Multiple sequence alignment - TraesCS7B01G341500

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 TraesCS7B01G341500 chr7B 100.000 2726 0 0 634 3359 596539322 596536597 0.000000e+00 5035.0
1 TraesCS7B01G341500 chr7B 96.247 1359 39 7 655 2002 596516475 596515118 0.000000e+00 2217.0
2 TraesCS7B01G341500 chr7B 96.585 820 24 3 2020 2839 596514977 596514162 0.000000e+00 1356.0
3 TraesCS7B01G341500 chr7B 93.326 869 51 6 2020 2885 596501821 596500957 0.000000e+00 1277.0
4 TraesCS7B01G341500 chr7B 86.292 1014 99 20 805 1799 595882367 595881375 0.000000e+00 1066.0
5 TraesCS7B01G341500 chr7B 96.516 488 14 2 2834 3319 596506000 596505514 0.000000e+00 804.0
6 TraesCS7B01G341500 chr7B 100.000 414 0 0 1 414 596539955 596539542 0.000000e+00 765.0
7 TraesCS7B01G341500 chr7B 81.652 823 105 27 2071 2882 595856395 595855608 2.830000e-180 641.0
8 TraesCS7B01G341500 chr7B 82.120 632 62 20 1190 1800 595993706 595993105 8.370000e-136 494.0
9 TraesCS7B01G341500 chr7B 87.220 313 20 8 3034 3342 596419049 596418753 4.150000e-89 339.0
10 TraesCS7B01G341500 chr7B 93.532 201 13 0 181 381 596517134 596516934 1.960000e-77 300.0
11 TraesCS7B01G341500 chr7B 92.021 188 13 1 806 991 595993941 595993754 2.570000e-66 263.0
12 TraesCS7B01G341500 chr7B 92.208 154 6 3 1849 2002 596502112 596501965 2.630000e-51 213.0
13 TraesCS7B01G341500 chr7B 87.013 154 16 4 640 791 426351152 426351001 1.600000e-38 171.0
14 TraesCS7B01G341500 chr7B 100.000 47 0 0 3313 3359 596502858 596502812 1.660000e-13 87.9
15 TraesCS7B01G341500 chr7B 90.909 55 5 0 1748 1802 596502283 596502229 1.290000e-09 75.0
16 TraesCS7B01G341500 chr7D 92.061 1184 64 12 634 1802 551604943 551603775 0.000000e+00 1639.0
17 TraesCS7B01G341500 chr7D 91.912 1187 63 13 634 1802 551501022 551499851 0.000000e+00 1629.0
18 TraesCS7B01G341500 chr7D 92.582 1038 62 8 1853 2885 551603660 551602633 0.000000e+00 1476.0
19 TraesCS7B01G341500 chr7D 92.316 924 59 9 1969 2885 551499654 551498736 0.000000e+00 1303.0
20 TraesCS7B01G341500 chr7D 85.771 1012 104 19 806 1799 551000535 550999546 0.000000e+00 1035.0
21 TraesCS7B01G341500 chr7D 83.593 835 85 28 876 1688 551928641 551927837 0.000000e+00 736.0
22 TraesCS7B01G341500 chr7D 82.826 821 99 22 2071 2882 550992033 550991246 0.000000e+00 697.0
23 TraesCS7B01G341500 chr7D 93.277 476 21 7 2887 3359 551602598 551602131 0.000000e+00 691.0
24 TraesCS7B01G341500 chr7D 93.038 474 23 7 2887 3357 551498700 551498234 0.000000e+00 684.0
25 TraesCS7B01G341500 chr7D 91.270 378 32 1 1 378 551504280 551503904 6.430000e-142 514.0
26 TraesCS7B01G341500 chr7D 90.741 378 34 1 1 378 551608208 551607832 1.390000e-138 503.0
27 TraesCS7B01G341500 chr7D 83.721 215 29 5 2071 2282 551110742 551110953 7.350000e-47 198.0
28 TraesCS7B01G341500 chr7D 95.349 86 4 0 1853 1938 551499736 551499651 1.630000e-28 137.0
29 TraesCS7B01G341500 chr7A 93.697 952 42 5 852 1802 637158006 637157072 0.000000e+00 1410.0
30 TraesCS7B01G341500 chr7A 91.563 806 58 8 2088 2885 637151647 637150844 0.000000e+00 1103.0
31 TraesCS7B01G341500 chr7A 89.135 902 74 7 634 1524 637078310 637077422 0.000000e+00 1101.0
32 TraesCS7B01G341500 chr7A 81.158 950 104 43 876 1792 637337031 637336124 0.000000e+00 693.0
33 TraesCS7B01G341500 chr7A 82.095 821 124 19 2071 2883 637074181 637074986 0.000000e+00 680.0
34 TraesCS7B01G341500 chr7A 81.973 821 107 18 2071 2883 636911319 636910532 0.000000e+00 658.0
35 TraesCS7B01G341500 chr7A 92.327 391 28 2 1 390 637172949 637172560 3.790000e-154 555.0
36 TraesCS7B01G341500 chr7A 90.746 389 33 3 1 388 637078733 637078347 1.790000e-142 516.0
37 TraesCS7B01G341500 chr7A 93.976 249 11 3 1852 2099 637151994 637151749 1.140000e-99 374.0
38 TraesCS7B01G341500 chr7A 88.525 305 29 4 806 1108 636920295 636919995 6.850000e-97 364.0
39 TraesCS7B01G341500 chr7A 85.356 239 17 13 634 859 637172399 637172166 7.250000e-57 231.0
40 TraesCS7B01G341500 chr7A 92.500 120 7 1 2887 3006 637150810 637150693 1.600000e-38 171.0
41 TraesCS7B01G341500 chr2A 86.592 358 41 6 4 360 780721424 780721073 4.060000e-104 388.0
42 TraesCS7B01G341500 chr2A 88.591 149 14 3 640 787 621387688 621387834 9.580000e-41 178.0
43 TraesCS7B01G341500 chr2A 86.792 159 18 3 639 796 608605553 608605397 1.240000e-39 174.0
44 TraesCS7B01G341500 chr2A 86.335 161 18 4 637 796 249754623 249754466 4.460000e-39 172.0
45 TraesCS7B01G341500 chr2A 87.919 149 15 3 640 787 698694372 698694226 4.460000e-39 172.0
46 TraesCS7B01G341500 chr6D 82.161 398 48 13 1 388 358209766 358210150 1.500000e-83 320.0
47 TraesCS7B01G341500 chr6D 87.861 173 21 0 99 271 430447032 430447204 1.580000e-48 204.0
48 TraesCS7B01G341500 chr1D 87.654 243 28 2 147 388 50915450 50915691 7.100000e-72 281.0
49 TraesCS7B01G341500 chr1D 87.919 149 14 4 640 787 73725589 73725734 4.460000e-39 172.0
50 TraesCS7B01G341500 chr1A 85.185 189 26 2 188 374 49971439 49971627 3.420000e-45 193.0
51 TraesCS7B01G341500 chr5D 87.500 152 16 3 637 787 486291196 486291345 4.460000e-39 172.0
52 TraesCS7B01G341500 chr5A 83.000 200 21 3 1 192 372155216 372155410 5.760000e-38 169.0
53 TraesCS7B01G341500 chr2B 86.164 159 19 3 637 794 249200330 249200174 5.760000e-38 169.0
54 TraesCS7B01G341500 chr6B 87.692 130 11 2 102 230 648723952 648724077 2.700000e-31 147.0


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 TraesCS7B01G341500 chr7B 596536597 596539955 3358 True 2900.000000 5035 100.000000 1 3359 2 chr7B.!!$R8 3358
1 TraesCS7B01G341500 chr7B 596514162 596517134 2972 True 1291.000000 2217 95.454667 181 2839 3 chr7B.!!$R7 2658
2 TraesCS7B01G341500 chr7B 595881375 595882367 992 True 1066.000000 1066 86.292000 805 1799 1 chr7B.!!$R3 994
3 TraesCS7B01G341500 chr7B 595855608 595856395 787 True 641.000000 641 81.652000 2071 2882 1 chr7B.!!$R2 811
4 TraesCS7B01G341500 chr7B 596500957 596506000 5043 True 491.380000 1277 94.591800 1748 3359 5 chr7B.!!$R6 1611
5 TraesCS7B01G341500 chr7B 595993105 595993941 836 True 378.500000 494 87.070500 806 1800 2 chr7B.!!$R5 994
6 TraesCS7B01G341500 chr7D 551602131 551608208 6077 True 1077.250000 1639 92.165250 1 3359 4 chr7D.!!$R5 3358
7 TraesCS7B01G341500 chr7D 550999546 551000535 989 True 1035.000000 1035 85.771000 806 1799 1 chr7D.!!$R2 993
8 TraesCS7B01G341500 chr7D 551498234 551504280 6046 True 853.400000 1629 92.777000 1 3357 5 chr7D.!!$R4 3356
9 TraesCS7B01G341500 chr7D 551927837 551928641 804 True 736.000000 736 83.593000 876 1688 1 chr7D.!!$R3 812
10 TraesCS7B01G341500 chr7D 550991246 550992033 787 True 697.000000 697 82.826000 2071 2882 1 chr7D.!!$R1 811
11 TraesCS7B01G341500 chr7A 637157072 637158006 934 True 1410.000000 1410 93.697000 852 1802 1 chr7A.!!$R3 950
12 TraesCS7B01G341500 chr7A 637077422 637078733 1311 True 808.500000 1101 89.940500 1 1524 2 chr7A.!!$R5 1523
13 TraesCS7B01G341500 chr7A 637336124 637337031 907 True 693.000000 693 81.158000 876 1792 1 chr7A.!!$R4 916
14 TraesCS7B01G341500 chr7A 637074181 637074986 805 False 680.000000 680 82.095000 2071 2883 1 chr7A.!!$F1 812
15 TraesCS7B01G341500 chr7A 636910532 636911319 787 True 658.000000 658 81.973000 2071 2883 1 chr7A.!!$R1 812
16 TraesCS7B01G341500 chr7A 637150693 637151994 1301 True 549.333333 1103 92.679667 1852 3006 3 chr7A.!!$R6 1154
17 TraesCS7B01G341500 chr7A 637172166 637172949 783 True 393.000000 555 88.841500 1 859 2 chr7A.!!$R7 858

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
105 106 1.061905 TCCGGAATGGATGCAGGGAT 61.062 55.000 0.0 0.0 43.74 3.85 F
298 299 2.169352 ACTGGCTCACAATCTAGCGAAT 59.831 45.455 0.0 0.0 39.71 3.34 F
1945 5321 2.286935 AAAGAGGGGCTCTATTGGGA 57.713 50.000 0.0 0.0 40.28 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 5304 0.470341 GTGTCCCAATAGAGCCCCTC 59.530 60.000 0.0 0.0 0.0 4.30 R
2111 5726 6.043938 CCCCTATCACCTATTACTTTTGCCTA 59.956 42.308 0.0 0.0 0.0 3.93 R
2934 6602 0.105039 GGTGAGAGGGTATTGGAGCG 59.895 60.000 0.0 0.0 0.0 5.03 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
43 44 2.918345 GCTGCGGCAACATGGTTCA 61.918 57.895 14.08 0.00 38.54 3.18
72 73 1.300931 GACCAGCGTTGACTCAGCA 60.301 57.895 0.00 0.00 0.00 4.41
78 79 2.095461 AGCGTTGACTCAGCAGAGATA 58.905 47.619 13.73 0.00 44.98 1.98
105 106 1.061905 TCCGGAATGGATGCAGGGAT 61.062 55.000 0.00 0.00 43.74 3.85
142 143 5.735285 AAGTGATCAGTGAGTCAGATTGA 57.265 39.130 3.18 0.00 0.00 2.57
186 187 4.298332 CAACAACCAGAAACTTATGTGGC 58.702 43.478 0.00 0.00 32.91 5.01
298 299 2.169352 ACTGGCTCACAATCTAGCGAAT 59.831 45.455 0.00 0.00 39.71 3.34
724 3962 6.215121 AGCGAATGAATGAATCTACTCTCTG 58.785 40.000 0.00 0.00 0.00 3.35
800 4047 5.887598 ACTTATATTTACAAAACGGACCCCC 59.112 40.000 0.00 0.00 0.00 5.40
801 4048 2.984435 ATTTACAAAACGGACCCCCT 57.016 45.000 0.00 0.00 0.00 4.79
1794 5098 8.163408 TGAAGGGATTTTCTCTACTGAAATCAA 58.837 33.333 9.43 0.00 36.07 2.57
1929 5304 6.128391 TGCTTAGTACGAAGGCAACATAAAAG 60.128 38.462 16.24 0.00 41.41 2.27
1945 5321 2.286935 AAAGAGGGGCTCTATTGGGA 57.713 50.000 0.00 0.00 40.28 4.37
2062 5564 7.272948 CAGAGCAAAGTTTTCTTAAGATGATGC 59.727 37.037 5.89 11.03 39.48 3.91
2079 5581 7.778083 AGATGATGCAGCAAAAGAATTATTGA 58.222 30.769 9.54 0.00 0.00 2.57
2131 5746 9.914834 TGTTTATAGGCAAAAGTAATAGGTGAT 57.085 29.630 0.00 0.00 0.00 3.06
2140 5755 7.013369 GCAAAAGTAATAGGTGATAGGGGAAAG 59.987 40.741 0.00 0.00 0.00 2.62
2207 5823 9.598517 AAAATCAAGCTTCAAAACTGTTATGAA 57.401 25.926 0.00 0.00 0.00 2.57
2473 6097 1.269051 CCGAAACTTGTGCCTTTGGAC 60.269 52.381 0.00 0.00 0.00 4.02
2690 6319 9.658475 TTTTATGTGTGTCGTTTTCAGATTTAG 57.342 29.630 0.00 0.00 0.00 1.85
2885 6519 3.460103 CAGGCTTTGCTTTGTGTTCAAT 58.540 40.909 0.00 0.00 33.32 2.57
2934 6602 0.311790 TTGCAAACTAGCTGCTGTGC 59.688 50.000 13.43 15.82 40.59 4.57
2946 6614 2.472909 GCTGTGCGCTCCAATACCC 61.473 63.158 9.73 0.00 35.14 3.69
2947 6615 1.221840 CTGTGCGCTCCAATACCCT 59.778 57.895 9.73 0.00 0.00 4.34
2974 6642 4.224818 ACCAGTTACTACCTACGAGAGAGT 59.775 45.833 0.00 0.00 0.00 3.24
3011 6679 6.645790 AGGATAACATATACGAAACCGAGT 57.354 37.500 0.00 0.00 0.00 4.18
3016 6684 3.698040 ACATATACGAAACCGAGTGGACT 59.302 43.478 0.00 0.00 39.21 3.85
3044 6713 2.551721 CCAGTGAGCAATAGCATAGGGG 60.552 54.545 0.00 0.00 45.49 4.79
3067 6736 4.163441 TCAAACCCAAACTCATCACTGA 57.837 40.909 0.00 0.00 0.00 3.41
3070 6739 1.270839 ACCCAAACTCATCACTGACGG 60.271 52.381 0.00 0.00 0.00 4.79
3141 6810 5.621193 ACATGGGTATTGACTATTGGTAGC 58.379 41.667 0.00 0.00 0.00 3.58
3161 6830 3.252458 AGCCCGTTTGTGAACTCATTAAC 59.748 43.478 0.00 0.00 33.51 2.01
3166 6835 4.664410 CGTTTGTGAACTCATTAACGTGTG 59.336 41.667 15.41 0.00 38.96 3.82
3219 6890 4.156008 TGGAGGCGAGAATTTAGAAAAAGC 59.844 41.667 0.00 0.00 0.00 3.51
3307 6978 5.581605 CCATGTAAACACAACATCCATAGC 58.418 41.667 0.00 0.00 35.39 2.97
3312 6983 0.028505 CACAACATCCATAGCAGCGC 59.971 55.000 0.00 0.00 0.00 5.92
3330 7001 2.225491 GCGCATGGACAAAAACTAGTCA 59.775 45.455 0.30 0.00 36.50 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.194781 ACGCTGGTCACCTGAGGAAT 61.195 55.000 4.99 0.00 0.00 3.01
72 73 4.501571 CCATTCCGGATCGTTGTTATCTCT 60.502 45.833 4.15 0.00 36.56 3.10
142 143 5.070001 TGCATTACTTCCACTACAAAGCTT 58.930 37.500 0.00 0.00 0.00 3.74
186 187 3.614092 AGTACCATTGCAACATCTGAGG 58.386 45.455 0.00 0.00 0.00 3.86
278 279 2.299993 TTCGCTAGATTGTGAGCCAG 57.700 50.000 0.00 0.00 35.13 4.85
678 3915 6.398918 GCTCCGTATGTAGTCCATTATTGAT 58.601 40.000 0.00 0.00 34.86 2.57
775 4013 7.053498 GGGGGTCCGTTTTGTAAATATAAGTA 58.947 38.462 0.00 0.00 0.00 2.24
1247 4504 3.801997 CGAGGGGCAGGCATTCCT 61.802 66.667 0.00 0.00 45.66 3.36
1663 4955 3.586461 CTGCCTGCTGAGACGCTGT 62.586 63.158 0.00 0.00 0.00 4.40
1929 5304 0.470341 GTGTCCCAATAGAGCCCCTC 59.530 60.000 0.00 0.00 0.00 4.30
2018 5489 7.194607 TGCTCTGCAATATAGCAACTTTATC 57.805 36.000 9.50 0.00 45.13 1.75
2036 5538 7.272948 GCATCATCTTAAGAAAACTTTGCTCTG 59.727 37.037 9.71 0.00 0.00 3.35
2062 5564 9.504710 CATCTCTTCTCAATAATTCTTTTGCTG 57.495 33.333 0.00 0.00 0.00 4.41
2111 5726 6.043938 CCCCTATCACCTATTACTTTTGCCTA 59.956 42.308 0.00 0.00 0.00 3.93
2131 5746 6.155565 TCGATTAGTTCATTCACTTTCCCCTA 59.844 38.462 0.00 0.00 0.00 3.53
2140 5755 9.262472 GTTAAATGTGTCGATTAGTTCATTCAC 57.738 33.333 0.00 0.00 0.00 3.18
2444 6066 3.490078 GGCACAAGTTTCGGTTTTCATGA 60.490 43.478 0.00 0.00 0.00 3.07
2473 6097 2.065899 TCTGGACCAAAGGTTTGTGG 57.934 50.000 0.00 0.00 35.25 4.17
2656 6285 7.617533 AAACGACACACATAAAATTTACTGC 57.382 32.000 0.00 0.00 0.00 4.40
2885 6519 0.179111 CCGCTCGTCAATGCTCCTTA 60.179 55.000 0.00 0.00 0.00 2.69
2934 6602 0.105039 GGTGAGAGGGTATTGGAGCG 59.895 60.000 0.00 0.00 0.00 5.03
2946 6614 4.511527 TCGTAGGTAGTAACTGGTGAGAG 58.488 47.826 0.00 0.00 0.00 3.20
2947 6615 4.223700 TCTCGTAGGTAGTAACTGGTGAGA 59.776 45.833 10.23 10.23 0.00 3.27
3006 6674 1.448540 GGCACATGAGTCCACTCGG 60.449 63.158 0.00 0.20 45.72 4.63
3011 6679 0.322648 CTCACTGGCACATGAGTCCA 59.677 55.000 13.53 2.88 38.35 4.02
3016 6684 2.635714 CTATTGCTCACTGGCACATGA 58.364 47.619 0.00 0.00 42.27 3.07
3044 6713 4.761739 TCAGTGATGAGTTTGGGTTTGATC 59.238 41.667 0.00 0.00 0.00 2.92
3103 6772 3.559238 CCATGTTTCGTTTGGGAAGAG 57.441 47.619 0.00 0.00 0.00 2.85
3141 6810 3.249080 ACGTTAATGAGTTCACAAACGGG 59.751 43.478 23.28 7.94 44.58 5.28
3161 6830 1.796151 GATGACATGGGTGCACACG 59.204 57.895 20.43 5.73 0.00 4.49
3166 6835 1.745232 TAAACCGATGACATGGGTGC 58.255 50.000 21.35 0.00 40.77 5.01
3249 6920 7.581213 ATGGTTTGTCATTTTGTCTAAGTCA 57.419 32.000 0.00 0.00 0.00 3.41
3307 6978 2.226437 ACTAGTTTTTGTCCATGCGCTG 59.774 45.455 9.73 4.25 0.00 5.18
3312 6983 4.455877 GGGTCTGACTAGTTTTTGTCCATG 59.544 45.833 7.85 0.00 32.67 3.66
3330 7001 0.400594 GCTAACTGGGTTGTGGGTCT 59.599 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.