Multiple sequence alignment - TraesCS4B01G266400

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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 TraesCS4B01G266400 chr4B 100.000 3547 0 0 1 3547 538384336 538387882 0.000000e+00 6551.0
1 TraesCS4B01G266400 chr4B 91.721 1534 88 12 2049 3547 538372061 538373590 0.000000e+00 2093.0
2 TraesCS4B01G266400 chr4B 86.446 1269 139 21 665 1921 538270395 538269148 0.000000e+00 1360.0
3 TraesCS4B01G266400 chr4B 85.856 1308 137 23 640 1925 538673144 538674425 0.000000e+00 1347.0
4 TraesCS4B01G266400 chr4B 94.465 813 39 4 907 1719 538370641 538371447 0.000000e+00 1247.0
5 TraesCS4B01G266400 chr4B 83.624 916 100 26 1925 2820 538674497 538675382 0.000000e+00 815.0
6 TraesCS4B01G266400 chr4B 82.642 795 90 27 1925 2704 538269080 538268319 0.000000e+00 660.0
7 TraesCS4B01G266400 chr4B 80.488 451 66 12 2054 2498 568411071 568411505 3.410000e-85 326.0
8 TraesCS4B01G266400 chr4B 92.271 207 14 2 1718 1924 538371704 538371908 3.460000e-75 292.0
9 TraesCS4B01G266400 chr4B 82.866 321 27 15 3227 3547 538675460 538675752 2.720000e-66 263.0
10 TraesCS4B01G266400 chr4B 90.256 195 16 2 2817 3008 209113928 209114122 5.880000e-63 252.0
11 TraesCS4B01G266400 chr4B 93.590 78 5 0 1925 2002 538371982 538372059 2.240000e-22 117.0
12 TraesCS4B01G266400 chr4D 93.597 1265 54 4 662 1925 436697053 436698291 0.000000e+00 1862.0
13 TraesCS4B01G266400 chr4D 86.261 1281 134 25 665 1925 436379165 436377907 0.000000e+00 1352.0
14 TraesCS4B01G266400 chr4D 86.330 1229 135 20 709 1925 436836762 436837969 0.000000e+00 1308.0
15 TraesCS4B01G266400 chr4D 90.501 979 50 18 2608 3547 436713037 436714011 0.000000e+00 1253.0
16 TraesCS4B01G266400 chr4D 95.080 691 31 3 1925 2612 436698366 436699056 0.000000e+00 1085.0
17 TraesCS4B01G266400 chr4D 84.083 823 81 25 1925 2725 436377833 436377039 0.000000e+00 749.0
18 TraesCS4B01G266400 chr4D 81.818 440 55 15 1925 2352 436838041 436838467 2.620000e-91 346.0
19 TraesCS4B01G266400 chr4D 89.706 272 23 3 2420 2686 436862597 436862868 3.390000e-90 342.0
20 TraesCS4B01G266400 chr4D 79.955 449 63 18 2054 2494 455319663 455320092 4.450000e-79 305.0
21 TraesCS4B01G266400 chr4D 84.191 272 27 10 3227 3497 436872763 436873019 2.110000e-62 250.0
22 TraesCS4B01G266400 chr4D 93.750 80 5 0 3468 3547 436376659 436376580 1.730000e-23 121.0
23 TraesCS4B01G266400 chr4D 92.105 76 6 0 640 715 436812844 436812919 1.350000e-19 108.0
24 TraesCS4B01G266400 chr4D 97.727 44 1 0 3504 3547 436874057 436874100 3.800000e-10 76.8
25 TraesCS4B01G266400 chr4A 86.620 1278 133 23 665 1925 31621475 31622731 0.000000e+00 1378.0
26 TraesCS4B01G266400 chr4A 84.977 1298 126 35 647 1925 31596569 31595322 0.000000e+00 1253.0
27 TraesCS4B01G266400 chr4A 84.428 822 79 26 1925 2725 31622806 31623599 0.000000e+00 763.0
28 TraesCS4B01G266400 chr4A 80.942 955 164 14 747 1689 12678780 12677832 0.000000e+00 739.0
29 TraesCS4B01G266400 chr4A 79.722 503 79 17 2054 2550 12677818 12677333 3.390000e-90 342.0
30 TraesCS4B01G266400 chr4A 82.195 410 44 12 1925 2322 31595250 31594858 3.410000e-85 326.0
31 TraesCS4B01G266400 chr6B 98.762 646 6 2 1 646 174630627 174629984 0.000000e+00 1147.0
32 TraesCS4B01G266400 chr6B 98.151 649 11 1 1 649 377669785 377669138 0.000000e+00 1131.0
33 TraesCS4B01G266400 chr6B 96.302 649 23 1 1 648 296421952 296422600 0.000000e+00 1064.0
34 TraesCS4B01G266400 chr6B 90.710 183 16 1 3002 3183 626863689 626863507 3.540000e-60 243.0
35 TraesCS4B01G266400 chr6B 79.394 330 40 14 1921 2228 236478510 236478833 1.290000e-49 207.0
36 TraesCS4B01G266400 chr6B 86.957 69 7 1 1952 2020 236478232 236478298 3.800000e-10 76.8
37 TraesCS4B01G266400 chr2B 96.451 648 22 1 1 648 524270376 524271022 0.000000e+00 1068.0
38 TraesCS4B01G266400 chr5B 96.302 649 22 2 1 648 674036627 674035980 0.000000e+00 1064.0
39 TraesCS4B01G266400 chr2A 95.884 656 23 4 1 655 245805293 245804641 0.000000e+00 1059.0
40 TraesCS4B01G266400 chr2A 95.719 654 25 3 1 653 433476642 433475991 0.000000e+00 1050.0
41 TraesCS4B01G266400 chr3B 95.994 649 25 1 1 648 28679037 28678389 0.000000e+00 1053.0
42 TraesCS4B01G266400 chr7B 95.699 651 26 2 1 649 138441393 138442043 0.000000e+00 1046.0
43 TraesCS4B01G266400 chr6A 79.399 1165 192 31 769 1912 178883207 178884344 0.000000e+00 778.0
44 TraesCS4B01G266400 chr6A 75.433 289 50 16 1929 2209 178884457 178884732 1.730000e-23 121.0
45 TraesCS4B01G266400 chr7D 92.308 182 13 1 3002 3182 579027048 579026867 1.260000e-64 257.0
46 TraesCS4B01G266400 chr1B 92.308 182 13 1 3002 3182 638749339 638749520 1.260000e-64 257.0
47 TraesCS4B01G266400 chrUn 90.256 195 16 3 2817 3008 216512963 216513157 5.880000e-63 252.0
48 TraesCS4B01G266400 chrUn 90.256 195 16 3 2817 3008 286270420 286270226 5.880000e-63 252.0
49 TraesCS4B01G266400 chrUn 90.256 195 16 3 2817 3008 379970740 379970934 5.880000e-63 252.0
50 TraesCS4B01G266400 chrUn 91.209 182 15 1 3002 3182 273319630 273319811 2.730000e-61 246.0
51 TraesCS4B01G266400 chr7A 91.758 182 14 1 3002 3182 60106326 60106507 5.880000e-63 252.0
52 TraesCS4B01G266400 chr6D 89.552 201 18 3 2817 3014 168263312 168263112 5.880000e-63 252.0
53 TraesCS4B01G266400 chr6D 91.209 182 15 1 3002 3182 108465018 108464837 2.730000e-61 246.0
54 TraesCS4B01G266400 chr5A 91.758 182 14 1 3002 3182 73032262 73032081 5.880000e-63 252.0
55 TraesCS4B01G266400 chr3A 91.758 182 14 1 3002 3182 122221856 122222037 5.880000e-63 252.0
56 TraesCS4B01G266400 chr1D 90.256 195 16 3 2817 3008 254389446 254389640 5.880000e-63 252.0
57 TraesCS4B01G266400 chr1D 90.256 195 16 3 2817 3008 254392465 254392659 5.880000e-63 252.0


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 TraesCS4B01G266400 chr4B 538384336 538387882 3546 False 6551.000000 6551 100.000000 1 3547 1 chr4B.!!$F2 3546
1 TraesCS4B01G266400 chr4B 538268319 538270395 2076 True 1010.000000 1360 84.544000 665 2704 2 chr4B.!!$R1 2039
2 TraesCS4B01G266400 chr4B 538370641 538373590 2949 False 937.250000 2093 93.011750 907 3547 4 chr4B.!!$F4 2640
3 TraesCS4B01G266400 chr4B 538673144 538675752 2608 False 808.333333 1347 84.115333 640 3547 3 chr4B.!!$F5 2907
4 TraesCS4B01G266400 chr4D 436697053 436699056 2003 False 1473.500000 1862 94.338500 662 2612 2 chr4D.!!$F5 1950
5 TraesCS4B01G266400 chr4D 436713037 436714011 974 False 1253.000000 1253 90.501000 2608 3547 1 chr4D.!!$F1 939
6 TraesCS4B01G266400 chr4D 436836762 436838467 1705 False 827.000000 1308 84.074000 709 2352 2 chr4D.!!$F6 1643
7 TraesCS4B01G266400 chr4D 436376580 436379165 2585 True 740.666667 1352 88.031333 665 3547 3 chr4D.!!$R1 2882
8 TraesCS4B01G266400 chr4A 31621475 31623599 2124 False 1070.500000 1378 85.524000 665 2725 2 chr4A.!!$F1 2060
9 TraesCS4B01G266400 chr4A 31594858 31596569 1711 True 789.500000 1253 83.586000 647 2322 2 chr4A.!!$R2 1675
10 TraesCS4B01G266400 chr4A 12677333 12678780 1447 True 540.500000 739 80.332000 747 2550 2 chr4A.!!$R1 1803
11 TraesCS4B01G266400 chr6B 174629984 174630627 643 True 1147.000000 1147 98.762000 1 646 1 chr6B.!!$R1 645
12 TraesCS4B01G266400 chr6B 377669138 377669785 647 True 1131.000000 1131 98.151000 1 649 1 chr6B.!!$R2 648
13 TraesCS4B01G266400 chr6B 296421952 296422600 648 False 1064.000000 1064 96.302000 1 648 1 chr6B.!!$F1 647
14 TraesCS4B01G266400 chr2B 524270376 524271022 646 False 1068.000000 1068 96.451000 1 648 1 chr2B.!!$F1 647
15 TraesCS4B01G266400 chr5B 674035980 674036627 647 True 1064.000000 1064 96.302000 1 648 1 chr5B.!!$R1 647
16 TraesCS4B01G266400 chr2A 245804641 245805293 652 True 1059.000000 1059 95.884000 1 655 1 chr2A.!!$R1 654
17 TraesCS4B01G266400 chr2A 433475991 433476642 651 True 1050.000000 1050 95.719000 1 653 1 chr2A.!!$R2 652
18 TraesCS4B01G266400 chr3B 28678389 28679037 648 True 1053.000000 1053 95.994000 1 648 1 chr3B.!!$R1 647
19 TraesCS4B01G266400 chr7B 138441393 138442043 650 False 1046.000000 1046 95.699000 1 649 1 chr7B.!!$F1 648
20 TraesCS4B01G266400 chr6A 178883207 178884732 1525 False 449.500000 778 77.416000 769 2209 2 chr6A.!!$F1 1440
21 TraesCS4B01G266400 chr1D 254389446 254392659 3213 False 252.000000 252 90.256000 2817 3008 2 chr1D.!!$F1 191

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
738 750 0.106769 TGCCTGAGCAGTTGGAAACA 60.107 50.0 0.00 0.0 45.96 2.83 F
1097 1114 0.460987 GAGCTGAACTAGGCGCACAT 60.461 55.0 10.83 0.0 0.00 3.21 F
1678 1707 0.820871 TTTGGTTGCCACTTGTGTCC 59.179 50.0 0.00 0.0 30.78 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1677 1.202348 TGGCAACCAAACATGTCAACG 60.202 47.619 0.0 0.0 0.00 4.10 R
2406 2872 1.361204 TGCCAGAACAGGAGGATCAA 58.639 50.000 0.0 0.0 36.25 2.57 R
3159 6658 0.988832 TGGCTCCCGACCAAACTAAT 59.011 50.000 0.0 0.0 33.12 1.73 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
252 255 8.684386 TGGAAACTTCATAACAAGTTGATACA 57.316 30.769 10.54 0.00 44.28 2.29
405 410 4.881850 CCTCGGGTAGTTTAAATGATGCTT 59.118 41.667 0.00 0.00 0.00 3.91
677 682 2.960384 GCTCCCTCTCTACTAACCTTCC 59.040 54.545 0.00 0.00 0.00 3.46
687 699 3.329929 ACTAACCTTCCGACCATGTTC 57.670 47.619 0.00 0.00 0.00 3.18
738 750 0.106769 TGCCTGAGCAGTTGGAAACA 60.107 50.000 0.00 0.00 45.96 2.83
848 860 4.181578 CAATCGTCTCCACCTATTTTCGT 58.818 43.478 0.00 0.00 0.00 3.85
1097 1114 0.460987 GAGCTGAACTAGGCGCACAT 60.461 55.000 10.83 0.00 0.00 3.21
1362 1381 1.448540 GACACAGTCCATGCCTCCG 60.449 63.158 0.00 0.00 0.00 4.63
1423 1442 4.719773 TCTTCCGAGAATTTTATGAGGGGA 59.280 41.667 0.00 0.00 0.00 4.81
1474 1499 7.762159 TCAATTTGACTACAAAAACCAAAGGAC 59.238 33.333 0.00 0.00 46.77 3.85
1649 1677 5.640732 ACAATTTGGCGTCACATTTATCTC 58.359 37.500 0.00 0.00 0.00 2.75
1656 1684 3.366724 GCGTCACATTTATCTCGTTGACA 59.633 43.478 0.00 0.00 0.00 3.58
1678 1707 0.820871 TTTGGTTGCCACTTGTGTCC 59.179 50.000 0.00 0.00 30.78 4.02
1724 2011 7.924412 CACTGTCCTTGAACTTTACTAGTACAA 59.076 37.037 0.91 2.62 35.54 2.41
1769 2057 4.973168 TGCCCATCCATAAATAGTGACTC 58.027 43.478 0.00 0.00 0.00 3.36
1827 2137 9.921637 TGGTAATGAAATGACTAAATGGTTTTC 57.078 29.630 0.00 0.00 0.00 2.29
1927 2348 2.708216 TGTTCACAAGCTTGACTGGA 57.292 45.000 32.50 19.31 0.00 3.86
2106 2550 7.042456 GCCATATGTACTGACTTTCTACACATG 60.042 40.741 1.24 0.00 28.98 3.21
2178 2623 2.363306 TTGAAGCACCCTGTTGATGT 57.637 45.000 0.00 0.00 0.00 3.06
2179 2624 1.608055 TGAAGCACCCTGTTGATGTG 58.392 50.000 0.00 0.00 0.00 3.21
2302 2759 1.147153 GGCTAGGCTGGTGGATGAC 59.853 63.158 9.46 0.00 0.00 3.06
2406 2872 1.366319 ATTCTCCTTCAGTGCCCTGT 58.634 50.000 0.00 0.00 39.82 4.00
2535 3003 2.104967 ACATTGTACCTGCTAGGCGTA 58.895 47.619 2.50 0.00 39.63 4.42
2650 3121 9.722056 GTTTCATTAGGTTCAAGCATTATAGTG 57.278 33.333 0.00 0.00 0.00 2.74
2666 3137 8.562892 GCATTATAGTGTTCTTACAATCTGCAT 58.437 33.333 0.00 0.00 35.69 3.96
2754 3225 4.202050 CCAACTTGTTCTTTTCCCTGTCAG 60.202 45.833 0.00 0.00 0.00 3.51
2791 3262 8.145122 TGCATCGTATTGACATATTACCAAGTA 58.855 33.333 0.00 0.00 0.00 2.24
2829 3300 7.856145 TTTCAAATTTCTCTATCTCTGAGGC 57.144 36.000 4.59 0.00 32.78 4.70
2832 3303 4.582701 ATTTCTCTATCTCTGAGGCGTG 57.417 45.455 4.59 0.00 32.78 5.34
2834 3305 3.840124 TCTCTATCTCTGAGGCGTGTA 57.160 47.619 4.59 0.00 32.78 2.90
2836 3307 3.388350 TCTCTATCTCTGAGGCGTGTAGA 59.612 47.826 4.59 5.09 32.78 2.59
2840 3311 3.784701 TCTCTGAGGCGTGTAGATTTC 57.215 47.619 4.59 0.00 0.00 2.17
2842 3313 1.816835 TCTGAGGCGTGTAGATTTCGT 59.183 47.619 0.00 0.00 0.00 3.85
2850 3321 4.624452 GGCGTGTAGATTTCGTAAAACTCT 59.376 41.667 0.00 0.00 0.00 3.24
2998 6491 5.240623 TCTTTATGTTCACGTGGATTTTGCT 59.759 36.000 17.00 0.00 0.00 3.91
3117 6616 1.354368 GAGGTCCCCCACTTTGATTCA 59.646 52.381 0.00 0.00 0.00 2.57
3119 6618 2.102578 GGTCCCCCACTTTGATTCATG 58.897 52.381 0.00 0.00 0.00 3.07
3136 6635 3.378512 TCATGTCCTGTTAGCATCTCCT 58.621 45.455 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 255 7.066307 ACCTTATTTGCATTTTCCTGAGTTT 57.934 32.000 0.00 0.00 0.00 2.66
405 410 7.332557 AGCATATCATTTGCATTCAGGAAAAA 58.667 30.769 2.71 0.00 41.06 1.94
677 682 1.361668 CCTGAAGCGGAACATGGTCG 61.362 60.000 4.29 1.34 0.00 4.79
706 718 5.163269 ACTGCTCAGGCACATCATAATAAGA 60.163 40.000 1.66 0.00 44.28 2.10
1097 1114 0.836606 TCAGCATCCGAAAGCCCATA 59.163 50.000 0.00 0.00 0.00 2.74
1362 1381 6.690194 AGTTCATATGCAAGATCCTGAAAC 57.310 37.500 0.00 0.00 0.00 2.78
1474 1499 1.603678 GCCACTGTGCAAACCATCTTG 60.604 52.381 1.29 0.00 0.00 3.02
1584 1612 4.261801 AGGTGGAAGAAATACCATTGTCG 58.738 43.478 0.00 0.00 38.48 4.35
1649 1677 1.202348 TGGCAACCAAACATGTCAACG 60.202 47.619 0.00 0.00 0.00 4.10
1656 1684 1.830477 ACACAAGTGGCAACCAAACAT 59.170 42.857 5.08 0.00 34.18 2.71
1678 1707 5.293814 CAGTGGATGAGATGAAGCTAAACAG 59.706 44.000 0.00 0.00 0.00 3.16
1827 2137 7.824289 TGAACAGAAGTTATCTAAGGTGGAATG 59.176 37.037 0.00 0.00 38.30 2.67
2178 2623 4.542525 AGTGACCCCCTTTGTATTTATCCA 59.457 41.667 0.00 0.00 0.00 3.41
2179 2624 5.104067 AGAGTGACCCCCTTTGTATTTATCC 60.104 44.000 0.00 0.00 0.00 2.59
2237 2682 2.949644 GGCCAGTAATAACATCACACCC 59.050 50.000 0.00 0.00 0.00 4.61
2302 2759 9.973450 ATGTTTATATATCTTAGCATAGCCTCG 57.027 33.333 0.00 0.00 0.00 4.63
2378 2840 5.006746 GGCACTGAAGGAGAATAATAACACG 59.993 44.000 0.00 0.00 0.00 4.49
2406 2872 1.361204 TGCCAGAACAGGAGGATCAA 58.639 50.000 0.00 0.00 36.25 2.57
2535 3003 3.137544 TGACAGGGTACTCAAACCAACAT 59.862 43.478 0.00 0.00 41.67 2.71
2586 3057 6.530019 TGAGTAGTGAGATCAAGCATTACA 57.470 37.500 13.98 0.00 31.87 2.41
2754 3225 5.286082 GTCAATACGATGCAAATCCACAAAC 59.714 40.000 0.00 0.00 0.00 2.93
2791 3262 9.387257 GAGAAATTTGAAATTGATTGCCCTAAT 57.613 29.630 3.62 0.00 0.00 1.73
2829 3300 6.686130 ACAGAGTTTTACGAAATCTACACG 57.314 37.500 0.00 0.00 0.00 4.49
2832 3303 8.961294 TGTCTACAGAGTTTTACGAAATCTAC 57.039 34.615 0.00 0.00 0.00 2.59
2834 3305 7.063544 GCATGTCTACAGAGTTTTACGAAATCT 59.936 37.037 0.00 0.00 0.00 2.40
2836 3307 6.649141 TGCATGTCTACAGAGTTTTACGAAAT 59.351 34.615 0.00 0.00 0.00 2.17
2840 3311 5.161358 TCTGCATGTCTACAGAGTTTTACG 58.839 41.667 0.00 0.00 37.99 3.18
2842 3313 6.993079 TCTTCTGCATGTCTACAGAGTTTTA 58.007 36.000 0.00 0.00 43.43 1.52
2850 3321 4.633126 GCATTTCTCTTCTGCATGTCTACA 59.367 41.667 0.00 0.00 35.96 2.74
2998 6491 8.124199 GTGAACAAAATCCAAAGTAACGAACTA 58.876 33.333 0.00 0.00 37.50 2.24
3073 6566 1.997874 GGCACCTGTCTCCCCAGAT 60.998 63.158 0.00 0.00 34.23 2.90
3117 6616 5.279206 CGAATAGGAGATGCTAACAGGACAT 60.279 44.000 0.00 0.00 0.00 3.06
3119 6618 4.278669 TCGAATAGGAGATGCTAACAGGAC 59.721 45.833 0.00 0.00 0.00 3.85
3136 6635 4.920640 GAGTCATCCCAACTCTCGAATA 57.079 45.455 0.00 0.00 40.03 1.75
3159 6658 0.988832 TGGCTCCCGACCAAACTAAT 59.011 50.000 0.00 0.00 33.12 1.73
3238 6768 1.952296 CTAACAATGCATCCTCCTGCC 59.048 52.381 0.00 0.00 41.58 4.85
3361 6971 7.157347 TCATTTTTGGCAATTTAGCATGTACA 58.843 30.769 0.00 0.00 35.83 2.90
3421 7031 8.464770 TTTGAAAATAGTGCAACAATATCAGC 57.535 30.769 0.00 0.00 41.43 4.26


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

AutoCloner maintained by Alex Coulton.