Multiple sequence alignment - TraesCS6D01G075700

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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 TraesCS6D01G075700 chr6D 100.000 3693 0 0 1 3693 39487415 39491107 0.000000e+00 6820.0
1 TraesCS6D01G075700 chr6D 87.636 2022 136 45 1234 3199 39673332 39671369 0.000000e+00 2244.0
2 TraesCS6D01G075700 chr6D 93.402 1364 70 13 459 1818 40062464 40061117 0.000000e+00 2002.0
3 TraesCS6D01G075700 chr6D 90.669 643 52 7 2198 2836 40060785 40060147 0.000000e+00 848.0
4 TraesCS6D01G075700 chr6D 77.204 658 109 28 1292 1936 88701842 88702471 2.730000e-91 346.0
5 TraesCS6D01G075700 chr6D 88.000 300 19 5 1914 2213 40061080 40060798 4.570000e-89 339.0
6 TraesCS6D01G075700 chr6D 79.897 388 73 5 80 464 88356481 88356866 2.810000e-71 279.0
7 TraesCS6D01G075700 chr6D 76.498 651 67 36 2602 3191 39777153 39776528 3.630000e-70 276.0
8 TraesCS6D01G075700 chr6D 80.625 320 40 14 3392 3693 39776407 39776092 1.030000e-55 228.0
9 TraesCS6D01G075700 chr6D 81.034 290 22 17 3422 3693 40059547 40059273 2.250000e-47 200.0
10 TraesCS6D01G075700 chr6D 94.595 37 2 0 1849 1885 40061109 40061073 1.430000e-04 58.4
11 TraesCS6D01G075700 chr6B 95.388 3708 131 25 1 3693 91198663 91202345 0.000000e+00 5864.0
12 TraesCS6D01G075700 chr6B 90.826 2082 142 30 783 2840 91621364 91619308 0.000000e+00 2741.0
13 TraesCS6D01G075700 chr6B 81.714 957 141 16 1026 1962 35378575 35377633 0.000000e+00 767.0
14 TraesCS6D01G075700 chr6B 79.734 676 120 12 2025 2690 35377509 35376841 1.200000e-129 473.0
15 TraesCS6D01G075700 chr6B 82.857 315 34 12 3393 3693 91618740 91618432 7.860000e-67 265.0
16 TraesCS6D01G075700 chr6A 92.425 2033 119 14 811 2840 51480394 51478394 0.000000e+00 2868.0
17 TraesCS6D01G075700 chr6A 81.118 1038 147 27 975 1987 19828935 19829948 0.000000e+00 785.0
18 TraesCS6D01G075700 chr6A 79.912 682 109 23 2025 2690 19830052 19830721 3.340000e-130 475.0
19 TraesCS6D01G075700 chr6A 75.722 935 161 43 1041 1936 106698215 106699122 3.430000e-110 409.0
20 TraesCS6D01G075700 chr6A 85.156 128 16 1 3392 3516 51477883 51477756 1.080000e-25 128.0
21 TraesCS6D01G075700 chr6A 85.882 85 11 1 3271 3355 51477966 51477883 5.080000e-14 89.8
22 TraesCS6D01G075700 chr2A 77.927 820 132 25 1118 1935 645823842 645824614 2.010000e-127 466.0
23 TraesCS6D01G075700 chr2A 91.525 59 5 0 2550 2608 57829653 57829595 8.500000e-12 82.4
24 TraesCS6D01G075700 chr7D 79.104 469 87 9 1 464 309576234 309575772 2.770000e-81 313.0
25 TraesCS6D01G075700 chr7D 78.972 214 43 2 248 459 419879811 419880024 1.070000e-30 145.0
26 TraesCS6D01G075700 chr4B 78.012 332 61 10 1 327 409048174 409047850 8.090000e-47 198.0
27 TraesCS6D01G075700 chr3D 77.976 336 59 13 1112 1441 89801158 89801484 2.910000e-46 196.0
28 TraesCS6D01G075700 chr3B 77.259 343 63 13 1105 1441 139222336 139222669 1.750000e-43 187.0
29 TraesCS6D01G075700 chr5D 82.028 217 34 5 1048 1260 58677762 58677977 2.930000e-41 180.0
30 TraesCS6D01G075700 chr5D 88.312 77 8 1 376 451 309882968 309883044 1.410000e-14 91.6
31 TraesCS6D01G075700 chr2D 79.310 145 21 4 2550 2694 56199710 56199575 3.930000e-15 93.5


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 TraesCS6D01G075700 chr6D 39487415 39491107 3692 False 6820.00 6820 100.0000 1 3693 1 chr6D.!!$F1 3692
1 TraesCS6D01G075700 chr6D 39671369 39673332 1963 True 2244.00 2244 87.6360 1234 3199 1 chr6D.!!$R1 1965
2 TraesCS6D01G075700 chr6D 40059273 40062464 3191 True 689.48 2002 89.5400 459 3693 5 chr6D.!!$R3 3234
3 TraesCS6D01G075700 chr6D 88701842 88702471 629 False 346.00 346 77.2040 1292 1936 1 chr6D.!!$F3 644
4 TraesCS6D01G075700 chr6D 39776092 39777153 1061 True 252.00 276 78.5615 2602 3693 2 chr6D.!!$R2 1091
5 TraesCS6D01G075700 chr6B 91198663 91202345 3682 False 5864.00 5864 95.3880 1 3693 1 chr6B.!!$F1 3692
6 TraesCS6D01G075700 chr6B 91618432 91621364 2932 True 1503.00 2741 86.8415 783 3693 2 chr6B.!!$R2 2910
7 TraesCS6D01G075700 chr6B 35376841 35378575 1734 True 620.00 767 80.7240 1026 2690 2 chr6B.!!$R1 1664
8 TraesCS6D01G075700 chr6A 51477756 51480394 2638 True 1028.60 2868 87.8210 811 3516 3 chr6A.!!$R1 2705
9 TraesCS6D01G075700 chr6A 19828935 19830721 1786 False 630.00 785 80.5150 975 2690 2 chr6A.!!$F2 1715
10 TraesCS6D01G075700 chr6A 106698215 106699122 907 False 409.00 409 75.7220 1041 1936 1 chr6A.!!$F1 895
11 TraesCS6D01G075700 chr2A 645823842 645824614 772 False 466.00 466 77.9270 1118 1935 1 chr2A.!!$F1 817

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
264 265 0.462047 CGGAGCAAAAGACGGCCTAT 60.462 55.0 0.00 0.0 0.00 2.57 F
774 775 0.467844 ACATTGCAACTGGTGGCTCA 60.468 50.0 0.00 0.0 0.00 4.26 F
1373 1452 0.959372 ATCGACGAGTCCAACGAGGT 60.959 55.0 3.01 0.0 38.12 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2143 1.133598 CCTGCACATCATCGCAACATT 59.866 47.619 0.00 0.0 37.76 2.71 R
2522 2783 0.460987 GTGGCCTCACGAATGGAGAG 60.461 60.000 3.32 0.0 34.24 3.20 R
3161 3533 0.396435 TCCACCTTGCGAACTGATGT 59.604 50.000 0.00 0.0 0.00 3.06 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
88 89 6.265196 TGTTTTTGTTGCATGTCTCCTCTATT 59.735 34.615 0.00 0.00 0.00 1.73
132 133 1.291877 CCAAACGTGAGGAGGAAGCG 61.292 60.000 0.33 0.00 0.00 4.68
136 137 1.667830 CGTGAGGAGGAAGCGCAAA 60.668 57.895 11.47 0.00 0.00 3.68
137 138 1.227999 CGTGAGGAGGAAGCGCAAAA 61.228 55.000 11.47 0.00 0.00 2.44
138 139 0.519077 GTGAGGAGGAAGCGCAAAAG 59.481 55.000 11.47 0.00 0.00 2.27
139 140 1.237285 TGAGGAGGAAGCGCAAAAGC 61.237 55.000 11.47 0.00 37.41 3.51
181 182 4.006319 CTCCAGGAGAAAAGATGGTGTTC 58.994 47.826 11.62 0.00 34.32 3.18
196 197 2.169769 GGTGTTCCATACGATCTTCCCA 59.830 50.000 0.00 0.00 0.00 4.37
199 200 3.517901 TGTTCCATACGATCTTCCCAGTT 59.482 43.478 0.00 0.00 0.00 3.16
207 208 2.160417 CGATCTTCCCAGTTGTTTGAGC 59.840 50.000 0.00 0.00 0.00 4.26
208 209 1.593196 TCTTCCCAGTTGTTTGAGCG 58.407 50.000 0.00 0.00 0.00 5.03
222 223 3.147595 AGCGCCCGTATGAGCTCA 61.148 61.111 20.79 20.79 34.48 4.26
264 265 0.462047 CGGAGCAAAAGACGGCCTAT 60.462 55.000 0.00 0.00 0.00 2.57
265 266 1.751437 GGAGCAAAAGACGGCCTATT 58.249 50.000 0.00 0.00 0.00 1.73
267 268 2.084546 GAGCAAAAGACGGCCTATTGT 58.915 47.619 0.00 0.00 0.00 2.71
270 271 2.227865 GCAAAAGACGGCCTATTGTTCA 59.772 45.455 0.00 0.00 0.00 3.18
274 275 3.134574 AGACGGCCTATTGTTCAAACA 57.865 42.857 0.00 0.00 37.08 2.83
280 281 2.724839 GCCTATTGTTCAAACACTCGCG 60.725 50.000 0.00 0.00 38.92 5.87
287 288 1.000233 TCAAACACTCGCGCTCGTAC 61.000 55.000 5.56 0.00 36.96 3.67
327 328 2.803492 GCGACCACAATGAGTATCTCCC 60.803 54.545 0.00 0.00 34.92 4.30
329 330 1.762957 ACCACAATGAGTATCTCCCGG 59.237 52.381 0.00 0.00 34.92 5.73
334 335 0.896019 ATGAGTATCTCCCGGAGCGG 60.896 60.000 9.87 0.00 41.13 5.52
373 374 1.960689 ACCGCAACTGGCAATTTTAGT 59.039 42.857 0.00 0.00 45.17 2.24
374 375 2.288152 ACCGCAACTGGCAATTTTAGTG 60.288 45.455 0.00 0.00 45.17 2.74
377 378 3.392882 GCAACTGGCAATTTTAGTGCTT 58.607 40.909 0.00 0.00 43.97 3.91
402 403 5.587388 ATGAAAGCAATAACACCTCCATG 57.413 39.130 0.00 0.00 0.00 3.66
403 404 4.406456 TGAAAGCAATAACACCTCCATGT 58.594 39.130 0.00 0.00 0.00 3.21
420 421 3.618594 CCATGTGATTCATTTCGACGTCT 59.381 43.478 14.70 0.00 34.09 4.18
445 446 3.551659 GGTCGACGAGGTGTTTTCTAACT 60.552 47.826 9.92 0.00 35.24 2.24
491 492 4.495690 AAAGCTTTAAAGTTTGCCCCAA 57.504 36.364 16.77 0.00 29.55 4.12
532 533 4.637276 TCGCCACTAATTTTCTGTCAAGA 58.363 39.130 0.00 0.00 0.00 3.02
551 552 8.421784 TGTCAAGACAGTACAAAGAAACTAGAT 58.578 33.333 0.00 0.00 36.21 1.98
585 586 6.718522 TTACATCCATATTCGTAGACCACA 57.281 37.500 0.00 0.00 34.32 4.17
730 731 7.985476 AGTTCAGAATAAAATCACAATACGGG 58.015 34.615 0.00 0.00 0.00 5.28
766 767 9.844790 TTTTCTAGAAATATCACATTGCAACTG 57.155 29.630 18.37 4.25 0.00 3.16
774 775 0.467844 ACATTGCAACTGGTGGCTCA 60.468 50.000 0.00 0.00 0.00 4.26
866 872 3.445096 CAGTGAGACCAAATCCATTTCCC 59.555 47.826 0.00 0.00 0.00 3.97
1073 1098 4.733725 CTCCCCGGTCTCCCCCAA 62.734 72.222 0.00 0.00 0.00 4.12
1126 1166 2.512515 GTGAGGACCGCATCAGCC 60.513 66.667 0.00 0.00 35.20 4.85
1128 1168 3.785859 GAGGACCGCATCAGCCCA 61.786 66.667 0.00 0.00 37.52 5.36
1373 1452 0.959372 ATCGACGAGTCCAACGAGGT 60.959 55.000 3.01 0.00 38.12 3.85
1590 1709 1.308216 CTTCCCCCACCTCCAGGAT 60.308 63.158 0.00 0.00 38.94 3.24
1989 2123 3.788333 ATCTGGTTTGATTTGCATCGG 57.212 42.857 0.00 0.00 31.08 4.18
2009 2143 5.857268 TCGGATTCTAGCATCAATTGATCA 58.143 37.500 18.16 5.93 31.21 2.92
2160 2366 3.238597 GAGATGCTTCCCTGGAGTAGAT 58.761 50.000 0.00 0.00 0.00 1.98
2201 2437 3.007614 GTGAGTTTTACCCTGTGGCTCTA 59.992 47.826 0.00 0.00 33.59 2.43
2234 2488 9.206870 TCTCTGCATTCAAAATTACCATTTTTC 57.793 29.630 0.00 0.00 40.09 2.29
2428 2689 3.680842 GGTGTTCGACCAGTTCACT 57.319 52.632 0.00 0.00 45.34 3.41
2768 3033 2.290641 CGTGTTTCCTTGTGAAAGGGAG 59.709 50.000 4.73 0.00 43.46 4.30
2912 3250 5.137403 GTGTTACTATTGTTGTGAGTTGCG 58.863 41.667 0.00 0.00 0.00 4.85
2978 3331 0.478072 TGGGAGCAGTGTTTCCATGT 59.522 50.000 2.18 0.00 35.09 3.21
3161 3533 0.887387 GCGTGGGCTCTGGTTTTGTA 60.887 55.000 0.00 0.00 35.83 2.41
3248 3622 1.610554 GCTGCATCCTGGGTTTGCAT 61.611 55.000 16.40 0.00 44.65 3.96
3365 3785 7.654116 ACTTGGTTAACCATTATTTGTTTTCCG 59.346 33.333 27.57 1.37 46.97 4.30
3370 3790 5.066968 ACCATTATTTGTTTTCCGCGATT 57.933 34.783 8.23 0.00 0.00 3.34
3375 3795 7.486551 CCATTATTTGTTTTCCGCGATTTAGAA 59.513 33.333 8.23 0.00 0.00 2.10
3455 3885 5.556355 ATCAAGATAATGCCGCATATGTG 57.444 39.130 6.22 9.39 0.00 3.21
3456 3886 4.388485 TCAAGATAATGCCGCATATGTGT 58.612 39.130 14.91 0.00 0.00 3.72
3457 3887 4.821260 TCAAGATAATGCCGCATATGTGTT 59.179 37.500 14.91 5.79 0.00 3.32
3544 3991 0.034756 CAATGACGGGGTGTGTGAGA 59.965 55.000 0.00 0.00 0.00 3.27
3688 4165 0.463654 AAGTTGCTGCGGTGAGAACA 60.464 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.227512 TGAAAACAACACAAAACCAACTCAAAT 59.772 29.630 0.00 0.00 0.00 2.32
136 137 5.767168 AGCTGTAGAACTTCATGAAAAGCTT 59.233 36.000 9.88 0.00 33.70 3.74
137 138 5.312079 AGCTGTAGAACTTCATGAAAAGCT 58.688 37.500 9.88 5.66 32.66 3.74
138 139 5.391416 GGAGCTGTAGAACTTCATGAAAAGC 60.391 44.000 9.88 3.24 0.00 3.51
139 140 5.702670 TGGAGCTGTAGAACTTCATGAAAAG 59.297 40.000 9.88 0.85 0.00 2.27
144 145 3.196469 TCCTGGAGCTGTAGAACTTCATG 59.804 47.826 0.00 0.00 0.00 3.07
181 182 3.543680 ACAACTGGGAAGATCGTATGG 57.456 47.619 0.00 0.00 0.00 2.74
187 188 2.160417 CGCTCAAACAACTGGGAAGATC 59.840 50.000 0.00 0.00 0.00 2.75
189 190 1.593196 CGCTCAAACAACTGGGAAGA 58.407 50.000 0.00 0.00 0.00 2.87
191 192 1.452145 GGCGCTCAAACAACTGGGAA 61.452 55.000 7.64 0.00 0.00 3.97
196 197 0.321298 ATACGGGCGCTCAAACAACT 60.321 50.000 8.62 0.00 0.00 3.16
199 200 0.739462 CTCATACGGGCGCTCAAACA 60.739 55.000 8.62 0.00 0.00 2.83
207 208 1.665916 CCATGAGCTCATACGGGCG 60.666 63.158 28.27 14.81 34.26 6.13
208 209 1.963338 GCCATGAGCTCATACGGGC 60.963 63.158 30.09 30.09 36.31 6.13
222 223 1.490490 TCTCCTATTTCTTGCGGCCAT 59.510 47.619 2.24 0.00 0.00 4.40
264 265 0.303493 GAGCGCGAGTGTTTGAACAA 59.697 50.000 12.10 0.00 41.21 2.83
265 266 1.817217 CGAGCGCGAGTGTTTGAACA 61.817 55.000 12.10 0.00 40.82 3.18
267 268 0.318022 TACGAGCGCGAGTGTTTGAA 60.318 50.000 19.05 0.00 41.64 2.69
270 271 2.078914 CGTACGAGCGCGAGTGTTT 61.079 57.895 19.05 0.00 41.64 2.83
287 288 1.361668 CCAGGTGAAATGACCGCTCG 61.362 60.000 0.00 0.00 41.35 5.03
327 328 3.642778 AACACCATCGTCCGCTCCG 62.643 63.158 0.00 0.00 0.00 4.63
329 330 0.454600 TAGAACACCATCGTCCGCTC 59.545 55.000 0.00 0.00 0.00 5.03
334 335 3.625938 GGTCGTATAGAACACCATCGTC 58.374 50.000 0.00 0.00 36.33 4.20
339 340 1.175654 TGCGGTCGTATAGAACACCA 58.824 50.000 0.00 0.00 35.97 4.17
377 378 5.565509 TGGAGGTGTTATTGCTTTCATACA 58.434 37.500 0.00 0.00 0.00 2.29
402 403 3.304559 CCTCAGACGTCGAAATGAATCAC 59.695 47.826 10.46 0.00 0.00 3.06
403 404 3.056821 ACCTCAGACGTCGAAATGAATCA 60.057 43.478 10.46 0.00 0.00 2.57
420 421 0.748450 AAAACACCTCGTCGACCTCA 59.252 50.000 10.58 0.00 0.00 3.86
491 492 5.710099 TGGCGAAGGAAGAAGAAAATTATGT 59.290 36.000 0.00 0.00 0.00 2.29
565 566 6.925211 ACTATGTGGTCTACGAATATGGATG 58.075 40.000 0.00 0.00 0.00 3.51
748 749 4.621274 GCCACCAGTTGCAATGTGATATTT 60.621 41.667 21.29 0.00 0.00 1.40
752 753 0.604578 GCCACCAGTTGCAATGTGAT 59.395 50.000 21.29 1.22 0.00 3.06
757 758 0.467844 TGTGAGCCACCAGTTGCAAT 60.468 50.000 0.59 0.00 32.73 3.56
762 763 1.102978 GTTTGTGTGAGCCACCAGTT 58.897 50.000 3.33 0.00 43.85 3.16
763 764 0.034574 TGTTTGTGTGAGCCACCAGT 60.035 50.000 3.33 0.00 43.85 4.00
766 767 1.102978 AGTTGTTTGTGTGAGCCACC 58.897 50.000 3.33 0.00 43.85 4.61
774 775 4.461198 CCTTCTCCCTTAGTTGTTTGTGT 58.539 43.478 0.00 0.00 0.00 3.72
782 783 1.203440 TCTGGGCCTTCTCCCTTAGTT 60.203 52.381 4.53 0.00 46.67 2.24
784 785 0.833949 GTCTGGGCCTTCTCCCTTAG 59.166 60.000 4.53 0.00 46.67 2.18
866 872 8.802267 TGAGATGGGGAGTAATAAAAACAAAAG 58.198 33.333 0.00 0.00 0.00 2.27
941 953 1.412505 GGGAAAGGTGTGGGTTTTCCT 60.413 52.381 13.16 0.00 45.78 3.36
1126 1166 3.391382 GAGGGTGTCGGGGAGTGG 61.391 72.222 0.00 0.00 0.00 4.00
1128 1168 3.602030 AGGAGGGTGTCGGGGAGT 61.602 66.667 0.00 0.00 0.00 3.85
1989 2123 9.181805 CAACATTGATCAATTGATGCTAGAATC 57.818 33.333 25.37 9.79 34.37 2.52
2009 2143 1.133598 CCTGCACATCATCGCAACATT 59.866 47.619 0.00 0.00 37.76 2.71
2160 2366 3.872696 CACAGCCATGATGTGTAAGGTA 58.127 45.455 17.93 0.00 43.74 3.08
2201 2437 7.498570 GGTAATTTTGAATGCAGAGAGAGAGAT 59.501 37.037 0.00 0.00 0.00 2.75
2234 2488 2.283298 ACGATGGAATGCAAGCAGTAG 58.717 47.619 0.00 0.00 0.00 2.57
2522 2783 0.460987 GTGGCCTCACGAATGGAGAG 60.461 60.000 3.32 0.00 34.24 3.20
2978 3331 0.472044 TGTAAGCCACAGCCACAGAA 59.528 50.000 0.00 0.00 41.25 3.02
3161 3533 0.396435 TCCACCTTGCGAACTGATGT 59.604 50.000 0.00 0.00 0.00 3.06
3248 3622 3.003897 GCAAAACAGTAAACCGACATCCA 59.996 43.478 0.00 0.00 0.00 3.41
3365 3785 4.558860 GCAAACCTGACATTTCTAAATCGC 59.441 41.667 0.00 0.00 0.00 4.58
3457 3887 8.824159 TGTGTCTTTCAAATCAAGAACAAAAA 57.176 26.923 0.00 0.00 31.98 1.94
3544 3991 1.207791 CTTGGGGAGAGCCAGTACAT 58.792 55.000 0.00 0.00 35.15 2.29
3616 4078 1.348008 TGCCCCAGATTAGCAGAGGG 61.348 60.000 0.00 0.00 39.29 4.30
3617 4079 0.769873 ATGCCCCAGATTAGCAGAGG 59.230 55.000 0.00 0.00 40.40 3.69
3620 4082 3.498774 AGTTATGCCCCAGATTAGCAG 57.501 47.619 0.00 0.00 40.40 4.24
3623 4085 6.966534 ATTTCAAGTTATGCCCCAGATTAG 57.033 37.500 0.00 0.00 0.00 1.73
3626 4095 6.322201 CAGTTATTTCAAGTTATGCCCCAGAT 59.678 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.