Multiple sequence alignment - TraesCS5A01G507400

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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 TraesCS5A01G507400 chr5A 100.000 3493 0 0 1 3493 671913692 671910200 0.000000e+00 6451
1 TraesCS5A01G507400 chr6B 94.395 3497 167 13 1 3493 706186749 706183278 0.000000e+00 5345
2 TraesCS5A01G507400 chr4A 93.757 2515 155 2 978 3492 28971548 28969036 0.000000e+00 3773
3 TraesCS5A01G507400 chr4A 95.816 980 40 1 1 980 28972557 28971579 0.000000e+00 1581
4 TraesCS5A01G507400 chr3B 90.143 1745 157 8 978 2717 648184261 648182527 0.000000e+00 2255
5 TraesCS5A01G507400 chr3B 90.332 993 82 8 1 980 648185283 648184292 0.000000e+00 1290
6 TraesCS5A01G507400 chr1A 93.548 217 13 1 1 216 13268049 13267833 4.350000e-84 322
7 TraesCS5A01G507400 chr1D 94.898 98 5 0 1 98 20332723 20332626 1.680000e-33 154


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 TraesCS5A01G507400 chr5A 671910200 671913692 3492 True 6451.0 6451 100.0000 1 3493 1 chr5A.!!$R1 3492
1 TraesCS5A01G507400 chr6B 706183278 706186749 3471 True 5345.0 5345 94.3950 1 3493 1 chr6B.!!$R1 3492
2 TraesCS5A01G507400 chr4A 28969036 28972557 3521 True 2677.0 3773 94.7865 1 3492 2 chr4A.!!$R1 3491
3 TraesCS5A01G507400 chr3B 648182527 648185283 2756 True 1772.5 2255 90.2375 1 2717 2 chr3B.!!$R1 2716

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
450 464 0.877071 CTGTTGCCCTGTGATGACAC 59.123 55.0 0.00 0.0 46.09 3.67 F
1720 1767 0.106708 TCCATTAGGGCTAGCTTGCG 59.893 55.0 15.72 0.0 36.21 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2246 0.532862 CGGCTTCGTCCCTGCATATT 60.533 55.0 0.0 0.0 0.0 1.28 R
3056 3111 0.527385 TTTCTGCTGTGTTTTGCCGC 60.527 50.0 0.0 0.0 0.0 6.53 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
64 65 5.249163 TGAGGAAGATGGTTGAGAAGATTGA 59.751 40.000 0.00 0.00 0.00 2.57
85 86 3.136641 AGTGAACATATCTCCTGGGGT 57.863 47.619 0.00 0.00 0.00 4.95
113 114 2.108362 CACGGGGGAGCGGTAATC 59.892 66.667 0.00 0.00 0.00 1.75
128 129 6.978338 AGCGGTAATCATCGTCTTCTTAATA 58.022 36.000 0.00 0.00 0.00 0.98
149 150 1.634702 TTGAAGTTTGCGGTTTGTGC 58.365 45.000 0.00 0.00 0.00 4.57
218 220 1.880027 CTGTTTGCTTTAGGTTCGGCT 59.120 47.619 0.00 0.00 0.00 5.52
252 254 1.093159 GCCAGCTGATTGAACTCCAG 58.907 55.000 17.39 0.00 0.00 3.86
331 334 1.965935 CATACCATCCACGCCAATGA 58.034 50.000 0.00 0.00 0.00 2.57
450 464 0.877071 CTGTTGCCCTGTGATGACAC 59.123 55.000 0.00 0.00 46.09 3.67
689 703 3.008157 TGCATTTTGAATGGTGAAGGCAT 59.992 39.130 3.16 0.00 34.40 4.40
725 739 4.202461 ACCACATCCTACAACATCAACAGT 60.202 41.667 0.00 0.00 0.00 3.55
740 754 4.531854 TCAACAGTCCAGAACCAATTCAA 58.468 39.130 0.00 0.00 37.29 2.69
832 846 4.918810 TGAAGCTTTTCCAAGAACTTCC 57.081 40.909 0.00 0.00 32.28 3.46
939 953 7.489239 AAGGGAAGGAAGTATATCATCTAGC 57.511 40.000 0.00 0.00 0.00 3.42
969 983 3.495331 TGGGTTAGCAAAGAAGCAATGA 58.505 40.909 0.00 0.00 36.85 2.57
1003 1050 1.985473 TGACAAGCAAAGCCAGATGT 58.015 45.000 0.00 0.00 0.00 3.06
1020 1067 3.713248 AGATGTCCATAGCACAGGATTCA 59.287 43.478 0.00 0.00 36.11 2.57
1043 1090 3.324846 TCGGTTATGGAGATTGCTAGCAT 59.675 43.478 20.13 8.84 0.00 3.79
1120 1167 2.202987 GGCCATCTCCTGAGTGCG 60.203 66.667 0.00 0.00 0.00 5.34
1140 1187 3.746492 GCGTCTTGTTTGGATCAACTACT 59.254 43.478 0.00 0.00 0.00 2.57
1333 1380 6.814954 AACATACACTGATGGGTCTCTAAT 57.185 37.500 0.00 0.00 0.00 1.73
1520 1567 2.158623 AGACTTGCCCAACTTGACATGA 60.159 45.455 0.00 0.00 0.00 3.07
1537 1584 3.817647 ACATGAGCTTCTCAAAAGACACC 59.182 43.478 0.00 0.00 44.04 4.16
1549 1596 3.652057 AAAGACACCCCTGGTATGATG 57.348 47.619 1.76 0.00 32.11 3.07
1601 1648 1.762370 TGAGCGACACCATCATACCAT 59.238 47.619 0.00 0.00 0.00 3.55
1615 1662 4.296912 TCATACCATGCCCCAATTTGAAT 58.703 39.130 0.00 0.00 0.00 2.57
1642 1689 1.328374 ACACGTTTTTACTGACCGCAC 59.672 47.619 0.00 0.00 0.00 5.34
1643 1690 0.939419 ACGTTTTTACTGACCGCACC 59.061 50.000 0.00 0.00 0.00 5.01
1693 1740 1.077501 CCAATGCCGACCCACTGAT 60.078 57.895 0.00 0.00 0.00 2.90
1718 1765 2.843701 CACTCCATTAGGGCTAGCTTG 58.156 52.381 15.72 5.10 36.21 4.01
1720 1767 0.106708 TCCATTAGGGCTAGCTTGCG 59.893 55.000 15.72 0.00 36.21 4.85
1902 1953 4.322650 GGGTGGTTTATGCATTTGACATGT 60.323 41.667 3.54 0.00 0.00 3.21
1937 1988 2.000447 GTCGTTTATGACCCTGCTGTC 59.000 52.381 0.00 0.00 35.77 3.51
2002 2053 4.717233 TTGTGAGCAACAAACTTCATGT 57.283 36.364 2.76 0.00 45.85 3.21
2024 2075 2.568956 TGCTCTGTTCAACTGCCTCTAT 59.431 45.455 0.00 0.00 0.00 1.98
2195 2246 8.923270 ACTTCTTGGTTTCCATTCTTTAATTCA 58.077 29.630 0.00 0.00 31.53 2.57
2219 2270 1.820581 CAGGGACGAAGCCGGATTA 59.179 57.895 4.14 0.00 40.78 1.75
2308 2359 5.620879 GCTCTTCAGATTGAATGAAACACCC 60.621 44.000 0.00 0.00 35.59 4.61
2403 2457 1.651240 ATCGCACAGCAACCTCATGC 61.651 55.000 0.00 0.00 46.78 4.06
2447 2501 4.677673 AGGAAATCAAACAAAAGCTGCT 57.322 36.364 0.00 0.00 0.00 4.24
2477 2531 2.747446 GCTCGAAGCAATTAAAGGGTCA 59.253 45.455 2.53 0.00 41.89 4.02
2521 2575 7.039313 ACATTGTTGTTTTAAGGAAGAGGTC 57.961 36.000 0.00 0.00 29.55 3.85
2532 2586 0.804989 GAAGAGGTCGCCATTTGTGG 59.195 55.000 0.00 0.00 0.00 4.17
2553 2608 3.643792 GGGACAGCTTGACTAGATATGGT 59.356 47.826 0.00 0.00 0.00 3.55
2563 2618 7.519008 GCTTGACTAGATATGGTATTTGTGTGC 60.519 40.741 0.00 0.00 0.00 4.57
2566 2621 7.289084 TGACTAGATATGGTATTTGTGTGCCTA 59.711 37.037 0.00 0.00 0.00 3.93
2573 2628 3.561725 GGTATTTGTGTGCCTAGCATCTC 59.438 47.826 0.00 0.00 41.91 2.75
2601 2656 9.835389 CCATTTTAATCCCATGTTGTAATGAAT 57.165 29.630 0.00 0.00 0.00 2.57
2632 2687 7.040478 TCAGAGCTAAATGCAAACAAGTTATGT 60.040 33.333 0.00 0.00 44.56 2.29
2706 2761 7.160049 TGTTTGGACACCAACGTTAGATATTA 58.840 34.615 0.00 0.00 43.82 0.98
2811 2866 1.073025 CCAGTAGCCACACCTTGCA 59.927 57.895 0.00 0.00 0.00 4.08
2855 2910 1.680735 AGCTAGACGATTCTCTGCCTG 59.319 52.381 0.00 0.00 34.00 4.85
2911 2966 4.878397 CCCTGTGTAGTTCAGAATTCATCC 59.122 45.833 8.44 0.00 35.20 3.51
2949 3004 3.438087 CCTTGTCTCGCAAATCAATCAGT 59.562 43.478 0.00 0.00 36.53 3.41
3056 3111 6.346439 GCACATCATATCAACTAGAAAGCTCG 60.346 42.308 0.00 0.00 0.00 5.03
3115 3170 1.086696 CTTACCCTTGACATGGCACG 58.913 55.000 0.00 0.00 0.00 5.34
3158 3213 2.494073 GTTCTCGTCACTCCAGGAGATT 59.506 50.000 24.45 0.00 37.20 2.40
3284 3339 2.273776 GGCCTGGAGGAAGAAGCC 59.726 66.667 0.00 0.00 37.39 4.35
3286 3341 2.586792 CCTGGAGGAAGAAGCCGG 59.413 66.667 0.00 0.00 37.39 6.13
3337 3392 1.231221 GCCGTTGGATGTGTGTGTTA 58.769 50.000 0.00 0.00 0.00 2.41
3382 3437 5.253991 TGGCATGGTCATTATATAGCCAA 57.746 39.130 0.00 0.00 46.76 4.52
3430 3485 0.860533 CAAATTTTGTGGCTGGTGCG 59.139 50.000 0.78 0.00 40.82 5.34
3449 3504 3.814268 CTCGCGGCACCCATTTGG 61.814 66.667 6.13 0.00 41.37 3.28
3453 3508 3.762247 CGGCACCCATTTGGCTGG 61.762 66.667 0.00 0.00 39.89 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.200825 CACCCCAGGAGATATGTTCACTT 59.799 47.826 0.00 0.00 0.00 3.16
85 86 0.252789 TCCCCCGTGGTAGGAAATCA 60.253 55.000 0.00 0.00 34.77 2.57
128 129 2.607180 GCACAAACCGCAAACTTCAATT 59.393 40.909 0.00 0.00 0.00 2.32
184 186 5.757850 AGCAAACAGTGAGAGTTTTTAGG 57.242 39.130 0.00 0.00 37.10 2.69
218 220 3.266240 TGGCTAACAGAGAGCTCGA 57.734 52.632 8.37 0.00 39.98 4.04
252 254 1.202698 AGGGAGCATGTATCTTTCGCC 60.203 52.381 0.00 0.00 0.00 5.54
450 464 5.589855 TGGTTAGTCACAAGGCATGAATATG 59.410 40.000 0.00 0.00 37.36 1.78
689 703 3.137544 AGGATGTGGTTGACAGTTGGTTA 59.862 43.478 0.00 0.00 38.23 2.85
725 739 3.138283 AGGAGTGTTGAATTGGTTCTGGA 59.862 43.478 0.00 0.00 35.33 3.86
740 754 4.976540 ACCTTGCTTACTAAAGGAGTGT 57.023 40.909 8.39 0.00 44.93 3.55
805 819 5.595952 AGTTCTTGGAAAAGCTTCATGTTCT 59.404 36.000 0.00 0.00 32.75 3.01
806 820 5.836347 AGTTCTTGGAAAAGCTTCATGTTC 58.164 37.500 0.00 0.00 32.75 3.18
832 846 4.414337 TGGGATTGTTTTGTTTCTTGGG 57.586 40.909 0.00 0.00 0.00 4.12
939 953 0.602638 TTGCTAACCCAGAGTGCACG 60.603 55.000 12.01 0.00 33.13 5.34
969 983 2.584492 TGTCAATCTCATCGCGTGAT 57.416 45.000 5.43 5.43 35.97 3.06
1003 1050 2.037641 CCGATGAATCCTGTGCTATGGA 59.962 50.000 0.00 0.00 36.72 3.41
1020 1067 3.324846 TGCTAGCAATCTCCATAACCGAT 59.675 43.478 16.84 0.00 0.00 4.18
1043 1090 4.664150 TCATCGTACATACTGGCAATCA 57.336 40.909 0.00 0.00 0.00 2.57
1120 1167 6.073003 CCTTCAGTAGTTGATCCAAACAAGAC 60.073 42.308 0.00 0.00 35.27 3.01
1333 1380 3.317993 GGTTAGTGCTTGCCTCTGAAAAA 59.682 43.478 0.00 0.00 0.00 1.94
1520 1567 1.777272 AGGGGTGTCTTTTGAGAAGCT 59.223 47.619 0.00 0.00 0.00 3.74
1537 1584 1.806496 TCCTCCACATCATACCAGGG 58.194 55.000 0.00 0.00 0.00 4.45
1549 1596 2.103263 AGGCTCGATGTATTTCCTCCAC 59.897 50.000 0.00 0.00 0.00 4.02
1585 1632 1.229428 GGCATGGTATGATGGTGTCG 58.771 55.000 0.00 0.00 0.00 4.35
1601 1648 5.936956 GTGTCATAAAATTCAAATTGGGGCA 59.063 36.000 0.00 0.00 0.00 5.36
1615 1662 6.420588 CGGTCAGTAAAAACGTGTCATAAAA 58.579 36.000 0.00 0.00 0.00 1.52
1642 1689 1.180029 CTGCACATTCAGAAAGGGGG 58.820 55.000 0.00 0.00 36.19 5.40
1643 1690 1.815003 GTCTGCACATTCAGAAAGGGG 59.185 52.381 0.00 0.00 43.89 4.79
1693 1740 0.698238 AGCCCTAATGGAGTGCACAA 59.302 50.000 21.04 4.31 35.39 3.33
1902 1953 2.474266 GACGATTCGCTTGCGCAA 59.526 55.556 23.48 23.48 35.30 4.85
1937 1988 0.677288 TACTGTATCCGAATGGGCCG 59.323 55.000 0.00 0.00 35.24 6.13
2002 2053 1.141657 AGAGGCAGTTGAACAGAGCAA 59.858 47.619 0.00 0.00 0.00 3.91
2122 2173 4.261801 GTTGTTCATGTATAGGCAGTGGT 58.738 43.478 0.00 0.00 0.00 4.16
2195 2246 0.532862 CGGCTTCGTCCCTGCATATT 60.533 55.000 0.00 0.00 0.00 1.28
2308 2359 3.582998 TTAAATCATCCTCAGGGGCTG 57.417 47.619 0.00 0.00 34.39 4.85
2354 2408 7.774157 AGTGTTTCCTACGAGATAAGATAGTCA 59.226 37.037 0.00 0.00 0.00 3.41
2403 2457 1.268285 CGTCCTCATCAGCTCGTACAG 60.268 57.143 0.00 0.00 0.00 2.74
2477 2531 3.880490 TGTTTGCCTACAGAACGACAAAT 59.120 39.130 0.00 0.00 30.59 2.32
2521 2575 1.526575 AAGCTGTCCCACAAATGGCG 61.527 55.000 0.00 0.00 45.76 5.69
2532 2586 4.946478 ACCATATCTAGTCAAGCTGTCC 57.054 45.455 0.00 0.00 0.00 4.02
2553 2608 3.433598 GGGAGATGCTAGGCACACAAATA 60.434 47.826 0.00 0.00 43.04 1.40
2563 2618 5.012893 GGATTAAAATGGGGAGATGCTAGG 58.987 45.833 0.00 0.00 0.00 3.02
2566 2621 3.207321 TGGGATTAAAATGGGGAGATGCT 59.793 43.478 0.00 0.00 0.00 3.79
2573 2628 6.552445 TTACAACATGGGATTAAAATGGGG 57.448 37.500 0.00 0.00 0.00 4.96
2601 2656 7.391554 ACTTGTTTGCATTTAGCTCTGATAAGA 59.608 33.333 0.00 0.00 45.94 2.10
2632 2687 4.337836 TGCAGCACATGAAAACTAGTTTGA 59.662 37.500 21.22 11.60 32.36 2.69
2706 2761 2.990740 TTTGGTAGCCCAGTTTGGAT 57.009 45.000 0.00 0.00 43.15 3.41
2746 2801 0.823356 GTGGCACTGGTGTGGAATGT 60.823 55.000 11.13 0.00 43.97 2.71
2747 2802 0.822944 TGTGGCACTGGTGTGGAATG 60.823 55.000 19.83 0.00 43.97 2.67
2811 2866 4.427661 GCTCGTCTGCCTGCGACT 62.428 66.667 10.65 0.00 33.33 4.18
2842 2897 1.363744 GTTGTCCAGGCAGAGAATCG 58.636 55.000 0.00 0.00 42.67 3.34
2855 2910 0.957888 GCAAGAGAGGCAGGTTGTCC 60.958 60.000 0.00 0.00 0.00 4.02
2911 2966 2.125350 GGTTCGCCTGCTGGAGAG 60.125 66.667 14.77 3.90 42.90 3.20
2939 2994 5.809001 TCCTGAAGCAACTACTGATTGATT 58.191 37.500 0.00 0.00 38.32 2.57
2949 3004 3.454858 AGATCCCTTCCTGAAGCAACTA 58.545 45.455 1.25 0.00 37.11 2.24
3056 3111 0.527385 TTTCTGCTGTGTTTTGCCGC 60.527 50.000 0.00 0.00 0.00 6.53
3115 3170 3.568430 CCCTGGAAGAAGGTACAAAACAC 59.432 47.826 0.00 0.00 35.34 3.32
3158 3213 1.667151 GCCAAAAGCAGCCATGTGA 59.333 52.632 0.00 0.00 42.97 3.58
3248 3303 0.686224 CTGGCTTCCATGGGCAAAAA 59.314 50.000 13.02 0.00 38.72 1.94
3284 3339 3.868077 CCATTTCTTCAAGCTCTAGACCG 59.132 47.826 0.00 0.00 0.00 4.79
3286 3341 8.723942 TTATTCCATTTCTTCAAGCTCTAGAC 57.276 34.615 0.00 0.00 0.00 2.59
3337 3392 3.790437 CCAGCGCCACCATCCTCT 61.790 66.667 2.29 0.00 0.00 3.69
3449 3504 3.864686 CCACATGTACGCGCCAGC 61.865 66.667 5.73 0.00 40.74 4.85
3453 3508 3.564027 GGCTCCACATGTACGCGC 61.564 66.667 5.73 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.