Multiple sequence alignment - TraesCS7D01G316800

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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 TraesCS7D01G316800 chr7D 100.000 3698 0 0 1 3698 403146194 403149891 0.000000e+00 6830.0
1 TraesCS7D01G316800 chr7D 87.500 312 29 9 411 713 403145808 403145498 5.880000e-93 351.0
2 TraesCS7D01G316800 chr2D 95.153 2249 82 8 715 2941 43245616 43247859 0.000000e+00 3524.0
3 TraesCS7D01G316800 chr2D 93.063 1701 69 16 1063 2725 91111164 91112853 0.000000e+00 2442.0
4 TraesCS7D01G316800 chr2D 94.780 977 23 2 2722 3698 91115631 91116579 0.000000e+00 1496.0
5 TraesCS7D01G316800 chr2D 98.047 717 14 0 2982 3698 43247857 43248573 0.000000e+00 1247.0
6 TraesCS7D01G316800 chr2D 92.917 240 17 0 1 240 22119716 22119477 2.110000e-92 350.0
7 TraesCS7D01G316800 chr2D 94.397 232 6 2 714 938 91110432 91110663 2.110000e-92 350.0
8 TraesCS7D01G316800 chr2D 88.750 240 27 0 1 240 22155613 22155374 1.000000e-75 294.0
9 TraesCS7D01G316800 chr2D 86.667 240 26 4 1 240 22144635 22144402 1.020000e-65 261.0
10 TraesCS7D01G316800 chr2D 91.304 46 4 0 1018 1063 91111039 91111084 3.080000e-06 63.9
11 TraesCS7D01G316800 chr3A 94.454 1749 75 7 1166 2897 125424486 125422743 0.000000e+00 2673.0
12 TraesCS7D01G316800 chr3A 97.395 806 21 0 2893 3698 125401485 125400680 0.000000e+00 1373.0
13 TraesCS7D01G316800 chr3A 93.909 394 17 2 715 1102 125424876 125424484 4.110000e-164 588.0
14 TraesCS7D01G316800 chr4A 94.231 1040 40 4 2660 3698 176614423 176615443 0.000000e+00 1570.0
15 TraesCS7D01G316800 chr4A 94.208 259 15 0 714 972 176609818 176610076 2.680000e-106 396.0
16 TraesCS7D01G316800 chr4A 86.462 325 38 1 2535 2853 113863562 113863238 5.880000e-93 351.0
17 TraesCS7D01G316800 chr4A 93.798 129 8 0 2535 2663 176610086 176610214 1.050000e-45 195.0
18 TraesCS7D01G316800 chr6B 96.811 878 28 0 2821 3698 704707962 704707085 0.000000e+00 1467.0
19 TraesCS7D01G316800 chr6B 83.755 554 59 19 2886 3431 217158525 217159055 2.570000e-136 496.0
20 TraesCS7D01G316800 chr6B 86.909 275 30 6 437 706 136916825 136916552 1.670000e-78 303.0
21 TraesCS7D01G316800 chr1B 96.811 878 27 1 2821 3698 459065831 459064955 0.000000e+00 1465.0
22 TraesCS7D01G316800 chr1B 91.292 689 41 7 1 671 298090866 298091553 0.000000e+00 922.0
23 TraesCS7D01G316800 chr1B 90.665 632 41 10 1070 1686 626713520 626714148 0.000000e+00 824.0
24 TraesCS7D01G316800 chr1B 85.714 756 82 11 2951 3696 456157907 456157168 0.000000e+00 774.0
25 TraesCS7D01G316800 chr1B 78.704 432 51 18 2130 2525 626723628 626724054 2.200000e-62 250.0
26 TraesCS7D01G316800 chr1B 98.113 53 1 0 972 1024 626713445 626713497 3.930000e-15 93.5
27 TraesCS7D01G316800 chr5B 95.444 878 29 1 2821 3698 325719937 325720803 0.000000e+00 1389.0
28 TraesCS7D01G316800 chr5B 92.275 712 51 2 6 714 580126039 580125329 0.000000e+00 1007.0
29 TraesCS7D01G316800 chr5B 90.833 240 20 2 1 240 84623350 84623587 1.660000e-83 320.0
30 TraesCS7D01G316800 chr5B 95.455 132 6 0 247 378 567776214 567776083 1.040000e-50 211.0
31 TraesCS7D01G316800 chr6D 95.112 716 32 1 1 713 29985608 29986323 0.000000e+00 1125.0
32 TraesCS7D01G316800 chr6D 83.725 553 61 18 2886 3431 123151781 123152311 2.570000e-136 496.0
33 TraesCS7D01G316800 chr6D 90.182 275 20 6 447 717 29985182 29984911 5.880000e-93 351.0
34 TraesCS7D01G316800 chr3D 95.609 706 20 2 714 1419 55086535 55087229 0.000000e+00 1122.0
35 TraesCS7D01G316800 chr3D 96.013 301 10 2 2553 2852 55087227 55087526 4.290000e-134 488.0
36 TraesCS7D01G316800 chr1A 90.303 825 54 15 972 1789 549846425 549847230 0.000000e+00 1057.0
37 TraesCS7D01G316800 chr1A 86.207 261 34 2 456 715 466028913 466029172 7.820000e-72 281.0
38 TraesCS7D01G316800 chr1A 77.212 452 60 21 2116 2531 549853766 549854210 1.340000e-54 224.0
39 TraesCS7D01G316800 chr1A 82.178 101 7 7 2221 2314 549850763 549850859 3.960000e-10 76.8
40 TraesCS7D01G316800 chr1D 90.152 792 55 12 972 1752 457151673 457152452 0.000000e+00 1009.0
41 TraesCS7D01G316800 chr1D 77.059 340 50 8 2116 2432 457176858 457177192 1.770000e-38 171.0
42 TraesCS7D01G316800 chr1D 77.206 272 19 13 2221 2475 457153249 457153494 6.490000e-23 119.0
43 TraesCS7D01G316800 chr5D 85.960 755 75 13 2951 3696 463016552 463017284 0.000000e+00 778.0
44 TraesCS7D01G316800 chr5D 95.000 240 11 1 1 240 75912850 75913088 3.490000e-100 375.0
45 TraesCS7D01G316800 chr5D 95.455 132 6 0 247 378 461877332 461877201 1.040000e-50 211.0
46 TraesCS7D01G316800 chrUn 87.013 693 83 7 3011 3696 94306612 94305920 0.000000e+00 774.0
47 TraesCS7D01G316800 chr2B 92.842 461 32 1 246 705 262908205 262907745 0.000000e+00 667.0
48 TraesCS7D01G316800 chr2B 85.494 324 33 11 403 713 262908714 262909036 3.560000e-85 326.0
49 TraesCS7D01G316800 chr2B 93.694 111 6 1 3 113 262908314 262908205 8.220000e-37 165.0
50 TraesCS7D01G316800 chr4B 87.117 326 36 1 2535 2854 434458665 434458990 7.550000e-97 364.0
51 TraesCS7D01G316800 chr4D 86.503 326 38 1 2535 2854 351457099 351457424 1.630000e-93 353.0
52 TraesCS7D01G316800 chr4D 85.000 60 6 1 757 813 400234805 400234864 1.430000e-04 58.4
53 TraesCS7D01G316800 chr2A 92.917 240 17 0 1 240 23959140 23958901 2.110000e-92 350.0
54 TraesCS7D01G316800 chr5A 92.424 132 10 0 247 378 581622154 581622023 4.880000e-44 189.0
55 TraesCS7D01G316800 chr3B 84.444 90 11 2 410 496 344666213 344666302 6.580000e-13 86.1


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 TraesCS7D01G316800 chr7D 403146194 403149891 3697 False 6830.000 6830 100.0000 1 3698 1 chr7D.!!$F1 3697
1 TraesCS7D01G316800 chr2D 43245616 43248573 2957 False 2385.500 3524 96.6000 715 3698 2 chr2D.!!$F1 2983
2 TraesCS7D01G316800 chr2D 91110432 91116579 6147 False 1087.975 2442 93.3860 714 3698 4 chr2D.!!$F2 2984
3 TraesCS7D01G316800 chr3A 125422743 125424876 2133 True 1630.500 2673 94.1815 715 2897 2 chr3A.!!$R2 2182
4 TraesCS7D01G316800 chr3A 125400680 125401485 805 True 1373.000 1373 97.3950 2893 3698 1 chr3A.!!$R1 805
5 TraesCS7D01G316800 chr4A 176614423 176615443 1020 False 1570.000 1570 94.2310 2660 3698 1 chr4A.!!$F1 1038
6 TraesCS7D01G316800 chr6B 704707085 704707962 877 True 1467.000 1467 96.8110 2821 3698 1 chr6B.!!$R2 877
7 TraesCS7D01G316800 chr6B 217158525 217159055 530 False 496.000 496 83.7550 2886 3431 1 chr6B.!!$F1 545
8 TraesCS7D01G316800 chr1B 459064955 459065831 876 True 1465.000 1465 96.8110 2821 3698 1 chr1B.!!$R2 877
9 TraesCS7D01G316800 chr1B 298090866 298091553 687 False 922.000 922 91.2920 1 671 1 chr1B.!!$F1 670
10 TraesCS7D01G316800 chr1B 456157168 456157907 739 True 774.000 774 85.7140 2951 3696 1 chr1B.!!$R1 745
11 TraesCS7D01G316800 chr1B 626713445 626714148 703 False 458.750 824 94.3890 972 1686 2 chr1B.!!$F3 714
12 TraesCS7D01G316800 chr5B 325719937 325720803 866 False 1389.000 1389 95.4440 2821 3698 1 chr5B.!!$F2 877
13 TraesCS7D01G316800 chr5B 580125329 580126039 710 True 1007.000 1007 92.2750 6 714 1 chr5B.!!$R2 708
14 TraesCS7D01G316800 chr6D 29985608 29986323 715 False 1125.000 1125 95.1120 1 713 1 chr6D.!!$F1 712
15 TraesCS7D01G316800 chr6D 123151781 123152311 530 False 496.000 496 83.7250 2886 3431 1 chr6D.!!$F2 545
16 TraesCS7D01G316800 chr3D 55086535 55087526 991 False 805.000 1122 95.8110 714 2852 2 chr3D.!!$F1 2138
17 TraesCS7D01G316800 chr1A 549846425 549854210 7785 False 452.600 1057 83.2310 972 2531 3 chr1A.!!$F2 1559
18 TraesCS7D01G316800 chr1D 457151673 457153494 1821 False 564.000 1009 83.6790 972 2475 2 chr1D.!!$F2 1503
19 TraesCS7D01G316800 chr5D 463016552 463017284 732 False 778.000 778 85.9600 2951 3696 1 chr5D.!!$F2 745
20 TraesCS7D01G316800 chrUn 94305920 94306612 692 True 774.000 774 87.0130 3011 3696 1 chrUn.!!$R1 685
21 TraesCS7D01G316800 chr2B 262907745 262908314 569 True 416.000 667 93.2680 3 705 2 chr2B.!!$R1 702

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
259 261 0.466372 TCGGGGTGTCAAATGCAACA 60.466 50.000 0.00 0.0 0.00 3.33 F
1032 1365 0.390209 GCGCCACTTGATGCCAAAAT 60.390 50.000 0.00 0.0 0.00 1.82 F
1339 1850 0.249322 GGATTTACGCTGCCGCTCTA 60.249 55.000 0.00 0.0 38.22 2.43 F
1413 1935 1.134401 CGGTTCCACTGGCTGTATCAT 60.134 52.381 0.00 0.0 0.00 2.45 F
1781 2313 1.143183 GAATAGAACCGAGGCCGCA 59.857 57.895 7.44 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1763 0.249398 GTGTACCTGGCATCGGTTCT 59.751 55.000 3.52 0.00 35.98 3.01 R
2114 9173 0.250945 AGGACGTGAGAGTCTCTGCA 60.251 55.000 20.64 2.61 40.76 4.41 R
2541 9664 1.114627 CGTCCTCATCCACATCCTCA 58.885 55.000 0.00 0.00 0.00 3.86 R
2624 9747 2.821366 CGTCCATGAGTGCCCAGC 60.821 66.667 0.00 0.00 0.00 4.85 R
3366 13301 3.692257 ACATCTCAGTCAAGGGAACTG 57.308 47.619 0.00 0.00 42.68 3.16 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
252 254 2.112297 GTGGCTCGGGGTGTCAAA 59.888 61.111 0.00 0.00 0.00 2.69
259 261 0.466372 TCGGGGTGTCAAATGCAACA 60.466 50.000 0.00 0.00 0.00 3.33
720 744 3.523606 TGGTTAAATACTCGCGCCTTA 57.476 42.857 0.00 0.00 0.00 2.69
735 759 1.508256 CCTTATCCTCCCCGTTCCTT 58.492 55.000 0.00 0.00 0.00 3.36
743 767 2.706190 CCTCCCCGTTCCTTTCTCATAT 59.294 50.000 0.00 0.00 0.00 1.78
807 835 1.333636 CCCCTCGTCTGAAGGAGCAT 61.334 60.000 0.00 0.00 36.33 3.79
915 952 1.867919 CTCGGAGTTGCCAGAGTCGT 61.868 60.000 0.00 0.00 34.61 4.34
950 987 3.148279 GAGTCGGCGGGGAGATGT 61.148 66.667 7.21 0.00 0.00 3.06
1032 1365 0.390209 GCGCCACTTGATGCCAAAAT 60.390 50.000 0.00 0.00 0.00 1.82
1260 1763 1.213296 GGGCTTCCTGAGGAATACCA 58.787 55.000 25.84 3.14 41.23 3.25
1339 1850 0.249322 GGATTTACGCTGCCGCTCTA 60.249 55.000 0.00 0.00 38.22 2.43
1413 1935 1.134401 CGGTTCCACTGGCTGTATCAT 60.134 52.381 0.00 0.00 0.00 2.45
1420 1942 3.254166 CCACTGGCTGTATCATAAATGCC 59.746 47.826 0.00 0.00 40.62 4.40
1468 1990 1.271856 TATCAAGACCGAGGCACCAA 58.728 50.000 0.00 0.00 0.00 3.67
1481 2003 3.505386 AGGCACCAAATTGTTCCATGTA 58.495 40.909 0.00 0.00 0.00 2.29
1599 2121 8.773645 TGCATATGTATAGTTGTGATGCTTAAC 58.226 33.333 4.29 0.00 39.13 2.01
1619 2142 2.224281 ACAAAGTCAGTTCGGAGCATGA 60.224 45.455 0.00 0.00 0.00 3.07
1705 2237 6.370453 TCTATGTAGTAGTAACAGCCATCCA 58.630 40.000 0.00 0.00 0.00 3.41
1745 2277 2.878406 TGCTTTAGGACAGTGCAAGAAC 59.122 45.455 0.00 0.00 0.00 3.01
1747 2279 3.187432 GCTTTAGGACAGTGCAAGAACTC 59.813 47.826 0.00 0.00 0.00 3.01
1750 2282 1.488957 GACAGTGCAAGAACTCGCG 59.511 57.895 0.00 0.00 0.00 5.87
1781 2313 1.143183 GAATAGAACCGAGGCCGCA 59.857 57.895 7.44 0.00 0.00 5.69
1901 2609 3.289704 TTCGCGACCAGCCGAATCA 62.290 57.895 9.15 0.00 44.76 2.57
2087 9145 3.753272 CCTTGGGTCTGATGTTGTTGTAG 59.247 47.826 0.00 0.00 0.00 2.74
2114 9173 1.895798 TGATGAAGCTTCTCGTGGTCT 59.104 47.619 26.09 2.21 0.00 3.85
2353 9453 2.505777 CTCGGAGCTGCGTCTGTG 60.506 66.667 27.20 9.75 0.00 3.66
2541 9664 1.255667 AACTGTACAGGTCCGCCGAT 61.256 55.000 26.12 0.00 40.50 4.18
2639 9762 4.100084 CGGCTGGGCACTCATGGA 62.100 66.667 0.00 0.00 0.00 3.41
2680 9803 2.741985 CCCACGACGCAGCATTCA 60.742 61.111 0.00 0.00 0.00 2.57
2839 12744 1.529010 CTTGACAGGGCCTGCAACA 60.529 57.895 33.04 25.31 34.37 3.33
3250 13159 2.811431 CACCATGTAAGTTTTGCTCCGA 59.189 45.455 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.050934 GCCGAGTACTTCTCCCGGT 61.051 63.158 18.07 0.00 39.84 5.28
275 277 4.100084 CTGCCCTCGCATCCACCA 62.100 66.667 0.00 0.00 46.11 4.17
642 666 4.944930 ACTACCACTTTACAACTTTGTGCA 59.055 37.500 4.82 0.00 42.31 4.57
650 674 4.023450 GCCCAGAAACTACCACTTTACAAC 60.023 45.833 0.00 0.00 0.00 3.32
720 744 1.205055 GAGAAAGGAACGGGGAGGAT 58.795 55.000 0.00 0.00 0.00 3.24
735 759 1.615883 GCTGGAGCTCGGATATGAGAA 59.384 52.381 7.83 0.00 38.28 2.87
950 987 0.037590 CTCCCGAATCCCAACACCAA 59.962 55.000 0.00 0.00 0.00 3.67
1032 1365 3.831323 TCAGAGGGAAATGCAGAAACAA 58.169 40.909 0.00 0.00 0.00 2.83
1121 1537 8.579850 AAAGAAATGTGGCATTAATACAGAGA 57.420 30.769 0.00 0.00 0.00 3.10
1242 1733 2.119495 TCTGGTATTCCTCAGGAAGCC 58.881 52.381 18.53 18.53 45.48 4.35
1260 1763 0.249398 GTGTACCTGGCATCGGTTCT 59.751 55.000 3.52 0.00 35.98 3.01
1362 1873 2.512485 TTCTTCCGCAGTCGTTACAA 57.488 45.000 0.00 0.00 0.00 2.41
1413 1935 2.044451 CCACAGGCGGGGCATTTA 60.044 61.111 0.00 0.00 0.00 1.40
1433 1955 6.220930 GTCTTGATAACTCTGGTGTTGTACA 58.779 40.000 0.00 0.00 0.00 2.90
1481 2003 3.314541 AACGACTCGCCTGTTAATTCT 57.685 42.857 0.00 0.00 0.00 2.40
1599 2121 2.416747 TCATGCTCCGAACTGACTTTG 58.583 47.619 0.00 0.00 0.00 2.77
1619 2142 2.351738 GCTGCTAACCAAAAGCGACATT 60.352 45.455 0.00 0.00 43.11 2.71
1705 2237 2.530701 CATTATCCTAGAGACGGGGCT 58.469 52.381 0.00 0.00 0.00 5.19
1745 2277 4.827087 ATGCTGCCAGACCGCGAG 62.827 66.667 8.23 0.00 0.00 5.03
1750 2282 2.615912 GTTCTATTCATGCTGCCAGACC 59.384 50.000 0.00 0.00 0.00 3.85
1781 2313 1.596934 CAGGGTGGCGTAGTGACAT 59.403 57.895 0.00 0.00 0.00 3.06
2076 9134 6.691754 TCATCAACAACACTACAACAACAT 57.308 33.333 0.00 0.00 0.00 2.71
2087 9145 3.248602 ACGAGAAGCTTCATCAACAACAC 59.751 43.478 27.57 0.00 0.00 3.32
2114 9173 0.250945 AGGACGTGAGAGTCTCTGCA 60.251 55.000 20.64 2.61 40.76 4.41
2353 9453 2.879103 TGGAACAGAGGGTCAATTCC 57.121 50.000 0.00 0.00 39.47 3.01
2496 9612 4.816925 GGCCTACTGATAAATCTTTTCGCT 59.183 41.667 0.00 0.00 0.00 4.93
2541 9664 1.114627 CGTCCTCATCCACATCCTCA 58.885 55.000 0.00 0.00 0.00 3.86
2624 9747 2.821366 CGTCCATGAGTGCCCAGC 60.821 66.667 0.00 0.00 0.00 4.85
2680 9803 4.589374 GGACCATTAGTGCAGGTAGACTAT 59.411 45.833 0.00 0.00 36.67 2.12
2762 12667 4.112634 ACCTGCTTAAATTGGTTGAGGA 57.887 40.909 0.00 0.00 0.00 3.71
2839 12744 5.013079 TCGGGAGTCAGGCAATAAATATCAT 59.987 40.000 0.00 0.00 0.00 2.45
3250 13159 6.823182 ACCAATTAGCTTTGCAAAAAGAAAGT 59.177 30.769 13.84 2.28 32.68 2.66
3366 13301 3.692257 ACATCTCAGTCAAGGGAACTG 57.308 47.619 0.00 0.00 42.68 3.16
3617 13559 4.233632 TCATGTCCTACCAATTGCATCA 57.766 40.909 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.