Multiple sequence alignment - TraesCS6B01G448500

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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 TraesCS6B01G448500 chr6B 100.000 2557 0 0 1 2557 708191255 708193811 0.000000e+00 4723
1 TraesCS6B01G448500 chr6B 99.675 924 1 2 1636 2557 708201066 708201989 0.000000e+00 1688
2 TraesCS6B01G448500 chr6B 99.346 918 5 1 1641 2557 422811327 422810410 0.000000e+00 1661
3 TraesCS6B01G448500 chr4A 94.883 1661 64 10 1 1641 44650140 44651799 0.000000e+00 2577
4 TraesCS6B01G448500 chr4A 93.405 1683 68 9 1 1641 44781614 44783295 0.000000e+00 2453
5 TraesCS6B01G448500 chr4A 94.382 979 40 4 1 965 44646327 44645350 0.000000e+00 1489
6 TraesCS6B01G448500 chr4A 94.705 491 20 4 1157 1641 44645353 44644863 0.000000e+00 758
7 TraesCS6B01G448500 chr3A 93.120 1686 69 23 1 1641 688613411 688611728 0.000000e+00 2427
8 TraesCS6B01G448500 chr3A 87.774 1595 126 26 60 1595 70485318 70483734 0.000000e+00 1801
9 TraesCS6B01G448500 chr3A 91.777 1131 43 12 541 1641 264036093 264037203 0.000000e+00 1528
10 TraesCS6B01G448500 chr6A 90.990 1687 103 25 1 1641 85351443 85353126 0.000000e+00 2228
11 TraesCS6B01G448500 chr1D 89.832 1485 93 22 1 1430 456809849 456811330 0.000000e+00 1853
12 TraesCS6B01G448500 chr1D 94.581 609 24 4 1042 1641 202978686 202979294 0.000000e+00 933
13 TraesCS6B01G448500 chr7A 99.564 917 4 0 1641 2557 73401452 73402368 0.000000e+00 1672
14 TraesCS6B01G448500 chr2A 99.351 924 4 2 1636 2557 504745917 504746840 0.000000e+00 1672
15 TraesCS6B01G448500 chr4B 99.242 924 5 2 1636 2557 2373107 2374030 0.000000e+00 1666
16 TraesCS6B01G448500 chr4B 99.455 917 5 0 1641 2557 283084365 283085281 0.000000e+00 1666
17 TraesCS6B01G448500 chr4B 99.346 918 6 0 1640 2557 329589633 329588716 0.000000e+00 1663
18 TraesCS6B01G448500 chr4B 99.238 919 7 0 1639 2557 283076212 283077130 0.000000e+00 1659
19 TraesCS6B01G448500 chr4B 99.346 917 5 1 1641 2557 329581061 329580146 0.000000e+00 1659
20 TraesCS6B01G448500 chr3D 93.168 805 48 5 843 1641 50895960 50896763 0.000000e+00 1175
21 TraesCS6B01G448500 chr3D 94.110 764 39 3 1 760 50895068 50895829 0.000000e+00 1157
22 TraesCS6B01G448500 chr1A 91.905 803 60 4 843 1641 516653141 516652340 0.000000e+00 1118
23 TraesCS6B01G448500 chr1A 88.318 428 25 13 443 847 516653630 516653205 8.220000e-135 490
24 TraesCS6B01G448500 chr7B 89.486 875 67 13 1 852 471226760 471225888 0.000000e+00 1083
25 TraesCS6B01G448500 chr6D 91.391 453 26 7 1201 1641 28691870 28691419 2.180000e-170 608


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 TraesCS6B01G448500 chr6B 708191255 708193811 2556 False 4723.0 4723 100.0000 1 2557 1 chr6B.!!$F1 2556
1 TraesCS6B01G448500 chr6B 708201066 708201989 923 False 1688.0 1688 99.6750 1636 2557 1 chr6B.!!$F2 921
2 TraesCS6B01G448500 chr6B 422810410 422811327 917 True 1661.0 1661 99.3460 1641 2557 1 chr6B.!!$R1 916
3 TraesCS6B01G448500 chr4A 44650140 44651799 1659 False 2577.0 2577 94.8830 1 1641 1 chr4A.!!$F1 1640
4 TraesCS6B01G448500 chr4A 44781614 44783295 1681 False 2453.0 2453 93.4050 1 1641 1 chr4A.!!$F2 1640
5 TraesCS6B01G448500 chr4A 44644863 44646327 1464 True 1123.5 1489 94.5435 1 1641 2 chr4A.!!$R1 1640
6 TraesCS6B01G448500 chr3A 688611728 688613411 1683 True 2427.0 2427 93.1200 1 1641 1 chr3A.!!$R2 1640
7 TraesCS6B01G448500 chr3A 70483734 70485318 1584 True 1801.0 1801 87.7740 60 1595 1 chr3A.!!$R1 1535
8 TraesCS6B01G448500 chr3A 264036093 264037203 1110 False 1528.0 1528 91.7770 541 1641 1 chr3A.!!$F1 1100
9 TraesCS6B01G448500 chr6A 85351443 85353126 1683 False 2228.0 2228 90.9900 1 1641 1 chr6A.!!$F1 1640
10 TraesCS6B01G448500 chr1D 456809849 456811330 1481 False 1853.0 1853 89.8320 1 1430 1 chr1D.!!$F2 1429
11 TraesCS6B01G448500 chr1D 202978686 202979294 608 False 933.0 933 94.5810 1042 1641 1 chr1D.!!$F1 599
12 TraesCS6B01G448500 chr7A 73401452 73402368 916 False 1672.0 1672 99.5640 1641 2557 1 chr7A.!!$F1 916
13 TraesCS6B01G448500 chr2A 504745917 504746840 923 False 1672.0 1672 99.3510 1636 2557 1 chr2A.!!$F1 921
14 TraesCS6B01G448500 chr4B 2373107 2374030 923 False 1666.0 1666 99.2420 1636 2557 1 chr4B.!!$F1 921
15 TraesCS6B01G448500 chr4B 283084365 283085281 916 False 1666.0 1666 99.4550 1641 2557 1 chr4B.!!$F3 916
16 TraesCS6B01G448500 chr4B 329588716 329589633 917 True 1663.0 1663 99.3460 1640 2557 1 chr4B.!!$R2 917
17 TraesCS6B01G448500 chr4B 283076212 283077130 918 False 1659.0 1659 99.2380 1639 2557 1 chr4B.!!$F2 918
18 TraesCS6B01G448500 chr4B 329580146 329581061 915 True 1659.0 1659 99.3460 1641 2557 1 chr4B.!!$R1 916
19 TraesCS6B01G448500 chr3D 50895068 50896763 1695 False 1166.0 1175 93.6390 1 1641 2 chr3D.!!$F1 1640
20 TraesCS6B01G448500 chr1A 516652340 516653630 1290 True 804.0 1118 90.1115 443 1641 2 chr1A.!!$R1 1198
21 TraesCS6B01G448500 chr7B 471225888 471226760 872 True 1083.0 1083 89.4860 1 852 1 chr7B.!!$R1 851

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
23 24 1.089112 TGATGCAATGAGGTTGAGCG 58.911 50.0 0.0 0.0 40.37 5.03 F
761 769 1.247567 CTTTGGTGGGATGTGTGGAC 58.752 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1686 1.131638 TTGTGGCACTTCAGGAGAGT 58.868 50.000 19.83 0.0 0.0 3.24 R
2015 2184 2.417719 GCATGTGTCCTTCTTCGTTCT 58.582 47.619 0.00 0.0 0.0 3.01 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 1.089112 TGATGCAATGAGGTTGAGCG 58.911 50.000 0.00 0.0 40.37 5.03
208 211 6.258230 TCGACTCGGTATCACTTAAAAGAA 57.742 37.500 0.00 0.0 0.00 2.52
232 235 3.412386 GGTATCAAGTCAACAACAGCCT 58.588 45.455 0.00 0.0 0.00 4.58
391 394 5.693961 TGTGTCCATATGGTGCTGAATAAT 58.306 37.500 21.28 0.0 36.34 1.28
392 395 5.532032 TGTGTCCATATGGTGCTGAATAATG 59.468 40.000 21.28 0.0 36.34 1.90
393 396 5.048504 GTGTCCATATGGTGCTGAATAATGG 60.049 44.000 21.28 0.0 36.34 3.16
394 397 5.072741 GTCCATATGGTGCTGAATAATGGT 58.927 41.667 21.28 0.0 36.34 3.55
395 398 5.048504 GTCCATATGGTGCTGAATAATGGTG 60.049 44.000 21.28 0.0 36.34 4.17
396 399 4.828939 CCATATGGTGCTGAATAATGGTGT 59.171 41.667 14.09 0.0 0.00 4.16
397 400 5.302568 CCATATGGTGCTGAATAATGGTGTT 59.697 40.000 14.09 0.0 0.00 3.32
398 401 4.989279 ATGGTGCTGAATAATGGTGTTC 57.011 40.909 0.00 0.0 0.00 3.18
399 402 4.032960 TGGTGCTGAATAATGGTGTTCT 57.967 40.909 0.00 0.0 0.00 3.01
402 405 4.702131 GGTGCTGAATAATGGTGTTCTCTT 59.298 41.667 0.00 0.0 0.00 2.85
429 432 7.887996 TGGAAAATGCTTATGATGAACAAAC 57.112 32.000 0.00 0.0 0.00 2.93
517 521 5.416083 CATGTGATGGATGATTTGTTGCTT 58.584 37.500 0.00 0.0 0.00 3.91
533 537 5.324409 TGTTGCTTGAGGAAGTGGATAATT 58.676 37.500 0.00 0.0 0.00 1.40
693 697 2.540383 AGAGTTGGAGTAGGATGTGCA 58.460 47.619 0.00 0.0 0.00 4.57
761 769 1.247567 CTTTGGTGGGATGTGTGGAC 58.752 55.000 0.00 0.0 0.00 4.02
776 784 4.202514 TGTGTGGACCAACCTTGATATGAA 60.203 41.667 0.00 0.0 39.86 2.57
785 793 5.395546 CCAACCTTGATATGAATTTGGTGGG 60.396 44.000 7.07 0.0 31.72 4.61
948 1078 4.016444 GCATTTTCTTGTAGGACCATGGA 58.984 43.478 21.47 0.0 0.00 3.41
1113 1251 6.399743 TGTTATAGGTAATGTGCGTGAGAAA 58.600 36.000 0.00 0.0 0.00 2.52
1141 1279 3.628017 GTGACCATCACAAAGGAAAACG 58.372 45.455 4.08 0.0 46.22 3.60
1154 1292 4.411256 AGGAAAACGTCAGTTCAAGGTA 57.589 40.909 8.35 0.0 40.18 3.08
1244 1382 5.627499 TGGATCAATAACAAGCTGTCAAC 57.373 39.130 0.00 0.0 0.00 3.18
1389 1556 3.351794 AGGCTAACAAGAAAGTAGGGC 57.648 47.619 0.00 0.0 0.00 5.19
1390 1557 2.642807 AGGCTAACAAGAAAGTAGGGCA 59.357 45.455 0.00 0.0 0.00 5.36
1391 1558 2.747989 GGCTAACAAGAAAGTAGGGCAC 59.252 50.000 0.00 0.0 0.00 5.01
1505 1672 6.408035 TGAAACTGTTGTAGAACCAACTACA 58.592 36.000 0.00 0.0 46.99 2.74
1519 1686 4.104102 ACCAACTACAGAACCCAATGAAGA 59.896 41.667 0.00 0.0 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.527565 ACGACAAATGCATCTTGGCC 59.472 50.000 19.12 0.00 0.00 5.36
163 166 4.581309 TCTGAATGGAGCAAGAAATCCT 57.419 40.909 0.00 0.00 36.50 3.24
208 211 3.758554 GCTGTTGTTGACTTGATACCCAT 59.241 43.478 0.00 0.00 0.00 4.00
232 235 4.640771 ATACAGCTCTTTGGGAGTTTGA 57.359 40.909 0.00 0.00 43.62 2.69
391 394 5.774690 AGCATTTTCCATTAAGAGAACACCA 59.225 36.000 0.00 0.00 0.00 4.17
392 395 6.272822 AGCATTTTCCATTAAGAGAACACC 57.727 37.500 0.00 0.00 0.00 4.16
393 396 9.294030 CATAAGCATTTTCCATTAAGAGAACAC 57.706 33.333 0.00 0.00 0.00 3.32
394 397 9.241919 TCATAAGCATTTTCCATTAAGAGAACA 57.758 29.630 0.00 0.00 0.00 3.18
397 400 9.631257 TCATCATAAGCATTTTCCATTAAGAGA 57.369 29.630 0.00 0.00 0.00 3.10
437 440 8.952278 ACAACAAGCATTAATAATTCGAACCTA 58.048 29.630 0.00 0.00 0.00 3.08
517 521 8.045720 AGGCTATTTAATTATCCACTTCCTCA 57.954 34.615 0.00 0.00 0.00 3.86
533 537 6.295349 GGATCATCTTCGGAAGAGGCTATTTA 60.295 42.308 23.57 9.11 41.61 1.40
693 697 5.202004 AGAACACCATTATCTAGTCGACCT 58.798 41.667 13.01 2.17 0.00 3.85
733 741 6.038603 CACACATCCCACCAAAGTAATATCAG 59.961 42.308 0.00 0.00 0.00 2.90
740 748 2.058705 TCCACACATCCCACCAAAGTA 58.941 47.619 0.00 0.00 0.00 2.24
761 769 5.395546 CCCACCAAATTCATATCAAGGTTGG 60.396 44.000 3.79 3.79 39.92 3.77
776 784 0.114954 AGGCACACATCCCACCAAAT 59.885 50.000 0.00 0.00 0.00 2.32
785 793 4.535526 AAATACCCAAAAGGCACACATC 57.464 40.909 0.00 0.00 40.58 3.06
838 885 8.437360 ACAAGGTAATGTCACACATACATATG 57.563 34.615 0.00 0.00 37.97 1.78
845 916 5.376625 AGACAACAAGGTAATGTCACACAT 58.623 37.500 7.75 0.00 44.55 3.21
1071 1202 1.552337 ACAGCACTGTAGACATGGGAG 59.448 52.381 0.35 0.00 42.90 4.30
1154 1292 5.099575 CGTAGTGCTTTTCAAAGGTTTTGT 58.900 37.500 1.55 0.00 36.53 2.83
1244 1382 4.134379 AGCCACACATCTTCACTATCAG 57.866 45.455 0.00 0.00 0.00 2.90
1389 1556 7.962964 TCTTAATGACCTTGTTCTTGTAGTG 57.037 36.000 0.00 0.00 0.00 2.74
1390 1557 9.574516 AATTCTTAATGACCTTGTTCTTGTAGT 57.425 29.630 0.00 0.00 0.00 2.73
1391 1558 9.831737 CAATTCTTAATGACCTTGTTCTTGTAG 57.168 33.333 0.00 0.00 0.00 2.74
1505 1672 3.262915 CAGGAGAGTCTTCATTGGGTTCT 59.737 47.826 0.06 0.00 0.00 3.01
1519 1686 1.131638 TTGTGGCACTTCAGGAGAGT 58.868 50.000 19.83 0.00 0.00 3.24
2015 2184 2.417719 GCATGTGTCCTTCTTCGTTCT 58.582 47.619 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.