Multiple sequence alignment - TraesCS1A01G406800

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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 TraesCS1A01G406800 chr1A 100.000 3084 0 0 1 3084 569357012 569353929 0.000000e+00 5696.0
1 TraesCS1A01G406800 chr1A 89.700 767 73 4 1447 2209 569377068 569376304 0.000000e+00 974.0
2 TraesCS1A01G406800 chr1A 84.360 422 20 18 751 1147 569377576 569377176 3.760000e-99 372.0
3 TraesCS1A01G406800 chr1A 100.000 35 0 0 717 751 569377696 569377662 7.140000e-07 65.8
4 TraesCS1A01G406800 chr4A 97.811 1782 25 4 751 2528 624746611 624748382 0.000000e+00 3062.0
5 TraesCS1A01G406800 chr4A 89.740 770 73 4 1444 2209 624733529 624734296 0.000000e+00 979.0
6 TraesCS1A01G406800 chr4A 97.993 548 7 1 2537 3084 624755366 624755909 0.000000e+00 948.0
7 TraesCS1A01G406800 chr4A 95.437 504 14 5 254 751 624746025 624746525 0.000000e+00 795.0
8 TraesCS1A01G406800 chr4A 92.727 550 39 1 2535 3084 624753086 624753634 0.000000e+00 793.0
9 TraesCS1A01G406800 chr4A 94.297 263 11 4 21 281 624745697 624745957 1.720000e-107 399.0
10 TraesCS1A01G406800 chr4A 83.886 422 21 17 751 1147 624733025 624733424 2.920000e-95 359.0
11 TraesCS1A01G406800 chr5D 96.018 1783 61 5 751 2528 544816590 544818367 0.000000e+00 2891.0
12 TraesCS1A01G406800 chr5D 91.067 806 65 5 1408 2209 544799322 544800124 0.000000e+00 1083.0
13 TraesCS1A01G406800 chr5D 93.285 551 35 2 2535 3084 544872550 544873099 0.000000e+00 811.0
14 TraesCS1A01G406800 chr5D 92.740 551 36 4 2535 3084 544874831 544875378 0.000000e+00 793.0
15 TraesCS1A01G406800 chr5D 92.559 551 34 3 2535 3084 544870271 544870815 0.000000e+00 784.0
16 TraesCS1A01G406800 chr5D 93.449 519 33 1 2566 3084 544877378 544877895 0.000000e+00 769.0
17 TraesCS1A01G406800 chr5D 89.111 551 55 5 2535 3084 544804258 544804804 0.000000e+00 680.0
18 TraesCS1A01G406800 chr5D 91.641 323 16 6 437 751 544809853 544810172 1.310000e-118 436.0
19 TraesCS1A01G406800 chr5D 94.964 278 11 2 11 286 544807611 544807887 1.700000e-117 433.0
20 TraesCS1A01G406800 chr5D 91.584 202 13 3 448 647 544816156 544816355 3.030000e-70 276.0
21 TraesCS1A01G406800 chr5D 94.886 176 8 1 273 448 544809195 544809369 1.090000e-69 274.0
22 TraesCS1A01G406800 chr5D 100.000 36 0 0 716 751 544798728 544798763 1.980000e-07 67.6
23 TraesCS1A01G406800 chr5B 92.485 1690 101 12 751 2430 687325730 687327403 0.000000e+00 2394.0
24 TraesCS1A01G406800 chr5B 86.802 1773 125 41 751 2491 687259380 687261075 0.000000e+00 1877.0
25 TraesCS1A01G406800 chr5B 95.582 679 26 3 1 676 687324438 687325115 0.000000e+00 1085.0
26 TraesCS1A01G406800 chr5B 89.591 807 76 6 1407 2209 687212960 687213762 0.000000e+00 1018.0
27 TraesCS1A01G406800 chr5B 90.885 746 59 7 1407 2147 687223956 687224697 0.000000e+00 992.0
28 TraesCS1A01G406800 chr5B 91.618 680 42 7 1 676 687339459 687340127 0.000000e+00 926.0
29 TraesCS1A01G406800 chr5B 90.973 565 34 6 751 1306 687342118 687342674 0.000000e+00 745.0
30 TraesCS1A01G406800 chr5B 90.000 540 38 8 140 676 687258611 687259137 0.000000e+00 684.0
31 TraesCS1A01G406800 chr5B 88.545 550 59 4 2535 3084 687263656 687264201 0.000000e+00 664.0
32 TraesCS1A01G406800 chr5B 86.207 551 65 5 2535 3084 687333305 687333845 1.230000e-163 586.0
33 TraesCS1A01G406800 chr5B 92.652 313 18 3 442 751 687325334 687325644 2.180000e-121 446.0
34 TraesCS1A01G406800 chr5B 83.710 442 29 13 751 1168 687223494 687223916 8.070000e-101 377.0
35 TraesCS1A01G406800 chr5B 83.173 416 41 15 752 1147 687212508 687212914 1.360000e-93 353.0
36 TraesCS1A01G406800 chr5B 90.123 81 4 2 673 751 687340207 687340285 5.440000e-18 102.0
37 TraesCS1A01G406800 chr5B 90.385 52 5 0 98 149 687241248 687241299 5.520000e-08 69.4
38 TraesCS1A01G406800 chr5B 100.000 35 0 0 717 751 687212421 687212455 7.140000e-07 65.8
39 TraesCS1A01G406800 chr4B 80.183 328 47 14 341 662 547308723 547309038 2.390000e-56 230.0
40 TraesCS1A01G406800 chr4D 77.444 399 56 24 375 751 441255171 441255557 1.120000e-49 207.0
41 TraesCS1A01G406800 chr6A 93.478 46 3 0 2221 2266 9358806 9358851 5.520000e-08 69.4


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 TraesCS1A01G406800 chr1A 569353929 569357012 3083 True 5696.000000 5696 100.000000 1 3084 1 chr1A.!!$R1 3083
1 TraesCS1A01G406800 chr1A 569376304 569377696 1392 True 470.600000 974 91.353333 717 2209 3 chr1A.!!$R2 1492
2 TraesCS1A01G406800 chr4A 624745697 624748382 2685 False 1418.666667 3062 95.848333 21 2528 3 chr4A.!!$F2 2507
3 TraesCS1A01G406800 chr4A 624753086 624755909 2823 False 870.500000 948 95.360000 2535 3084 2 chr4A.!!$F3 549
4 TraesCS1A01G406800 chr4A 624733025 624734296 1271 False 669.000000 979 86.813000 751 2209 2 chr4A.!!$F1 1458
5 TraesCS1A01G406800 chr5D 544816156 544818367 2211 False 1583.500000 2891 93.801000 448 2528 2 chr5D.!!$F3 2080
6 TraesCS1A01G406800 chr5D 544870271 544877895 7624 False 789.250000 811 93.008250 2535 3084 4 chr5D.!!$F4 549
7 TraesCS1A01G406800 chr5D 544798728 544800124 1396 False 575.300000 1083 95.533500 716 2209 2 chr5D.!!$F1 1493
8 TraesCS1A01G406800 chr5D 544804258 544810172 5914 False 455.750000 680 92.650500 11 3084 4 chr5D.!!$F2 3073
9 TraesCS1A01G406800 chr5B 687324438 687327403 2965 False 1308.333333 2394 93.573000 1 2430 3 chr5B.!!$F6 2429
10 TraesCS1A01G406800 chr5B 687258611 687264201 5590 False 1075.000000 1877 88.449000 140 3084 3 chr5B.!!$F5 2944
11 TraesCS1A01G406800 chr5B 687223494 687224697 1203 False 684.500000 992 87.297500 751 2147 2 chr5B.!!$F4 1396
12 TraesCS1A01G406800 chr5B 687339459 687342674 3215 False 591.000000 926 90.904667 1 1306 3 chr5B.!!$F7 1305
13 TraesCS1A01G406800 chr5B 687333305 687333845 540 False 586.000000 586 86.207000 2535 3084 1 chr5B.!!$F2 549
14 TraesCS1A01G406800 chr5B 687212421 687213762 1341 False 478.933333 1018 90.921333 717 2209 3 chr5B.!!$F3 1492

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
573 5747 0.242017 GCATCTTCTGTGGTGCCAAC 59.758 55.0 0.00 0.0 0.0 3.77 F
809 8365 0.673985 TGGAACCGCGATCTCATAGG 59.326 55.0 8.23 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 8998 1.240641 TTGCATTGCGTACCAGGTGG 61.241 55.0 0.76 0.0 42.17 4.61 R
2529 10203 1.441732 AAACCGAGGAAAAACGCGCT 61.442 50.0 5.73 0.0 0.00 5.92 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
230 3580 6.382859 TCTGAGTGTAATTCTATGCCTTGGTA 59.617 38.462 0.00 0.00 0.00 3.25
286 4957 5.118990 GTCCTTATCATGCTTCTTGTGCTA 58.881 41.667 0.00 0.00 0.00 3.49
307 4978 8.642885 GTGCTATAATCTGATGAGTGTAATTCG 58.357 37.037 0.00 0.00 0.00 3.34
308 4979 7.814587 TGCTATAATCTGATGAGTGTAATTCGG 59.185 37.037 0.00 0.00 0.00 4.30
573 5747 0.242017 GCATCTTCTGTGGTGCCAAC 59.758 55.000 0.00 0.00 0.00 3.77
667 5843 4.065789 AGCCCTCTTTCAGAAACGTTTAG 58.934 43.478 14.65 9.96 0.00 1.85
706 6423 0.875059 GCACCAGCCAGACTTTGTAC 59.125 55.000 0.00 0.00 33.58 2.90
808 8364 2.128035 GTTGGAACCGCGATCTCATAG 58.872 52.381 8.23 0.00 0.00 2.23
809 8365 0.673985 TGGAACCGCGATCTCATAGG 59.326 55.000 8.23 0.00 0.00 2.57
810 8366 0.674534 GGAACCGCGATCTCATAGGT 59.325 55.000 8.23 0.00 36.66 3.08
811 8367 1.884579 GGAACCGCGATCTCATAGGTA 59.115 52.381 8.23 0.00 34.35 3.08
812 8368 2.492484 GGAACCGCGATCTCATAGGTAT 59.508 50.000 8.23 0.00 34.35 2.73
821 8378 5.634020 GCGATCTCATAGGTATGTTAACACC 59.366 44.000 11.22 8.82 35.26 4.16
1026 8616 1.953559 CTGGGATGCGCTTAAGCTTA 58.046 50.000 24.33 13.61 39.32 3.09
1110 8700 4.559502 GCCCATGCCACGTTCTAT 57.440 55.556 0.00 0.00 0.00 1.98
2529 10203 1.730192 CGCGCTTTGCTGCATCAAA 60.730 52.632 14.51 14.51 43.27 2.69
2533 10207 2.067616 CTTTGCTGCATCAAAGCGC 58.932 52.632 25.19 7.45 44.11 5.92
2534 10208 1.670971 CTTTGCTGCATCAAAGCGCG 61.671 55.000 25.19 0.00 44.11 6.86
2535 10209 2.405061 TTTGCTGCATCAAAGCGCGT 62.405 50.000 11.52 0.00 43.88 6.01
2536 10210 2.126734 GCTGCATCAAAGCGCGTT 60.127 55.556 8.43 1.67 37.31 4.84
2537 10211 1.730547 GCTGCATCAAAGCGCGTTT 60.731 52.632 5.64 4.71 37.31 3.60
2538 10212 1.277495 GCTGCATCAAAGCGCGTTTT 61.277 50.000 15.55 15.55 37.31 2.43
2779 18289 6.279882 TGTTCAAGGCATTTCTCGAATTTTT 58.720 32.000 0.00 0.00 0.00 1.94
2974 18484 1.602191 AATCGTTGTTTTGATCGCGC 58.398 45.000 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 3551 9.499479 CAAGGCATAGAATTACACTCAGATTAT 57.501 33.333 0.00 0.00 0.00 1.28
286 4957 9.265901 CTTTCCGAATTACACTCATCAGATTAT 57.734 33.333 0.00 0.00 0.00 1.28
307 4978 7.826690 TCTTTGGTAGTTGAATTATGCTTTCC 58.173 34.615 0.00 0.00 0.00 3.13
308 4979 7.970614 CCTCTTTGGTAGTTGAATTATGCTTTC 59.029 37.037 0.00 0.00 0.00 2.62
355 5026 0.901580 ATTGCAAGCCCAACTCCCTG 60.902 55.000 4.94 0.00 0.00 4.45
573 5747 1.098050 GCCTGGCCAACTTATGTCTG 58.902 55.000 7.01 0.00 0.00 3.51
702 6415 5.487488 ACATTCTTCCAGGGATTAGTGTACA 59.513 40.000 0.00 0.00 0.00 2.90
706 6423 5.102953 TGACATTCTTCCAGGGATTAGTG 57.897 43.478 0.00 0.00 0.00 2.74
808 8364 7.120579 TGAGAATGATTGTGGTGTTAACATACC 59.879 37.037 12.26 9.85 37.48 2.73
809 8365 8.039603 TGAGAATGATTGTGGTGTTAACATAC 57.960 34.615 12.26 14.10 0.00 2.39
810 8366 8.806429 ATGAGAATGATTGTGGTGTTAACATA 57.194 30.769 12.26 1.36 0.00 2.29
811 8367 7.707624 ATGAGAATGATTGTGGTGTTAACAT 57.292 32.000 12.26 0.00 0.00 2.71
812 8368 7.448161 AGAATGAGAATGATTGTGGTGTTAACA 59.552 33.333 3.59 3.59 0.00 2.41
821 8378 6.766467 TGATGGAGAGAATGAGAATGATTGTG 59.234 38.462 0.00 0.00 0.00 3.33
1382 8998 1.240641 TTGCATTGCGTACCAGGTGG 61.241 55.000 0.76 0.00 42.17 4.61
2529 10203 1.441732 AAACCGAGGAAAAACGCGCT 61.442 50.000 5.73 0.00 0.00 5.92
2531 10205 1.830086 AAAAACCGAGGAAAAACGCG 58.170 45.000 3.53 3.53 0.00 6.01
2889 18399 7.453393 AGACATCACAGAAACAAGGAGAAATA 58.547 34.615 0.00 0.00 0.00 1.40
2890 18400 6.302269 AGACATCACAGAAACAAGGAGAAAT 58.698 36.000 0.00 0.00 0.00 2.17
2974 18484 6.951062 AGAAGAAGAAAGGAAAAACTCTGG 57.049 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.