Multiple sequence alignment - TraesCS6A01G251500

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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 TraesCS6A01G251500 chr6A 100.000 2456 0 0 1 2456 466087373 466089828 0.000000e+00 4536.0
1 TraesCS6A01G251500 chr6A 86.417 1016 84 27 914 1903 455822289 455821302 0.000000e+00 1062.0
2 TraesCS6A01G251500 chr6A 91.667 96 7 1 2170 2265 455821114 455821020 5.510000e-27 132.0
3 TraesCS6A01G251500 chr6A 89.041 73 2 6 2011 2082 455821226 455821159 4.350000e-13 86.1
4 TraesCS6A01G251500 chr6B 92.171 1571 74 16 904 2456 494093916 494092377 0.000000e+00 2174.0
5 TraesCS6A01G251500 chr6B 85.897 1014 76 27 923 1903 505908480 505909459 0.000000e+00 1018.0
6 TraesCS6A01G251500 chr6B 90.289 484 34 12 433 904 643392607 643392125 2.680000e-174 621.0
7 TraesCS6A01G251500 chr6B 87.212 477 47 6 1 466 683171472 683170999 4.650000e-147 531.0
8 TraesCS6A01G251500 chr6B 88.034 351 25 11 564 904 643388441 643388098 1.370000e-107 399.0
9 TraesCS6A01G251500 chr6B 81.579 494 71 10 64 540 643392924 643392434 8.230000e-105 390.0
10 TraesCS6A01G251500 chr6B 94.690 113 6 0 2153 2265 505909600 505909712 2.510000e-40 176.0
11 TraesCS6A01G251500 chr6D 96.254 1148 28 8 904 2047 327343506 327344642 0.000000e+00 1868.0
12 TraesCS6A01G251500 chr6D 87.634 930 81 13 1 905 97786509 97785589 0.000000e+00 1050.0
13 TraesCS6A01G251500 chr6D 90.865 416 24 8 2042 2456 327347822 327348224 1.660000e-151 545.0
14 TraesCS6A01G251500 chr6D 82.803 628 68 18 919 1532 318260953 318260352 2.160000e-145 525.0
15 TraesCS6A01G251500 chr5A 97.715 919 18 3 1 917 492566452 492565535 0.000000e+00 1578.0
16 TraesCS6A01G251500 chr5A 86.703 925 96 12 1 905 530013823 530014740 0.000000e+00 1002.0
17 TraesCS6A01G251500 chr3A 97.901 905 17 2 1 905 622452858 622453760 0.000000e+00 1565.0
18 TraesCS6A01G251500 chr3A 76.667 480 83 25 442 905 111082160 111081694 3.160000e-59 239.0
19 TraesCS6A01G251500 chr1A 97.685 907 19 2 1 906 374674515 374673610 0.000000e+00 1557.0
20 TraesCS6A01G251500 chr1A 92.366 131 10 0 1235 1365 402260153 402260283 1.160000e-43 187.0
21 TraesCS6A01G251500 chr3D 88.973 925 73 20 1 905 81181037 81180122 0.000000e+00 1116.0
22 TraesCS6A01G251500 chr3D 87.136 894 64 20 36 909 550421008 550421870 0.000000e+00 966.0
23 TraesCS6A01G251500 chr3D 86.022 930 86 27 1 905 468972335 468973245 0.000000e+00 957.0
24 TraesCS6A01G251500 chr4A 87.368 665 56 7 205 856 706559990 706559341 0.000000e+00 737.0
25 TraesCS6A01G251500 chr7D 93.130 131 9 0 1235 1365 629783409 629783539 2.490000e-45 193.0
26 TraesCS6A01G251500 chr1B 91.603 131 11 0 1235 1365 317589506 317589636 5.400000e-42 182.0
27 TraesCS6A01G251500 chr2B 92.800 125 7 1 1241 1365 212347225 212347103 1.940000e-41 180.0
28 TraesCS6A01G251500 chr2D 73.569 594 102 38 351 905 456962476 456961899 2.510000e-40 176.0


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 TraesCS6A01G251500 chr6A 466087373 466089828 2455 False 4536.0 4536 100.000000 1 2456 1 chr6A.!!$F1 2455
1 TraesCS6A01G251500 chr6A 455821020 455822289 1269 True 426.7 1062 89.041667 914 2265 3 chr6A.!!$R1 1351
2 TraesCS6A01G251500 chr6B 494092377 494093916 1539 True 2174.0 2174 92.171000 904 2456 1 chr6B.!!$R1 1552
3 TraesCS6A01G251500 chr6B 505908480 505909712 1232 False 597.0 1018 90.293500 923 2265 2 chr6B.!!$F1 1342
4 TraesCS6A01G251500 chr6B 643388098 643392924 4826 True 470.0 621 86.634000 64 904 3 chr6B.!!$R3 840
5 TraesCS6A01G251500 chr6D 327343506 327348224 4718 False 1206.5 1868 93.559500 904 2456 2 chr6D.!!$F1 1552
6 TraesCS6A01G251500 chr6D 97785589 97786509 920 True 1050.0 1050 87.634000 1 905 1 chr6D.!!$R1 904
7 TraesCS6A01G251500 chr6D 318260352 318260953 601 True 525.0 525 82.803000 919 1532 1 chr6D.!!$R2 613
8 TraesCS6A01G251500 chr5A 492565535 492566452 917 True 1578.0 1578 97.715000 1 917 1 chr5A.!!$R1 916
9 TraesCS6A01G251500 chr5A 530013823 530014740 917 False 1002.0 1002 86.703000 1 905 1 chr5A.!!$F1 904
10 TraesCS6A01G251500 chr3A 622452858 622453760 902 False 1565.0 1565 97.901000 1 905 1 chr3A.!!$F1 904
11 TraesCS6A01G251500 chr1A 374673610 374674515 905 True 1557.0 1557 97.685000 1 906 1 chr1A.!!$R1 905
12 TraesCS6A01G251500 chr3D 81180122 81181037 915 True 1116.0 1116 88.973000 1 905 1 chr3D.!!$R1 904
13 TraesCS6A01G251500 chr3D 550421008 550421870 862 False 966.0 966 87.136000 36 909 1 chr3D.!!$F2 873
14 TraesCS6A01G251500 chr3D 468972335 468973245 910 False 957.0 957 86.022000 1 905 1 chr3D.!!$F1 904
15 TraesCS6A01G251500 chr4A 706559341 706559990 649 True 737.0 737 87.368000 205 856 1 chr4A.!!$R1 651

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
816 4883 1.075542 CAGCGAACGAATAACAGGCA 58.924 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 9612 0.102844 GTCTGGCAAAGCAGCAACAA 59.897 50.0 0.0 0.0 35.83 2.83 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
111 114 9.977762 CCTTCAAAATTTTCAGTTTTTCTTGAG 57.022 29.630 0.00 0.00 0.00 3.02
816 4883 1.075542 CAGCGAACGAATAACAGGCA 58.924 50.000 0.00 0.00 0.00 4.75
1505 5602 3.319137 TCTTGACGATTCTTGGTCTGG 57.681 47.619 0.00 0.00 32.30 3.86
1609 5726 6.957631 ACATGGTTGTGTATAGGATTCTTGA 58.042 36.000 0.00 0.00 33.85 3.02
1612 5729 6.177610 TGGTTGTGTATAGGATTCTTGAACC 58.822 40.000 0.00 0.00 0.00 3.62
1682 5799 6.676237 TTTTTGCAGATTTGGTTCCTTTTC 57.324 33.333 0.00 0.00 0.00 2.29
1683 5800 5.612725 TTTGCAGATTTGGTTCCTTTTCT 57.387 34.783 0.00 0.00 0.00 2.52
1685 5802 5.200368 TGCAGATTTGGTTCCTTTTCTTC 57.800 39.130 0.00 0.00 0.00 2.87
1686 5803 4.895297 TGCAGATTTGGTTCCTTTTCTTCT 59.105 37.500 0.00 0.00 0.00 2.85
1687 5804 6.068010 TGCAGATTTGGTTCCTTTTCTTCTA 58.932 36.000 0.00 0.00 0.00 2.10
1798 5915 8.707938 TGTTTGATAGCATATCGATCCTATTG 57.292 34.615 0.00 0.00 0.00 1.90
1811 5928 4.556898 CGATCCTATTGATCCGACGTTCTT 60.557 45.833 0.00 0.00 46.06 2.52
1880 5997 4.142578 TGAAAACATACTGCAAACGTGTGT 60.143 37.500 7.72 1.79 38.17 3.72
1913 6030 4.332543 TGAAGCGGATACTAACATTTGCAG 59.667 41.667 0.00 0.00 0.00 4.41
1965 6084 6.912591 CGTTATGCCTTCATGGTTCTTTAATC 59.087 38.462 0.00 0.00 38.35 1.75
2005 6124 7.510549 ACTCTTCTGCTTAAGTTAATTTGCA 57.489 32.000 4.02 7.56 0.00 4.08
2036 6155 6.688637 TTCAGATCAAATGCTCCATAGTTG 57.311 37.500 0.00 0.00 0.00 3.16
2081 9386 9.353431 TGTGGCATATTGTTATCTTGTGATATT 57.647 29.630 0.00 0.00 35.36 1.28
2149 9454 8.247562 TCCTTTACATATTGTATGGTGTTTTGC 58.752 33.333 2.42 0.00 32.20 3.68
2150 9455 7.491048 CCTTTACATATTGTATGGTGTTTTGCC 59.509 37.037 2.42 0.00 32.20 4.52
2151 9456 5.337578 ACATATTGTATGGTGTTTTGCCC 57.662 39.130 2.42 0.00 0.00 5.36
2203 9508 1.542108 GGGCATCACTATCTGTGGCTC 60.542 57.143 0.00 0.00 46.20 4.70
2307 9612 4.142160 GCTCAAGTTTCTTGGTTTTGGACT 60.142 41.667 9.18 0.00 0.00 3.85
2321 9626 0.102844 TGGACTTGTTGCTGCTTTGC 59.897 50.000 0.00 0.00 0.00 3.68
2325 9630 0.386476 CTTGTTGCTGCTTTGCCAGA 59.614 50.000 0.00 0.00 34.77 3.86
2369 9674 4.795268 TCAGTCTAATAAGCTAATCCGCG 58.205 43.478 0.00 0.00 34.40 6.46
2377 9682 2.969238 CTAATCCGCGGCCTGCTG 60.969 66.667 23.51 10.47 43.27 4.41
2393 9698 0.989890 GCTGTGTTAGGCTAACGACG 59.010 55.000 27.20 19.27 41.50 5.12
2397 9702 2.162208 TGTGTTAGGCTAACGACGTAGG 59.838 50.000 27.20 0.00 41.50 3.18
2401 9706 2.643933 AGGCTAACGACGTAGGTTTC 57.356 50.000 0.00 3.52 0.00 2.78
2407 9712 4.094146 GCTAACGACGTAGGTTTCTCTAGT 59.906 45.833 0.00 0.00 0.00 2.57
2417 9722 8.242739 ACGTAGGTTTCTCTAGTTCAGATAAAC 58.757 37.037 0.00 6.69 44.08 2.01
2425 9730 5.706916 TCTAGTTCAGATAAACGAACGCTT 58.293 37.500 0.00 0.00 44.94 4.68
2445 9750 3.678056 TGTTCAGCTAAGTGTACTGGG 57.322 47.619 0.00 0.00 32.19 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1222 5309 4.194720 CTCCTCCTCGCCGTTCGG 62.195 72.222 6.90 6.90 39.05 4.30
1231 5318 1.293683 ACCTCCTCCTCCTCCTCCTC 61.294 65.000 0.00 0.00 0.00 3.71
1232 5319 1.230819 ACCTCCTCCTCCTCCTCCT 60.231 63.158 0.00 0.00 0.00 3.69
1233 5320 1.075600 CACCTCCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1421 5517 4.704833 GAGCAGTCTTGGCCGCCA 62.705 66.667 8.43 8.43 0.00 5.69
1442 5538 1.077930 CCATGTCAGCACCCTGGAG 60.078 63.158 0.00 0.00 39.61 3.86
1505 5602 3.784701 TCGTAATCAGAGGTTCAGAGC 57.215 47.619 0.00 0.00 0.00 4.09
1609 5726 1.267121 ACTACATGCAGTCTCCGGTT 58.733 50.000 0.00 0.00 0.00 4.44
1612 5729 3.439293 CAGTAACTACATGCAGTCTCCG 58.561 50.000 0.00 0.00 0.00 4.63
1682 5799 7.148672 GCCAAATGTGACGATCTGATATAGAAG 60.149 40.741 0.00 0.00 39.30 2.85
1683 5800 6.646653 GCCAAATGTGACGATCTGATATAGAA 59.353 38.462 0.00 0.00 39.30 2.10
1685 5802 5.349817 GGCCAAATGTGACGATCTGATATAG 59.650 44.000 0.00 0.00 0.00 1.31
1686 5803 5.237815 GGCCAAATGTGACGATCTGATATA 58.762 41.667 0.00 0.00 0.00 0.86
1687 5804 4.067896 GGCCAAATGTGACGATCTGATAT 58.932 43.478 0.00 0.00 0.00 1.63
1798 5915 4.174009 TCAGAATTGAAGAACGTCGGATC 58.826 43.478 0.00 0.00 0.00 3.36
1811 5928 9.695526 AATCAAAATCGACAAAATCAGAATTGA 57.304 25.926 6.37 0.00 37.81 2.57
1898 6015 5.102953 TCTCAGGCTGCAAATGTTAGTAT 57.897 39.130 10.34 0.00 0.00 2.12
1913 6030 5.355350 AGCACTGTAAATTGTAATCTCAGGC 59.645 40.000 0.00 0.00 0.00 4.85
1965 6084 3.791973 AGAGTAACCGCTGATCTTCTG 57.208 47.619 0.00 0.00 0.00 3.02
2036 6155 4.022849 CCACAGAACAGGAAACAAGAATCC 60.023 45.833 0.00 0.00 35.88 3.01
2081 9386 5.606505 TGCTAGTACTCACAATTCACACAA 58.393 37.500 0.00 0.00 0.00 3.33
2082 9387 5.010617 TCTGCTAGTACTCACAATTCACACA 59.989 40.000 0.00 0.00 0.00 3.72
2092 9397 4.420168 CTTCAAGCTCTGCTAGTACTCAC 58.580 47.826 0.00 0.00 38.25 3.51
2134 9439 3.070302 GGAAAGGGCAAAACACCATACAA 59.930 43.478 0.00 0.00 0.00 2.41
2138 9443 1.970640 GAGGAAAGGGCAAAACACCAT 59.029 47.619 0.00 0.00 0.00 3.55
2139 9444 1.342474 TGAGGAAAGGGCAAAACACCA 60.342 47.619 0.00 0.00 0.00 4.17
2142 9447 3.454082 ACATTTGAGGAAAGGGCAAAACA 59.546 39.130 0.00 0.00 35.44 2.83
2143 9448 4.058124 GACATTTGAGGAAAGGGCAAAAC 58.942 43.478 0.00 0.00 35.44 2.43
2144 9449 3.708631 TGACATTTGAGGAAAGGGCAAAA 59.291 39.130 0.00 0.00 37.93 2.44
2145 9450 3.303938 TGACATTTGAGGAAAGGGCAAA 58.696 40.909 0.00 0.00 37.93 3.68
2146 9451 2.956132 TGACATTTGAGGAAAGGGCAA 58.044 42.857 0.00 0.00 37.93 4.52
2147 9452 2.673775 TGACATTTGAGGAAAGGGCA 57.326 45.000 0.00 0.00 38.55 5.36
2148 9453 4.541973 AAATGACATTTGAGGAAAGGGC 57.458 40.909 12.62 0.00 31.12 5.19
2203 9508 3.735237 AGCATCTGACCATACCTAACG 57.265 47.619 0.00 0.00 0.00 3.18
2266 9571 3.277715 GAGCATTGCCTTCTAAGAGCTT 58.722 45.455 4.70 0.00 0.00 3.74
2307 9612 0.102844 GTCTGGCAAAGCAGCAACAA 59.897 50.000 0.00 0.00 35.83 2.83
2321 9626 2.593978 CATGGGAGGGCAGTCTGG 59.406 66.667 1.14 0.00 0.00 3.86
2325 9630 0.475906 GAATAGCATGGGAGGGCAGT 59.524 55.000 0.00 0.00 0.00 4.40
2377 9682 2.162408 ACCTACGTCGTTAGCCTAACAC 59.838 50.000 14.59 10.23 38.57 3.32
2386 9691 5.700832 TGAACTAGAGAAACCTACGTCGTTA 59.299 40.000 1.78 0.00 0.00 3.18
2401 9706 5.333513 AGCGTTCGTTTATCTGAACTAGAG 58.666 41.667 0.00 0.00 41.74 2.43
2407 9712 5.013861 GAACAAGCGTTCGTTTATCTGAA 57.986 39.130 0.00 0.00 42.05 3.02
2425 9730 2.969950 ACCCAGTACACTTAGCTGAACA 59.030 45.455 0.00 0.00 32.39 3.18


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

AutoCloner maintained by Alex Coulton.