Multiple sequence alignment - TraesCS7A01G531800

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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 TraesCS7A01G531800 chr7A 100.000 2711 0 0 1 2711 709999971 709997261 0.000000e+00 5007
1 TraesCS7A01G531800 chr7A 87.024 709 62 19 945 1644 709674312 709674999 0.000000e+00 773
2 TraesCS7A01G531800 chr7A 88.427 337 22 8 908 1241 710995419 710995097 9.100000e-105 390
3 TraesCS7A01G531800 chr7A 89.610 231 24 0 669 899 710079506 710079736 7.340000e-76 294
4 TraesCS7A01G531800 chr4A 99.273 963 7 0 1749 2711 673480044 673479082 0.000000e+00 1740
5 TraesCS7A01G531800 chr4A 97.425 971 23 2 1742 2711 731199362 731200331 0.000000e+00 1653
6 TraesCS7A01G531800 chr3D 96.384 968 32 2 1746 2711 118416331 118417297 0.000000e+00 1591
7 TraesCS7A01G531800 chr3D 84.829 936 85 23 1 900 479631993 479631079 0.000000e+00 889
8 TraesCS7A01G531800 chr7D 96.473 964 29 4 1748 2711 7472505 7473463 0.000000e+00 1587
9 TraesCS7A01G531800 chr7D 95.167 869 21 10 900 1749 617117166 617116300 0.000000e+00 1352
10 TraesCS7A01G531800 chr7D 90.112 627 50 6 1 620 392361232 392361853 0.000000e+00 804
11 TraesCS7A01G531800 chr7D 85.472 709 73 20 945 1644 616908052 616908739 0.000000e+00 712
12 TraesCS7A01G531800 chr7D 90.654 535 39 2 908 1440 617374519 617373994 0.000000e+00 701
13 TraesCS7A01G531800 chr7D 82.746 539 63 15 1748 2265 554200687 554200158 1.140000e-123 453
14 TraesCS7A01G531800 chr7D 90.129 233 21 2 669 900 392267629 392267398 4.390000e-78 302
15 TraesCS7A01G531800 chr7D 86.475 244 30 2 2255 2498 554200243 554200003 5.760000e-67 265
16 TraesCS7A01G531800 chr7D 82.266 203 27 3 2308 2502 497343676 497343877 1.670000e-37 167
17 TraesCS7A01G531800 chr7B 91.487 881 35 9 907 1749 711485650 711484772 0.000000e+00 1175
18 TraesCS7A01G531800 chr7B 86.214 914 86 17 15 900 161900380 161901281 0.000000e+00 953
19 TraesCS7A01G531800 chr7B 84.432 880 104 12 1 868 254826847 254827705 0.000000e+00 835
20 TraesCS7A01G531800 chr7B 88.966 435 42 4 1210 1644 711000738 711001166 1.430000e-147 532
21 TraesCS7A01G531800 chr7B 82.983 523 57 10 1752 2251 600800616 600801129 6.890000e-121 444
22 TraesCS7A01G531800 chr7B 80.608 263 38 5 2256 2507 525827545 525827285 9.910000e-45 191
23 TraesCS7A01G531800 chr7B 78.113 265 35 11 2254 2507 525701943 525702195 2.180000e-31 147
24 TraesCS7A01G531800 chr7B 77.736 265 36 11 2254 2507 525622891 525623143 1.010000e-29 141
25 TraesCS7A01G531800 chr2D 96.197 710 25 2 2002 2711 447248499 447247792 0.000000e+00 1160
26 TraesCS7A01G531800 chr2D 93.032 531 35 2 1749 2279 433211214 433211742 0.000000e+00 774
27 TraesCS7A01G531800 chr3A 89.978 908 71 12 1 900 465530288 465531183 0.000000e+00 1155
28 TraesCS7A01G531800 chr6B 87.957 847 52 12 88 902 685210700 685209872 0.000000e+00 953
29 TraesCS7A01G531800 chr6B 84.375 928 104 19 1 900 29005199 29004285 0.000000e+00 872
30 TraesCS7A01G531800 chr6B 84.290 923 106 13 3 901 256304625 256303718 0.000000e+00 865
31 TraesCS7A01G531800 chr6B 92.182 307 23 1 1973 2279 480390111 480389806 1.490000e-117 433
32 TraesCS7A01G531800 chr6B 89.732 224 20 3 1747 1968 143434396 143434618 1.590000e-72 283
33 TraesCS7A01G531800 chr5B 85.316 933 92 19 1 905 397856845 397855930 0.000000e+00 922
34 TraesCS7A01G531800 chr5B 84.951 917 90 22 15 900 441661504 441662403 0.000000e+00 885
35 TraesCS7A01G531800 chr5B 83.995 731 69 21 200 899 442785884 442785171 0.000000e+00 658
36 TraesCS7A01G531800 chr6D 84.182 923 112 14 1 901 143869386 143868476 0.000000e+00 865
37 TraesCS7A01G531800 chr1B 82.577 947 110 27 1 907 557422774 557423705 0.000000e+00 784
38 TraesCS7A01G531800 chr2B 91.857 307 24 1 1973 2279 761996394 761996699 6.940000e-116 427
39 TraesCS7A01G531800 chr2B 90.129 233 22 1 669 900 181719267 181719499 4.390000e-78 302


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 TraesCS7A01G531800 chr7A 709997261 709999971 2710 True 5007 5007 100.0000 1 2711 1 chr7A.!!$R1 2710
1 TraesCS7A01G531800 chr7A 709674312 709674999 687 False 773 773 87.0240 945 1644 1 chr7A.!!$F1 699
2 TraesCS7A01G531800 chr4A 673479082 673480044 962 True 1740 1740 99.2730 1749 2711 1 chr4A.!!$R1 962
3 TraesCS7A01G531800 chr4A 731199362 731200331 969 False 1653 1653 97.4250 1742 2711 1 chr4A.!!$F1 969
4 TraesCS7A01G531800 chr3D 118416331 118417297 966 False 1591 1591 96.3840 1746 2711 1 chr3D.!!$F1 965
5 TraesCS7A01G531800 chr3D 479631079 479631993 914 True 889 889 84.8290 1 900 1 chr3D.!!$R1 899
6 TraesCS7A01G531800 chr7D 7472505 7473463 958 False 1587 1587 96.4730 1748 2711 1 chr7D.!!$F1 963
7 TraesCS7A01G531800 chr7D 617116300 617117166 866 True 1352 1352 95.1670 900 1749 1 chr7D.!!$R2 849
8 TraesCS7A01G531800 chr7D 392361232 392361853 621 False 804 804 90.1120 1 620 1 chr7D.!!$F2 619
9 TraesCS7A01G531800 chr7D 616908052 616908739 687 False 712 712 85.4720 945 1644 1 chr7D.!!$F4 699
10 TraesCS7A01G531800 chr7D 617373994 617374519 525 True 701 701 90.6540 908 1440 1 chr7D.!!$R3 532
11 TraesCS7A01G531800 chr7D 554200003 554200687 684 True 359 453 84.6105 1748 2498 2 chr7D.!!$R4 750
12 TraesCS7A01G531800 chr7B 711484772 711485650 878 True 1175 1175 91.4870 907 1749 1 chr7B.!!$R2 842
13 TraesCS7A01G531800 chr7B 161900380 161901281 901 False 953 953 86.2140 15 900 1 chr7B.!!$F1 885
14 TraesCS7A01G531800 chr7B 254826847 254827705 858 False 835 835 84.4320 1 868 1 chr7B.!!$F2 867
15 TraesCS7A01G531800 chr7B 600800616 600801129 513 False 444 444 82.9830 1752 2251 1 chr7B.!!$F5 499
16 TraesCS7A01G531800 chr2D 447247792 447248499 707 True 1160 1160 96.1970 2002 2711 1 chr2D.!!$R1 709
17 TraesCS7A01G531800 chr2D 433211214 433211742 528 False 774 774 93.0320 1749 2279 1 chr2D.!!$F1 530
18 TraesCS7A01G531800 chr3A 465530288 465531183 895 False 1155 1155 89.9780 1 900 1 chr3A.!!$F1 899
19 TraesCS7A01G531800 chr6B 685209872 685210700 828 True 953 953 87.9570 88 902 1 chr6B.!!$R4 814
20 TraesCS7A01G531800 chr6B 29004285 29005199 914 True 872 872 84.3750 1 900 1 chr6B.!!$R1 899
21 TraesCS7A01G531800 chr6B 256303718 256304625 907 True 865 865 84.2900 3 901 1 chr6B.!!$R2 898
22 TraesCS7A01G531800 chr5B 397855930 397856845 915 True 922 922 85.3160 1 905 1 chr5B.!!$R1 904
23 TraesCS7A01G531800 chr5B 441661504 441662403 899 False 885 885 84.9510 15 900 1 chr5B.!!$F1 885
24 TraesCS7A01G531800 chr5B 442785171 442785884 713 True 658 658 83.9950 200 899 1 chr5B.!!$R2 699
25 TraesCS7A01G531800 chr6D 143868476 143869386 910 True 865 865 84.1820 1 901 1 chr6D.!!$R1 900
26 TraesCS7A01G531800 chr1B 557422774 557423705 931 False 784 784 82.5770 1 907 1 chr1B.!!$F1 906

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
297 311 0.889186 CCCTACCCCATATGCGCAAC 60.889 60.0 17.11 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2020 1.542915 CTTGATGGTGAACAAGCCAGG 59.457 52.381 0.0 0.0 38.27 4.45 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
47 53 1.570813 ACATATGGTCGACGCATGTG 58.429 50.000 26.64 26.64 0.00 3.21
71 77 7.755373 GTGACCTAATTGAAGCTAACATTTTCC 59.245 37.037 0.00 0.00 0.00 3.13
72 78 7.450014 TGACCTAATTGAAGCTAACATTTTCCA 59.550 33.333 0.00 0.00 0.00 3.53
227 235 2.107950 TCACCATCCACGGCTAAAAG 57.892 50.000 0.00 0.00 0.00 2.27
268 281 1.068588 GTGACCAAAAAGAGGGCCAAC 59.931 52.381 6.18 0.00 31.11 3.77
297 311 0.889186 CCCTACCCCATATGCGCAAC 60.889 60.000 17.11 0.00 0.00 4.17
309 323 1.080705 GCGCAACTGAGTAGGACGT 60.081 57.895 0.30 0.00 0.00 4.34
343 357 3.490933 CGGAGCTAAAATGGACAGATCGA 60.491 47.826 0.00 0.00 0.00 3.59
603 655 2.876219 GACTCGGTCTGGTCGGTC 59.124 66.667 0.00 0.00 0.00 4.79
604 656 1.674980 GACTCGGTCTGGTCGGTCT 60.675 63.158 0.00 0.00 0.00 3.85
605 657 1.924320 GACTCGGTCTGGTCGGTCTG 61.924 65.000 0.00 0.00 0.00 3.51
653 728 3.749665 TCCCTGGTGATTTTGCAAAAG 57.250 42.857 27.08 13.87 0.00 2.27
659 740 2.549992 GGTGATTTTGCAAAAGACCCCC 60.550 50.000 29.39 21.93 32.30 5.40
767 848 1.295357 CCGCCAAATCAGCACGTACA 61.295 55.000 0.00 0.00 0.00 2.90
875 956 3.177249 GGCCAACGCGACGAGTAC 61.177 66.667 15.93 0.00 35.02 2.73
989 1074 3.634397 ATTTCCCATCATGTCGACACT 57.366 42.857 22.71 7.55 0.00 3.55
993 1078 2.567169 TCCCATCATGTCGACACTTTCT 59.433 45.455 22.71 0.56 0.00 2.52
1133 1233 1.507174 GGCAGCTACTTCGACGACT 59.493 57.895 0.00 0.00 0.00 4.18
1708 1843 3.335579 ACTTTGGATACGTTGCCTTCTC 58.664 45.455 0.00 0.00 42.51 2.87
1728 1863 9.472361 CCTTCTCAGATAAATTTTATGCCATTG 57.528 33.333 6.38 0.00 0.00 2.82
1736 1871 9.900264 GATAAATTTTATGCCATTGTCGTTTTC 57.100 29.630 6.38 0.00 0.00 2.29
1737 1872 6.720012 AATTTTATGCCATTGTCGTTTTCC 57.280 33.333 0.00 0.00 0.00 3.13
1742 1877 4.920640 TGCCATTGTCGTTTTCCTTTTA 57.079 36.364 0.00 0.00 0.00 1.52
1743 1878 5.461032 TGCCATTGTCGTTTTCCTTTTAT 57.539 34.783 0.00 0.00 0.00 1.40
1744 1879 6.576662 TGCCATTGTCGTTTTCCTTTTATA 57.423 33.333 0.00 0.00 0.00 0.98
1884 2020 4.600692 AACACAATTAGCAGAAAACCCC 57.399 40.909 0.00 0.00 0.00 4.95
2021 2158 2.029739 TGCCTTTAGACGTCAACGATGA 60.030 45.455 19.50 0.00 43.02 2.92
2327 2585 7.808381 CGTCTAAATCTTCAGAGTACTCAACAA 59.192 37.037 24.44 12.25 0.00 2.83
2660 2918 3.947196 TGAACATGCTAACACCCATGATC 59.053 43.478 7.53 5.92 40.92 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 24 5.547341 CGTCGACCATATGTTGTTTTGTAG 58.453 41.667 10.58 0.00 0.00 2.74
19 25 4.143073 GCGTCGACCATATGTTGTTTTGTA 60.143 41.667 10.58 0.00 0.00 2.41
47 53 7.755373 GTGGAAAATGTTAGCTTCAATTAGGTC 59.245 37.037 0.00 0.00 0.00 3.85
268 281 1.374572 TGGGGTAGGGTTTAGGGTTG 58.625 55.000 0.00 0.00 0.00 3.77
297 311 1.169577 AGAGTGCACGTCCTACTCAG 58.830 55.000 19.53 0.00 42.44 3.35
309 323 0.902984 TAGCTCCGGGAAAGAGTGCA 60.903 55.000 0.00 0.00 33.69 4.57
343 357 0.827925 TCGTCACCACCTTCTCTGCT 60.828 55.000 0.00 0.00 0.00 4.24
477 496 3.356639 GACCGCCATGAGCTCGTCA 62.357 63.158 5.16 0.00 40.39 4.35
666 747 3.120086 ATTCGGGGGAATGCGGGAG 62.120 63.158 0.00 0.00 0.00 4.30
667 748 3.093835 ATTCGGGGGAATGCGGGA 61.094 61.111 0.00 0.00 0.00 5.14
733 814 1.672356 GCGGTTGACTGGCATGTCT 60.672 57.895 14.98 0.00 37.79 3.41
767 848 7.495055 ACGGTCCAATATACGTTTTCTTCTAT 58.505 34.615 0.00 0.00 35.90 1.98
875 956 2.770164 AAATTCACTCCAGGTCCTCG 57.230 50.000 0.00 0.00 0.00 4.63
1677 1812 7.081976 GCAACGTATCCAAAGTAAAATTCTGT 58.918 34.615 0.00 0.00 0.00 3.41
1708 1843 8.633075 AACGACAATGGCATAAAATTTATCTG 57.367 30.769 0.00 0.00 0.00 2.90
1737 1872 9.438291 CACATGATACTTCGCCTTTTATAAAAG 57.562 33.333 25.01 25.01 43.82 2.27
1742 1877 7.624360 TTTCACATGATACTTCGCCTTTTAT 57.376 32.000 0.00 0.00 0.00 1.40
1743 1878 7.441890 TTTTCACATGATACTTCGCCTTTTA 57.558 32.000 0.00 0.00 0.00 1.52
1744 1879 5.957842 TTTCACATGATACTTCGCCTTTT 57.042 34.783 0.00 0.00 0.00 2.27
1760 1895 8.918202 ATTTTCACTGAGTACCTATTTTCACA 57.082 30.769 0.00 0.00 0.00 3.58
1884 2020 1.542915 CTTGATGGTGAACAAGCCAGG 59.457 52.381 0.00 0.00 38.27 4.45
2021 2158 2.377810 TTGCTGCCATCGGAGGGAT 61.378 57.895 13.78 0.00 35.09 3.85
2327 2585 0.387367 GTGTCAGTCACGAGCGATGT 60.387 55.000 0.00 0.00 37.31 3.06
2660 2918 3.377172 TCATGCTCAATCTGTGATGCAAG 59.623 43.478 0.00 0.00 40.99 4.01


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

AutoCloner maintained by Alex Coulton.