Multiple sequence alignment - TraesCS1A01G339100

Loading Multiple Alignment...

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 TraesCS1A01G339100 chr1A 100.000 2450 0 0 1 2450 529127690 529125241 0.000000e+00 4525.0
1 TraesCS1A01G339100 chr1A 88.474 616 63 5 1 610 529132431 529131818 0.000000e+00 737.0
2 TraesCS1A01G339100 chr1A 87.825 616 67 7 1 610 529165420 529164807 0.000000e+00 715.0
3 TraesCS1A01G339100 chr1A 87.662 616 68 7 1 610 529191968 529191355 0.000000e+00 710.0
4 TraesCS1A01G339100 chr1A 86.992 615 74 5 1 610 529189707 529189094 0.000000e+00 688.0
5 TraesCS1A01G339100 chr1A 85.246 610 75 9 9 610 529195159 529194557 4.480000e-172 614.0
6 TraesCS1A01G339100 chr1A 92.079 101 8 0 1 101 529187440 529187340 2.540000e-30 143.0
7 TraesCS1A01G339100 chr1A 80.460 87 13 4 1316 1400 280603691 280603607 2.030000e-06 63.9
8 TraesCS1A01G339100 chr1B 92.054 2454 127 28 11 2450 582023215 582020816 0.000000e+00 3389.0
9 TraesCS1A01G339100 chr1B 86.379 602 68 8 15 608 582025940 582025345 0.000000e+00 645.0
10 TraesCS1A01G339100 chr1B 82.353 68 10 2 1334 1400 312249237 312249171 9.460000e-05 58.4
11 TraesCS1A01G339100 chr1D 90.459 2484 122 51 9 2450 430862410 430860000 0.000000e+00 3168.0
12 TraesCS1A01G339100 chr1D 87.439 613 65 8 7 610 430865944 430865335 0.000000e+00 695.0
13 TraesCS1A01G339100 chr1D 82.353 68 10 2 1334 1400 218409904 218409838 9.460000e-05 58.4


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 TraesCS1A01G339100 chr1A 529125241 529127690 2449 True 4525.00 4525 100.00000 1 2450 1 chr1A.!!$R2 2449
1 TraesCS1A01G339100 chr1A 529131818 529132431 613 True 737.00 737 88.47400 1 610 1 chr1A.!!$R3 609
2 TraesCS1A01G339100 chr1A 529164807 529165420 613 True 715.00 715 87.82500 1 610 1 chr1A.!!$R4 609
3 TraesCS1A01G339100 chr1A 529187340 529195159 7819 True 538.75 710 87.99475 1 610 4 chr1A.!!$R5 609
4 TraesCS1A01G339100 chr1B 582020816 582025940 5124 True 2017.00 3389 89.21650 11 2450 2 chr1B.!!$R2 2439
5 TraesCS1A01G339100 chr1D 430860000 430865944 5944 True 1931.50 3168 88.94900 7 2450 2 chr1D.!!$R2 2443

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
677 10124 0.588252 CTCGCAGTGGGTTTCAAGTG 59.412 55.0 7.12 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 12691 0.53065 CGCATATGGACGAACAGCCT 60.531 55.0 4.56 0.0 0.0 4.58 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
29 3221 1.429463 CAGTCGGCTAGCGTTTTCTT 58.571 50.000 9.00 0.00 0.00 2.52
257 5718 0.740868 TGCATGCAGACCTCGTAAGC 60.741 55.000 18.46 0.00 37.18 3.09
258 5719 0.740868 GCATGCAGACCTCGTAAGCA 60.741 55.000 14.21 0.00 39.79 3.91
267 5728 3.195610 AGACCTCGTAAGCAACATCATGA 59.804 43.478 0.00 0.00 37.18 3.07
271 5732 1.004610 CGTAAGCAACATCATGAGGCG 60.005 52.381 7.40 0.00 0.00 5.52
277 5738 0.679002 AACATCATGAGGCGCTTGCT 60.679 50.000 7.64 0.00 39.13 3.91
294 5755 2.285083 TGCTCGCAACGGCTTATAAAT 58.715 42.857 0.00 0.00 38.10 1.40
302 5763 4.480541 CAACGGCTTATAAATTGTGCACA 58.519 39.130 17.42 17.42 0.00 4.57
303 5764 4.981806 ACGGCTTATAAATTGTGCACAT 57.018 36.364 22.39 8.69 0.00 3.21
305 5766 4.202010 ACGGCTTATAAATTGTGCACATCC 60.202 41.667 22.39 9.40 0.00 3.51
306 5767 4.202000 CGGCTTATAAATTGTGCACATCCA 60.202 41.667 22.39 6.21 0.00 3.41
322 5783 3.515104 ACATCCAAAACAAGGCAATAGGG 59.485 43.478 0.00 0.00 0.00 3.53
334 5795 4.273318 AGGCAATAGGGAAAATGAGACAC 58.727 43.478 0.00 0.00 0.00 3.67
335 5796 4.016444 GGCAATAGGGAAAATGAGACACA 58.984 43.478 0.00 0.00 0.00 3.72
357 5818 4.525912 ACAATTGAAGCAATTCAGGACC 57.474 40.909 13.59 0.00 41.40 4.46
376 5837 1.440476 GGGATAAGTGGTCGACCGG 59.560 63.158 28.70 0.00 39.43 5.28
379 5840 1.673808 GATAAGTGGTCGACCGGCCT 61.674 60.000 28.70 20.59 41.25 5.19
393 5854 0.804364 CGGCCTTTTAAACCCGTACC 59.196 55.000 0.00 0.00 36.18 3.34
411 5872 1.202533 ACCGAGGGAGTAATGCATTCG 60.203 52.381 16.86 11.40 0.00 3.34
412 5873 1.502231 CGAGGGAGTAATGCATTCGG 58.498 55.000 16.86 0.00 0.00 4.30
434 5895 1.541588 GTTTCATGTGGGCTCACTTCC 59.458 52.381 19.48 0.00 43.94 3.46
446 5907 4.339530 GGGCTCACTTCCCTCATTTTTATC 59.660 45.833 0.00 0.00 40.66 1.75
501 5962 4.828387 AGCCCCTTATCGAACTAACTCTAG 59.172 45.833 0.00 0.00 0.00 2.43
508 5969 7.014038 CCTTATCGAACTAACTCTAGGCCTTAA 59.986 40.741 12.58 0.00 0.00 1.85
520 5981 1.821136 AGGCCTTAAGTTGCTTGATGC 59.179 47.619 0.00 0.00 43.25 3.91
530 5991 3.316308 AGTTGCTTGATGCGAAAAAGACT 59.684 39.130 0.00 0.00 46.63 3.24
538 5999 6.712241 TGATGCGAAAAAGACTCTAGAAAG 57.288 37.500 0.00 0.00 0.00 2.62
545 6006 8.536407 GCGAAAAAGACTCTAGAAAGATCATAC 58.464 37.037 0.00 0.00 0.00 2.39
546 6007 9.026074 CGAAAAAGACTCTAGAAAGATCATACC 57.974 37.037 0.00 0.00 0.00 2.73
547 6008 9.320352 GAAAAAGACTCTAGAAAGATCATACCC 57.680 37.037 0.00 0.00 0.00 3.69
549 6010 4.521256 AGACTCTAGAAAGATCATACCCGC 59.479 45.833 0.00 0.00 0.00 6.13
550 6011 4.215908 ACTCTAGAAAGATCATACCCGCA 58.784 43.478 0.00 0.00 0.00 5.69
551 6012 4.649674 ACTCTAGAAAGATCATACCCGCAA 59.350 41.667 0.00 0.00 0.00 4.85
553 6014 5.601662 TCTAGAAAGATCATACCCGCAAAG 58.398 41.667 0.00 0.00 0.00 2.77
557 6022 5.355350 AGAAAGATCATACCCGCAAAGAAAG 59.645 40.000 0.00 0.00 0.00 2.62
561 6026 4.280436 TCATACCCGCAAAGAAAGAAGA 57.720 40.909 0.00 0.00 0.00 2.87
660 10107 3.019564 ACTATTGGCCATGAAACAGCTC 58.980 45.455 6.09 0.00 0.00 4.09
670 10117 1.152963 AAACAGCTCGCAGTGGGTT 60.153 52.632 7.12 0.00 0.00 4.11
677 10124 0.588252 CTCGCAGTGGGTTTCAAGTG 59.412 55.000 7.12 0.00 0.00 3.16
718 10165 1.489230 CTTAACCCCCACCGCTAAGAT 59.511 52.381 0.00 0.00 0.00 2.40
989 10436 4.609247 GTCGATCGTCTCCGGCGG 62.609 72.222 22.51 22.51 34.59 6.13
991 10438 3.274586 CGATCGTCTCCGGCGGTA 61.275 66.667 27.32 12.96 33.95 4.02
1076 10523 0.109342 CCTGTCCAAGTGCAAGACCT 59.891 55.000 0.00 0.00 0.00 3.85
1077 10524 1.477558 CCTGTCCAAGTGCAAGACCTT 60.478 52.381 0.00 0.00 0.00 3.50
1408 11502 3.839432 CCGGCTTCCTCGAGACCC 61.839 72.222 15.71 7.24 0.00 4.46
1438 11538 0.249073 GATCCATCGAGTCACCACCG 60.249 60.000 0.00 0.00 0.00 4.94
1439 11539 0.970937 ATCCATCGAGTCACCACCGT 60.971 55.000 0.00 0.00 0.00 4.83
1522 11623 2.103094 TCCGAGTCCATTCCATGCTTAG 59.897 50.000 0.00 0.00 0.00 2.18
1542 11645 7.922811 TGCTTAGTTATGATATGAGTGTCAGTG 59.077 37.037 0.00 0.00 0.00 3.66
1648 12063 9.667107 AAACTCCAATCGATTCTAGATGTTTTA 57.333 29.630 18.58 0.00 0.00 1.52
1886 12301 0.896226 GCTCGGGTTTGGACTCTAGT 59.104 55.000 0.00 0.00 0.00 2.57
1887 12302 2.097825 GCTCGGGTTTGGACTCTAGTA 58.902 52.381 0.00 0.00 0.00 1.82
1888 12303 2.099427 GCTCGGGTTTGGACTCTAGTAG 59.901 54.545 0.00 0.00 0.00 2.57
1889 12304 2.097825 TCGGGTTTGGACTCTAGTAGC 58.902 52.381 0.00 0.00 0.00 3.58
1890 12305 1.822990 CGGGTTTGGACTCTAGTAGCA 59.177 52.381 0.00 0.00 0.00 3.49
1891 12306 2.159226 CGGGTTTGGACTCTAGTAGCAG 60.159 54.545 0.00 0.00 0.00 4.24
1892 12307 2.418884 GGGTTTGGACTCTAGTAGCAGC 60.419 54.545 0.00 0.00 0.00 5.25
1893 12308 2.498078 GGTTTGGACTCTAGTAGCAGCT 59.502 50.000 0.00 0.00 0.00 4.24
1894 12309 3.516615 GTTTGGACTCTAGTAGCAGCTG 58.483 50.000 10.11 10.11 0.00 4.24
1895 12310 1.107114 TGGACTCTAGTAGCAGCTGC 58.893 55.000 31.53 31.53 42.49 5.25
1913 12329 2.687200 TACCTGCCAGCCACCGAT 60.687 61.111 0.00 0.00 0.00 4.18
1935 12351 6.687105 CGATTTCTTTTCTGAAAGTTCGTTGT 59.313 34.615 2.75 0.00 42.32 3.32
1936 12352 7.304849 CGATTTCTTTTCTGAAAGTTCGTTGTG 60.305 37.037 2.75 0.00 42.32 3.33
1938 12354 2.730183 TTCTGAAAGTTCGTTGTGCG 57.270 45.000 0.00 0.00 37.27 5.34
2247 12666 2.223876 TGCTGGGACGACGGATTATTAC 60.224 50.000 0.00 0.00 0.00 1.89
2265 12684 2.730626 CGCTGTTCGTCCTCTTCTG 58.269 57.895 0.00 0.00 0.00 3.02
2266 12685 0.241213 CGCTGTTCGTCCTCTTCTGA 59.759 55.000 0.00 0.00 0.00 3.27
2267 12686 1.335964 CGCTGTTCGTCCTCTTCTGAA 60.336 52.381 0.00 0.00 0.00 3.02
2268 12687 2.755650 GCTGTTCGTCCTCTTCTGAAA 58.244 47.619 0.00 0.00 0.00 2.69
2269 12688 3.131396 GCTGTTCGTCCTCTTCTGAAAA 58.869 45.455 0.00 0.00 0.00 2.29
2270 12689 3.560068 GCTGTTCGTCCTCTTCTGAAAAA 59.440 43.478 0.00 0.00 0.00 1.94
2289 12708 4.701956 AAAAAGGCTGTTCGTCCATATG 57.298 40.909 0.00 0.00 0.00 1.78
2290 12709 1.668419 AAGGCTGTTCGTCCATATGC 58.332 50.000 0.00 0.00 0.00 3.14
2291 12710 0.530650 AGGCTGTTCGTCCATATGCG 60.531 55.000 0.00 0.00 0.00 4.73
2312 12731 1.896660 TCGCACTCCAAAGGCCAAC 60.897 57.895 5.01 0.00 0.00 3.77
2416 12841 1.217882 CTCAACGGTGTGTGGAGTTC 58.782 55.000 0.00 0.00 42.80 3.01
2430 12855 0.530870 GAGTTCGCTAGGTGATGCCC 60.531 60.000 0.00 0.00 38.26 5.36
2441 12866 0.811616 GTGATGCCCGTCATGTCTCC 60.812 60.000 0.00 0.00 35.05 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 3199 2.725203 AAAACGCTAGCCGACTGCCA 62.725 55.000 9.66 0.00 42.71 4.92
106 3305 6.823689 AGTTGTCTTGTTTTGAAGCTAAGAGA 59.176 34.615 0.00 0.00 0.00 3.10
257 5718 0.524816 GCAAGCGCCTCATGATGTTG 60.525 55.000 2.29 0.00 0.00 3.33
258 5719 0.679002 AGCAAGCGCCTCATGATGTT 60.679 50.000 2.29 0.00 39.83 2.71
271 5732 1.982073 ATAAGCCGTTGCGAGCAAGC 61.982 55.000 11.09 11.79 44.33 4.01
277 5738 3.729462 GCACAATTTATAAGCCGTTGCGA 60.729 43.478 0.00 0.00 44.33 5.10
294 5755 2.741228 GCCTTGTTTTGGATGTGCACAA 60.741 45.455 25.72 4.24 0.00 3.33
302 5763 4.059773 TCCCTATTGCCTTGTTTTGGAT 57.940 40.909 0.00 0.00 0.00 3.41
303 5764 3.534357 TCCCTATTGCCTTGTTTTGGA 57.466 42.857 0.00 0.00 0.00 3.53
305 5766 6.229733 TCATTTTCCCTATTGCCTTGTTTTG 58.770 36.000 0.00 0.00 0.00 2.44
306 5767 6.269769 TCTCATTTTCCCTATTGCCTTGTTTT 59.730 34.615 0.00 0.00 0.00 2.43
322 5783 6.476380 TGCTTCAATTGTTGTGTCTCATTTTC 59.524 34.615 5.13 0.00 0.00 2.29
334 5795 4.687483 GGTCCTGAATTGCTTCAATTGTTG 59.313 41.667 9.24 0.89 43.05 3.33
335 5796 4.559300 CGGTCCTGAATTGCTTCAATTGTT 60.559 41.667 9.24 0.00 43.05 2.83
357 5818 1.065273 CGGTCGACCACTTATCCCG 59.935 63.158 32.80 12.98 35.14 5.14
393 5854 1.068588 TCCGAATGCATTACTCCCTCG 59.931 52.381 12.97 9.78 0.00 4.63
411 5872 1.168714 GTGAGCCCACATGAAACTCC 58.831 55.000 0.00 0.00 42.72 3.85
412 5873 2.191128 AGTGAGCCCACATGAAACTC 57.809 50.000 0.00 1.26 45.54 3.01
446 5907 7.116948 CCCGCTTAACTATATGAAGTGAAGATG 59.883 40.741 6.86 0.12 39.47 2.90
489 5950 5.581479 GCAACTTAAGGCCTAGAGTTAGTTC 59.419 44.000 25.11 14.81 31.58 3.01
501 5962 1.468054 CGCATCAAGCAACTTAAGGCC 60.468 52.381 7.53 0.00 46.13 5.19
508 5969 3.316308 AGTCTTTTTCGCATCAAGCAACT 59.684 39.130 0.00 0.00 46.13 3.16
520 5981 9.026074 GGTATGATCTTTCTAGAGTCTTTTTCG 57.974 37.037 0.00 0.00 32.92 3.46
530 5991 5.362717 TCTTTGCGGGTATGATCTTTCTAGA 59.637 40.000 0.00 0.00 34.21 2.43
538 5999 4.876107 TCTTCTTTCTTTGCGGGTATGATC 59.124 41.667 0.00 0.00 0.00 2.92
545 6006 9.273016 TCTTATATAATCTTCTTTCTTTGCGGG 57.727 33.333 0.00 0.00 0.00 6.13
561 6026 9.838339 CTCACCCACTCTTTTGTCTTATATAAT 57.162 33.333 0.00 0.00 0.00 1.28
660 10107 1.654220 CCACTTGAAACCCACTGCG 59.346 57.895 0.00 0.00 0.00 5.18
718 10165 2.190841 TGCGCGAGGATCCGATGTA 61.191 57.895 12.10 0.00 31.82 2.29
754 10201 3.842925 ATGGTTCGGTTGGTGCGCT 62.843 57.895 9.73 0.00 0.00 5.92
822 10269 2.092882 GCACACTCGCGAGTAACCC 61.093 63.158 38.75 23.24 40.20 4.11
989 10436 4.256180 CCTCCATGGCCGCCCTAC 62.256 72.222 6.96 0.00 0.00 3.18
990 10437 4.490606 TCCTCCATGGCCGCCCTA 62.491 66.667 6.96 0.00 35.26 3.53
1042 10489 0.040603 ACAGGTTCTTCGTCGTCGTC 60.041 55.000 1.33 0.00 38.33 4.20
1047 10494 1.269621 ACTTGGACAGGTTCTTCGTCG 60.270 52.381 0.00 0.00 0.00 5.12
1076 10523 3.351416 CACGCTGCTGCTGCTGAA 61.351 61.111 25.43 0.00 40.01 3.02
1077 10524 4.614112 ACACGCTGCTGCTGCTGA 62.614 61.111 25.43 1.16 40.01 4.26
1189 10636 4.847198 CCATAATCCATCATCATCGGGAA 58.153 43.478 0.00 0.00 32.25 3.97
1190 10637 3.370846 GCCATAATCCATCATCATCGGGA 60.371 47.826 0.00 0.00 0.00 5.14
1408 11502 3.559657 GATGGATCGACGGCCCTCG 62.560 68.421 16.94 16.94 45.88 4.63
1436 11536 2.296692 CTGAAATCAAGCGCGGACGG 62.297 60.000 8.83 0.00 40.57 4.79
1438 11538 1.226128 GCTGAAATCAAGCGCGGAC 60.226 57.895 8.83 0.00 0.00 4.79
1439 11539 1.026182 ATGCTGAAATCAAGCGCGGA 61.026 50.000 8.83 4.15 0.00 5.54
1522 11623 8.768955 GGAATTCACTGACACTCATATCATAAC 58.231 37.037 7.93 0.00 0.00 1.89
1542 11645 5.048013 ACTCCATTTTGTTTCTCGGGAATTC 60.048 40.000 0.00 0.00 0.00 2.17
1895 12310 2.257409 AATCGGTGGCTGGCAGGTAG 62.257 60.000 17.64 0.00 0.00 3.18
1896 12311 1.847798 AAATCGGTGGCTGGCAGGTA 61.848 55.000 17.64 0.00 0.00 3.08
1913 12329 5.571357 GCACAACGAACTTTCAGAAAAGAAA 59.429 36.000 4.99 0.00 43.90 2.52
2007 12426 0.645355 CATGGACATCGTGTACACGC 59.355 55.000 37.13 24.88 45.23 5.34
2013 12432 3.874873 CACGCATGGACATCGTGT 58.125 55.556 19.50 10.16 45.75 4.49
2268 12687 3.119495 GCATATGGACGAACAGCCTTTTT 60.119 43.478 4.56 0.00 0.00 1.94
2269 12688 2.423538 GCATATGGACGAACAGCCTTTT 59.576 45.455 4.56 0.00 0.00 2.27
2270 12689 2.017049 GCATATGGACGAACAGCCTTT 58.983 47.619 4.56 0.00 0.00 3.11
2272 12691 0.530650 CGCATATGGACGAACAGCCT 60.531 55.000 4.56 0.00 0.00 4.58
2273 12692 1.934463 CGCATATGGACGAACAGCC 59.066 57.895 4.56 0.00 0.00 4.85
2274 12693 1.276844 GCGCATATGGACGAACAGC 59.723 57.895 0.30 0.00 0.00 4.40
2275 12694 1.145759 ACGCGCATATGGACGAACAG 61.146 55.000 5.73 0.00 0.00 3.16
2276 12695 1.143373 GACGCGCATATGGACGAACA 61.143 55.000 5.73 0.00 0.00 3.18
2277 12696 1.558383 GACGCGCATATGGACGAAC 59.442 57.895 5.73 0.00 0.00 3.95
2278 12697 1.942223 CGACGCGCATATGGACGAA 60.942 57.895 5.73 0.00 0.00 3.85
2279 12698 2.353030 CGACGCGCATATGGACGA 60.353 61.111 5.73 0.00 0.00 4.20
2290 12709 3.777925 CCTTTGGAGTGCGACGCG 61.778 66.667 16.14 3.53 0.00 6.01
2291 12710 4.090057 GCCTTTGGAGTGCGACGC 62.090 66.667 14.19 14.19 0.00 5.19
2312 12731 0.965439 TGGCGAACCCCTTGAATTTG 59.035 50.000 0.00 0.00 33.59 2.32
2416 12841 2.279517 GACGGGCATCACCTAGCG 60.280 66.667 0.00 0.00 39.10 4.26


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

AutoCloner maintained by Alex Coulton.