Multiple sequence alignment - TraesCS7D01G246900

Loading Multiple Alignment...

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 TraesCS7D01G246900 chr7D 100.000 3179 0 0 454 3632 216085288 216082110 0.000000e+00 5871.0
1 TraesCS7D01G246900 chr7D 100.000 198 0 0 1 198 216085741 216085544 2.310000e-97 366.0
2 TraesCS7D01G246900 chr7D 100.000 168 0 0 3902 4069 216081840 216081673 1.100000e-80 311.0
3 TraesCS7D01G246900 chr7A 97.610 2636 52 5 1001 3632 229145667 229143039 0.000000e+00 4508.0
4 TraesCS7D01G246900 chr7A 86.032 315 40 4 454 767 229176839 229176528 6.520000e-88 335.0
5 TraesCS7D01G246900 chr7A 91.765 170 12 1 3902 4069 229143028 229142859 6.800000e-58 235.0
6 TraesCS7D01G246900 chr7A 91.429 140 7 3 859 998 229145840 229145706 1.930000e-43 187.0
7 TraesCS7D01G246900 chr7B 97.040 2635 67 5 1001 3632 184296956 184299582 0.000000e+00 4423.0
8 TraesCS7D01G246900 chr7B 93.855 358 21 1 454 810 184295820 184296177 4.630000e-149 538.0
9 TraesCS7D01G246900 chr7B 90.576 191 15 3 1 189 184295586 184295775 2.430000e-62 250.0
10 TraesCS7D01G246900 chr7B 91.813 171 11 2 3902 4069 184299594 184299764 6.800000e-58 235.0
11 TraesCS7D01G246900 chr7B 93.860 114 4 2 807 920 184296306 184296416 6.990000e-38 169.0
12 TraesCS7D01G246900 chr7B 91.304 92 4 3 907 998 184296830 184296917 5.520000e-24 122.0
13 TraesCS7D01G246900 chr5B 92.347 196 15 0 3399 3594 450842129 450841934 3.100000e-71 279.0
14 TraesCS7D01G246900 chr5D 93.122 189 13 0 3406 3594 377534597 377534409 1.110000e-70 278.0
15 TraesCS7D01G246900 chr5A 93.122 189 13 0 3406 3594 478322171 478321983 1.110000e-70 278.0
16 TraesCS7D01G246900 chr1D 83.750 80 8 4 658 732 255707144 255707223 2.030000e-08 71.3
17 TraesCS7D01G246900 chr1A 90.196 51 5 0 682 732 328087553 328087603 2.620000e-07 67.6


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 TraesCS7D01G246900 chr7D 216081673 216085741 4068 True 2182.666667 5871 100.000000 1 4069 3 chr7D.!!$R1 4068
1 TraesCS7D01G246900 chr7A 229142859 229145840 2981 True 1643.333333 4508 93.601333 859 4069 3 chr7A.!!$R2 3210
2 TraesCS7D01G246900 chr7B 184295586 184299764 4178 False 956.166667 4423 93.074667 1 4069 6 chr7B.!!$F1 4068

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
795 798 0.180406 AAGGTGACGTGGTTGAAGCT 59.820 50.0 0.00 0.0 0.00 3.74 F
998 1560 0.241481 GTCGATCTAAGCCTAGCGGG 59.759 60.0 0.00 0.0 38.36 6.13 F
999 1561 0.894184 TCGATCTAAGCCTAGCGGGG 60.894 60.0 1.23 0.0 35.12 5.73 F
1501 2099 0.895530 TGGACATGAAGAGGGACGAC 59.104 55.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2397 1.065418 CAAGGTACCCTGGTTAGCTGG 60.065 57.143 8.74 0.0 32.13 4.85 R
2932 3530 0.035534 TTGCCAGTGTGTGTCAGTGT 60.036 50.000 0.00 0.0 43.72 3.55 R
2934 3532 0.464373 CCTTGCCAGTGTGTGTCAGT 60.464 55.000 0.00 0.0 0.00 3.41 R
3206 3809 0.544697 GGGAAAGAGATACGGCCCAA 59.455 55.000 0.00 0.0 35.63 4.12 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
21 22 1.176527 CATTGACGGGCCATCAGTTT 58.823 50.000 4.39 0.00 0.00 2.66
29 30 4.517663 CCATCAGTTTGGCCCACA 57.482 55.556 0.00 0.00 0.00 4.17
31 32 0.251297 CCATCAGTTTGGCCCACAGA 60.251 55.000 0.00 0.00 0.00 3.41
74 75 1.154016 CTAGTCCAGCACACCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
128 130 2.932614 CAATTAGTGGCCAAGAGAGACG 59.067 50.000 7.24 0.00 0.00 4.18
140 142 4.498241 CAAGAGAGACGTCCAATCAATCA 58.502 43.478 13.01 0.00 0.00 2.57
163 165 3.484742 GACGATCGCCGAGCCATGA 62.485 63.158 16.60 0.00 41.76 3.07
175 177 2.771089 GAGCCATGACTCTGTTCAACA 58.229 47.619 1.16 0.00 33.69 3.33
176 178 2.481952 GAGCCATGACTCTGTTCAACAC 59.518 50.000 1.16 0.00 33.69 3.32
182 184 0.249911 ACTCTGTTCAACACTCGGGC 60.250 55.000 0.00 0.00 0.00 6.13
184 186 2.954753 CTGTTCAACACTCGGGCGC 61.955 63.158 0.00 0.00 0.00 6.53
185 187 4.072088 GTTCAACACTCGGGCGCG 62.072 66.667 18.21 18.21 0.00 6.86
473 475 1.320507 GTCCCTCTCGACTACATCCC 58.679 60.000 0.00 0.00 0.00 3.85
490 492 4.253257 CTAGGCGGCTCGACGACC 62.253 72.222 17.67 0.00 44.75 4.79
497 499 3.485431 GCTCGACGACCGTCTCGA 61.485 66.667 18.60 16.81 46.14 4.04
526 528 1.928706 GCTACGCCGGCCAAAATTGA 61.929 55.000 23.46 0.00 0.00 2.57
550 552 1.838112 GATGCCCTGACAACCATCAA 58.162 50.000 0.00 0.00 35.38 2.57
553 555 2.607499 TGCCCTGACAACCATCAAATT 58.393 42.857 0.00 0.00 0.00 1.82
626 629 1.178276 TTGGGCGCCGATTTTACATT 58.822 45.000 22.54 0.00 0.00 2.71
667 670 1.407618 GAAGCGGTGTCCAAAAACCTT 59.592 47.619 0.00 0.00 34.06 3.50
675 678 4.645136 GGTGTCCAAAAACCTTCTTTCTCT 59.355 41.667 0.00 0.00 33.40 3.10
690 693 7.928167 CCTTCTTTCTCTTTGGCTAATTGTTTT 59.072 33.333 0.00 0.00 0.00 2.43
694 697 9.196552 CTTTCTCTTTGGCTAATTGTTTTTAGG 57.803 33.333 0.00 0.00 31.19 2.69
695 698 7.227049 TCTCTTTGGCTAATTGTTTTTAGGG 57.773 36.000 0.00 0.00 31.19 3.53
716 719 5.359009 AGGGCATCAAGTTTTACATCATCAG 59.641 40.000 0.00 0.00 0.00 2.90
767 770 5.185828 GGTCCTTGTTATTCTTCAATGGCTT 59.814 40.000 0.00 0.00 0.00 4.35
783 786 6.983890 TCAATGGCTTTTCTTTTTAAGGTGAC 59.016 34.615 0.00 0.00 0.00 3.67
795 798 0.180406 AAGGTGACGTGGTTGAAGCT 59.820 50.000 0.00 0.00 0.00 3.74
813 948 6.003950 TGAAGCTGCATTAGGAGTTAGTTTT 58.996 36.000 1.02 0.00 35.34 2.43
850 985 6.213600 AGAATAGGACATACATATGGTCACCC 59.786 42.308 7.80 2.90 38.00 4.61
944 1506 5.997129 ACCCTTTTGATAATTTGCCTTTGTG 59.003 36.000 0.00 0.00 0.00 3.33
945 1507 5.997129 CCCTTTTGATAATTTGCCTTTGTGT 59.003 36.000 0.00 0.00 0.00 3.72
949 1511 7.630470 TTTGATAATTTGCCTTTGTGTTACG 57.370 32.000 0.00 0.00 0.00 3.18
965 1527 3.680937 TGTTACGTTGATTCGGTTCCATC 59.319 43.478 0.00 0.00 34.94 3.51
976 1538 1.280457 GGTTCCATCTCCCACAGTCT 58.720 55.000 0.00 0.00 0.00 3.24
998 1560 0.241481 GTCGATCTAAGCCTAGCGGG 59.759 60.000 0.00 0.00 38.36 6.13
999 1561 0.894184 TCGATCTAAGCCTAGCGGGG 60.894 60.000 1.23 0.00 35.12 5.73
1012 1610 2.264124 GCGGGGTATGAGATCGCTA 58.736 57.895 0.00 0.00 42.62 4.26
1351 1949 2.419990 CCTCATCTCCATGTACGCCAAA 60.420 50.000 0.00 0.00 0.00 3.28
1460 2058 3.995506 AATGCCGGCGGGAGGAAAG 62.996 63.158 29.48 0.00 34.06 2.62
1501 2099 0.895530 TGGACATGAAGAGGGACGAC 59.104 55.000 0.00 0.00 0.00 4.34
1723 2321 4.927978 TTTGGTTGTGTGGAATTCGATT 57.072 36.364 0.00 0.00 0.00 3.34
1799 2397 2.573915 AGGATGAAGGAGTCTGGTTTCC 59.426 50.000 0.00 0.00 0.00 3.13
2164 2762 1.304381 TGGCTTGGTGGAAGATGGC 60.304 57.895 0.00 0.00 32.82 4.40
2252 2850 0.902531 GGTTGATCTCCTTGGTCGGA 59.097 55.000 0.00 0.00 0.00 4.55
2308 2906 2.237143 TGAGATGAACTTTGAGCCGGAT 59.763 45.455 5.05 0.00 0.00 4.18
2419 3017 2.742372 CCGGAAGACCAAGGTGCG 60.742 66.667 0.00 0.00 35.59 5.34
2627 3225 3.194968 GGAACTGAACCGACTAATCAGGA 59.805 47.826 6.92 0.00 43.79 3.86
2728 3326 6.414408 CTGAAATATCACAGCGAGAAACTT 57.586 37.500 0.00 0.00 0.00 2.66
2866 3464 4.508047 GGCAAGGTGATCATAATCAGGGAT 60.508 45.833 0.00 0.00 42.53 3.85
2929 3527 3.130693 GTGGCGACTATTGGTAGAGAAGT 59.869 47.826 0.00 0.00 0.00 3.01
2932 3530 5.419788 TGGCGACTATTGGTAGAGAAGTTAA 59.580 40.000 0.00 0.00 0.00 2.01
2933 3531 5.747675 GGCGACTATTGGTAGAGAAGTTAAC 59.252 44.000 0.00 0.00 0.00 2.01
2934 3532 6.327934 GCGACTATTGGTAGAGAAGTTAACA 58.672 40.000 8.61 0.00 0.00 2.41
2935 3533 6.253083 GCGACTATTGGTAGAGAAGTTAACAC 59.747 42.308 8.61 1.57 0.00 3.32
2936 3534 7.536855 CGACTATTGGTAGAGAAGTTAACACT 58.463 38.462 8.61 6.70 33.11 3.55
2937 3535 7.485277 CGACTATTGGTAGAGAAGTTAACACTG 59.515 40.741 8.61 0.00 31.60 3.66
3017 3615 3.648339 TTTCTTTGCAACTCAGATGCC 57.352 42.857 4.19 0.00 43.16 4.40
3132 3731 8.840321 CAGTCAAAAGAACAAAGATAAAGGAGA 58.160 33.333 0.00 0.00 0.00 3.71
3206 3809 1.109323 GCGGCCATAAAGAAGCCCAT 61.109 55.000 2.24 0.00 44.13 4.00
3249 3854 0.749091 CATCCGCCTCATCCAAGCAA 60.749 55.000 0.00 0.00 0.00 3.91
3269 3874 1.748493 AGCAAAGCCGAAACAGAACAA 59.252 42.857 0.00 0.00 0.00 2.83
3287 3892 1.792118 AAGGAAAGAAACGCGCCCAC 61.792 55.000 5.73 0.00 0.00 4.61
3310 3915 0.810426 GAATTCCGGCGTCCTCTTCC 60.810 60.000 6.01 0.00 0.00 3.46
3455 4060 1.124780 TGGACAGGTTCGTGAAGGAA 58.875 50.000 0.00 0.00 0.00 3.36
3581 4186 2.038007 TGGAAGGCCGAGCTCTCT 59.962 61.111 12.85 3.75 36.79 3.10
3930 4536 2.741985 CGCCACCGTGATCAGCAA 60.742 61.111 0.00 0.00 0.00 3.91
3932 4538 1.647545 CGCCACCGTGATCAGCAATT 61.648 55.000 0.00 0.00 0.00 2.32
3969 4575 2.146342 CGATCGAGAATGGGGGAAATG 58.854 52.381 10.26 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.611673 CCTAGTCTGTGGGCCAAACTG 60.612 57.143 21.45 6.72 0.00 3.16
21 22 4.130255 GACCTAGTCTGTGGGCCA 57.870 61.111 0.00 0.00 0.00 5.36
29 30 2.444010 CCTAGCCTAGTGGACCTAGTCT 59.556 54.545 0.00 0.00 41.48 3.24
31 32 2.175284 GTCCTAGCCTAGTGGACCTAGT 59.825 54.545 0.00 0.00 43.10 2.57
63 64 4.065281 GGCTACCGACGGTGTGCT 62.065 66.667 31.20 11.80 36.19 4.40
65 66 4.446413 GGGGCTACCGACGGTGTG 62.446 72.222 29.55 21.22 36.19 3.82
74 75 1.421480 AGATAAGTTCGGGGGCTACC 58.579 55.000 0.00 0.00 39.11 3.18
120 122 4.499183 GTTGATTGATTGGACGTCTCTCT 58.501 43.478 16.46 0.00 0.00 3.10
121 123 3.304559 CGTTGATTGATTGGACGTCTCTC 59.695 47.826 16.46 10.15 0.00 3.20
128 130 2.734606 TCGTCACGTTGATTGATTGGAC 59.265 45.455 0.00 0.00 0.00 4.02
140 142 2.202440 CTCGGCGATCGTCACGTT 60.202 61.111 21.12 0.00 40.32 3.99
144 146 3.527427 ATGGCTCGGCGATCGTCA 61.527 61.111 21.12 8.19 40.32 4.35
163 165 0.249911 GCCCGAGTGTTGAACAGAGT 60.250 55.000 0.00 0.00 0.00 3.24
465 467 1.867919 CGAGCCGCCTAGGGATGTAG 61.868 65.000 11.72 0.00 41.48 2.74
473 475 4.253257 GGTCGTCGAGCCGCCTAG 62.253 72.222 13.42 0.00 0.00 3.02
526 528 1.296715 GTTGTCAGGGCATCGACCT 59.703 57.895 0.00 0.00 45.50 3.85
532 534 2.307496 TTTGATGGTTGTCAGGGCAT 57.693 45.000 0.00 0.00 0.00 4.40
613 616 7.902917 GCTTTTTCCAAATAATGTAAAATCGGC 59.097 33.333 0.00 0.00 0.00 5.54
626 629 6.257630 GCTTCTGTTGTTGCTTTTTCCAAATA 59.742 34.615 0.00 0.00 0.00 1.40
644 647 1.404035 GTTTTTGGACACCGCTTCTGT 59.596 47.619 0.00 0.00 0.00 3.41
667 670 9.965824 CTAAAAACAATTAGCCAAAGAGAAAGA 57.034 29.630 0.00 0.00 0.00 2.52
675 678 5.552870 TGCCCTAAAAACAATTAGCCAAA 57.447 34.783 0.00 0.00 32.62 3.28
690 693 6.889177 TGATGATGTAAAACTTGATGCCCTAA 59.111 34.615 0.00 0.00 0.00 2.69
694 697 6.199937 ACTGATGATGTAAAACTTGATGCC 57.800 37.500 0.00 0.00 0.00 4.40
695 698 7.307694 TCAACTGATGATGTAAAACTTGATGC 58.692 34.615 0.00 0.00 31.50 3.91
767 770 5.415077 TCAACCACGTCACCTTAAAAAGAAA 59.585 36.000 0.00 0.00 0.00 2.52
783 786 1.131126 CCTAATGCAGCTTCAACCACG 59.869 52.381 0.00 0.00 0.00 4.94
900 1035 9.636789 AAAGGGTCACTAAACTACAGTTATTTT 57.363 29.630 0.00 0.00 37.25 1.82
944 1506 3.930848 AGATGGAACCGAATCAACGTAAC 59.069 43.478 0.00 0.00 0.00 2.50
945 1507 4.178540 GAGATGGAACCGAATCAACGTAA 58.821 43.478 0.00 0.00 0.00 3.18
949 1511 2.289565 GGGAGATGGAACCGAATCAAC 58.710 52.381 0.00 0.00 0.00 3.18
965 1527 1.403679 GATCGACTCAGACTGTGGGAG 59.596 57.143 9.22 4.31 34.85 4.30
976 1538 1.874231 CGCTAGGCTTAGATCGACTCA 59.126 52.381 7.11 0.00 0.00 3.41
1012 1610 2.639327 GCAAGGCAGGCGGTTGAAT 61.639 57.895 8.64 0.00 0.00 2.57
1069 1667 2.034221 GGTTGGGAGTGGGAGTGC 59.966 66.667 0.00 0.00 0.00 4.40
1351 1949 1.741770 GTCGTGGAGCAAGCCGAAT 60.742 57.895 0.00 0.00 0.00 3.34
1460 2058 1.448717 GAAACCTGAGCGCCTCCTC 60.449 63.158 2.29 0.00 0.00 3.71
1501 2099 0.250124 TGTAACTGTTGGGAGCCACG 60.250 55.000 2.69 0.00 30.78 4.94
1744 2342 3.061848 GCCCCAACACCATCACCG 61.062 66.667 0.00 0.00 0.00 4.94
1799 2397 1.065418 CAAGGTACCCTGGTTAGCTGG 60.065 57.143 8.74 0.00 32.13 4.85
2067 2665 4.934075 TCAGATTGCATCAAGTCGAAAG 57.066 40.909 0.00 0.00 0.00 2.62
2164 2762 6.326583 TCTCCATGGACCTAAAGTAATACCAG 59.673 42.308 11.44 0.00 0.00 4.00
2252 2850 3.614399 CTTCGTCAAGCTTCCCTGT 57.386 52.632 0.00 0.00 0.00 4.00
2308 2906 4.956700 AGAAGAGTTCTCCATATGACCGAA 59.043 41.667 3.65 1.00 34.07 4.30
2419 3017 7.409661 GCATATGTATTTGACAACAATATGCGC 60.410 37.037 18.30 0.00 42.78 6.09
2815 3413 0.039437 TGGAGACGAGCTTCACGAAC 60.039 55.000 0.00 0.00 34.70 3.95
2929 3527 2.285083 GCCAGTGTGTGTCAGTGTTAA 58.715 47.619 0.00 0.00 43.72 2.01
2932 3530 0.035534 TTGCCAGTGTGTGTCAGTGT 60.036 50.000 0.00 0.00 43.72 3.55
2933 3531 0.659427 CTTGCCAGTGTGTGTCAGTG 59.341 55.000 0.00 0.00 44.54 3.66
2934 3532 0.464373 CCTTGCCAGTGTGTGTCAGT 60.464 55.000 0.00 0.00 0.00 3.41
2935 3533 1.789078 GCCTTGCCAGTGTGTGTCAG 61.789 60.000 0.00 0.00 0.00 3.51
2936 3534 1.823470 GCCTTGCCAGTGTGTGTCA 60.823 57.895 0.00 0.00 0.00 3.58
2937 3535 1.510480 GAGCCTTGCCAGTGTGTGTC 61.510 60.000 0.00 0.00 0.00 3.67
3206 3809 0.544697 GGGAAAGAGATACGGCCCAA 59.455 55.000 0.00 0.00 35.63 4.12
3249 3854 1.388547 TGTTCTGTTTCGGCTTTGCT 58.611 45.000 0.00 0.00 0.00 3.91
3269 3874 2.112297 TGGGCGCGTTTCTTTCCT 59.888 55.556 8.43 0.00 0.00 3.36
3287 3892 2.585247 GGACGCCGGAATTCCTCG 60.585 66.667 25.00 25.00 36.31 4.63
3310 3915 2.514824 GGCTTCTAGGGCTTGCGG 60.515 66.667 8.14 0.00 0.00 5.69
3384 3989 2.551912 GCCTCAACAACCACCACCG 61.552 63.158 0.00 0.00 0.00 4.94
3455 4060 2.604686 TCCAGCGCCTCCTTGAGT 60.605 61.111 2.29 0.00 0.00 3.41
3581 4186 4.170062 CTCGTTACCTCGCGGCGA 62.170 66.667 24.84 24.84 0.00 5.54
3912 4517 2.520465 ATTGCTGATCACGGTGGCGA 62.520 55.000 8.50 3.97 0.00 5.54
3913 4518 1.647545 AATTGCTGATCACGGTGGCG 61.648 55.000 8.50 0.00 0.00 5.69
3920 4526 4.933330 AGATGATGCAAATTGCTGATCAC 58.067 39.130 18.93 13.93 45.31 3.06
3969 4575 3.126879 TGCCGCTGCAGCATACAC 61.127 61.111 36.03 20.38 44.23 2.90
3989 4595 6.861065 ATAGTACACTGAAACACAAACCAG 57.139 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.