Multiple sequence alignment - TraesCS7A01G297800

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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 TraesCS7A01G297800 chr7A 100.000 3143 0 0 1 3143 401612434 401615576 0.000000e+00 5805.0
1 TraesCS7A01G297800 chr7A 97.479 1904 44 3 876 2778 26975507 26973607 0.000000e+00 3247.0
2 TraesCS7A01G297800 chr7A 92.180 1202 82 11 1942 3136 9092518 9091322 0.000000e+00 1688.0
3 TraesCS7A01G297800 chr7A 96.739 368 12 0 2776 3143 26964943 26964576 5.760000e-172 614.0
4 TraesCS7A01G297800 chr7B 91.898 2271 179 5 876 3143 405675594 405673326 0.000000e+00 3169.0
5 TraesCS7A01G297800 chr7B 95.391 499 22 1 1 498 264477770 264478268 0.000000e+00 793.0
6 TraesCS7A01G297800 chr7B 93.333 375 20 1 494 863 264480942 264481316 1.650000e-152 549.0
7 TraesCS7A01G297800 chr7B 100.000 32 0 0 874 905 405675627 405675596 3.390000e-05 60.2
8 TraesCS7A01G297800 chr3A 91.758 2269 178 4 876 3143 266559504 266557244 0.000000e+00 3145.0
9 TraesCS7A01G297800 chr3A 86.737 475 48 6 136 598 267362986 267362515 6.010000e-142 514.0
10 TraesCS7A01G297800 chr3A 88.060 201 13 2 408 598 560151194 560150995 8.770000e-56 228.0
11 TraesCS7A01G297800 chr3D 89.943 2277 214 9 869 3143 31652479 31654742 0.000000e+00 2922.0
12 TraesCS7A01G297800 chr3D 100.000 30 0 0 876 905 31652453 31652482 4.380000e-04 56.5
13 TraesCS7A01G297800 chr6B 89.696 1844 174 5 869 2710 87634149 87635978 0.000000e+00 2338.0
14 TraesCS7A01G297800 chr6B 88.174 482 46 7 130 600 715735021 715734540 5.880000e-157 564.0
15 TraesCS7A01G297800 chr6B 90.736 421 39 0 2706 3126 87644285 87644705 2.120000e-156 562.0
16 TraesCS7A01G297800 chr6B 85.806 465 42 13 102 544 333175377 333175839 3.670000e-129 472.0
17 TraesCS7A01G297800 chr6B 84.783 460 47 12 102 540 257975606 257975149 1.030000e-119 440.0
18 TraesCS7A01G297800 chr2A 96.848 1174 34 3 869 2042 3364466 3365636 0.000000e+00 1960.0
19 TraesCS7A01G297800 chr2A 97.959 1029 20 1 2116 3143 3365877 3366905 0.000000e+00 1783.0
20 TraesCS7A01G297800 chr2A 79.869 765 84 32 102 851 172782586 172783295 2.180000e-136 496.0
21 TraesCS7A01G297800 chr1A 97.683 863 17 1 1 863 276860766 276859907 0.000000e+00 1480.0
22 TraesCS7A01G297800 chr7D 96.524 863 30 0 1 863 283700067 283699205 0.000000e+00 1428.0
23 TraesCS7A01G297800 chr3B 92.841 866 56 2 1 860 283129133 283129998 0.000000e+00 1251.0
24 TraesCS7A01G297800 chr3B 86.576 812 80 13 62 863 613744083 613743291 0.000000e+00 869.0
25 TraesCS7A01G297800 chr2B 89.778 812 82 1 2328 3138 104786234 104787045 0.000000e+00 1038.0
26 TraesCS7A01G297800 chr2B 83.913 460 48 14 102 540 546452264 546452718 1.740000e-112 416.0
27 TraesCS7A01G297800 chr2B 84.438 347 33 11 531 860 546452780 546453122 3.910000e-84 322.0
28 TraesCS7A01G297800 chr2D 84.074 653 61 12 249 863 641570906 641570259 9.710000e-165 590.0
29 TraesCS7A01G297800 chr5B 81.491 778 82 34 102 863 134987110 134987841 1.620000e-162 582.0
30 TraesCS7A01G297800 chr5B 81.462 383 56 14 876 1254 243768790 243769161 1.830000e-77 300.0
31 TraesCS7A01G297800 chr1B 80.092 653 69 23 250 863 363216990 363216360 2.240000e-116 429.0
32 TraesCS7A01G297800 chr1D 74.632 816 183 22 2245 3047 5476636 5477440 3.880000e-89 339.0
33 TraesCS7A01G297800 chr4B 74.502 251 52 3 2241 2491 463586037 463586275 7.170000e-17 99.0
34 TraesCS7A01G297800 chr6D 92.063 63 3 2 2217 2278 106662688 106662749 1.550000e-13 87.9


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 TraesCS7A01G297800 chr7A 401612434 401615576 3142 False 5805.00 5805 100.0000 1 3143 1 chr7A.!!$F1 3142
1 TraesCS7A01G297800 chr7A 26973607 26975507 1900 True 3247.00 3247 97.4790 876 2778 1 chr7A.!!$R3 1902
2 TraesCS7A01G297800 chr7A 9091322 9092518 1196 True 1688.00 1688 92.1800 1942 3136 1 chr7A.!!$R1 1194
3 TraesCS7A01G297800 chr7B 405673326 405675627 2301 True 1614.60 3169 95.9490 874 3143 2 chr7B.!!$R1 2269
4 TraesCS7A01G297800 chr7B 264477770 264481316 3546 False 671.00 793 94.3620 1 863 2 chr7B.!!$F1 862
5 TraesCS7A01G297800 chr3A 266557244 266559504 2260 True 3145.00 3145 91.7580 876 3143 1 chr3A.!!$R1 2267
6 TraesCS7A01G297800 chr3D 31652453 31654742 2289 False 1489.25 2922 94.9715 869 3143 2 chr3D.!!$F1 2274
7 TraesCS7A01G297800 chr6B 87634149 87635978 1829 False 2338.00 2338 89.6960 869 2710 1 chr6B.!!$F1 1841
8 TraesCS7A01G297800 chr2A 3364466 3366905 2439 False 1871.50 1960 97.4035 869 3143 2 chr2A.!!$F2 2274
9 TraesCS7A01G297800 chr2A 172782586 172783295 709 False 496.00 496 79.8690 102 851 1 chr2A.!!$F1 749
10 TraesCS7A01G297800 chr1A 276859907 276860766 859 True 1480.00 1480 97.6830 1 863 1 chr1A.!!$R1 862
11 TraesCS7A01G297800 chr7D 283699205 283700067 862 True 1428.00 1428 96.5240 1 863 1 chr7D.!!$R1 862
12 TraesCS7A01G297800 chr3B 283129133 283129998 865 False 1251.00 1251 92.8410 1 860 1 chr3B.!!$F1 859
13 TraesCS7A01G297800 chr3B 613743291 613744083 792 True 869.00 869 86.5760 62 863 1 chr3B.!!$R1 801
14 TraesCS7A01G297800 chr2B 104786234 104787045 811 False 1038.00 1038 89.7780 2328 3138 1 chr2B.!!$F1 810
15 TraesCS7A01G297800 chr2B 546452264 546453122 858 False 369.00 416 84.1755 102 860 2 chr2B.!!$F2 758
16 TraesCS7A01G297800 chr2D 641570259 641570906 647 True 590.00 590 84.0740 249 863 1 chr2D.!!$R1 614
17 TraesCS7A01G297800 chr5B 134987110 134987841 731 False 582.00 582 81.4910 102 863 1 chr5B.!!$F1 761
18 TraesCS7A01G297800 chr1B 363216360 363216990 630 True 429.00 429 80.0920 250 863 1 chr1B.!!$R1 613
19 TraesCS7A01G297800 chr1D 5476636 5477440 804 False 339.00 339 74.6320 2245 3047 1 chr1D.!!$F1 802

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
992 3909 0.174389 GTCTGCGCTCATCAAGGAGA 59.826 55.0 9.73 0.0 37.05 3.71 F
1027 3944 0.960364 TGCAGGGAAGGAAACGATGC 60.960 55.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 4952 0.112995 AGGAAGCCAAGATGTGCCAA 59.887 50.000 0.0 0.0 0.0 4.52 R
2190 5276 3.764434 CTGGTTGTAGCTGTCTCTTCCTA 59.236 47.826 0.0 0.0 0.0 2.94 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
81 82 8.504409 ACAGTCTATACTCCCTCTGTAAACTAT 58.496 37.037 0.00 0.00 34.95 2.12
247 253 2.493278 GGAACCATTGTGCTTGCTGTAT 59.507 45.455 0.00 0.00 0.00 2.29
475 536 3.133003 GCTCCACAACCTTAGCAGAGATA 59.867 47.826 0.00 0.00 35.05 1.98
601 3473 4.154942 AGAAGGTGGCACAAAATCTCATT 58.845 39.130 20.82 0.00 44.16 2.57
603 3475 3.499338 AGGTGGCACAAAATCTCATTCA 58.501 40.909 20.82 0.00 44.16 2.57
863 3750 3.555956 ACGTTTGTCTCTGTAAACAGCAG 59.444 43.478 5.21 4.64 43.46 4.24
864 3751 3.555956 CGTTTGTCTCTGTAAACAGCAGT 59.444 43.478 5.21 0.00 43.46 4.40
865 3752 4.550831 CGTTTGTCTCTGTAAACAGCAGTG 60.551 45.833 5.21 0.00 43.46 3.66
866 3753 2.483876 TGTCTCTGTAAACAGCAGTGC 58.516 47.619 7.13 7.13 43.46 4.40
867 3754 2.103094 TGTCTCTGTAAACAGCAGTGCT 59.897 45.455 13.14 13.14 43.46 4.40
868 3755 2.734079 GTCTCTGTAAACAGCAGTGCTC 59.266 50.000 16.58 4.00 43.46 4.26
869 3756 2.072298 CTCTGTAAACAGCAGTGCTCC 58.928 52.381 16.58 1.52 43.46 4.70
870 3757 1.694150 TCTGTAAACAGCAGTGCTCCT 59.306 47.619 16.58 1.53 43.46 3.69
871 3758 2.104792 TCTGTAAACAGCAGTGCTCCTT 59.895 45.455 16.58 13.65 43.46 3.36
872 3759 2.221169 TGTAAACAGCAGTGCTCCTTG 58.779 47.619 16.58 7.68 36.40 3.61
936 3853 0.320073 TCCACCTAAAACTCACGCCG 60.320 55.000 0.00 0.00 0.00 6.46
946 3863 3.664025 CTCACGCCGGATCCTTGCA 62.664 63.158 19.48 3.53 0.00 4.08
986 3903 2.125952 CCGTGTCTGCGCTCATCA 60.126 61.111 9.73 0.00 0.00 3.07
992 3909 0.174389 GTCTGCGCTCATCAAGGAGA 59.826 55.000 9.73 0.00 37.05 3.71
1027 3944 0.960364 TGCAGGGAAGGAAACGATGC 60.960 55.000 0.00 0.00 0.00 3.91
1501 4418 1.484444 GGCGAGGATTATGGGCCTCT 61.484 60.000 4.53 0.00 46.75 3.69
1711 4629 3.732048 ACCCGGTGGAGTATGAAAAAT 57.268 42.857 0.00 0.00 34.81 1.82
1838 4756 2.323999 AACTTTGATGCCCCCAATGA 57.676 45.000 0.00 0.00 0.00 2.57
1940 4859 4.224594 AGAGCAGAATCTGAATGAGGACAA 59.775 41.667 15.38 0.00 32.44 3.18
2033 4952 6.909550 TGGCAAAGTTAATAGTCCAAATGT 57.090 33.333 0.00 0.00 0.00 2.71
2055 4974 1.941999 GCACATCTTGGCTTCCTGGC 61.942 60.000 0.00 0.00 42.18 4.85
2123 5209 2.087646 GAAGGCAATGGAAGTGAGACC 58.912 52.381 0.00 0.00 30.28 3.85
2190 5276 1.761784 AGCGAAGGAGAGCAGATCATT 59.238 47.619 0.00 0.00 35.48 2.57
2262 5348 2.478879 CGCCGGGACCAATGAAAATAAC 60.479 50.000 2.18 0.00 0.00 1.89
2677 5767 5.177511 GTGATCGGCGATTTTAATGAGATCA 59.822 40.000 24.81 10.51 40.29 2.92
2789 5879 1.268992 TTGGGGTACGAGGGTGATGG 61.269 60.000 0.00 0.00 0.00 3.51
3029 6120 7.391833 GGAGACTGTGGAAGAGATTGTTAAAAT 59.608 37.037 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.817809 CACTAAAGATTGTAGCTTGGAGTATAA 57.182 33.333 0.00 0.00 0.00 0.98
475 536 5.047590 TGCATCTCAGCTGATTGATTGTTTT 60.048 36.000 23.80 1.02 34.99 2.43
601 3473 0.461548 CTTAGCTGATCGCCCTGTGA 59.538 55.000 0.00 0.00 40.39 3.58
603 3475 1.137872 CTTCTTAGCTGATCGCCCTGT 59.862 52.381 0.00 0.00 40.39 4.00
652 3529 2.115427 TCCTAGGATGCATTTGACCGA 58.885 47.619 7.62 0.00 0.00 4.69
863 3750 1.298014 CAGGGGAGTCAAGGAGCAC 59.702 63.158 0.00 0.00 0.00 4.40
864 3751 1.920325 CCAGGGGAGTCAAGGAGCA 60.920 63.158 0.00 0.00 0.00 4.26
865 3752 2.993853 CCAGGGGAGTCAAGGAGC 59.006 66.667 0.00 0.00 0.00 4.70
866 3753 2.993853 GCCAGGGGAGTCAAGGAG 59.006 66.667 0.00 0.00 0.00 3.69
867 3754 3.003173 CGCCAGGGGAGTCAAGGA 61.003 66.667 0.00 0.00 0.00 3.36
868 3755 4.101448 CCGCCAGGGGAGTCAAGG 62.101 72.222 4.70 0.00 0.00 3.61
869 3756 4.785453 GCCGCCAGGGGAGTCAAG 62.785 72.222 4.70 0.00 38.20 3.02
870 3757 3.916438 TAGCCGCCAGGGGAGTCAA 62.916 63.158 4.70 0.00 38.20 3.18
871 3758 4.392166 TAGCCGCCAGGGGAGTCA 62.392 66.667 4.70 0.00 38.20 3.41
872 3759 3.851128 GTAGCCGCCAGGGGAGTC 61.851 72.222 4.70 0.00 38.20 3.36
908 3825 2.781174 AGTTTTAGGTGGAGTTGGGTGA 59.219 45.455 0.00 0.00 0.00 4.02
986 3903 2.744202 GTCAACATGCAATCGTCTCCTT 59.256 45.455 0.00 0.00 0.00 3.36
1305 4222 5.630121 TCCTTCTTAGCCTTGAAAATCACA 58.370 37.500 0.00 0.00 0.00 3.58
1711 4629 4.560513 GCAAAAATCACAGAAATCGGGGAA 60.561 41.667 0.00 0.00 0.00 3.97
1940 4859 7.384524 TGATTTGAGTCCATCTCCATATCTT 57.615 36.000 0.00 0.00 42.12 2.40
2033 4952 0.112995 AGGAAGCCAAGATGTGCCAA 59.887 50.000 0.00 0.00 0.00 4.52
2123 5209 3.805971 TGCTCATCGTGCTCTTATCAATG 59.194 43.478 0.00 0.00 0.00 2.82
2190 5276 3.764434 CTGGTTGTAGCTGTCTCTTCCTA 59.236 47.826 0.00 0.00 0.00 2.94
3029 6120 3.604667 CAGCCTTTTGCCACGCCA 61.605 61.111 0.00 0.00 42.71 5.69


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

AutoCloner maintained by Alex Coulton.