 0.00 0.00 0.00 4.37
3633 4513 7.876068 CACTACAACTGAGTAAACTAATGGGAA 59.124 37.037 0.00 0.00 0.00 3.97
3707 4587 8.810041 AGAAAAGCAAATTCAACCTATGAGAAT 58.190 29.630 0.00 0.00 39.77 2.40
3953 4839 8.531146 CCCTTGGCTTTGAAAAGATCTTTATTA 58.469 33.333 20.76 7.83 38.28 0.98
4116 5002 2.777913 TCTCTAGCCCTAGACCTCTCA 58.222 52.381 0.97 0.00 37.28 3.27
4586 5473 9.547753 CTATGTATAGTGGACATAATAATGCCC 57.452 37.037 0.00 0.00 38.87 5.36
4638 5525 9.710818 TCCTAGAGGAAAGCTTAATTTCTAGTA 57.289 33.333 22.39 12.99 42.18 1.82
4811 5704 2.854185 GAGAAATTACGCTTTGCATGCC 59.146 45.455 16.68 0.00 0.00 4.40
4954 5962 0.478072 ACTCCAACCAAGATGCCACA 59.522 50.000 0.00 0.00 0.00 4.17
5422 6433 3.366052 TGCCCATTTTCTAGGACTTCC 57.634 47.619 0.00 0.00 0.00 3.46
5470 6481 5.046288 AGTAAGCTCACCGGTAGTACTAT 57.954 43.478 6.87 0.00 0.00 2.12
5524 6536 5.003804 ACACGAAAGTTCCTAGATGCAATT 58.996 37.500 0.00 0.00 46.40 2.32
5728 6742 1.628846 TGCTAGGGAGTTGGAGAAACC 59.371 52.381 0.00 0.00 39.85 3.27
5997 7016 4.534500 TCCTTGTAATGAGCCCAAGAACTA 59.466 41.667 0.00 0.00 38.23 2.24
6053 7072 7.414436 TGAAGAAGTGGAAATTTACAACTTCG 58.586 34.615 24.48 0.00 35.83 3.79
6447 7468 7.817418 TTACCTGTAATATTCCTTGAATGGC 57.183 36.000 0.00 0.00 33.95 4.40
6520 7541 0.382636 GCTTGTTGTTTCGACCGTCG 60.383 55.000 14.94 14.94 42.10 5.12
6601 7622 5.200483 TCATATGTTTTTGTCATCCTCCCC 58.800 41.667 1.90 0.00 0.00 4.81
6627 7648 4.942852 ACTCCTTCATTTATCTCAGCTCG 58.057 43.478 0.00 0.00 0.00 5.03
6782 7803 3.096092 GGGGGATGCAAGATGTTTGTTA 58.904 45.455 0.00 0.00 0.00 2.41
6791 7812 5.181811 TGCAAGATGTTTGTTAGGTCTCATG 59.818 40.000 0.00 0.00 0.00 3.07
6908 7929 7.186021 TCTCGTCTCATTCTTGTTTTAAACC 57.814 36.000 5.32 0.00 0.00 3.27
6935 7956 9.696917 CTTTTTAGTTCCTTAGCACATTTGATT 57.303 29.630 0.00 0.00 0.00 2.57
6997 8018 7.915397 GGTGAAGTGTTTGCATATTATTAGTGG 59.085 37.037 0.00 0.00 0.00 4.00
6998 8019 7.915397 GTGAAGTGTTTGCATATTATTAGTGGG 59.085 37.037 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.115052 AACGCCACCATCCTGCAA 59.885 55.556 0.00 0.00 0.00 4.08
496 508 2.038329 TCGGACGACCCCCTTGAT 59.962 61.111 0.00 0.00 0.00 2.57
553 565 2.012673 CCTTCTCAATTGCTCGGAAGG 58.987 52.381 22.21 22.21 44.28 3.46
566 578 1.612146 TCGCCACATCCCCTTCTCA 60.612 57.895 0.00 0.00 0.00 3.27
655 667 3.377253 ACATGTCCTCGAACCCTAGTA 57.623 47.619 0.00 0.00 0.00 1.82
878 899 5.679906 CGAAGCAATAATATCCACCTTTCG 58.320 41.667 0.00 0.00 0.00 3.46
1056 1084 1.827399 CTCCCGTACAACCCTGTGCT 61.827 60.000 0.00 0.00 36.13 4.40
1205 1233 1.680989 TCGTGGAAGATGAGCCCGA 60.681 57.895 0.00 0.00 0.00 5.14
1359 1515 2.360801 GGCCTTGCACAACAACTTCTTA 59.639 45.455 0.00 0.00 33.68 2.10
1395 1551 0.820871 GGACGAACATGAGCTCCTCT 59.179 55.000 12.15 0.00 0.00 3.69
1407 1563 4.790861 GACCGCGGGAGGACGAAC 62.791 72.222 31.76 5.04 35.47 3.95
1529 1685 1.019673 CGCATGAAGGATCTGGTTGG 58.980 55.000 0.00 0.00 0.00 3.77
1544 1700 1.143620 GAGAGCCTCTCAAGCGCAT 59.856 57.895 16.86 0.00 42.90 4.73
1619 1777 2.524394 AGGTGACCCTGAGCACGT 60.524 61.111 0.00 0.00 40.58 4.49
1649 1807 0.037882 CTCTTCGAGCAAGACAGGCA 60.038 55.000 0.00 0.00 36.08 4.75
1861 2019 1.603171 TGCGAGGAAAGCATGGCAA 60.603 52.632 0.00 0.00 36.62 4.52
2187 2358 2.354103 CCAGATGGACACGTTGATGTCT 60.354 50.000 5.92 0.00 46.85 3.41
2755 3632 3.747854 GGTTGCCTACCTACTATCCAC 57.252 52.381 0.00 0.00 44.10 4.02
2861 3738 2.496899 TTGTGGAGAGAAGGCATTCC 57.503 50.000 7.63 0.00 35.94 3.01
3228 4105 1.064825 GGAACCCCTTTCACCTCTCA 58.935 55.000 0.00 0.00 35.70 3.27
3531 4411 3.055591 CGCATAGGCAGTAATCACTCTG 58.944 50.000 0.00 0.00 41.24 3.35
3953 4839 8.697292 ACTTCCTCGATCTAGCTAGTAATTTTT 58.303 33.333 20.10 0.00 0.00 1.94
4116 5002 2.548464 AAGAGGAGACCAGAGCTCAT 57.452 50.000 17.77 0.00 34.07 2.90
4180 5067 4.067896 TGAGATCTTTGGAGCAAGAACAC 58.932 43.478 0.00 0.00 0.00 3.32
4586 5473 2.356135 ACTTGCGCTAATAACCAGGTG 58.644 47.619 9.73 0.00 0.00 4.00
4638 5525 5.994416 ACTTGGGTGGATATATGGAGTTT 57.006 39.130 0.00 0.00 0.00 2.66
4811 5704 9.014297 GTTATTGTTTATGGATCCCCTTATGAG 57.986 37.037 9.90 0.00 0.00 2.90
5452 6463 3.136077 TGAGATAGTACTACCGGTGAGCT 59.864 47.826 19.93 12.32 0.00 4.09
5470 6481 7.451501 TTCATAACATGACTTGCAAATGAGA 57.548 32.000 14.91 4.29 39.39 3.27
6053 7072 2.305343 CAATCTCATGATCCCCTCCTCC 59.695 54.545 0.00 0.00 31.51 4.30
6404 7424 7.038302 ACAGGTAATAGAAGTTCCACATTCAGA 60.038 37.037 0.00 0.00 0.00 3.27
6446 7467 5.904362 AGTTGAATCTCCCATACAAAAGC 57.096 39.130 0.00 0.00 0.00 3.51
6447 7468 9.793252 CAAATAGTTGAATCTCCCATACAAAAG 57.207 33.333 0.00 0.00 36.83 2.27
6491 7512 4.514816 TCGAAACAACAAGCATGAGATGAA 59.485 37.500 0.00 0.00 0.00 2.57
6601 7622 6.347696 AGCTGAGATAAATGAAGGAGTTGAG 58.652 40.000 0.00 0.00 0.00 3.02
6627 7648 2.497273 AGAGCATTGTGCCAATTTACCC 59.503 45.455 0.00 0.00 46.52 3.69
6722 7743 5.070770 TGTTGCACTCAAAACTTCATGTT 57.929 34.783 0.00 0.00 41.29 2.71
6782 7803 3.220110 CATTAAGCATGGCATGAGACCT 58.780 45.455 30.69 14.97 0.00 3.85
6791 7812 4.021719 AGCATATTCCACATTAAGCATGGC 60.022 41.667 0.00 0.00 37.17 4.40
6833 7854 5.623956 TCTCCCATACGGTTAACATTCAT 57.376 39.130 8.10 0.00 0.00 2.57
6842 7863 5.888982 ATAGTTGAATCTCCCATACGGTT 57.111 39.130 0.00 0.00 0.00 4.44
6843 7864 5.888982 AATAGTTGAATCTCCCATACGGT 57.111 39.130 0.00 0.00 0.00 4.83
6908 7929 7.657336 TCAAATGTGCTAAGGAACTAAAAAGG 58.343 34.615 0.00 0.00 38.49 3.11


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

AutoCloner maintained by Alex Coulton.