Multiple sequence alignment - TraesCS3D01G128700

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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 TraesCS3D01G128700 chr3D 100.000 5021 0 0 1 5021 86940106 86935086 0.000000e+00 9273
1 TraesCS3D01G128700 chr3B 95.130 4661 103 43 1 4613 136804460 136799876 0.000000e+00 7236
2 TraesCS3D01G128700 chr3B 92.874 435 7 11 4596 5021 136799832 136799413 1.200000e-170 610
3 TraesCS3D01G128700 chr3A 96.170 3264 75 17 1801 5021 103620697 103617441 0.000000e+00 5289
4 TraesCS3D01G128700 chr3A 90.641 1528 37 29 244 1693 103622632 103621133 0.000000e+00 1932
5 TraesCS3D01G128700 chr3A 92.248 258 8 4 1 246 103623157 103622900 6.180000e-94 355
6 TraesCS3D01G128700 chr7A 84.988 413 56 4 3572 3981 546262187 546261778 1.010000e-111 414
7 TraesCS3D01G128700 chr7A 83.761 234 35 2 1047 1280 546263809 546263579 8.460000e-53 219
8 TraesCS3D01G128700 chr7A 81.579 190 33 2 3271 3459 546262545 546262357 6.730000e-34 156
9 TraesCS3D01G128700 chr7D 82.979 423 64 5 3563 3981 450245478 450245060 4.750000e-100 375
10 TraesCS3D01G128700 chr7D 83.333 198 27 6 3265 3459 450245815 450245621 1.440000e-40 178
11 TraesCS3D01G128700 chr7B 82.979 423 64 5 3563 3981 468406089 468405671 4.750000e-100 375
12 TraesCS3D01G128700 chr7B 82.745 255 38 5 1029 1280 468407679 468407428 6.540000e-54 222
13 TraesCS3D01G128700 chr7B 83.684 190 29 2 3271 3459 468406409 468406221 1.440000e-40 178
14 TraesCS3D01G128700 chr6D 89.362 141 15 0 3265 3405 149304720 149304860 1.440000e-40 178
15 TraesCS3D01G128700 chr6B 86.525 141 19 0 3265 3405 262275174 262275314 6.730000e-34 156
16 TraesCS3D01G128700 chr2A 76.211 227 45 7 1066 1290 84944386 84944167 1.480000e-20 111


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 TraesCS3D01G128700 chr3D 86935086 86940106 5020 True 9273.000000 9273 100.000000 1 5021 1 chr3D.!!$R1 5020
1 TraesCS3D01G128700 chr3B 136799413 136804460 5047 True 3923.000000 7236 94.002000 1 5021 2 chr3B.!!$R1 5020
2 TraesCS3D01G128700 chr3A 103617441 103623157 5716 True 2525.333333 5289 93.019667 1 5021 3 chr3A.!!$R1 5020
3 TraesCS3D01G128700 chr7A 546261778 546263809 2031 True 263.000000 414 83.442667 1047 3981 3 chr7A.!!$R1 2934
4 TraesCS3D01G128700 chr7D 450245060 450245815 755 True 276.500000 375 83.156000 3265 3981 2 chr7D.!!$R1 716
5 TraesCS3D01G128700 chr7B 468405671 468407679 2008 True 258.333333 375 83.136000 1029 3981 3 chr7B.!!$R1 2952

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
130 135 0.106769 ACTGACATGCCACACAACCA 60.107 50.000 0.00 0.0 0.00 3.67 F
338 633 0.461961 AATCCTCTCTGTAGCACGCC 59.538 55.000 0.00 0.0 0.00 5.68 F
466 761 0.470766 GGCTCGAGGGAGAGAGACTA 59.529 60.000 15.58 0.0 43.27 2.59 F
1726 2120 0.541863 CACGGGTCTATTCCCTGCTT 59.458 55.000 0.25 0.0 44.95 3.91 F
1995 2719 2.421424 CTGTAACTCATCTTGCTTGGGC 59.579 50.000 0.00 0.0 39.26 5.36 F
3882 4754 1.750399 GCTCACGGTGGCCATCATT 60.750 57.895 18.15 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1859 0.331278 TTTGCCACCGATCCCATTCT 59.669 50.000 0.00 0.0 0.00 2.40 R
2168 2912 0.453390 GTTACTGGTACCGCTACGCT 59.547 55.000 7.57 0.0 0.00 5.07 R
2169 2913 0.526310 GGTTACTGGTACCGCTACGC 60.526 60.000 7.57 0.0 0.00 4.42 R
3518 4348 1.000506 TCAGGTCACGCACTACTTTCC 59.999 52.381 0.00 0.0 0.00 3.13 R
3930 4802 1.142748 GAGGAGCATCAGGACCGTG 59.857 63.158 0.00 0.0 36.25 4.94 R
4737 5685 1.334869 GCACACTACCATTGCTATGCC 59.665 52.381 2.27 0.0 33.26 4.40 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
130 135 0.106769 ACTGACATGCCACACAACCA 60.107 50.000 0.00 0.00 0.00 3.67
188 193 7.667575 AGGATAATTACACACACAGAGAGAT 57.332 36.000 0.00 0.00 0.00 2.75
190 195 8.634444 AGGATAATTACACACACAGAGAGATAC 58.366 37.037 0.00 0.00 0.00 2.24
287 570 4.120331 GGCACGGCAGCAATGTCC 62.120 66.667 0.00 0.00 35.83 4.02
288 571 3.364441 GCACGGCAGCAATGTCCA 61.364 61.111 0.00 0.00 0.00 4.02
289 572 2.703798 GCACGGCAGCAATGTCCAT 61.704 57.895 0.00 0.00 0.00 3.41
290 573 1.430632 CACGGCAGCAATGTCCATC 59.569 57.895 0.00 0.00 0.00 3.51
291 574 1.028330 CACGGCAGCAATGTCCATCT 61.028 55.000 0.00 0.00 0.00 2.90
338 633 0.461961 AATCCTCTCTGTAGCACGCC 59.538 55.000 0.00 0.00 0.00 5.68
341 636 3.342370 CTCTCTGTAGCACGCCGCA 62.342 63.158 0.00 0.00 46.13 5.69
342 637 2.432456 CTCTGTAGCACGCCGCAA 60.432 61.111 0.00 0.00 46.13 4.85
344 639 3.788766 CTGTAGCACGCCGCAACC 61.789 66.667 0.00 0.00 46.13 3.77
465 760 1.226262 GGCTCGAGGGAGAGAGACT 59.774 63.158 15.58 0.00 43.27 3.24
466 761 0.470766 GGCTCGAGGGAGAGAGACTA 59.529 60.000 15.58 0.00 43.27 2.59
495 792 5.013547 AGAAAGGTCGAGAGAGAGAAATGA 58.986 41.667 0.00 0.00 43.49 2.57
497 794 4.229304 AGGTCGAGAGAGAGAAATGAGA 57.771 45.455 0.00 0.00 43.49 3.27
498 795 4.594970 AGGTCGAGAGAGAGAAATGAGAA 58.405 43.478 0.00 0.00 43.49 2.87
499 796 4.640201 AGGTCGAGAGAGAGAAATGAGAAG 59.360 45.833 0.00 0.00 43.49 2.85
501 798 3.380004 TCGAGAGAGAGAAATGAGAAGGC 59.620 47.826 0.00 0.00 34.84 4.35
736 1055 5.347364 GCTTTCAGCGATGATACTAATCCTC 59.653 44.000 3.25 0.00 0.00 3.71
886 1215 2.951642 CCTCTCTCCTCTGCTTCTACTG 59.048 54.545 0.00 0.00 0.00 2.74
952 1293 0.963355 GAGTGAGTGAGGCGAGAGGT 60.963 60.000 0.00 0.00 0.00 3.85
967 1317 3.700038 CGAGAGGTGGGGGATATACATAC 59.300 52.174 0.00 0.00 0.00 2.39
968 1318 4.684724 GAGAGGTGGGGGATATACATACA 58.315 47.826 0.00 0.00 0.00 2.29
969 1319 5.281314 GAGAGGTGGGGGATATACATACAT 58.719 45.833 0.00 0.00 0.00 2.29
970 1320 6.432190 AGAGGTGGGGGATATACATACATA 57.568 41.667 0.00 0.00 0.00 2.29
1293 1654 4.009675 TCTACGGTAAACACATACGTCCT 58.990 43.478 0.00 0.00 38.79 3.85
1301 1662 4.811969 AACACATACGTCCTCAACCATA 57.188 40.909 0.00 0.00 0.00 2.74
1361 1742 3.209410 CACACTCTGCTTCTTCCTTTGT 58.791 45.455 0.00 0.00 0.00 2.83
1399 1784 6.469275 CCAACGACAAACTCTTTTTCTTCTTC 59.531 38.462 0.00 0.00 0.00 2.87
1400 1785 6.986904 ACGACAAACTCTTTTTCTTCTTCT 57.013 33.333 0.00 0.00 0.00 2.85
1471 1859 8.925161 AACAAAATTCAGAACGAAAATCAAGA 57.075 26.923 0.00 0.00 37.12 3.02
1517 1905 3.270027 CAGAGAGAAGAGAGAAGAGCGA 58.730 50.000 0.00 0.00 0.00 4.93
1726 2120 0.541863 CACGGGTCTATTCCCTGCTT 59.458 55.000 0.25 0.00 44.95 3.91
1995 2719 2.421424 CTGTAACTCATCTTGCTTGGGC 59.579 50.000 0.00 0.00 39.26 5.36
2021 2745 3.741344 AGTTTTGCAGCTTAGTAGTCGTG 59.259 43.478 0.00 0.00 0.00 4.35
2057 2781 6.518369 GCCACCTTGCTGTATGTATGTATCTA 60.518 42.308 0.00 0.00 0.00 1.98
2058 2782 7.615403 CCACCTTGCTGTATGTATGTATCTAT 58.385 38.462 0.00 0.00 0.00 1.98
2059 2783 7.547019 CCACCTTGCTGTATGTATGTATCTATG 59.453 40.741 0.00 0.00 0.00 2.23
2060 2784 8.090831 CACCTTGCTGTATGTATGTATCTATGT 58.909 37.037 0.00 0.00 0.00 2.29
2061 2785 9.309224 ACCTTGCTGTATGTATGTATCTATGTA 57.691 33.333 0.00 0.00 0.00 2.29
2083 2807 7.192913 TGTATTTATGCCTGCATTTTTCTACG 58.807 34.615 10.27 0.00 37.82 3.51
2086 2810 6.935741 TTATGCCTGCATTTTTCTACGTAT 57.064 33.333 10.27 0.00 37.82 3.06
2091 2815 6.136071 GCCTGCATTTTTCTACGTATATGTG 58.864 40.000 7.89 0.00 0.00 3.21
2167 2911 5.620429 GCATTGGCATTTTTGCAGCTTAATT 60.620 36.000 0.00 0.00 40.72 1.40
2168 2912 6.403418 GCATTGGCATTTTTGCAGCTTAATTA 60.403 34.615 0.00 0.00 40.72 1.40
2169 2913 6.724694 TTGGCATTTTTGCAGCTTAATTAG 57.275 33.333 0.00 0.00 36.33 1.73
2319 3077 3.397482 CTCGTCAATCATTGATCCCCTC 58.603 50.000 2.67 0.00 42.47 4.30
3518 4348 2.045926 CAAACCAGCCTCCTCCCG 60.046 66.667 0.00 0.00 0.00 5.14
3882 4754 1.750399 GCTCACGGTGGCCATCATT 60.750 57.895 18.15 0.00 0.00 2.57
3930 4802 4.729856 AAGTACGTCCACGCGCCC 62.730 66.667 5.73 0.00 44.43 6.13
4008 4880 0.531532 CATCATCCCAGACGCCAGAC 60.532 60.000 0.00 0.00 0.00 3.51
4010 4882 3.461773 ATCCCAGACGCCAGACCG 61.462 66.667 0.00 0.00 0.00 4.79
4139 5011 0.947244 GCTTTGTCATATCCAGGGCG 59.053 55.000 0.00 0.00 0.00 6.13
4393 5269 5.062558 GGAAGATTGCAAATTGTACACATGC 59.937 40.000 16.04 16.04 37.52 4.06
4419 5295 3.177997 TCCTTTTGTTCTTTGGCAAGC 57.822 42.857 0.00 0.00 0.00 4.01
4737 5685 9.434420 GAAGGGTAGAAGATAGATTTGATCATG 57.566 37.037 0.00 0.00 0.00 3.07
4751 5705 4.370094 TGATCATGGCATAGCAATGGTA 57.630 40.909 0.00 0.00 40.15 3.25
4772 5726 4.447989 TGCGCCTGCTCTGCTCTC 62.448 66.667 4.18 0.00 43.34 3.20
4842 5796 0.102120 AACAACGCAACACACATGGG 59.898 50.000 0.00 0.00 36.84 4.00
4843 5797 0.749818 ACAACGCAACACACATGGGA 60.750 50.000 0.00 0.00 35.02 4.37
4844 5798 0.317770 CAACGCAACACACATGGGAC 60.318 55.000 0.00 0.00 35.02 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 99 2.143122 CAGTCAGGTTGTTATGTGCGT 58.857 47.619 0.00 0.00 0.00 5.24
130 135 4.694233 CTGCTCCGCACTGTGCCT 62.694 66.667 25.61 0.00 41.12 4.75
188 193 5.111989 GCTCACTCATTCATGTTGCTAGTA 58.888 41.667 0.00 0.00 0.00 1.82
190 195 3.001026 CGCTCACTCATTCATGTTGCTAG 59.999 47.826 0.00 0.00 0.00 3.42
282 565 0.401105 CCCTCCCCTCAGATGGACAT 60.401 60.000 0.00 0.00 0.00 3.06
283 566 1.003442 CCCTCCCCTCAGATGGACA 59.997 63.158 0.00 0.00 0.00 4.02
284 567 1.003573 ACCCTCCCCTCAGATGGAC 59.996 63.158 0.00 0.00 0.00 4.02
285 568 1.003442 CACCCTCCCCTCAGATGGA 59.997 63.158 0.00 0.00 0.00 3.41
287 570 1.692042 AGCACCCTCCCCTCAGATG 60.692 63.158 0.00 0.00 0.00 2.90
288 571 1.692042 CAGCACCCTCCCCTCAGAT 60.692 63.158 0.00 0.00 0.00 2.90
289 572 2.284921 CAGCACCCTCCCCTCAGA 60.285 66.667 0.00 0.00 0.00 3.27
290 573 2.284921 TCAGCACCCTCCCCTCAG 60.285 66.667 0.00 0.00 0.00 3.35
291 574 2.284921 CTCAGCACCCTCCCCTCA 60.285 66.667 0.00 0.00 0.00 3.86
465 760 4.712829 TCTCTCTCGACCTTTCTCTCTCTA 59.287 45.833 0.00 0.00 0.00 2.43
466 761 3.517901 TCTCTCTCGACCTTTCTCTCTCT 59.482 47.826 0.00 0.00 0.00 3.10
495 792 2.969300 TTCGTTTTGGCCCGCCTTCT 62.969 55.000 7.35 0.00 36.94 2.85
497 794 2.082629 CTTTCGTTTTGGCCCGCCTT 62.083 55.000 7.35 0.00 36.94 4.35
498 795 2.519780 TTTCGTTTTGGCCCGCCT 60.520 55.556 7.35 0.00 36.94 5.52
499 796 2.049526 CTTTCGTTTTGGCCCGCC 60.050 61.111 0.00 0.00 0.00 6.13
501 798 0.948678 TTCTCTTTCGTTTTGGCCCG 59.051 50.000 0.00 0.00 0.00 6.13
736 1055 3.447586 ACCAGCATGTGTGTAGTAGTAGG 59.552 47.826 0.00 0.00 0.00 3.18
858 1187 1.750778 GCAGAGGAGAGAGGAACAGAG 59.249 57.143 0.00 0.00 0.00 3.35
859 1188 1.357420 AGCAGAGGAGAGAGGAACAGA 59.643 52.381 0.00 0.00 0.00 3.41
860 1189 1.851304 AGCAGAGGAGAGAGGAACAG 58.149 55.000 0.00 0.00 0.00 3.16
886 1215 3.580731 CGTCCTCAGAGAAGAAGAAACC 58.419 50.000 0.00 0.00 0.00 3.27
952 1293 9.967559 ATTCTATGTATGTATGTATATCCCCCA 57.032 33.333 0.00 0.00 0.00 4.96
967 1317 4.060900 AGCACCGCTCAATTCTATGTATG 58.939 43.478 0.00 0.00 30.62 2.39
968 1318 4.060900 CAGCACCGCTCAATTCTATGTAT 58.939 43.478 0.00 0.00 36.40 2.29
969 1319 3.118775 ACAGCACCGCTCAATTCTATGTA 60.119 43.478 0.00 0.00 36.40 2.29
970 1320 2.283298 CAGCACCGCTCAATTCTATGT 58.717 47.619 0.00 0.00 36.40 2.29
1361 1742 2.151202 GTCGTTGGGAGATCAAGCAAA 58.849 47.619 0.00 0.00 0.00 3.68
1399 1784 7.605449 TCATCAGATTAAAAGGAGGCAAAAAG 58.395 34.615 0.00 0.00 0.00 2.27
1400 1785 7.537596 TCATCAGATTAAAAGGAGGCAAAAA 57.462 32.000 0.00 0.00 0.00 1.94
1405 1790 6.949352 TCATTCATCAGATTAAAAGGAGGC 57.051 37.500 0.00 0.00 0.00 4.70
1471 1859 0.331278 TTTGCCACCGATCCCATTCT 59.669 50.000 0.00 0.00 0.00 2.40
1631 2024 1.672356 CCACTCCGACAAGCCAAGG 60.672 63.158 0.00 0.00 0.00 3.61
1696 2089 3.617143 GACCCGTGGCCACCTAACC 62.617 68.421 29.95 11.79 0.00 2.85
1995 2719 5.005779 CGACTACTAAGCTGCAAAACTATGG 59.994 44.000 1.02 0.00 0.00 2.74
2021 2745 0.890683 CAAGGTGGCAATCAGTTCCC 59.109 55.000 0.00 0.00 0.00 3.97
2057 2781 7.862372 CGTAGAAAAATGCAGGCATAAATACAT 59.138 33.333 7.26 0.00 35.31 2.29
2058 2782 7.148154 ACGTAGAAAAATGCAGGCATAAATACA 60.148 33.333 7.26 0.00 35.31 2.29
2059 2783 7.193595 ACGTAGAAAAATGCAGGCATAAATAC 58.806 34.615 7.26 6.19 35.31 1.89
2060 2784 7.328277 ACGTAGAAAAATGCAGGCATAAATA 57.672 32.000 7.26 0.00 35.31 1.40
2061 2785 6.207691 ACGTAGAAAAATGCAGGCATAAAT 57.792 33.333 7.26 0.00 35.31 1.40
2083 2807 4.079980 TGGCATGGGTACACACATATAC 57.920 45.455 0.00 0.00 38.04 1.47
2086 2810 2.929641 CATGGCATGGGTACACACATA 58.070 47.619 19.80 0.00 38.04 2.29
2091 2815 1.379710 TGGCATGGCATGGGTACAC 60.380 57.895 27.48 10.44 0.00 2.90
2167 2911 1.670811 GTTACTGGTACCGCTACGCTA 59.329 52.381 7.57 0.00 0.00 4.26
2168 2912 0.453390 GTTACTGGTACCGCTACGCT 59.547 55.000 7.57 0.00 0.00 5.07
2169 2913 0.526310 GGTTACTGGTACCGCTACGC 60.526 60.000 7.57 0.00 0.00 4.42
2170 2914 1.098050 AGGTTACTGGTACCGCTACG 58.902 55.000 7.57 0.00 40.69 3.51
2171 2915 2.884827 CAAGGTTACTGGTACCGCTAC 58.115 52.381 7.57 2.69 40.69 3.58
2261 3010 1.065636 CACATCAGCATCCACCAGACT 60.066 52.381 0.00 0.00 0.00 3.24
2319 3077 0.936297 GACAAGCAGGCAAGCAAACG 60.936 55.000 4.78 0.00 36.85 3.60
2461 3222 1.507174 GTAGCGGTCGAAGTGCTCT 59.493 57.895 10.19 0.00 40.06 4.09
2861 3622 4.435970 TCCTCGTAGCTCCGGCCA 62.436 66.667 2.24 0.00 39.73 5.36
3518 4348 1.000506 TCAGGTCACGCACTACTTTCC 59.999 52.381 0.00 0.00 0.00 3.13
3882 4754 1.585006 GAACTCGAACCGCTGGAGA 59.415 57.895 1.50 0.00 34.18 3.71
3930 4802 1.142748 GAGGAGCATCAGGACCGTG 59.857 63.158 0.00 0.00 36.25 4.94
4008 4880 4.392754 TCATCATCTTTTCACACATGACGG 59.607 41.667 0.00 0.00 33.38 4.79
4010 4882 6.906659 AGTTCATCATCTTTTCACACATGAC 58.093 36.000 0.00 0.00 33.38 3.06
4014 4886 6.057533 AGTGAGTTCATCATCTTTTCACACA 58.942 36.000 0.00 0.00 40.92 3.72
4015 4887 6.551385 AGTGAGTTCATCATCTTTTCACAC 57.449 37.500 4.77 0.00 40.92 3.82
4079 4951 0.608856 AGCACATGGTCATTTCGGCA 60.609 50.000 0.00 0.00 0.00 5.69
4139 5011 1.065564 AGCTTTGCTCCAGTGATCTCC 60.066 52.381 0.00 0.00 30.62 3.71
4163 5035 5.401531 TGTAGTCATTCTCTTGGTGGTAC 57.598 43.478 0.00 0.00 0.00 3.34
4165 5037 4.593206 TCTTGTAGTCATTCTCTTGGTGGT 59.407 41.667 0.00 0.00 0.00 4.16
4393 5269 3.809279 GCCAAAGAACAAAAGGAACATGG 59.191 43.478 0.00 0.00 0.00 3.66
4419 5295 1.299926 CTCCGTTTATCCCCTCGCG 60.300 63.158 0.00 0.00 0.00 5.87
4709 5657 5.844004 TCAAATCTATCTTCTACCCTTCGC 58.156 41.667 0.00 0.00 0.00 4.70
4737 5685 1.334869 GCACACTACCATTGCTATGCC 59.665 52.381 2.27 0.00 33.26 4.40
4923 5881 1.741327 TTATCGGCCGCTACAGTCCC 61.741 60.000 23.51 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.