Multiple sequence alignment - TraesCS6B01G052100

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 TraesCS6B01G052100 chr6B 100.000 2411 0 0 1 2411 31277607 31280017 0.000000e+00 4453
1 TraesCS6B01G052100 chr6B 91.147 994 31 13 15 1002 30804792 30805734 0.000000e+00 1295
2 TraesCS6B01G052100 chr6B 91.046 994 32 13 15 1002 30725824 30726766 0.000000e+00 1290
3 TraesCS6B01G052100 chr6B 91.046 994 32 13 15 1002 30870140 30871082 0.000000e+00 1290
4 TraesCS6B01G052100 chr6B 90.106 758 22 11 842 1590 30872796 30873509 0.000000e+00 935
5 TraesCS6B01G052100 chr6B 90.702 484 20 11 524 1002 30638567 30639030 2.630000e-174 621
6 TraesCS6B01G052100 chr6B 87.426 509 46 5 1097 1591 31717308 31716804 9.670000e-159 569
7 TraesCS6B01G052100 chr6B 86.414 449 9 12 1150 1591 30643017 30643420 6.120000e-121 444
8 TraesCS6B01G052100 chr6B 86.192 449 11 11 1150 1591 30731014 30731418 2.850000e-119 438
9 TraesCS6B01G052100 chr6B 85.746 449 12 12 1150 1591 30809959 30810362 6.160000e-116 427
10 TraesCS6B01G052100 chr6B 86.082 388 38 9 702 1086 30794847 30795221 1.040000e-108 403
11 TraesCS6B01G052100 chr6B 85.572 402 38 12 688 1086 30859675 30860059 1.040000e-108 403
12 TraesCS6B01G052100 chr6B 85.075 402 40 12 688 1086 30715824 30716208 2.250000e-105 392
13 TraesCS6B01G052100 chr6B 92.500 280 8 1 201 480 30638291 30638557 2.910000e-104 388
14 TraesCS6B01G052100 chr6B 98.438 192 3 0 15 206 30623175 30623366 2.970000e-89 339
15 TraesCS6B01G052100 chr6B 91.139 237 16 4 1360 1591 30716320 30716556 1.390000e-82 316
16 TraesCS6B01G052100 chr6B 91.139 237 16 4 1360 1591 30860171 30860407 1.390000e-82 316
17 TraesCS6B01G052100 chr6B 90.717 237 17 4 1360 1591 30795333 30795569 6.470000e-81 311
18 TraesCS6B01G052100 chr6B 80.597 402 57 9 1210 1591 30718949 30719349 8.430000e-75 291
19 TraesCS6B01G052100 chr6B 87.347 245 31 0 1210 1454 31713937 31713693 5.070000e-72 281
20 TraesCS6B01G052100 chr6B 80.000 405 57 13 1210 1591 30862790 30863193 6.560000e-71 278
21 TraesCS6B01G052100 chr6B 85.660 265 27 5 114 372 30745055 30745314 3.950000e-68 268
22 TraesCS6B01G052100 chr6B 79.506 405 59 13 1210 1591 30797955 30798358 1.420000e-67 267
23 TraesCS6B01G052100 chr6B 79.319 411 61 12 1204 1591 30877774 30878183 1.420000e-67 267
24 TraesCS6B01G052100 chr6B 79.506 405 58 15 1210 1591 31361887 31362289 5.110000e-67 265
25 TraesCS6B01G052100 chr6B 79.455 404 58 14 1211 1591 31396188 31396589 1.840000e-66 263
26 TraesCS6B01G052100 chr6B 84.962 266 28 5 114 372 30667112 30667372 2.380000e-65 259
27 TraesCS6B01G052100 chr6B 96.774 155 5 0 1002 1156 30728956 30729110 2.380000e-65 259
28 TraesCS6B01G052100 chr6B 96.774 155 5 0 1002 1156 30807925 30808079 2.380000e-65 259
29 TraesCS6B01G052100 chr6B 84.528 265 30 5 114 372 30680428 30680687 3.980000e-63 252
30 TraesCS6B01G052100 chr6B 84.151 265 31 5 114 372 30823701 30823960 1.850000e-61 246
31 TraesCS6B01G052100 chr6B 94.194 155 9 0 1002 1156 30641194 30641348 1.110000e-58 237
32 TraesCS6B01G052100 chr5D 90.898 824 67 7 1591 2411 55076334 55075516 0.000000e+00 1099
33 TraesCS6B01G052100 chr5D 89.309 608 57 7 1807 2411 505105555 505104953 0.000000e+00 756
34 TraesCS6B01G052100 chr3D 89.468 864 43 15 1591 2411 566091056 566090198 0.000000e+00 1048
35 TraesCS6B01G052100 chr3D 93.333 540 27 8 1875 2411 569210227 569210760 0.000000e+00 789
36 TraesCS6B01G052100 chr3D 90.208 480 43 4 1590 2067 5237641 5238118 7.320000e-175 623
37 TraesCS6B01G052100 chr3D 76.667 600 90 35 824 1412 306074010 306073450 1.090000e-73 287
38 TraesCS6B01G052100 chr1D 89.480 846 57 10 1591 2408 453823864 453824705 0.000000e+00 1040
39 TraesCS6B01G052100 chr1D 89.596 817 68 13 1602 2411 7581888 7581082 0.000000e+00 1022
40 TraesCS6B01G052100 chr3B 91.516 719 51 7 1694 2411 819235879 819236588 0.000000e+00 981
41 TraesCS6B01G052100 chr3A 87.574 845 76 13 1591 2411 707197508 707198347 0.000000e+00 952
42 TraesCS6B01G052100 chr5A 86.682 871 65 14 1591 2411 544771848 544772717 0.000000e+00 918
43 TraesCS6B01G052100 chr2B 87.074 851 59 15 1591 2411 99555390 99554561 0.000000e+00 915
44 TraesCS6B01G052100 chr4D 90.764 563 24 7 1875 2411 426782714 426782154 0.000000e+00 726
45 TraesCS6B01G052100 chr6D 95.153 392 15 4 2021 2411 46622455 46622067 1.220000e-172 616
46 TraesCS6B01G052100 chr6D 88.247 519 47 8 1090 1595 17485829 17486346 2.050000e-170 608
47 TraesCS6B01G052100 chr6D 91.375 429 34 3 1591 2017 16718210 16717783 3.450000e-163 584
48 TraesCS6B01G052100 chr6D 91.086 359 26 3 15 372 17484813 17485166 4.660000e-132 481
49 TraesCS6B01G052100 chr6D 80.675 533 46 29 570 1088 17485368 17485857 6.340000e-96 361
50 TraesCS6B01G052100 chr6D 75.840 774 116 48 861 1591 17821986 17822731 6.430000e-86 327
51 TraesCS6B01G052100 chr6D 90.062 161 12 2 629 789 17482670 17482826 3.140000e-49 206
52 TraesCS6B01G052100 chr6D 78.879 232 31 10 861 1088 17491619 17491836 8.990000e-30 141
53 TraesCS6B01G052100 chr6A 83.841 427 50 14 15 433 18359224 18359639 2.910000e-104 388
54 TraesCS6B01G052100 chr6A 87.616 323 15 6 771 1086 18359884 18360188 3.810000e-93 351
55 TraesCS6B01G052100 chr6A 76.124 712 117 38 910 1582 18439396 18440093 8.310000e-85 324
56 TraesCS6B01G052100 chr6A 96.923 65 2 0 1118 1182 18360190 18360254 2.530000e-20 110


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 TraesCS6B01G052100 chr6B 31277607 31280017 2410 False 4453.000000 4453 100.000000 1 2411 1 chr6B.!!$F7 2410
1 TraesCS6B01G052100 chr6B 30870140 30873509 3369 False 1112.500000 1290 90.576000 15 1590 2 chr6B.!!$F16 1575
2 TraesCS6B01G052100 chr6B 30725824 30731418 5594 False 662.333333 1290 91.337333 15 1591 3 chr6B.!!$F12 1576
3 TraesCS6B01G052100 chr6B 30804792 30810362 5570 False 660.333333 1295 91.222333 15 1591 3 chr6B.!!$F14 1576
4 TraesCS6B01G052100 chr6B 31713693 31717308 3615 True 425.000000 569 87.386500 1097 1591 2 chr6B.!!$R1 494
5 TraesCS6B01G052100 chr6B 30638291 30643420 5129 False 422.500000 621 90.952500 201 1591 4 chr6B.!!$F10 1390
6 TraesCS6B01G052100 chr6B 30715824 30719349 3525 False 333.000000 392 85.603667 688 1591 3 chr6B.!!$F11 903
7 TraesCS6B01G052100 chr6B 30859675 30863193 3518 False 332.333333 403 85.570333 688 1591 3 chr6B.!!$F15 903
8 TraesCS6B01G052100 chr6B 30794847 30798358 3511 False 327.000000 403 85.435000 702 1591 3 chr6B.!!$F13 889
9 TraesCS6B01G052100 chr5D 55075516 55076334 818 True 1099.000000 1099 90.898000 1591 2411 1 chr5D.!!$R1 820
10 TraesCS6B01G052100 chr5D 505104953 505105555 602 True 756.000000 756 89.309000 1807 2411 1 chr5D.!!$R2 604
11 TraesCS6B01G052100 chr3D 566090198 566091056 858 True 1048.000000 1048 89.468000 1591 2411 1 chr3D.!!$R2 820
12 TraesCS6B01G052100 chr3D 569210227 569210760 533 False 789.000000 789 93.333000 1875 2411 1 chr3D.!!$F2 536
13 TraesCS6B01G052100 chr3D 306073450 306074010 560 True 287.000000 287 76.667000 824 1412 1 chr3D.!!$R1 588
14 TraesCS6B01G052100 chr1D 453823864 453824705 841 False 1040.000000 1040 89.480000 1591 2408 1 chr1D.!!$F1 817
15 TraesCS6B01G052100 chr1D 7581082 7581888 806 True 1022.000000 1022 89.596000 1602 2411 1 chr1D.!!$R1 809
16 TraesCS6B01G052100 chr3B 819235879 819236588 709 False 981.000000 981 91.516000 1694 2411 1 chr3B.!!$F1 717
17 TraesCS6B01G052100 chr3A 707197508 707198347 839 False 952.000000 952 87.574000 1591 2411 1 chr3A.!!$F1 820
18 TraesCS6B01G052100 chr5A 544771848 544772717 869 False 918.000000 918 86.682000 1591 2411 1 chr5A.!!$F1 820
19 TraesCS6B01G052100 chr2B 99554561 99555390 829 True 915.000000 915 87.074000 1591 2411 1 chr2B.!!$R1 820
20 TraesCS6B01G052100 chr4D 426782154 426782714 560 True 726.000000 726 90.764000 1875 2411 1 chr4D.!!$R1 536
21 TraesCS6B01G052100 chr6D 17482670 17486346 3676 False 414.000000 608 87.517500 15 1595 4 chr6D.!!$F3 1580
22 TraesCS6B01G052100 chr6D 17821986 17822731 745 False 327.000000 327 75.840000 861 1591 1 chr6D.!!$F2 730
23 TraesCS6B01G052100 chr6A 18439396 18440093 697 False 324.000000 324 76.124000 910 1582 1 chr6A.!!$F1 672
24 TraesCS6B01G052100 chr6A 18359224 18360254 1030 False 283.000000 388 89.460000 15 1182 3 chr6A.!!$F2 1167

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
67 2201 1.192534 GCGACGAAGAAAGTTGGACAG 59.807 52.381 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 14806 0.321346 ATCGGTGATATGGCATGCGA 59.679 50.0 12.44 8.58 0.0 5.1 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
32 2162 7.921786 AAAAAGATACGAGATCAAATCACCA 57.078 32.000 0.00 0.00 0.00 4.17
67 2201 1.192534 GCGACGAAGAAAGTTGGACAG 59.807 52.381 0.00 0.00 0.00 3.51
331 2492 3.318017 TCAACGCTGAGTTTCTAGAAGC 58.682 45.455 11.09 11.09 42.02 3.86
423 2617 2.557555 TCCCTCCTGTCATCATCAGT 57.442 50.000 0.00 0.00 0.00 3.41
460 2654 4.274214 TGTTATAGTACGGGTGAGATGACG 59.726 45.833 0.00 0.00 0.00 4.35
617 2834 7.949690 AATCCAACATTTGAGATCAGAATCA 57.050 32.000 0.00 0.00 34.07 2.57
620 2837 7.170277 TCCAACATTTGAGATCAGAATCAGAA 58.830 34.615 0.00 0.00 34.07 3.02
621 2838 7.832685 TCCAACATTTGAGATCAGAATCAGAAT 59.167 33.333 0.00 0.00 34.07 2.40
622 2839 8.129840 CCAACATTTGAGATCAGAATCAGAATC 58.870 37.037 0.00 0.00 34.07 2.52
623 2840 8.894731 CAACATTTGAGATCAGAATCAGAATCT 58.105 33.333 0.00 0.00 34.07 2.40
624 2841 9.463902 AACATTTGAGATCAGAATCAGAATCTT 57.536 29.630 0.00 0.00 34.07 2.40
696 2916 4.853924 CCTCAACAGGCATTTGTTTACT 57.146 40.909 0.00 0.00 39.17 2.24
700 2920 6.012658 TCAACAGGCATTTGTTTACTGATC 57.987 37.500 0.00 0.00 39.17 2.92
769 2989 3.963665 TGTTTGTTTTCGCATCTTCCTG 58.036 40.909 0.00 0.00 0.00 3.86
790 3010 3.011595 TGTCCATTTCCATCCATGAACCT 59.988 43.478 0.00 0.00 0.00 3.50
843 3067 4.862092 CGGCATCGTCAGCTCGCT 62.862 66.667 0.00 0.00 0.00 4.93
844 3068 2.959071 GGCATCGTCAGCTCGCTC 60.959 66.667 0.00 0.00 0.00 5.03
845 3069 3.318555 GCATCGTCAGCTCGCTCG 61.319 66.667 0.00 0.00 0.00 5.03
846 3070 3.318555 CATCGTCAGCTCGCTCGC 61.319 66.667 0.00 0.00 0.00 5.03
1088 7447 3.394836 GAGCAAGGAGAGCGGGGT 61.395 66.667 0.00 0.00 37.01 4.95
1380 14243 0.037303 TGGGAAGGCTCTGCTTCTTG 59.963 55.000 0.00 0.00 0.00 3.02
1475 14353 4.098416 GCAGGTTGCATCGACTATTTTTC 58.902 43.478 0.00 0.00 44.26 2.29
1556 14446 0.704076 TGTAAATGCCCTTCAGCCCT 59.296 50.000 0.00 0.00 0.00 5.19
1761 14652 0.798776 GAACGACCGTCGACCTAGAA 59.201 55.000 27.03 0.00 43.74 2.10
1772 14663 0.243907 GACCTAGAAGCAGACACGCA 59.756 55.000 0.00 0.00 0.00 5.24
1777 14668 0.319728 AGAAGCAGACACGCAGACAT 59.680 50.000 0.00 0.00 0.00 3.06
1784 14675 3.857854 CACGCAGACATCAGCCGC 61.858 66.667 0.00 0.00 0.00 6.53
1800 14725 2.046314 GCCAGCATACGTGTGGGT 60.046 61.111 14.49 0.00 31.35 4.51
1805 14730 3.009192 GCATACGTGTGGGTCCGGA 62.009 63.158 14.49 0.00 0.00 5.14
1831 14756 2.509336 CCGTGACCAGCGGCTAAG 60.509 66.667 0.26 0.00 42.82 2.18
1833 14758 2.663196 GTGACCAGCGGCTAAGGT 59.337 61.111 11.44 11.44 38.63 3.50
1838 14763 2.579787 CAGCGGCTAAGGTCGTCG 60.580 66.667 0.26 0.00 43.14 5.12
1903 14828 1.339438 GCATGCCATATCACCGATCCT 60.339 52.381 6.36 0.00 0.00 3.24
2248 15248 4.196193 CACAGAAGTTTAGTGGTGGTTGA 58.804 43.478 1.80 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.921786 TGGTGATTTGATCTCGTATCTTTTT 57.078 32.000 0.00 0.00 0.00 1.94
11 12 8.400947 CAAAATGGTGATTTGATCTCGTATCTT 58.599 33.333 0.00 0.00 39.56 2.40
32 2162 1.197721 CGTCGCCTTGCTCTTCAAAAT 59.802 47.619 0.00 0.00 33.65 1.82
67 2201 0.466922 CTTCCTGGATGTGGGATGGC 60.467 60.000 0.00 0.00 0.00 4.40
423 2617 8.283992 CCGTACTATAACATTGTTTGTTTGACA 58.716 33.333 7.45 0.00 46.51 3.58
441 2635 3.204306 TCGTCATCTCACCCGTACTAT 57.796 47.619 0.00 0.00 0.00 2.12
460 2654 6.590234 ATTCTTAGGTTGGTCAATTGGTTC 57.410 37.500 5.42 0.00 0.00 3.62
610 2827 2.871022 CGGCTGGAAGATTCTGATTCTG 59.129 50.000 3.07 0.00 34.07 3.02
612 2829 2.911484 ACGGCTGGAAGATTCTGATTC 58.089 47.619 0.00 0.00 34.07 2.52
615 2832 2.859165 AAACGGCTGGAAGATTCTGA 57.141 45.000 0.00 0.00 34.07 3.27
616 2833 2.162408 GGAAAACGGCTGGAAGATTCTG 59.838 50.000 0.00 0.00 34.07 3.02
617 2834 2.224769 TGGAAAACGGCTGGAAGATTCT 60.225 45.455 0.00 0.00 34.07 2.40
620 2837 1.351017 TCTGGAAAACGGCTGGAAGAT 59.649 47.619 0.00 0.00 34.07 2.40
621 2838 0.762418 TCTGGAAAACGGCTGGAAGA 59.238 50.000 0.00 0.00 34.07 2.87
622 2839 1.740025 GATCTGGAAAACGGCTGGAAG 59.260 52.381 0.00 0.00 0.00 3.46
623 2840 1.073125 TGATCTGGAAAACGGCTGGAA 59.927 47.619 0.00 0.00 0.00 3.53
624 2841 0.690192 TGATCTGGAAAACGGCTGGA 59.310 50.000 0.00 0.00 0.00 3.86
694 2914 2.060980 GGAGGCCTGGTCGATCAGT 61.061 63.158 23.64 5.94 33.14 3.41
695 2915 2.818132 GGAGGCCTGGTCGATCAG 59.182 66.667 19.14 19.14 34.70 2.90
696 2916 3.147595 CGGAGGCCTGGTCGATCA 61.148 66.667 12.00 0.00 0.00 2.92
700 2920 2.742372 CAAACGGAGGCCTGGTCG 60.742 66.667 12.00 14.38 0.00 4.79
769 2989 3.382546 CAGGTTCATGGATGGAAATGGAC 59.617 47.826 0.00 0.00 32.37 4.02
790 3010 5.340803 CGTGTAGACTACGTAGTACCTACA 58.659 45.833 32.68 32.68 44.33 2.74
803 3023 2.742589 CAGTCTGAGTGCGTGTAGACTA 59.257 50.000 11.54 0.00 45.84 2.59
809 3029 2.029666 GCCAGTCTGAGTGCGTGT 59.970 61.111 6.98 0.00 0.00 4.49
810 3030 3.108289 CGCCAGTCTGAGTGCGTG 61.108 66.667 12.22 9.39 41.95 5.34
1380 14243 3.446175 GAAGCCGAAGCGCATGAGC 62.446 63.158 14.17 14.17 46.67 4.26
1464 14341 9.476202 AAAGAAAAATGAAGGGAAAAATAGTCG 57.524 29.630 0.00 0.00 0.00 4.18
1475 14353 6.238456 GGCACAAAAGAAAGAAAAATGAAGGG 60.238 38.462 0.00 0.00 0.00 3.95
1747 14638 0.322277 TCTGCTTCTAGGTCGACGGT 60.322 55.000 9.92 1.52 0.00 4.83
1761 14652 0.389556 CTGATGTCTGCGTGTCTGCT 60.390 55.000 0.00 0.00 35.36 4.24
1772 14663 1.689243 TATGCTGGCGGCTGATGTCT 61.689 55.000 20.66 1.34 42.39 3.41
1777 14668 3.770040 ACGTATGCTGGCGGCTGA 61.770 61.111 20.66 4.08 42.39 4.26
1784 14675 1.449601 GGACCCACACGTATGCTGG 60.450 63.158 0.00 0.00 0.00 4.85
1786 14677 2.577059 CGGACCCACACGTATGCT 59.423 61.111 0.00 0.00 0.00 3.79
1831 14756 1.588139 CGGCATAGGTTCGACGACC 60.588 63.158 0.00 2.51 40.11 4.79
1833 14758 1.430632 GTCGGCATAGGTTCGACGA 59.569 57.895 8.93 0.00 42.60 4.20
1838 14763 1.588139 CGACCGTCGGCATAGGTTC 60.588 63.158 12.28 0.00 38.57 3.62
1881 14806 0.321346 ATCGGTGATATGGCATGCGA 59.679 50.000 12.44 8.58 0.00 5.10
1963 14888 3.541713 GGGTTTTGGTGGGCGCAA 61.542 61.111 10.83 0.00 0.00 4.85
2226 15226 4.196193 TCAACCACCACTAAACTTCTGTG 58.804 43.478 0.00 0.00 0.00 3.66
2242 15242 1.820056 TGCCGAGCGTTTTCAACCA 60.820 52.632 0.00 0.00 0.00 3.67
2360 15360 1.895231 GCAACGTCCCCTCCGTTTT 60.895 57.895 0.00 0.00 45.46 2.43


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

AutoCloner maintained by Alex Coulton.