Multiple sequence alignment - TraesCS3B01G446600

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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 TraesCS3B01G446600 chr3B 100.000 2972 0 0 1 2972 685942604 685939633 0.000000e+00 5489
1 TraesCS3B01G446600 chr3B 93.340 2162 127 7 1 2156 685981057 685978907 0.000000e+00 3179
2 TraesCS3B01G446600 chr3B 87.546 1622 143 31 569 2182 686044976 686043406 0.000000e+00 1821
3 TraesCS3B01G446600 chr3B 87.061 1538 152 21 567 2089 685910539 685909034 0.000000e+00 1694
4 TraesCS3B01G446600 chr3B 89.529 1337 124 10 1006 2329 686021957 686020624 0.000000e+00 1679
5 TraesCS3B01G446600 chr3B 85.624 1579 164 26 618 2178 685875546 685874013 0.000000e+00 1600
6 TraesCS3B01G446600 chr3B 86.804 1311 136 13 791 2090 685763762 685762478 0.000000e+00 1428
7 TraesCS3B01G446600 chr3B 92.823 627 39 2 2346 2972 738284923 738285543 0.000000e+00 904
8 TraesCS3B01G446600 chr3D 95.293 1657 68 4 690 2342 520684435 520682785 0.000000e+00 2619
9 TraesCS3B01G446600 chr3D 86.947 1762 181 25 592 2329 520703919 520702183 0.000000e+00 1934
10 TraesCS3B01G446600 chr3D 87.386 1538 148 19 567 2089 520678623 520677117 0.000000e+00 1724
11 TraesCS3B01G446600 chr3D 93.829 632 38 1 2342 2972 170543174 170543805 0.000000e+00 950
12 TraesCS3B01G446600 chr3D 93.485 307 10 5 391 696 520685032 520684735 5.840000e-122 448
13 TraesCS3B01G446600 chr3D 93.103 261 14 3 1 260 520700970 520700713 2.160000e-101 379
14 TraesCS3B01G446600 chr3D 85.756 344 30 13 618 950 520642203 520641868 2.190000e-91 346
15 TraesCS3B01G446600 chr3D 90.260 154 9 1 258 405 520690910 520690757 2.340000e-46 196
16 TraesCS3B01G446600 chr3A 85.642 1588 166 25 609 2178 658186488 658188031 0.000000e+00 1613
17 TraesCS3B01G446600 chr3A 86.591 1499 150 22 609 2089 655936991 655935526 0.000000e+00 1607
18 TraesCS3B01G446600 chr3A 84.501 471 58 9 1855 2321 655944089 655943630 4.520000e-123 451
19 TraesCS3B01G446600 chr7B 93.038 632 43 1 2342 2972 517318215 517318846 0.000000e+00 922
20 TraesCS3B01G446600 chr7B 92.210 629 48 1 2342 2969 231724371 231723743 0.000000e+00 889
21 TraesCS3B01G446600 chr6B 92.698 630 45 1 2341 2969 173799722 173799093 0.000000e+00 907
22 TraesCS3B01G446600 chr2B 92.575 633 45 2 2340 2970 565068106 565067474 0.000000e+00 907
23 TraesCS3B01G446600 chr5B 92.429 634 46 2 2340 2972 282083082 282083714 0.000000e+00 904
24 TraesCS3B01G446600 chr6D 92.417 633 44 3 2341 2972 84236144 84236773 0.000000e+00 900
25 TraesCS3B01G446600 chr5D 92.089 632 48 1 2341 2972 370715422 370716051 0.000000e+00 889


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 TraesCS3B01G446600 chr3B 685939633 685942604 2971 True 5489.0 5489 100.000 1 2972 1 chr3B.!!$R4 2971
1 TraesCS3B01G446600 chr3B 685978907 685981057 2150 True 3179.0 3179 93.340 1 2156 1 chr3B.!!$R5 2155
2 TraesCS3B01G446600 chr3B 686043406 686044976 1570 True 1821.0 1821 87.546 569 2182 1 chr3B.!!$R7 1613
3 TraesCS3B01G446600 chr3B 685909034 685910539 1505 True 1694.0 1694 87.061 567 2089 1 chr3B.!!$R3 1522
4 TraesCS3B01G446600 chr3B 686020624 686021957 1333 True 1679.0 1679 89.529 1006 2329 1 chr3B.!!$R6 1323
5 TraesCS3B01G446600 chr3B 685874013 685875546 1533 True 1600.0 1600 85.624 618 2178 1 chr3B.!!$R2 1560
6 TraesCS3B01G446600 chr3B 685762478 685763762 1284 True 1428.0 1428 86.804 791 2090 1 chr3B.!!$R1 1299
7 TraesCS3B01G446600 chr3B 738284923 738285543 620 False 904.0 904 92.823 2346 2972 1 chr3B.!!$F1 626
8 TraesCS3B01G446600 chr3D 520677117 520678623 1506 True 1724.0 1724 87.386 567 2089 1 chr3D.!!$R2 1522
9 TraesCS3B01G446600 chr3D 520682785 520685032 2247 True 1533.5 2619 94.389 391 2342 2 chr3D.!!$R4 1951
10 TraesCS3B01G446600 chr3D 520700713 520703919 3206 True 1156.5 1934 90.025 1 2329 2 chr3D.!!$R5 2328
11 TraesCS3B01G446600 chr3D 170543174 170543805 631 False 950.0 950 93.829 2342 2972 1 chr3D.!!$F1 630
12 TraesCS3B01G446600 chr3A 658186488 658188031 1543 False 1613.0 1613 85.642 609 2178 1 chr3A.!!$F1 1569
13 TraesCS3B01G446600 chr3A 655935526 655936991 1465 True 1607.0 1607 86.591 609 2089 1 chr3A.!!$R1 1480
14 TraesCS3B01G446600 chr7B 517318215 517318846 631 False 922.0 922 93.038 2342 2972 1 chr7B.!!$F1 630
15 TraesCS3B01G446600 chr7B 231723743 231724371 628 True 889.0 889 92.210 2342 2969 1 chr7B.!!$R1 627
16 TraesCS3B01G446600 chr6B 173799093 173799722 629 True 907.0 907 92.698 2341 2969 1 chr6B.!!$R1 628
17 TraesCS3B01G446600 chr2B 565067474 565068106 632 True 907.0 907 92.575 2340 2970 1 chr2B.!!$R1 630
18 TraesCS3B01G446600 chr5B 282083082 282083714 632 False 904.0 904 92.429 2340 2972 1 chr5B.!!$F1 632
19 TraesCS3B01G446600 chr6D 84236144 84236773 629 False 900.0 900 92.417 2341 2972 1 chr6D.!!$F1 631
20 TraesCS3B01G446600 chr5D 370715422 370716051 629 False 889.0 889 92.089 2341 2972 1 chr5D.!!$F1 631

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
941 1286 1.066143 TCTAGCAGCTAGGTTGCCAAC 60.066 52.381 26.28 0.0 40.57 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 2982 1.135731 CTCTGACTCTCGTGTCGGC 59.864 63.158 8.95 0.0 41.67 5.54 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
146 147 4.846779 ATTACACGCATCAACCAAAGTT 57.153 36.364 0.00 0.00 36.33 2.66
160 161 7.701445 TCAACCAAAGTTAAAAATGCAAATGG 58.299 30.769 0.00 0.00 33.27 3.16
266 267 2.115343 TAACATAACATGTGGCCGCA 57.885 45.000 23.66 23.66 44.07 5.69
267 268 1.252175 AACATAACATGTGGCCGCAA 58.748 45.000 25.33 7.03 44.07 4.85
310 311 6.827586 TCTAAACCAAAACTGTTGTCTGTT 57.172 33.333 0.00 0.00 37.33 3.16
348 349 7.271539 CGTGTATAAAATATGACCTTCGTTCG 58.728 38.462 0.00 0.00 0.00 3.95
376 377 2.766828 AGACGTTTCTTAGGCTAGGCAT 59.233 45.455 19.70 6.29 0.00 4.40
383 384 5.693769 TTCTTAGGCTAGGCATAACAAGT 57.306 39.130 19.70 0.00 31.57 3.16
606 609 1.069973 CGCCACCATACGCAACATATG 60.070 52.381 0.00 0.00 0.00 1.78
847 1187 2.627699 AGTTCAACATCCCGCAAAATGT 59.372 40.909 0.00 0.00 37.71 2.71
933 1278 2.968574 TCATTCCCTTCTAGCAGCTAGG 59.031 50.000 26.28 15.23 35.03 3.02
941 1286 1.066143 TCTAGCAGCTAGGTTGCCAAC 60.066 52.381 26.28 0.00 40.57 3.77
1299 1659 3.998672 GACAACGACCTCCCGGCA 61.999 66.667 0.00 0.00 0.00 5.69
1344 1704 0.172578 CCAACGATAGGTCAGCACGA 59.827 55.000 0.00 0.00 43.77 4.35
1720 2080 1.796017 TGACACAGTCACCCCTAACA 58.204 50.000 0.00 0.00 37.67 2.41
1779 2139 1.977293 GCGCCCCTCTTCCTTCAGAT 61.977 60.000 0.00 0.00 0.00 2.90
1872 2232 7.539436 GTCAAAAGGACTTCTTCAAGAACTTT 58.461 34.615 7.94 7.94 43.46 2.66
1964 2324 1.210967 TCGGAGGGTGAACAACAAACT 59.789 47.619 0.00 0.00 0.00 2.66
1965 2325 2.435069 TCGGAGGGTGAACAACAAACTA 59.565 45.455 0.00 0.00 0.00 2.24
2018 2378 4.814234 TGTGAACTCATTGTCCTTGTGTAC 59.186 41.667 0.00 0.00 0.00 2.90
2237 2607 2.309764 GACATGTCATGGAACCGCGC 62.310 60.000 21.07 0.00 33.60 6.86
2246 2617 1.295792 TGGAACCGCGCATCTATTTC 58.704 50.000 8.75 0.00 0.00 2.17
2258 2632 6.542852 GCGCATCTATTTCTGTTAGTTTTGA 58.457 36.000 0.30 0.00 0.00 2.69
2325 2701 7.389330 TGGAATGTCGTATTAACAAAGTGACAT 59.611 33.333 0.00 0.00 44.78 3.06
2334 2710 9.410556 GTATTAACAAAGTGACATGAAGCAAAT 57.589 29.630 0.00 0.00 0.00 2.32
2342 2718 7.197071 AGTGACATGAAGCAAATACGTTTTA 57.803 32.000 0.00 0.00 0.00 1.52
2343 2719 7.075741 AGTGACATGAAGCAAATACGTTTTAC 58.924 34.615 0.00 0.00 0.00 2.01
2344 2720 6.304683 GTGACATGAAGCAAATACGTTTTACC 59.695 38.462 0.00 0.00 0.00 2.85
2372 2748 4.309254 GCTTTCGCCTCGCTTTATATAC 57.691 45.455 0.00 0.00 0.00 1.47
2390 2766 4.685169 ATACAAAGCATCGACCAACAAG 57.315 40.909 0.00 0.00 0.00 3.16
2414 2790 2.248835 GGTACAAACGCACGCCACT 61.249 57.895 0.00 0.00 0.00 4.00
2417 2793 0.945265 TACAAACGCACGCCACTACC 60.945 55.000 0.00 0.00 0.00 3.18
2436 2812 1.675972 ACACACGCACACACCCAAA 60.676 52.632 0.00 0.00 0.00 3.28
2455 2831 4.511454 CCAAAGCAAGATACATAAGCGCTA 59.489 41.667 12.05 0.00 0.00 4.26
2497 2874 1.609501 ACTACAAGAGCAGCCGGGA 60.610 57.895 2.18 0.00 0.00 5.14
2550 2927 2.279741 GAAGCTGCATATGACGAACCA 58.720 47.619 6.97 0.00 0.00 3.67
2562 2939 1.299648 CGAACCATGGGCTCCAAGA 59.700 57.895 18.09 0.00 36.95 3.02
2679 3056 1.585006 GACGACGCCTTCAGGAAGA 59.415 57.895 10.52 0.00 40.79 2.87
2698 3075 2.796425 GAGCGAGCTACGTCGTCGA 61.796 63.158 15.84 0.00 42.17 4.20
2719 3096 3.757270 ACGATCCGTCTGAAGATAGGAT 58.243 45.455 15.72 15.72 42.74 3.24
2757 3134 1.537814 ATACTCACCGCCACCGAACA 61.538 55.000 0.00 0.00 36.29 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.263905 TGGACTAGCATTTTTCTGATGGGT 60.264 41.667 0.00 0.00 0.00 4.51
40 41 5.221185 CCATGGACTAGCATTTTTCTGATGG 60.221 44.000 5.56 0.00 0.00 3.51
146 147 6.236409 TGCCATCTTTCCATTTGCATTTTTA 58.764 32.000 0.00 0.00 0.00 1.52
160 161 6.091986 GCTATCTAGCTATGTTGCCATCTTTC 59.908 42.308 0.00 0.00 45.62 2.62
244 245 2.422127 GCGGCCACATGTTATGTTAAGT 59.578 45.455 2.24 0.00 42.70 2.24
245 246 2.421775 TGCGGCCACATGTTATGTTAAG 59.578 45.455 2.24 0.00 42.70 1.85
266 267 3.589951 ATTCCACTAGCCATGCTGATT 57.410 42.857 0.00 0.00 40.10 2.57
267 268 3.137913 AGAATTCCACTAGCCATGCTGAT 59.862 43.478 0.65 0.00 40.10 2.90
337 338 2.728318 GTCTTTGGTACGAACGAAGGTC 59.272 50.000 0.14 0.00 0.00 3.85
383 384 9.451002 TCTTTCGATAAAGAGAGAGACTTTCTA 57.549 33.333 0.00 0.00 44.85 2.10
606 609 5.350365 TCCTCACGAAATATTGTGTTGTAGC 59.650 40.000 5.98 0.00 41.10 3.58
933 1278 0.819582 CTGATGGATGGGTTGGCAAC 59.180 55.000 21.92 21.92 0.00 4.17
1003 1357 1.678970 AAGAGGAAACGGCCATGGC 60.679 57.895 29.47 29.47 41.06 4.40
1004 1358 0.609131 ACAAGAGGAAACGGCCATGG 60.609 55.000 7.63 7.63 0.00 3.66
1074 1428 1.144716 GACTCCATGGCTCATCGCA 59.855 57.895 6.96 0.00 41.67 5.10
1091 1445 2.271821 CACCGGCATGACCATGGA 59.728 61.111 21.47 0.00 39.16 3.41
1119 1479 3.374220 TCGTAAAAGGACGAGCTCAAA 57.626 42.857 15.40 0.00 46.43 2.69
1164 1524 1.590525 GATGACGCGCCGGACAATA 60.591 57.895 5.05 0.00 0.00 1.90
1299 1659 2.432510 GACCTCCTTCTCGGTCATGATT 59.567 50.000 0.00 0.00 46.98 2.57
1720 2080 5.109903 GCCATAGTACTTGTTGTCGAAGAT 58.890 41.667 0.00 0.00 40.67 2.40
1779 2139 3.104512 AGGATCGGACAACATTACCTGA 58.895 45.455 0.00 0.00 0.00 3.86
1828 2188 4.160329 TGACTACCAGAGAACCTGTGAAT 58.840 43.478 0.00 0.00 41.33 2.57
1869 2229 2.436646 ACCATCGAGGCCGCAAAG 60.437 61.111 7.44 0.00 43.14 2.77
1872 2232 2.739849 TTTTGACCATCGAGGCCGCA 62.740 55.000 7.44 0.00 43.14 5.69
2108 2476 9.221775 GTATGAAAATAATGGATTCACGACAAC 57.778 33.333 0.00 0.00 36.03 3.32
2258 2632 7.225784 TGCATGTTTGGTAAGTTAATGACAT 57.774 32.000 0.00 0.00 0.00 3.06
2294 2670 9.095065 ACTTTGTTAATACGACATTCCAGATAC 57.905 33.333 0.00 0.00 0.00 2.24
2298 2674 7.095397 TGTCACTTTGTTAATACGACATTCCAG 60.095 37.037 0.00 0.00 0.00 3.86
2306 2682 6.425417 TGCTTCATGTCACTTTGTTAATACGA 59.575 34.615 0.00 0.00 0.00 3.43
2325 2701 7.222999 CCTTTTTGGTAAAACGTATTTGCTTCA 59.777 33.333 0.00 0.00 0.00 3.02
2334 2710 5.272397 CGAAAGCCTTTTTGGTAAAACGTA 58.728 37.500 0.00 0.00 38.35 3.57
2372 2748 3.300009 GTTCTTGTTGGTCGATGCTTTG 58.700 45.455 0.00 0.00 0.00 2.77
2390 2766 1.570967 GTGCGTTTGTACCGGGTTC 59.429 57.895 4.31 0.00 0.00 3.62
2414 2790 1.521906 GGTGTGTGCGTGTGTGGTA 60.522 57.895 0.00 0.00 0.00 3.25
2417 2793 1.927608 TTTGGGTGTGTGCGTGTGTG 61.928 55.000 0.00 0.00 0.00 3.82
2436 2812 3.743396 GCTTAGCGCTTATGTATCTTGCT 59.257 43.478 18.68 0.00 35.14 3.91
2455 2831 3.595758 GGTGGTGTTGCTGCGCTT 61.596 61.111 9.73 0.00 0.00 4.68
2497 2874 2.333938 CGTGTTCACGGTCGAGGT 59.666 61.111 16.17 0.00 0.00 3.85
2550 2927 2.671070 CACCGTCTTGGAGCCCAT 59.329 61.111 0.00 0.00 42.00 4.00
2605 2982 1.135731 CTCTGACTCTCGTGTCGGC 59.864 63.158 8.95 0.00 41.67 5.54
2611 2988 1.203075 AGGGGAAACTCTGACTCTCGT 60.203 52.381 0.00 0.00 42.28 4.18
2679 3056 2.800581 CGACGACGTAGCTCGCTCT 61.801 63.158 0.00 0.00 44.19 4.09
2698 3075 3.210232 TCCTATCTTCAGACGGATCGT 57.790 47.619 0.00 0.00 45.10 3.73
2701 3078 5.263872 ACCTATCCTATCTTCAGACGGAT 57.736 43.478 12.02 12.02 39.51 4.18
2719 3096 2.758434 GGCCGGGGTGAAAACCTA 59.242 61.111 2.18 0.00 0.00 3.08
2954 4063 3.655211 CCAGTTGGGGGCAGCTCT 61.655 66.667 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.