Multiple sequence alignment - TraesCS7B01G349400

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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 TraesCS7B01G349400 chr7B 100.000 2540 0 0 1 2540 606185087 606187626 0.000000e+00 4691.0
1 TraesCS7B01G349400 chr7B 92.532 2571 117 33 1 2540 606135345 606137871 0.000000e+00 3615.0
2 TraesCS7B01G349400 chr7B 80.150 267 46 6 1044 1308 605874158 605874419 2.580000e-45 193.0
3 TraesCS7B01G349400 chr7B 91.045 134 12 0 483 616 1062824 1062691 5.580000e-42 182.0
4 TraesCS7B01G349400 chr7B 77.174 276 49 11 1049 1317 606039373 606039641 5.660000e-32 148.0
5 TraesCS7B01G349400 chr7B 90.323 93 6 2 610 702 450564933 450565022 4.440000e-23 119.0
6 TraesCS7B01G349400 chr7B 81.301 123 23 0 1082 1204 606533579 606533701 1.610000e-17 100.0
7 TraesCS7B01G349400 chr7B 75.115 217 42 11 1108 1317 605969056 605969267 9.680000e-15 91.6
8 TraesCS7B01G349400 chr7D 92.683 1066 47 9 822 1859 558161104 558162166 0.000000e+00 1507.0
9 TraesCS7B01G349400 chr7D 87.664 608 45 13 1961 2540 558162271 558162876 0.000000e+00 680.0
10 TraesCS7B01G349400 chr7D 77.500 280 51 10 1044 1317 557893125 557893398 9.410000e-35 158.0
11 TraesCS7B01G349400 chr7D 78.022 273 42 11 943 1204 558168495 558168760 3.380000e-34 156.0
12 TraesCS7B01G349400 chr7D 78.862 123 20 5 1082 1204 558922402 558922518 7.530000e-11 78.7
13 TraesCS7B01G349400 chr7A 89.754 1015 81 14 822 1832 643634552 643635547 0.000000e+00 1277.0
14 TraesCS7B01G349400 chr7A 79.268 246 41 7 973 1209 643603146 643603390 2.020000e-36 163.0
15 TraesCS7B01G349400 chr7A 84.049 163 23 3 1043 1204 643645174 643645334 1.220000e-33 154.0
16 TraesCS7B01G349400 chr4B 94.253 87 5 0 615 701 519258920 519259006 1.590000e-27 134.0
17 TraesCS7B01G349400 chr4B 92.135 89 7 0 614 702 116875066 116875154 2.650000e-25 126.0
18 TraesCS7B01G349400 chr4B 93.023 86 6 0 615 700 308049641 308049726 2.650000e-25 126.0
19 TraesCS7B01G349400 chr1B 94.118 85 5 0 615 699 528405017 528405101 2.050000e-26 130.0
20 TraesCS7B01G349400 chr6B 93.103 87 6 0 614 700 96970759 96970845 7.380000e-26 128.0
21 TraesCS7B01G349400 chr2D 89.583 96 10 0 613 708 511922602 511922697 3.430000e-24 122.0
22 TraesCS7B01G349400 chr1A 88.119 101 8 4 610 709 48977253 48977156 1.600000e-22 117.0


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 TraesCS7B01G349400 chr7B 606185087 606187626 2539 False 4691.0 4691 100.0000 1 2540 1 chr7B.!!$F6 2539
1 TraesCS7B01G349400 chr7B 606135345 606137871 2526 False 3615.0 3615 92.5320 1 2540 1 chr7B.!!$F5 2539
2 TraesCS7B01G349400 chr7D 558161104 558162876 1772 False 1093.5 1507 90.1735 822 2540 2 chr7D.!!$F4 1718
3 TraesCS7B01G349400 chr7A 643634552 643635547 995 False 1277.0 1277 89.7540 822 1832 1 chr7A.!!$F2 1010

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
90 91 0.031585 CTGGAACCAGACGAACGTCA 59.968 55.0 25.13 6.35 46.3 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2158 0.621862 CTCTCCCACCTAGCCCCTTT 60.622 60.0 0.0 0.0 0.0 3.11 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
56 57 4.445718 CGAGCGACATAAATTGCTACATCT 59.554 41.667 0.00 0.00 39.57 2.90
90 91 0.031585 CTGGAACCAGACGAACGTCA 59.968 55.000 25.13 6.35 46.30 4.35
165 166 3.485947 GTTGCATCAAATTGCTACGGA 57.514 42.857 0.00 0.00 43.18 4.69
166 167 3.171277 GTTGCATCAAATTGCTACGGAC 58.829 45.455 0.00 0.00 43.18 4.79
307 308 1.079127 CACCAGAGTTGCTACCGGG 60.079 63.158 6.32 0.00 0.00 5.73
603 604 1.226945 AACGCAAGCGCTTTTTGCT 60.227 47.368 25.32 12.92 46.62 3.91
619 620 0.324943 TGCTGGAACCAAGCTACTCC 59.675 55.000 13.25 0.00 0.00 3.85
620 621 0.324943 GCTGGAACCAAGCTACTCCA 59.675 55.000 6.01 6.01 36.53 3.86
641 642 5.129650 TCCATTCGTCCCATAATGTAAGACA 59.870 40.000 0.00 0.00 32.34 3.41
642 643 5.236478 CCATTCGTCCCATAATGTAAGACAC 59.764 44.000 0.00 0.00 32.34 3.67
722 723 3.081061 TGTGAAACGAGGCATGCTAAAT 58.919 40.909 18.92 0.96 42.39 1.40
728 729 1.526887 CGAGGCATGCTAAATACGTGG 59.473 52.381 18.92 0.00 0.00 4.94
1247 1248 5.236282 CGGTGAGATATGCATCTTTCTGAT 58.764 41.667 0.19 0.00 41.78 2.90
1373 1374 2.480416 CCTATTCGAGCAGAGACGCTTT 60.480 50.000 0.00 0.00 44.01 3.51
1387 1388 1.895231 GCTTTGACGTCGGGGGTTT 60.895 57.895 11.62 0.00 0.00 3.27
1394 1395 1.070105 CGTCGGGGGTTTGTCTCAA 59.930 57.895 0.00 0.00 0.00 3.02
1406 1407 0.889638 TGTCTCAACGAGAGGAGCGT 60.890 55.000 9.18 0.00 44.81 5.07
1422 1423 2.401766 CGTGCTGGAAGGATGTGGC 61.402 63.158 0.00 0.00 35.94 5.01
1628 1645 0.894835 TGAGTGCCGATGCTGAGTAA 59.105 50.000 0.00 0.00 38.71 2.24
1720 1747 4.929479 ACCTACCAATGCCAAGTTCATTA 58.071 39.130 0.00 0.00 33.27 1.90
1852 1891 4.340894 TGATTTGAATACTGAAGCACGC 57.659 40.909 0.00 0.00 0.00 5.34
1859 1898 1.890876 TACTGAAGCACGCCATGTTT 58.109 45.000 0.00 0.00 33.87 2.83
1860 1899 1.032014 ACTGAAGCACGCCATGTTTT 58.968 45.000 0.00 0.00 30.84 2.43
1884 1956 0.744414 ACCATCCATTTCTGCGTCCG 60.744 55.000 0.00 0.00 0.00 4.79
1886 1958 0.744414 CATCCATTTCTGCGTCCGGT 60.744 55.000 0.00 0.00 0.00 5.28
1888 1960 0.672401 TCCATTTCTGCGTCCGGTTC 60.672 55.000 0.00 0.00 0.00 3.62
1898 1970 1.593196 CGTCCGGTTCCATGCATAAT 58.407 50.000 0.00 0.00 0.00 1.28
1899 1971 1.946768 CGTCCGGTTCCATGCATAATT 59.053 47.619 0.00 0.00 0.00 1.40
1933 2005 0.861837 GGCTTTCGATATGTCAGGCG 59.138 55.000 0.00 0.00 0.00 5.52
1952 2024 1.291132 GTGATAGCCAACGAAGGAGC 58.709 55.000 0.00 0.00 0.00 4.70
2010 2082 7.901029 CAGCAATAGGTGAAGGAGATAATAGA 58.099 38.462 0.00 0.00 45.95 1.98
2071 2145 1.482177 CCTTGGGTTTGACATTCCCCA 60.482 52.381 11.42 7.79 45.36 4.96
2080 2154 3.439540 CATTCCCCAACGCACCGG 61.440 66.667 0.00 0.00 0.00 5.28
2116 2191 3.262151 GGTGGGAGAGCCTTATTCTATCC 59.738 52.174 0.00 0.00 40.31 2.59
2125 2200 7.995663 AGAGCCTTATTCTATCCTTAGAGAGA 58.004 38.462 0.00 0.00 38.58 3.10
2151 2226 2.955068 GCCTCGCGTTCCTAAGTAC 58.045 57.895 5.77 0.00 0.00 2.73
2255 2331 6.868864 TCACAACATTCGAAAAAGTTTCCAAA 59.131 30.769 0.00 0.00 0.00 3.28
2395 2483 9.520204 TTCACAAAAATTGAAAAGTTTGCAAAA 57.480 22.222 14.67 0.00 44.05 2.44
2455 2544 8.062512 AACTGGGAAAGTTCCACAAATTTGAAG 61.063 37.037 24.64 15.20 46.60 3.02
2463 2552 8.479313 AGTTCCACAAATTTGAAGAAAAAGAC 57.521 30.769 24.64 13.26 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.550275 TGTAGCAATTTATGTCGCTCGAC 59.450 43.478 14.77 14.77 44.77 4.20
56 57 2.712539 CAGCAAAACACGACGCCA 59.287 55.556 0.00 0.00 0.00 5.69
90 91 0.033504 CTATGCCAACGCCCGTAGAT 59.966 55.000 0.00 0.00 0.00 1.98
97 98 2.828128 GCTCTGCTATGCCAACGCC 61.828 63.158 0.00 0.00 0.00 5.68
165 166 0.749649 TCCAGCAAAACAAATGCCGT 59.250 45.000 0.00 0.00 44.91 5.68
166 167 1.526464 GTTCCAGCAAAACAAATGCCG 59.474 47.619 0.00 0.00 44.91 5.69
204 205 3.564218 ATGGATGGAGCTCCGCCC 61.564 66.667 30.85 29.18 38.21 6.13
603 604 2.354704 CGAATGGAGTAGCTTGGTTCCA 60.355 50.000 9.64 9.64 43.36 3.53
619 620 6.049149 AGTGTCTTACATTATGGGACGAATG 58.951 40.000 0.00 0.00 39.31 2.67
620 621 6.235231 AGTGTCTTACATTATGGGACGAAT 57.765 37.500 0.00 0.00 0.00 3.34
669 670 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
672 673 4.100498 TCCTTCCGTCCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
688 689 3.119602 TCGTTTCACATCTACTCCTTCCG 60.120 47.826 0.00 0.00 0.00 4.30
690 691 4.425520 CCTCGTTTCACATCTACTCCTTC 58.574 47.826 0.00 0.00 0.00 3.46
722 723 2.158928 CCGTTGGATTTATCCCCACGTA 60.159 50.000 20.44 0.00 46.59 3.57
1247 1248 2.965147 GCATCGGCGTCAACAAGCA 61.965 57.895 6.85 0.00 34.54 3.91
1373 1374 2.091102 GAGACAAACCCCCGACGTCA 62.091 60.000 17.16 0.00 0.00 4.35
1387 1388 0.889638 ACGCTCCTCTCGTTGAGACA 60.890 55.000 9.16 0.00 45.39 3.41
1394 1395 3.753434 CCAGCACGCTCCTCTCGT 61.753 66.667 0.00 0.00 41.28 4.18
1406 1407 1.141657 GATAGCCACATCCTTCCAGCA 59.858 52.381 0.00 0.00 0.00 4.41
1422 1423 2.853731 AAGCGTCGTCCTTCAGATAG 57.146 50.000 0.00 0.00 0.00 2.08
1720 1747 5.184096 AGACGCCATAATAGACGAAGATCAT 59.816 40.000 0.00 0.00 0.00 2.45
1859 1898 3.320541 ACGCAGAAATGGATGGTCAAAAA 59.679 39.130 0.00 0.00 0.00 1.94
1860 1899 2.890311 ACGCAGAAATGGATGGTCAAAA 59.110 40.909 0.00 0.00 0.00 2.44
1933 2005 1.291132 GCTCCTTCGTTGGCTATCAC 58.709 55.000 0.00 0.00 0.00 3.06
2080 2154 3.134127 CACCTAGCCCCTTTGCGC 61.134 66.667 0.00 0.00 36.02 6.09
2084 2158 0.621862 CTCTCCCACCTAGCCCCTTT 60.622 60.000 0.00 0.00 0.00 3.11
2116 2191 2.011222 AGGCGACGACTTCTCTCTAAG 58.989 52.381 0.00 0.00 0.00 2.18
2368 2456 9.688592 TTTGCAAACTTTTCAATTTTTGTGAAT 57.311 22.222 8.05 0.00 35.03 2.57
2512 2612 2.767644 ACTGGGCTGGGTTTTTAGTT 57.232 45.000 0.00 0.00 0.00 2.24
2516 2616 2.698274 CAGTTTACTGGGCTGGGTTTTT 59.302 45.455 1.88 0.00 40.20 1.94


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

AutoCloner maintained by Alex Coulton.