Multiple sequence alignment - TraesCS3A01G216600

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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 TraesCS3A01G216600 chr3A 100.000 2381 0 0 1 2381 394722091 394719711 0.000000e+00 4397
1 TraesCS3A01G216600 chr3D 92.861 1905 107 13 494 2381 297719124 297717232 0.000000e+00 2737
2 TraesCS3A01G216600 chr3D 90.233 430 42 0 1 430 297719561 297719132 1.600000e-156 562
3 TraesCS3A01G216600 chr3B 91.812 1380 79 18 661 2033 392839429 392838077 0.000000e+00 1892
4 TraesCS3A01G216600 chr3B 90.892 538 49 0 1 538 392850517 392849980 0.000000e+00 723
5 TraesCS3A01G216600 chr1A 75.457 656 141 8 1 648 583134076 583133433 3.850000e-78 302
6 TraesCS3A01G216600 chr6D 78.889 180 32 6 1689 1865 423390498 423390674 1.500000e-22 117
7 TraesCS3A01G216600 chr4D 81.679 131 18 6 1691 1819 13562106 13561980 1.160000e-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 TraesCS3A01G216600 chr3A 394719711 394722091 2380 True 4397.0 4397 100.000 1 2381 1 chr3A.!!$R1 2380
1 TraesCS3A01G216600 chr3D 297717232 297719561 2329 True 1649.5 2737 91.547 1 2381 2 chr3D.!!$R1 2380
2 TraesCS3A01G216600 chr3B 392838077 392839429 1352 True 1892.0 1892 91.812 661 2033 1 chr3B.!!$R1 1372
3 TraesCS3A01G216600 chr3B 392849980 392850517 537 True 723.0 723 90.892 1 538 1 chr3B.!!$R2 537
4 TraesCS3A01G216600 chr1A 583133433 583134076 643 True 302.0 302 75.457 1 648 1 chr1A.!!$R1 647

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
305 307 0.459585 TTGACCGCTTACTGCCGATC 60.46 55.0 0.0 0.0 38.78 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1743 0.098728 GAACGTGATTTGATGGCCGG 59.901 55.0 0.0 0.0 0.0 6.13 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
60 61 9.914131 CAGATGATAAAGTAAGTATGGATTCGA 57.086 33.333 0.00 0.00 0.00 3.71
133 134 1.607148 GGAACAAACCAAGACCCTTCG 59.393 52.381 0.00 0.00 0.00 3.79
197 198 3.108881 CAATACCGATGTGAGTGTCTCG 58.891 50.000 0.00 0.00 32.35 4.04
209 210 3.187700 GAGTGTCTCGTGTGTTGAAAGT 58.812 45.455 0.00 0.00 0.00 2.66
260 261 4.194640 CACCTACTACATTCATTGCTGCT 58.805 43.478 0.00 0.00 0.00 4.24
305 307 0.459585 TTGACCGCTTACTGCCGATC 60.460 55.000 0.00 0.00 38.78 3.69
318 320 3.130693 ACTGCCGATCCTACAACTCTAAC 59.869 47.826 0.00 0.00 0.00 2.34
348 350 3.924686 GTGATTTTCGCTAAACTCCGAGA 59.075 43.478 1.33 0.00 34.68 4.04
356 358 3.731264 CGCTAAACTCCGAGATCTTTCGT 60.731 47.826 1.33 0.00 38.88 3.85
371 373 6.884295 AGATCTTTCGTGAATGGTAATGGAAA 59.116 34.615 0.00 0.00 0.00 3.13
407 409 4.204799 GGTGGTAAACCTCTCAAACTTGT 58.795 43.478 0.02 0.00 46.55 3.16
416 418 4.273480 ACCTCTCAAACTTGTGACAATTCG 59.727 41.667 0.00 0.00 0.00 3.34
418 420 3.625313 TCTCAAACTTGTGACAATTCGCA 59.375 39.130 0.00 0.00 40.61 5.10
434 436 1.609072 TCGCACGCTCTCTTATAGCAT 59.391 47.619 0.00 0.00 40.08 3.79
483 485 9.895138 ACTAGCCTTATCGTTTATTTCCTTTTA 57.105 29.630 0.00 0.00 0.00 1.52
585 593 3.593942 TGAACTCCCCCTAGTTTCTTCA 58.406 45.455 0.00 0.00 39.78 3.02
588 596 3.532102 ACTCCCCCTAGTTTCTTCATGT 58.468 45.455 0.00 0.00 0.00 3.21
590 598 3.777522 CTCCCCCTAGTTTCTTCATGTCT 59.222 47.826 0.00 0.00 0.00 3.41
592 600 3.519510 CCCCCTAGTTTCTTCATGTCTCA 59.480 47.826 0.00 0.00 0.00 3.27
648 656 6.428771 TGGTTGAATAAAGTCCTAAGTTTCCG 59.571 38.462 0.00 0.00 30.64 4.30
651 659 2.873094 AAAGTCCTAAGTTTCCGGGG 57.127 50.000 0.00 0.00 0.00 5.73
652 660 0.989602 AAGTCCTAAGTTTCCGGGGG 59.010 55.000 0.00 0.00 0.00 5.40
654 662 0.540454 GTCCTAAGTTTCCGGGGGAG 59.460 60.000 0.00 0.00 31.21 4.30
655 663 0.619543 TCCTAAGTTTCCGGGGGAGG 60.620 60.000 0.00 0.24 31.21 4.30
656 664 1.632965 CCTAAGTTTCCGGGGGAGGG 61.633 65.000 0.00 0.00 31.21 4.30
657 665 1.617233 TAAGTTTCCGGGGGAGGGG 60.617 63.158 0.00 0.00 31.21 4.79
907 915 7.215719 TCCATCTATAATTGAGTACTCCGTG 57.784 40.000 20.11 5.71 0.00 4.94
955 963 2.275134 TTCTTGCACTCTCCATTGCA 57.725 45.000 0.00 0.00 46.93 4.08
962 970 2.875672 GCACTCTCCATTGCACAACCTA 60.876 50.000 0.00 0.00 38.68 3.08
1212 1220 0.760567 AGATACTGATGGGGCAGCGA 60.761 55.000 0.00 0.00 39.51 4.93
1361 1369 0.375803 GTCGCGTGTCCAACAAAGTT 59.624 50.000 5.77 0.00 0.00 2.66
1430 1438 1.608336 TCCGGTGTGGTGACTAGGG 60.608 63.158 0.00 0.00 39.52 3.53
1449 1457 4.467769 AGGGATATGAAAATGGCTGTCTG 58.532 43.478 0.00 0.00 0.00 3.51
1459 1467 2.839486 TGGCTGTCTGGTGAAAGTAG 57.161 50.000 0.00 0.00 30.25 2.57
1461 1469 1.623811 GGCTGTCTGGTGAAAGTAGGA 59.376 52.381 0.00 0.00 30.25 2.94
1462 1470 2.038557 GGCTGTCTGGTGAAAGTAGGAA 59.961 50.000 0.00 0.00 30.25 3.36
1502 1510 8.632679 TCAGGAGAAAATGCCAATGTTATTATC 58.367 33.333 0.00 0.00 0.00 1.75
1503 1511 8.636213 CAGGAGAAAATGCCAATGTTATTATCT 58.364 33.333 0.00 0.00 0.00 1.98
1504 1512 9.866655 AGGAGAAAATGCCAATGTTATTATCTA 57.133 29.630 0.00 0.00 0.00 1.98
1726 1743 8.575649 TCCAAAGAAGTAAATCCAAGTAATCC 57.424 34.615 0.00 0.00 0.00 3.01
1744 1761 1.312371 CCCGGCCATCAAATCACGTT 61.312 55.000 2.24 0.00 0.00 3.99
1763 1781 3.851098 GTTCTCCAACGAGCTAGATTGT 58.149 45.455 0.00 0.00 35.94 2.71
1771 1789 5.327091 CAACGAGCTAGATTGTTTCAATGG 58.673 41.667 10.97 0.00 0.00 3.16
1890 1908 4.157656 TCCTAAACAAAATCCTGCCGAATG 59.842 41.667 0.00 0.00 0.00 2.67
1894 1912 2.489329 ACAAAATCCTGCCGAATGTCAG 59.511 45.455 0.00 0.00 0.00 3.51
1947 1966 5.163447 CGATGAATCTTTCCTACACCCTACA 60.163 44.000 0.00 0.00 0.00 2.74
1970 1989 5.068460 CACTTCTTGATCCCTACCTACTCAG 59.932 48.000 0.00 0.00 0.00 3.35
2025 2044 3.067106 CAATTCACACTAGCGAAGGTGT 58.933 45.455 0.00 0.00 45.96 4.16
2073 2092 6.537301 TGTTTTCTCGTGAAACAACTATGAGT 59.463 34.615 11.92 0.00 41.34 3.41
2087 2106 9.802039 AACAACTATGAGTGGGTTATTTCTTAA 57.198 29.630 0.00 0.00 28.69 1.85
2167 2186 7.962918 CACAGAAAAAGAGGGTAATGTTATTCG 59.037 37.037 0.00 0.00 0.00 3.34
2190 2209 1.299976 GTTCCAAGCCCGGACTCAT 59.700 57.895 0.73 0.00 33.75 2.90
2220 2239 3.411517 CCACCGCCCTCCTCCAAT 61.412 66.667 0.00 0.00 0.00 3.16
2264 2283 2.368439 TGTGGGTATTGAGCATCTTGC 58.632 47.619 0.00 0.00 45.46 4.01
2297 2316 9.532494 TTCTTCCCAATAATTTTCAGATCTTCA 57.468 29.630 0.00 0.00 0.00 3.02
2327 2346 4.702831 GTTCTTTCCTCATCTCCATCCTC 58.297 47.826 0.00 0.00 0.00 3.71
2347 2366 5.900123 TCCTCTAAATCTGCTACTAGCCTTT 59.100 40.000 5.58 5.80 41.51 3.11
2375 2394 4.292186 TCCACTTCTTTTCATCCTCCTG 57.708 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.551305 ATTGTTCCTCGATGTCCATATCA 57.449 39.130 0.00 0.00 0.00 2.15
17 18 6.410942 TCATCTGTGATATTGTTCCTCGAT 57.589 37.500 0.00 0.00 0.00 3.59
57 58 4.600692 TCCACTTCAAAGACTGAATCGA 57.399 40.909 0.00 0.00 43.20 3.59
60 61 7.911651 TCTCTAATCCACTTCAAAGACTGAAT 58.088 34.615 0.00 0.00 43.20 2.57
169 170 5.063438 ACACTCACATCGGTATTGATTTTCG 59.937 40.000 0.00 0.00 0.00 3.46
197 198 4.024809 GCTCCACTCTTACTTTCAACACAC 60.025 45.833 0.00 0.00 0.00 3.82
209 210 0.683504 GACCTCCGGCTCCACTCTTA 60.684 60.000 0.00 0.00 0.00 2.10
260 261 6.839134 TGATGTTAGGATAGAGCTTACTCCAA 59.161 38.462 10.81 2.81 44.65 3.53
271 272 4.588951 AGCGGTCAATGATGTTAGGATAGA 59.411 41.667 0.00 0.00 0.00 1.98
305 307 2.102588 CCCCATCCGTTAGAGTTGTAGG 59.897 54.545 0.00 0.00 0.00 3.18
318 320 0.748005 AGCGAAAATCACCCCATCCG 60.748 55.000 0.00 0.00 0.00 4.18
348 350 7.461182 TTTTCCATTACCATTCACGAAAGAT 57.539 32.000 0.00 0.00 0.00 2.40
356 358 9.217278 CAAACAATCATTTTCCATTACCATTCA 57.783 29.630 0.00 0.00 0.00 2.57
371 373 5.011635 GGTTTACCACCTCCAAACAATCATT 59.988 40.000 0.00 0.00 43.29 2.57
399 401 2.463653 CGTGCGAATTGTCACAAGTTTG 59.536 45.455 0.00 0.00 33.03 2.93
405 407 0.599991 AGAGCGTGCGAATTGTCACA 60.600 50.000 0.00 0.00 33.03 3.58
407 409 0.038251 AGAGAGCGTGCGAATTGTCA 60.038 50.000 0.00 0.00 0.00 3.58
416 418 3.057596 AGAGATGCTATAAGAGAGCGTGC 60.058 47.826 0.00 0.00 43.19 5.34
418 420 5.556915 AGTAGAGATGCTATAAGAGAGCGT 58.443 41.667 0.00 0.00 43.19 5.07
483 485 6.992715 GGCATTTCTAGTTACATGGTGAGTAT 59.007 38.462 0.00 0.00 0.00 2.12
490 492 5.415701 AGTGTTGGCATTTCTAGTTACATGG 59.584 40.000 0.00 0.00 0.00 3.66
531 533 4.053295 AGTGAGTGTGCATGCAAATTTTC 58.947 39.130 24.58 16.18 0.00 2.29
585 593 4.313282 CGATCAGCCATAACATGAGACAT 58.687 43.478 0.00 0.00 0.00 3.06
588 596 2.759191 GCGATCAGCCATAACATGAGA 58.241 47.619 0.00 0.00 40.81 3.27
590 598 1.501169 CGCGATCAGCCATAACATGA 58.499 50.000 0.00 0.00 44.76 3.07
592 600 0.250038 AGCGCGATCAGCCATAACAT 60.250 50.000 12.10 0.00 44.76 2.71
615 623 4.457949 GGACTTTATTCAACCAATGTCGGT 59.542 41.667 0.00 0.00 42.71 4.69
655 663 3.816994 AGAACGCAATATAGTTTCCCCC 58.183 45.455 0.00 0.00 0.00 5.40
656 664 5.830000 AAAGAACGCAATATAGTTTCCCC 57.170 39.130 0.00 0.00 0.00 4.81
657 665 7.085052 AGAAAAGAACGCAATATAGTTTCCC 57.915 36.000 0.00 0.00 0.00 3.97
658 666 7.748847 TGAGAAAAGAACGCAATATAGTTTCC 58.251 34.615 0.00 0.00 0.00 3.13
659 667 9.774742 ATTGAGAAAAGAACGCAATATAGTTTC 57.225 29.630 0.00 0.00 36.39 2.78
698 706 4.009675 GGGTTTCTGCATGACACAATCTA 58.990 43.478 0.00 0.00 0.00 1.98
705 713 1.514678 GCGTGGGTTTCTGCATGACA 61.515 55.000 0.00 0.00 0.00 3.58
898 906 8.355169 TGGACTTCATATTTATACACGGAGTAC 58.645 37.037 0.00 0.00 41.61 2.73
955 963 3.786553 TCAGTCAGGGTATGTAGGTTGT 58.213 45.455 0.00 0.00 0.00 3.32
962 970 3.526931 CGTGATTCAGTCAGGGTATGT 57.473 47.619 0.00 0.00 38.69 2.29
1212 1220 0.322975 AGAAGTTGAGTGGCTCGCAT 59.677 50.000 0.00 0.00 32.35 4.73
1361 1369 8.253113 GCATTAACTAACTACCAGGTACAGTTA 58.747 37.037 12.61 12.61 34.48 2.24
1430 1438 4.883585 TCACCAGACAGCCATTTTCATATC 59.116 41.667 0.00 0.00 0.00 1.63
1468 1476 6.196918 TGGCATTTTCTCCTGATATCAGAT 57.803 37.500 30.40 14.09 46.59 2.90
1477 1485 8.636213 AGATAATAACATTGGCATTTTCTCCTG 58.364 33.333 0.00 0.00 0.00 3.86
1516 1524 9.301153 CACACTATTTGGGTCTTTTTATATTGC 57.699 33.333 0.00 0.00 0.00 3.56
1538 1546 0.392193 AGCTAGCTCATGTGCCACAC 60.392 55.000 12.68 4.16 34.56 3.82
1585 1593 0.237761 GGATCGTCGTCCCATCTACG 59.762 60.000 0.00 0.00 41.64 3.51
1659 1676 4.079787 AGGGAATGACATGGCTAGCTTTAA 60.080 41.667 15.72 0.00 0.00 1.52
1702 1719 7.415206 CGGGATTACTTGGATTTACTTCTTTGG 60.415 40.741 0.00 0.00 0.00 3.28
1707 1724 4.275196 GCCGGGATTACTTGGATTTACTTC 59.725 45.833 2.18 0.00 0.00 3.01
1708 1725 4.204799 GCCGGGATTACTTGGATTTACTT 58.795 43.478 2.18 0.00 0.00 2.24
1711 1728 2.510382 TGGCCGGGATTACTTGGATTTA 59.490 45.455 2.18 0.00 0.00 1.40
1726 1743 0.098728 GAACGTGATTTGATGGCCGG 59.901 55.000 0.00 0.00 0.00 6.13
1744 1761 4.021456 TGAAACAATCTAGCTCGTTGGAGA 60.021 41.667 0.00 0.00 43.27 3.71
1763 1781 1.266718 GTTGAGCGCTCACCATTGAAA 59.733 47.619 38.36 19.46 39.66 2.69
1771 1789 2.286950 TGAAAACATGTTGAGCGCTCAC 60.287 45.455 38.36 29.97 39.66 3.51
1890 1908 4.556942 TGCATACTAATTGCATGCTGAC 57.443 40.909 20.33 3.47 44.73 3.51
1921 1939 3.531538 GGTGTAGGAAAGATTCATCGCA 58.468 45.455 0.00 0.00 0.00 5.10
1947 1966 5.205056 CTGAGTAGGTAGGGATCAAGAAGT 58.795 45.833 0.00 0.00 0.00 3.01
1970 1989 0.250381 AGATCTAGCAGCAGCATGGC 60.250 55.000 3.17 0.00 45.49 4.40
2025 2044 8.586570 ACAAAAATACAAATTTCATCTTGCGA 57.413 26.923 0.00 0.00 34.12 5.10
2135 2154 9.227777 ACATTACCCTCTTTTTCTGTGTTATAC 57.772 33.333 0.00 0.00 0.00 1.47
2167 2186 2.359975 CCGGGCTTGGAACAGACC 60.360 66.667 0.00 0.00 42.39 3.85
2194 2213 2.034048 GAGGGCGGTGGGAGAAGATC 62.034 65.000 0.00 0.00 0.00 2.75
2195 2214 2.041265 AGGGCGGTGGGAGAAGAT 59.959 61.111 0.00 0.00 0.00 2.40
2220 2239 2.433604 GGAGTCATCATCAGAAGAGCCA 59.566 50.000 0.00 0.00 0.00 4.75
2260 2279 2.795231 TGGGAAGAATCAGGAGCAAG 57.205 50.000 0.00 0.00 0.00 4.01
2264 2283 8.297470 TGAAAATTATTGGGAAGAATCAGGAG 57.703 34.615 0.00 0.00 0.00 3.69
2268 2287 9.705103 AGATCTGAAAATTATTGGGAAGAATCA 57.295 29.630 0.00 0.00 0.00 2.57
2296 2315 6.183360 GGAGATGAGGAAAGAACGAAAAGATG 60.183 42.308 0.00 0.00 0.00 2.90
2297 2316 5.877564 GGAGATGAGGAAAGAACGAAAAGAT 59.122 40.000 0.00 0.00 0.00 2.40
2327 2346 6.341316 TGTGAAAGGCTAGTAGCAGATTTAG 58.659 40.000 23.24 0.00 44.75 1.85
2347 2366 6.070656 AGGATGAAAAGAAGTGGATTTGTGA 58.929 36.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.