Multiple sequence alignment - TraesCS2A01G289000

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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 TraesCS2A01G289000 chr2A 100.000 2735 0 0 1 2735 497435423 497438157 0.000000e+00 5051.0
1 TraesCS2A01G289000 chr2A 84.856 1664 135 49 1 1624 155628463 155626877 0.000000e+00 1568.0
2 TraesCS2A01G289000 chr2A 88.330 497 40 11 1 482 524832243 524832736 5.080000e-162 580.0
3 TraesCS2A01G289000 chr2A 91.034 435 31 7 1 429 610160983 610160551 5.080000e-162 580.0
4 TraesCS2A01G289000 chr5D 92.230 2780 159 22 1 2735 17807213 17809980 0.000000e+00 3884.0
5 TraesCS2A01G289000 chr5D 92.569 471 33 2 1 470 223990781 223991250 0.000000e+00 675.0
6 TraesCS2A01G289000 chr5D 89.520 458 41 6 1 457 540870330 540869879 8.500000e-160 573.0
7 TraesCS2A01G289000 chr1B 94.120 2075 100 10 677 2735 29816021 29813953 0.000000e+00 3136.0
8 TraesCS2A01G289000 chr1B 95.011 441 22 0 2295 2735 242727109 242727549 0.000000e+00 693.0
9 TraesCS2A01G289000 chr1B 85.426 446 42 16 1 443 643126631 643126206 2.500000e-120 442.0
10 TraesCS2A01G289000 chr1B 87.395 119 11 2 436 550 29816131 29816013 1.710000e-27 134.0
11 TraesCS2A01G289000 chr3D 93.779 1945 82 16 799 2735 53984284 53986197 0.000000e+00 2885.0
12 TraesCS2A01G289000 chr5B 90.586 2220 132 28 1 2164 615378892 615376694 0.000000e+00 2870.0
13 TraesCS2A01G289000 chr5B 92.575 633 27 2 2106 2735 615376699 615376084 0.000000e+00 891.0
14 TraesCS2A01G289000 chr5B 84.524 84 7 4 626 703 316613120 316613203 8.120000e-11 78.7
15 TraesCS2A01G289000 chr5B 82.051 78 8 4 582 657 247244087 247244014 8.180000e-06 62.1
16 TraesCS2A01G289000 chr7B 89.986 2197 139 34 1 2164 149635686 149633538 0.000000e+00 2763.0
17 TraesCS2A01G289000 chr7B 92.540 630 30 1 2106 2735 149633543 149632931 0.000000e+00 887.0
18 TraesCS2A01G289000 chr7B 88.249 434 50 1 37 470 567025363 567024931 4.040000e-143 518.0
19 TraesCS2A01G289000 chr4B 89.455 2219 152 29 1 2164 655814487 655816678 0.000000e+00 2726.0
20 TraesCS2A01G289000 chr4B 88.632 475 41 6 1 470 577158413 577158879 1.420000e-157 566.0
21 TraesCS2A01G289000 chr4B 86.170 94 6 5 626 716 577159083 577159172 8.060000e-16 95.3
22 TraesCS2A01G289000 chr4D 92.055 1951 115 15 799 2735 370058198 370056274 0.000000e+00 2708.0
23 TraesCS2A01G289000 chr4D 92.313 1379 82 17 958 2317 506698887 506700260 0.000000e+00 1938.0
24 TraesCS2A01G289000 chr4D 88.428 458 41 6 1 455 506697862 506698310 2.400000e-150 542.0
25 TraesCS2A01G289000 chr3A 91.375 1797 101 28 958 2735 455722966 455721205 0.000000e+00 2410.0
26 TraesCS2A01G289000 chr2B 90.591 1828 115 19 962 2735 644602519 644600695 0.000000e+00 2370.0
27 TraesCS2A01G289000 chr2B 85.106 94 7 5 626 716 545002706 545002617 3.750000e-14 89.8
28 TraesCS2A01G289000 chr1A 93.893 1572 64 11 1166 2735 95534528 95532987 0.000000e+00 2342.0
29 TraesCS2A01G289000 chr6D 94.016 1270 61 11 1061 2317 15592421 15591154 0.000000e+00 1910.0
30 TraesCS2A01G289000 chr6B 87.537 1685 140 29 1 1665 62826373 62824739 0.000000e+00 1884.0
31 TraesCS2A01G289000 chr6B 94.805 77 3 1 680 756 633630501 633630426 4.780000e-23 119.0
32 TraesCS2A01G289000 chr6B 84.615 78 10 2 582 657 633630675 633630598 2.920000e-10 76.8
33 TraesCS2A01G289000 chrUn 85.640 766 52 23 544 1258 101572728 101573486 0.000000e+00 752.0
34 TraesCS2A01G289000 chrUn 90.769 455 25 8 1 438 101503506 101503960 2.350000e-165 592.0
35 TraesCS2A01G289000 chrUn 89.831 118 10 1 436 551 101541117 101541234 1.700000e-32 150.0
36 TraesCS2A01G289000 chr4A 93.905 443 22 3 2296 2735 741252022 741251582 0.000000e+00 664.0


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 TraesCS2A01G289000 chr2A 497435423 497438157 2734 False 5051.00 5051 100.0000 1 2735 1 chr2A.!!$F1 2734
1 TraesCS2A01G289000 chr2A 155626877 155628463 1586 True 1568.00 1568 84.8560 1 1624 1 chr2A.!!$R1 1623
2 TraesCS2A01G289000 chr5D 17807213 17809980 2767 False 3884.00 3884 92.2300 1 2735 1 chr5D.!!$F1 2734
3 TraesCS2A01G289000 chr1B 29813953 29816131 2178 True 1635.00 3136 90.7575 436 2735 2 chr1B.!!$R2 2299
4 TraesCS2A01G289000 chr3D 53984284 53986197 1913 False 2885.00 2885 93.7790 799 2735 1 chr3D.!!$F1 1936
5 TraesCS2A01G289000 chr5B 615376084 615378892 2808 True 1880.50 2870 91.5805 1 2735 2 chr5B.!!$R2 2734
6 TraesCS2A01G289000 chr7B 149632931 149635686 2755 True 1825.00 2763 91.2630 1 2735 2 chr7B.!!$R2 2734
7 TraesCS2A01G289000 chr4B 655814487 655816678 2191 False 2726.00 2726 89.4550 1 2164 1 chr4B.!!$F1 2163
8 TraesCS2A01G289000 chr4B 577158413 577159172 759 False 330.65 566 87.4010 1 716 2 chr4B.!!$F2 715
9 TraesCS2A01G289000 chr4D 370056274 370058198 1924 True 2708.00 2708 92.0550 799 2735 1 chr4D.!!$R1 1936
10 TraesCS2A01G289000 chr4D 506697862 506700260 2398 False 1240.00 1938 90.3705 1 2317 2 chr4D.!!$F1 2316
11 TraesCS2A01G289000 chr3A 455721205 455722966 1761 True 2410.00 2410 91.3750 958 2735 1 chr3A.!!$R1 1777
12 TraesCS2A01G289000 chr2B 644600695 644602519 1824 True 2370.00 2370 90.5910 962 2735 1 chr2B.!!$R2 1773
13 TraesCS2A01G289000 chr1A 95532987 95534528 1541 True 2342.00 2342 93.8930 1166 2735 1 chr1A.!!$R1 1569
14 TraesCS2A01G289000 chr6D 15591154 15592421 1267 True 1910.00 1910 94.0160 1061 2317 1 chr6D.!!$R1 1256
15 TraesCS2A01G289000 chr6B 62824739 62826373 1634 True 1884.00 1884 87.5370 1 1665 1 chr6B.!!$R1 1664
16 TraesCS2A01G289000 chrUn 101572728 101573486 758 False 752.00 752 85.6400 544 1258 1 chrUn.!!$F3 714

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
227 229 0.466007 TTGCAGCACAGCCAAAGAGA 60.466 50.0 0.0 0.0 0.0 3.1 F
296 298 2.744494 GCGCCTCCAGAAGATGAAGAAT 60.744 50.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1983 0.962356 CCAGGACACCATGGTTGCTC 60.962 60.000 16.84 9.97 0.00 4.26 R
2065 2950 1.064463 CAGCATCCCCTTAAGCTTCCA 60.064 52.381 0.00 0.00 34.61 3.53 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
93 95 2.606213 TCCAGATGGTGACGCCCA 60.606 61.111 1.74 0.00 39.27 5.36
117 119 1.462238 AGGGAGGGTGACAAGCACT 60.462 57.895 0.00 0.00 46.86 4.40
135 137 2.511600 GCCCCATTGACGTCGAGG 60.512 66.667 11.90 11.21 0.00 4.63
143 145 1.740332 TTGACGTCGAGGTGCTTCCA 61.740 55.000 16.63 3.94 39.02 3.53
153 155 1.280421 AGGTGCTTCCAGATGTTCCTC 59.720 52.381 1.79 0.00 39.02 3.71
167 169 2.143122 GTTCCTCACATCGTCAAGCAA 58.857 47.619 0.00 0.00 0.00 3.91
207 209 1.679139 CCTGGAAGCACAAGTTGACA 58.321 50.000 10.54 0.00 0.00 3.58
227 229 0.466007 TTGCAGCACAGCCAAAGAGA 60.466 50.000 0.00 0.00 0.00 3.10
296 298 2.744494 GCGCCTCCAGAAGATGAAGAAT 60.744 50.000 0.00 0.00 0.00 2.40
297 299 3.493350 GCGCCTCCAGAAGATGAAGAATA 60.493 47.826 0.00 0.00 0.00 1.75
299 301 4.689812 CGCCTCCAGAAGATGAAGAATATG 59.310 45.833 0.00 0.00 0.00 1.78
328 364 3.349927 CCAACATGAAGAAGATGGCAGA 58.650 45.455 0.00 0.00 0.00 4.26
348 384 4.752101 CAGATGCAGTTAGTTAGGTATGCC 59.248 45.833 0.00 0.00 32.77 4.40
461 508 3.568007 TCTGTTGGCAATGTTGAAGTACC 59.432 43.478 1.92 0.00 0.00 3.34
512 660 8.264347 TGATGGAGTGCTATGAACTTATGTTTA 58.736 33.333 0.00 0.00 36.39 2.01
517 665 9.261180 GAGTGCTATGAACTTATGTTTATGCTA 57.739 33.333 8.50 1.74 36.39 3.49
540 688 7.856398 GCTATTGATGATGTTGTCTTCTTGATG 59.144 37.037 0.00 0.00 33.39 3.07
541 689 7.698506 ATTGATGATGTTGTCTTCTTGATGT 57.301 32.000 0.00 0.00 33.39 3.06
542 690 7.514784 TTGATGATGTTGTCTTCTTGATGTT 57.485 32.000 0.00 0.00 33.39 2.71
554 702 6.634436 GTCTTCTTGATGTTGTTGATGTTGTC 59.366 38.462 0.00 0.00 0.00 3.18
579 727 4.588899 TGCTACTGGCTTGTTGATGTTAT 58.411 39.130 0.00 0.00 42.39 1.89
618 766 8.484641 TGTCTTGTTGATCTTATCTGTTGATC 57.515 34.615 0.00 0.00 37.63 2.92
665 847 5.278957 GGCAACAATCCAAAAGAAGAAGCTA 60.279 40.000 0.00 0.00 0.00 3.32
676 858 9.232473 CCAAAAGAAGAAGCTACTAAGGTTATT 57.768 33.333 0.00 0.00 44.82 1.40
818 1081 9.719355 TCAACTTTGTCTTGTTGCTATATAAGA 57.281 29.630 0.00 0.00 42.11 2.10
852 1310 8.511321 CCAAAAGTGTGTTGTTGCTATATAAGA 58.489 33.333 0.00 0.00 0.00 2.10
858 1316 8.808529 GTGTGTTGTTGCTATATAAGACTACAG 58.191 37.037 7.06 0.00 29.39 2.74
1003 1671 5.299279 GCACACCCTATAACTTGCATTATGT 59.701 40.000 3.31 0.00 0.00 2.29
1157 1983 0.326264 CTGTTCCCCTGGTCTCCAAG 59.674 60.000 0.00 0.00 30.80 3.61
1277 2121 6.209986 GGGTTAAACAACAGCTAGGGTTAAAT 59.790 38.462 0.00 0.00 0.00 1.40
1366 2221 1.792757 AAGAATGGACTGGCCTGGCA 61.793 55.000 22.05 3.71 37.63 4.92
1386 2241 3.941483 GCAACAGATCTGCCTAGCTTTAA 59.059 43.478 22.83 0.00 33.51 1.52
1704 2588 4.900635 TGAAGAGGAGACAAAACAAAGC 57.099 40.909 0.00 0.00 0.00 3.51
1725 2609 5.532557 AGCCTAAAAGAAAATGTGTTGAGC 58.467 37.500 0.00 0.00 0.00 4.26
1726 2610 5.068987 AGCCTAAAAGAAAATGTGTTGAGCA 59.931 36.000 0.00 0.00 0.00 4.26
1927 2812 9.467258 CTGACAAATCAGTAACAAACATTCATT 57.533 29.630 0.00 0.00 46.39 2.57
2065 2950 5.417170 AGAGGAGACCAAGGAGAAGATAT 57.583 43.478 0.00 0.00 0.00 1.63
2241 3180 9.877178 TTTGGTTTTCAACTGTAATATGTTGTT 57.123 25.926 0.00 0.00 42.71 2.83
2526 3510 9.719355 TCATAACTACTATGAAACACAACACAT 57.281 29.630 0.00 0.00 42.85 3.21
2544 3528 6.398234 ACACATAAAGCACCATAACAACAA 57.602 33.333 0.00 0.00 0.00 2.83
2593 3577 6.158695 AGGATTTCTCTACCTAATCCAAGCAA 59.841 38.462 13.73 0.00 46.29 3.91
2618 3602 3.961816 GCAACTTGCTGCTTGGTAGCG 62.962 57.143 6.50 0.00 43.95 4.26
2680 3667 3.325753 GCCAGCACCTCTCCCAGT 61.326 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 3.083997 GTCACCCTCCCTGGCGAT 61.084 66.667 0.00 0.00 0.00 4.58
117 119 2.264480 CTCGACGTCAATGGGGCA 59.736 61.111 17.16 0.00 0.00 5.36
135 137 2.079925 GTGAGGAACATCTGGAAGCAC 58.920 52.381 0.00 0.00 0.00 4.40
153 155 1.462283 CACCTCTTGCTTGACGATGTG 59.538 52.381 0.00 0.00 0.00 3.21
167 169 0.838122 CCAAGACCACCTCCACCTCT 60.838 60.000 0.00 0.00 0.00 3.69
207 209 0.601558 CTCTTTGGCTGTGCTGCAAT 59.398 50.000 2.77 0.00 34.04 3.56
227 229 4.410555 ACTGTCACCTTCCTCTTCTTCTTT 59.589 41.667 0.00 0.00 0.00 2.52
328 364 3.386726 TCGGCATACCTAACTAACTGCAT 59.613 43.478 0.00 0.00 0.00 3.96
461 508 8.533965 CATTGACACTTAGTTCAACAACAAATG 58.466 33.333 10.46 3.14 34.60 2.32
512 660 7.555195 TCAAGAAGACAACATCATCAATAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
517 665 7.698506 ACATCAAGAAGACAACATCATCAAT 57.301 32.000 0.00 0.00 0.00 2.57
524 672 6.698008 TCAACAACATCAAGAAGACAACAT 57.302 33.333 0.00 0.00 0.00 2.71
540 688 3.542712 AGCATCGACAACATCAACAAC 57.457 42.857 0.00 0.00 0.00 3.32
541 689 4.152223 CAGTAGCATCGACAACATCAACAA 59.848 41.667 0.00 0.00 0.00 2.83
542 690 3.679502 CAGTAGCATCGACAACATCAACA 59.320 43.478 0.00 0.00 0.00 3.33
579 727 2.158769 ACAAGACAGCACCATCAACAGA 60.159 45.455 0.00 0.00 0.00 3.41
618 766 6.514048 GCCTTATATAGCAACAAGAAAGCAGG 60.514 42.308 0.00 0.00 0.00 4.85
676 858 8.397906 CAGACAAAGTTCAGTTAAGATCAACAA 58.602 33.333 0.00 0.00 0.00 2.83
773 959 5.527582 AGTTGAACTACTCAATGTTGACCAC 59.472 40.000 0.00 0.00 45.74 4.16
818 1081 6.329496 CAACAACACACTTTTGGATAGTTGT 58.671 36.000 0.00 0.00 46.82 3.32
852 1310 7.562135 TCAGTTAACTTCTTTTGGACTGTAGT 58.438 34.615 5.07 0.00 35.68 2.73
858 1316 9.366216 ACAAAATTCAGTTAACTTCTTTTGGAC 57.634 29.630 28.76 0.26 36.77 4.02
1157 1983 0.962356 CCAGGACACCATGGTTGCTC 60.962 60.000 16.84 9.97 0.00 4.26
1366 2221 6.094603 CACATTTAAAGCTAGGCAGATCTGTT 59.905 38.462 23.38 14.52 0.00 3.16
1386 2241 4.082408 CACACAAAGATCCATGCTCACATT 60.082 41.667 0.00 0.00 32.87 2.71
1725 2609 7.767659 TCCATGATCTTCAAGTTCTATTCAGTG 59.232 37.037 0.00 0.00 0.00 3.66
1726 2610 7.855375 TCCATGATCTTCAAGTTCTATTCAGT 58.145 34.615 0.00 0.00 0.00 3.41
1927 2812 2.972713 CTGCCTTAGCCCTGAATACCTA 59.027 50.000 0.00 0.00 38.69 3.08
2065 2950 1.064463 CAGCATCCCCTTAAGCTTCCA 60.064 52.381 0.00 0.00 34.61 3.53
2254 3193 5.093457 GCAACACATCATGTCTCAATTCAG 58.907 41.667 0.00 0.00 42.31 3.02
2305 3246 7.441157 TCTTGGAATGTCGAATATGTACCAATC 59.559 37.037 0.00 0.00 35.00 2.67
2526 3510 5.536538 TGATGGTTGTTGTTATGGTGCTTTA 59.463 36.000 0.00 0.00 0.00 1.85
2544 3528 0.322277 CTGCTGAAGCTGGTGATGGT 60.322 55.000 3.61 0.00 42.66 3.55
2680 3667 1.202734 GCATAGCTGGAAGAGGCATGA 60.203 52.381 0.00 0.00 34.07 3.07


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

AutoCloner maintained by Alex Coulton.