Multiple sequence alignment - TraesCS2A01G169600

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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 TraesCS2A01G169600 chr2A 100.000 2805 0 0 1 2805 124389902 124392706 0.000000 5180.0
1 TraesCS2A01G169600 chr2D 94.191 2789 131 19 1 2770 120564368 120567144 0.000000 4224.0
2 TraesCS2A01G169600 chr2B 91.984 2807 135 38 1 2770 173484253 173487006 0.000000 3855.0
3 TraesCS2A01G169600 chr4A 100.000 32 0 0 2769 2800 598154737 598154768 0.000030 60.2
4 TraesCS2A01G169600 chr6D 100.000 31 0 0 2769 2799 38435417 38435447 0.000109 58.4
5 TraesCS2A01G169600 chr6D 100.000 31 0 0 2769 2799 38448681 38448711 0.000109 58.4
6 TraesCS2A01G169600 chr5D 100.000 31 0 0 2769 2799 314438854 314438824 0.000109 58.4
7 TraesCS2A01G169600 chr5D 100.000 31 0 0 2769 2799 482408016 482408046 0.000109 58.4
8 TraesCS2A01G169600 chr3D 100.000 31 0 0 2769 2799 12286489 12286519 0.000109 58.4
9 TraesCS2A01G169600 chr3D 100.000 31 0 0 2769 2799 428136945 428136975 0.000109 58.4
10 TraesCS2A01G169600 chr3D 100.000 31 0 0 2769 2799 473754383 473754353 0.000109 58.4
11 TraesCS2A01G169600 chr1D 100.000 31 0 0 2769 2799 495441944 495441914 0.000109 58.4


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 TraesCS2A01G169600 chr2A 124389902 124392706 2804 False 5180 5180 100.000 1 2805 1 chr2A.!!$F1 2804
1 TraesCS2A01G169600 chr2D 120564368 120567144 2776 False 4224 4224 94.191 1 2770 1 chr2D.!!$F1 2769
2 TraesCS2A01G169600 chr2B 173484253 173487006 2753 False 3855 3855 91.984 1 2770 1 chr2B.!!$F1 2769

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
953 985 0.249489 CAGTCGATCGGTTGGGGATC 60.249 60.0 16.41 0.0 37.52 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2245 0.457851 TGTTGGACGTTTTGCCTTGG 59.542 50.0 0.0 0.0 0.0 3.61 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
29 30 0.723414 CAGTACAAGCATGTCAGGCG 59.277 55.000 3.45 0.00 41.05 5.52
70 71 3.016736 GCCCATAAGCTCAAAGTTGCTA 58.983 45.455 0.00 0.00 38.75 3.49
75 76 6.488006 CCCATAAGCTCAAAGTTGCTATGTAT 59.512 38.462 0.00 0.00 38.75 2.29
76 77 7.013655 CCCATAAGCTCAAAGTTGCTATGTATT 59.986 37.037 0.00 0.00 38.75 1.89
214 216 1.203441 ATGCCCAGAGTTGCTCCTCA 61.203 55.000 6.08 0.00 33.75 3.86
305 307 9.365311 CAAGGTATAAATTTAAATACTGACGCG 57.635 33.333 3.53 3.53 0.00 6.01
320 322 4.156556 ACTGACGCGTTATGAAACCTACTA 59.843 41.667 15.53 0.00 31.46 1.82
378 381 1.434555 TCTTTGTACGCGGACAATGG 58.565 50.000 35.75 29.52 39.04 3.16
401 404 6.267242 TGGTGGTCAAATTTCAGATGATTTCA 59.733 34.615 0.00 0.00 0.00 2.69
417 420 6.005583 TGATTTCAAGTGAATTCTCTGTGC 57.994 37.500 10.64 0.12 36.15 4.57
418 421 5.766670 TGATTTCAAGTGAATTCTCTGTGCT 59.233 36.000 10.64 0.00 36.15 4.40
432 435 5.724328 TCTCTGTGCTAATACAAGGTTCAG 58.276 41.667 0.00 0.00 0.00 3.02
462 465 5.157940 ACATCGGGATTTCATGGAGATAG 57.842 43.478 0.00 0.00 0.00 2.08
477 480 8.937835 TCATGGAGATAGTATCTTCCATTTTCA 58.062 33.333 25.85 15.48 41.30 2.69
611 616 3.651803 ACTCTTGAGAGACAAACGAGG 57.348 47.619 14.61 0.00 44.74 4.63
615 620 3.887110 TCTTGAGAGACAAACGAGGTACA 59.113 43.478 0.00 0.00 38.08 2.90
617 622 4.659111 TGAGAGACAAACGAGGTACAAA 57.341 40.909 0.00 0.00 0.00 2.83
628 638 9.275398 ACAAACGAGGTACAAAGTGATATTAAA 57.725 29.630 0.00 0.00 0.00 1.52
661 671 2.298446 TGAGCAGACAGAAGGTTCTCAG 59.702 50.000 0.00 0.00 34.74 3.35
760 771 4.271776 GGTAAATATTCCAAGAACGTCCCG 59.728 45.833 0.00 0.00 0.00 5.14
877 899 2.268076 ATCAACACCACCGCTTGCC 61.268 57.895 0.00 0.00 0.00 4.52
905 937 1.080569 GTTGTTGCATTGCCCTCGG 60.081 57.895 6.12 0.00 0.00 4.63
928 960 4.500035 GGGAGACGAGGTCATTAGTTGATC 60.500 50.000 0.00 0.00 36.54 2.92
935 967 3.264193 AGGTCATTAGTTGATCACCAGCA 59.736 43.478 0.00 0.00 37.99 4.41
937 969 4.256920 GTCATTAGTTGATCACCAGCAGT 58.743 43.478 0.00 0.00 36.54 4.40
948 980 1.811266 CCAGCAGTCGATCGGTTGG 60.811 63.158 16.41 12.85 36.52 3.77
953 985 0.249489 CAGTCGATCGGTTGGGGATC 60.249 60.000 16.41 0.00 37.52 3.36
957 989 1.070134 TCGATCGGTTGGGGATCAATC 59.930 52.381 16.41 0.00 40.21 2.67
1198 1230 3.686726 GGAGTTCTTCATCATCACACACC 59.313 47.826 0.00 0.00 0.00 4.16
1233 1269 0.174389 CTGATCACTGTCCAGACCCG 59.826 60.000 0.40 0.00 0.00 5.28
1269 1305 1.656095 CTGCGAATTTCTCTGACGGTC 59.344 52.381 0.00 0.00 0.00 4.79
1271 1307 1.656095 GCGAATTTCTCTGACGGTCTG 59.344 52.381 9.88 9.18 0.00 3.51
1293 1329 0.376852 CGTTCTTGGTGGTGTGTGTG 59.623 55.000 0.00 0.00 0.00 3.82
1304 1340 2.029666 GTGTGTGCGAGCAGGAGT 59.970 61.111 0.00 0.00 0.00 3.85
1480 1516 3.055094 TGGCCAAGATCCTCAAGAAGTAC 60.055 47.826 0.61 0.00 0.00 2.73
1531 1567 1.869574 CGTGATCGAGACCGTGCTG 60.870 63.158 0.00 0.00 39.71 4.41
1832 1869 1.455587 CCCATTCCCCGTCCAATGG 60.456 63.158 0.00 0.00 46.10 3.16
2127 2165 2.973694 ATTCAAACTGCCATGATGCC 57.026 45.000 0.00 0.00 0.00 4.40
2184 2222 5.048434 ACAAACTAGCAATTCTTTCAGCTCC 60.048 40.000 0.00 0.00 38.47 4.70
2207 2245 0.752054 CTCCTGATGAGTCCAGAGGC 59.248 60.000 0.00 0.00 36.27 4.70
2246 2285 3.506067 ACAGAAATTGATCGTTCCCCAAC 59.494 43.478 0.00 0.00 0.00 3.77
2279 2318 6.437928 TGTTTCAGAATTTTCAGACCAATCG 58.562 36.000 0.00 0.00 0.00 3.34
2408 2447 0.940126 CAAGATGATTCCTTCGCCGG 59.060 55.000 0.00 0.00 0.00 6.13
2504 2543 0.673333 TCAATGTGCACAGCCTACGG 60.673 55.000 25.84 8.93 0.00 4.02
2559 2599 4.410492 AAATTGTTGCAGCGAGTAAGAG 57.590 40.909 0.00 0.00 0.00 2.85
2562 2602 0.718343 GTTGCAGCGAGTAAGAGCAG 59.282 55.000 0.00 0.00 36.47 4.24
2655 2695 5.105146 GGTATATTCTTGCTCCAGGATCGAT 60.105 44.000 0.00 0.00 0.00 3.59
2770 2810 2.159170 AGATAGCAAGCCGAGTCTGTTC 60.159 50.000 0.00 0.00 0.00 3.18
2771 2811 0.109272 TAGCAAGCCGAGTCTGTTCG 60.109 55.000 0.00 0.00 40.18 3.95
2772 2812 1.664965 GCAAGCCGAGTCTGTTCGT 60.665 57.895 0.00 0.00 38.88 3.85
2773 2813 0.388134 GCAAGCCGAGTCTGTTCGTA 60.388 55.000 0.00 0.00 38.88 3.43
2774 2814 1.933500 GCAAGCCGAGTCTGTTCGTAA 60.934 52.381 0.00 0.00 38.88 3.18
2775 2815 2.400399 CAAGCCGAGTCTGTTCGTAAA 58.600 47.619 0.00 0.00 38.88 2.01
2776 2816 2.993899 CAAGCCGAGTCTGTTCGTAAAT 59.006 45.455 0.00 0.00 38.88 1.40
2777 2817 2.877335 AGCCGAGTCTGTTCGTAAATC 58.123 47.619 0.00 0.00 38.88 2.17
2778 2818 2.492484 AGCCGAGTCTGTTCGTAAATCT 59.508 45.455 0.00 0.00 38.88 2.40
2779 2819 2.853003 GCCGAGTCTGTTCGTAAATCTC 59.147 50.000 0.00 0.00 38.88 2.75
2780 2820 3.672511 GCCGAGTCTGTTCGTAAATCTCA 60.673 47.826 0.00 0.00 38.88 3.27
2781 2821 4.482386 CCGAGTCTGTTCGTAAATCTCAA 58.518 43.478 0.00 0.00 38.88 3.02
2782 2822 4.559251 CCGAGTCTGTTCGTAAATCTCAAG 59.441 45.833 0.00 0.00 38.88 3.02
2783 2823 5.391449 CGAGTCTGTTCGTAAATCTCAAGA 58.609 41.667 0.00 0.00 35.91 3.02
2784 2824 6.030849 CGAGTCTGTTCGTAAATCTCAAGAT 58.969 40.000 0.00 0.00 35.91 2.40
2785 2825 7.187480 CGAGTCTGTTCGTAAATCTCAAGATA 58.813 38.462 0.00 0.00 35.91 1.98
2786 2826 7.696872 CGAGTCTGTTCGTAAATCTCAAGATAA 59.303 37.037 0.00 0.00 35.91 1.75
2787 2827 9.522804 GAGTCTGTTCGTAAATCTCAAGATAAT 57.477 33.333 0.00 0.00 33.73 1.28
2792 2832 8.988934 TGTTCGTAAATCTCAAGATAATATGCC 58.011 33.333 0.00 0.00 33.73 4.40
2793 2833 7.812309 TCGTAAATCTCAAGATAATATGCCG 57.188 36.000 0.00 0.00 33.73 5.69
2794 2834 6.811665 TCGTAAATCTCAAGATAATATGCCGG 59.188 38.462 0.00 0.00 33.73 6.13
2795 2835 5.886960 AAATCTCAAGATAATATGCCGGC 57.113 39.130 22.73 22.73 33.73 6.13
2796 2836 4.833478 ATCTCAAGATAATATGCCGGCT 57.167 40.909 29.70 15.76 32.01 5.52
2797 2837 4.193826 TCTCAAGATAATATGCCGGCTC 57.806 45.455 29.70 15.82 0.00 4.70
2798 2838 3.578282 TCTCAAGATAATATGCCGGCTCA 59.422 43.478 29.70 15.91 0.00 4.26
2799 2839 4.040339 TCTCAAGATAATATGCCGGCTCAA 59.960 41.667 29.70 13.42 0.00 3.02
2800 2840 4.318332 TCAAGATAATATGCCGGCTCAAG 58.682 43.478 29.70 11.67 0.00 3.02
2801 2841 2.704572 AGATAATATGCCGGCTCAAGC 58.295 47.619 29.70 11.31 41.14 4.01
2802 2842 2.304180 AGATAATATGCCGGCTCAAGCT 59.696 45.455 29.70 13.49 41.70 3.74
2803 2843 2.638480 TAATATGCCGGCTCAAGCTT 57.362 45.000 29.70 14.20 41.70 3.74
2804 2844 1.312815 AATATGCCGGCTCAAGCTTC 58.687 50.000 29.70 0.00 41.70 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.865446 CCTGACATGCTTGTACTGATGA 58.135 45.455 5.05 0.00 35.79 2.92
11 12 1.021390 GCGCCTGACATGCTTGTACT 61.021 55.000 5.05 0.00 35.79 2.73
19 20 2.177531 GCAAGTGCGCCTGACATG 59.822 61.111 4.18 0.35 0.00 3.21
29 30 1.987770 CGGATCATTTTGTGCAAGTGC 59.012 47.619 0.00 0.00 42.50 4.40
70 71 4.085357 TGCGGGCTCTATTGAAATACAT 57.915 40.909 0.00 0.00 0.00 2.29
75 76 2.790433 ACTTTGCGGGCTCTATTGAAA 58.210 42.857 0.00 0.00 0.00 2.69
76 77 2.489938 ACTTTGCGGGCTCTATTGAA 57.510 45.000 0.00 0.00 0.00 2.69
84 85 0.820871 TGTTTGAAACTTTGCGGGCT 59.179 45.000 9.69 0.00 0.00 5.19
123 124 7.448748 AACTATTCAACCTCATGTTTACACC 57.551 36.000 0.00 0.00 34.00 4.16
155 156 3.068024 TGCAATTGAGTCCCACAAACTTC 59.932 43.478 10.34 0.00 0.00 3.01
305 307 7.384477 ACCAGACAAGTAGTAGGTTTCATAAC 58.616 38.462 0.00 0.00 35.78 1.89
320 322 0.320697 GTAGGCCGAACCAGACAAGT 59.679 55.000 0.00 0.00 43.14 3.16
378 381 7.869429 ACTTGAAATCATCTGAAATTTGACCAC 59.131 33.333 0.00 0.00 0.00 4.16
401 404 7.335422 CCTTGTATTAGCACAGAGAATTCACTT 59.665 37.037 8.44 0.00 0.00 3.16
410 413 5.724328 TCTGAACCTTGTATTAGCACAGAG 58.276 41.667 0.00 0.00 0.00 3.35
432 435 6.486657 TCCATGAAATCCCGATGTTTAGAATC 59.513 38.462 0.00 0.00 0.00 2.52
462 465 5.484173 TGTCGCATGAAAATGGAAGATAC 57.516 39.130 0.00 0.00 0.00 2.24
477 480 9.230122 TCAAATATTTATGTATGGATGTCGCAT 57.770 29.630 0.00 0.00 0.00 4.73
592 597 3.651803 ACCTCGTTTGTCTCTCAAGAG 57.348 47.619 0.33 0.33 43.36 2.85
640 650 2.298446 CTGAGAACCTTCTGTCTGCTCA 59.702 50.000 0.00 0.00 37.73 4.26
642 652 1.001860 GCTGAGAACCTTCTGTCTGCT 59.998 52.381 0.00 0.00 37.73 4.24
643 653 1.437625 GCTGAGAACCTTCTGTCTGC 58.562 55.000 0.00 0.00 37.73 4.26
644 654 1.345741 TGGCTGAGAACCTTCTGTCTG 59.654 52.381 0.00 0.00 37.73 3.51
647 657 0.398318 GGTGGCTGAGAACCTTCTGT 59.602 55.000 0.00 0.00 37.73 3.41
760 771 1.900545 CGGTTGGGGAGGAAGAGGAC 61.901 65.000 0.00 0.00 0.00 3.85
807 827 1.475280 CTGGTAATATAGGCGCGGCTA 59.525 52.381 39.34 39.34 0.00 3.93
808 828 0.246635 CTGGTAATATAGGCGCGGCT 59.753 55.000 37.69 37.69 0.00 5.52
877 899 1.269012 ATGCAACAACATGAAGGGGG 58.731 50.000 0.00 0.00 0.00 5.40
905 937 2.758979 TCAACTAATGACCTCGTCTCCC 59.241 50.000 0.00 0.00 33.15 4.30
928 960 1.079819 AACCGATCGACTGCTGGTG 60.080 57.895 18.66 0.00 32.14 4.17
935 967 0.686441 TGATCCCCAACCGATCGACT 60.686 55.000 18.66 0.00 39.23 4.18
937 969 1.070134 GATTGATCCCCAACCGATCGA 59.930 52.381 18.66 0.00 39.23 3.59
948 980 1.943340 GCCTTCTGTTCGATTGATCCC 59.057 52.381 0.00 0.00 0.00 3.85
953 985 1.391485 CGACTGCCTTCTGTTCGATTG 59.609 52.381 0.00 0.00 0.00 2.67
957 989 1.006102 ACCGACTGCCTTCTGTTCG 60.006 57.895 0.00 0.00 0.00 3.95
959 991 0.687354 ATCACCGACTGCCTTCTGTT 59.313 50.000 0.00 0.00 0.00 3.16
960 992 0.247736 GATCACCGACTGCCTTCTGT 59.752 55.000 0.00 0.00 0.00 3.41
1198 1230 0.239082 TCAGCGCATATACGTACCCG 59.761 55.000 11.47 0.00 40.83 5.28
1252 1288 2.663602 CACAGACCGTCAGAGAAATTCG 59.336 50.000 0.40 0.00 0.00 3.34
1269 1305 1.095228 ACACCACCAAGAACGCACAG 61.095 55.000 0.00 0.00 0.00 3.66
1271 1307 1.355210 CACACCACCAAGAACGCAC 59.645 57.895 0.00 0.00 0.00 5.34
1304 1340 4.113815 CCTGATCGCCCCCTGCAA 62.114 66.667 0.00 0.00 41.33 4.08
1531 1567 3.673599 GTGAAGAAGGGCTGCACC 58.326 61.111 0.00 0.00 45.97 5.01
1958 1995 9.739276 TCACATCTTGTTACCATCTTAATTCTT 57.261 29.630 0.00 0.00 0.00 2.52
1959 1996 9.388506 CTCACATCTTGTTACCATCTTAATTCT 57.611 33.333 0.00 0.00 0.00 2.40
1960 1997 8.125448 GCTCACATCTTGTTACCATCTTAATTC 58.875 37.037 0.00 0.00 0.00 2.17
1961 1998 7.611467 TGCTCACATCTTGTTACCATCTTAATT 59.389 33.333 0.00 0.00 0.00 1.40
1962 1999 7.112122 TGCTCACATCTTGTTACCATCTTAAT 58.888 34.615 0.00 0.00 0.00 1.40
1963 2000 6.472016 TGCTCACATCTTGTTACCATCTTAA 58.528 36.000 0.00 0.00 0.00 1.85
2057 2094 8.296713 TCAACCATATTTAAGCAGAAACTCAAC 58.703 33.333 0.00 0.00 0.00 3.18
2165 2203 3.626670 CCAGGAGCTGAAAGAATTGCTAG 59.373 47.826 0.00 0.00 35.76 3.42
2207 2245 0.457851 TGTTGGACGTTTTGCCTTGG 59.542 50.000 0.00 0.00 0.00 3.61
2246 2285 8.717821 TCTGAAAATTCTGAAACAGTATAACCG 58.282 33.333 0.00 0.00 33.11 4.44
2279 2318 4.985409 CCTCAGACTAATGGATTAACTCGC 59.015 45.833 0.00 0.00 0.00 5.03
2504 2543 3.858503 GCTGCTGAATCTCCAACCAAAAC 60.859 47.826 0.00 0.00 0.00 2.43
2559 2599 2.006772 CGCGGACTATGAAACCTGC 58.993 57.895 0.00 0.00 0.00 4.85
2562 2602 2.522638 CGGCGCGGACTATGAAACC 61.523 63.158 9.72 0.00 0.00 3.27
2629 2669 5.623368 CGATCCTGGAGCAAGAATATACCTC 60.623 48.000 13.04 0.00 0.00 3.85
2655 2695 2.835764 CCTTTGCACCTACTACCTACCA 59.164 50.000 0.00 0.00 0.00 3.25
2770 2810 6.455646 GCCGGCATATTATCTTGAGATTTACG 60.456 42.308 24.80 0.00 36.05 3.18
2771 2811 6.595716 AGCCGGCATATTATCTTGAGATTTAC 59.404 38.462 31.54 0.00 36.05 2.01
2772 2812 6.711277 AGCCGGCATATTATCTTGAGATTTA 58.289 36.000 31.54 0.00 36.05 1.40
2773 2813 5.564550 AGCCGGCATATTATCTTGAGATTT 58.435 37.500 31.54 0.00 36.05 2.17
2774 2814 5.171339 AGCCGGCATATTATCTTGAGATT 57.829 39.130 31.54 0.00 36.05 2.40
2775 2815 4.223700 TGAGCCGGCATATTATCTTGAGAT 59.776 41.667 31.54 0.06 38.51 2.75
2776 2816 3.578282 TGAGCCGGCATATTATCTTGAGA 59.422 43.478 31.54 0.00 0.00 3.27
2777 2817 3.930336 TGAGCCGGCATATTATCTTGAG 58.070 45.455 31.54 0.00 0.00 3.02
2778 2818 4.318332 CTTGAGCCGGCATATTATCTTGA 58.682 43.478 31.54 5.81 0.00 3.02
2779 2819 3.120060 GCTTGAGCCGGCATATTATCTTG 60.120 47.826 31.54 13.27 34.31 3.02
2780 2820 3.077359 GCTTGAGCCGGCATATTATCTT 58.923 45.455 31.54 3.33 34.31 2.40
2781 2821 2.304180 AGCTTGAGCCGGCATATTATCT 59.696 45.455 31.54 13.24 43.38 1.98
2782 2822 2.704572 AGCTTGAGCCGGCATATTATC 58.295 47.619 31.54 16.99 43.38 1.75
2783 2823 2.867109 AGCTTGAGCCGGCATATTAT 57.133 45.000 31.54 6.18 43.38 1.28
2784 2824 2.494059 GAAGCTTGAGCCGGCATATTA 58.506 47.619 31.54 6.61 43.38 0.98
2785 2825 1.312815 GAAGCTTGAGCCGGCATATT 58.687 50.000 31.54 13.97 43.38 1.28
2786 2826 3.012560 GAAGCTTGAGCCGGCATAT 57.987 52.632 31.54 8.11 43.38 1.78
2787 2827 4.540153 GAAGCTTGAGCCGGCATA 57.460 55.556 31.54 14.63 43.38 3.14


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

AutoCloner maintained by Alex Coulton.