Multiple sequence alignment - TraesCS1B01G434800

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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 TraesCS1B01G434800 chr1B 100.000 2495 0 0 1 2495 659001566 659004060 0.000000e+00 4608
1 TraesCS1B01G434800 chr1B 92.675 1488 68 19 990 2460 659033653 659035116 0.000000e+00 2106
2 TraesCS1B01G434800 chr1B 92.389 1511 56 17 990 2476 659294562 659296037 0.000000e+00 2098
3 TraesCS1B01G434800 chr1B 90.500 1379 52 29 990 2349 659285896 659287214 0.000000e+00 1748
4 TraesCS1B01G434800 chr1B 91.619 1229 55 16 1136 2342 659073582 659074784 0.000000e+00 1655
5 TraesCS1B01G434800 chr1B 96.643 983 30 3 1 982 659292344 659293324 0.000000e+00 1629
6 TraesCS1B01G434800 chr1B 99.202 877 7 0 1619 2495 658969601 658970477 0.000000e+00 1581
7 TraesCS1B01G434800 chr1B 95.547 988 17 5 1 982 659281533 659282499 0.000000e+00 1555
8 TraesCS1B01G434800 chr1B 95.122 984 25 3 1 982 659031404 659032366 0.000000e+00 1530
9 TraesCS1B01G434800 chr1B 97.178 567 10 1 416 982 659178514 659179074 0.000000e+00 953
10 TraesCS1B01G434800 chr1B 91.089 606 29 4 988 1593 658969030 658969610 0.000000e+00 797
11 TraesCS1B01G434800 chr1B 86.676 728 43 24 990 1688 659182353 659183055 0.000000e+00 758
12 TraesCS1B01G434800 chr1B 85.385 650 71 9 1837 2476 659327172 659327807 0.000000e+00 652
13 TraesCS1B01G434800 chr1B 91.781 438 9 4 1 432 659177583 659177999 3.580000e-163 584
14 TraesCS1B01G434800 chr1B 79.399 898 97 36 1623 2458 659317674 659318545 1.010000e-153 553
15 TraesCS1B01G434800 chr1B 86.335 483 48 13 1 479 659068543 659069011 6.160000e-141 510
16 TraesCS1B01G434800 chr1B 84.250 527 45 14 472 981 658966755 658967260 1.740000e-131 479
17 TraesCS1B01G434800 chr1B 96.691 272 8 1 2206 2476 659190872 659191143 3.780000e-123 451
18 TraesCS1B01G434800 chr1B 96.324 272 9 1 2206 2476 659083060 659083331 1.760000e-121 446
19 TraesCS1B01G434800 chr1B 88.136 236 20 3 750 982 659069643 659069873 8.790000e-70 274
20 TraesCS1B01G434800 chr1B 83.895 267 24 4 472 724 659069384 659069645 1.150000e-58 237
21 TraesCS1B01G434800 chr1A 92.129 775 37 9 992 1764 568265903 568266655 0.000000e+00 1072
22 TraesCS1B01G434800 chr1A 85.978 649 66 10 1839 2476 568399455 568400089 0.000000e+00 671
23 TraesCS1B01G434800 chr1A 92.952 454 22 4 992 1445 568327861 568328304 0.000000e+00 652
24 TraesCS1B01G434800 chr1A 92.809 445 31 1 1809 2252 568266926 568267370 0.000000e+00 643
25 TraesCS1B01G434800 chr1A 82.263 654 77 21 1837 2476 568384182 568384810 1.700000e-146 529
26 TraesCS1B01G434800 chr1A 85.038 528 51 12 472 981 568325443 568325960 1.710000e-141 512
27 TraesCS1B01G434800 chr1A 85.009 527 48 12 476 982 568263617 568264132 7.960000e-140 507
28 TraesCS1B01G434800 chr1A 83.759 431 40 15 558 981 568114555 568114962 5.040000e-102 381
29 TraesCS1B01G434800 chr1A 82.229 332 25 15 6 333 568262699 568263000 3.180000e-64 255
30 TraesCS1B01G434800 chr1D 86.918 1009 50 33 1507 2476 473961549 473962514 0.000000e+00 1057
31 TraesCS1B01G434800 chr1D 85.820 677 47 21 1080 1731 473879749 473880401 0.000000e+00 673
32 TraesCS1B01G434800 chr1D 82.975 652 75 19 1837 2476 473966754 473967381 7.800000e-155 556
33 TraesCS1B01G434800 chr1D 85.579 527 49 7 472 981 473958788 473959304 6.110000e-146 527
34 TraesCS1B01G434800 chr1D 84.153 549 67 10 1936 2476 473998118 473998654 4.760000e-142 514
35 TraesCS1B01G434800 chr1D 85.386 479 42 14 6 479 473957920 473958375 2.900000e-129 472
36 TraesCS1B01G434800 chr1D 87.398 246 18 6 1837 2082 473997879 473998111 1.140000e-68 270


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 TraesCS1B01G434800 chr1B 659001566 659004060 2494 False 4608.000000 4608 100.000000 1 2495 1 chr1B.!!$F1 2494
1 TraesCS1B01G434800 chr1B 659292344 659296037 3693 False 1863.500000 2098 94.516000 1 2476 2 chr1B.!!$F11 2475
2 TraesCS1B01G434800 chr1B 659031404 659035116 3712 False 1818.000000 2106 93.898500 1 2460 2 chr1B.!!$F7 2459
3 TraesCS1B01G434800 chr1B 659281533 659287214 5681 False 1651.500000 1748 93.023500 1 2349 2 chr1B.!!$F10 2348
4 TraesCS1B01G434800 chr1B 658966755 658970477 3722 False 952.333333 1581 91.513667 472 2495 3 chr1B.!!$F6 2023
5 TraesCS1B01G434800 chr1B 659177583 659183055 5472 False 765.000000 953 91.878333 1 1688 3 chr1B.!!$F9 1687
6 TraesCS1B01G434800 chr1B 659068543 659074784 6241 False 669.000000 1655 87.496250 1 2342 4 chr1B.!!$F8 2341
7 TraesCS1B01G434800 chr1B 659327172 659327807 635 False 652.000000 652 85.385000 1837 2476 1 chr1B.!!$F5 639
8 TraesCS1B01G434800 chr1B 659317674 659318545 871 False 553.000000 553 79.399000 1623 2458 1 chr1B.!!$F4 835
9 TraesCS1B01G434800 chr1A 568399455 568400089 634 False 671.000000 671 85.978000 1839 2476 1 chr1A.!!$F3 637
10 TraesCS1B01G434800 chr1A 568262699 568267370 4671 False 619.250000 1072 88.044000 6 2252 4 chr1A.!!$F4 2246
11 TraesCS1B01G434800 chr1A 568325443 568328304 2861 False 582.000000 652 88.995000 472 1445 2 chr1A.!!$F5 973
12 TraesCS1B01G434800 chr1A 568384182 568384810 628 False 529.000000 529 82.263000 1837 2476 1 chr1A.!!$F2 639
13 TraesCS1B01G434800 chr1D 473957920 473962514 4594 False 685.333333 1057 85.961000 6 2476 3 chr1D.!!$F3 2470
14 TraesCS1B01G434800 chr1D 473879749 473880401 652 False 673.000000 673 85.820000 1080 1731 1 chr1D.!!$F1 651
15 TraesCS1B01G434800 chr1D 473966754 473967381 627 False 556.000000 556 82.975000 1837 2476 1 chr1D.!!$F2 639
16 TraesCS1B01G434800 chr1D 473997879 473998654 775 False 392.000000 514 85.775500 1837 2476 2 chr1D.!!$F4 639

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
670 1722 1.94334 GATGAAAAGATCTCCGGTGGC 59.057 52.381 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 8177 2.440409 CCCAGCAAGCAGACAAATACT 58.56 47.619 0.0 0.0 0.0 2.12 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
347 358 5.277345 CGCAGGGTTAATTAGAAATCCGAAG 60.277 44.000 0.00 0.00 0.00 3.79
524 1564 8.792830 ATAGAAACTGCTTGCAGAAATACTAA 57.207 30.769 26.71 6.80 0.00 2.24
636 1688 3.534357 TCTTTCCCATGGCCTTTTACA 57.466 42.857 6.09 0.00 0.00 2.41
670 1722 1.943340 GATGAAAAGATCTCCGGTGGC 59.057 52.381 0.00 0.00 0.00 5.01
819 1873 3.474570 AAGCTAGGCGCCAGGAGG 61.475 66.667 31.54 14.07 40.39 4.30
982 2357 6.506538 ACATGTAAAGAATGGAGGCTCTAT 57.493 37.500 15.23 11.47 0.00 1.98
983 2358 6.904626 ACATGTAAAGAATGGAGGCTCTATT 58.095 36.000 23.96 23.96 29.85 1.73
984 2359 7.349598 ACATGTAAAGAATGGAGGCTCTATTT 58.650 34.615 24.42 13.82 27.21 1.40
985 2360 8.494433 ACATGTAAAGAATGGAGGCTCTATTTA 58.506 33.333 24.42 12.91 27.21 1.40
986 2361 9.512588 CATGTAAAGAATGGAGGCTCTATTTAT 57.487 33.333 24.42 14.91 27.21 1.40
996 7650 4.704403 AGGCTCTATTTATAGGCTCCCAT 58.296 43.478 0.00 0.00 44.60 4.00
1015 7669 3.561960 CCATGGCCTATAAATAGCAGCCA 60.562 47.826 17.11 17.11 45.37 4.75
1069 7723 4.067896 CCAGAGCTTCTACAAGAGCAAAA 58.932 43.478 0.00 0.00 0.00 2.44
1156 7815 4.468765 AGAACATCACATCTCACCTGAG 57.531 45.455 0.00 0.00 43.36 3.35
1178 7837 3.425713 TCTTCCGGGTCGTCGTCG 61.426 66.667 0.00 0.00 38.55 5.12
1481 8142 6.197282 GCTTTGCTTCTAACAAGTTTTCAGTC 59.803 38.462 0.00 0.00 0.00 3.51
1486 8147 4.945246 TCTAACAAGTTTTCAGTCGAGCT 58.055 39.130 0.00 0.00 0.00 4.09
1488 8149 3.951979 ACAAGTTTTCAGTCGAGCTTG 57.048 42.857 0.00 0.00 39.16 4.01
1489 8150 3.531538 ACAAGTTTTCAGTCGAGCTTGA 58.468 40.909 0.00 0.00 37.39 3.02
1490 8151 3.557595 ACAAGTTTTCAGTCGAGCTTGAG 59.442 43.478 3.10 0.00 37.39 3.02
1491 8152 2.139118 AGTTTTCAGTCGAGCTTGAGC 58.861 47.619 3.10 0.00 42.49 4.26
1492 8153 1.867233 GTTTTCAGTCGAGCTTGAGCA 59.133 47.619 3.10 0.00 45.16 4.26
1516 8177 7.255104 GCATAATAAAGCATACCAGTTACTGCA 60.255 37.037 6.88 0.00 37.09 4.41
1540 8219 2.282745 GTCTGCTTGCTGGGGCTT 60.283 61.111 0.00 0.00 39.59 4.35
1577 8272 4.040445 TGCTTTAACTCAAAAGGCACAC 57.960 40.909 0.00 0.00 37.03 3.82
1598 8297 5.104109 ACACCATGCAGGGTATTTATGTACT 60.104 40.000 24.77 0.00 43.89 2.73
1599 8298 6.100569 ACACCATGCAGGGTATTTATGTACTA 59.899 38.462 24.77 0.00 43.89 1.82
1600 8299 6.426937 CACCATGCAGGGTATTTATGTACTAC 59.573 42.308 24.77 0.00 43.89 2.73
1631 8330 9.398538 TGTTTTTCTTTAGAGGTTACTTAGCAA 57.601 29.630 0.00 0.00 0.00 3.91
1657 8368 2.680913 GCATGACGACTGGCACCAC 61.681 63.158 0.00 0.00 0.00 4.16
1658 8369 1.301637 CATGACGACTGGCACCACA 60.302 57.895 0.00 0.00 0.00 4.17
2033 9027 5.520748 ACAGGAAGGAATGGAGTATTGTT 57.479 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 211 1.707427 AGGAGGGGGCATCACATATTC 59.293 52.381 0.00 0.00 0.00 1.75
295 306 2.577449 ACGGAAGCTTGGTTTGTTTG 57.423 45.000 2.10 0.00 0.00 2.93
524 1564 8.736244 ACCAGCAAAATACGTACTTATTTCATT 58.264 29.630 15.40 1.04 31.67 2.57
636 1688 9.401058 AGATCTTTTCATCGGAATTAAATCTGT 57.599 29.630 0.00 0.00 31.93 3.41
670 1722 2.584608 GACCGGTCCACCATCCAG 59.415 66.667 24.75 0.00 35.14 3.86
692 1746 1.531739 GGGTTTGATTCTTGCGGGCA 61.532 55.000 0.00 0.00 0.00 5.36
819 1873 1.340248 CATTGCCAGAATGCCATCCTC 59.660 52.381 0.00 0.00 31.97 3.71
996 7650 3.330405 TGATGGCTGCTATTTATAGGCCA 59.670 43.478 16.80 16.80 45.37 5.36
1015 7669 2.507058 TGGTGGCTCTCTTTGCTATGAT 59.493 45.455 0.00 0.00 0.00 2.45
1069 7723 2.886391 GCTCCTGGAAGTGAGGTAGTCT 60.886 54.545 0.00 0.00 33.54 3.24
1156 7815 1.141234 GACGACCCGGAAGACATCC 59.859 63.158 0.73 0.00 45.57 3.51
1481 8142 4.801147 TGCTTTATTATGCTCAAGCTCG 57.199 40.909 3.32 0.00 41.89 5.03
1486 8147 7.880160 AACTGGTATGCTTTATTATGCTCAA 57.120 32.000 0.00 0.00 0.00 3.02
1488 8149 8.499162 CAGTAACTGGTATGCTTTATTATGCTC 58.501 37.037 0.00 0.00 0.00 4.26
1489 8150 7.041098 GCAGTAACTGGTATGCTTTATTATGCT 60.041 37.037 0.00 0.00 35.78 3.79
1490 8151 7.078228 GCAGTAACTGGTATGCTTTATTATGC 58.922 38.462 0.00 0.00 35.78 3.14
1491 8152 8.153479 TGCAGTAACTGGTATGCTTTATTATG 57.847 34.615 0.00 0.00 39.42 1.90
1492 8153 7.993183 ACTGCAGTAACTGGTATGCTTTATTAT 59.007 33.333 20.16 0.00 39.42 1.28
1516 8177 2.440409 CCCAGCAAGCAGACAAATACT 58.560 47.619 0.00 0.00 0.00 2.12
1577 8272 6.769512 AGTAGTACATAAATACCCTGCATGG 58.230 40.000 6.46 6.46 0.00 3.66
1657 8368 8.660373 CAGTTTGGCTTATAGAGAGTTAGTTTG 58.340 37.037 0.00 0.00 0.00 2.93
1658 8369 7.334671 GCAGTTTGGCTTATAGAGAGTTAGTTT 59.665 37.037 0.00 0.00 0.00 2.66
2033 9027 7.392113 CCTAACCATACTTTGTCCACACAATAA 59.608 37.037 0.00 0.00 42.28 1.40


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

AutoCloner maintained by Alex Coulton.