Multiple sequence alignment - TraesCS4D01G239300

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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 TraesCS4D01G239300 chr4D 100.000 3928 0 0 1 3928 401416001 401419928 0.000000e+00 7254.0
1 TraesCS4D01G239300 chr4D 98.729 1889 19 2 1281 3165 417813336 417815223 0.000000e+00 3350.0
2 TraesCS4D01G239300 chr4D 97.983 347 7 0 3582 3928 417815222 417815568 1.560000e-168 603.0
3 TraesCS4D01G239300 chr4D 92.621 393 13 11 858 1250 417812869 417813245 5.740000e-153 551.0
4 TraesCS4D01G239300 chr4B 94.693 2619 115 7 1313 3928 496463545 496466142 0.000000e+00 4045.0
5 TraesCS4D01G239300 chr4B 96.739 368 11 1 892 1258 496462885 496463252 2.590000e-171 612.0
6 TraesCS4D01G239300 chr4A 93.564 2626 129 19 1330 3928 59244562 59247174 0.000000e+00 3877.0
7 TraesCS4D01G239300 chr4A 100.000 414 0 0 1281 1694 59244120 59244533 0.000000e+00 765.0
8 TraesCS4D01G239300 chr4A 91.286 482 24 10 781 1257 59243604 59244072 3.310000e-180 641.0
9 TraesCS4D01G239300 chr7D 98.805 837 9 1 3092 3928 340167902 340168737 0.000000e+00 1489.0
10 TraesCS4D01G239300 chr7D 97.328 711 18 1 1 711 70150280 70150989 0.000000e+00 1206.0
11 TraesCS4D01G239300 chr7D 94.000 50 2 1 709 757 96047986 96048035 1.510000e-09 75.0
12 TraesCS4D01G239300 chr6B 96.062 711 27 1 1 711 545224074 545223365 0.000000e+00 1157.0
13 TraesCS4D01G239300 chr2B 94.568 718 38 1 1 718 379118332 379119048 0.000000e+00 1109.0
14 TraesCS4D01G239300 chr7B 93.803 710 34 2 1 710 491198235 491198934 0.000000e+00 1059.0
15 TraesCS4D01G239300 chr7B 97.163 141 3 1 571 711 537842095 537841956 1.820000e-58 237.0
16 TraesCS4D01G239300 chr3D 97.858 607 12 1 55 661 395670129 395669524 0.000000e+00 1048.0
17 TraesCS4D01G239300 chr5A 93.287 715 36 3 1 713 552379012 552378308 0.000000e+00 1044.0
18 TraesCS4D01G239300 chr5D 96.179 602 22 1 4 604 437083844 437083243 0.000000e+00 983.0
19 TraesCS4D01G239300 chr3A 91.573 712 51 7 1 712 468005698 468004996 0.000000e+00 974.0
20 TraesCS4D01G239300 chr7A 91.639 598 45 3 113 710 634478324 634478916 0.000000e+00 822.0
21 TraesCS4D01G239300 chr2A 83.942 137 19 3 3594 3729 748694844 748694978 1.150000e-25 128.0
22 TraesCS4D01G239300 chr1B 83.333 126 19 2 3600 3724 623885213 623885089 8.920000e-22 115.0
23 TraesCS4D01G239300 chr1B 93.103 58 4 0 1 58 478719433 478719490 6.990000e-13 86.1
24 TraesCS4D01G239300 chr1A 96.552 58 2 0 1 58 456938677 456938734 3.230000e-16 97.1
25 TraesCS4D01G239300 chr2D 96.491 57 0 2 706 760 646827878 646827934 4.180000e-15 93.5
26 TraesCS4D01G239300 chr2D 94.737 57 1 2 706 760 646846239 646846295 1.940000e-13 87.9
27 TraesCS4D01G239300 chr2D 94.737 57 1 2 706 760 646996160 646996216 1.940000e-13 87.9
28 TraesCS4D01G239300 chr5B 86.486 74 10 0 3589 3662 551422078 551422005 9.050000e-12 82.4


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 TraesCS4D01G239300 chr4D 401416001 401419928 3927 False 7254.000000 7254 100.000000 1 3928 1 chr4D.!!$F1 3927
1 TraesCS4D01G239300 chr4D 417812869 417815568 2699 False 1501.333333 3350 96.444333 858 3928 3 chr4D.!!$F2 3070
2 TraesCS4D01G239300 chr4B 496462885 496466142 3257 False 2328.500000 4045 95.716000 892 3928 2 chr4B.!!$F1 3036
3 TraesCS4D01G239300 chr4A 59243604 59247174 3570 False 1761.000000 3877 94.950000 781 3928 3 chr4A.!!$F1 3147
4 TraesCS4D01G239300 chr7D 340167902 340168737 835 False 1489.000000 1489 98.805000 3092 3928 1 chr7D.!!$F3 836
5 TraesCS4D01G239300 chr7D 70150280 70150989 709 False 1206.000000 1206 97.328000 1 711 1 chr7D.!!$F1 710
6 TraesCS4D01G239300 chr6B 545223365 545224074 709 True 1157.000000 1157 96.062000 1 711 1 chr6B.!!$R1 710
7 TraesCS4D01G239300 chr2B 379118332 379119048 716 False 1109.000000 1109 94.568000 1 718 1 chr2B.!!$F1 717
8 TraesCS4D01G239300 chr7B 491198235 491198934 699 False 1059.000000 1059 93.803000 1 710 1 chr7B.!!$F1 709
9 TraesCS4D01G239300 chr3D 395669524 395670129 605 True 1048.000000 1048 97.858000 55 661 1 chr3D.!!$R1 606
10 TraesCS4D01G239300 chr5A 552378308 552379012 704 True 1044.000000 1044 93.287000 1 713 1 chr5A.!!$R1 712
11 TraesCS4D01G239300 chr5D 437083243 437083844 601 True 983.000000 983 96.179000 4 604 1 chr5D.!!$R1 600
12 TraesCS4D01G239300 chr3A 468004996 468005698 702 True 974.000000 974 91.573000 1 712 1 chr3A.!!$R1 711
13 TraesCS4D01G239300 chr7A 634478324 634478916 592 False 822.000000 822 91.639000 113 710 1 chr7A.!!$F1 597

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
993 1002 2.391389 CCAGTTCCGCTTCGCCTTC 61.391 63.158 0.00 0.0 0.0 3.46 F
1050 1059 1.076549 GTCCAAACCAGATGCCCCA 59.923 57.895 0.00 0.0 0.0 4.96 F
2117 2771 1.220169 CGCGCAGAGGATGATGAAGG 61.220 60.000 8.75 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2901 0.168788 CAACAACACGCCAGCATAGG 59.831 55.000 0.00 0.0 0.00 2.57 R
2793 3455 4.083696 GCAAATACCGGGTGTATATTTCCG 60.084 45.833 10.66 0.0 39.28 4.30 R
3296 3970 2.734606 CAGGCATCAACAACTTGCATTG 59.265 45.455 0.00 0.0 38.12 2.82 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
53 54 3.451178 TGAGGGAGACAATAGCAACTACC 59.549 47.826 0.00 0.00 33.87 3.18
234 235 9.273016 CACGGTCAGGATATATGAAACTTAATT 57.727 33.333 0.00 0.00 0.00 1.40
539 543 7.269435 GTCGCTAGACTTTAATCACGTTTTA 57.731 36.000 0.00 0.00 43.80 1.52
649 653 4.736473 TCACCTCCGGATGAGATTATACA 58.264 43.478 14.21 0.00 44.42 2.29
706 710 6.830873 AAGGAGGAGATGATTTGTCAAAAG 57.169 37.500 1.31 0.00 0.00 2.27
731 735 5.973899 AAAAACAAAGTGGCCACAAAAAT 57.026 30.435 36.39 17.29 0.00 1.82
732 736 5.973899 AAAACAAAGTGGCCACAAAAATT 57.026 30.435 36.39 21.81 0.00 1.82
733 737 4.961435 AACAAAGTGGCCACAAAAATTG 57.039 36.364 36.39 29.01 0.00 2.32
734 738 4.213564 ACAAAGTGGCCACAAAAATTGA 57.786 36.364 36.39 0.00 0.00 2.57
735 739 4.779696 ACAAAGTGGCCACAAAAATTGAT 58.220 34.783 36.39 18.09 0.00 2.57
736 740 4.575645 ACAAAGTGGCCACAAAAATTGATG 59.424 37.500 36.39 18.91 0.00 3.07
737 741 4.686191 AAGTGGCCACAAAAATTGATGA 57.314 36.364 36.39 0.00 0.00 2.92
738 742 3.993920 AGTGGCCACAAAAATTGATGAC 58.006 40.909 36.39 5.31 0.00 3.06
739 743 3.387374 AGTGGCCACAAAAATTGATGACA 59.613 39.130 36.39 0.00 0.00 3.58
740 744 4.040706 AGTGGCCACAAAAATTGATGACAT 59.959 37.500 36.39 8.02 0.00 3.06
741 745 4.389687 GTGGCCACAAAAATTGATGACATC 59.610 41.667 31.23 8.59 0.00 3.06
742 746 4.040095 TGGCCACAAAAATTGATGACATCA 59.960 37.500 14.24 14.24 37.55 3.07
743 747 5.180271 GGCCACAAAAATTGATGACATCAT 58.820 37.500 18.62 2.27 39.39 2.45
744 748 6.070938 TGGCCACAAAAATTGATGACATCATA 60.071 34.615 18.62 10.20 39.39 2.15
745 749 6.987992 GGCCACAAAAATTGATGACATCATAT 59.012 34.615 18.62 11.86 39.39 1.78
746 750 7.496591 GGCCACAAAAATTGATGACATCATATT 59.503 33.333 18.62 16.24 39.39 1.28
747 751 8.885722 GCCACAAAAATTGATGACATCATATTT 58.114 29.630 18.62 20.02 39.39 1.40
772 776 3.220110 TGTGAGATACATAGACGGACCC 58.780 50.000 0.00 0.00 33.42 4.46
773 777 3.117625 TGTGAGATACATAGACGGACCCT 60.118 47.826 0.00 0.00 33.42 4.34
774 778 3.890147 GTGAGATACATAGACGGACCCTT 59.110 47.826 0.00 0.00 0.00 3.95
775 779 4.341520 GTGAGATACATAGACGGACCCTTT 59.658 45.833 0.00 0.00 0.00 3.11
776 780 4.960469 TGAGATACATAGACGGACCCTTTT 59.040 41.667 0.00 0.00 0.00 2.27
777 781 6.040166 GTGAGATACATAGACGGACCCTTTTA 59.960 42.308 0.00 0.00 0.00 1.52
778 782 6.608405 TGAGATACATAGACGGACCCTTTTAA 59.392 38.462 0.00 0.00 0.00 1.52
779 783 7.124599 TGAGATACATAGACGGACCCTTTTAAA 59.875 37.037 0.00 0.00 0.00 1.52
786 790 8.706035 CATAGACGGACCCTTTTAAAATATACG 58.294 37.037 0.09 5.36 0.00 3.06
812 816 9.638300 GATGAACTATTTTTAGCATACGTTGAG 57.362 33.333 0.00 0.00 0.00 3.02
817 821 8.122952 ACTATTTTTAGCATACGTTGAGCATTC 58.877 33.333 0.00 0.00 0.00 2.67
826 830 8.285394 AGCATACGTTGAGCATTCTTTAATATG 58.715 33.333 0.00 0.00 0.00 1.78
917 926 8.628280 AGAAGAAAAGAAAAATCTCAAGTGAGG 58.372 33.333 8.42 0.00 42.30 3.86
993 1002 2.391389 CCAGTTCCGCTTCGCCTTC 61.391 63.158 0.00 0.00 0.00 3.46
1050 1059 1.076549 GTCCAAACCAGATGCCCCA 59.923 57.895 0.00 0.00 0.00 4.96
1258 1281 2.428085 GCTCCTCTCCCTCCGGTTC 61.428 68.421 0.00 0.00 0.00 3.62
1259 1282 1.758906 CTCCTCTCCCTCCGGTTCC 60.759 68.421 0.00 0.00 0.00 3.62
1260 1283 2.231540 CTCCTCTCCCTCCGGTTCCT 62.232 65.000 0.00 0.00 0.00 3.36
1261 1284 2.060980 CCTCTCCCTCCGGTTCCTG 61.061 68.421 0.00 0.00 0.00 3.86
1262 1285 2.683933 TCTCCCTCCGGTTCCTGC 60.684 66.667 0.00 0.00 0.00 4.85
1263 1286 2.685380 CTCCCTCCGGTTCCTGCT 60.685 66.667 0.00 0.00 0.00 4.24
1264 1287 2.683933 TCCCTCCGGTTCCTGCTC 60.684 66.667 0.00 0.00 0.00 4.26
1265 1288 2.685380 CCCTCCGGTTCCTGCTCT 60.685 66.667 0.00 0.00 0.00 4.09
1266 1289 2.581354 CCTCCGGTTCCTGCTCTG 59.419 66.667 0.00 0.00 0.00 3.35
1267 1290 2.581354 CTCCGGTTCCTGCTCTGG 59.419 66.667 0.00 0.00 0.00 3.86
1268 1291 3.672295 CTCCGGTTCCTGCTCTGGC 62.672 68.421 0.00 0.00 39.26 4.85
1272 1295 4.400961 GTTCCTGCTCTGGCGCCT 62.401 66.667 29.70 0.00 42.25 5.52
1273 1296 4.399395 TTCCTGCTCTGGCGCCTG 62.399 66.667 29.70 27.77 42.25 4.85
1694 2348 3.062500 TTTGGATGCGCGGCCAATC 62.063 57.895 27.43 14.05 43.19 2.67
1819 2473 1.530419 TGTGCCCAATGTGGTGTCC 60.530 57.895 0.00 0.00 35.17 4.02
2117 2771 1.220169 CGCGCAGAGGATGATGAAGG 61.220 60.000 8.75 0.00 0.00 3.46
2221 2875 4.019051 TGTTGGTTGAGACTGATGGATGAT 60.019 41.667 0.00 0.00 0.00 2.45
2247 2901 1.669779 GGTGCTCTGTGATTCTGATGC 59.330 52.381 0.00 0.00 0.00 3.91
2483 3145 3.316029 TGGTTCTGTGCTCAATTCTTGTG 59.684 43.478 0.00 0.00 0.00 3.33
3296 3970 1.270839 TGCCAGCTTCAGTTGAGTACC 60.271 52.381 0.00 0.00 0.00 3.34
3720 4404 3.245948 CTGGTGCTGCTTCGTGTGC 62.246 63.158 0.00 0.00 0.00 4.57
3721 4405 2.974698 GGTGCTGCTTCGTGTGCT 60.975 61.111 0.00 0.00 0.00 4.40
3735 4420 1.405105 GTGTGCTTTCTTTGCTGACCA 59.595 47.619 0.00 0.00 0.00 4.02
3857 4542 1.343465 GTTCGAACCTGAGACCTCCAA 59.657 52.381 17.68 0.00 0.00 3.53
3908 4593 6.549364 TCACCAGGAGATGTTTTGTGTTTAAT 59.451 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.883275 TCAAACCACAAATACCAGGCG 59.117 47.619 0.00 0.00 0.00 5.52
209 210 9.847224 AAATTAAGTTTCATATATCCTGACCGT 57.153 29.630 0.00 0.00 0.00 4.83
234 235 4.883585 GTCATGATCAAACCCAGCATCTAA 59.116 41.667 0.00 0.00 0.00 2.10
713 717 4.213564 TCAATTTTTGTGGCCACTTTGT 57.786 36.364 34.75 15.36 0.00 2.83
714 718 4.815308 TCATCAATTTTTGTGGCCACTTTG 59.185 37.500 34.75 25.97 0.00 2.77
717 721 3.387374 TGTCATCAATTTTTGTGGCCACT 59.613 39.130 34.75 13.35 0.00 4.00
718 722 3.726607 TGTCATCAATTTTTGTGGCCAC 58.273 40.909 29.67 29.67 0.00 5.01
719 723 4.040095 TGATGTCATCAATTTTTGTGGCCA 59.960 37.500 13.25 0.00 36.11 5.36
720 724 4.567971 TGATGTCATCAATTTTTGTGGCC 58.432 39.130 13.25 0.00 36.11 5.36
721 725 8.428186 AATATGATGTCATCAATTTTTGTGGC 57.572 30.769 19.17 0.00 43.50 5.01
743 747 9.734984 TCCGTCTATGTATCTCACATCTAAATA 57.265 33.333 0.00 0.00 44.99 1.40
744 748 8.516234 GTCCGTCTATGTATCTCACATCTAAAT 58.484 37.037 0.00 0.00 44.99 1.40
745 749 7.040617 GGTCCGTCTATGTATCTCACATCTAAA 60.041 40.741 0.00 0.00 44.99 1.85
746 750 6.430308 GGTCCGTCTATGTATCTCACATCTAA 59.570 42.308 0.00 0.00 44.99 2.10
747 751 5.938710 GGTCCGTCTATGTATCTCACATCTA 59.061 44.000 0.00 0.00 44.99 1.98
748 752 4.762765 GGTCCGTCTATGTATCTCACATCT 59.237 45.833 0.00 0.00 44.99 2.90
749 753 4.082679 GGGTCCGTCTATGTATCTCACATC 60.083 50.000 0.00 0.00 44.99 3.06
751 755 3.117625 AGGGTCCGTCTATGTATCTCACA 60.118 47.826 0.00 0.00 42.69 3.58
752 756 3.488363 AGGGTCCGTCTATGTATCTCAC 58.512 50.000 0.00 0.00 0.00 3.51
753 757 3.878237 AGGGTCCGTCTATGTATCTCA 57.122 47.619 0.00 0.00 0.00 3.27
754 758 5.532664 AAAAGGGTCCGTCTATGTATCTC 57.467 43.478 0.00 0.00 0.00 2.75
755 759 7.427989 TTTAAAAGGGTCCGTCTATGTATCT 57.572 36.000 0.00 0.00 0.00 1.98
756 760 8.672823 ATTTTAAAAGGGTCCGTCTATGTATC 57.327 34.615 6.79 0.00 0.00 2.24
759 763 9.551734 GTATATTTTAAAAGGGTCCGTCTATGT 57.448 33.333 6.79 0.00 0.00 2.29
760 764 8.706035 CGTATATTTTAAAAGGGTCCGTCTATG 58.294 37.037 6.79 0.00 0.00 2.23
761 765 8.641541 TCGTATATTTTAAAAGGGTCCGTCTAT 58.358 33.333 6.79 0.00 0.00 1.98
762 766 8.006298 TCGTATATTTTAAAAGGGTCCGTCTA 57.994 34.615 6.79 0.00 0.00 2.59
763 767 6.877236 TCGTATATTTTAAAAGGGTCCGTCT 58.123 36.000 6.79 0.00 0.00 4.18
764 768 7.439056 TCATCGTATATTTTAAAAGGGTCCGTC 59.561 37.037 6.79 0.00 0.00 4.79
765 769 7.274447 TCATCGTATATTTTAAAAGGGTCCGT 58.726 34.615 6.79 0.00 0.00 4.69
766 770 7.718272 TCATCGTATATTTTAAAAGGGTCCG 57.282 36.000 6.79 5.38 0.00 4.79
767 771 9.117183 AGTTCATCGTATATTTTAAAAGGGTCC 57.883 33.333 6.79 0.00 0.00 4.46
786 790 9.638300 CTCAACGTATGCTAAAAATAGTTCATC 57.362 33.333 0.00 0.00 0.00 2.92
802 806 8.069574 TGCATATTAAAGAATGCTCAACGTATG 58.930 33.333 16.85 0.00 46.87 2.39
803 807 8.153479 TGCATATTAAAGAATGCTCAACGTAT 57.847 30.769 16.85 0.00 46.87 3.06
806 810 9.449550 TTTATGCATATTAAAGAATGCTCAACG 57.550 29.630 7.36 0.00 46.87 4.10
826 830 9.961266 AGTTCGTGTTTTTAAAAAGTTTTATGC 57.039 25.926 13.58 0.80 33.12 3.14
859 863 5.324409 TGCCTGTTGGATGTTTTTATCTCT 58.676 37.500 0.00 0.00 34.57 3.10
860 864 5.183904 ACTGCCTGTTGGATGTTTTTATCTC 59.816 40.000 0.00 0.00 34.57 2.75
862 866 5.391312 ACTGCCTGTTGGATGTTTTTATC 57.609 39.130 0.00 0.00 34.57 1.75
869 873 3.091545 CCATAAACTGCCTGTTGGATGT 58.908 45.455 8.06 0.00 39.13 3.06
1050 1059 2.722201 CGGAGGAGGGTTAAGCGCT 61.722 63.158 2.64 2.64 43.54 5.92
1186 1209 4.332543 TGGAGGGGGAAGGCGTCT 62.333 66.667 0.00 0.00 0.00 4.18
1192 1215 3.316573 GAGCGTGTGGAGGGGGAAG 62.317 68.421 0.00 0.00 0.00 3.46
1819 2473 2.916716 GCATTTCGCCAAACATGTGTAG 59.083 45.455 0.00 0.00 32.94 2.74
2221 2875 2.846206 AGAATCACAGAGCACCCCATTA 59.154 45.455 0.00 0.00 0.00 1.90
2247 2901 0.168788 CAACAACACGCCAGCATAGG 59.831 55.000 0.00 0.00 0.00 2.57
2483 3145 6.183360 TGTTCTTGTTCTTCAAACCATCTTCC 60.183 38.462 0.00 0.00 35.48 3.46
2793 3455 4.083696 GCAAATACCGGGTGTATATTTCCG 60.084 45.833 10.66 0.00 39.28 4.30
2972 3638 5.065731 GCAGTTGCTTGTATATGAGCTCTTT 59.934 40.000 16.19 5.11 39.60 2.52
3166 3840 4.828296 GATGCAGGTGGCCAGGGG 62.828 72.222 5.11 0.00 43.89 4.79
3296 3970 2.734606 CAGGCATCAACAACTTGCATTG 59.265 45.455 0.00 0.00 38.12 2.82
3487 4161 7.280876 GTCCAATTAAGTCATACTGCAATGAGA 59.719 37.037 1.21 0.00 36.57 3.27
3488 4162 7.066163 TGTCCAATTAAGTCATACTGCAATGAG 59.934 37.037 1.21 0.00 36.57 2.90
3720 4404 2.856222 ACTCCTGGTCAGCAAAGAAAG 58.144 47.619 0.00 0.00 0.00 2.62
3721 4405 3.391296 ACTACTCCTGGTCAGCAAAGAAA 59.609 43.478 0.00 0.00 0.00 2.52
3857 4542 3.686726 GCTAGCTTGTGCACTCTTTATGT 59.313 43.478 19.41 0.00 42.74 2.29


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

AutoCloner maintained by Alex Coulton.