Multiple sequence alignment - TraesCS7A01G216900

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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 TraesCS7A01G216900 chr7A 100.000 4580 0 0 1 4580 183645215 183640636 0.000000e+00 8458
1 TraesCS7A01G216900 chr7A 76.212 1547 273 58 691 2164 183483716 183482192 0.000000e+00 730
2 TraesCS7A01G216900 chr7A 83.386 638 98 7 1180 1816 183655920 183655290 6.600000e-163 584
3 TraesCS7A01G216900 chr7A 77.164 1086 190 41 746 1816 182857273 182856231 3.070000e-161 579
4 TraesCS7A01G216900 chr7A 81.649 643 103 11 1177 1816 183308912 183308282 1.890000e-143 520
5 TraesCS7A01G216900 chr7A 81.620 321 57 2 3979 4298 183480399 183480080 9.770000e-67 265
6 TraesCS7A01G216900 chr7A 81.757 296 47 5 3539 3832 183480878 183480588 1.650000e-59 241
7 TraesCS7A01G216900 chr7A 80.656 305 54 3 3979 4282 183652960 183652660 9.910000e-57 231
8 TraesCS7A01G216900 chr7A 80.198 303 53 5 3540 3840 183653438 183653141 2.150000e-53 220
9 TraesCS7A01G216900 chr7A 79.421 311 57 5 3540 3848 183306340 183306035 3.590000e-51 213
10 TraesCS7A01G216900 chr7A 77.879 330 70 2 1718 2047 182720937 182720611 7.770000e-48 202
11 TraesCS7A01G216900 chr7D 96.725 3542 98 5 1 3542 178992989 178989466 0.000000e+00 5882
12 TraesCS7A01G216900 chr7D 97.508 602 15 0 3979 4580 178988871 178988270 0.000000e+00 1029
13 TraesCS7A01G216900 chr7D 96.854 445 14 0 3539 3983 178989356 178988912 0.000000e+00 745
14 TraesCS7A01G216900 chr7D 78.418 1024 173 29 1177 2164 178940646 178939635 1.400000e-174 623
15 TraesCS7A01G216900 chr7D 82.445 638 104 7 1180 1816 179123521 179122891 6.700000e-153 551
16 TraesCS7A01G216900 chr7D 82.243 642 100 12 1177 1816 178861840 178861211 4.030000e-150 542
17 TraesCS7A01G216900 chr7D 82.951 305 50 2 3979 4282 178937842 178937539 1.620000e-69 274
18 TraesCS7A01G216900 chr7D 81.419 296 48 5 3539 3832 178938321 178938031 7.660000e-58 235
19 TraesCS7A01G216900 chr7D 80.064 311 55 5 3540 3848 178859363 178859058 1.660000e-54 224
20 TraesCS7A01G216900 chr7B 95.018 3553 144 13 1 3542 145031592 145028062 0.000000e+00 5550
21 TraesCS7A01G216900 chr7B 92.053 604 46 2 3979 4580 145027467 145026864 0.000000e+00 848
22 TraesCS7A01G216900 chr7B 76.611 1552 275 52 682 2164 144813871 144812339 0.000000e+00 774
23 TraesCS7A01G216900 chr7B 94.104 441 26 0 3539 3979 145027952 145027512 0.000000e+00 671
24 TraesCS7A01G216900 chr7B 82.602 638 103 7 1180 1816 145055154 145054524 1.440000e-154 556
25 TraesCS7A01G216900 chr7B 82.680 306 49 4 3979 4282 144733519 144733216 7.550000e-68 268
26 TraesCS7A01G216900 chr7B 81.633 294 47 5 3540 3831 144811024 144810736 2.130000e-58 237
27 TraesCS7A01G216900 chr7B 80.592 304 52 5 3539 3840 145052649 145052351 1.280000e-55 228
28 TraesCS7A01G216900 chr7B 76.970 330 73 2 1718 2047 144707278 144706952 7.820000e-43 185


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 TraesCS7A01G216900 chr7A 183640636 183645215 4579 True 8458.000000 8458 100.000000 1 4580 1 chr7A.!!$R3 4579
1 TraesCS7A01G216900 chr7A 182856231 182857273 1042 True 579.000000 579 77.164000 746 1816 1 chr7A.!!$R2 1070
2 TraesCS7A01G216900 chr7A 183480080 183483716 3636 True 412.000000 730 79.863000 691 4298 3 chr7A.!!$R5 3607
3 TraesCS7A01G216900 chr7A 183306035 183308912 2877 True 366.500000 520 80.535000 1177 3848 2 chr7A.!!$R4 2671
4 TraesCS7A01G216900 chr7A 183652660 183655920 3260 True 345.000000 584 81.413333 1180 4282 3 chr7A.!!$R6 3102
5 TraesCS7A01G216900 chr7D 178988270 178992989 4719 True 2552.000000 5882 97.029000 1 4580 3 chr7D.!!$R4 4579
6 TraesCS7A01G216900 chr7D 179122891 179123521 630 True 551.000000 551 82.445000 1180 1816 1 chr7D.!!$R1 636
7 TraesCS7A01G216900 chr7D 178859058 178861840 2782 True 383.000000 542 81.153500 1177 3848 2 chr7D.!!$R2 2671
8 TraesCS7A01G216900 chr7D 178937539 178940646 3107 True 377.333333 623 80.929333 1177 4282 3 chr7D.!!$R3 3105
9 TraesCS7A01G216900 chr7B 145026864 145031592 4728 True 2356.333333 5550 93.725000 1 4580 3 chr7B.!!$R4 4579
10 TraesCS7A01G216900 chr7B 144810736 144813871 3135 True 505.500000 774 79.122000 682 3831 2 chr7B.!!$R3 3149
11 TraesCS7A01G216900 chr7B 145052351 145055154 2803 True 392.000000 556 81.597000 1180 3840 2 chr7B.!!$R5 2660

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
322 324 1.468520 CCTTTGAAGCATACGGGTGTG 59.531 52.381 0.0 0.0 0.00 3.82 F
1050 1081 0.770499 TTGATCTGCCCAACACTGGA 59.230 50.000 0.0 0.0 46.92 3.86 F
2165 2242 2.298163 ACTGGCTGCAAAAGATCAAAGG 59.702 45.455 0.5 0.0 0.00 3.11 F
3016 3336 1.899814 TGAAGAAGTCCCGCACATACT 59.100 47.619 0.0 0.0 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1731 1.132643 CTCTGGATTGCTGCTTGCTTC 59.867 52.381 0.0 1.93 43.37 3.86 R
2421 2660 0.734889 CATTGACCGATGGTTGCTCC 59.265 55.000 0.0 0.00 35.25 4.70 R
3076 3396 1.211703 TGTTCTTGACCAGAAGCCACA 59.788 47.619 0.0 0.00 42.55 4.17 R
4144 4640 2.370189 ACCCTTCTTCCTCACAGACTTG 59.630 50.000 0.0 0.00 0.00 3.16 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
317 319 2.609459 CAGCTACCTTTGAAGCATACGG 59.391 50.000 0.00 0.00 41.32 4.02
322 324 1.468520 CCTTTGAAGCATACGGGTGTG 59.531 52.381 0.00 0.00 0.00 3.82
490 493 8.274322 ACATAGATGTATGACTTCCATTTCCAA 58.726 33.333 16.26 0.00 38.76 3.53
619 622 4.022849 CCTATGTAGGCTGCTTATTTTGGC 60.023 45.833 3.77 0.00 36.53 4.52
620 623 2.801483 TGTAGGCTGCTTATTTTGGCA 58.199 42.857 3.77 0.00 36.94 4.92
798 805 4.156008 ACGCAGTCTCTTTCTGTTGTTTTT 59.844 37.500 0.00 0.00 29.74 1.94
811 818 9.706691 TTTCTGTTGTTTTTGTTTGGTGTATAA 57.293 25.926 0.00 0.00 0.00 0.98
825 832 6.182507 TGGTGTATAAACCTCACAAAGTCT 57.817 37.500 13.44 0.00 41.16 3.24
983 990 4.322567 AGAGGTTGAGACTTGCAATCTTC 58.677 43.478 0.00 0.00 36.86 2.87
1050 1081 0.770499 TTGATCTGCCCAACACTGGA 59.230 50.000 0.00 0.00 46.92 3.86
1411 1455 6.763355 TCTCTTGTCTTAGTCATCTTGCTTT 58.237 36.000 0.00 0.00 0.00 3.51
1555 1599 7.675161 TCCATTTACATCTGGATTCTAGTCA 57.325 36.000 0.00 0.00 36.63 3.41
1626 1670 9.050154 AGGGTTATTCCAAAATCATTGAGAAAT 57.950 29.630 0.00 0.00 38.11 2.17
1639 1683 6.938507 TCATTGAGAAATAGGCTGCAAAAAT 58.061 32.000 0.50 0.00 0.00 1.82
2110 2187 3.365265 GGGTCTGCTTTGCGGTGG 61.365 66.667 0.00 0.00 36.18 4.61
2165 2242 2.298163 ACTGGCTGCAAAAGATCAAAGG 59.702 45.455 0.50 0.00 0.00 3.11
2181 2264 6.888632 AGATCAAAGGTCATAAGTGCTTCAAT 59.111 34.615 0.00 0.00 0.00 2.57
2214 2312 4.646572 GTCTCTTTTCACTGGAATCAGGT 58.353 43.478 0.00 0.00 44.99 4.00
2217 2315 6.710744 GTCTCTTTTCACTGGAATCAGGTAAA 59.289 38.462 0.00 0.00 44.99 2.01
2218 2316 7.228706 GTCTCTTTTCACTGGAATCAGGTAAAA 59.771 37.037 0.00 0.00 44.99 1.52
2219 2317 7.777910 TCTCTTTTCACTGGAATCAGGTAAAAA 59.222 33.333 0.00 0.00 44.99 1.94
2243 2341 7.951347 AAATATCAGGAAATTCTGAGCAAGT 57.049 32.000 3.55 0.00 45.60 3.16
2256 2354 2.751259 TGAGCAAGTTCATTCTCATGCC 59.249 45.455 0.00 0.00 34.44 4.40
2470 2709 7.415765 CGCAACCAGGAAATACCACAAATATTA 60.416 37.037 0.00 0.00 42.04 0.98
2473 2712 7.951591 ACCAGGAAATACCACAAATATTATGC 58.048 34.615 0.00 0.00 42.04 3.14
2474 2713 7.563188 ACCAGGAAATACCACAAATATTATGCA 59.437 33.333 0.00 0.00 42.04 3.96
2548 2787 2.564504 TCTGACACAGGACATCCTTCAG 59.435 50.000 17.04 17.04 46.09 3.02
2790 3056 5.277779 GGATGATTCGTCTGAACAAACAACA 60.278 40.000 5.88 0.00 36.81 3.33
2802 3068 9.234827 TCTGAACAAACAACATCAGATAATCAT 57.765 29.630 0.46 0.00 42.36 2.45
2806 3072 9.630098 AACAAACAACATCAGATAATCATTGTC 57.370 29.630 0.00 0.00 0.00 3.18
2939 3259 3.569701 GGCAATGTTGACAAGAAAGGAGA 59.430 43.478 0.00 0.00 35.83 3.71
3016 3336 1.899814 TGAAGAAGTCCCGCACATACT 59.100 47.619 0.00 0.00 0.00 2.12
3076 3396 2.428171 CAATCAGGTTTGAATCCGCCAT 59.572 45.455 0.00 0.00 36.78 4.40
3371 3691 0.468400 TTGTTGGTGGGCCTTGTACC 60.468 55.000 4.53 4.13 35.27 3.34
3476 3799 3.573598 TCTTATGCAAACATTTGTGGCG 58.426 40.909 6.24 0.00 40.24 5.69
3483 3806 1.452145 AACATTTGTGGCGCGAACCT 61.452 50.000 12.10 0.00 0.00 3.50
3495 3818 1.813859 CGAACCTCATCAGGCCGTA 59.186 57.895 0.00 0.00 45.05 4.02
3601 4052 7.812309 TGATGTGTTCTACTACTCAAATTCG 57.188 36.000 0.00 0.00 0.00 3.34
3604 4055 6.154445 TGTGTTCTACTACTCAAATTCGGTC 58.846 40.000 0.00 0.00 0.00 4.79
3637 4088 7.588123 GTGTCATCTGTAGTTATCACGATACTG 59.412 40.741 0.00 0.00 0.00 2.74
3766 4217 6.594788 TGCAGGAAAGCAAAAGAATCTAAT 57.405 33.333 0.00 0.00 42.46 1.73
3768 4219 7.444299 TGCAGGAAAGCAAAAGAATCTAATTT 58.556 30.769 0.00 0.00 42.46 1.82
3797 4248 1.150827 CATCGCTGTTGCAGTTCTGA 58.849 50.000 3.84 0.00 39.64 3.27
3942 4393 0.593128 GCTTCTGAGCGGCAAGAAAA 59.407 50.000 15.91 0.07 39.48 2.29
4144 4640 5.140177 GTCGTGATCATGTTTCTGTTGAAC 58.860 41.667 14.52 0.00 31.02 3.18
4201 4697 9.440773 GAGGTATTGCATTTGATCATGATACTA 57.559 33.333 8.54 0.00 0.00 1.82
4500 4996 7.432869 TGTATTATCTGCAAATAATTGGTGCC 58.567 34.615 10.44 0.00 37.48 5.01
4547 5045 9.807921 TTCCTAAAGTCCAGATTAACTTGAAAT 57.192 29.630 0.00 0.00 35.93 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 319 1.599542 GCTCAGACAAGTGAACACACC 59.400 52.381 7.68 0.00 35.39 4.16
322 324 1.876322 AGCTGCTCAGACAAGTGAAC 58.124 50.000 0.00 0.00 0.00 3.18
490 493 4.276431 GCAAGCGGAGAAGTAGTAGACTAT 59.724 45.833 0.00 0.00 37.44 2.12
649 652 5.118990 TCTCAAGAAAGAAGGTGTGAGTTG 58.881 41.667 0.00 0.00 35.20 3.16
798 805 6.603997 ACTTTGTGAGGTTTATACACCAAACA 59.396 34.615 10.65 10.43 39.62 2.83
811 818 3.970640 AGGAAGAGAGACTTTGTGAGGTT 59.029 43.478 0.00 0.00 39.13 3.50
825 832 4.929479 AGAAGACAGCTAGAAGGAAGAGA 58.071 43.478 0.00 0.00 0.00 3.10
983 990 1.931841 CCATGTGATTGCTCTCTGACG 59.068 52.381 0.00 0.00 0.00 4.35
1050 1081 5.204409 TGCTGCTTTCACTCAAATGATTT 57.796 34.783 0.00 0.00 0.00 2.17
1411 1455 4.224433 CGCTTCGTCACACTCTTACTTAA 58.776 43.478 0.00 0.00 0.00 1.85
1523 1567 5.684704 TCCAGATGTAAATGGATGACTTCC 58.315 41.667 0.30 0.30 40.70 3.46
1555 1599 6.336566 TCACAACATACACAAAAACAGCAAT 58.663 32.000 0.00 0.00 0.00 3.56
1626 1670 6.788598 TTATCCATCAATTTTTGCAGCCTA 57.211 33.333 0.00 0.00 0.00 3.93
1628 1672 6.740411 TTTTATCCATCAATTTTTGCAGCC 57.260 33.333 0.00 0.00 0.00 4.85
1687 1731 1.132643 CTCTGGATTGCTGCTTGCTTC 59.867 52.381 0.00 1.93 43.37 3.86
2110 2187 2.095466 TGTAAACAAATGCCGCAGCTAC 60.095 45.455 0.00 0.00 40.80 3.58
2142 2219 1.538047 TGATCTTTTGCAGCCAGTCC 58.462 50.000 0.00 0.00 0.00 3.85
2165 2242 8.986477 ACCAATTTTATTGAAGCACTTATGAC 57.014 30.769 1.11 0.00 0.00 3.06
2181 2264 6.017440 CCAGTGAAAAGAGACGACCAATTTTA 60.017 38.462 0.00 0.00 0.00 1.52
2217 2315 8.810041 ACTTGCTCAGAATTTCCTGATATTTTT 58.190 29.630 0.00 0.00 41.79 1.94
2218 2316 8.358582 ACTTGCTCAGAATTTCCTGATATTTT 57.641 30.769 0.00 0.00 41.79 1.82
2219 2317 7.951347 ACTTGCTCAGAATTTCCTGATATTT 57.049 32.000 0.00 0.00 41.79 1.40
2220 2318 7.613022 TGAACTTGCTCAGAATTTCCTGATATT 59.387 33.333 0.00 0.00 41.79 1.28
2221 2319 7.114754 TGAACTTGCTCAGAATTTCCTGATAT 58.885 34.615 0.00 0.00 41.79 1.63
2222 2320 6.475504 TGAACTTGCTCAGAATTTCCTGATA 58.524 36.000 0.00 0.00 41.79 2.15
2223 2321 5.319453 TGAACTTGCTCAGAATTTCCTGAT 58.681 37.500 0.00 0.00 41.79 2.90
2224 2322 4.717877 TGAACTTGCTCAGAATTTCCTGA 58.282 39.130 0.00 0.00 40.57 3.86
2225 2323 5.640189 ATGAACTTGCTCAGAATTTCCTG 57.360 39.130 0.00 0.00 35.55 3.86
2226 2324 6.008960 AGAATGAACTTGCTCAGAATTTCCT 58.991 36.000 0.00 0.00 0.00 3.36
2227 2325 6.072286 TGAGAATGAACTTGCTCAGAATTTCC 60.072 38.462 0.00 0.00 32.85 3.13
2228 2326 6.906659 TGAGAATGAACTTGCTCAGAATTTC 58.093 36.000 0.00 0.00 32.85 2.17
2229 2327 6.889301 TGAGAATGAACTTGCTCAGAATTT 57.111 33.333 0.00 0.00 32.85 1.82
2230 2328 6.625300 GCATGAGAATGAACTTGCTCAGAATT 60.625 38.462 0.00 0.00 40.34 2.17
2231 2329 5.163642 GCATGAGAATGAACTTGCTCAGAAT 60.164 40.000 0.00 0.00 40.34 2.40
2235 2333 2.751259 GGCATGAGAATGAACTTGCTCA 59.249 45.455 0.00 0.00 41.14 4.26
2243 2341 2.040145 TGACCAGTGGCATGAGAATGAA 59.960 45.455 9.78 0.00 0.00 2.57
2256 2354 3.775202 GTCTGTAGTATGCTGACCAGTG 58.225 50.000 0.00 0.00 42.21 3.66
2421 2660 0.734889 CATTGACCGATGGTTGCTCC 59.265 55.000 0.00 0.00 35.25 4.70
2470 2709 0.994247 TGATCCTCTGGGTTGTGCAT 59.006 50.000 0.00 0.00 0.00 3.96
2473 2712 1.349026 ACACTGATCCTCTGGGTTGTG 59.651 52.381 0.00 0.00 26.65 3.33
2474 2713 1.734655 ACACTGATCCTCTGGGTTGT 58.265 50.000 0.00 0.00 26.65 3.32
2515 2754 3.188492 CTGTGTCAGAGACTGCATCATC 58.812 50.000 0.00 0.00 32.44 2.92
2548 2787 1.885887 TGTAGCTTGGTGGCATTTGAC 59.114 47.619 0.00 0.00 34.17 3.18
2667 2906 7.592533 GGCATATAGTCAACAATATTTGCAGTG 59.407 37.037 8.96 0.00 37.79 3.66
2790 3056 5.944599 GGCTCCATGACAATGATTATCTGAT 59.055 40.000 0.00 0.00 35.67 2.90
2802 3068 1.303561 GCTGGTGGCTCCATGACAA 60.304 57.895 9.01 0.00 46.12 3.18
2806 3072 1.890979 GATCGCTGGTGGCTCCATG 60.891 63.158 9.01 5.27 46.12 3.66
2905 3222 2.749076 CAACATTGCCATTCTCGGAAGA 59.251 45.455 0.00 0.00 39.12 2.87
2939 3259 2.121948 TGCTGCTATCTTCAGTGGGAT 58.878 47.619 0.00 0.00 34.21 3.85
2985 3305 2.535331 GACTTCTTCAGATGCTCCGAC 58.465 52.381 0.00 0.00 0.00 4.79
3076 3396 1.211703 TGTTCTTGACCAGAAGCCACA 59.788 47.619 0.00 0.00 42.55 4.17
3146 3466 8.090831 TCAGATAGAAGAATGCAATATAACGCT 58.909 33.333 0.00 0.00 0.00 5.07
3371 3691 4.527509 AGATGGATACCGACATAAGCAG 57.472 45.455 0.00 0.00 0.00 4.24
3459 3782 1.283613 CGCGCCACAAATGTTTGCAT 61.284 50.000 0.00 0.00 41.79 3.96
3476 3799 2.292794 TACGGCCTGATGAGGTTCGC 62.293 60.000 13.72 0.00 42.15 4.70
3483 3806 1.626321 TGGTTTTCTACGGCCTGATGA 59.374 47.619 0.00 0.00 0.00 2.92
3495 3818 2.040412 GACATCCCCAGTCTGGTTTTCT 59.960 50.000 17.85 0.00 35.17 2.52
3721 4172 2.029623 CTTCCTGCAGCATAGGCAATT 58.970 47.619 8.66 0.00 44.61 2.32
3766 4217 4.437794 GCAACAGCGATGATGATGAGAAAA 60.438 41.667 15.55 0.00 0.00 2.29
3768 4219 2.610833 GCAACAGCGATGATGATGAGAA 59.389 45.455 15.55 0.00 0.00 2.87
3942 4393 7.881751 TCTTTTCTTTCTCATCATGACATGAGT 59.118 33.333 22.00 8.94 46.91 3.41
4144 4640 2.370189 ACCCTTCTTCCTCACAGACTTG 59.630 50.000 0.00 0.00 0.00 3.16
4201 4697 4.022068 GCTGTCATAAGAGCTAGCAGATCT 60.022 45.833 18.83 8.41 43.81 2.75
4500 4996 7.762382 AGGAAGAAAAACAAACTGACTACAAG 58.238 34.615 0.00 0.00 0.00 3.16
4547 5045 7.392953 TGTTCAGAAATATACAACAATGCCAGA 59.607 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.