Multiple sequence alignment - TraesCS3B01G303000

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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 TraesCS3B01G303000 chr3B 100.000 3382 0 0 1 3382 487051207 487047826 0.000000e+00 6246.0
1 TraesCS3B01G303000 chr3B 82.500 80 13 1 3012 3091 157239769 157239691 6.060000e-08 69.4
2 TraesCS3B01G303000 chr3D 89.814 1934 149 30 1 1918 373330633 373328732 0.000000e+00 2436.0
3 TraesCS3B01G303000 chr3D 93.126 1382 69 14 2015 3382 373328581 373327212 0.000000e+00 2002.0
4 TraesCS3B01G303000 chr3D 81.791 659 105 14 48 698 424894806 424895457 3.840000e-149 538.0
5 TraesCS3B01G303000 chr3D 84.146 82 11 2 3012 3093 326964040 326963961 1.010000e-10 78.7
6 TraesCS3B01G303000 chr3A 96.830 1388 32 6 1996 3382 494729157 494727781 0.000000e+00 2309.0
7 TraesCS3B01G303000 chr3A 91.524 1640 77 18 367 1992 494730794 494729203 0.000000e+00 2202.0
8 TraesCS3B01G303000 chr2B 83.673 588 80 10 37 620 286977744 286977169 1.070000e-149 540.0
9 TraesCS3B01G303000 chr2B 91.176 102 8 1 1919 2020 216462908 216462808 1.640000e-28 137.0
10 TraesCS3B01G303000 chr2D 82.770 592 85 10 37 617 262456774 262457359 2.330000e-141 512.0
11 TraesCS3B01G303000 chr6B 80.775 645 108 13 48 683 575324457 575325094 1.090000e-134 490.0
12 TraesCS3B01G303000 chr6B 79.518 664 124 11 44 701 88329120 88328463 2.380000e-126 462.0
13 TraesCS3B01G303000 chr5D 81.270 614 105 8 48 657 543226985 543226378 3.920000e-134 488.0
14 TraesCS3B01G303000 chr1B 79.882 676 121 13 35 701 534219963 534219294 6.560000e-132 481.0
15 TraesCS3B01G303000 chr2A 78.420 709 132 20 48 745 770277569 770278267 3.100000e-120 442.0
16 TraesCS3B01G303000 chr2A 91.262 103 8 1 1919 2021 559118510 559118409 4.550000e-29 139.0
17 TraesCS3B01G303000 chr7A 94.059 101 5 1 1919 2019 692371746 692371845 5.840000e-33 152.0
18 TraesCS3B01G303000 chr7A 94.059 101 5 1 1919 2019 692395592 692395691 5.840000e-33 152.0
19 TraesCS3B01G303000 chr7A 91.176 102 8 1 1919 2020 48103080 48103180 1.640000e-28 137.0
20 TraesCS3B01G303000 chr7A 86.441 59 7 1 3037 3095 572872216 572872159 2.820000e-06 63.9
21 TraesCS3B01G303000 chr5B 91.176 102 8 1 1919 2020 55371038 55370938 1.640000e-28 137.0
22 TraesCS3B01G303000 chr4B 90.291 103 9 1 1919 2021 71586835 71586936 2.120000e-27 134.0
23 TraesCS3B01G303000 chr1A 90.196 102 9 1 1919 2020 106228175 106228075 7.610000e-27 132.0
24 TraesCS3B01G303000 chr7D 85.526 76 9 2 3011 3086 41820308 41820381 1.010000e-10 78.7
25 TraesCS3B01G303000 chr7D 86.885 61 7 1 3011 3070 136417279 136417339 2.180000e-07 67.6
26 TraesCS3B01G303000 chr1D 82.667 75 12 1 3012 3086 111724560 111724487 7.830000e-07 65.8


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 TraesCS3B01G303000 chr3B 487047826 487051207 3381 True 6246.0 6246 100.000 1 3382 1 chr3B.!!$R2 3381
1 TraesCS3B01G303000 chr3D 373327212 373330633 3421 True 2219.0 2436 91.470 1 3382 2 chr3D.!!$R2 3381
2 TraesCS3B01G303000 chr3D 424894806 424895457 651 False 538.0 538 81.791 48 698 1 chr3D.!!$F1 650
3 TraesCS3B01G303000 chr3A 494727781 494730794 3013 True 2255.5 2309 94.177 367 3382 2 chr3A.!!$R1 3015
4 TraesCS3B01G303000 chr2B 286977169 286977744 575 True 540.0 540 83.673 37 620 1 chr2B.!!$R2 583
5 TraesCS3B01G303000 chr2D 262456774 262457359 585 False 512.0 512 82.770 37 617 1 chr2D.!!$F1 580
6 TraesCS3B01G303000 chr6B 575324457 575325094 637 False 490.0 490 80.775 48 683 1 chr6B.!!$F1 635
7 TraesCS3B01G303000 chr6B 88328463 88329120 657 True 462.0 462 79.518 44 701 1 chr6B.!!$R1 657
8 TraesCS3B01G303000 chr5D 543226378 543226985 607 True 488.0 488 81.270 48 657 1 chr5D.!!$R1 609
9 TraesCS3B01G303000 chr1B 534219294 534219963 669 True 481.0 481 79.882 35 701 1 chr1B.!!$R1 666
10 TraesCS3B01G303000 chr2A 770277569 770278267 698 False 442.0 442 78.420 48 745 1 chr2A.!!$F1 697

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
318 338 1.132500 AATGGGACCCGGAGATCTTC 58.868 55.000 0.73 0.0 0.0 2.87 F
1162 1205 1.078637 GGTACCGCACTTCCCTTCC 60.079 63.158 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1534 0.038343 CCCATTTTCACCAAGGCACG 60.038 55.0 0.0 0.0 0.0 5.34 R
2924 3083 0.336737 AGAGGAGGGTCAGGTAGGTG 59.663 60.0 0.0 0.0 0.0 4.00 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
41 42 3.064324 ACTGGATTTGGCAGCGGC 61.064 61.111 0.00 0.00 40.13 6.53
62 64 3.624777 CCTCCATGTTTGCTAGGTTGAT 58.375 45.455 0.00 0.00 0.00 2.57
63 65 3.629398 CCTCCATGTTTGCTAGGTTGATC 59.371 47.826 0.00 0.00 0.00 2.92
64 66 4.264253 CTCCATGTTTGCTAGGTTGATCA 58.736 43.478 0.00 0.00 0.00 2.92
97 102 3.507411 TCCTCCTAGCAACTACACTGTT 58.493 45.455 0.00 0.00 0.00 3.16
118 128 7.391554 ACTGTTAATGTGCATCAGTAGAACATT 59.608 33.333 5.03 5.03 42.46 2.71
220 234 8.870075 AAGAGCTCACTTTAACCAAAGATAAT 57.130 30.769 17.77 0.00 43.32 1.28
221 235 9.959721 AAGAGCTCACTTTAACCAAAGATAATA 57.040 29.630 17.77 0.00 43.32 0.98
222 236 9.959721 AGAGCTCACTTTAACCAAAGATAATAA 57.040 29.630 17.77 0.00 43.32 1.40
235 252 8.993424 ACCAAAGATAATAAGGAGCTAGAAAGA 58.007 33.333 0.00 0.00 0.00 2.52
242 259 3.274095 AGGAGCTAGAAAGAATGTGGC 57.726 47.619 0.00 0.00 0.00 5.01
318 338 1.132500 AATGGGACCCGGAGATCTTC 58.868 55.000 0.73 0.00 0.00 2.87
467 491 6.039941 TCCGGTCATGTTTGATAAGTTTGTTT 59.960 34.615 0.00 0.00 33.56 2.83
706 742 1.519408 TGAGTTTGCGGGCTCTTAAC 58.481 50.000 0.00 0.00 33.22 2.01
728 765 1.134670 ACAGAGGCGATGTTTAGAGGC 60.135 52.381 0.00 0.00 0.00 4.70
768 805 2.427453 GTCCGTATCACTGTCTGTGGAT 59.573 50.000 9.69 5.40 46.20 3.41
778 815 1.899142 TGTCTGTGGATCGGATTCACA 59.101 47.619 26.28 26.28 38.84 3.58
792 829 5.753438 TCGGATTCACAGATAAGTACAATGC 59.247 40.000 0.00 0.00 0.00 3.56
799 836 4.634443 ACAGATAAGTACAATGCCCGTTTC 59.366 41.667 0.00 0.00 0.00 2.78
902 945 4.335647 CGCCTTCAGCCCCACAGT 62.336 66.667 0.00 0.00 38.78 3.55
903 946 2.674380 GCCTTCAGCCCCACAGTG 60.674 66.667 0.00 0.00 34.35 3.66
1162 1205 1.078637 GGTACCGCACTTCCCTTCC 60.079 63.158 0.00 0.00 0.00 3.46
1314 1358 2.045926 CCGCCCAAGACTGGAAGG 60.046 66.667 0.00 0.00 46.92 3.46
1365 1409 2.079158 CAGAATGACAGACACCGCATT 58.921 47.619 0.00 0.00 39.69 3.56
1416 1460 3.008049 GCACCCGGATGAAGAAGGTATAT 59.992 47.826 0.00 0.00 0.00 0.86
1417 1461 4.222145 GCACCCGGATGAAGAAGGTATATA 59.778 45.833 0.00 0.00 0.00 0.86
1453 1497 1.694696 GGCGTATCCCTTTCTCCATCT 59.305 52.381 0.00 0.00 0.00 2.90
1478 1522 8.865590 TTTCAAGTTTTGCCACTAAAATACTC 57.134 30.769 0.00 0.00 32.71 2.59
1483 1527 8.816640 AGTTTTGCCACTAAAATACTCAATTG 57.183 30.769 0.00 0.00 32.71 2.32
1490 1534 5.801947 CACTAAAATACTCAATTGGCACTGC 59.198 40.000 5.42 0.00 0.00 4.40
1491 1535 3.492421 AAATACTCAATTGGCACTGCG 57.508 42.857 5.42 0.00 0.00 5.18
1492 1536 2.113860 ATACTCAATTGGCACTGCGT 57.886 45.000 5.42 0.00 0.00 5.24
1493 1537 1.155889 TACTCAATTGGCACTGCGTG 58.844 50.000 5.42 4.61 36.51 5.34
1514 1558 3.103742 GCCTTGGTGAAAATGGGGAATA 58.896 45.455 0.00 0.00 0.00 1.75
1564 1623 3.135712 GTGTTTTGGGGAATTTTGAGGGT 59.864 43.478 0.00 0.00 0.00 4.34
1565 1624 3.783082 TGTTTTGGGGAATTTTGAGGGTT 59.217 39.130 0.00 0.00 0.00 4.11
1669 1728 5.280654 ACATTTTGGAGTTGCATTCTGTT 57.719 34.783 0.00 0.00 0.00 3.16
1764 1823 7.766738 TGATTGTACAAGGCGAGTGATTAATTA 59.233 33.333 14.65 0.00 0.00 1.40
1937 1996 9.799106 ATATAAACTCCATCCTGAATTAGTTGG 57.201 33.333 0.00 0.00 32.01 3.77
1969 2069 7.233389 ACGGATGTATCTAGCACTGAAATAT 57.767 36.000 0.00 0.00 0.00 1.28
1992 2092 5.532557 TGTCTAGATACATCCATTTGAGCG 58.467 41.667 0.00 0.00 0.00 5.03
1993 2093 5.069119 TGTCTAGATACATCCATTTGAGCGT 59.931 40.000 0.00 0.00 0.00 5.07
2005 2147 4.334443 CATTTGAGCGTCAACTAATTCCG 58.666 43.478 0.76 0.00 35.89 4.30
2012 2154 2.537401 GTCAACTAATTCCGGACGGAG 58.463 52.381 13.64 3.57 46.06 4.63
2048 2190 8.695456 GGTTATTGGTATGAAGATGGTTTCATT 58.305 33.333 6.56 0.00 43.41 2.57
2740 2894 7.038154 TCTGTTTTCTTTTGTACTCCAATGG 57.962 36.000 0.00 0.00 31.81 3.16
2766 2925 5.687166 AATACGACCCTGGAAAAGACATA 57.313 39.130 0.00 0.00 0.00 2.29
2767 2926 3.329929 ACGACCCTGGAAAAGACATAC 57.670 47.619 0.00 0.00 0.00 2.39
2768 2927 2.635915 ACGACCCTGGAAAAGACATACA 59.364 45.455 0.00 0.00 0.00 2.29
2769 2928 3.262420 CGACCCTGGAAAAGACATACAG 58.738 50.000 0.00 0.00 0.00 2.74
2770 2929 3.306780 CGACCCTGGAAAAGACATACAGT 60.307 47.826 0.00 0.00 0.00 3.55
2788 2947 3.322254 ACAGTATAATCCTTCCTGAGCGG 59.678 47.826 0.00 0.00 0.00 5.52
2908 3067 6.034591 CCCTAGTGAACTTGTATTAGACACG 58.965 44.000 0.00 0.00 37.96 4.49
2924 3083 8.684973 ATTAGACACGGTATATTTTAGATCGC 57.315 34.615 0.00 0.00 0.00 4.58
2925 3084 6.080648 AGACACGGTATATTTTAGATCGCA 57.919 37.500 0.00 0.00 0.00 5.10
3069 3228 2.593346 TGCAATGAAACGCAAAGGTT 57.407 40.000 0.00 0.00 34.59 3.50
3142 3302 5.542635 ACCTGAGACTGGTTCAATACTGTTA 59.457 40.000 0.00 0.00 31.67 2.41
3143 3303 6.213600 ACCTGAGACTGGTTCAATACTGTTAT 59.786 38.462 0.00 0.00 31.67 1.89
3144 3304 7.399191 ACCTGAGACTGGTTCAATACTGTTATA 59.601 37.037 0.00 0.00 31.67 0.98
3145 3305 7.707035 CCTGAGACTGGTTCAATACTGTTATAC 59.293 40.741 0.00 0.00 0.00 1.47
3146 3306 8.129496 TGAGACTGGTTCAATACTGTTATACA 57.871 34.615 0.00 0.00 0.00 2.29
3281 3441 8.853126 ACATGATATTTGCATTATTACTGTGCT 58.147 29.630 0.00 0.00 39.52 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.064324 GCCGCTGCCAAATCCAGT 61.064 61.111 0.00 0.0 32.93 4.00
41 42 3.071874 TCAACCTAGCAAACATGGAGG 57.928 47.619 0.00 0.0 0.00 4.30
75 77 3.093057 ACAGTGTAGTTGCTAGGAGGAG 58.907 50.000 0.00 0.0 0.00 3.69
76 78 3.170991 ACAGTGTAGTTGCTAGGAGGA 57.829 47.619 0.00 0.0 0.00 3.71
77 79 3.963428 AACAGTGTAGTTGCTAGGAGG 57.037 47.619 0.00 0.0 0.00 4.30
83 88 4.133820 TGCACATTAACAGTGTAGTTGCT 58.866 39.130 0.00 0.0 39.17 3.91
97 102 7.105588 AGTCAATGTTCTACTGATGCACATTA 58.894 34.615 0.00 0.0 36.21 1.90
220 234 4.680708 CGCCACATTCTTTCTAGCTCCTTA 60.681 45.833 0.00 0.0 0.00 2.69
221 235 3.615155 GCCACATTCTTTCTAGCTCCTT 58.385 45.455 0.00 0.0 0.00 3.36
222 236 2.419297 CGCCACATTCTTTCTAGCTCCT 60.419 50.000 0.00 0.0 0.00 3.69
235 252 0.247185 CCAAATGCCTTCGCCACATT 59.753 50.000 0.00 0.0 35.59 2.71
242 259 0.449388 GAGCACTCCAAATGCCTTCG 59.551 55.000 0.00 0.0 44.53 3.79
264 281 1.462791 GAACAACTGCAAAACGGACG 58.537 50.000 0.00 0.0 0.00 4.79
318 338 3.572632 AACATGTCATCATCTCCCCTG 57.427 47.619 0.00 0.0 31.15 4.45
391 413 3.445096 CCATGTTCTCAAATTCCAGACCC 59.555 47.826 0.00 0.0 0.00 4.46
467 491 6.073819 CGATGCCGAATTTGTTGATGTATCTA 60.074 38.462 0.00 0.0 38.22 1.98
472 496 2.746904 TCGATGCCGAATTTGTTGATGT 59.253 40.909 0.00 0.0 42.51 3.06
706 742 2.932614 CCTCTAAACATCGCCTCTGTTG 59.067 50.000 0.00 0.0 36.95 3.33
768 805 5.753438 GCATTGTACTTATCTGTGAATCCGA 59.247 40.000 0.00 0.0 0.00 4.55
778 815 3.869246 CGAAACGGGCATTGTACTTATCT 59.131 43.478 0.00 0.0 0.00 1.98
799 836 1.452108 GTCTTCAAGCCCATCCCCG 60.452 63.158 0.00 0.0 0.00 5.73
804 841 0.779997 AAGGGTGTCTTCAAGCCCAT 59.220 50.000 1.75 0.0 43.42 4.00
902 945 2.570302 GGAAGTAGTAGGTTTGCTCCCA 59.430 50.000 0.00 0.0 0.00 4.37
903 946 2.093075 GGGAAGTAGTAGGTTTGCTCCC 60.093 54.545 0.00 0.0 0.00 4.30
909 952 2.629017 TCCGGGGAAGTAGTAGGTTT 57.371 50.000 0.00 0.0 0.00 3.27
1251 1295 0.831307 CCCTCCTCCTAAACCTTCCG 59.169 60.000 0.00 0.0 0.00 4.30
1260 1304 3.694697 TGCAGCCCCCTCCTCCTA 61.695 66.667 0.00 0.0 0.00 2.94
1314 1358 4.373116 TTGACCGAGTCCGCCTGC 62.373 66.667 2.23 0.0 0.00 4.85
1318 1362 0.456995 CTCTTCTTGACCGAGTCCGC 60.457 60.000 2.23 0.0 0.00 5.54
1453 1497 8.470805 TGAGTATTTTAGTGGCAAAACTTGAAA 58.529 29.630 0.00 0.0 30.57 2.69
1490 1534 0.038343 CCCATTTTCACCAAGGCACG 60.038 55.000 0.00 0.0 0.00 5.34
1491 1535 0.321346 CCCCATTTTCACCAAGGCAC 59.679 55.000 0.00 0.0 0.00 5.01
1492 1536 0.189574 TCCCCATTTTCACCAAGGCA 59.810 50.000 0.00 0.0 0.00 4.75
1493 1537 1.347062 TTCCCCATTTTCACCAAGGC 58.653 50.000 0.00 0.0 0.00 4.35
1494 1538 3.706086 CCTATTCCCCATTTTCACCAAGG 59.294 47.826 0.00 0.0 0.00 3.61
1534 1585 1.561643 TCCCCAAAACACAGCAACAA 58.438 45.000 0.00 0.0 0.00 2.83
1546 1605 2.708325 CCAACCCTCAAAATTCCCCAAA 59.292 45.455 0.00 0.0 0.00 3.28
1548 1607 1.484065 CCCAACCCTCAAAATTCCCCA 60.484 52.381 0.00 0.0 0.00 4.96
1721 1780 9.751542 TGTACAATCAAATTTAATCCGTTTGTT 57.248 25.926 0.00 0.0 35.09 2.83
1764 1823 8.950210 CCGATAATAAATCCACTTGCAATATCT 58.050 33.333 0.00 0.0 0.00 1.98
1922 1981 4.574674 TGAGTGCCAACTAATTCAGGAT 57.425 40.909 0.00 0.0 36.52 3.24
1937 1996 3.491267 GCTAGATACATCCGTTTGAGTGC 59.509 47.826 0.00 0.0 0.00 4.40
1969 2069 5.069119 ACGCTCAAATGGATGTATCTAGACA 59.931 40.000 0.00 0.0 0.00 3.41
1988 2088 1.925185 GTCCGGAATTAGTTGACGCTC 59.075 52.381 5.23 0.0 0.00 5.03
1992 2092 2.537401 CTCCGTCCGGAATTAGTTGAC 58.463 52.381 5.23 0.0 44.66 3.18
1993 2093 1.479323 CCTCCGTCCGGAATTAGTTGA 59.521 52.381 5.23 0.0 44.66 3.18
2005 2147 1.757340 CCAGTACTCCCCTCCGTCC 60.757 68.421 0.00 0.0 0.00 4.79
2012 2154 4.657039 TCATACCAATAACCAGTACTCCCC 59.343 45.833 0.00 0.0 0.00 4.81
2740 2894 4.155462 GTCTTTTCCAGGGTCGTATTTTCC 59.845 45.833 0.00 0.0 0.00 3.13
2766 2925 3.322254 CCGCTCAGGAAGGATTATACTGT 59.678 47.826 0.00 0.0 45.00 3.55
2767 2926 3.322254 ACCGCTCAGGAAGGATTATACTG 59.678 47.826 0.00 0.0 45.00 2.74
2768 2927 3.322254 CACCGCTCAGGAAGGATTATACT 59.678 47.826 0.00 0.0 45.00 2.12
2769 2928 3.069729 ACACCGCTCAGGAAGGATTATAC 59.930 47.826 0.00 0.0 45.00 1.47
2770 2929 3.305720 ACACCGCTCAGGAAGGATTATA 58.694 45.455 0.00 0.0 45.00 0.98
2788 2947 2.990066 ACAGGCCTAGAGCAATACAC 57.010 50.000 3.98 0.0 46.50 2.90
2908 3067 6.812160 CAGGTAGGTGCGATCTAAAATATACC 59.188 42.308 0.00 0.0 0.00 2.73
2922 3081 2.722201 GGAGGGTCAGGTAGGTGCG 61.722 68.421 0.00 0.0 0.00 5.34
2924 3083 0.336737 AGAGGAGGGTCAGGTAGGTG 59.663 60.000 0.00 0.0 0.00 4.00
2925 3084 0.336737 CAGAGGAGGGTCAGGTAGGT 59.663 60.000 0.00 0.0 0.00 3.08
3142 3302 6.569228 CGAGAACGTGTTGACATTATGTAT 57.431 37.500 0.00 0.0 34.56 2.29
3144 3304 4.903638 CGAGAACGTGTTGACATTATGT 57.096 40.909 0.00 0.0 34.56 2.29
3281 3441 7.178628 GGGTCAAAGATATCATGCTACCTACTA 59.821 40.741 5.32 0.0 0.00 1.82
3282 3442 6.014156 GGGTCAAAGATATCATGCTACCTACT 60.014 42.308 5.32 0.0 0.00 2.57
3283 3443 6.166982 GGGTCAAAGATATCATGCTACCTAC 58.833 44.000 5.32 0.0 0.00 3.18


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

AutoCloner maintained by Alex Coulton.