Multiple sequence alignment - TraesCS6D01G050200

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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 TraesCS6D01G050200 chr6D 100.000 2495 0 0 1 2495 24255873 24258367 0.000000e+00 4608
1 TraesCS6D01G050200 chr6D 89.794 2332 100 49 1 2231 447818185 447820479 0.000000e+00 2861
2 TraesCS6D01G050200 chr6D 97.647 255 6 0 2240 2494 447823077 447823331 2.950000e-119 438
3 TraesCS6D01G050200 chr3D 98.799 2498 27 1 1 2495 216428087 216430584 0.000000e+00 4444
4 TraesCS6D01G050200 chr3D 86.892 2342 151 60 1 2234 502047858 502045565 0.000000e+00 2481
5 TraesCS6D01G050200 chr3D 85.355 2349 151 83 1 2231 20288789 20291062 0.000000e+00 2254
6 TraesCS6D01G050200 chr3D 85.893 1836 129 60 1 1743 523400582 523402380 0.000000e+00 1836
7 TraesCS6D01G050200 chr3D 86.749 1698 102 52 1 1609 532071116 532069453 0.000000e+00 1775
8 TraesCS6D01G050200 chr3D 83.450 1142 80 41 1 1060 160913206 160914320 0.000000e+00 961
9 TraesCS6D01G050200 chr3D 89.378 386 17 2 1872 2234 575251022 575250638 4.860000e-127 464
10 TraesCS6D01G050200 chr5D 94.069 2293 71 14 2 2239 398263460 398261178 0.000000e+00 3421
11 TraesCS6D01G050200 chr5D 90.004 2351 103 44 1 2234 114472188 114469853 0.000000e+00 2918
12 TraesCS6D01G050200 chr5D 87.248 2329 152 56 6 2235 274114294 274116576 0.000000e+00 2521
13 TraesCS6D01G050200 chr5D 85.997 2321 167 66 1 2234 494245281 494243032 0.000000e+00 2340
14 TraesCS6D01G050200 chr5D 86.875 1821 143 39 1 1757 382518252 382520040 0.000000e+00 1951
15 TraesCS6D01G050200 chr5D 91.531 614 25 6 1642 2235 545534949 545535555 0.000000e+00 821
16 TraesCS6D01G050200 chr5D 98.039 255 5 0 2240 2494 398260244 398259990 6.330000e-121 444
17 TraesCS6D01G050200 chr5D 97.647 255 6 0 2240 2494 408550264 408550010 2.950000e-119 438
18 TraesCS6D01G050200 chr7D 89.234 2220 119 51 118 2231 46570638 46572843 0.000000e+00 2665
19 TraesCS6D01G050200 chr7D 87.066 1268 89 34 1 1199 545665802 545667063 0.000000e+00 1363
20 TraesCS6D01G050200 chr7D 91.531 614 26 6 1642 2235 625180408 625179801 0.000000e+00 822
21 TraesCS6D01G050200 chr7D 97.647 255 6 0 2240 2494 631813565 631813311 2.950000e-119 438
22 TraesCS6D01G050200 chr5A 89.354 2104 112 51 59 2070 574041123 574039040 0.000000e+00 2542
23 TraesCS6D01G050200 chr5A 97.647 255 6 0 2240 2494 567302791 567302537 2.950000e-119 438
24 TraesCS6D01G050200 chr4D 93.418 1732 58 15 1 1698 97481026 97479317 0.000000e+00 2516
25 TraesCS6D01G050200 chr4D 88.000 525 22 14 31 520 496936299 496935781 1.290000e-162 582
26 TraesCS6D01G050200 chr4D 98.039 255 5 0 2240 2494 375072787 375073041 6.330000e-121 444
27 TraesCS6D01G050200 chr4D 97.647 255 6 0 2240 2494 97476272 97476018 2.950000e-119 438
28 TraesCS6D01G050200 chr2D 91.408 1839 95 27 1 1788 601106515 601104689 0.000000e+00 2462
29 TraesCS6D01G050200 chr2D 89.320 206 16 4 2029 2234 147379364 147379165 1.150000e-63 254
30 TraesCS6D01G050200 chrUn 92.752 1421 71 6 844 2235 97175492 97176909 0.000000e+00 2025
31 TraesCS6D01G050200 chrUn 92.151 1427 74 14 844 2235 97255836 97257259 0.000000e+00 1980
32 TraesCS6D01G050200 chrUn 87.974 1713 137 44 116 1796 70158325 70156650 0.000000e+00 1958
33 TraesCS6D01G050200 chrUn 90.747 616 24 8 1642 2234 70156826 70156221 0.000000e+00 791
34 TraesCS6D01G050200 chr6A 93.939 1254 46 4 1005 2231 536675996 536677246 0.000000e+00 1868
35 TraesCS6D01G050200 chr6A 88.668 1006 71 29 31 1007 536666098 536667089 0.000000e+00 1186
36 TraesCS6D01G050200 chr6A 89.806 206 15 4 2029 2234 56127870 56127671 2.460000e-65 259
37 TraesCS6D01G050200 chr3A 88.725 1490 105 28 353 1788 573968679 573967199 0.000000e+00 1762
38 TraesCS6D01G050200 chr1D 85.658 1792 123 57 3 1718 829089 830822 0.000000e+00 1762
39 TraesCS6D01G050200 chr7A 88.155 1241 75 44 59 1238 563240726 563239497 0.000000e+00 1411
40 TraesCS6D01G050200 chr4A 87.231 791 64 21 1 763 630836430 630837211 0.000000e+00 867
41 TraesCS6D01G050200 chr4A 97.647 255 6 0 2240 2494 708330336 708330082 2.950000e-119 438
42 TraesCS6D01G050200 chr2A 86.108 799 55 25 1 763 165245050 165245828 0.000000e+00 809
43 TraesCS6D01G050200 chr1B 87.270 652 47 19 136 763 557113927 557114566 0.000000e+00 712
44 TraesCS6D01G050200 chr1B 90.463 367 16 6 458 805 529699126 529698760 1.350000e-127 466


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 TraesCS6D01G050200 chr6D 24255873 24258367 2494 False 4608.0 4608 100.0000 1 2495 1 chr6D.!!$F1 2494
1 TraesCS6D01G050200 chr6D 447818185 447823331 5146 False 1649.5 2861 93.7205 1 2494 2 chr6D.!!$F2 2493
2 TraesCS6D01G050200 chr3D 216428087 216430584 2497 False 4444.0 4444 98.7990 1 2495 1 chr3D.!!$F3 2494
3 TraesCS6D01G050200 chr3D 502045565 502047858 2293 True 2481.0 2481 86.8920 1 2234 1 chr3D.!!$R1 2233
4 TraesCS6D01G050200 chr3D 20288789 20291062 2273 False 2254.0 2254 85.3550 1 2231 1 chr3D.!!$F1 2230
5 TraesCS6D01G050200 chr3D 523400582 523402380 1798 False 1836.0 1836 85.8930 1 1743 1 chr3D.!!$F4 1742
6 TraesCS6D01G050200 chr3D 532069453 532071116 1663 True 1775.0 1775 86.7490 1 1609 1 chr3D.!!$R2 1608
7 TraesCS6D01G050200 chr3D 160913206 160914320 1114 False 961.0 961 83.4500 1 1060 1 chr3D.!!$F2 1059
8 TraesCS6D01G050200 chr5D 114469853 114472188 2335 True 2918.0 2918 90.0040 1 2234 1 chr5D.!!$R1 2233
9 TraesCS6D01G050200 chr5D 274114294 274116576 2282 False 2521.0 2521 87.2480 6 2235 1 chr5D.!!$F1 2229
10 TraesCS6D01G050200 chr5D 494243032 494245281 2249 True 2340.0 2340 85.9970 1 2234 1 chr5D.!!$R3 2233
11 TraesCS6D01G050200 chr5D 382518252 382520040 1788 False 1951.0 1951 86.8750 1 1757 1 chr5D.!!$F2 1756
12 TraesCS6D01G050200 chr5D 398259990 398263460 3470 True 1932.5 3421 96.0540 2 2494 2 chr5D.!!$R4 2492
13 TraesCS6D01G050200 chr5D 545534949 545535555 606 False 821.0 821 91.5310 1642 2235 1 chr5D.!!$F3 593
14 TraesCS6D01G050200 chr7D 46570638 46572843 2205 False 2665.0 2665 89.2340 118 2231 1 chr7D.!!$F1 2113
15 TraesCS6D01G050200 chr7D 545665802 545667063 1261 False 1363.0 1363 87.0660 1 1199 1 chr7D.!!$F2 1198
16 TraesCS6D01G050200 chr7D 625179801 625180408 607 True 822.0 822 91.5310 1642 2235 1 chr7D.!!$R1 593
17 TraesCS6D01G050200 chr5A 574039040 574041123 2083 True 2542.0 2542 89.3540 59 2070 1 chr5A.!!$R2 2011
18 TraesCS6D01G050200 chr4D 97476018 97481026 5008 True 1477.0 2516 95.5325 1 2494 2 chr4D.!!$R2 2493
19 TraesCS6D01G050200 chr4D 496935781 496936299 518 True 582.0 582 88.0000 31 520 1 chr4D.!!$R1 489
20 TraesCS6D01G050200 chr2D 601104689 601106515 1826 True 2462.0 2462 91.4080 1 1788 1 chr2D.!!$R2 1787
21 TraesCS6D01G050200 chrUn 97175492 97176909 1417 False 2025.0 2025 92.7520 844 2235 1 chrUn.!!$F1 1391
22 TraesCS6D01G050200 chrUn 97255836 97257259 1423 False 1980.0 1980 92.1510 844 2235 1 chrUn.!!$F2 1391
23 TraesCS6D01G050200 chrUn 70156221 70158325 2104 True 1374.5 1958 89.3605 116 2234 2 chrUn.!!$R1 2118
24 TraesCS6D01G050200 chr6A 536675996 536677246 1250 False 1868.0 1868 93.9390 1005 2231 1 chr6A.!!$F2 1226
25 TraesCS6D01G050200 chr6A 536666098 536667089 991 False 1186.0 1186 88.6680 31 1007 1 chr6A.!!$F1 976
26 TraesCS6D01G050200 chr3A 573967199 573968679 1480 True 1762.0 1762 88.7250 353 1788 1 chr3A.!!$R1 1435
27 TraesCS6D01G050200 chr1D 829089 830822 1733 False 1762.0 1762 85.6580 3 1718 1 chr1D.!!$F1 1715
28 TraesCS6D01G050200 chr7A 563239497 563240726 1229 True 1411.0 1411 88.1550 59 1238 1 chr7A.!!$R1 1179
29 TraesCS6D01G050200 chr4A 630836430 630837211 781 False 867.0 867 87.2310 1 763 1 chr4A.!!$F1 762
30 TraesCS6D01G050200 chr2A 165245050 165245828 778 False 809.0 809 86.1080 1 763 1 chr2A.!!$F1 762
31 TraesCS6D01G050200 chr1B 557113927 557114566 639 False 712.0 712 87.2700 136 763 1 chr1B.!!$F1 627

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
684 912 2.009774 CAGGAAGGCGTTTCTATGGTG 58.99 52.381 0.0 0.0 36.03 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2463 0.747852 GGTTTTCTTTTGGGTGGCGA 59.252 50.0 0.0 0.0 0.0 5.54 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
684 912 2.009774 CAGGAAGGCGTTTCTATGGTG 58.990 52.381 0.00 0.0 36.03 4.17
996 1370 5.423290 TCAGAGATGTCTTTCCAAGCTATGA 59.577 40.000 0.00 0.0 0.00 2.15
1068 1442 0.251077 AGAAGGAGTTGGCCAAGCTG 60.251 55.000 21.21 0.0 0.00 4.24
1640 2080 9.677567 TCATGCATTTGAACTTTAGTTTCTTAC 57.322 29.630 0.00 0.0 38.56 2.34
1980 2463 0.399949 TTCCCAGTGACTCCACCAGT 60.400 55.000 0.00 0.0 44.22 4.00
2213 2762 1.064463 GCAGGGGAAGGACATTCATGA 60.064 52.381 1.83 0.0 39.91 3.07
2328 5517 4.475345 TGGCAACCCAATTAACTGTAACT 58.525 39.130 0.00 0.0 38.46 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.335647 ACTGAACCGGCCTGCCTG 62.336 66.667 0.0 1.94 0.00 4.85
684 912 0.181350 CATCTAACCTGGACTGGGCC 59.819 60.000 0.0 0.00 0.00 5.80
1068 1442 4.137543 ACTCCCTTTCATGTTCACACTTC 58.862 43.478 0.0 0.00 0.00 3.01
1640 2080 8.488651 ACAACATAGGAAATAAGGTTCTTACG 57.511 34.615 0.0 0.00 0.00 3.18
1980 2463 0.747852 GGTTTTCTTTTGGGTGGCGA 59.252 50.000 0.0 0.00 0.00 5.54
2031 2528 4.890306 GCCTCCCCCTCCTCCTCC 62.890 77.778 0.0 0.00 0.00 4.30
2213 2762 1.144503 CCCTGCCCAGCTAATGATCTT 59.855 52.381 0.0 0.00 0.00 2.40
2328 5517 1.815408 GCAAGTGGAGAGAGCACCAAA 60.815 52.381 0.0 0.00 36.49 3.28


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

AutoCloner maintained by Alex Coulton.