Multiple sequence alignment - TraesCS2A01G173900

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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 TraesCS2A01G173900 chr2A 100.000 2370 0 0 1 2370 131919830 131917461 0.000000e+00 4377
1 TraesCS2A01G173900 chr2A 94.093 237 13 1 1713 1948 374157204 374157440 2.240000e-95 359
2 TraesCS2A01G173900 chr2A 93.780 209 9 4 1368 1573 399661727 399661520 6.360000e-81 311
3 TraesCS2A01G173900 chr2A 81.538 390 36 18 20 375 397621182 397621569 2.980000e-74 289
4 TraesCS2A01G173900 chr4D 95.424 2382 89 8 1 2370 37445130 37442757 0.000000e+00 3777
5 TraesCS2A01G173900 chr4D 84.072 609 88 8 769 1372 484588979 484588375 1.580000e-161 579
6 TraesCS2A01G173900 chr4D 83.077 390 31 15 20 375 332637748 332637360 2.940000e-84 322
7 TraesCS2A01G173900 chr6A 91.099 1966 143 16 1 1948 327889981 327891932 0.000000e+00 2632
8 TraesCS2A01G173900 chr6A 95.187 374 13 3 1997 2370 327892117 327892485 9.440000e-164 586
9 TraesCS2A01G173900 chr5A 90.789 1965 152 11 1 1948 492065055 492063103 0.000000e+00 2599
10 TraesCS2A01G173900 chr5A 88.310 787 70 11 1 771 384457699 384458479 0.000000e+00 924
11 TraesCS2A01G173900 chr5A 93.583 374 18 4 1997 2366 492062918 492062547 9.570000e-154 553
12 TraesCS2A01G173900 chr5A 91.603 131 11 0 1570 1700 384460712 384460842 5.200000e-42 182
13 TraesCS2A01G173900 chr7A 92.568 1682 108 8 269 1948 384488132 384489798 0.000000e+00 2398
14 TraesCS2A01G173900 chr7A 96.257 374 10 2 1997 2370 384489982 384490351 5.600000e-171 610
15 TraesCS2A01G173900 chr7A 95.021 241 10 2 1710 1948 84493765 84493525 6.180000e-101 377
16 TraesCS2A01G173900 chr7A 85.507 276 35 2 1 275 384487928 384488199 1.390000e-72 283
17 TraesCS2A01G173900 chr5B 92.258 1692 113 8 28 1707 414451345 414449660 0.000000e+00 2383
18 TraesCS2A01G173900 chr5B 81.538 390 36 16 20 375 159191826 159191439 2.980000e-74 289
19 TraesCS2A01G173900 chr6B 91.967 1718 109 14 1 1707 257285468 257287167 0.000000e+00 2381
20 TraesCS2A01G173900 chr6B 95.000 240 11 1 1710 1948 129867376 129867615 2.220000e-100 375
21 TraesCS2A01G173900 chr6B 86.939 245 21 5 131 365 269785634 269785877 5.020000e-67 265
22 TraesCS2A01G173900 chr1D 93.511 786 37 4 1 778 361460988 361461767 0.000000e+00 1157
23 TraesCS2A01G173900 chr1D 97.037 405 8 4 1968 2370 361472229 361472631 0.000000e+00 678
24 TraesCS2A01G173900 chr6D 87.467 766 61 11 15 756 248003131 248003885 0.000000e+00 850
25 TraesCS2A01G173900 chr6D 92.481 133 9 1 1570 1702 248006235 248006366 3.110000e-44 189
26 TraesCS2A01G173900 chr2B 92.012 338 19 6 1368 1701 145535605 145535938 3.570000e-128 468
27 TraesCS2A01G173900 chr2B 93.396 212 9 5 1368 1575 392819735 392819525 2.290000e-80 309
28 TraesCS2A01G173900 chr2D 94.681 282 13 2 2089 2370 298539806 298539527 1.010000e-118 436
29 TraesCS2A01G173900 chr2D 95.455 88 0 3 2026 2111 298541360 298541275 1.140000e-28 137
30 TraesCS2A01G173900 chr3B 91.857 307 20 3 775 1079 343253549 343253246 7.830000e-115 424
31 TraesCS2A01G173900 chr3B 94.093 237 13 1 1713 1948 343251951 343251715 2.240000e-95 359
32 TraesCS2A01G173900 chr4A 94.583 240 12 1 1710 1948 585124692 585124453 1.030000e-98 370
33 TraesCS2A01G173900 chr4B 94.167 240 12 2 1710 1948 527927263 527927501 4.810000e-97 364
34 TraesCS2A01G173900 chr4B 81.538 390 37 15 20 376 357424802 357424415 2.980000e-74 289


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 TraesCS2A01G173900 chr2A 131917461 131919830 2369 True 4377.0 4377 100.0000 1 2370 1 chr2A.!!$R1 2369
1 TraesCS2A01G173900 chr4D 37442757 37445130 2373 True 3777.0 3777 95.4240 1 2370 1 chr4D.!!$R1 2369
2 TraesCS2A01G173900 chr4D 484588375 484588979 604 True 579.0 579 84.0720 769 1372 1 chr4D.!!$R3 603
3 TraesCS2A01G173900 chr6A 327889981 327892485 2504 False 1609.0 2632 93.1430 1 2370 2 chr6A.!!$F1 2369
4 TraesCS2A01G173900 chr5A 492062547 492065055 2508 True 1576.0 2599 92.1860 1 2366 2 chr5A.!!$R1 2365
5 TraesCS2A01G173900 chr5A 384457699 384460842 3143 False 553.0 924 89.9565 1 1700 2 chr5A.!!$F1 1699
6 TraesCS2A01G173900 chr7A 384487928 384490351 2423 False 1097.0 2398 91.4440 1 2370 3 chr7A.!!$F1 2369
7 TraesCS2A01G173900 chr5B 414449660 414451345 1685 True 2383.0 2383 92.2580 28 1707 1 chr5B.!!$R2 1679
8 TraesCS2A01G173900 chr6B 257285468 257287167 1699 False 2381.0 2381 91.9670 1 1707 1 chr6B.!!$F2 1706
9 TraesCS2A01G173900 chr1D 361460988 361461767 779 False 1157.0 1157 93.5110 1 778 1 chr1D.!!$F1 777
10 TraesCS2A01G173900 chr6D 248003131 248006366 3235 False 519.5 850 89.9740 15 1702 2 chr6D.!!$F1 1687
11 TraesCS2A01G173900 chr2D 298539527 298541360 1833 True 286.5 436 95.0680 2026 2370 2 chr2D.!!$R1 344
12 TraesCS2A01G173900 chr3B 343251715 343253549 1834 True 391.5 424 92.9750 775 1948 2 chr3B.!!$R1 1173

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
101 112 0.543749 CCCAAGATCCTCGGCTTCTT 59.456 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 6661 0.955919 CGTCCAGGTTCAAAGAGGGC 60.956 60.0 0.0 0.0 0.0 5.19 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
22 23 0.975556 TCCTAGTTGCAGCGATGGGA 60.976 55.000 1.46 0.00 0.00 4.37
26 27 1.375908 GTTGCAGCGATGGGAGACA 60.376 57.895 1.46 0.00 0.00 3.41
69 80 4.858433 CCGGCGGCGACATCGTAA 62.858 66.667 34.49 0.00 42.22 3.18
92 103 3.470888 CGACCCGCCCAAGATCCT 61.471 66.667 0.00 0.00 0.00 3.24
101 112 0.543749 CCCAAGATCCTCGGCTTCTT 59.456 55.000 0.00 0.00 0.00 2.52
106 117 1.902508 AGATCCTCGGCTTCTTGAACA 59.097 47.619 0.00 0.00 0.00 3.18
124 149 1.396996 ACAATTTCATGCTCGTACGCC 59.603 47.619 11.24 4.54 0.00 5.68
125 150 1.014352 AATTTCATGCTCGTACGCCC 58.986 50.000 11.24 4.15 0.00 6.13
126 151 0.814010 ATTTCATGCTCGTACGCCCC 60.814 55.000 11.24 1.45 0.00 5.80
127 152 2.862674 TTTCATGCTCGTACGCCCCC 62.863 60.000 11.24 0.00 0.00 5.40
375 429 3.322466 CTGGCCGTTCCTCACCCT 61.322 66.667 0.00 0.00 35.26 4.34
475 529 1.135489 GGTTCATGTCGTCGTCTGCTA 60.135 52.381 0.00 0.00 0.00 3.49
497 551 7.913297 TGCTACAGTTCACTATTTTGTGTTTTC 59.087 33.333 0.00 0.00 38.90 2.29
704 768 2.307768 CCTCCGCTGTCCATAGTTCTA 58.692 52.381 0.00 0.00 0.00 2.10
742 806 9.733219 GAGTACTTGTTAATGTATGTCTAGGTC 57.267 37.037 0.00 0.00 0.00 3.85
818 882 1.136695 CTGTTGTTCAGCCCAAGCAAA 59.863 47.619 0.00 0.00 43.56 3.68
913 977 4.196193 CCTTTTATGCGGATACTGGACAA 58.804 43.478 0.00 0.00 0.00 3.18
921 985 2.679082 GGATACTGGACAAGGAGCCTA 58.321 52.381 0.00 0.00 42.70 3.93
1024 1090 3.138304 CCGAGACAATGACAGGTTTGAA 58.862 45.455 0.00 0.00 0.00 2.69
1245 1426 1.737793 CCCATGAACTAGCCGTGTTTC 59.262 52.381 0.00 0.00 0.00 2.78
1303 1484 1.972872 CAGGCTCCAGACTGTGTTTT 58.027 50.000 0.70 0.00 45.99 2.43
1423 1606 6.932400 TGAAAGATTTAACAACGAGAAGGCTA 59.068 34.615 0.00 0.00 0.00 3.93
1485 1668 4.162320 TGTCTCTGACCTCTTTCTTGTGTT 59.838 41.667 0.00 0.00 0.00 3.32
1500 1683 2.100197 TGTGTTCCTGTCGCTAGCTAT 58.900 47.619 13.93 0.00 0.00 2.97
1848 6620 9.479549 AATCATACAGAATATTGTCAAAACCCT 57.520 29.630 0.00 0.00 32.56 4.34
1889 6661 9.677567 AAAACAAACTTATGTACTTGCATACAG 57.322 29.630 6.35 0.00 38.43 2.74
1913 6685 0.817634 CTTTGAACCTGGACGGCACA 60.818 55.000 0.00 0.00 35.61 4.57
2303 8706 7.254761 CCATTCCCTTGTTTTAAAAACTTCTGC 60.255 37.037 1.31 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.078918 CTGTCTCCCATCGCTGCAA 60.079 57.895 0.00 0.00 0.00 4.08
69 80 3.000819 TTGGGCGGGTCGATGTCT 61.001 61.111 0.00 0.00 0.00 3.41
79 90 4.918201 GCCGAGGATCTTGGGCGG 62.918 72.222 14.96 7.07 44.47 6.13
92 103 4.797471 CATGAAATTGTTCAAGAAGCCGA 58.203 39.130 0.00 0.00 46.66 5.54
106 117 1.014352 GGGCGTACGAGCATGAAATT 58.986 50.000 21.65 0.00 39.27 1.82
128 153 4.179599 GAGGAGGGGGAGGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
149 190 2.657237 CACTCGCTCGGGAAAGGT 59.343 61.111 0.00 0.00 0.00 3.50
245 291 0.617535 TTCAGAATCGGGAGGCTCCA 60.618 55.000 33.27 15.98 38.64 3.86
384 438 2.028484 GGTGGACAGCGTCGTTGA 59.972 61.111 16.42 0.00 32.65 3.18
475 529 8.184192 CAGAGAAAACACAAAATAGTGAACTGT 58.816 33.333 0.57 0.00 42.05 3.55
497 551 6.748333 TTGCACTTCCATTTATCTTCAGAG 57.252 37.500 0.00 0.00 0.00 3.35
704 768 9.823647 CATTAACAAGTACTCAGAGAATACCAT 57.176 33.333 3.79 0.00 0.00 3.55
742 806 1.020861 TAGCACATCAGCGCACTTGG 61.021 55.000 11.47 0.00 40.15 3.61
913 977 0.475828 AAACACACCCCTAGGCTCCT 60.476 55.000 2.05 0.00 36.11 3.69
921 985 2.021457 CTGAACGAAAAACACACCCCT 58.979 47.619 0.00 0.00 0.00 4.79
1024 1090 2.047465 CACTCGCTTCTGCTGCCT 60.047 61.111 0.00 0.00 36.97 4.75
1201 1382 6.410504 GGCCACCTTATTAGAGTCCCTTTTAT 60.411 42.308 0.00 0.00 0.00 1.40
1213 1394 4.170468 AGTTCATGGGCCACCTTATTAG 57.830 45.455 9.28 0.00 37.76 1.73
1365 1548 6.847421 AGGCAATTCTCAGCTTCTTTTTAT 57.153 33.333 0.00 0.00 0.00 1.40
1366 1549 7.944729 ATAGGCAATTCTCAGCTTCTTTTTA 57.055 32.000 0.00 0.00 0.00 1.52
1423 1606 3.290710 TGAAGGAAGCTTGCTCAAACTT 58.709 40.909 21.63 3.92 0.00 2.66
1485 1668 3.700198 TCGATAGCTAGCGACAGGA 57.300 52.632 28.71 7.84 39.36 3.86
1578 5223 6.980577 TCCCCCTCATAAAAATACAATCAGT 58.019 36.000 0.00 0.00 0.00 3.41
1612 5318 2.483877 TGGCGTGATGAACTGCTAAAAG 59.516 45.455 0.00 0.00 0.00 2.27
1848 6620 8.770438 AAGTTTGTTTTAGTGAGAAAAATGCA 57.230 26.923 0.00 0.00 30.36 3.96
1889 6661 0.955919 CGTCCAGGTTCAAAGAGGGC 60.956 60.000 0.00 0.00 0.00 5.19
1913 6685 3.195610 TCATCGTCCAAGTTGAGCACTAT 59.804 43.478 3.87 0.00 32.94 2.12
2261 8662 9.196139 CAAGGGAATGGTAAAAATATAAGTCCA 57.804 33.333 0.00 0.00 0.00 4.02
2303 8706 4.686554 CGGTAGAAAGTGTGGAGAAGAAAG 59.313 45.833 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.