Multiple sequence alignment - TraesCS3A01G317800

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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 TraesCS3A01G317800 chr3A 100.000 4040 0 0 1 4040 558894421 558890382 0.000000e+00 7461.0
1 TraesCS3A01G317800 chr3B 95.342 3199 104 17 853 4037 557086897 557090064 0.000000e+00 5040.0
2 TraesCS3A01G317800 chr3B 83.455 822 97 18 7 806 557047596 557048400 0.000000e+00 728.0
3 TraesCS3A01G317800 chr3D 94.013 3374 114 24 712 4040 427445288 427448618 0.000000e+00 5031.0
4 TraesCS3A01G317800 chr3D 87.483 719 54 14 1 706 427444248 427444943 0.000000e+00 797.0
5 TraesCS3A01G317800 chr5B 72.230 713 159 33 2138 2826 63260868 63260171 2.480000e-42 183.0
6 TraesCS3A01G317800 chr7B 86.957 92 12 0 442 533 62762880 62762971 1.990000e-18 104.0
7 TraesCS3A01G317800 chr7B 100.000 30 0 0 2569 2598 682843861 682843890 5.640000e-04 56.5
8 TraesCS3A01G317800 chr7B 100.000 30 0 0 2569 2598 683152190 683152219 5.640000e-04 56.5
9 TraesCS3A01G317800 chr4D 82.114 123 21 1 2338 2460 81909031 81909152 1.990000e-18 104.0
10 TraesCS3A01G317800 chr4B 81.301 123 22 1 2338 2460 115530201 115530322 9.240000e-17 99.0
11 TraesCS3A01G317800 chr1D 73.298 191 48 2 2105 2295 462335956 462336143 2.610000e-07 67.6
12 TraesCS3A01G317800 chr7A 100.000 29 0 0 2570 2598 694198131 694198159 2.000000e-03 54.7


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 TraesCS3A01G317800 chr3A 558890382 558894421 4039 True 7461 7461 100.000 1 4040 1 chr3A.!!$R1 4039
1 TraesCS3A01G317800 chr3B 557086897 557090064 3167 False 5040 5040 95.342 853 4037 1 chr3B.!!$F2 3184
2 TraesCS3A01G317800 chr3B 557047596 557048400 804 False 728 728 83.455 7 806 1 chr3B.!!$F1 799
3 TraesCS3A01G317800 chr3D 427444248 427448618 4370 False 2914 5031 90.748 1 4040 2 chr3D.!!$F1 4039

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
322 323 0.032515 TATGGAAGGAGAGGGACGCA 60.033 55.000 0.00 0.00 0.00 5.24 F
654 670 1.125930 CGCCCGCTTTTGTTTATTTGC 59.874 47.619 0.00 0.00 0.00 3.68 F
1836 2225 0.696501 GGGTGGTACTGGGATTGTGT 59.303 55.000 0.00 0.00 0.00 3.72 F
2616 3005 0.033781 TGGCACTGGAAATTGCTTGC 59.966 50.000 3.77 3.77 38.85 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1763 0.833287 CGGATCTGTTGGGGATGACT 59.167 55.0 0.00 0.0 0.0 3.41 R
2367 2756 0.976641 ACTGAAGGCATTCCTCGTGA 59.023 50.0 8.88 0.0 43.4 4.35 R
2922 3311 0.320771 ACGCACCTCCAACTGATGAC 60.321 55.0 0.00 0.0 0.0 3.06 R
3852 4257 1.250840 AAAAGCGGGAGATGGTTGCC 61.251 55.0 0.00 0.0 0.0 4.52 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
79 80 2.359230 GGCGAAAGAGCTGCAGGT 60.359 61.111 20.31 20.31 37.29 4.00
92 93 2.590575 CAGGTGTCGCCGGTGTTT 60.591 61.111 16.01 0.00 43.70 2.83
164 165 0.383231 GCTCATGAAGGGGCAAATCG 59.617 55.000 0.00 0.00 0.00 3.34
178 179 0.108186 AAATCGTCGATGAGCAGGCA 60.108 50.000 13.65 0.00 0.00 4.75
237 238 0.463474 GACTTCCTGGATGAGCAGCC 60.463 60.000 15.76 0.00 37.40 4.85
247 248 0.179073 ATGAGCAGCCGGTGATGTAC 60.179 55.000 1.90 0.00 0.00 2.90
322 323 0.032515 TATGGAAGGAGAGGGACGCA 60.033 55.000 0.00 0.00 0.00 5.24
363 364 3.462678 GTGGCCGGAGAGGAGGTC 61.463 72.222 5.05 0.00 45.00 3.85
369 370 2.039624 GGAGAGGAGGTCCAGGCA 59.960 66.667 0.00 0.00 38.89 4.75
432 433 4.129737 CGGCCACGACCACGAGAT 62.130 66.667 2.24 0.00 44.60 2.75
437 438 3.060000 ACGACCACGAGATCGGCA 61.060 61.111 0.68 0.00 44.95 5.69
440 441 1.658717 GACCACGAGATCGGCATCG 60.659 63.158 7.22 0.94 44.95 3.84
504 520 3.338275 GCCATGGCTTGGGTACCGA 62.338 63.158 29.98 0.00 46.55 4.69
531 547 2.360854 CCACTCCTATTCTTCCCCTCCT 60.361 54.545 0.00 0.00 0.00 3.69
544 560 2.401766 CCTCCTGTTGATGCACCGC 61.402 63.158 0.00 0.00 0.00 5.68
565 581 1.736645 GCGAGCTTGCCAGACGTAA 60.737 57.895 15.66 0.00 0.00 3.18
654 670 1.125930 CGCCCGCTTTTGTTTATTTGC 59.874 47.619 0.00 0.00 0.00 3.68
670 686 8.006590 TGTTTATTTGCAATGTATGAAAAACGC 58.993 29.630 0.00 0.00 40.02 4.84
689 705 6.456447 AACGCAATGAATTTGATCTGTTTG 57.544 33.333 0.00 0.00 37.53 2.93
767 1123 1.195442 TGGACACGGTTGGATAGCCA 61.195 55.000 0.00 0.00 44.17 4.75
774 1130 2.224670 ACGGTTGGATAGCCAGTTTTCA 60.225 45.455 0.00 0.00 46.91 2.69
780 1136 4.661222 TGGATAGCCAGTTTTCACATCAA 58.339 39.130 0.00 0.00 39.92 2.57
786 1142 3.005684 GCCAGTTTTCACATCAATGTCCA 59.994 43.478 0.00 0.00 39.39 4.02
798 1154 2.644299 TCAATGTCCATGAACTGGTCCT 59.356 45.455 0.00 0.00 46.08 3.85
838 1194 2.735772 ATGGCCGCGTTGGAGAGAT 61.736 57.895 4.92 0.00 42.00 2.75
914 1303 5.008118 GGTCTCAAGCAGTAGGATTTTATGC 59.992 44.000 0.00 0.00 37.15 3.14
999 1388 1.306226 GGCTCACCCTACCCACTCT 60.306 63.158 0.00 0.00 0.00 3.24
1040 1429 2.018086 CCTCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1041 1430 1.541672 CTCCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1042 1431 2.015726 TCCCTCCTCCTCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
1043 1432 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1044 1433 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1045 1434 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1374 1763 2.038975 CTCTCCCCGTTCCCCTCA 59.961 66.667 0.00 0.00 0.00 3.86
1836 2225 0.696501 GGGTGGTACTGGGATTGTGT 59.303 55.000 0.00 0.00 0.00 3.72
1854 2243 2.030805 GTGTGGATTCCTTGTTGTGCTC 60.031 50.000 3.95 0.00 0.00 4.26
1953 2342 0.806102 CAATGGGGTACGACGAGCTG 60.806 60.000 0.00 0.00 0.00 4.24
1987 2376 3.952508 TGCAGAGCGGGCCAAGAA 61.953 61.111 4.39 0.00 0.00 2.52
2009 2398 2.479560 GGTTCCGTTATGCTGAATTGGC 60.480 50.000 0.00 0.00 0.00 4.52
2346 2735 1.973281 CGACATTGCACTGGGCCTT 60.973 57.895 9.06 0.00 43.89 4.35
2367 2756 0.179000 CCTCGGCATTGCTCTACCTT 59.821 55.000 8.82 0.00 0.00 3.50
2433 2822 0.594028 GCAATGTGATGCTGGATGCG 60.594 55.000 0.00 0.00 46.63 4.73
2616 3005 0.033781 TGGCACTGGAAATTGCTTGC 59.966 50.000 3.77 3.77 38.85 4.01
2685 3074 2.505982 CCGTGGGTATGGGAGCTG 59.494 66.667 0.00 0.00 0.00 4.24
2692 3081 0.693049 GGTATGGGAGCTGTATGGGG 59.307 60.000 0.00 0.00 0.00 4.96
2694 3083 2.054799 GTATGGGAGCTGTATGGGGAA 58.945 52.381 0.00 0.00 0.00 3.97
2715 3104 4.760047 GCCCTTCTCGAAGCGGCA 62.760 66.667 22.89 0.00 45.66 5.69
2841 3230 1.755783 GGCCCTGAATGCCCTGAAG 60.756 63.158 0.00 0.00 43.33 3.02
2922 3311 0.954449 CTGACTTGGCTGCTCTGGTG 60.954 60.000 0.00 0.00 0.00 4.17
2953 3342 2.542907 GGTGCGTCCAACACACAGG 61.543 63.158 1.25 0.00 39.87 4.00
3081 3470 3.362831 GCTGCTTTCACGATGATTTTGTG 59.637 43.478 0.00 0.00 40.61 3.33
3099 3488 1.396996 GTGTGTTTCGTCTTGTGCTGT 59.603 47.619 0.00 0.00 0.00 4.40
3109 3498 3.664107 GTCTTGTGCTGTAACATGGAGA 58.336 45.455 0.00 0.00 0.00 3.71
3240 3632 5.246307 GCAGTTTGAGGTATTAGGTTGAGT 58.754 41.667 0.00 0.00 0.00 3.41
3241 3633 5.351740 GCAGTTTGAGGTATTAGGTTGAGTC 59.648 44.000 0.00 0.00 0.00 3.36
3242 3634 6.464222 CAGTTTGAGGTATTAGGTTGAGTCA 58.536 40.000 0.00 0.00 0.00 3.41
3313 3718 3.556513 GATACGAGCCAACTAGATGTCG 58.443 50.000 10.27 10.27 0.00 4.35
3399 3804 8.394877 CGCTCAAACTTTCACATGGTTATATAA 58.605 33.333 0.00 0.00 0.00 0.98
3413 3818 6.425577 GGTTATATAAAACCGCACTGAACA 57.574 37.500 0.00 0.00 39.62 3.18
3414 3819 6.483687 GGTTATATAAAACCGCACTGAACAG 58.516 40.000 0.00 0.00 39.62 3.16
3423 3828 1.880601 GCACTGAACAGACAGACGCG 61.881 60.000 3.53 3.53 40.63 6.01
3585 3990 1.075374 TCCCTACTTGCAGTGCCAAAT 59.925 47.619 13.72 0.00 0.00 2.32
3586 3991 1.895131 CCCTACTTGCAGTGCCAAATT 59.105 47.619 13.72 0.00 0.00 1.82
3616 4021 4.724399 TGGTCTAACAACCACAATGACAT 58.276 39.130 0.00 0.00 44.40 3.06
3620 4025 6.016276 GGTCTAACAACCACAATGACATCTTT 60.016 38.462 0.00 0.00 39.27 2.52
3702 4107 3.782656 TTGTTACCTCCCCTGAGAAAC 57.217 47.619 0.00 0.00 41.42 2.78
3780 4185 2.947652 CAGGAGGTGATGCTAAACCATG 59.052 50.000 5.30 0.00 39.05 3.66
3852 4257 5.890419 AGATTTATCTTCCCCAAAAGCTGAG 59.110 40.000 0.00 0.00 31.97 3.35
4025 4434 3.008049 AGGATTTAACCGAGTGAGCAGTT 59.992 43.478 0.00 0.00 34.73 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.963338 GCGACACCTGCAGCTCTTT 60.963 57.895 8.66 0.00 0.00 2.52
79 80 1.707239 GAACACAAACACCGGCGACA 61.707 55.000 9.30 0.00 0.00 4.35
92 93 2.599281 TCCTCCCGCGAGAACACA 60.599 61.111 8.23 0.00 38.52 3.72
164 165 1.014044 TCGTTTGCCTGCTCATCGAC 61.014 55.000 0.00 0.00 0.00 4.20
304 305 0.692419 ATGCGTCCCTCTCCTTCCAT 60.692 55.000 0.00 0.00 0.00 3.41
305 306 1.306141 ATGCGTCCCTCTCCTTCCA 60.306 57.895 0.00 0.00 0.00 3.53
322 323 3.814842 TCTGTGTCGATCTTTGCAAACAT 59.185 39.130 8.05 3.23 0.00 2.71
335 336 3.680786 CGGCCACCTCTGTGTCGA 61.681 66.667 2.24 0.00 41.09 4.20
338 339 3.314331 CTCCGGCCACCTCTGTGT 61.314 66.667 2.24 0.00 41.09 3.72
353 354 1.599576 GTTGCCTGGACCTCCTCTC 59.400 63.158 0.00 0.00 36.82 3.20
363 364 3.052082 CTGTCTGCGGTTGCCTGG 61.052 66.667 0.00 0.00 41.78 4.45
416 417 2.202756 GATCTCGTGGTCGTGGCC 60.203 66.667 0.00 0.00 38.33 5.36
431 432 2.413351 CCTGTCGACGATGCCGAT 59.587 61.111 11.62 0.00 38.38 4.18
432 433 3.822192 CCCTGTCGACGATGCCGA 61.822 66.667 11.62 0.00 39.50 5.54
437 438 4.796231 GTGCGCCCTGTCGACGAT 62.796 66.667 11.62 0.00 0.00 3.73
467 483 2.048503 GCGTCCCGTGTGCTACTT 60.049 61.111 0.00 0.00 0.00 2.24
490 506 1.550130 CCTTCTCGGTACCCAAGCCA 61.550 60.000 6.25 0.00 0.00 4.75
562 578 5.117287 GTGTCACACATCTCGTCTTCTTTAC 59.883 44.000 2.00 0.00 34.08 2.01
565 581 3.643763 GTGTCACACATCTCGTCTTCTT 58.356 45.455 2.00 0.00 34.08 2.52
630 646 4.911514 AATAAACAAAAGCGGGCGATAT 57.088 36.364 0.00 0.00 0.00 1.63
654 670 9.042632 CAAATTCATTGCGTTTTTCATACATTG 57.957 29.630 0.00 0.00 31.00 2.82
735 1090 4.647611 ACCGTGTCCATACATTTCAAAGA 58.352 39.130 0.00 0.00 38.08 2.52
767 1123 6.266103 AGTTCATGGACATTGATGTGAAAACT 59.734 34.615 6.96 2.33 41.95 2.66
798 1154 6.426633 CCATGTATTTATCTGCGTATTGGTCA 59.573 38.462 0.00 0.00 0.00 4.02
807 1163 1.135972 GCGGCCATGTATTTATCTGCG 60.136 52.381 2.24 0.00 0.00 5.18
838 1194 6.218019 GCTTGTATTATACGTATGGTCACCA 58.782 40.000 18.37 0.00 38.19 4.17
914 1303 1.471119 ACAAGGCATGAGCTGGATTG 58.529 50.000 0.00 0.00 41.70 2.67
999 1388 1.906824 GGCGACGGAGATCCCCATA 60.907 63.158 0.00 0.00 0.00 2.74
1040 1429 4.816984 GGGCGACGGAGAGGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
1041 1430 4.824515 AGGGCGACGGAGAGGAGG 62.825 72.222 0.00 0.00 0.00 4.30
1042 1431 3.213402 GAGGGCGACGGAGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
1043 1432 4.816984 GGAGGGCGACGGAGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
1044 1433 4.824515 AGGAGGGCGACGGAGAGG 62.825 72.222 0.00 0.00 0.00 3.69
1045 1434 3.213402 GAGGAGGGCGACGGAGAG 61.213 72.222 0.00 0.00 0.00 3.20
1374 1763 0.833287 CGGATCTGTTGGGGATGACT 59.167 55.000 0.00 0.00 0.00 3.41
1836 2225 1.202758 ACGAGCACAACAAGGAATCCA 60.203 47.619 0.61 0.00 0.00 3.41
1854 2243 1.234615 AAACAATCCCTGCACCGACG 61.235 55.000 0.00 0.00 0.00 5.12
1987 2376 3.016736 CCAATTCAGCATAACGGAACCT 58.983 45.455 0.00 0.00 35.20 3.50
2009 2398 1.134175 AGAAATTATTGGTTGCCGCCG 59.866 47.619 0.00 0.00 0.00 6.46
2235 2624 3.358775 CTCATAGACGAGCAAGAAGTCG 58.641 50.000 0.00 0.00 42.04 4.18
2328 2717 1.973281 AAGGCCCAGTGCAATGTCG 60.973 57.895 13.82 3.75 43.89 4.35
2349 2738 1.134699 TGAAGGTAGAGCAATGCCGAG 60.135 52.381 0.00 0.00 0.00 4.63
2367 2756 0.976641 ACTGAAGGCATTCCTCGTGA 59.023 50.000 8.88 0.00 43.40 4.35
2391 2780 2.280457 TTGATGTCGCGGTGCACA 60.280 55.556 20.43 2.92 0.00 4.57
2433 2822 1.294659 CGAGCTTGGCACTGAAGGTC 61.295 60.000 6.13 6.13 42.15 3.85
2616 3005 3.758088 CTCCGATGGCTGTCGTCCG 62.758 68.421 10.89 0.00 39.89 4.79
2676 3065 1.607225 TTTCCCCATACAGCTCCCAT 58.393 50.000 0.00 0.00 0.00 4.00
2692 3081 1.135944 CGCTTCGAGAAGGGCTTTTTC 60.136 52.381 15.23 0.00 42.91 2.29
2694 3083 0.955919 CCGCTTCGAGAAGGGCTTTT 60.956 55.000 20.19 0.00 46.25 2.27
2715 3104 0.842467 CCCCCTTCAACCTCCAGTCT 60.842 60.000 0.00 0.00 0.00 3.24
2922 3311 0.320771 ACGCACCTCCAACTGATGAC 60.321 55.000 0.00 0.00 0.00 3.06
2953 3342 4.078516 AGTAACGCCGCCTGGGTC 62.079 66.667 0.00 0.00 39.59 4.46
3081 3470 3.062909 TGTTACAGCACAAGACGAAACAC 59.937 43.478 0.00 0.00 0.00 3.32
3099 3488 8.046107 TGTACAATCAATCACATCTCCATGTTA 58.954 33.333 0.00 0.00 40.66 2.41
3240 3632 3.920231 AGCAGCTTTATCACCTGATGA 57.080 42.857 0.00 0.00 43.13 2.92
3241 3633 4.953667 TCTAGCAGCTTTATCACCTGATG 58.046 43.478 0.00 0.00 36.05 3.07
3242 3634 5.822132 ATCTAGCAGCTTTATCACCTGAT 57.178 39.130 0.00 0.00 38.51 2.90
3399 3804 1.134521 TCTGTCTGTTCAGTGCGGTTT 60.135 47.619 0.00 0.00 36.85 3.27
3411 3816 0.663568 GCTTACACGCGTCTGTCTGT 60.664 55.000 9.86 5.79 0.00 3.41
3412 3817 1.344942 GGCTTACACGCGTCTGTCTG 61.345 60.000 9.86 0.00 0.00 3.51
3413 3818 1.080705 GGCTTACACGCGTCTGTCT 60.081 57.895 9.86 0.00 0.00 3.41
3414 3819 0.942410 TTGGCTTACACGCGTCTGTC 60.942 55.000 9.86 1.40 0.00 3.51
3423 3828 9.774742 CATTCTAATCTACTTTTTGGCTTACAC 57.225 33.333 0.00 0.00 0.00 2.90
3616 4021 7.556275 AGGTGTTGAGATTTTGTAGTTGAAAGA 59.444 33.333 0.00 0.00 0.00 2.52
3620 4025 6.119536 ACAGGTGTTGAGATTTTGTAGTTGA 58.880 36.000 0.00 0.00 0.00 3.18
3702 4107 8.321353 TGTAATAGGGGCAGTGATAGATAAATG 58.679 37.037 0.00 0.00 0.00 2.32
3780 4185 8.299570 ACAGTGGATGACTTGAATTATTTGTTC 58.700 33.333 0.00 0.00 29.75 3.18
3798 4203 1.815613 CAGACTCGACTGACAGTGGAT 59.184 52.381 19.09 10.50 39.94 3.41
3852 4257 1.250840 AAAAGCGGGAGATGGTTGCC 61.251 55.000 0.00 0.00 0.00 4.52
3899 4304 1.877637 ACTGTTTCATGCAGTGCGTA 58.122 45.000 10.08 0.00 44.52 4.42
3949 4357 6.533012 CGACGAGAGGGTACTATTTATCGATA 59.467 42.308 0.00 0.00 33.43 2.92


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

AutoCloner maintained by Alex Coulton.