Multiple sequence alignment - TraesCS6A01G049100

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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 TraesCS6A01G049100 chr6A 100.000 3035 0 0 1 3035 25106445 25109479 0.000000e+00 5605.0
1 TraesCS6A01G049100 chr6A 95.642 2478 62 11 1 2434 25524703 25527178 0.000000e+00 3936.0
2 TraesCS6A01G049100 chr6A 97.253 2257 52 7 1 2250 25313175 25315428 0.000000e+00 3816.0
3 TraesCS6A01G049100 chr6A 97.007 2172 50 6 286 2456 25580359 25582516 0.000000e+00 3637.0
4 TraesCS6A01G049100 chr6A 96.383 2184 64 5 286 2456 25472022 25474203 0.000000e+00 3581.0
5 TraesCS6A01G049100 chr6A 94.395 1891 71 10 275 2139 25069687 25071568 0.000000e+00 2872.0
6 TraesCS6A01G049100 chr6A 97.328 1497 32 3 1 1495 25202392 25203882 0.000000e+00 2536.0
7 TraesCS6A01G049100 chr6A 92.214 1811 103 23 1243 3035 25203705 25205495 0.000000e+00 2529.0
8 TraesCS6A01G049100 chr6A 96.450 1493 32 3 985 2456 25408352 25409844 0.000000e+00 2444.0
9 TraesCS6A01G049100 chr6A 95.869 581 24 0 2455 3035 25212199 25212779 0.000000e+00 941.0
10 TraesCS6A01G049100 chr6A 95.738 305 12 1 1 304 25407483 25407787 9.780000e-135 490.0
11 TraesCS6A01G049100 chr6A 96.512 258 8 1 1 257 25471769 25472026 2.800000e-115 425.0
12 TraesCS6A01G049100 chr6A 96.512 258 8 1 1 257 25580106 25580363 2.800000e-115 425.0
13 TraesCS6A01G049100 chr6A 96.133 181 7 0 2276 2456 25315421 25315601 2.290000e-76 296.0
14 TraesCS6A01G049100 chr6A 86.905 84 8 2 1 83 565053041 565053122 1.160000e-14 91.6
15 TraesCS6A01G049100 chrUn 94.221 1644 91 3 482 2124 94374281 94375921 0.000000e+00 2507.0
16 TraesCS6A01G049100 chrUn 94.221 1644 88 4 482 2124 94456416 94458053 0.000000e+00 2503.0
17 TraesCS6A01G049100 chrUn 92.926 1668 90 8 482 2124 94279963 94281627 0.000000e+00 2401.0
18 TraesCS6A01G049100 chrUn 90.202 1235 95 11 899 2124 94682709 94683926 0.000000e+00 1587.0
19 TraesCS6A01G049100 chr6B 91.500 1247 89 7 482 1727 62653139 62654369 0.000000e+00 1700.0
20 TraesCS6A01G049100 chr6B 88.907 1235 119 7 899 2124 62657570 62658795 0.000000e+00 1506.0
21 TraesCS6A01G049100 chr6B 86.905 84 8 2 1 83 149020819 149020738 1.160000e-14 91.6
22 TraesCS6A01G049100 chr4A 96.082 587 17 1 2455 3035 529271443 529272029 0.000000e+00 952.0
23 TraesCS6A01G049100 chr4A 95.385 585 21 1 2457 3035 529257225 529257809 0.000000e+00 926.0
24 TraesCS6A01G049100 chr7A 96.068 585 17 1 2457 3035 547917853 547917269 0.000000e+00 948.0
25 TraesCS6A01G049100 chr7A 95.214 585 22 1 2457 3035 103525136 103524552 0.000000e+00 920.0
26 TraesCS6A01G049100 chr5A 95.586 589 19 2 2453 3035 198212267 198211680 0.000000e+00 937.0
27 TraesCS6A01G049100 chr5A 95.230 587 22 3 2455 3035 419556390 419555804 0.000000e+00 924.0
28 TraesCS6A01G049100 chr3A 95.377 584 21 1 2458 3035 619344959 619344376 0.000000e+00 924.0
29 TraesCS6A01G049100 chr3A 90.476 84 5 2 1 83 472418347 472418428 1.150000e-19 108.0
30 TraesCS6A01G049100 chr4D 95.816 239 10 0 2139 2377 495450877 495450639 1.320000e-103 387.0
31 TraesCS6A01G049100 chr4D 95.671 231 10 0 2133 2363 495451414 495451184 3.700000e-99 372.0
32 TraesCS6A01G049100 chr4D 89.691 194 19 1 88 280 105123154 105122961 2.340000e-61 246.0
33 TraesCS6A01G049100 chr5B 88.444 225 23 3 2134 2358 658337974 658338195 4.990000e-68 268.0
34 TraesCS6A01G049100 chr2B 87.556 225 25 3 2134 2358 756018165 756018386 1.080000e-64 257.0
35 TraesCS6A01G049100 chr3D 89.000 200 20 2 85 284 441025616 441025813 2.340000e-61 246.0
36 TraesCS6A01G049100 chr3D 80.503 159 20 11 2127 2280 608946218 608946370 8.890000e-21 111.0
37 TraesCS6A01G049100 chr7D 89.286 196 20 1 85 280 497318686 497318880 8.410000e-61 244.0


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 TraesCS6A01G049100 chr6A 25106445 25109479 3034 False 5605.0 5605 100.0000 1 3035 1 chr6A.!!$F2 3034
1 TraesCS6A01G049100 chr6A 25524703 25527178 2475 False 3936.0 3936 95.6420 1 2434 1 chr6A.!!$F4 2433
2 TraesCS6A01G049100 chr6A 25069687 25071568 1881 False 2872.0 2872 94.3950 275 2139 1 chr6A.!!$F1 1864
3 TraesCS6A01G049100 chr6A 25202392 25205495 3103 False 2532.5 2536 94.7710 1 3035 2 chr6A.!!$F6 3034
4 TraesCS6A01G049100 chr6A 25313175 25315601 2426 False 2056.0 3816 96.6930 1 2456 2 chr6A.!!$F7 2455
5 TraesCS6A01G049100 chr6A 25580106 25582516 2410 False 2031.0 3637 96.7595 1 2456 2 chr6A.!!$F10 2455
6 TraesCS6A01G049100 chr6A 25471769 25474203 2434 False 2003.0 3581 96.4475 1 2456 2 chr6A.!!$F9 2455
7 TraesCS6A01G049100 chr6A 25407483 25409844 2361 False 1467.0 2444 96.0940 1 2456 2 chr6A.!!$F8 2455
8 TraesCS6A01G049100 chr6A 25212199 25212779 580 False 941.0 941 95.8690 2455 3035 1 chr6A.!!$F3 580
9 TraesCS6A01G049100 chrUn 94374281 94375921 1640 False 2507.0 2507 94.2210 482 2124 1 chrUn.!!$F2 1642
10 TraesCS6A01G049100 chrUn 94456416 94458053 1637 False 2503.0 2503 94.2210 482 2124 1 chrUn.!!$F3 1642
11 TraesCS6A01G049100 chrUn 94279963 94281627 1664 False 2401.0 2401 92.9260 482 2124 1 chrUn.!!$F1 1642
12 TraesCS6A01G049100 chrUn 94682709 94683926 1217 False 1587.0 1587 90.2020 899 2124 1 chrUn.!!$F4 1225
13 TraesCS6A01G049100 chr6B 62653139 62658795 5656 False 1603.0 1700 90.2035 482 2124 2 chr6B.!!$F1 1642
14 TraesCS6A01G049100 chr4A 529271443 529272029 586 False 952.0 952 96.0820 2455 3035 1 chr4A.!!$F2 580
15 TraesCS6A01G049100 chr4A 529257225 529257809 584 False 926.0 926 95.3850 2457 3035 1 chr4A.!!$F1 578
16 TraesCS6A01G049100 chr7A 547917269 547917853 584 True 948.0 948 96.0680 2457 3035 1 chr7A.!!$R2 578
17 TraesCS6A01G049100 chr7A 103524552 103525136 584 True 920.0 920 95.2140 2457 3035 1 chr7A.!!$R1 578
18 TraesCS6A01G049100 chr5A 198211680 198212267 587 True 937.0 937 95.5860 2453 3035 1 chr5A.!!$R1 582
19 TraesCS6A01G049100 chr5A 419555804 419556390 586 True 924.0 924 95.2300 2455 3035 1 chr5A.!!$R2 580
20 TraesCS6A01G049100 chr3A 619344376 619344959 583 True 924.0 924 95.3770 2458 3035 1 chr3A.!!$R1 577
21 TraesCS6A01G049100 chr4D 495450639 495451414 775 True 379.5 387 95.7435 2133 2377 2 chr4D.!!$R2 244

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
708 750 0.973632 AAGTACCGTGACAGCCATGA 59.026 50.0 0.0 0.0 33.6 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 7254 0.185416 TTACCCCGGCAAGGTTTTCA 59.815 50.0 6.17 0.0 38.89 2.69 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
67 68 4.548346 GCGTACTGAATGTATGAGAAACGC 60.548 45.833 0.00 0.0 39.81 4.84
633 673 3.362706 ACGAGTCATGGCCTACTAAAGA 58.637 45.455 3.32 0.0 0.00 2.52
687 729 9.436957 CTTAATAGACCACACAAGACTACAAAT 57.563 33.333 0.00 0.0 0.00 2.32
708 750 0.973632 AAGTACCGTGACAGCCATGA 59.026 50.000 0.00 0.0 33.60 3.07
1216 1260 4.022589 CACAAAATCCATCTCAGCAACAGT 60.023 41.667 0.00 0.0 0.00 3.55
1422 1471 0.753479 ATCCACAACCGCAACCACAA 60.753 50.000 0.00 0.0 0.00 3.33
1440 1489 4.484236 CACAATATTCGCAACCACAACAT 58.516 39.130 0.00 0.0 0.00 2.71
1497 1636 8.491152 CAACAACAACAACAAGAACAACAAATA 58.509 29.630 0.00 0.0 0.00 1.40
1700 1839 5.809464 TGTTGTTCATGCTATTATTCTGCG 58.191 37.500 0.00 0.0 0.00 5.18
1955 2241 6.601613 CCATTTGGCATCTTTGGTACTAACTA 59.398 38.462 0.00 0.0 0.00 2.24
2129 6351 7.495934 ACACAGGTCTTGTCTACATATTTATGC 59.504 37.037 0.00 0.0 38.16 3.14
2187 6940 4.170468 ACCAGGAGCAAGGTAAATATGG 57.830 45.455 0.00 0.0 36.07 2.74
2329 7082 0.436150 CGTGACACATCTGAACGCAG 59.564 55.000 6.37 0.0 43.67 5.18
2564 7317 2.594592 GTGTGAAGGCTTGCCGGT 60.595 61.111 3.46 0.0 0.00 5.28
2849 7609 4.829492 GGATGGAAAAATGATCTACAGGGG 59.171 45.833 0.00 0.0 0.00 4.79
2919 7679 5.123186 TCAAATCCGAGTTCGTATGCAAAAT 59.877 36.000 0.00 0.0 37.74 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 269 9.793259 TGCCTCTACTTCCCATTTATATAAAAG 57.207 33.333 11.80 7.63 0.00 2.27
655 697 9.427821 AGTCTTGTGTGGTCTATTAAGATAGAT 57.572 33.333 0.01 0.00 44.46 1.98
656 698 8.824756 AGTCTTGTGTGGTCTATTAAGATAGA 57.175 34.615 0.00 0.00 41.46 1.98
666 708 8.426489 ACTTAATTTGTAGTCTTGTGTGGTCTA 58.574 33.333 0.00 0.00 0.00 2.59
687 729 2.563620 TCATGGCTGTCACGGTACTTAA 59.436 45.455 0.00 0.00 0.00 1.85
883 926 6.014413 TGGTGGCACTACTTACAAGTGTATTA 60.014 38.462 18.45 0.00 45.01 0.98
1216 1260 2.886523 CCAATGGAACTTGCTCTTGTGA 59.113 45.455 0.00 0.00 0.00 3.58
1422 1471 3.351740 TGGATGTTGTGGTTGCGAATAT 58.648 40.909 0.00 0.00 0.00 1.28
1440 1489 0.599558 GCTGCTGCTGTGAAATTGGA 59.400 50.000 8.53 0.00 36.03 3.53
1497 1636 6.551385 TGTTGTTGCAAAATTTGTTGAAGT 57.449 29.167 0.00 0.00 0.00 3.01
1700 1839 6.478588 TGTTGTTGTTGTTTTTGTTGTTGAC 58.521 32.000 0.00 0.00 0.00 3.18
2292 7045 1.874345 CGTACAGTCGTTGGAGGCCT 61.874 60.000 3.86 3.86 0.00 5.19
2449 7202 6.370593 CACTTTTAAGCATCAACACACGTAT 58.629 36.000 0.00 0.00 0.00 3.06
2477 7230 2.621526 CTGGCATGCTGCTTTATGATCA 59.378 45.455 18.92 0.00 44.28 2.92
2497 7250 1.530655 CCGGCAAGGTTTTCACCCT 60.531 57.895 0.00 0.00 45.63 4.34
2501 7254 0.185416 TTACCCCGGCAAGGTTTTCA 59.815 50.000 6.17 0.00 38.89 2.69
2564 7317 3.294493 GCCGGCAAGCTTTCCACA 61.294 61.111 24.80 0.00 0.00 4.17
2849 7609 2.028287 TTCGACGAGACGAAGACAAC 57.972 50.000 6.33 0.00 45.21 3.32
2919 7679 2.621338 CTGCACTCCGATTGCTCTAAA 58.379 47.619 11.56 0.00 40.86 1.85
2975 7735 1.337823 GCTACCCGTCAGACATGTGTT 60.338 52.381 1.15 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.