Multiple sequence alignment - TraesCS6B01G205700

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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 TraesCS6B01G205700 chr6B 100.000 4026 0 0 1 4026 257783981 257779956 0.000000e+00 7435
1 TraesCS6B01G205700 chr6B 91.801 3732 182 43 341 4026 228758164 228754511 0.000000e+00 5083
2 TraesCS6B01G205700 chr6B 92.651 3157 166 29 891 4026 230602356 230605467 0.000000e+00 4484
3 TraesCS6B01G205700 chr6B 87.607 1396 120 24 917 2305 213521194 213522543 0.000000e+00 1570
4 TraesCS6B01G205700 chr6B 89.542 153 16 0 186 338 257792805 257792653 1.140000e-45 195
5 TraesCS6B01G205700 chr6B 88.722 133 7 7 699 823 257792712 257792580 5.390000e-34 156
6 TraesCS6B01G205700 chr6D 97.482 3654 64 7 399 4026 146506060 146509711 0.000000e+00 6213
7 TraesCS6B01G205700 chr6D 97.962 3091 44 4 949 4026 131032865 131029781 0.000000e+00 5341
8 TraesCS6B01G205700 chr6D 94.473 3094 100 17 387 3436 130214235 130211169 0.000000e+00 4700
9 TraesCS6B01G205700 chr6D 86.733 603 56 13 338 919 131033466 131032867 0.000000e+00 649
10 TraesCS6B01G205700 chr6D 86.139 606 34 19 3424 4026 130211153 130210595 3.440000e-170 608
11 TraesCS6B01G205700 chr6D 92.537 402 30 0 2 403 146504074 146504475 9.700000e-161 577
12 TraesCS6B01G205700 chr6D 87.349 332 41 1 5 336 130391133 130390803 2.940000e-101 379
13 TraesCS6B01G205700 chr6D 86.350 337 46 0 2 338 146387379 146387715 6.360000e-98 368
14 TraesCS6B01G205700 chr6D 87.970 133 7 8 699 823 130390859 130390728 9.020000e-32 148
15 TraesCS6B01G205700 chr6D 86.869 99 13 0 342 440 146390512 146390610 1.180000e-20 111
16 TraesCS6B01G205700 chr6A 92.828 3179 139 33 868 4026 171738696 171741805 0.000000e+00 4525
17 TraesCS6B01G205700 chr6A 93.973 1908 71 18 699 2585 169226964 169225080 0.000000e+00 2846
18 TraesCS6B01G205700 chr6A 93.515 1465 62 10 2581 4026 169221052 169219602 0.000000e+00 2148
19 TraesCS6B01G205700 chr6A 88.994 1163 57 31 1024 2179 162911123 162912221 0.000000e+00 1373
20 TraesCS6B01G205700 chr6A 87.685 812 73 13 3084 3893 162913701 162914487 0.000000e+00 920
21 TraesCS6B01G205700 chr6A 93.548 620 27 2 2410 3018 162913035 162913652 0.000000e+00 911
22 TraesCS6B01G205700 chr6A 85.583 652 69 12 441 1074 169254958 169254314 0.000000e+00 660
23 TraesCS6B01G205700 chr6A 87.281 456 45 8 245 690 169227477 169227025 3.590000e-140 508
24 TraesCS6B01G205700 chr6A 92.308 156 12 0 2263 2418 162912224 162912379 5.240000e-54 222
25 TraesCS6B01G205700 chr6A 94.118 102 2 3 836 936 171738604 171738702 6.970000e-33 152
26 TraesCS6B01G205700 chr6A 95.604 91 4 0 3936 4026 162914481 162914571 3.240000e-31 147
27 TraesCS6B01G205700 chr6A 77.941 204 29 10 785 984 162909501 162909692 3.290000e-21 113
28 TraesCS6B01G205700 chr5B 94.440 1133 53 4 1898 3021 84884569 84883438 0.000000e+00 1735
29 TraesCS6B01G205700 chr5B 92.317 859 49 7 3170 4026 84883226 84882383 0.000000e+00 1205
30 TraesCS6B01G205700 chr5B 86.391 338 40 4 2 335 84891897 84891562 8.220000e-97 364
31 TraesCS6B01G205700 chr5B 87.248 149 5 2 3037 3173 84883451 84883305 1.500000e-34 158
32 TraesCS6B01G205700 chr1D 87.218 133 8 7 699 823 266787784 266787653 4.190000e-30 143


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 TraesCS6B01G205700 chr6B 257779956 257783981 4025 True 7435.000000 7435 100.000000 1 4026 1 chr6B.!!$R2 4025
1 TraesCS6B01G205700 chr6B 228754511 228758164 3653 True 5083.000000 5083 91.801000 341 4026 1 chr6B.!!$R1 3685
2 TraesCS6B01G205700 chr6B 230602356 230605467 3111 False 4484.000000 4484 92.651000 891 4026 1 chr6B.!!$F2 3135
3 TraesCS6B01G205700 chr6B 213521194 213522543 1349 False 1570.000000 1570 87.607000 917 2305 1 chr6B.!!$F1 1388
4 TraesCS6B01G205700 chr6D 146504074 146509711 5637 False 3395.000000 6213 95.009500 2 4026 2 chr6D.!!$F2 4024
5 TraesCS6B01G205700 chr6D 131029781 131033466 3685 True 2995.000000 5341 92.347500 338 4026 2 chr6D.!!$R3 3688
6 TraesCS6B01G205700 chr6D 130210595 130214235 3640 True 2654.000000 4700 90.306000 387 4026 2 chr6D.!!$R1 3639
7 TraesCS6B01G205700 chr6D 146387379 146390610 3231 False 239.500000 368 86.609500 2 440 2 chr6D.!!$F1 438
8 TraesCS6B01G205700 chr6A 171738604 171741805 3201 False 2338.500000 4525 93.473000 836 4026 2 chr6A.!!$F2 3190
9 TraesCS6B01G205700 chr6A 169219602 169221052 1450 True 2148.000000 2148 93.515000 2581 4026 1 chr6A.!!$R1 1445
10 TraesCS6B01G205700 chr6A 169225080 169227477 2397 True 1677.000000 2846 90.627000 245 2585 2 chr6A.!!$R3 2340
11 TraesCS6B01G205700 chr6A 169254314 169254958 644 True 660.000000 660 85.583000 441 1074 1 chr6A.!!$R2 633
12 TraesCS6B01G205700 chr6A 162909501 162914571 5070 False 614.333333 1373 89.346667 785 4026 6 chr6A.!!$F1 3241
13 TraesCS6B01G205700 chr5B 84882383 84884569 2186 True 1032.666667 1735 91.335000 1898 4026 3 chr5B.!!$R2 2128

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
210 211 0.244994 CTATTGCTAGAGCGGCCGAT 59.755 55.00 33.48 27.37 45.83 4.18 F
888 2637 0.674895 CCAGCCTGACTCGGGAAAAG 60.675 60.00 8.24 0.00 29.82 2.27 F
1927 5114 0.398318 GTCAGGAGGAAGCACCAAGT 59.602 55.00 2.96 0.00 42.04 3.16 F
2355 5623 5.069501 AGAAGCCATCAAAATCTTTGCTC 57.930 39.13 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 4816 1.000771 CGAGGAGGTGGAGGAGTGA 60.001 63.158 0.00 0.00 0.00 3.41 R
2355 5623 0.443869 CAACAGAAATGACGGGCTCG 59.556 55.000 3.27 3.27 43.02 5.03 R
2806 6935 1.142060 TCCGACACCAAACCATCTTGT 59.858 47.619 0.00 0.00 0.00 3.16 R
3685 9693 1.431243 AGCCACCCAGACCCAAAAATA 59.569 47.619 0.00 0.00 0.00 1.40 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
23 24 0.833287 GATGCTACAAGCCAGGAGGA 59.167 55.000 0.00 0.00 41.51 3.71
49 50 0.478072 ACAAGGTGGGTGATGCTTCA 59.522 50.000 0.00 0.00 0.00 3.02
71 72 3.487563 GGTGTTGAACCGGATTGATTC 57.512 47.619 9.46 0.60 39.81 2.52
81 82 2.193447 CGGATTGATTCGACGACACAT 58.807 47.619 0.00 0.00 0.00 3.21
188 189 1.501170 AGATCCGAGATTCCTCCTCCA 59.499 52.381 0.00 0.00 36.04 3.86
192 193 2.447429 TCCGAGATTCCTCCTCCATACT 59.553 50.000 0.00 0.00 36.04 2.12
193 194 3.656264 TCCGAGATTCCTCCTCCATACTA 59.344 47.826 0.00 0.00 36.04 1.82
210 211 0.244994 CTATTGCTAGAGCGGCCGAT 59.755 55.000 33.48 27.37 45.83 4.18
347 348 2.741985 CAACACATGGAGCGGCGA 60.742 61.111 12.98 0.00 0.00 5.54
533 2148 3.637273 GTGGGAGGTGAAGCCGGT 61.637 66.667 1.90 0.00 43.70 5.28
558 2173 1.670083 GGGTTCGGGACAACGGAAG 60.670 63.158 0.00 0.00 33.72 3.46
617 2236 1.819632 GAATTGGGCTCGCGGATGT 60.820 57.895 6.13 0.00 0.00 3.06
690 2310 2.694303 GCCGGGGATATAGGATGGATCT 60.694 54.545 2.18 0.00 0.00 2.75
888 2637 0.674895 CCAGCCTGACTCGGGAAAAG 60.675 60.000 8.24 0.00 29.82 2.27
1018 2794 4.093408 CGAAATCTCAATCTTTCGCCTTCA 59.907 41.667 4.73 0.00 44.70 3.02
1629 4816 1.741770 CCAAGCGCCGCTCTTACTT 60.742 57.895 14.01 0.00 38.25 2.24
1927 5114 0.398318 GTCAGGAGGAAGCACCAAGT 59.602 55.000 2.96 0.00 42.04 3.16
2355 5623 5.069501 AGAAGCCATCAAAATCTTTGCTC 57.930 39.130 0.00 0.00 0.00 4.26
2806 6935 5.815581 ACAATATCCTTCAGCTGTTAACCA 58.184 37.500 14.67 0.00 0.00 3.67
3003 7741 8.974060 TCTTAAATTGGATGGTATACACCTTC 57.026 34.615 5.01 0.00 45.98 3.46
3412 9371 9.900112 AGAAGAGGGAGTATAATAATAACCTGT 57.100 33.333 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.231736 ACCCACCTTGTCGCGTCT 61.232 61.111 5.77 0.00 0.00 4.18
70 71 1.333931 GATAGAGCCATGTGTCGTCGA 59.666 52.381 0.00 0.00 0.00 4.20
71 72 1.335182 AGATAGAGCCATGTGTCGTCG 59.665 52.381 0.00 0.00 0.00 5.12
81 82 3.619900 ACCAGACCATAGATAGAGCCA 57.380 47.619 0.00 0.00 0.00 4.75
121 122 4.393990 GGGTTAGGGTTGATTAAGACGTTG 59.606 45.833 0.00 0.00 0.00 4.10
188 189 1.202582 CGGCCGCTCTAGCAATAGTAT 59.797 52.381 14.67 0.00 42.21 2.12
192 193 0.038251 CATCGGCCGCTCTAGCAATA 60.038 55.000 23.51 0.00 42.21 1.90
193 194 1.301244 CATCGGCCGCTCTAGCAAT 60.301 57.895 23.51 2.39 42.21 3.56
210 211 0.693049 GCTGGTTTCCTCTCCCTTCA 59.307 55.000 0.00 0.00 0.00 3.02
243 244 2.954611 GACAGGGTCCTTTTGCGC 59.045 61.111 0.00 0.00 0.00 6.09
347 348 1.078426 CCGCTCCAATTCCTTCCGT 60.078 57.895 0.00 0.00 0.00 4.69
455 2053 2.106683 CCTCGCGGCTCCGAAATTT 61.107 57.895 13.11 0.00 42.83 1.82
477 2075 2.282958 TCCTCTGACCTCGCCGTT 60.283 61.111 0.00 0.00 0.00 4.44
533 2148 1.345415 GTTGTCCCGAACCCACTTCTA 59.655 52.381 0.00 0.00 0.00 2.10
558 2173 1.109323 CCCGATTTTGCTGATCCCCC 61.109 60.000 0.00 0.00 0.00 5.40
589 2208 1.537202 GAGCCCAATTCCGTCATATGC 59.463 52.381 0.00 0.00 0.00 3.14
643 2263 4.819105 ACAGATACTTCAAATCGGGTCA 57.181 40.909 0.00 0.00 0.00 4.02
645 2265 5.160607 TGAACAGATACTTCAAATCGGGT 57.839 39.130 0.00 0.00 0.00 5.28
690 2310 1.271488 CGGTTAGGGTTAGGGTTTGCA 60.271 52.381 0.00 0.00 0.00 4.08
727 2399 4.807643 GCCTTCTAACTCCAAATCCACACT 60.808 45.833 0.00 0.00 0.00 3.55
792 2482 0.533755 ATTACGATCAGGCAGGCTGC 60.534 55.000 30.93 30.93 44.08 5.25
888 2637 2.657184 CGAACACGGATTGGGTTTTTC 58.343 47.619 0.00 0.00 0.00 2.29
1564 4751 1.141019 GAAGGCGGCAGACGTATGA 59.859 57.895 15.63 0.00 46.52 2.15
1629 4816 1.000771 CGAGGAGGTGGAGGAGTGA 60.001 63.158 0.00 0.00 0.00 3.41
1664 4851 3.181438 CGGAGAAGGAGAAGGAGGATCTA 60.181 52.174 0.00 0.00 33.73 1.98
1927 5114 3.042682 TGACCCCTAGTGTGACAAGAAA 58.957 45.455 0.00 0.00 0.00 2.52
2355 5623 0.443869 CAACAGAAATGACGGGCTCG 59.556 55.000 3.27 3.27 43.02 5.03
2806 6935 1.142060 TCCGACACCAAACCATCTTGT 59.858 47.619 0.00 0.00 0.00 3.16
3035 7776 4.572978 TCCCCATCAACCTAAAGCCTATA 58.427 43.478 0.00 0.00 0.00 1.31
3068 7809 2.884639 GGGAGTAAGCAACACACACATT 59.115 45.455 0.00 0.00 0.00 2.71
3412 9371 7.255242 GCTAACTATTGATAGGCAAAATGCTCA 60.255 37.037 2.00 0.00 44.28 4.26
3422 9381 6.927294 ACAAACTGCTAACTATTGATAGGC 57.073 37.500 3.30 0.00 34.69 3.93
3681 9689 4.263287 GCCACCCAGACCCAAAAATAAAAT 60.263 41.667 0.00 0.00 0.00 1.82
3682 9690 3.071747 GCCACCCAGACCCAAAAATAAAA 59.928 43.478 0.00 0.00 0.00 1.52
3683 9691 2.635427 GCCACCCAGACCCAAAAATAAA 59.365 45.455 0.00 0.00 0.00 1.40
3684 9692 2.158234 AGCCACCCAGACCCAAAAATAA 60.158 45.455 0.00 0.00 0.00 1.40
3685 9693 1.431243 AGCCACCCAGACCCAAAAATA 59.569 47.619 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.