Multiple sequence alignment - TraesCS5D01G433500

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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 TraesCS5D01G433500 chr5D 100.000 2998 0 0 1 2998 489300939 489303936 0.000000e+00 5537
1 TraesCS5D01G433500 chr5D 88.242 825 82 9 1 818 286931474 286932290 0.000000e+00 972
2 TraesCS5D01G433500 chr5D 79.452 292 51 8 2024 2311 483516513 483516799 6.560000e-47 198
3 TraesCS5D01G433500 chr6D 97.228 974 27 0 2025 2998 418730767 418731740 0.000000e+00 1650
4 TraesCS5D01G433500 chr6D 89.709 826 70 8 1 818 144604074 144603256 0.000000e+00 1040
5 TraesCS5D01G433500 chr6D 87.681 828 86 9 1 820 335610240 335611059 0.000000e+00 950
6 TraesCS5D01G433500 chr5A 90.834 1211 37 19 864 2024 610455817 610457003 0.000000e+00 1554
7 TraesCS5D01G433500 chr5B 86.571 1184 82 31 864 2006 603451176 603452323 0.000000e+00 1234
8 TraesCS5D01G433500 chr4A 89.915 823 70 6 1 820 631640582 631641394 0.000000e+00 1048
9 TraesCS5D01G433500 chr2D 89.455 825 74 9 1 822 340278211 340277397 0.000000e+00 1029
10 TraesCS5D01G433500 chr3D 89.359 827 68 12 1 820 368854368 368853555 0.000000e+00 1022
11 TraesCS5D01G433500 chr3D 78.912 294 54 7 2024 2314 567295129 567294841 3.050000e-45 193
12 TraesCS5D01G433500 chr4D 89.115 836 69 12 1 822 69136055 69135228 0.000000e+00 1020
13 TraesCS5D01G433500 chr6B 88.443 822 81 10 1 820 599726283 599727092 0.000000e+00 979
14 TraesCS5D01G433500 chr6B 88.164 828 79 13 1 822 184716496 184717310 0.000000e+00 968
15 TraesCS5D01G433500 chr7D 88.235 544 61 3 2025 2567 72533286 72532745 0.000000e+00 647
16 TraesCS5D01G433500 chr7D 79.795 292 55 3 2025 2314 109614006 109613717 3.030000e-50 209
17 TraesCS5D01G433500 chr7D 89.404 151 16 0 2548 2698 72532846 72532696 1.100000e-44 191
18 TraesCS5D01G433500 chr7A 87.402 508 61 3 2025 2530 77619876 77619370 5.570000e-162 580
19 TraesCS5D01G433500 chr1B 80.198 303 56 4 2022 2324 16795826 16796124 1.080000e-54 224
20 TraesCS5D01G433500 chr7B 80.000 295 50 8 2021 2311 691192281 691192570 3.030000e-50 209
21 TraesCS5D01G433500 chr4B 78.983 295 52 10 2024 2314 259539906 259539618 3.050000e-45 193


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 TraesCS5D01G433500 chr5D 489300939 489303936 2997 False 5537 5537 100.0000 1 2998 1 chr5D.!!$F3 2997
1 TraesCS5D01G433500 chr5D 286931474 286932290 816 False 972 972 88.2420 1 818 1 chr5D.!!$F1 817
2 TraesCS5D01G433500 chr6D 418730767 418731740 973 False 1650 1650 97.2280 2025 2998 1 chr6D.!!$F2 973
3 TraesCS5D01G433500 chr6D 144603256 144604074 818 True 1040 1040 89.7090 1 818 1 chr6D.!!$R1 817
4 TraesCS5D01G433500 chr6D 335610240 335611059 819 False 950 950 87.6810 1 820 1 chr6D.!!$F1 819
5 TraesCS5D01G433500 chr5A 610455817 610457003 1186 False 1554 1554 90.8340 864 2024 1 chr5A.!!$F1 1160
6 TraesCS5D01G433500 chr5B 603451176 603452323 1147 False 1234 1234 86.5710 864 2006 1 chr5B.!!$F1 1142
7 TraesCS5D01G433500 chr4A 631640582 631641394 812 False 1048 1048 89.9150 1 820 1 chr4A.!!$F1 819
8 TraesCS5D01G433500 chr2D 340277397 340278211 814 True 1029 1029 89.4550 1 822 1 chr2D.!!$R1 821
9 TraesCS5D01G433500 chr3D 368853555 368854368 813 True 1022 1022 89.3590 1 820 1 chr3D.!!$R1 819
10 TraesCS5D01G433500 chr4D 69135228 69136055 827 True 1020 1020 89.1150 1 822 1 chr4D.!!$R1 821
11 TraesCS5D01G433500 chr6B 599726283 599727092 809 False 979 979 88.4430 1 820 1 chr6B.!!$F2 819
12 TraesCS5D01G433500 chr6B 184716496 184717310 814 False 968 968 88.1640 1 822 1 chr6B.!!$F1 821
13 TraesCS5D01G433500 chr7D 72532696 72533286 590 True 419 647 88.8195 2025 2698 2 chr7D.!!$R2 673
14 TraesCS5D01G433500 chr7A 77619370 77619876 506 True 580 580 87.4020 2025 2530 1 chr7A.!!$R1 505

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
854 882 0.106149 GACCCGGGTCGCATAAGATT 59.894 55.0 36.87 4.37 35.3 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2735 2861 2.342279 CACGCCCGTTCCTCTTGA 59.658 61.111 0.0 0.0 0.0 3.02 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
44 45 4.379243 CACCCCGCTCTTCGTGCT 62.379 66.667 0.00 0.00 36.19 4.40
98 106 2.031516 CAGAGCTGGACCAACGCAG 61.032 63.158 8.32 0.00 0.00 5.18
129 137 3.636231 CTCCACCCACTTGGCCGA 61.636 66.667 0.00 0.00 37.83 5.54
152 160 1.760875 GGCCTACTCATGGACGGGA 60.761 63.158 0.00 0.00 0.00 5.14
612 630 1.440938 CTTTGACCGGCGTTTGACCA 61.441 55.000 6.01 0.00 0.00 4.02
636 656 9.086336 CCAGCCACTTATGTTTAATTATGTTTG 57.914 33.333 0.00 0.00 0.00 2.93
655 676 7.083502 TGTTTGTTTATGTTTATTTCGTGCG 57.916 32.000 0.00 0.00 0.00 5.34
657 678 7.112287 TGTTTGTTTATGTTTATTTCGTGCGAG 59.888 33.333 0.00 0.00 0.00 5.03
658 679 5.083389 TGTTTATGTTTATTTCGTGCGAGC 58.917 37.500 0.00 0.00 0.00 5.03
689 717 2.502130 TCACGCTGGTATATTTGGGTCA 59.498 45.455 0.00 0.00 0.00 4.02
701 729 1.083895 TGGGTCAGCCTCCCCATTA 59.916 57.895 0.00 0.00 46.06 1.90
723 751 2.710902 GGCCAAGCCGACCCATTTC 61.711 63.158 0.00 0.00 39.62 2.17
725 753 1.883021 CCAAGCCGACCCATTTCAC 59.117 57.895 0.00 0.00 0.00 3.18
766 794 1.876497 CTGGCCAACCCAAACGGATG 61.876 60.000 7.01 0.00 44.81 3.51
782 810 1.269448 GGATGAAAAGCGGACAAAGCA 59.731 47.619 0.00 0.00 37.01 3.91
820 848 1.354368 CCCCCTTGGAGTTGCTCTTAA 59.646 52.381 0.00 0.00 35.39 1.85
821 849 2.619074 CCCCCTTGGAGTTGCTCTTAAG 60.619 54.545 0.00 0.00 35.39 1.85
822 850 2.305927 CCCCTTGGAGTTGCTCTTAAGA 59.694 50.000 4.81 4.81 31.56 2.10
823 851 3.054065 CCCCTTGGAGTTGCTCTTAAGAT 60.054 47.826 5.44 0.00 31.56 2.40
824 852 3.944015 CCCTTGGAGTTGCTCTTAAGATG 59.056 47.826 5.44 1.81 31.56 2.90
825 853 3.376546 CCTTGGAGTTGCTCTTAAGATGC 59.623 47.826 5.44 11.99 31.56 3.91
826 854 3.701205 TGGAGTTGCTCTTAAGATGCA 57.299 42.857 19.33 19.33 34.69 3.96
827 855 3.603532 TGGAGTTGCTCTTAAGATGCAG 58.396 45.455 21.03 7.22 38.01 4.41
828 856 2.941720 GGAGTTGCTCTTAAGATGCAGG 59.058 50.000 21.03 6.92 38.01 4.85
829 857 3.369892 GGAGTTGCTCTTAAGATGCAGGA 60.370 47.826 21.03 11.09 38.01 3.86
830 858 3.604582 AGTTGCTCTTAAGATGCAGGAC 58.395 45.455 21.03 18.43 38.01 3.85
831 859 2.299993 TGCTCTTAAGATGCAGGACG 57.700 50.000 19.33 3.42 32.55 4.79
832 860 1.550524 TGCTCTTAAGATGCAGGACGT 59.449 47.619 19.33 0.00 32.55 4.34
833 861 1.929836 GCTCTTAAGATGCAGGACGTG 59.070 52.381 16.99 0.00 0.00 4.49
852 880 3.213264 GACCCGGGTCGCATAAGA 58.787 61.111 36.87 0.00 35.30 2.10
853 881 1.746517 GACCCGGGTCGCATAAGAT 59.253 57.895 36.87 5.01 35.30 2.40
854 882 0.106149 GACCCGGGTCGCATAAGATT 59.894 55.000 36.87 4.37 35.30 2.40
855 883 0.544697 ACCCGGGTCGCATAAGATTT 59.455 50.000 24.16 0.00 0.00 2.17
856 884 1.064979 ACCCGGGTCGCATAAGATTTT 60.065 47.619 24.16 0.00 0.00 1.82
857 885 2.021457 CCCGGGTCGCATAAGATTTTT 58.979 47.619 14.18 0.00 0.00 1.94
884 918 5.365025 TCCTAATTCAAGGACCTCTGATCTG 59.635 44.000 0.00 0.00 40.86 2.90
901 935 3.319137 TCTGCAATGCTCGGTATATCC 57.681 47.619 6.82 0.00 0.00 2.59
1322 1384 2.432628 GCACGGAGGAACCTCACG 60.433 66.667 20.39 20.75 44.40 4.35
1327 1389 0.460284 CGGAGGAACCTCACGATTGG 60.460 60.000 20.39 0.00 44.40 3.16
1378 1440 1.076014 TGGTCGAGCTACAGGTCCA 59.924 57.895 16.64 0.00 39.23 4.02
1389 1451 1.830279 ACAGGTCCATCAACATGCAG 58.170 50.000 0.00 0.00 34.40 4.41
1390 1452 1.352017 ACAGGTCCATCAACATGCAGA 59.648 47.619 0.00 0.00 34.40 4.26
1446 1508 2.827051 CGCCATGAATGAGCGGTGG 61.827 63.158 14.47 0.00 40.91 4.61
1618 1711 1.539560 CGAGGGCATCTCCGGATCAT 61.540 60.000 3.57 0.00 39.30 2.45
1629 1722 2.281070 GGATCATGGCGGCATCGT 60.281 61.111 23.19 13.43 38.89 3.73
1632 1725 3.405093 ATCATGGCGGCATCGTGGT 62.405 57.895 23.19 6.20 38.89 4.16
1798 1891 0.315251 GATGATCTGATCGTCCCGCA 59.685 55.000 23.38 2.52 38.98 5.69
1983 2107 1.527311 GCTTTGCTTCGGTATCGATCC 59.473 52.381 0.00 2.28 45.51 3.36
1984 2108 2.821546 CTTTGCTTCGGTATCGATCCA 58.178 47.619 0.00 0.00 45.51 3.41
2051 2175 6.801377 GTGAATTGCAGAAAACATCGACATTA 59.199 34.615 0.00 0.00 0.00 1.90
2056 2180 5.471797 TGCAGAAAACATCGACATTAAAGGA 59.528 36.000 0.00 0.00 0.00 3.36
2059 2183 8.181573 GCAGAAAACATCGACATTAAAGGATAA 58.818 33.333 0.00 0.00 0.00 1.75
2099 2223 9.777297 ACAATTCTACAGTTTTATGCCAAAAAT 57.223 25.926 0.00 0.00 31.43 1.82
2177 2303 6.292649 CGTTTTAAGCACGATTATGATAGGCA 60.293 38.462 3.75 0.00 40.20 4.75
2239 2365 6.540438 AGACGTTGTTAGATGAGGGATTTA 57.460 37.500 0.00 0.00 0.00 1.40
2736 2862 4.899239 CGGACAGGGATGGCGCTC 62.899 72.222 7.64 0.00 34.72 5.03
2739 2865 1.817099 GACAGGGATGGCGCTCAAG 60.817 63.158 7.64 0.00 34.72 3.02
2833 2959 1.546476 CTACGACACAGCCTCTTCCTT 59.454 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 88 1.758440 TTCTGCGTTGGTCCAGCTCT 61.758 55.000 4.03 0.00 0.00 4.09
129 137 1.501582 GTCCATGAGTAGGCCTCCTT 58.498 55.000 9.68 0.00 39.65 3.36
143 151 1.740285 GCGATACTGTCCCGTCCAT 59.260 57.895 0.00 0.00 0.00 3.41
152 160 0.963856 TCACCCACTCGCGATACTGT 60.964 55.000 10.36 0.00 0.00 3.55
176 184 3.379445 GCGAAGTGGACGGGAGGA 61.379 66.667 0.00 0.00 0.00 3.71
218 226 1.668294 CTTCCAGCACTCGAGGTGT 59.332 57.895 18.41 0.00 46.86 4.16
313 321 4.208686 CCTCGAGCCGTAGCACCC 62.209 72.222 6.99 0.00 43.56 4.61
316 324 2.829003 CCTCCTCGAGCCGTAGCA 60.829 66.667 6.99 0.00 43.56 3.49
320 328 3.707640 CTCCTCCTCCTCGAGCCGT 62.708 68.421 6.99 0.00 0.00 5.68
441 456 1.095600 TCGGTGAGGTCGATGAAGAG 58.904 55.000 0.00 0.00 0.00 2.85
469 484 4.680237 TGCCCTTGCCGTCGACAG 62.680 66.667 17.16 5.18 36.33 3.51
470 485 4.243008 TTGCCCTTGCCGTCGACA 62.243 61.111 17.16 0.00 36.33 4.35
471 486 3.423154 CTTGCCCTTGCCGTCGAC 61.423 66.667 5.18 5.18 36.33 4.20
472 487 4.697756 CCTTGCCCTTGCCGTCGA 62.698 66.667 0.00 0.00 36.33 4.20
478 493 3.698820 CCTTGCCCTTGCCCTTGC 61.699 66.667 0.00 0.00 36.33 4.01
577 595 5.178809 CGGTCAAAGTCCACTTAAACCTAAG 59.821 44.000 15.83 0.00 37.97 2.18
587 605 2.030562 CGCCGGTCAAAGTCCACT 59.969 61.111 1.90 0.00 0.00 4.00
636 656 5.225129 CAGCTCGCACGAAATAAACATAAAC 59.775 40.000 0.00 0.00 0.00 2.01
674 702 2.441750 GGAGGCTGACCCAAATATACCA 59.558 50.000 0.00 0.00 36.11 3.25
707 735 0.893270 TGTGAAATGGGTCGGCTTGG 60.893 55.000 0.00 0.00 0.00 3.61
723 751 2.476051 GTGCTCGTCCGCATTGTG 59.524 61.111 0.76 0.00 42.62 3.33
766 794 1.268778 GCGTGCTTTGTCCGCTTTTC 61.269 55.000 0.00 0.00 43.81 2.29
804 832 4.005650 TGCATCTTAAGAGCAACTCCAAG 58.994 43.478 20.34 0.00 34.97 3.61
835 863 0.106149 AATCTTATGCGACCCGGGTC 59.894 55.000 39.19 39.19 41.40 4.46
836 864 0.544697 AAATCTTATGCGACCCGGGT 59.455 50.000 30.81 30.81 0.00 5.28
837 865 1.675552 AAAATCTTATGCGACCCGGG 58.324 50.000 22.25 22.25 0.00 5.73
856 884 6.848069 TCAGAGGTCCTTGAATTAGGAAAAA 58.152 36.000 0.00 0.00 45.62 1.94
857 885 6.448369 TCAGAGGTCCTTGAATTAGGAAAA 57.552 37.500 0.00 0.00 45.62 2.29
858 886 6.445139 AGATCAGAGGTCCTTGAATTAGGAAA 59.555 38.462 0.00 0.00 45.62 3.13
859 887 5.966935 AGATCAGAGGTCCTTGAATTAGGAA 59.033 40.000 0.00 0.00 45.62 3.36
860 888 5.365025 CAGATCAGAGGTCCTTGAATTAGGA 59.635 44.000 0.00 0.00 42.02 2.94
861 889 5.609423 CAGATCAGAGGTCCTTGAATTAGG 58.391 45.833 0.00 0.00 36.59 2.69
862 890 5.055812 GCAGATCAGAGGTCCTTGAATTAG 58.944 45.833 0.00 0.00 0.00 1.73
865 893 2.842496 TGCAGATCAGAGGTCCTTGAAT 59.158 45.455 0.00 0.00 0.00 2.57
879 911 3.868077 GGATATACCGAGCATTGCAGATC 59.132 47.826 11.91 1.96 0.00 2.75
884 918 2.263077 CGAGGATATACCGAGCATTGC 58.737 52.381 0.00 0.00 44.74 3.56
901 935 1.679680 TCCCCTGTATTTAGCGACGAG 59.320 52.381 0.00 0.00 0.00 4.18
1322 1384 2.960129 CGCCGGTCGTAGCCAATC 60.960 66.667 1.90 0.00 0.00 2.67
1591 1684 4.554036 GATGCCCTCGTCTGCCCC 62.554 72.222 0.00 0.00 0.00 5.80
1593 1686 2.107953 GAGATGCCCTCGTCTGCC 59.892 66.667 0.00 0.00 38.62 4.85
1660 1753 2.854214 CGAGCGCTTCATCGACAGC 61.854 63.158 13.26 3.48 41.40 4.40
1798 1891 2.920645 CGGCGACACCTGTCTGTCT 61.921 63.158 0.00 0.00 42.66 3.41
1983 2107 2.510874 TCGCGTGTTTTTCAAACAGTG 58.489 42.857 5.77 4.74 0.00 3.66
1984 2108 2.904011 TCGCGTGTTTTTCAAACAGT 57.096 40.000 5.77 0.00 0.00 3.55
2051 2175 4.706962 GTGGATTCTGCAACCTTATCCTTT 59.293 41.667 0.00 0.00 36.55 3.11
2056 2180 6.212888 GAATTGTGGATTCTGCAACCTTAT 57.787 37.500 0.00 0.00 40.83 1.73
2089 2213 6.183360 GGCTAGGAATTAGTGATTTTTGGCAT 60.183 38.462 0.00 0.00 0.00 4.40
2137 2263 5.220605 GCTTAAAACGAACTAAGCCATCGAT 60.221 40.000 12.85 0.00 42.71 3.59
2239 2365 4.753107 CGTGGACTGTTTGGTAAATGTAGT 59.247 41.667 0.00 0.00 0.00 2.73
2735 2861 2.342279 CACGCCCGTTCCTCTTGA 59.658 61.111 0.00 0.00 0.00 3.02
2736 2862 2.742372 CCACGCCCGTTCCTCTTG 60.742 66.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.