Multiple sequence alignment - TraesCS2B01G382800

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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 TraesCS2B01G382800 chr2B 100.000 2264 0 0 1 2264 546619168 546621431 0.000000e+00 4181.0
1 TraesCS2B01G382800 chr2B 91.310 840 44 9 1450 2264 465663596 465662761 0.000000e+00 1120.0
2 TraesCS2B01G382800 chr2B 83.787 845 82 23 1450 2264 215848666 215849485 0.000000e+00 750.0
3 TraesCS2B01G382800 chr2B 90.618 469 34 6 1450 1911 430230965 430230500 4.130000e-172 614.0
4 TraesCS2B01G382800 chr2B 90.741 54 3 2 1421 1474 682791582 682791531 1.120000e-08 71.3
5 TraesCS2B01G382800 chr2D 93.818 1472 79 3 1 1467 476789253 476790717 0.000000e+00 2204.0
6 TraesCS2B01G382800 chr2D 93.729 1467 82 4 1 1465 632766142 632767600 0.000000e+00 2191.0
7 TraesCS2B01G382800 chr6B 93.524 1467 86 3 2 1466 281223409 281221950 0.000000e+00 2174.0
8 TraesCS2B01G382800 chr6B 91.859 823 41 8 1466 2264 605818314 605819134 0.000000e+00 1125.0
9 TraesCS2B01G382800 chr6B 85.976 164 18 4 2103 2264 157835564 157835724 1.080000e-38 171.0
10 TraesCS2B01G382800 chr5B 93.071 1472 90 4 1 1467 89726820 89728284 0.000000e+00 2143.0
11 TraesCS2B01G382800 chr5B 92.386 1471 104 5 1 1468 64293433 64294898 0.000000e+00 2089.0
12 TraesCS2B01G382800 chr5B 92.114 1471 108 5 1 1468 584816927 584815462 0.000000e+00 2067.0
13 TraesCS2B01G382800 chr1D 92.944 1474 94 4 2 1474 14674863 14673399 0.000000e+00 2137.0
14 TraesCS2B01G382800 chr4A 93.417 1428 83 5 42 1467 564697234 564698652 0.000000e+00 2106.0
15 TraesCS2B01G382800 chr5A 92.742 1433 96 5 1 1431 690039125 690040551 0.000000e+00 2063.0
16 TraesCS2B01G382800 chr1B 90.047 844 48 8 1450 2264 549917418 549916582 0.000000e+00 1061.0
17 TraesCS2B01G382800 chr1B 93.103 464 30 2 1450 1912 540298650 540298188 0.000000e+00 678.0
18 TraesCS2B01G382800 chr1B 87.687 601 48 5 1450 2027 540289073 540288476 0.000000e+00 676.0
19 TraesCS2B01G382800 chr1B 94.799 423 22 0 1467 1889 504246434 504246012 0.000000e+00 660.0
20 TraesCS2B01G382800 chr1B 89.859 355 30 6 1912 2264 504245680 504245330 3.430000e-123 451.0
21 TraesCS2B01G382800 chr1B 92.357 157 10 2 2110 2264 540287906 540287750 2.930000e-54 222.0
22 TraesCS2B01G382800 chr3B 89.869 839 48 8 1450 2264 809558230 809557405 0.000000e+00 1044.0
23 TraesCS2B01G382800 chr3B 79.787 188 29 6 1958 2142 732875967 732876148 6.560000e-26 128.0
24 TraesCS2B01G382800 chr4B 89.590 634 35 9 1519 2129 9634866 9635491 0.000000e+00 776.0
25 TraesCS2B01G382800 chr4B 94.545 110 4 2 2156 2264 9635817 9635925 3.870000e-38 169.0
26 TraesCS2B01G382800 chr2A 85.095 369 31 7 1466 1830 764944589 764944241 2.770000e-94 355.0


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 TraesCS2B01G382800 chr2B 546619168 546621431 2263 False 4181.0 4181 100.0000 1 2264 1 chr2B.!!$F2 2263
1 TraesCS2B01G382800 chr2B 465662761 465663596 835 True 1120.0 1120 91.3100 1450 2264 1 chr2B.!!$R2 814
2 TraesCS2B01G382800 chr2B 215848666 215849485 819 False 750.0 750 83.7870 1450 2264 1 chr2B.!!$F1 814
3 TraesCS2B01G382800 chr2D 476789253 476790717 1464 False 2204.0 2204 93.8180 1 1467 1 chr2D.!!$F1 1466
4 TraesCS2B01G382800 chr2D 632766142 632767600 1458 False 2191.0 2191 93.7290 1 1465 1 chr2D.!!$F2 1464
5 TraesCS2B01G382800 chr6B 281221950 281223409 1459 True 2174.0 2174 93.5240 2 1466 1 chr6B.!!$R1 1464
6 TraesCS2B01G382800 chr6B 605818314 605819134 820 False 1125.0 1125 91.8590 1466 2264 1 chr6B.!!$F2 798
7 TraesCS2B01G382800 chr5B 89726820 89728284 1464 False 2143.0 2143 93.0710 1 1467 1 chr5B.!!$F2 1466
8 TraesCS2B01G382800 chr5B 64293433 64294898 1465 False 2089.0 2089 92.3860 1 1468 1 chr5B.!!$F1 1467
9 TraesCS2B01G382800 chr5B 584815462 584816927 1465 True 2067.0 2067 92.1140 1 1468 1 chr5B.!!$R1 1467
10 TraesCS2B01G382800 chr1D 14673399 14674863 1464 True 2137.0 2137 92.9440 2 1474 1 chr1D.!!$R1 1472
11 TraesCS2B01G382800 chr4A 564697234 564698652 1418 False 2106.0 2106 93.4170 42 1467 1 chr4A.!!$F1 1425
12 TraesCS2B01G382800 chr5A 690039125 690040551 1426 False 2063.0 2063 92.7420 1 1431 1 chr5A.!!$F1 1430
13 TraesCS2B01G382800 chr1B 549916582 549917418 836 True 1061.0 1061 90.0470 1450 2264 1 chr1B.!!$R2 814
14 TraesCS2B01G382800 chr1B 504245330 504246434 1104 True 555.5 660 92.3290 1467 2264 2 chr1B.!!$R3 797
15 TraesCS2B01G382800 chr1B 540287750 540289073 1323 True 449.0 676 90.0220 1450 2264 2 chr1B.!!$R4 814
16 TraesCS2B01G382800 chr3B 809557405 809558230 825 True 1044.0 1044 89.8690 1450 2264 1 chr3B.!!$R1 814
17 TraesCS2B01G382800 chr4B 9634866 9635925 1059 False 472.5 776 92.0675 1519 2264 2 chr4B.!!$F1 745

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
862 868 0.559205 TAGGGGAAGGCCTATCGACA 59.441 55.0 5.16 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2253 0.037734 CCAAGGGCTCCGGTTTTACT 59.962 55.0 0.0 0.0 0.0 2.24 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
22 23 3.592059 GGTGACCGCAATACTCAAGTAA 58.408 45.455 0.00 0.00 33.76 2.24
46 47 4.926238 ACTTTCATCAAGCTCAACGAGTAG 59.074 41.667 0.00 0.00 35.65 2.57
152 153 1.132640 GCGCGTAAGTCTGCCAAAG 59.867 57.895 8.43 0.00 41.68 2.77
214 216 3.391665 GATGAGCCGGGTGGGACAG 62.392 68.421 12.94 0.00 41.80 3.51
306 308 3.264193 AGAGGCCACACAAGTATCATTGA 59.736 43.478 5.01 0.00 34.20 2.57
450 452 2.108075 TCCTTTCCTTGATGCCTCACAA 59.892 45.455 0.00 0.00 0.00 3.33
543 545 4.714308 AGAAAGAAGAGATTCCGGAGTGAT 59.286 41.667 3.25 0.00 0.00 3.06
582 584 5.298276 TGGATACACCGGAATAAAGCAATTC 59.702 40.000 9.46 0.00 46.17 2.17
623 625 2.156098 GCCACCGGAGAACAACAATTA 58.844 47.619 9.46 0.00 0.00 1.40
770 775 3.953775 CCTTGGAGGTGGCCGTGT 61.954 66.667 0.00 0.00 0.00 4.49
862 868 0.559205 TAGGGGAAGGCCTATCGACA 59.441 55.000 5.16 0.00 0.00 4.35
924 934 9.609346 GGTACTACTTTTAATATGTCCATGTGT 57.391 33.333 0.00 0.00 0.00 3.72
927 937 9.733556 ACTACTTTTAATATGTCCATGTGTTCA 57.266 29.630 0.00 0.00 0.00 3.18
928 938 9.988350 CTACTTTTAATATGTCCATGTGTTCAC 57.012 33.333 0.00 0.00 0.00 3.18
929 939 8.635765 ACTTTTAATATGTCCATGTGTTCACT 57.364 30.769 4.59 0.00 0.00 3.41
930 940 9.077885 ACTTTTAATATGTCCATGTGTTCACTT 57.922 29.630 4.59 0.00 0.00 3.16
1298 1314 8.559536 CATGTTACTCTAAAATGTGTGTCAACT 58.440 33.333 0.00 0.00 30.41 3.16
1350 1366 4.160439 CCTCCTCTATGCAAGTACTTCACA 59.840 45.833 4.77 7.72 0.00 3.58
1359 1375 5.419542 TGCAAGTACTTCACATGGATAGAC 58.580 41.667 4.77 0.00 0.00 2.59
1383 1399 2.289882 TGAAGTGCCAGAAGATGTCCAG 60.290 50.000 0.00 0.00 0.00 3.86
1414 1430 3.550437 ATCAAGATTGTCTTAGGCGCT 57.450 42.857 7.64 0.00 33.78 5.92
1499 1515 1.544825 CGTGAGGAGGAGAGGGCAAA 61.545 60.000 0.00 0.00 0.00 3.68
1544 1560 0.907486 CAAGAGGAGGATGAGGCACA 59.093 55.000 0.00 0.00 0.00 4.57
1602 1618 0.250338 GCCTTCACTTCGGTGGACTT 60.250 55.000 0.00 0.00 45.34 3.01
1729 1745 4.747540 TTGAATTTGGTGTCGAGATGTG 57.252 40.909 0.00 0.00 0.00 3.21
1774 1790 7.547227 ACTTTAGTTTGTCAGCAATTTCTGTT 58.453 30.769 4.99 0.00 35.63 3.16
1928 2253 0.396435 CAGCCAACCCTACTGTGACA 59.604 55.000 0.00 0.00 0.00 3.58
1978 2305 1.591703 CTACCGCCACAGCTTCTGA 59.408 57.895 0.29 0.00 36.60 3.27
1984 2312 1.371183 CCACAGCTTCTGACGGGAA 59.629 57.895 0.29 0.00 35.18 3.97
1993 2321 0.895530 TCTGACGGGAAGGTCATCAC 59.104 55.000 0.00 0.00 45.23 3.06
2205 3327 3.561241 TGCACCCTACCGCCACAA 61.561 61.111 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.130118 ACTCGTTGAGCTTGATGAAAGTT 58.870 39.130 0.00 0.00 38.25 2.66
46 47 5.157067 GTGCTTTCAGAATGCTTTAGGAAC 58.843 41.667 18.99 6.23 34.76 3.62
139 140 4.776349 TCACTTGTTCTTTGGCAGACTTA 58.224 39.130 0.00 0.00 0.00 2.24
214 216 1.188863 TAAGACCTACCGTCCCTTGC 58.811 55.000 0.00 0.00 43.08 4.01
306 308 1.470098 GTCATCAAATGCGAGCAAGGT 59.530 47.619 0.57 0.00 0.00 3.50
373 375 2.296752 CCAATGTGAACTCATGCAACCA 59.703 45.455 0.00 0.00 0.00 3.67
450 452 0.106519 GCCCAACATACTCAGGCCAT 60.107 55.000 5.01 0.00 37.66 4.40
543 545 5.658634 GGTGTATCCAGCTAGATCATCCATA 59.341 44.000 0.00 0.00 36.16 2.74
573 575 3.134574 TGACCACTACCGAATTGCTTT 57.865 42.857 0.00 0.00 0.00 3.51
623 625 2.079158 CTGTGTCGTTGCATTCTCCAT 58.921 47.619 0.00 0.00 0.00 3.41
770 775 1.120530 GCTAATCCTTCCTCCACGGA 58.879 55.000 0.00 0.00 41.06 4.69
862 868 1.064463 ACCATCCGGATTGAGCAACAT 60.064 47.619 21.66 0.00 35.59 2.71
983 993 5.937975 AGCCATGCCTACAACAATTAAAT 57.062 34.783 0.00 0.00 0.00 1.40
1298 1314 6.883756 TGACTGCATACAAAATGGATGTTAGA 59.116 34.615 12.68 0.00 40.81 2.10
1359 1375 2.681848 GACATCTTCTGGCACTTCATGG 59.318 50.000 0.00 0.00 30.81 3.66
1383 1399 7.872113 AAGACAATCTTGATATTGGTCCTTC 57.128 36.000 0.00 0.00 40.48 3.46
1396 1412 2.541762 GCTAGCGCCTAAGACAATCTTG 59.458 50.000 2.29 0.00 37.29 3.02
1414 1430 1.671850 CCTTTCTTCGAACAGGCGCTA 60.672 52.381 7.64 0.00 0.00 4.26
1419 1435 4.893424 TTGAAACCTTTCTTCGAACAGG 57.107 40.909 10.50 10.50 38.02 4.00
1499 1515 0.598419 GCGAGCCTTTGCAAGCTTTT 60.598 50.000 13.77 0.00 40.11 2.27
1544 1560 3.438520 GGGCCATTTCCCCTTCTTATCAT 60.439 47.826 4.39 0.00 40.51 2.45
1602 1618 2.627945 GCTTCATCCGGTTACATGACA 58.372 47.619 0.00 0.00 0.00 3.58
1729 1745 3.254166 AGTTCATTCATGACACCTTGCAC 59.746 43.478 0.00 0.00 36.36 4.57
1774 1790 8.959548 ACAATTCACAGATATTGCAGACAAATA 58.040 29.630 0.00 0.00 39.77 1.40
1928 2253 0.037734 CCAAGGGCTCCGGTTTTACT 59.962 55.000 0.00 0.00 0.00 2.24
1978 2305 2.298661 GGGGTGATGACCTTCCCGT 61.299 63.158 0.00 0.00 42.66 5.28
1984 2312 1.382695 CGGTAGGGGGTGATGACCT 60.383 63.158 0.00 0.00 42.66 3.85
1993 2321 1.688187 AGGCACTAACGGTAGGGGG 60.688 63.158 12.63 1.68 36.02 5.40
2027 2357 1.542547 CCGTCACAGCAAGTTTACCCT 60.543 52.381 0.00 0.00 0.00 4.34
2030 2360 2.206750 TCACCGTCACAGCAAGTTTAC 58.793 47.619 0.00 0.00 0.00 2.01
2205 3327 2.481441 TCAATCCCTACTGCCAGATGT 58.519 47.619 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.