Multiple sequence alignment - TraesCS2B01G121300

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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 TraesCS2B01G121300 chr2B 100.000 4057 0 0 1 4057 88852990 88857046 0.000000e+00 7492.0
1 TraesCS2B01G121300 chr2B 87.224 1088 58 37 536 1580 774768688 774769737 0.000000e+00 1164.0
2 TraesCS2B01G121300 chr2B 93.191 705 38 5 1683 2382 38263232 38262533 0.000000e+00 1027.0
3 TraesCS2B01G121300 chr2B 96.270 429 16 0 3629 4057 655488064 655487636 0.000000e+00 704.0
4 TraesCS2B01G121300 chr2B 93.962 265 16 0 2666 2930 38260475 38260211 6.320000e-108 401.0
5 TraesCS2B01G121300 chr4B 97.841 3566 70 6 1 3561 475802131 475798568 0.000000e+00 6152.0
6 TraesCS2B01G121300 chr4B 94.083 507 19 1 3562 4057 582037220 582037726 0.000000e+00 760.0
7 TraesCS2B01G121300 chr4B 90.426 188 15 3 2012 2198 446508575 446508760 1.130000e-60 244.0
8 TraesCS2B01G121300 chr3B 97.447 3564 81 7 2 3559 491826133 491822574 0.000000e+00 6069.0
9 TraesCS2B01G121300 chr3B 94.325 511 18 1 3558 4057 446410384 446410894 0.000000e+00 773.0
10 TraesCS2B01G121300 chr3B 93.750 416 25 1 102 517 115400785 115401199 1.240000e-174 623.0
11 TraesCS2B01G121300 chr7A 97.107 3560 74 4 4 3559 576086858 576090392 0.000000e+00 5976.0
12 TraesCS2B01G121300 chr7A 96.015 3563 94 15 1 3559 39479350 39482868 0.000000e+00 5749.0
13 TraesCS2B01G121300 chr3A 96.089 2020 46 5 1 2018 35094186 35092198 0.000000e+00 3262.0
14 TraesCS2B01G121300 chr3A 97.558 1515 31 2 2046 3559 35092071 35090562 0.000000e+00 2588.0
15 TraesCS2B01G121300 chr3A 98.125 800 6 1 1219 2018 35150393 35149603 0.000000e+00 1386.0
16 TraesCS2B01G121300 chr3A 95.759 731 30 1 1 731 35152316 35151587 0.000000e+00 1177.0
17 TraesCS2B01G121300 chr3A 97.383 535 12 2 3026 3559 35148932 35148399 0.000000e+00 909.0
18 TraesCS2B01G121300 chrUn 97.624 1515 30 2 2046 3559 309099466 309100975 0.000000e+00 2593.0
19 TraesCS2B01G121300 chrUn 97.558 1515 31 2 2046 3559 309113731 309112222 0.000000e+00 2588.0
20 TraesCS2B01G121300 chrUn 98.125 800 6 1 1219 2018 309098549 309099339 0.000000e+00 1386.0
21 TraesCS2B01G121300 chrUn 98.125 800 6 1 1219 2018 309114648 309113858 0.000000e+00 1386.0
22 TraesCS2B01G121300 chrUn 95.072 629 11 2 733 1359 472255659 472256269 0.000000e+00 972.0
23 TraesCS2B01G121300 chr5A 96.025 1434 36 3 1 1431 637188226 637186811 0.000000e+00 2313.0
24 TraesCS2B01G121300 chr5A 96.285 942 23 2 2619 3559 637185501 637184571 0.000000e+00 1535.0
25 TraesCS2B01G121300 chr5A 88.110 471 45 5 2204 2664 249850533 249850064 2.130000e-152 549.0
26 TraesCS2B01G121300 chr1D 92.458 716 33 7 536 1240 432637431 432636726 0.000000e+00 1003.0
27 TraesCS2B01G121300 chr1D 96.066 305 3 3 1287 1582 432636729 432636425 4.710000e-134 488.0
28 TraesCS2B01G121300 chr1B 95.069 507 14 1 3562 4057 646709495 646710001 0.000000e+00 787.0
29 TraesCS2B01G121300 chr1B 94.675 507 15 2 3562 4057 94673236 94673741 0.000000e+00 776.0
30 TraesCS2B01G121300 chr1B 93.151 511 22 4 3558 4057 432076074 432076582 0.000000e+00 737.0
31 TraesCS2B01G121300 chr1B 92.023 514 28 2 3557 4057 587574464 587574977 0.000000e+00 710.0
32 TraesCS2B01G121300 chr1B 91.440 514 31 3 3556 4057 369732561 369733073 0.000000e+00 693.0
33 TraesCS2B01G121300 chr1B 91.194 511 28 2 3558 4057 679264061 679263557 0.000000e+00 678.0
34 TraesCS2B01G121300 chr1B 89.237 511 26 3 3558 4057 679203304 679202812 2.680000e-171 612.0
35 TraesCS2B01G121300 chr1B 89.894 188 16 3 2012 2198 61403136 61402951 5.240000e-59 239.0
36 TraesCS2B01G121300 chr7B 94.872 507 14 3 3562 4057 728569916 728570421 0.000000e+00 782.0
37 TraesCS2B01G121300 chr7B 94.675 507 15 2 3562 4057 623334714 623335219 0.000000e+00 776.0
38 TraesCS2B01G121300 chr7B 89.729 516 25 10 3556 4057 266498061 266497560 5.720000e-178 634.0
39 TraesCS2B01G121300 chr7B 93.990 416 24 1 102 517 388872421 388872835 2.660000e-176 628.0
40 TraesCS2B01G121300 chr7B 91.408 419 24 4 3552 3959 337083038 337082621 7.610000e-157 564.0
41 TraesCS2B01G121300 chr5B 94.675 507 13 3 3562 4057 591133172 591132669 0.000000e+00 774.0
42 TraesCS2B01G121300 chr5B 92.564 511 26 2 3558 4057 120283299 120282790 0.000000e+00 723.0
43 TraesCS2B01G121300 chr4A 94.094 508 18 2 3562 4057 733018291 733018798 0.000000e+00 761.0
44 TraesCS2B01G121300 chr4A 91.538 520 30 6 3550 4057 731707100 731707617 0.000000e+00 704.0
45 TraesCS2B01G121300 chr2D 96.146 467 16 2 1 466 14792011 14792476 0.000000e+00 761.0
46 TraesCS2B01G121300 chr2D 94.872 390 14 4 536 919 631285769 631286158 4.490000e-169 604.0
47 TraesCS2B01G121300 chr5D 90.944 519 27 5 3552 4057 53705967 53706478 0.000000e+00 680.0
48 TraesCS2B01G121300 chr3D 96.774 403 13 0 64 466 461429302 461429704 0.000000e+00 673.0
49 TraesCS2B01G121300 chr1A 89.474 456 36 6 2204 2649 90167642 90167189 2.120000e-157 566.0
50 TraesCS2B01G121300 chr1A 89.773 264 21 3 2668 2930 90165859 90165601 2.340000e-87 333.0
51 TraesCS2B01G121300 chr1A 89.894 188 16 3 2012 2198 367001353 367001168 5.240000e-59 239.0
52 TraesCS2B01G121300 chr6A 83.377 385 37 12 805 1177 31593295 31593664 8.400000e-87 331.0
53 TraesCS2B01G121300 chr2A 89.362 188 17 3 2012 2198 500498628 500498813 2.440000e-57 233.0
54 TraesCS2B01G121300 chr2A 88.298 188 19 3 2012 2198 677082311 677082496 5.280000e-54 222.0
55 TraesCS2B01G121300 chr6D 84.507 71 6 4 2130 2197 86853098 86853166 9.410000e-07 65.8


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 TraesCS2B01G121300 chr2B 88852990 88857046 4056 False 7492.000000 7492 100.0000 1 4057 1 chr2B.!!$F1 4056
1 TraesCS2B01G121300 chr2B 774768688 774769737 1049 False 1164.000000 1164 87.2240 536 1580 1 chr2B.!!$F2 1044
2 TraesCS2B01G121300 chr2B 38260211 38263232 3021 True 714.000000 1027 93.5765 1683 2930 2 chr2B.!!$R2 1247
3 TraesCS2B01G121300 chr4B 475798568 475802131 3563 True 6152.000000 6152 97.8410 1 3561 1 chr4B.!!$R1 3560
4 TraesCS2B01G121300 chr4B 582037220 582037726 506 False 760.000000 760 94.0830 3562 4057 1 chr4B.!!$F2 495
5 TraesCS2B01G121300 chr3B 491822574 491826133 3559 True 6069.000000 6069 97.4470 2 3559 1 chr3B.!!$R1 3557
6 TraesCS2B01G121300 chr3B 446410384 446410894 510 False 773.000000 773 94.3250 3558 4057 1 chr3B.!!$F2 499
7 TraesCS2B01G121300 chr7A 576086858 576090392 3534 False 5976.000000 5976 97.1070 4 3559 1 chr7A.!!$F2 3555
8 TraesCS2B01G121300 chr7A 39479350 39482868 3518 False 5749.000000 5749 96.0150 1 3559 1 chr7A.!!$F1 3558
9 TraesCS2B01G121300 chr3A 35090562 35094186 3624 True 2925.000000 3262 96.8235 1 3559 2 chr3A.!!$R1 3558
10 TraesCS2B01G121300 chr3A 35148399 35152316 3917 True 1157.333333 1386 97.0890 1 3559 3 chr3A.!!$R2 3558
11 TraesCS2B01G121300 chrUn 309098549 309100975 2426 False 1989.500000 2593 97.8745 1219 3559 2 chrUn.!!$F2 2340
12 TraesCS2B01G121300 chrUn 309112222 309114648 2426 True 1987.000000 2588 97.8415 1219 3559 2 chrUn.!!$R1 2340
13 TraesCS2B01G121300 chrUn 472255659 472256269 610 False 972.000000 972 95.0720 733 1359 1 chrUn.!!$F1 626
14 TraesCS2B01G121300 chr5A 637184571 637188226 3655 True 1924.000000 2313 96.1550 1 3559 2 chr5A.!!$R2 3558
15 TraesCS2B01G121300 chr1D 432636425 432637431 1006 True 745.500000 1003 94.2620 536 1582 2 chr1D.!!$R1 1046
16 TraesCS2B01G121300 chr1B 646709495 646710001 506 False 787.000000 787 95.0690 3562 4057 1 chr1B.!!$F5 495
17 TraesCS2B01G121300 chr1B 94673236 94673741 505 False 776.000000 776 94.6750 3562 4057 1 chr1B.!!$F1 495
18 TraesCS2B01G121300 chr1B 432076074 432076582 508 False 737.000000 737 93.1510 3558 4057 1 chr1B.!!$F3 499
19 TraesCS2B01G121300 chr1B 587574464 587574977 513 False 710.000000 710 92.0230 3557 4057 1 chr1B.!!$F4 500
20 TraesCS2B01G121300 chr1B 369732561 369733073 512 False 693.000000 693 91.4400 3556 4057 1 chr1B.!!$F2 501
21 TraesCS2B01G121300 chr1B 679263557 679264061 504 True 678.000000 678 91.1940 3558 4057 1 chr1B.!!$R3 499
22 TraesCS2B01G121300 chr7B 728569916 728570421 505 False 782.000000 782 94.8720 3562 4057 1 chr7B.!!$F3 495
23 TraesCS2B01G121300 chr7B 623334714 623335219 505 False 776.000000 776 94.6750 3562 4057 1 chr7B.!!$F2 495
24 TraesCS2B01G121300 chr7B 266497560 266498061 501 True 634.000000 634 89.7290 3556 4057 1 chr7B.!!$R1 501
25 TraesCS2B01G121300 chr5B 591132669 591133172 503 True 774.000000 774 94.6750 3562 4057 1 chr5B.!!$R2 495
26 TraesCS2B01G121300 chr5B 120282790 120283299 509 True 723.000000 723 92.5640 3558 4057 1 chr5B.!!$R1 499
27 TraesCS2B01G121300 chr4A 733018291 733018798 507 False 761.000000 761 94.0940 3562 4057 1 chr4A.!!$F2 495
28 TraesCS2B01G121300 chr4A 731707100 731707617 517 False 704.000000 704 91.5380 3550 4057 1 chr4A.!!$F1 507
29 TraesCS2B01G121300 chr5D 53705967 53706478 511 False 680.000000 680 90.9440 3552 4057 1 chr5D.!!$F1 505
30 TraesCS2B01G121300 chr1A 90165601 90167642 2041 True 449.500000 566 89.6235 2204 2930 2 chr1A.!!$R2 726

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
215 217 0.338120 CTCCCCCTCACCTTCTCTCT 59.662 60.0 0.0 0.0 0.00 3.10 F
1021 1046 0.250295 GGCTATGACGCTATGCCCAA 60.250 55.0 0.0 0.0 37.81 4.12 F
2615 5872 0.738389 AAACAAGTTGTCCTGTGGCG 59.262 50.0 9.4 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 3006 5.058490 AGAACGAAAATAAACCAACGGAGA 58.942 37.500 0.00 0.0 0.00 3.71 R
2985 7556 1.279846 TGCAGCATGAGAATCCTGACA 59.720 47.619 0.00 0.0 39.69 3.58 R
3545 8117 0.034380 AGTGCAAGCTCCATCTGCAT 60.034 50.000 12.83 0.9 37.83 3.96 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
215 217 0.338120 CTCCCCCTCACCTTCTCTCT 59.662 60.000 0.00 0.00 0.00 3.10
369 371 2.086426 GCGACAACGATGAGCGACA 61.086 57.895 14.27 0.00 44.57 4.35
418 420 1.589414 CCCCAACTCATCTTCTCCCT 58.411 55.000 0.00 0.00 0.00 4.20
422 424 3.713764 CCCAACTCATCTTCTCCCTGTAT 59.286 47.826 0.00 0.00 0.00 2.29
459 462 1.127343 CCAGGTTCTCCTCTCCCATC 58.873 60.000 0.00 0.00 43.07 3.51
517 520 2.383245 CTGGTGGAGCAACGGACAGT 62.383 60.000 0.00 0.00 26.80 3.55
531 534 2.219325 GACAGTGAGAGGCGGGACAG 62.219 65.000 0.00 0.00 0.00 3.51
601 604 1.211190 CTTGGCGCCTGCTTCTTTC 59.789 57.895 29.70 0.00 42.25 2.62
602 605 1.228245 TTGGCGCCTGCTTCTTTCT 60.228 52.632 29.70 0.00 42.25 2.52
809 819 2.293399 GGTTTGTTCATGGGTGTGAGAC 59.707 50.000 0.00 0.00 0.00 3.36
1021 1046 0.250295 GGCTATGACGCTATGCCCAA 60.250 55.000 0.00 0.00 37.81 4.12
1638 3006 5.088680 TCTACGGTTAATTTTCGTCCCAT 57.911 39.130 4.19 0.00 38.19 4.00
1643 3011 3.311596 GGTTAATTTTCGTCCCATCTCCG 59.688 47.826 0.00 0.00 0.00 4.63
1644 3012 2.781681 AATTTTCGTCCCATCTCCGT 57.218 45.000 0.00 0.00 0.00 4.69
2263 3770 9.086336 GAGATGAAAATTGTGTTTCTTTGTGAA 57.914 29.630 0.00 0.00 38.17 3.18
2475 5728 6.202954 ACGTAATGGTATATTTCTTGCTCTGC 59.797 38.462 0.00 0.00 0.00 4.26
2615 5872 0.738389 AAACAAGTTGTCCTGTGGCG 59.262 50.000 9.40 0.00 0.00 5.69
2849 7420 9.730705 ATGGATATACTGTGATGTTATTTCTGG 57.269 33.333 0.00 0.00 0.00 3.86
2985 7556 4.210746 GCTCGGTCGAGTTTTTCTTAACTT 59.789 41.667 19.56 0.00 43.70 2.66
3092 7663 3.392616 AGGGAGATCATAAACCATCGCTT 59.607 43.478 0.00 0.00 0.00 4.68
3146 7717 5.048504 TGAAGGAGCTGTCAATTGTTGAATC 60.049 40.000 5.13 0.31 42.15 2.52
3212 7783 5.729510 TCACCATGATTTTACATCGAGACA 58.270 37.500 0.00 0.00 0.00 3.41
3355 7926 0.804989 GGCAGTGCTTTCGTTATGCT 59.195 50.000 16.11 0.00 34.19 3.79
3374 7945 9.226345 GTTATGCTTATGATGCTTTCAGTTTAC 57.774 33.333 0.00 0.00 37.89 2.01
3375 7946 5.868257 TGCTTATGATGCTTTCAGTTTACG 58.132 37.500 0.00 0.00 37.89 3.18
3452 8024 6.017852 GTGATAACCTTTATAAGCTGGACTGC 60.018 42.308 0.00 0.00 0.00 4.40
3496 8068 8.599055 TTGTAATAACCGTTGTTGTACATACA 57.401 30.769 0.00 1.49 36.75 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
357 359 1.079819 CTGGGTTGTCGCTCATCGT 60.080 57.895 0.00 0.00 39.67 3.73
369 371 1.761198 GGAGATAGCGTTACCTGGGTT 59.239 52.381 0.00 0.00 0.00 4.11
418 420 0.099968 GCGCGTGAGTACAGGATACA 59.900 55.000 8.43 0.00 41.41 2.29
422 424 3.755628 GGGCGCGTGAGTACAGGA 61.756 66.667 8.43 0.00 34.32 3.86
480 483 2.359850 TTGGTGTCCCGCATCTGC 60.360 61.111 0.00 0.00 37.78 4.26
505 508 1.668294 CCTCTCACTGTCCGTTGCT 59.332 57.895 0.00 0.00 0.00 3.91
517 520 2.922503 TTGCTGTCCCGCCTCTCA 60.923 61.111 0.00 0.00 0.00 3.27
574 577 1.024579 CAGGCGCCAAGGTAAACGAT 61.025 55.000 31.54 0.00 0.00 3.73
601 604 2.415010 CGGGGATCGCTGAGTCAG 59.585 66.667 16.21 16.21 34.12 3.51
681 685 2.404186 CGTCCCGTCATCCTCGTCA 61.404 63.158 0.00 0.00 0.00 4.35
809 819 2.504996 AGGGGAGAAGAATTGCTCTCAG 59.495 50.000 13.00 0.00 33.22 3.35
925 935 3.807538 CGACGACGACCCCGATGT 61.808 66.667 0.00 0.00 42.66 3.06
927 937 3.503363 GACGACGACGACCCCGAT 61.503 66.667 15.32 0.00 42.66 4.18
1207 1238 8.970020 TCTAGCAACATACCAAATTGAATCAAT 58.030 29.630 2.07 2.07 35.39 2.57
1589 2957 7.285629 ACGGAGACTATCAAATGAGACATTAGA 59.714 37.037 0.00 0.00 0.00 2.10
1638 3006 5.058490 AGAACGAAAATAAACCAACGGAGA 58.942 37.500 0.00 0.00 0.00 3.71
1643 3011 6.090783 GGATGGAGAACGAAAATAAACCAAC 58.909 40.000 0.00 0.00 0.00 3.77
1644 3012 5.184287 GGGATGGAGAACGAAAATAAACCAA 59.816 40.000 0.00 0.00 0.00 3.67
2263 3770 5.950758 TGCGGTGTTTGATGTAAAATAGT 57.049 34.783 0.00 0.00 0.00 2.12
2985 7556 1.279846 TGCAGCATGAGAATCCTGACA 59.720 47.619 0.00 0.00 39.69 3.58
3092 7663 5.109331 TCAACAATTGATGTGCTGCAGCA 62.109 43.478 36.78 36.78 42.99 4.41
3146 7717 0.535102 AACACACCTCCTTCAAGCGG 60.535 55.000 0.00 0.00 0.00 5.52
3212 7783 6.554605 TCATCCCCTTTTGAAGAAGAAACATT 59.445 34.615 0.00 0.00 0.00 2.71
3257 7828 0.769247 ACAGGCGGGTAAAGTTCCTT 59.231 50.000 0.00 0.00 0.00 3.36
3355 7926 7.389330 TCTTTCCGTAAACTGAAAGCATCATAA 59.611 33.333 17.30 1.99 42.84 1.90
3444 8016 2.182842 GCGCCCATAAGCAGTCCAG 61.183 63.158 0.00 0.00 0.00 3.86
3452 8024 0.179000 AGACTTCCAGCGCCCATAAG 59.821 55.000 2.29 5.78 0.00 1.73
3545 8117 0.034380 AGTGCAAGCTCCATCTGCAT 60.034 50.000 12.83 0.90 37.83 3.96
3932 8518 2.935676 GCGCTACAGCTAACCCTTTCTT 60.936 50.000 0.00 0.00 39.32 2.52


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

AutoCloner maintained by Alex Coulton.