Multiple sequence alignment - TraesCS1B01G180600

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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 TraesCS1B01G180600 chr1B 100.000 4885 0 0 1 4885 327346090 327350974 0.000000e+00 9022.0
1 TraesCS1B01G180600 chr1B 89.993 1469 123 10 2670 4117 665244982 665243517 0.000000e+00 1877.0
2 TraesCS1B01G180600 chr1B 84.436 816 62 21 1833 2630 665246287 665245519 0.000000e+00 743.0
3 TraesCS1B01G180600 chr1B 76.937 1110 116 73 334 1393 665247633 665246614 2.030000e-138 503.0
4 TraesCS1B01G180600 chr1D 97.148 4909 85 21 1 4885 208412355 208407478 0.000000e+00 8239.0
5 TraesCS1B01G180600 chr1D 96.579 1900 46 5 2035 3918 227653418 227655314 0.000000e+00 3131.0
6 TraesCS1B01G180600 chr1D 93.454 718 26 7 839 1555 227652181 227652878 0.000000e+00 1046.0
7 TraesCS1B01G180600 chr1D 90.181 662 62 2 3255 3913 477789530 477788869 0.000000e+00 859.0
8 TraesCS1B01G180600 chr1D 87.857 700 47 13 145 836 227650824 227651493 0.000000e+00 787.0
9 TraesCS1B01G180600 chr1D 91.927 545 43 1 2670 3213 477790072 477789528 0.000000e+00 761.0
10 TraesCS1B01G180600 chr1D 84.796 809 65 19 1833 2630 477791039 477790278 0.000000e+00 760.0
11 TraesCS1B01G180600 chr1D 97.493 359 9 0 1680 2038 227652902 227653260 8.990000e-172 614.0
12 TraesCS1B01G180600 chr1D 98.068 207 4 0 3915 4121 227655416 227655622 1.290000e-95 361.0
13 TraesCS1B01G180600 chr1D 83.166 398 58 8 2711 3103 223163464 223163857 6.010000e-94 355.0
14 TraesCS1B01G180600 chr1D 90.741 162 9 3 1 159 227650473 227650631 1.380000e-50 211.0
15 TraesCS1B01G180600 chr1D 77.377 305 52 12 1720 2021 457582422 457582712 1.090000e-36 165.0
16 TraesCS1B01G180600 chr1D 93.578 109 7 0 1685 1793 477791138 477791030 3.910000e-36 163.0
17 TraesCS1B01G180600 chr1D 88.372 129 12 1 1179 1304 477791786 477791658 8.470000e-33 152.0
18 TraesCS1B01G180600 chr1D 100.000 29 0 0 1365 1393 477791602 477791574 2.000000e-03 54.7
19 TraesCS1B01G180600 chr1A 95.692 1950 51 7 2141 4071 294514588 294516523 0.000000e+00 3105.0
20 TraesCS1B01G180600 chr1A 91.332 1869 77 23 297 2144 294512662 294514466 0.000000e+00 2475.0
21 TraesCS1B01G180600 chr1A 93.035 761 53 0 4125 4885 249063273 249064033 0.000000e+00 1112.0
22 TraesCS1B01G180600 chr1A 86.640 988 113 12 3138 4116 574271927 574270950 0.000000e+00 1075.0
23 TraesCS1B01G180600 chr1A 84.920 809 64 21 1833 2630 574273361 574272600 0.000000e+00 765.0
24 TraesCS1B01G180600 chr1A 91.405 477 40 1 2670 3145 574272515 574272039 0.000000e+00 652.0
25 TraesCS1B01G180600 chr1A 81.994 622 63 28 757 1355 574274337 574273742 2.640000e-132 483.0
26 TraesCS1B01G180600 chr1A 83.376 391 64 1 2714 3103 294040638 294041028 1.290000e-95 361.0
27 TraesCS1B01G180600 chr1A 82.960 223 22 8 143 356 294512463 294512678 2.320000e-43 187.0
28 TraesCS1B01G180600 chr1A 79.279 222 39 6 1829 2050 550298280 550298494 1.100000e-31 148.0
29 TraesCS1B01G180600 chr3D 96.058 761 30 0 4125 4885 612007365 612006605 0.000000e+00 1240.0
30 TraesCS1B01G180600 chr3D 94.087 761 45 0 4125 4885 577965657 577966417 0.000000e+00 1157.0
31 TraesCS1B01G180600 chr7D 96.058 761 29 1 4125 4885 530942965 530942206 0.000000e+00 1238.0
32 TraesCS1B01G180600 chr7D 84.615 169 20 4 1837 2000 90408584 90408751 3.910000e-36 163.0
33 TraesCS1B01G180600 chr4D 95.926 761 27 2 4125 4885 214679987 214679231 0.000000e+00 1230.0
34 TraesCS1B01G180600 chr6B 95.007 761 38 0 4125 4885 16388951 16388191 0.000000e+00 1195.0
35 TraesCS1B01G180600 chr4B 94.350 761 33 3 4125 4885 65980930 65980180 0.000000e+00 1158.0
36 TraesCS1B01G180600 chr4B 100.000 42 0 0 1640 1681 273429729 273429688 1.460000e-10 78.7
37 TraesCS1B01G180600 chr4B 94.231 52 1 2 1640 1690 483504878 483504928 1.460000e-10 78.7
38 TraesCS1B01G180600 chr5D 92.904 761 54 0 4125 4885 562695648 562696408 0.000000e+00 1107.0
39 TraesCS1B01G180600 chr2D 90.646 759 69 1 4127 4885 640835982 640836738 0.000000e+00 1007.0
40 TraesCS1B01G180600 chr7B 83.797 395 59 5 2762 3155 41285512 41285902 2.150000e-98 370.0
41 TraesCS1B01G180600 chr4A 100.000 43 0 0 1640 1682 455277528 455277570 4.050000e-11 80.5
42 TraesCS1B01G180600 chr2A 95.745 47 2 0 1640 1686 385679781 385679735 5.240000e-10 76.8
43 TraesCS1B01G180600 chr7A 95.652 46 2 0 1639 1684 438993281 438993236 1.890000e-09 75.0
44 TraesCS1B01G180600 chrUn 92.157 51 3 1 1640 1689 5996372 5996422 2.440000e-08 71.3
45 TraesCS1B01G180600 chr3A 89.286 56 5 1 1631 1685 606010362 606010417 8.770000e-08 69.4


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 TraesCS1B01G180600 chr1B 327346090 327350974 4884 False 9022.000000 9022 100.000000 1 4885 1 chr1B.!!$F1 4884
1 TraesCS1B01G180600 chr1B 665243517 665247633 4116 True 1041.000000 1877 83.788667 334 4117 3 chr1B.!!$R1 3783
2 TraesCS1B01G180600 chr1D 208407478 208412355 4877 True 8239.000000 8239 97.148000 1 4885 1 chr1D.!!$R1 4884
3 TraesCS1B01G180600 chr1D 227650473 227655622 5149 False 1025.000000 3131 94.032000 1 4121 6 chr1D.!!$F3 4120
4 TraesCS1B01G180600 chr1D 477788869 477791786 2917 True 458.283333 859 91.475667 1179 3913 6 chr1D.!!$R2 2734
5 TraesCS1B01G180600 chr1A 294512463 294516523 4060 False 1922.333333 3105 89.994667 143 4071 3 chr1A.!!$F4 3928
6 TraesCS1B01G180600 chr1A 249063273 249064033 760 False 1112.000000 1112 93.035000 4125 4885 1 chr1A.!!$F1 760
7 TraesCS1B01G180600 chr1A 574270950 574274337 3387 True 743.750000 1075 86.239750 757 4116 4 chr1A.!!$R1 3359
8 TraesCS1B01G180600 chr3D 612006605 612007365 760 True 1240.000000 1240 96.058000 4125 4885 1 chr3D.!!$R1 760
9 TraesCS1B01G180600 chr3D 577965657 577966417 760 False 1157.000000 1157 94.087000 4125 4885 1 chr3D.!!$F1 760
10 TraesCS1B01G180600 chr7D 530942206 530942965 759 True 1238.000000 1238 96.058000 4125 4885 1 chr7D.!!$R1 760
11 TraesCS1B01G180600 chr4D 214679231 214679987 756 True 1230.000000 1230 95.926000 4125 4885 1 chr4D.!!$R1 760
12 TraesCS1B01G180600 chr6B 16388191 16388951 760 True 1195.000000 1195 95.007000 4125 4885 1 chr6B.!!$R1 760
13 TraesCS1B01G180600 chr4B 65980180 65980930 750 True 1158.000000 1158 94.350000 4125 4885 1 chr4B.!!$R1 760
14 TraesCS1B01G180600 chr5D 562695648 562696408 760 False 1107.000000 1107 92.904000 4125 4885 1 chr5D.!!$F1 760
15 TraesCS1B01G180600 chr2D 640835982 640836738 756 False 1007.000000 1007 90.646000 4127 4885 1 chr2D.!!$F1 758

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
274 484 0.041833 TCCAGGAGGAGGAGAACCAG 59.958 60.000 0.00 0.0 39.61 4.00 F
283 494 0.252103 AGGAGAACCAGAGGGCGTTA 60.252 55.000 0.00 0.0 37.90 3.18 F
287 498 0.794473 GAACCAGAGGGCGTTAAACG 59.206 55.000 0.00 0.0 45.88 3.60 F
895 1878 1.400494 GGTGATTTATCTTTGCGCGGT 59.600 47.619 8.83 0.0 0.00 5.68 F
1352 2379 3.211045 TCGTGATCATGGTCGTCTGATA 58.789 45.455 14.91 0.0 32.36 2.15 F
2798 5069 3.874392 ATGCAGCTACCCACAATTTTC 57.126 42.857 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 2337 1.328374 TCGATGATTGTTGCATGAGCG 59.672 47.619 0.00 0.00 46.23 5.03 R
1352 2379 2.576832 GGTGGCAGCCAAAGCACAT 61.577 57.895 18.28 0.00 43.56 3.21 R
2381 4003 2.679837 CAACATATGGAGTTTCAGCGCT 59.320 45.455 2.64 2.64 0.00 5.92 R
2798 5069 5.740569 CCTTCGAGCATGTATTGTTCAAATG 59.259 40.000 0.00 0.00 35.44 2.32 R
3221 5611 1.376543 TAGAGCACGGGAGAAGTACG 58.623 55.000 0.00 0.00 0.00 3.67 R
4530 7067 0.329596 GCCAAGTGTCCTCCCAGAAT 59.670 55.000 0.00 0.00 0.00 2.40 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
274 484 0.041833 TCCAGGAGGAGGAGAACCAG 59.958 60.000 0.00 0.00 39.61 4.00
283 494 0.252103 AGGAGAACCAGAGGGCGTTA 60.252 55.000 0.00 0.00 37.90 3.18
287 498 0.794473 GAACCAGAGGGCGTTAAACG 59.206 55.000 0.00 0.00 45.88 3.60
332 585 2.560981 CCAGGGGTTTGTTGTGGATAAC 59.439 50.000 0.00 0.00 0.00 1.89
475 746 2.677228 CCTCCATTCCCCAGCGTT 59.323 61.111 0.00 0.00 0.00 4.84
518 796 2.419198 CTTCGATCTGCCCCCGAG 59.581 66.667 0.00 0.00 33.66 4.63
630 914 2.550180 GCCTCTCTGTGGAAAGAACAAC 59.450 50.000 0.00 0.00 0.00 3.32
697 981 5.353938 GTTTTAGGGGGTTTCAGTTCAAAC 58.646 41.667 0.00 0.00 35.79 2.93
707 991 6.095021 GGGTTTCAGTTCAAACTACAAGTTCT 59.905 38.462 0.00 0.00 37.47 3.01
746 1034 6.642707 ATTATTTTCGACAAACCTGAACCA 57.357 33.333 0.00 0.00 0.00 3.67
747 1035 3.768468 TTTTCGACAAACCTGAACCAC 57.232 42.857 0.00 0.00 0.00 4.16
775 1063 7.489160 GGTTTATGTTTATGGAGTGGGATTTC 58.511 38.462 0.00 0.00 0.00 2.17
787 1075 5.246981 AGTGGGATTTCACTTCTTGATCA 57.753 39.130 0.00 0.00 44.74 2.92
858 1841 9.642327 CAAATTGATTGATTTACATCCAAGTGA 57.358 29.630 0.00 0.00 41.85 3.41
890 1873 9.252962 CATTAAGGAATGGTGATTTATCTTTGC 57.747 33.333 0.00 0.00 39.10 3.68
895 1878 1.400494 GGTGATTTATCTTTGCGCGGT 59.600 47.619 8.83 0.00 0.00 5.68
930 1922 5.638596 TCGTCAAGATTTGCACTACTCTA 57.361 39.130 0.00 0.00 0.00 2.43
931 1923 5.399858 TCGTCAAGATTTGCACTACTCTAC 58.600 41.667 0.00 0.00 0.00 2.59
932 1924 5.183331 TCGTCAAGATTTGCACTACTCTACT 59.817 40.000 0.00 0.00 0.00 2.57
933 1925 5.864474 CGTCAAGATTTGCACTACTCTACTT 59.136 40.000 0.00 0.00 0.00 2.24
1246 2255 4.338682 ACTGTAACTAGCCAGACGATTAGG 59.661 45.833 10.62 0.00 32.93 2.69
1352 2379 3.211045 TCGTGATCATGGTCGTCTGATA 58.789 45.455 14.91 0.00 32.36 2.15
2381 4003 3.900601 ACCACCAATGCATCAAAAACCTA 59.099 39.130 0.00 0.00 0.00 3.08
2582 4204 4.304659 GGATTCCCTTCCCTAGTCCTTTA 58.695 47.826 0.00 0.00 0.00 1.85
2798 5069 3.874392 ATGCAGCTACCCACAATTTTC 57.126 42.857 0.00 0.00 0.00 2.29
3221 5611 2.199236 CTAATTTCGTAGTGGCCGGAC 58.801 52.381 5.05 0.56 0.00 4.79
3564 5970 2.160721 TGGAGTCCTCGGATAAGCTT 57.839 50.000 11.33 3.48 0.00 3.74
4261 6782 1.986378 GACTCGCGAAATGGGATATCG 59.014 52.381 11.33 0.00 39.05 2.92
4427 6964 2.899256 CCAAAACATTGTCCCAGGTGAT 59.101 45.455 0.00 0.00 0.00 3.06
4435 6972 1.078823 TGTCCCAGGTGATAGTGAGGT 59.921 52.381 0.00 0.00 0.00 3.85
4460 6997 3.888930 ACTGATTCGCCTTTTTGGAAAGA 59.111 39.130 0.70 0.00 44.03 2.52
4530 7067 2.884012 TGAAAACGGTACTACCACGAGA 59.116 45.455 6.06 0.00 38.47 4.04
4738 7276 2.196595 TGGAGGTCGATCTTTCCCAAT 58.803 47.619 0.00 0.00 0.00 3.16
4858 7396 5.098893 CGAAACATGTGTGGAAAGTCAAAA 58.901 37.500 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 360 9.806203 TTTACATTGAACCATGATTCATCAATC 57.194 29.630 2.55 3.72 38.34 2.67
215 425 1.002544 CGGACAAAGGAAAGAGCCTCT 59.997 52.381 0.00 0.00 37.26 3.69
269 479 2.922779 CGTTTAACGCCCTCTGGTT 58.077 52.632 4.11 0.00 33.65 3.67
283 494 3.832615 AGTTTGGACTAGGACACGTTT 57.167 42.857 0.00 0.00 33.32 3.60
287 498 6.594547 GGAGAAATTAGTTTGGACTAGGACAC 59.405 42.308 0.00 0.00 39.43 3.67
399 663 5.371176 GGGGATTCCTTCCTCTATCTTTTCT 59.629 44.000 2.01 0.00 42.41 2.52
405 669 2.300437 CGTGGGGATTCCTTCCTCTATC 59.700 54.545 2.01 0.00 46.38 2.08
407 671 1.289830 TCGTGGGGATTCCTTCCTCTA 59.710 52.381 2.01 0.00 46.38 2.43
532 812 2.131067 GGAGGCGAGGGAGGAGAAG 61.131 68.421 0.00 0.00 0.00 2.85
721 1005 8.077386 GTGGTTCAGGTTTGTCGAAAATAATTA 58.923 33.333 0.00 0.00 0.00 1.40
746 1034 4.266714 CACTCCATAAACATAAACCGGGT 58.733 43.478 6.32 0.00 0.00 5.28
747 1035 3.630312 CCACTCCATAAACATAAACCGGG 59.370 47.826 6.32 0.00 0.00 5.73
805 1096 3.954258 GGACAAAATTTCCCCGATGATCT 59.046 43.478 0.00 0.00 0.00 2.75
807 1098 3.954258 GAGGACAAAATTTCCCCGATGAT 59.046 43.478 0.00 0.00 33.01 2.45
890 1873 2.349275 ACGAAATAATAACCACACCGCG 59.651 45.455 0.00 0.00 0.00 6.46
895 1878 7.753132 GCAAATCTTGACGAAATAATAACCACA 59.247 33.333 0.00 0.00 0.00 4.17
1128 2135 5.263968 AGCGCTACAATTCATGTACTACT 57.736 39.130 8.99 0.00 43.63 2.57
1129 2136 5.968387 AAGCGCTACAATTCATGTACTAC 57.032 39.130 12.05 0.00 43.63 2.73
1130 2137 8.657074 AATTAAGCGCTACAATTCATGTACTA 57.343 30.769 12.05 0.00 43.63 1.82
1310 2337 1.328374 TCGATGATTGTTGCATGAGCG 59.672 47.619 0.00 0.00 46.23 5.03
1352 2379 2.576832 GGTGGCAGCCAAAGCACAT 61.577 57.895 18.28 0.00 43.56 3.21
2381 4003 2.679837 CAACATATGGAGTTTCAGCGCT 59.320 45.455 2.64 2.64 0.00 5.92
2582 4204 7.504403 AGCTCAAACTTATGTAGCATAGACAT 58.496 34.615 5.19 0.00 40.59 3.06
2798 5069 5.740569 CCTTCGAGCATGTATTGTTCAAATG 59.259 40.000 0.00 0.00 35.44 2.32
3221 5611 1.376543 TAGAGCACGGGAGAAGTACG 58.623 55.000 0.00 0.00 0.00 3.67
3564 5970 1.663739 CTTCCCGGACTCGTCACAA 59.336 57.895 0.73 0.00 33.95 3.33
4036 6552 4.279671 ACATCACACTGCCCGAAATAAAAA 59.720 37.500 0.00 0.00 0.00 1.94
4261 6782 1.305201 TGGTCTTTCGGTCTGCAAAC 58.695 50.000 0.00 0.00 0.00 2.93
4435 6972 7.264817 CTTTCCAAAAAGGCGAATCAGTCGA 62.265 44.000 0.00 0.00 43.81 4.20
4460 6997 4.019501 AGGCTGATTTCACTCTCATCAGTT 60.020 41.667 9.52 0.00 44.00 3.16
4511 7048 4.219288 AGAATCTCGTGGTAGTACCGTTTT 59.781 41.667 14.67 2.70 42.58 2.43
4530 7067 0.329596 GCCAAGTGTCCTCCCAGAAT 59.670 55.000 0.00 0.00 0.00 2.40
4669 7206 2.422803 CCTCCCAATGATTTCCCGCTAA 60.423 50.000 0.00 0.00 0.00 3.09
4858 7396 9.643693 CATAAACACTTTGATTTTTAGAGGCAT 57.356 29.630 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.