Multiple sequence alignment - TraesCS3B01G466100

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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 TraesCS3B01G466100 chr3B 100.000 2156 0 0 1 2156 708715940 708718095 0.000000e+00 3982
1 TraesCS3B01G466100 chr3B 95.797 690 26 3 1467 2156 225991773 225992459 0.000000e+00 1110
2 TraesCS3B01G466100 chr3B 94.032 687 26 6 1 687 225177588 225176917 0.000000e+00 1027
3 TraesCS3B01G466100 chr3B 94.483 145 8 0 1198 1342 225991014 225991158 7.740000e-55 224
4 TraesCS3B01G466100 chr3B 95.614 114 5 0 1908 2021 647524470 647524357 1.310000e-42 183
5 TraesCS3B01G466100 chr5B 96.429 2156 45 2 1 2156 473282603 473280480 0.000000e+00 3526
6 TraesCS3B01G466100 chr5B 92.258 155 8 3 2005 2156 467180021 467180174 1.300000e-52 217
7 TraesCS3B01G466100 chr7D 96.361 687 18 4 1470 2156 477930635 477929956 0.000000e+00 1123
8 TraesCS3B01G466100 chr7D 95.376 173 8 0 1 173 272826573 272826401 2.110000e-70 276
9 TraesCS3B01G466100 chr7D 96.471 85 3 0 271 355 272826406 272826322 8.020000e-30 141
10 TraesCS3B01G466100 chr4A 94.913 688 30 4 1470 2156 92766538 92765855 0.000000e+00 1072
11 TraesCS3B01G466100 chr4A 87.371 483 58 1 689 1168 95386974 95386492 3.130000e-153 551
12 TraesCS3B01G466100 chr4A 92.857 210 13 2 1471 1680 717673303 717673096 9.670000e-79 303
13 TraesCS3B01G466100 chr4A 96.350 137 4 1 2020 2156 594067871 594068006 7.740000e-55 224
14 TraesCS3B01G466100 chr3D 94.614 687 30 5 1 687 189777763 189778442 0.000000e+00 1057
15 TraesCS3B01G466100 chr3D 94.469 687 23 6 1 687 153510430 153509759 0.000000e+00 1044
16 TraesCS3B01G466100 chr3D 93.404 470 28 2 699 1168 189781184 189781650 0.000000e+00 693
17 TraesCS3B01G466100 chr3D 92.903 155 7 3 2005 2156 394065137 394064984 2.790000e-54 222
18 TraesCS3B01G466100 chr3A 94.006 684 26 5 1 684 176144560 176145228 0.000000e+00 1022
19 TraesCS3B01G466100 chr1D 95.516 446 20 0 716 1161 442107961 442107516 0.000000e+00 713
20 TraesCS3B01G466100 chr1D 85.340 382 36 7 1470 1831 390680761 390680380 5.620000e-101 377
21 TraesCS3B01G466100 chr1D 87.845 181 15 3 1166 1340 390666908 390667087 2.800000e-49 206
22 TraesCS3B01G466100 chr1D 87.097 186 16 6 1166 1345 390681987 390681804 1.010000e-48 204
23 TraesCS3B01G466100 chr1D 95.402 87 3 1 1827 1912 390668117 390668203 1.040000e-28 137
24 TraesCS3B01G466100 chr1D 93.333 90 4 2 1827 1914 390679693 390679604 4.830000e-27 132
25 TraesCS3B01G466100 chr1B 90.591 457 43 0 705 1161 439537991 439537535 6.580000e-170 606
26 TraesCS3B01G466100 chr1B 93.629 361 21 2 1471 1831 523010751 523011109 2.430000e-149 538
27 TraesCS3B01G466100 chr1B 90.055 362 36 0 1470 1831 523148664 523148303 9.010000e-129 470
28 TraesCS3B01G466100 chr1B 92.258 155 8 3 2005 2156 155426494 155426341 1.300000e-52 217
29 TraesCS3B01G466100 chr1B 91.613 155 9 3 2005 2156 155697408 155697561 6.030000e-51 211
30 TraesCS3B01G466100 chr1B 95.000 120 6 0 1908 2027 155426650 155426531 2.820000e-44 189
31 TraesCS3B01G466100 chr1B 95.000 120 6 0 1908 2027 155697252 155697371 2.820000e-44 189
32 TraesCS3B01G466100 chr1B 98.851 87 0 1 1827 1912 523011770 523011856 1.030000e-33 154
33 TraesCS3B01G466100 chr1B 95.556 90 2 2 1827 1914 523147640 523147551 2.230000e-30 143
34 TraesCS3B01G466100 chr6B 86.975 476 59 1 689 1161 172267848 172267373 1.130000e-147 532
35 TraesCS3B01G466100 chr1A 93.094 362 22 2 1470 1831 488226845 488226487 5.270000e-146 527
36 TraesCS3B01G466100 chr1A 94.737 171 9 0 1661 1831 142891117 142891287 1.270000e-67 267
37 TraesCS3B01G466100 chr1A 89.130 184 15 2 1166 1345 488227656 488227474 7.740000e-55 224
38 TraesCS3B01G466100 chr7B 86.765 476 56 3 689 1161 336597947 336597476 6.820000e-145 523
39 TraesCS3B01G466100 chr7B 86.128 483 64 1 689 1168 209400688 209401170 3.170000e-143 518
40 TraesCS3B01G466100 chr7B 97.475 198 5 0 1 198 209397330 209397527 2.650000e-89 339
41 TraesCS3B01G466100 chr7B 93.810 210 10 2 1471 1680 426807798 426807592 1.610000e-81 313
42 TraesCS3B01G466100 chr7B 94.410 161 9 0 527 687 474731790 474731950 4.600000e-62 248
43 TraesCS3B01G466100 chr7B 95.620 137 6 0 1206 1342 209401313 209401449 1.000000e-53 220
44 TraesCS3B01G466100 chr7B 98.551 69 1 0 1 69 332400399 332400467 2.910000e-24 122
45 TraesCS3B01G466100 chr2D 86.526 475 61 1 697 1168 110056727 110056253 8.820000e-144 520
46 TraesCS3B01G466100 chr2D 88.636 176 11 6 354 529 548888271 548888437 2.800000e-49 206
47 TraesCS3B01G466100 chr7A 93.082 318 15 2 370 687 579007868 579008178 1.950000e-125 459
48 TraesCS3B01G466100 chr7A 95.858 169 7 0 177 345 579007268 579007436 7.580000e-70 274
49 TraesCS3B01G466100 chr5A 93.617 235 10 2 455 685 129146987 129147220 1.580000e-91 346
50 TraesCS3B01G466100 chr6A 95.706 163 7 0 183 345 531299544 531299382 1.640000e-66 263
51 TraesCS3B01G466100 chr6A 89.655 174 11 5 369 542 531298040 531297874 4.660000e-52 215
52 TraesCS3B01G466100 chr4B 90.683 161 15 0 527 687 195445525 195445685 4.660000e-52 215
53 TraesCS3B01G466100 chrUn 97.368 114 3 0 1908 2021 317015990 317016103 6.070000e-46 195
54 TraesCS3B01G466100 chr2A 95.000 120 6 0 1908 2027 718256026 718256145 2.820000e-44 189


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 TraesCS3B01G466100 chr3B 708715940 708718095 2155 False 3982.000000 3982 100.000000 1 2156 1 chr3B.!!$F1 2155
1 TraesCS3B01G466100 chr3B 225176917 225177588 671 True 1027.000000 1027 94.032000 1 687 1 chr3B.!!$R1 686
2 TraesCS3B01G466100 chr3B 225991014 225992459 1445 False 667.000000 1110 95.140000 1198 2156 2 chr3B.!!$F2 958
3 TraesCS3B01G466100 chr5B 473280480 473282603 2123 True 3526.000000 3526 96.429000 1 2156 1 chr5B.!!$R1 2155
4 TraesCS3B01G466100 chr7D 477929956 477930635 679 True 1123.000000 1123 96.361000 1470 2156 1 chr7D.!!$R1 686
5 TraesCS3B01G466100 chr4A 92765855 92766538 683 True 1072.000000 1072 94.913000 1470 2156 1 chr4A.!!$R1 686
6 TraesCS3B01G466100 chr3D 153509759 153510430 671 True 1044.000000 1044 94.469000 1 687 1 chr3D.!!$R1 686
7 TraesCS3B01G466100 chr3D 189777763 189781650 3887 False 875.000000 1057 94.009000 1 1168 2 chr3D.!!$F1 1167
8 TraesCS3B01G466100 chr3A 176144560 176145228 668 False 1022.000000 1022 94.006000 1 684 1 chr3A.!!$F1 683
9 TraesCS3B01G466100 chr1D 390679604 390681987 2383 True 237.666667 377 88.590000 1166 1914 3 chr1D.!!$R2 748
10 TraesCS3B01G466100 chr1B 523010751 523011856 1105 False 346.000000 538 96.240000 1471 1912 2 chr1B.!!$F2 441
11 TraesCS3B01G466100 chr1B 523147551 523148664 1113 True 306.500000 470 92.805500 1470 1914 2 chr1B.!!$R3 444
12 TraesCS3B01G466100 chr1A 488226487 488227656 1169 True 375.500000 527 91.112000 1166 1831 2 chr1A.!!$R1 665
13 TraesCS3B01G466100 chr7B 209397330 209401449 4119 False 359.000000 518 93.074333 1 1342 3 chr7B.!!$F3 1341
14 TraesCS3B01G466100 chr7A 579007268 579008178 910 False 366.500000 459 94.470000 177 687 2 chr7A.!!$F1 510
15 TraesCS3B01G466100 chr6A 531297874 531299544 1670 True 239.000000 263 92.680500 183 542 2 chr6A.!!$R1 359

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
771 4948 0.106819 ATGGTCCAAGAGATGCTGCC 60.107 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 7022 3.596214 TCTCCTTCTACACGCAAAATCC 58.404 45.455 0.0 0.0 0.0 3.01 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
114 115 4.741781 CGCCAGAGTTTTGCCGCG 62.742 66.667 0.00 0.00 0.00 6.46
199 216 2.792674 CTGTTTGCTGCTGTTTGATGTG 59.207 45.455 0.00 0.00 0.00 3.21
349 389 5.081728 TGTCTGGTCCTAACTGTTAAGCTA 58.918 41.667 1.46 0.00 0.00 3.32
457 1794 9.881649 GCCTGAACTGAAAGATATGATATGATA 57.118 33.333 0.00 0.00 37.43 2.15
765 4942 3.641434 CCAAGTGATGGTCCAAGAGAT 57.359 47.619 0.00 0.00 44.85 2.75
766 4943 3.276857 CCAAGTGATGGTCCAAGAGATG 58.723 50.000 0.00 0.00 44.85 2.90
767 4944 2.681848 CAAGTGATGGTCCAAGAGATGC 59.318 50.000 0.00 0.00 0.00 3.91
768 4945 2.194859 AGTGATGGTCCAAGAGATGCT 58.805 47.619 0.00 0.00 0.00 3.79
769 4946 2.093075 AGTGATGGTCCAAGAGATGCTG 60.093 50.000 0.00 0.00 0.00 4.41
770 4947 1.307097 GATGGTCCAAGAGATGCTGC 58.693 55.000 0.00 0.00 0.00 5.25
771 4948 0.106819 ATGGTCCAAGAGATGCTGCC 60.107 55.000 0.00 0.00 0.00 4.85
772 4949 1.452833 GGTCCAAGAGATGCTGCCC 60.453 63.158 0.00 0.00 0.00 5.36
773 4950 1.452833 GTCCAAGAGATGCTGCCCC 60.453 63.158 0.00 0.00 0.00 5.80
774 4951 1.924939 TCCAAGAGATGCTGCCCCA 60.925 57.895 0.00 0.00 0.00 4.96
775 4952 1.000521 CCAAGAGATGCTGCCCCAA 60.001 57.895 0.00 0.00 0.00 4.12
776 4953 1.035932 CCAAGAGATGCTGCCCCAAG 61.036 60.000 0.00 0.00 0.00 3.61
777 4954 0.323178 CAAGAGATGCTGCCCCAAGT 60.323 55.000 0.00 0.00 0.00 3.16
778 4955 0.323178 AAGAGATGCTGCCCCAAGTG 60.323 55.000 0.00 0.00 0.00 3.16
779 4956 1.203441 AGAGATGCTGCCCCAAGTGA 61.203 55.000 0.00 0.00 0.00 3.41
780 4957 0.106819 GAGATGCTGCCCCAAGTGAT 60.107 55.000 0.00 0.00 0.00 3.06
781 4958 0.395311 AGATGCTGCCCCAAGTGATG 60.395 55.000 0.00 0.00 0.00 3.07
889 5069 0.632835 AATGGTGGAGGTGATGGCAT 59.367 50.000 0.00 0.00 0.00 4.40
907 5087 7.891712 TGATGGCATAATATGTGGAGATCAAAT 59.108 33.333 0.00 0.00 0.00 2.32
920 5100 1.922545 GATCAAATGAAAGCAAGCGGC 59.077 47.619 0.00 0.00 45.30 6.53
951 5132 2.276201 GTTTTGTTGGCAGGGTCAAAC 58.724 47.619 8.07 2.86 31.07 2.93
1121 5302 0.815213 AGTGCTGCTGCGTTTCTTCA 60.815 50.000 11.21 0.00 43.34 3.02
1195 5376 7.149973 TCTTGTGGTCAACTACAACTACATAC 58.850 38.462 7.85 0.00 41.40 2.39
1224 5514 5.221621 GGAGAAGTGCATCTAAGCTAGGAAT 60.222 44.000 0.00 0.00 34.99 3.01
1451 6627 7.613801 TGTGCCTTGGTACTATAAATTGTGATT 59.386 33.333 9.16 0.00 0.00 2.57
1646 6891 6.683974 ATTACTGTAACATGTTCTGCCATC 57.316 37.500 15.85 0.00 0.00 3.51
1665 6910 7.503549 TGCCATCTCAAGCCATATATACTATG 58.496 38.462 0.00 0.00 0.00 2.23
1777 7022 2.159338 CGCCTGACATGATCAAAAAGGG 60.159 50.000 15.11 9.84 36.69 3.95
1795 7040 1.743394 GGGGATTTTGCGTGTAGAAGG 59.257 52.381 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 8.897752 AGATAGCAGTAAACAGAAATGAAATCC 58.102 33.333 0.00 0.00 0.00 3.01
199 216 8.144478 TCAAGATGTTAGATTCTACACATAGCC 58.856 37.037 15.41 8.41 29.81 3.93
349 389 6.594788 ATCTGGCAAACTGTCATTTTACAT 57.405 33.333 0.00 0.00 28.30 2.29
365 405 8.885693 ACTCACAGTATCTATATAATCTGGCA 57.114 34.615 0.00 0.00 0.00 4.92
760 4937 1.203441 TCACTTGGGGCAGCATCTCT 61.203 55.000 0.00 0.00 0.00 3.10
761 4938 0.106819 ATCACTTGGGGCAGCATCTC 60.107 55.000 0.00 0.00 0.00 2.75
762 4939 0.395311 CATCACTTGGGGCAGCATCT 60.395 55.000 0.00 0.00 0.00 2.90
763 4940 1.389609 CCATCACTTGGGGCAGCATC 61.390 60.000 0.00 0.00 42.33 3.91
764 4941 1.380785 CCATCACTTGGGGCAGCAT 60.381 57.895 0.00 0.00 42.33 3.79
765 4942 2.036098 CCATCACTTGGGGCAGCA 59.964 61.111 0.00 0.00 42.33 4.41
773 4950 2.681848 GCATCTCTTGGACCATCACTTG 59.318 50.000 0.00 0.00 0.00 3.16
774 4951 2.575279 AGCATCTCTTGGACCATCACTT 59.425 45.455 0.00 0.00 0.00 3.16
775 4952 2.093075 CAGCATCTCTTGGACCATCACT 60.093 50.000 0.00 0.00 0.00 3.41
776 4953 2.286872 CAGCATCTCTTGGACCATCAC 58.713 52.381 0.00 0.00 0.00 3.06
777 4954 1.407851 GCAGCATCTCTTGGACCATCA 60.408 52.381 0.00 0.00 0.00 3.07
778 4955 1.307097 GCAGCATCTCTTGGACCATC 58.693 55.000 0.00 0.00 0.00 3.51
779 4956 0.106819 GGCAGCATCTCTTGGACCAT 60.107 55.000 0.00 0.00 0.00 3.55
780 4957 1.300963 GGCAGCATCTCTTGGACCA 59.699 57.895 0.00 0.00 0.00 4.02
781 4958 1.452833 GGGCAGCATCTCTTGGACC 60.453 63.158 0.00 0.00 0.00 4.46
782 4959 0.322816 TTGGGCAGCATCTCTTGGAC 60.323 55.000 0.00 0.00 0.00 4.02
783 4960 0.405198 TTTGGGCAGCATCTCTTGGA 59.595 50.000 0.00 0.00 0.00 3.53
784 4961 0.529378 GTTTGGGCAGCATCTCTTGG 59.471 55.000 0.00 0.00 0.00 3.61
785 4962 1.201647 CTGTTTGGGCAGCATCTCTTG 59.798 52.381 0.00 0.00 0.00 3.02
786 4963 1.542492 CTGTTTGGGCAGCATCTCTT 58.458 50.000 0.00 0.00 0.00 2.85
889 5069 8.750515 TGCTTTCATTTGATCTCCACATATTA 57.249 30.769 0.00 0.00 0.00 0.98
907 5087 3.049674 CTCCGCCGCTTGCTTTCA 61.050 61.111 0.00 0.00 38.05 2.69
920 5100 1.873591 CCAACAAAACAGACTCCTCCG 59.126 52.381 0.00 0.00 0.00 4.63
951 5132 2.205022 TGGAGAACTCTTGGGCATTG 57.795 50.000 1.86 0.00 0.00 2.82
988 5169 4.339872 TGCTTTCCATCTTGTGCAAAAT 57.660 36.364 0.00 0.00 0.00 1.82
1018 5199 1.669779 GTAGGCAGCAGCTCTTTCATG 59.330 52.381 0.00 0.00 41.70 3.07
1121 5302 1.021390 CAACTCGGCCATTTCGCTCT 61.021 55.000 2.24 0.00 0.00 4.09
1195 5376 3.740764 GCTTAGATGCACTTCTCCTCTGG 60.741 52.174 0.00 0.00 0.00 3.86
1393 6401 6.479001 CACTCTTACGACCAAGAAGAAGAAAA 59.521 38.462 0.00 0.00 34.22 2.29
1451 6627 1.373435 CAGTCCGGTACCAAGGCAA 59.627 57.895 13.54 0.00 0.00 4.52
1596 6824 6.832384 AGATGAATGAAATGCATAAGTGTCCT 59.168 34.615 0.00 0.00 44.65 3.85
1597 6825 7.035840 AGATGAATGAAATGCATAAGTGTCC 57.964 36.000 0.00 0.00 44.65 4.02
1646 6891 8.005192 TCTCTGCATAGTATATATGGCTTGAG 57.995 38.462 0.00 0.00 0.00 3.02
1777 7022 3.596214 TCTCCTTCTACACGCAAAATCC 58.404 45.455 0.00 0.00 0.00 3.01
1795 7040 3.924144 ACACTTCACTTCATCAGCTCTC 58.076 45.455 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.