Multiple sequence alignment - TraesCS1A01G375000

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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 TraesCS1A01G375000 chr1A 100.000 2933 0 0 1 2933 549934031 549931099 0.000000e+00 5417
1 TraesCS1A01G375000 chr1D 90.279 2613 133 43 353 2933 457248180 457245657 0.000000e+00 3306
2 TraesCS1A01G375000 chr1D 88.973 263 5 12 1 240 457248560 457248299 1.320000e-78 303
3 TraesCS1A01G375000 chr1D 95.181 83 4 0 240 322 457248260 457248178 6.600000e-27 132
4 TraesCS1A01G375000 chr1B 89.647 2666 126 63 240 2834 626855836 626853250 0.000000e+00 3256
5 TraesCS1A01G375000 chr1B 88.031 259 11 10 1 240 626856137 626855880 3.700000e-74 289


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 TraesCS1A01G375000 chr1A 549931099 549934031 2932 True 5417.0 5417 100.000000 1 2933 1 chr1A.!!$R1 2932
1 TraesCS1A01G375000 chr1D 457245657 457248560 2903 True 1247.0 3306 91.477667 1 2933 3 chr1D.!!$R1 2932
2 TraesCS1A01G375000 chr1B 626853250 626856137 2887 True 1772.5 3256 88.839000 1 2834 2 chr1B.!!$R1 2833

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
709 801 0.039708 GTATAGGCCGTGGCGTACTC 60.04 60.0 14.88 7.95 42.92 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2401 0.247576 CTGACCGAGTAGCACGTACG 60.248 60.0 15.01 15.01 36.66 3.67 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
57 64 1.389106 GAGATCGAACGAACCGGTTTG 59.611 52.381 29.51 29.51 33.43 2.93
305 374 0.750850 TCCGACCAAATCCGATCTCC 59.249 55.000 0.00 0.00 0.00 3.71
331 400 1.670967 GCAGCCAGCACTTGATTTTCC 60.671 52.381 0.00 0.00 44.79 3.13
348 417 4.609247 CGATCCTCCGGTCGTCGC 62.609 72.222 0.00 0.00 37.59 5.19
405 479 4.785453 CGGGAAGACTGGCCAGGC 62.785 72.222 35.42 34.23 36.46 4.85
412 486 3.077556 ACTGGCCAGGCGGTCTAG 61.078 66.667 35.42 9.59 37.98 2.43
451 526 1.868987 TACAGTCGCGTGCCAAGCTA 61.869 55.000 5.77 0.00 0.00 3.32
597 673 1.615392 AGCTTCACATCCTTGGTTTGC 59.385 47.619 0.00 0.00 0.00 3.68
606 682 5.593909 CACATCCTTGGTTTGCTGGATATAA 59.406 40.000 0.00 0.00 37.22 0.98
678 755 1.529826 GCGACAGCATTTTCTAAGCGG 60.530 52.381 0.00 0.00 44.35 5.52
679 756 1.062587 CGACAGCATTTTCTAAGCGGG 59.937 52.381 0.00 0.00 0.00 6.13
697 789 1.268948 GGGACGACGACAAGTATAGGC 60.269 57.143 0.00 0.00 0.00 3.93
698 790 1.268948 GGACGACGACAAGTATAGGCC 60.269 57.143 0.00 0.00 0.00 5.19
699 791 0.379669 ACGACGACAAGTATAGGCCG 59.620 55.000 0.00 0.00 0.00 6.13
700 792 0.379669 CGACGACAAGTATAGGCCGT 59.620 55.000 0.00 0.00 0.00 5.68
701 793 1.836383 GACGACAAGTATAGGCCGTG 58.164 55.000 0.00 0.00 0.00 4.94
702 794 0.458669 ACGACAAGTATAGGCCGTGG 59.541 55.000 0.00 0.00 0.00 4.94
703 795 0.874607 CGACAAGTATAGGCCGTGGC 60.875 60.000 1.16 1.16 41.06 5.01
704 796 0.874607 GACAAGTATAGGCCGTGGCG 60.875 60.000 4.53 0.00 43.06 5.69
705 797 1.143183 CAAGTATAGGCCGTGGCGT 59.857 57.895 11.23 11.23 43.06 5.68
706 798 0.386476 CAAGTATAGGCCGTGGCGTA 59.614 55.000 14.93 14.93 43.98 4.42
707 799 0.386838 AAGTATAGGCCGTGGCGTAC 59.613 55.000 14.88 12.13 42.92 3.67
708 800 0.466922 AGTATAGGCCGTGGCGTACT 60.467 55.000 14.88 13.92 42.92 2.73
709 801 0.039708 GTATAGGCCGTGGCGTACTC 60.040 60.000 14.88 7.95 42.92 2.59
710 802 1.174712 TATAGGCCGTGGCGTACTCC 61.175 60.000 14.88 0.00 42.92 3.85
711 803 3.813562 TATAGGCCGTGGCGTACTCCA 62.814 57.143 14.88 0.00 42.92 3.86
739 831 3.616721 ACGGGTCAGCGAGCTTGT 61.617 61.111 2.14 4.75 0.00 3.16
740 832 3.114616 CGGGTCAGCGAGCTTGTG 61.115 66.667 2.14 0.20 0.00 3.33
746 838 0.947660 TCAGCGAGCTTGTGCAGAAG 60.948 55.000 18.83 18.83 42.74 2.85
756 852 1.730501 TGTGCAGAAGCTGTCTATGC 58.269 50.000 0.00 0.00 42.74 3.14
758 854 0.907486 TGCAGAAGCTGTCTATGCCT 59.093 50.000 1.30 0.00 42.74 4.75
883 984 4.050719 GCTTTTGCGCTGCGTTGC 62.051 61.111 24.04 15.68 34.86 4.17
1367 1480 3.003763 ACCTCCCACGGAAGAGCC 61.004 66.667 0.00 0.00 0.00 4.70
1377 1490 3.780173 GAAGAGCCGCAGCCTCCT 61.780 66.667 0.00 0.00 41.25 3.69
1510 1623 4.083862 GCGCCCCTTTCTCCGTCT 62.084 66.667 0.00 0.00 0.00 4.18
1516 1629 0.905337 CCCTTTCTCCGTCTCCCTGT 60.905 60.000 0.00 0.00 0.00 4.00
1517 1630 0.533032 CCTTTCTCCGTCTCCCTGTC 59.467 60.000 0.00 0.00 0.00 3.51
1667 1780 5.589050 GCCTTTCCCAACCATTTAGTACTAG 59.411 44.000 2.23 0.00 0.00 2.57
1671 1784 9.159364 CTTTCCCAACCATTTAGTACTAGTAAC 57.841 37.037 3.61 0.00 0.00 2.50
1685 1798 4.676546 ACTAGTAACGCTCGAATTTACCC 58.323 43.478 0.00 0.00 0.00 3.69
1797 1910 1.202394 TGTGTTGTGTGCAAGAATGGC 60.202 47.619 0.00 0.00 34.94 4.40
2013 2152 1.143183 TCGCAGGTAGCCCGAATTC 59.857 57.895 3.20 0.00 41.38 2.17
2018 2157 2.417719 CAGGTAGCCCGAATTCATAGC 58.582 52.381 6.22 4.81 35.12 2.97
2021 2160 2.808543 GGTAGCCCGAATTCATAGCAAG 59.191 50.000 6.22 0.00 0.00 4.01
2095 2234 7.031372 TGTACTCGTGTTCACCAGTTATTATC 58.969 38.462 8.30 0.00 0.00 1.75
2103 2242 9.821662 GTGTTCACCAGTTATTATCAAGTTTAC 57.178 33.333 0.00 0.00 0.00 2.01
2104 2243 9.562408 TGTTCACCAGTTATTATCAAGTTTACA 57.438 29.630 0.00 0.00 0.00 2.41
2110 2249 9.840427 CCAGTTATTATCAAGTTTACAACAAGG 57.160 33.333 0.00 0.00 0.00 3.61
2205 2349 5.838531 ACAATCTACTGCTGGTAGTACTC 57.161 43.478 0.00 0.00 45.86 2.59
2253 2398 2.887151 AACCTCTTCCATCCTGGTTG 57.113 50.000 0.00 0.00 39.26 3.77
2254 2399 1.747444 ACCTCTTCCATCCTGGTTGT 58.253 50.000 4.19 0.00 39.03 3.32
2255 2400 2.915869 ACCTCTTCCATCCTGGTTGTA 58.084 47.619 4.19 0.00 39.03 2.41
2256 2401 2.572104 ACCTCTTCCATCCTGGTTGTAC 59.428 50.000 4.19 0.00 39.03 2.90
2279 2431 0.097325 CGTGCTACTCGGTCAGTCTC 59.903 60.000 0.00 0.00 36.43 3.36
2380 2539 2.041819 GGGTCAGGTCCCGATCCT 60.042 66.667 0.00 0.00 37.93 3.24
2381 2540 2.134933 GGGTCAGGTCCCGATCCTC 61.135 68.421 0.00 0.00 37.93 3.71
2382 2541 2.134933 GGTCAGGTCCCGATCCTCC 61.135 68.421 0.00 0.00 32.37 4.30
2383 2542 2.134933 GTCAGGTCCCGATCCTCCC 61.135 68.421 0.00 0.00 32.37 4.30
2391 2550 1.623542 CCCGATCCTCCCCTTCGTTT 61.624 60.000 0.00 0.00 0.00 3.60
2480 2647 1.467713 GCTCGTTCGTTCTCTGGGTAG 60.468 57.143 0.00 0.00 0.00 3.18
2481 2648 1.132643 CTCGTTCGTTCTCTGGGTAGG 59.867 57.143 0.00 0.00 0.00 3.18
2482 2649 0.172803 CGTTCGTTCTCTGGGTAGGG 59.827 60.000 0.00 0.00 0.00 3.53
2483 2650 1.264295 GTTCGTTCTCTGGGTAGGGT 58.736 55.000 0.00 0.00 0.00 4.34
2484 2651 1.067071 GTTCGTTCTCTGGGTAGGGTG 60.067 57.143 0.00 0.00 0.00 4.61
2519 2686 3.224324 GGCCCTCGTGCTATCCGA 61.224 66.667 0.00 0.00 0.00 4.55
2520 2687 2.027751 GCCCTCGTGCTATCCGAC 59.972 66.667 0.00 0.00 0.00 4.79
2522 2689 2.331805 CCTCGTGCTATCCGACGG 59.668 66.667 7.84 7.84 36.23 4.79
2625 2797 0.091511 GAGCTTTTCGCGTCGTCTTC 59.908 55.000 5.77 0.00 45.59 2.87
2636 2808 1.469940 CGTCGTCTTCCTCCCAATCAG 60.470 57.143 0.00 0.00 0.00 2.90
2794 2989 1.329372 CGTGCATACGTACGTGTTCA 58.671 50.000 30.25 21.39 44.97 3.18
2836 3031 0.109873 AGAGAAACGCGTGTACGGAG 60.110 55.000 14.98 0.00 40.23 4.63
2838 3033 0.874390 AGAAACGCGTGTACGGAGTA 59.126 50.000 14.98 0.00 45.11 2.59
2873 3068 2.409948 AAGTTAGCACCAGCATCTCC 57.590 50.000 0.00 0.00 45.49 3.71
2874 3069 1.279496 AGTTAGCACCAGCATCTCCA 58.721 50.000 0.00 0.00 45.49 3.86
2875 3070 1.065854 AGTTAGCACCAGCATCTCCAC 60.066 52.381 0.00 0.00 45.49 4.02
2876 3071 1.065854 GTTAGCACCAGCATCTCCACT 60.066 52.381 0.00 0.00 45.49 4.00
2881 3076 2.491621 CAGCATCTCCACTCGCGA 59.508 61.111 9.26 9.26 0.00 5.87
2882 3077 1.067084 CAGCATCTCCACTCGCGAT 59.933 57.895 10.36 0.00 0.00 4.58
2883 3078 0.312102 CAGCATCTCCACTCGCGATA 59.688 55.000 10.36 0.00 0.00 2.92
2884 3079 0.312416 AGCATCTCCACTCGCGATAC 59.688 55.000 10.36 0.00 0.00 2.24
2885 3080 0.999228 GCATCTCCACTCGCGATACG 60.999 60.000 10.36 0.00 45.62 3.06
2886 3081 0.386100 CATCTCCACTCGCGATACGG 60.386 60.000 10.36 10.95 43.89 4.02
2887 3082 0.818445 ATCTCCACTCGCGATACGGT 60.818 55.000 10.36 0.00 43.89 4.83
2888 3083 1.009900 CTCCACTCGCGATACGGTC 60.010 63.158 10.36 0.00 43.89 4.79
2895 3090 2.078914 CGCGATACGGTCATACGGC 61.079 63.158 0.00 0.00 38.44 5.68
2915 3110 2.176546 GCCTCGTGCACGTACGTA 59.823 61.111 35.74 17.62 44.06 3.57
2921 3116 0.827125 CGTGCACGTACGTATACACG 59.173 55.000 34.94 34.94 43.34 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 1.594836 TCCCAAACCGGTTCGTTCG 60.595 57.895 22.53 6.89 0.00 3.95
222 247 1.308783 GGAAAGAAAGAGCAGCGGGG 61.309 60.000 0.00 0.00 0.00 5.73
353 422 2.917751 ATCATCGGCCGATCGGGT 60.918 61.111 37.10 21.24 38.44 5.28
606 682 6.234177 GCCAATCTGTTATTAGCAGTAGGAT 58.766 40.000 14.58 0.00 35.60 3.24
676 753 1.003116 CCTATACTTGTCGTCGTCCCG 60.003 57.143 0.00 0.00 0.00 5.14
678 755 1.268948 GGCCTATACTTGTCGTCGTCC 60.269 57.143 0.00 0.00 0.00 4.79
679 756 1.596464 CGGCCTATACTTGTCGTCGTC 60.596 57.143 0.00 0.00 0.00 4.20
739 831 0.907486 AGGCATAGACAGCTTCTGCA 59.093 50.000 8.21 0.00 42.74 4.41
740 832 1.669779 CAAGGCATAGACAGCTTCTGC 59.330 52.381 8.21 5.55 35.55 4.26
746 838 2.828128 GCGGCAAGGCATAGACAGC 61.828 63.158 0.00 0.00 0.00 4.40
773 869 3.964347 CGTACGTATACAATCACTGACCG 59.036 47.826 7.22 0.00 0.00 4.79
884 985 0.667453 TTTTTGTTACCGCCCGGAAC 59.333 50.000 14.44 12.98 38.96 3.62
885 986 0.667453 GTTTTTGTTACCGCCCGGAA 59.333 50.000 14.44 0.83 38.96 4.30
886 987 0.465097 TGTTTTTGTTACCGCCCGGA 60.465 50.000 14.44 0.00 38.96 5.14
891 992 1.072670 CGCGTTTGTTTTTGTTACCGC 60.073 47.619 0.00 0.00 36.78 5.68
949 1050 3.160748 GAGCAGGAGGAGGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
1218 1331 2.048603 GTGGCCCATGAGCTTCACC 61.049 63.158 0.00 0.00 0.00 4.02
1322 1435 4.790962 CCATGCGCTCTGGCTGGT 62.791 66.667 9.73 0.00 36.09 4.00
1516 1629 2.592001 CTCGATCTCCTCCGGCGA 60.592 66.667 9.30 0.00 0.00 5.54
1517 1630 3.665226 CCTCGATCTCCTCCGGCG 61.665 72.222 0.00 0.00 0.00 6.46
1667 1780 4.870221 ATTGGGTAAATTCGAGCGTTAC 57.130 40.909 6.47 6.47 0.00 2.50
1671 1784 2.450160 GCAATTGGGTAAATTCGAGCG 58.550 47.619 7.72 0.00 36.28 5.03
1701 1814 2.169832 AAAGCGTATCGATGGGATGG 57.830 50.000 8.54 0.00 36.55 3.51
1702 1815 3.062639 GCATAAAGCGTATCGATGGGATG 59.937 47.826 8.54 3.46 36.55 3.51
1741 1854 3.996150 TTACTATACTGGTGCTACGCC 57.004 47.619 0.00 0.00 34.12 5.68
1797 1910 1.006805 GGATCGGAGGATGAGCGTG 60.007 63.158 0.00 0.00 31.51 5.34
1800 1913 1.273886 GTTAGGGATCGGAGGATGAGC 59.726 57.143 0.00 0.00 31.51 4.26
2013 2152 4.626042 CCTAGCTACTCCAACTTGCTATG 58.374 47.826 0.00 0.00 35.96 2.23
2018 2157 1.204941 ACGCCTAGCTACTCCAACTTG 59.795 52.381 0.00 0.00 0.00 3.16
2021 2160 2.033174 GTCTACGCCTAGCTACTCCAAC 59.967 54.545 0.00 0.00 0.00 3.77
2095 2234 7.093992 TGGAGTTTTTCCTTGTTGTAAACTTG 58.906 34.615 0.00 0.00 46.75 3.16
2103 2242 4.261614 GGTAGCTGGAGTTTTTCCTTGTTG 60.262 45.833 0.00 0.00 46.92 3.33
2104 2243 3.889538 GGTAGCTGGAGTTTTTCCTTGTT 59.110 43.478 0.00 0.00 46.92 2.83
2109 2248 2.074576 GTCGGTAGCTGGAGTTTTTCC 58.925 52.381 0.00 0.00 46.98 3.13
2110 2249 3.041508 AGTCGGTAGCTGGAGTTTTTC 57.958 47.619 0.00 0.00 0.00 2.29
2253 2398 0.721718 ACCGAGTAGCACGTACGTAC 59.278 55.000 22.34 16.33 36.66 3.67
2254 2399 0.999406 GACCGAGTAGCACGTACGTA 59.001 55.000 22.34 2.28 36.66 3.57
2255 2400 0.950555 TGACCGAGTAGCACGTACGT 60.951 55.000 16.72 16.72 36.66 3.57
2256 2401 0.247576 CTGACCGAGTAGCACGTACG 60.248 60.000 15.01 15.01 36.66 3.67
2344 2503 1.450531 CGAAAGCCATGCCATCCCTC 61.451 60.000 0.00 0.00 0.00 4.30
2353 2512 1.002134 ACCTGACCCGAAAGCCATG 60.002 57.895 0.00 0.00 0.00 3.66
2380 2539 1.921857 GGGGAGGAAACGAAGGGGA 60.922 63.158 0.00 0.00 0.00 4.81
2381 2540 1.498176 AAGGGGAGGAAACGAAGGGG 61.498 60.000 0.00 0.00 0.00 4.79
2382 2541 0.404426 AAAGGGGAGGAAACGAAGGG 59.596 55.000 0.00 0.00 0.00 3.95
2383 2542 1.534729 CAAAGGGGAGGAAACGAAGG 58.465 55.000 0.00 0.00 0.00 3.46
2391 2550 2.282180 GCAACGCAAAGGGGAGGA 60.282 61.111 0.00 0.00 0.00 3.71
2480 2647 1.695239 CCCTAACCCTACCCCACCC 60.695 68.421 0.00 0.00 0.00 4.61
2481 2648 0.550884 AACCCTAACCCTACCCCACC 60.551 60.000 0.00 0.00 0.00 4.61
2482 2649 0.622136 CAACCCTAACCCTACCCCAC 59.378 60.000 0.00 0.00 0.00 4.61
2483 2650 0.550638 CCAACCCTAACCCTACCCCA 60.551 60.000 0.00 0.00 0.00 4.96
2484 2651 1.284111 CCCAACCCTAACCCTACCCC 61.284 65.000 0.00 0.00 0.00 4.95
2608 2780 1.130009 GGAAGACGACGCGAAAAGC 59.870 57.895 15.93 0.00 43.95 3.51
2625 2797 1.561542 ACTAGGTTGCTGATTGGGAGG 59.438 52.381 0.00 0.00 0.00 4.30
2636 2808 1.536284 CCAGTAGCGCTACTAGGTTGC 60.536 57.143 41.19 18.03 43.98 4.17
2786 2981 3.185797 GCTAAGGAAAACGATGAACACGT 59.814 43.478 0.00 0.00 45.89 4.49
2788 2983 3.500680 TGGCTAAGGAAAACGATGAACAC 59.499 43.478 0.00 0.00 0.00 3.32
2789 2984 3.745799 TGGCTAAGGAAAACGATGAACA 58.254 40.909 0.00 0.00 0.00 3.18
2790 2985 4.156008 ACATGGCTAAGGAAAACGATGAAC 59.844 41.667 0.00 0.00 0.00 3.18
2791 2986 4.331968 ACATGGCTAAGGAAAACGATGAA 58.668 39.130 0.00 0.00 0.00 2.57
2792 2987 3.938963 GACATGGCTAAGGAAAACGATGA 59.061 43.478 0.00 0.00 0.00 2.92
2793 2988 3.242413 CGACATGGCTAAGGAAAACGATG 60.242 47.826 0.00 0.00 0.00 3.84
2794 2989 2.936498 CGACATGGCTAAGGAAAACGAT 59.064 45.455 0.00 0.00 0.00 3.73
2864 3059 0.312102 TATCGCGAGTGGAGATGCTG 59.688 55.000 16.66 0.00 35.80 4.41
2873 3068 1.671469 GTATGACCGTATCGCGAGTG 58.329 55.000 16.66 6.49 44.77 3.51
2874 3069 0.234106 CGTATGACCGTATCGCGAGT 59.766 55.000 16.66 6.71 44.77 4.18
2875 3070 0.452287 CCGTATGACCGTATCGCGAG 60.452 60.000 16.66 2.71 44.77 5.03
2876 3071 1.570967 CCGTATGACCGTATCGCGA 59.429 57.895 13.09 13.09 44.77 5.87
2885 3080 4.603946 GAGGCCGGCCGTATGACC 62.604 72.222 38.88 18.71 41.95 4.02
2886 3081 4.944372 CGAGGCCGGCCGTATGAC 62.944 72.222 38.88 23.69 41.95 3.06
2915 3110 2.897972 GGTTCGCCTCCCGTGTAT 59.102 61.111 0.00 0.00 38.35 2.29


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

AutoCloner maintained by Alex Coulton.