Multiple sequence alignment - TraesCS3D01G469900

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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 TraesCS3D01G469900 chr3D 100.000 2468 0 0 1 2468 571677281 571679748 0.000000e+00 4558.0
1 TraesCS3D01G469900 chr3D 94.863 1538 73 5 146 1678 571117326 571118862 0.000000e+00 2398.0
2 TraesCS3D01G469900 chr3D 89.204 1695 157 15 1 1678 571513215 571514900 0.000000e+00 2093.0
3 TraesCS3D01G469900 chr3D 80.926 1447 205 40 379 1812 571208066 571209454 0.000000e+00 1077.0
4 TraesCS3D01G469900 chr3D 90.752 638 36 13 1679 2296 571118895 571119529 0.000000e+00 830.0
5 TraesCS3D01G469900 chr3D 80.744 618 54 29 1818 2399 571492794 571493382 2.930000e-114 422.0
6 TraesCS3D01G469900 chrUn 92.330 2073 116 25 436 2468 352871305 352873374 0.000000e+00 2907.0
7 TraesCS3D01G469900 chrUn 93.671 1343 66 11 436 1759 409139747 409141089 0.000000e+00 1991.0
8 TraesCS3D01G469900 chrUn 95.883 1166 47 1 472 1636 427478523 427479688 0.000000e+00 1886.0
9 TraesCS3D01G469900 chrUn 90.695 806 51 14 1684 2468 349530626 349529824 0.000000e+00 1051.0
10 TraesCS3D01G469900 chrUn 90.000 670 43 14 1820 2468 357850997 357851663 0.000000e+00 845.0
11 TraesCS3D01G469900 chrUn 91.350 474 34 6 1 470 408637778 408638248 2.070000e-180 641.0
12 TraesCS3D01G469900 chrUn 91.350 474 34 6 1 470 408638819 408638349 2.070000e-180 641.0
13 TraesCS3D01G469900 chrUn 90.909 297 19 7 1 293 380838432 380838140 2.300000e-105 392.0
14 TraesCS3D01G469900 chr3A 95.009 1683 78 6 1 1678 703938815 703940496 0.000000e+00 2638.0
15 TraesCS3D01G469900 chr3A 90.447 806 53 14 1684 2468 703940538 703941340 0.000000e+00 1040.0
16 TraesCS3D01G469900 chr3B 92.308 1534 114 4 148 1678 758435304 758436836 0.000000e+00 2176.0
17 TraesCS3D01G469900 chr3B 90.508 748 43 11 1674 2394 758436864 758437610 0.000000e+00 963.0
18 TraesCS3D01G469900 chr3B 88.889 324 31 3 2119 2437 758165772 758166095 6.400000e-106 394.0
19 TraesCS3D01G469900 chr3B 87.395 238 26 4 1818 2054 758434676 758434910 1.120000e-68 270.0
20 TraesCS3D01G469900 chr3B 86.975 238 27 4 1818 2054 758338908 758339142 5.230000e-67 265.0
21 TraesCS3D01G469900 chr3B 87.500 72 9 0 2230 2301 758371952 758372023 1.570000e-12 84.2
22 TraesCS3D01G469900 chr3B 91.525 59 5 0 1271 1329 778490122 778490064 5.660000e-12 82.4
23 TraesCS3D01G469900 chr4B 79.787 188 34 4 74 259 672594501 672594316 1.540000e-27 134.0
24 TraesCS3D01G469900 chr6B 79.348 184 34 3 75 256 649007880 649008061 2.580000e-25 126.0


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 TraesCS3D01G469900 chr3D 571677281 571679748 2467 False 4558.000000 4558 100.000000 1 2468 1 chr3D.!!$F4 2467
1 TraesCS3D01G469900 chr3D 571513215 571514900 1685 False 2093.000000 2093 89.204000 1 1678 1 chr3D.!!$F3 1677
2 TraesCS3D01G469900 chr3D 571117326 571119529 2203 False 1614.000000 2398 92.807500 146 2296 2 chr3D.!!$F5 2150
3 TraesCS3D01G469900 chr3D 571208066 571209454 1388 False 1077.000000 1077 80.926000 379 1812 1 chr3D.!!$F1 1433
4 TraesCS3D01G469900 chr3D 571492794 571493382 588 False 422.000000 422 80.744000 1818 2399 1 chr3D.!!$F2 581
5 TraesCS3D01G469900 chrUn 352871305 352873374 2069 False 2907.000000 2907 92.330000 436 2468 1 chrUn.!!$F1 2032
6 TraesCS3D01G469900 chrUn 409139747 409141089 1342 False 1991.000000 1991 93.671000 436 1759 1 chrUn.!!$F4 1323
7 TraesCS3D01G469900 chrUn 427478523 427479688 1165 False 1886.000000 1886 95.883000 472 1636 1 chrUn.!!$F5 1164
8 TraesCS3D01G469900 chrUn 349529824 349530626 802 True 1051.000000 1051 90.695000 1684 2468 1 chrUn.!!$R1 784
9 TraesCS3D01G469900 chrUn 357850997 357851663 666 False 845.000000 845 90.000000 1820 2468 1 chrUn.!!$F2 648
10 TraesCS3D01G469900 chr3A 703938815 703941340 2525 False 1839.000000 2638 92.728000 1 2468 2 chr3A.!!$F1 2467
11 TraesCS3D01G469900 chr3B 758434676 758437610 2934 False 1136.333333 2176 90.070333 148 2394 3 chr3B.!!$F4 2246

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
279 764 0.030101 AACACGGCAAATCCAACACG 59.97 50.0 0.0 0.0 34.01 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2679 0.38852 AAAAGATTCGCAAAGCCGCC 60.389 50.0 0.0 0.0 0.0 6.13 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
279 764 0.030101 AACACGGCAAATCCAACACG 59.970 50.000 0.00 0.00 34.01 4.49
299 784 0.036732 TCACCCAGCAACAGATCCAC 59.963 55.000 0.00 0.00 0.00 4.02
374 859 1.058428 CATCATGGCCTCCTCCTCCA 61.058 60.000 3.32 0.00 0.00 3.86
385 870 1.229336 CTCCTCCACCACCACCTCT 60.229 63.158 0.00 0.00 0.00 3.69
433 918 1.358787 TCACCCTACTTCCTACCCGAA 59.641 52.381 0.00 0.00 0.00 4.30
970 1466 1.030457 CGGCCTATGTTACCGTCTCT 58.970 55.000 0.00 0.00 42.01 3.10
1000 1496 5.412594 GCCAATCTGTCAGACAAGAATACAA 59.587 40.000 4.21 0.00 0.00 2.41
1179 1675 4.342359 GGAAGTGGACAAGGACTACTAGA 58.658 47.826 0.00 0.00 0.00 2.43
1246 1742 2.140717 GTGTTGTTCCGACGAAAGGAT 58.859 47.619 0.00 0.00 37.65 3.24
1340 1838 6.208402 TGCTTATACTTCACAGATGCCAAAAA 59.792 34.615 0.00 0.00 0.00 1.94
1470 1968 2.183478 TTCCGAGCATGTGTTGATGT 57.817 45.000 0.00 0.00 0.00 3.06
1632 2133 6.203915 TGTGTTACATATTGGGCATATCGTTC 59.796 38.462 0.00 0.00 0.00 3.95
1636 2137 5.060506 ACATATTGGGCATATCGTTCGAAA 58.939 37.500 0.00 0.00 0.00 3.46
1759 2301 2.907695 TACATGCATGCCCGCACCAT 62.908 55.000 26.53 6.25 46.56 3.55
1834 2376 1.068055 CACTGGCATCCTCAGTTTTGC 60.068 52.381 0.00 0.00 42.87 3.68
1883 2425 6.426980 TGAGAATTGAATGTTTCATCCTCG 57.573 37.500 0.00 0.00 39.84 4.63
2110 2679 3.727726 TCAGCATGGGTATGTAATGTCG 58.272 45.455 0.00 0.00 36.65 4.35
2140 2718 2.268730 GAATCTTTTCGGCAAGCCTG 57.731 50.000 9.73 3.19 0.00 4.85
2141 2719 1.541588 GAATCTTTTCGGCAAGCCTGT 59.458 47.619 9.73 0.00 0.00 4.00
2142 2720 2.489938 ATCTTTTCGGCAAGCCTGTA 57.510 45.000 9.73 0.00 0.00 2.74
2143 2721 2.264005 TCTTTTCGGCAAGCCTGTAA 57.736 45.000 9.73 0.82 0.00 2.41
2144 2722 2.151202 TCTTTTCGGCAAGCCTGTAAG 58.849 47.619 9.73 9.07 0.00 2.34
2226 2804 7.989416 AGAGAAATAATGTTGGTTTACCGAA 57.011 32.000 0.00 0.00 39.43 4.30
2228 2806 7.881232 AGAGAAATAATGTTGGTTTACCGAAGA 59.119 33.333 0.00 0.00 39.43 2.87
2281 2859 2.485814 GTGTCAATCTTTCAGGCTCACC 59.514 50.000 0.00 0.00 0.00 4.02
2317 2895 4.026052 TCAGTATGTGAGAGATGCTTCCA 58.974 43.478 0.00 0.00 37.40 3.53
2386 2974 1.287041 GACCCACGTTGCGACCTAAC 61.287 60.000 0.00 0.00 0.00 2.34
2399 2987 3.061161 GCGACCTAACGAATTTAAGCGAA 59.939 43.478 0.00 0.00 35.09 4.70
2401 2989 5.011370 CGACCTAACGAATTTAAGCGAAAC 58.989 41.667 0.00 0.00 35.09 2.78
2402 2990 5.287170 ACCTAACGAATTTAAGCGAAACC 57.713 39.130 0.00 0.00 0.00 3.27
2411 3000 6.466097 CGAATTTAAGCGAAACCTTGAGAATC 59.534 38.462 0.00 0.00 0.00 2.52
2446 3035 2.700773 GGCGATCAAACTGCACCCC 61.701 63.158 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 5.313506 AGTCCCAAATTATCTCCCTATTCCC 59.686 44.000 0.00 0.00 0.00 3.97
15 17 4.384208 CGAACAGTCCCAAATTATCTCCCT 60.384 45.833 0.00 0.00 0.00 4.20
135 137 8.146053 TCTTCCTTCCTTGACACTTATATCAA 57.854 34.615 0.00 0.00 33.82 2.57
279 764 0.036732 TGGATCTGTTGCTGGGTGAC 59.963 55.000 0.00 0.00 0.00 3.67
299 784 2.663602 CCGACTTCGTCATTTCACTCAG 59.336 50.000 0.00 0.00 37.74 3.35
374 859 0.996762 TTTGGGGAAGAGGTGGTGGT 60.997 55.000 0.00 0.00 0.00 4.16
385 870 0.699399 TTGCTACGGGATTTGGGGAA 59.301 50.000 0.00 0.00 0.00 3.97
696 1190 1.427592 GACGAAGCTGAGCTCATGGC 61.428 60.000 18.63 18.15 38.25 4.40
970 1466 1.191489 TCTGACAGATTGGCCACGGA 61.191 55.000 3.88 0.00 0.00 4.69
1000 1496 6.884295 TGATCTCCAAGAAACGTTAATTCCAT 59.116 34.615 0.00 0.00 0.00 3.41
1179 1675 2.057137 ACAATGTGCAGTCACCAAGT 57.943 45.000 0.00 0.00 42.46 3.16
1246 1742 7.759489 AGTAATAACCTGAAAAGCATGTCAA 57.241 32.000 0.00 0.00 0.00 3.18
1340 1838 5.186198 CCAAGGAATACTCGATCCACTTTT 58.814 41.667 5.61 0.00 38.23 2.27
1470 1968 3.921104 AGCTCTGTGATCCATAGGAGAA 58.079 45.455 0.00 0.00 34.05 2.87
1632 2133 6.864685 AGCATGTCCATTTATATGCAATTTCG 59.135 34.615 10.23 0.00 43.97 3.46
1636 2137 5.245301 AGCAGCATGTCCATTTATATGCAAT 59.755 36.000 10.23 0.00 43.97 3.56
1730 2272 3.181497 GGGCATGCATGTACACTTACTTG 60.181 47.826 26.79 0.00 36.74 3.16
1746 2288 3.274586 CGAGATGGTGCGGGCATG 61.275 66.667 0.00 0.00 0.00 4.06
1759 2301 7.609760 AATTTGTATACATTGACTTGCGAGA 57.390 32.000 8.31 0.00 0.00 4.04
1834 2376 5.106157 ACCATAATTGAAAAGAGAACGGCAG 60.106 40.000 0.00 0.00 0.00 4.85
1892 2434 7.324178 AGACAAACGACTTTCTATAAGATGCT 58.676 34.615 0.00 0.00 0.00 3.79
2110 2679 0.388520 AAAAGATTCGCAAAGCCGCC 60.389 50.000 0.00 0.00 0.00 6.13
2137 2715 5.531287 GGGAAACAGTATTATGCCTTACAGG 59.469 44.000 0.00 0.00 38.80 4.00
2138 2716 5.236478 CGGGAAACAGTATTATGCCTTACAG 59.764 44.000 0.00 0.00 0.00 2.74
2139 2717 5.120399 CGGGAAACAGTATTATGCCTTACA 58.880 41.667 0.00 0.00 0.00 2.41
2140 2718 4.514066 CCGGGAAACAGTATTATGCCTTAC 59.486 45.833 0.00 0.00 0.00 2.34
2141 2719 4.409574 TCCGGGAAACAGTATTATGCCTTA 59.590 41.667 0.00 0.00 0.00 2.69
2142 2720 3.201266 TCCGGGAAACAGTATTATGCCTT 59.799 43.478 0.00 0.00 0.00 4.35
2143 2721 2.775384 TCCGGGAAACAGTATTATGCCT 59.225 45.455 0.00 0.00 0.00 4.75
2144 2722 3.202829 TCCGGGAAACAGTATTATGCC 57.797 47.619 0.00 0.00 0.00 4.40
2145 2723 4.385825 TCATCCGGGAAACAGTATTATGC 58.614 43.478 0.00 0.00 0.00 3.14
2226 2804 4.703575 GCACATGATATGCCCAATATGTCT 59.296 41.667 0.00 0.00 37.08 3.41
2228 2806 4.409187 TGCACATGATATGCCCAATATGT 58.591 39.130 0.00 0.00 42.69 2.29
2281 2859 5.874810 TCACATACTGAAGAAGGGAAATTCG 59.125 40.000 0.00 0.00 34.27 3.34
2317 2895 2.683742 CGCATCTCCCACCCTAAAACAT 60.684 50.000 0.00 0.00 0.00 2.71
2386 2974 5.277601 TCTCAAGGTTTCGCTTAAATTCG 57.722 39.130 0.00 0.00 0.00 3.34
2399 2987 5.186198 CCTTATTCCGTGATTCTCAAGGTT 58.814 41.667 8.60 2.19 44.70 3.50
2401 2989 4.770795 ACCTTATTCCGTGATTCTCAAGG 58.229 43.478 3.08 3.08 45.57 3.61
2402 2990 7.843490 TTTACCTTATTCCGTGATTCTCAAG 57.157 36.000 0.00 0.00 0.00 3.02
2411 3000 3.199677 TCGCCATTTACCTTATTCCGTG 58.800 45.455 0.00 0.00 0.00 4.94
2412 3001 3.547054 TCGCCATTTACCTTATTCCGT 57.453 42.857 0.00 0.00 0.00 4.69
2420 3009 2.423538 GCAGTTTGATCGCCATTTACCT 59.576 45.455 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.