Multiple sequence alignment - TraesCS6B01G193900

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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 TraesCS6B01G193900 chr6B 100.000 3173 0 0 1 3173 228758403 228755231 0.000000e+00 5860.0
1 TraesCS6B01G193900 chr6B 92.691 2969 139 27 240 3173 257783641 257780716 0.000000e+00 4209.0
2 TraesCS6B01G193900 chr6B 95.456 2377 80 12 809 3173 230602352 230604712 0.000000e+00 3766.0
3 TraesCS6B01G193900 chr6B 87.246 1380 132 18 838 2203 213521194 213522543 0.000000e+00 1533.0
4 TraesCS6B01G193900 chr6B 81.333 150 23 5 460 605 613582458 613582310 2.000000e-22 117.0
5 TraesCS6B01G193900 chr6D 93.232 3221 132 28 1 3173 131033718 131030536 0.000000e+00 4662.0
6 TraesCS6B01G193900 chr6D 93.714 2927 111 25 286 3171 130214235 130211341 0.000000e+00 4318.0
7 TraesCS6B01G193900 chr6D 93.365 2909 126 25 298 3167 146506060 146508940 0.000000e+00 4241.0
8 TraesCS6B01G193900 chr6D 88.321 137 12 4 608 744 146387656 146387788 9.110000e-36 161.0
9 TraesCS6B01G193900 chr6D 88.235 102 12 0 76 177 130214334 130214233 4.300000e-24 122.0
10 TraesCS6B01G193900 chr6D 79.861 144 25 4 465 605 408898062 408897920 5.600000e-18 102.0
11 TraesCS6B01G193900 chr6A 94.468 2151 76 8 789 2918 171738696 171740824 0.000000e+00 3273.0
12 TraesCS6B01G193900 chr6A 94.509 1894 77 15 608 2483 169226964 169225080 0.000000e+00 2896.0
13 TraesCS6B01G193900 chr6A 88.697 1159 69 14 926 2077 162911118 162912221 0.000000e+00 1358.0
14 TraesCS6B01G193900 chr6A 94.901 706 22 7 2479 3173 169221052 169220350 0.000000e+00 1092.0
15 TraesCS6B01G193900 chr6A 92.605 622 31 3 2308 2918 162913035 162913652 0.000000e+00 880.0
16 TraesCS6B01G193900 chr6A 84.441 662 68 15 340 983 169254958 169254314 1.250000e-173 619.0
17 TraesCS6B01G193900 chr6A 91.566 249 10 5 2936 3173 171740812 171741060 1.820000e-87 333.0
18 TraesCS6B01G193900 chr6A 92.308 156 12 0 2161 2316 162912224 162912379 4.120000e-54 222.0
19 TraesCS6B01G193900 chr6A 83.884 242 30 3 2936 3171 162913640 162913878 4.120000e-54 222.0
20 TraesCS6B01G193900 chr6A 76.357 258 38 17 654 901 162909448 162909692 2.000000e-22 117.0
21 TraesCS6B01G193900 chr6A 86.408 103 9 4 756 857 171738604 171738702 1.200000e-19 108.0
22 TraesCS6B01G193900 chr5B 94.626 1135 49 5 1793 2918 84884572 84883441 0.000000e+00 1748.0
23 TraesCS6B01G193900 chr5B 90.177 621 45 7 978 1592 84890690 84890080 0.000000e+00 795.0
24 TraesCS6B01G193900 chr5B 95.364 151 5 1 2936 3086 84883453 84883305 4.090000e-59 239.0
25 TraesCS6B01G193900 chr5B 97.260 73 2 0 3101 3173 84883202 84883130 1.200000e-24 124.0
26 TraesCS6B01G193900 chr5D 77.037 540 95 21 76 606 449127515 449128034 1.860000e-72 283.0
27 TraesCS6B01G193900 chr5D 88.710 62 6 1 76 137 27269476 27269416 1.220000e-09 75.0
28 TraesCS6B01G193900 chr4D 75.451 554 95 32 76 605 48695694 48696230 6.840000e-57 231.0
29 TraesCS6B01G193900 chr1B 73.496 532 97 22 76 589 672424496 672425001 9.110000e-36 161.0
30 TraesCS6B01G193900 chr4A 83.240 179 20 6 76 248 60031536 60031362 4.240000e-34 156.0
31 TraesCS6B01G193900 chr4A 92.857 70 5 0 1 70 61624798 61624729 5.600000e-18 102.0
32 TraesCS6B01G193900 chr1D 87.591 137 12 5 608 744 266787784 266787653 1.520000e-33 154.0
33 TraesCS6B01G193900 chr1D 79.000 200 29 4 76 263 465340805 465341003 1.200000e-24 124.0
34 TraesCS6B01G193900 chr1D 91.304 69 6 0 2 70 320033717 320033649 9.370000e-16 95.3
35 TraesCS6B01G193900 chr1A 86.607 112 12 2 490 600 514543087 514543196 1.550000e-23 121.0
36 TraesCS6B01G193900 chr4B 95.714 70 3 0 1 70 186136633 186136564 2.590000e-21 113.0
37 TraesCS6B01G193900 chr2B 94.286 70 4 0 1 70 202291046 202291115 1.200000e-19 108.0
38 TraesCS6B01G193900 chr2A 94.286 70 4 0 1 70 376191932 376192001 1.200000e-19 108.0
39 TraesCS6B01G193900 chr2A 93.846 65 4 0 2 66 236103358 236103422 7.240000e-17 99.0
40 TraesCS6B01G193900 chr2D 94.203 69 4 0 1 69 214234349 214234281 4.330000e-19 106.0
41 TraesCS6B01G193900 chr3A 91.429 70 6 0 1 70 303015365 303015296 2.610000e-16 97.1
42 TraesCS6B01G193900 chr7D 90.323 62 6 0 76 137 463972774 463972835 7.290000e-12 82.4


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 TraesCS6B01G193900 chr6B 228755231 228758403 3172 True 5860.000000 5860 100.0000 1 3173 1 chr6B.!!$R1 3172
1 TraesCS6B01G193900 chr6B 257780716 257783641 2925 True 4209.000000 4209 92.6910 240 3173 1 chr6B.!!$R2 2933
2 TraesCS6B01G193900 chr6B 230602352 230604712 2360 False 3766.000000 3766 95.4560 809 3173 1 chr6B.!!$F2 2364
3 TraesCS6B01G193900 chr6B 213521194 213522543 1349 False 1533.000000 1533 87.2460 838 2203 1 chr6B.!!$F1 1365
4 TraesCS6B01G193900 chr6D 131030536 131033718 3182 True 4662.000000 4662 93.2320 1 3173 1 chr6D.!!$R1 3172
5 TraesCS6B01G193900 chr6D 146506060 146508940 2880 False 4241.000000 4241 93.3650 298 3167 1 chr6D.!!$F2 2869
6 TraesCS6B01G193900 chr6D 130211341 130214334 2993 True 2220.000000 4318 90.9745 76 3171 2 chr6D.!!$R3 3095
7 TraesCS6B01G193900 chr6A 169225080 169226964 1884 True 2896.000000 2896 94.5090 608 2483 1 chr6A.!!$R2 1875
8 TraesCS6B01G193900 chr6A 171738604 171741060 2456 False 1238.000000 3273 90.8140 756 3173 3 chr6A.!!$F2 2417
9 TraesCS6B01G193900 chr6A 169220350 169221052 702 True 1092.000000 1092 94.9010 2479 3173 1 chr6A.!!$R1 694
10 TraesCS6B01G193900 chr6A 169254314 169254958 644 True 619.000000 619 84.4410 340 983 1 chr6A.!!$R3 643
11 TraesCS6B01G193900 chr6A 162909448 162913878 4430 False 559.800000 1358 86.7702 654 3171 5 chr6A.!!$F1 2517
12 TraesCS6B01G193900 chr5B 84890080 84890690 610 True 795.000000 795 90.1770 978 1592 1 chr5B.!!$R1 614
13 TraesCS6B01G193900 chr5B 84883130 84884572 1442 True 703.666667 1748 95.7500 1793 3173 3 chr5B.!!$R2 1380
14 TraesCS6B01G193900 chr5D 449127515 449128034 519 False 283.000000 283 77.0370 76 606 1 chr5D.!!$F1 530
15 TraesCS6B01G193900 chr4D 48695694 48696230 536 False 231.000000 231 75.4510 76 605 1 chr4D.!!$F1 529

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
237 259 0.109597 CGCTTTCCTGTTGATGGTGC 60.110 55.0 0.0 0.0 0.0 5.01 F
384 436 0.596577 CTGTGAGGAAGGACGACGAA 59.403 55.0 0.0 0.0 0.0 3.85 F
1236 2814 0.182537 CCCCGCAATCCCAATACTCA 59.817 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 2793 1.073923 GAGTATTGGGATTGCGGGGAT 59.926 52.381 0.0 0.00 0.00 3.85 R
1884 3474 2.228343 AGAAGATTCAGCTTGCTGTTGC 59.772 45.455 20.2 11.39 40.20 4.17 R
2372 4708 2.359230 GCTGCGGGCTCTTCAACT 60.359 61.111 0.0 0.00 38.06 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
20 21 1.375523 GGTCGGGTTCTTCGCACAT 60.376 57.895 0.00 0.0 0.00 3.21
25 26 1.675641 GGTTCTTCGCACATGCCCT 60.676 57.895 0.00 0.0 37.91 5.19
32 33 0.613260 TCGCACATGCCCTAGAGTTT 59.387 50.000 0.00 0.0 37.91 2.66
47 48 2.959030 AGAGTTTGAACCTTTCTTGGGC 59.041 45.455 0.00 0.0 0.00 5.36
180 202 2.347490 GACACTCGGTGGTGCCAT 59.653 61.111 8.57 0.0 40.52 4.40
213 235 0.250234 CCTTGAACGAGATGGCTCCA 59.750 55.000 0.00 0.0 37.91 3.86
237 259 0.109597 CGCTTTCCTGTTGATGGTGC 60.110 55.000 0.00 0.0 0.00 5.01
380 432 2.962569 CGCTGTGAGGAAGGACGA 59.037 61.111 0.00 0.0 0.00 4.20
384 436 0.596577 CTGTGAGGAAGGACGACGAA 59.403 55.000 0.00 0.0 0.00 3.85
519 583 2.846206 ACATATGAAGGAGTTGGGCTCA 59.154 45.455 10.38 0.0 45.88 4.26
619 690 2.092592 CCGCAAATCCTAACCCTAACCT 60.093 50.000 0.00 0.0 0.00 3.50
623 694 4.686396 GCAAATCCTAACCCTAACCTCTCC 60.686 50.000 0.00 0.0 0.00 3.71
645 716 2.125326 CGGAGGCTCGGTGTGGATA 61.125 63.158 13.45 0.0 0.00 2.59
674 745 9.793252 GAGTTAGAAGGTGACACGTTTTATATA 57.207 33.333 14.28 0.0 0.00 0.86
1196 2762 2.032681 GCCCTTCCTGTTCGCTGT 59.967 61.111 0.00 0.0 0.00 4.40
1207 2779 0.850856 GTTCGCTGTCGACTTTTCGT 59.149 50.000 17.92 0.0 45.43 3.85
1215 2793 3.926497 GACTTTTCGTCGTCGCCA 58.074 55.556 0.00 0.0 36.96 5.69
1236 2814 0.182537 CCCCGCAATCCCAATACTCA 59.817 55.000 0.00 0.0 0.00 3.41
1242 2820 3.365472 GCAATCCCAATACTCACCCTTT 58.635 45.455 0.00 0.0 0.00 3.11
1431 3021 4.137615 TCCTCCCCGGCGAGATCA 62.138 66.667 17.94 0.0 30.97 2.92
1539 3129 2.886391 GCTCTTACTCCACTCCTCCACT 60.886 54.545 0.00 0.0 0.00 4.00
1713 3303 2.036475 CCTTCAGTGCCTGTATCGCTAT 59.964 50.000 2.68 0.0 32.61 2.97
1884 3474 1.244019 CCTCCCTTGCAACCTTTCGG 61.244 60.000 0.00 0.0 0.00 4.30
2300 3971 2.425668 GCGTTGGCCAAATATACCTTGT 59.574 45.455 22.47 0.0 0.00 3.16
2610 4954 3.429547 CGATCAACCTCGACTCAAAGGAT 60.430 47.826 0.00 0.0 41.12 3.24
2697 5041 8.090788 AGGTTAAAGACAATATCCTTCAGCTA 57.909 34.615 0.00 0.0 0.00 3.32
2751 5095 2.559381 ACCCTCATTAGCTCCAGTCT 57.441 50.000 0.00 0.0 0.00 3.24
2790 5134 4.230964 ACTGGTAAGATCTACCACCTCTCT 59.769 45.833 15.83 0.0 42.21 3.10
2921 5276 8.563123 ACACCTTTTAAATAGGCTTTAGTCTC 57.437 34.615 13.25 0.0 36.17 3.36
3046 5403 4.647399 GCCCCCATAATGCAACTTTTACTA 59.353 41.667 0.00 0.0 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.394606 AGAAAGGTTCAAACTCTAGGGCA 59.605 43.478 0.00 0.00 0.00 5.36
25 26 4.142038 GCCCAAGAAAGGTTCAAACTCTA 58.858 43.478 0.00 0.00 0.00 2.43
32 33 0.827507 GCAGGCCCAAGAAAGGTTCA 60.828 55.000 0.00 0.00 0.00 3.18
213 235 1.203052 CATCAACAGGAAAGCGGCAAT 59.797 47.619 1.45 0.00 0.00 3.56
221 243 2.436417 GCTAGCACCATCAACAGGAAA 58.564 47.619 10.63 0.00 0.00 3.13
270 292 1.528309 CCACGGCCACAACTCCTTT 60.528 57.895 2.24 0.00 0.00 3.11
352 404 1.298157 CTCACAGCGCCGGAATTCAA 61.298 55.000 5.05 0.00 0.00 2.69
380 432 0.974383 AATCCGTCCTCCAACTTCGT 59.026 50.000 0.00 0.00 0.00 3.85
384 436 1.299976 GCCAATCCGTCCTCCAACT 59.700 57.895 0.00 0.00 0.00 3.16
563 628 1.299165 CGGCCCGAACAGATACTCG 60.299 63.158 0.00 0.00 34.83 4.18
605 676 2.246849 GAGGGAGAGGTTAGGGTTAGGA 59.753 54.545 0.00 0.00 0.00 2.94
645 716 2.897969 ACGTGTCACCTTCTAACTCCAT 59.102 45.455 0.00 0.00 0.00 3.41
788 874 4.735132 TTTCGAGTCGGGCTGGCG 62.735 66.667 13.54 0.00 0.00 5.69
816 961 0.869730 CCGACCCGAACACGAATTTT 59.130 50.000 0.00 0.00 0.00 1.82
817 962 0.952010 CCCGACCCGAACACGAATTT 60.952 55.000 0.00 0.00 0.00 1.82
821 966 3.673484 GACCCGACCCGAACACGA 61.673 66.667 0.00 0.00 0.00 4.35
1215 2793 1.073923 GAGTATTGGGATTGCGGGGAT 59.926 52.381 0.00 0.00 0.00 3.85
1386 2976 3.535629 CTGGAAGGCACAGACGGCA 62.536 63.158 0.00 0.00 38.20 5.69
1884 3474 2.228343 AGAAGATTCAGCTTGCTGTTGC 59.772 45.455 20.20 11.39 40.20 4.17
2170 3841 5.567423 CGACATCTATGACAGCCATCCATTA 60.567 44.000 0.00 0.00 36.71 1.90
2300 3971 3.194542 CGAGGGGGCAAAATCATAACAAA 59.805 43.478 0.00 0.00 0.00 2.83
2372 4708 2.359230 GCTGCGGGCTCTTCAACT 60.359 61.111 0.00 0.00 38.06 3.16
2502 4838 5.335661 CCAAGCTTGGTATTTGTAGTGGTTC 60.336 44.000 33.46 0.00 43.43 3.62
2697 5041 3.440173 CACCGAACCATCTTGCAGTTAAT 59.560 43.478 0.00 0.00 0.00 1.40
2751 5095 2.703536 ACCAGTGTGTGTTACCTGATCA 59.296 45.455 0.00 0.00 32.55 2.92
2926 5282 9.303116 TCAACCTAAAGCCTATTTTATTCACAA 57.697 29.630 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.