Multiple sequence alignment - TraesCS6A01G023400

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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 TraesCS6A01G023400 chr6A 100.000 4501 0 0 1 4501 11682611 11678111 0.000000e+00 8312
1 TraesCS6A01G023400 chr6A 98.991 3172 30 2 1331 4501 11732792 11729622 0.000000e+00 5679
2 TraesCS6A01G023400 chr6A 97.935 920 17 2 2 919 11756740 11755821 0.000000e+00 1592
3 TraesCS6A01G023400 chr6A 83.738 1193 119 31 265 1431 11467397 11468540 0.000000e+00 1059
4 TraesCS6A01G023400 chr6A 99.762 420 1 0 914 1333 11747317 11746898 0.000000e+00 771
5 TraesCS6A01G023400 chr6A 75.422 1245 250 33 3175 4375 11007211 11005979 1.830000e-153 553
6 TraesCS6A01G023400 chr6A 76.907 931 176 24 2165 3068 10931946 10931028 4.050000e-135 492
7 TraesCS6A01G023400 chr6A 77.733 247 40 11 3537 3780 10930570 10930336 2.180000e-28 137
8 TraesCS6A01G023400 chr6D 84.256 2890 324 57 361 3157 10311549 10308698 0.000000e+00 2695
9 TraesCS6A01G023400 chr6D 82.832 2959 368 88 264 3157 9911983 9914866 0.000000e+00 2521
10 TraesCS6A01G023400 chr6D 80.484 1901 315 35 1207 3068 9852705 9850822 0.000000e+00 1404
11 TraesCS6A01G023400 chr6D 75.948 1239 241 35 3175 4368 9858704 9857478 6.490000e-163 584
12 TraesCS6A01G023400 chr6D 75.329 1293 256 52 3247 4498 9914953 9916223 3.040000e-156 562
13 TraesCS6A01G023400 chr6D 89.922 129 11 1 4373 4501 10307498 10307372 1.000000e-36 165
14 TraesCS6A01G023400 chr6D 77.642 246 42 9 3537 3780 9850359 9850125 2.180000e-28 137
15 TraesCS6A01G023400 chrUn 83.293 2041 251 54 286 2306 240890851 240892821 0.000000e+00 1797
16 TraesCS6A01G023400 chrUn 83.268 2044 252 55 289 2312 268933046 268931073 0.000000e+00 1797
17 TraesCS6A01G023400 chrUn 86.200 1558 134 40 265 1797 300672796 300674297 0.000000e+00 1611
18 TraesCS6A01G023400 chrUn 86.082 388 41 5 265 650 240889595 240889971 5.420000e-109 405
19 TraesCS6A01G023400 chrUn 86.082 388 41 5 265 650 268934305 268933929 5.420000e-109 405
20 TraesCS6A01G023400 chrUn 74.651 789 152 29 3185 3948 240893644 240894409 5.660000e-79 305
21 TraesCS6A01G023400 chrUn 74.651 789 152 29 3185 3948 268930256 268929491 5.660000e-79 305
22 TraesCS6A01G023400 chr6B 82.667 1852 279 27 1342 3157 18225431 18227276 0.000000e+00 1604
23 TraesCS6A01G023400 chr6B 80.702 1938 313 37 1185 3080 17729257 17727339 0.000000e+00 1450
24 TraesCS6A01G023400 chr6B 80.459 1919 317 35 1185 3068 18015433 18017328 0.000000e+00 1413
25 TraesCS6A01G023400 chr6B 79.396 1854 301 41 1342 3157 18812736 18814546 0.000000e+00 1232
26 TraesCS6A01G023400 chr6B 78.831 1899 348 27 1297 3157 18266420 18268302 0.000000e+00 1230
27 TraesCS6A01G023400 chr6B 77.343 1227 222 39 3176 4369 18268288 18269491 0.000000e+00 675
28 TraesCS6A01G023400 chr6B 75.481 1248 244 35 3175 4375 18000583 18001815 1.830000e-153 553
29 TraesCS6A01G023400 chr6B 75.600 1209 234 35 3185 4364 18166871 18168047 3.960000e-150 542
30 TraesCS6A01G023400 chr6B 75.221 1247 249 33 3175 4375 17762641 17761409 1.840000e-148 536
31 TraesCS6A01G023400 chr6B 82.098 553 65 14 3979 4501 18816949 18817497 4.130000e-120 442
32 TraesCS6A01G023400 chr6B 76.634 826 108 39 337 1131 18014454 18015225 1.180000e-100 377
33 TraesCS6A01G023400 chr6B 83.249 394 60 5 3979 4367 18431739 18432131 1.540000e-94 357
34 TraesCS6A01G023400 chr6B 76.735 735 98 34 416 1131 17730145 17729465 4.310000e-90 342
35 TraesCS6A01G023400 chr6B 79.015 467 88 8 3895 4359 18018137 18018595 1.220000e-80 311
36 TraesCS6A01G023400 chr6B 79.093 397 37 27 859 1244 18812321 18812682 9.740000e-57 231
37 TraesCS6A01G023400 chr6B 80.851 235 41 3 3539 3771 18431284 18431516 9.950000e-42 182
38 TraesCS6A01G023400 chr2A 95.745 282 9 3 1 279 776470833 776471114 6.870000e-123 451
39 TraesCS6A01G023400 chr2A 96.029 277 9 2 1 275 565291593 565291317 2.470000e-122 449
40 TraesCS6A01G023400 chr1A 96.029 277 9 2 1 275 10527960 10527684 2.470000e-122 449
41 TraesCS6A01G023400 chr7A 96.014 276 9 2 1 274 715080562 715080837 8.880000e-122 448
42 TraesCS6A01G023400 chr7A 96.000 275 9 2 1 273 74112308 74112582 3.190000e-121 446
43 TraesCS6A01G023400 chr7A 95.683 278 10 2 1 276 681910934 681911211 3.190000e-121 446
44 TraesCS6A01G023400 chr5A 95.699 279 10 2 1 277 560799355 560799077 8.880000e-122 448
45 TraesCS6A01G023400 chr5A 95.406 283 10 3 1 280 665657546 665657264 8.880000e-122 448


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 TraesCS6A01G023400 chr6A 11678111 11682611 4500 True 8312.000000 8312 100.000000 1 4501 1 chr6A.!!$R2 4500
1 TraesCS6A01G023400 chr6A 11729622 11732792 3170 True 5679.000000 5679 98.991000 1331 4501 1 chr6A.!!$R3 3170
2 TraesCS6A01G023400 chr6A 11755821 11756740 919 True 1592.000000 1592 97.935000 2 919 1 chr6A.!!$R5 917
3 TraesCS6A01G023400 chr6A 11467397 11468540 1143 False 1059.000000 1059 83.738000 265 1431 1 chr6A.!!$F1 1166
4 TraesCS6A01G023400 chr6A 11005979 11007211 1232 True 553.000000 553 75.422000 3175 4375 1 chr6A.!!$R1 1200
5 TraesCS6A01G023400 chr6A 10930336 10931946 1610 True 314.500000 492 77.320000 2165 3780 2 chr6A.!!$R6 1615
6 TraesCS6A01G023400 chr6D 9911983 9916223 4240 False 1541.500000 2521 79.080500 264 4498 2 chr6D.!!$F1 4234
7 TraesCS6A01G023400 chr6D 10307372 10311549 4177 True 1430.000000 2695 87.089000 361 4501 2 chr6D.!!$R3 4140
8 TraesCS6A01G023400 chr6D 9850125 9852705 2580 True 770.500000 1404 79.063000 1207 3780 2 chr6D.!!$R2 2573
9 TraesCS6A01G023400 chr6D 9857478 9858704 1226 True 584.000000 584 75.948000 3175 4368 1 chr6D.!!$R1 1193
10 TraesCS6A01G023400 chrUn 300672796 300674297 1501 False 1611.000000 1611 86.200000 265 1797 1 chrUn.!!$F1 1532
11 TraesCS6A01G023400 chrUn 240889595 240894409 4814 False 835.666667 1797 81.342000 265 3948 3 chrUn.!!$F2 3683
12 TraesCS6A01G023400 chrUn 268929491 268934305 4814 True 835.666667 1797 81.333667 265 3948 3 chrUn.!!$R1 3683
13 TraesCS6A01G023400 chr6B 18225431 18227276 1845 False 1604.000000 1604 82.667000 1342 3157 1 chr6B.!!$F3 1815
14 TraesCS6A01G023400 chr6B 18266420 18269491 3071 False 952.500000 1230 78.087000 1297 4369 2 chr6B.!!$F5 3072
15 TraesCS6A01G023400 chr6B 17727339 17730145 2806 True 896.000000 1450 78.718500 416 3080 2 chr6B.!!$R2 2664
16 TraesCS6A01G023400 chr6B 18014454 18018595 4141 False 700.333333 1413 78.702667 337 4359 3 chr6B.!!$F4 4022
17 TraesCS6A01G023400 chr6B 18812321 18817497 5176 False 635.000000 1232 80.195667 859 4501 3 chr6B.!!$F7 3642
18 TraesCS6A01G023400 chr6B 18000583 18001815 1232 False 553.000000 553 75.481000 3175 4375 1 chr6B.!!$F1 1200
19 TraesCS6A01G023400 chr6B 18166871 18168047 1176 False 542.000000 542 75.600000 3185 4364 1 chr6B.!!$F2 1179
20 TraesCS6A01G023400 chr6B 17761409 17762641 1232 True 536.000000 536 75.221000 3175 4375 1 chr6B.!!$R1 1200
21 TraesCS6A01G023400 chr6B 18431284 18432131 847 False 269.500000 357 82.050000 3539 4367 2 chr6B.!!$F6 828

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
172 174 0.391597 ACCGGTACTAATGATGCCCG 59.608 55.000 4.49 0.0 35.32 6.13 F
886 2208 2.028020 GGAAGTCCGGAACTGATCAACT 60.028 50.000 5.23 0.0 38.58 3.16 F
980 2302 2.039216 TCATCTAGAGGCTAGAGACCGG 59.961 54.545 0.00 0.0 0.00 5.28 F
2233 3775 3.573538 CCATTCTTGAACATTGACACCCA 59.426 43.478 0.00 0.0 0.00 4.51 F
2774 4346 0.753262 AGTCCACGTGCTTCTTCAGT 59.247 50.000 10.91 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 3775 5.765677 CCTGCTGATTCATCATTCTTGAGAT 59.234 40.000 0.00 0.00 36.02 2.75 R
2773 4345 1.067565 TCTCCGAGAGCATGTTGTCAC 60.068 52.381 7.46 0.00 0.00 3.67 R
2774 4346 1.256812 TCTCCGAGAGCATGTTGTCA 58.743 50.000 7.46 0.00 0.00 3.58 R
3068 4673 0.894141 GTGCCCATACAATTGTGCCA 59.106 50.000 21.42 1.21 0.00 4.92 R
3962 7317 5.940617 TCTAGGGTAATCAAATGGGTCATG 58.059 41.667 0.00 0.00 0.00 3.07 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
95 97 2.513204 CCAGCCTGATCACAGCCG 60.513 66.667 8.95 0.21 42.25 5.52
115 117 1.475213 GCACTGGCCTCATTAGTACCC 60.475 57.143 3.32 0.00 0.00 3.69
121 123 1.135721 GCCTCATTAGTACCCGTTCGT 59.864 52.381 0.00 0.00 0.00 3.85
135 137 1.228003 TTCGTGGCATGAACCGGTT 60.228 52.632 22.50 22.50 0.00 4.44
172 174 0.391597 ACCGGTACTAATGATGCCCG 59.608 55.000 4.49 0.00 35.32 6.13
224 227 3.684788 GTCACATTAGTGCCGACTCAAAT 59.315 43.478 2.28 0.00 45.49 2.32
241 244 4.804108 TCAAATTCAAACCGGCACTAATG 58.196 39.130 0.00 0.00 0.00 1.90
886 2208 2.028020 GGAAGTCCGGAACTGATCAACT 60.028 50.000 5.23 0.00 38.58 3.16
888 2210 3.870633 AGTCCGGAACTGATCAACTAC 57.129 47.619 5.23 0.00 36.65 2.73
891 2213 2.496070 TCCGGAACTGATCAACTACTGG 59.504 50.000 0.00 3.87 0.00 4.00
892 2214 2.233922 CCGGAACTGATCAACTACTGGT 59.766 50.000 0.00 0.00 0.00 4.00
893 2215 3.512680 CGGAACTGATCAACTACTGGTC 58.487 50.000 0.00 0.00 35.51 4.02
894 2216 3.056821 CGGAACTGATCAACTACTGGTCA 60.057 47.826 0.00 0.00 43.18 4.02
895 2217 4.560716 CGGAACTGATCAACTACTGGTCAA 60.561 45.833 0.00 0.00 44.74 3.18
896 2218 4.691216 GGAACTGATCAACTACTGGTCAAC 59.309 45.833 0.00 0.00 44.74 3.18
897 2219 4.955811 ACTGATCAACTACTGGTCAACA 57.044 40.909 0.00 0.00 44.74 3.33
898 2220 5.489792 ACTGATCAACTACTGGTCAACAT 57.510 39.130 0.00 0.00 44.74 2.71
899 2221 6.605471 ACTGATCAACTACTGGTCAACATA 57.395 37.500 0.00 0.00 44.74 2.29
900 2222 7.187824 ACTGATCAACTACTGGTCAACATAT 57.812 36.000 0.00 0.00 44.74 1.78
901 2223 7.624549 ACTGATCAACTACTGGTCAACATATT 58.375 34.615 0.00 0.00 44.74 1.28
902 2224 8.758829 ACTGATCAACTACTGGTCAACATATTA 58.241 33.333 0.00 0.00 44.74 0.98
903 2225 9.254133 CTGATCAACTACTGGTCAACATATTAG 57.746 37.037 0.00 0.00 44.74 1.73
904 2226 8.758829 TGATCAACTACTGGTCAACATATTAGT 58.241 33.333 0.00 0.00 42.42 2.24
980 2302 2.039216 TCATCTAGAGGCTAGAGACCGG 59.961 54.545 0.00 0.00 0.00 5.28
1046 2375 7.086376 CACTTACAAATCACCTTTCATTCCAG 58.914 38.462 0.00 0.00 0.00 3.86
1269 2784 5.221925 CCAATACATGGGTCACCTTATAGCT 60.222 44.000 0.00 0.00 46.27 3.32
2233 3775 3.573538 CCATTCTTGAACATTGACACCCA 59.426 43.478 0.00 0.00 0.00 4.51
2773 4345 1.871080 AAGTCCACGTGCTTCTTCAG 58.129 50.000 10.91 0.00 0.00 3.02
2774 4346 0.753262 AGTCCACGTGCTTCTTCAGT 59.247 50.000 10.91 0.00 0.00 3.41
2775 4347 0.861837 GTCCACGTGCTTCTTCAGTG 59.138 55.000 10.91 0.00 0.00 3.66
2820 4395 8.253113 TGGAAAATATGGAGCTTCTTGATTTTC 58.747 33.333 20.32 20.32 39.43 2.29
2983 4585 2.680352 GGAGCTGGACCTGTCGGA 60.680 66.667 0.00 0.00 0.00 4.55
3500 5178 6.712095 GCCCAGTTGAAGTGATGATTATATGA 59.288 38.462 0.68 0.00 0.00 2.15
3567 5272 2.592102 AAAGGTGATCATGCACAGGT 57.408 45.000 0.00 0.00 40.52 4.00
4011 7399 0.530870 GTGGTGCGGAGATCTTAGGC 60.531 60.000 0.00 1.48 0.00 3.93
4422 7869 7.377766 TGTGCTGAACCAAATTATTACTCTC 57.622 36.000 0.00 0.00 0.00 3.20
4427 7874 9.346725 GCTGAACCAAATTATTACTCTCTTTTG 57.653 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.745232 TTCATGGCATGAACCGGTAC 58.255 50.000 33.06 0.00 43.84 3.34
95 97 1.475213 GGGTACTAATGAGGCCAGTGC 60.475 57.143 5.01 2.10 0.00 4.40
115 117 2.474266 CGGTTCATGCCACGAACG 59.526 61.111 0.00 0.00 43.00 3.95
121 123 2.432444 CTTTAGAACCGGTTCATGCCA 58.568 47.619 40.66 22.33 41.84 4.92
172 174 4.770874 TTCCAACGGCTAGGCGGC 62.771 66.667 37.39 0.00 32.02 6.53
183 186 0.808755 CCATTAGTGCCGGTTCCAAC 59.191 55.000 1.90 0.00 0.00 3.77
241 244 4.211164 GCAAAAGGGTTAAATGTGAAGCAC 59.789 41.667 0.00 0.00 34.56 4.40
248 251 7.002276 ACACTAGTAGCAAAAGGGTTAAATGT 58.998 34.615 0.00 0.00 0.00 2.71
259 262 7.175816 TGAATTGCCATTACACTAGTAGCAAAA 59.824 33.333 13.15 0.00 40.22 2.44
901 2223 8.690884 GCTCTTCAGCAATCTCCATATATACTA 58.309 37.037 0.00 0.00 46.06 1.82
902 2224 7.555087 GCTCTTCAGCAATCTCCATATATACT 58.445 38.462 0.00 0.00 46.06 2.12
903 2225 7.769272 GCTCTTCAGCAATCTCCATATATAC 57.231 40.000 0.00 0.00 46.06 1.47
980 2302 2.564771 TGATGAATTGATCGGGTCTGC 58.435 47.619 0.30 0.00 0.00 4.26
2233 3775 5.765677 CCTGCTGATTCATCATTCTTGAGAT 59.234 40.000 0.00 0.00 36.02 2.75
2773 4345 1.067565 TCTCCGAGAGCATGTTGTCAC 60.068 52.381 7.46 0.00 0.00 3.67
2774 4346 1.256812 TCTCCGAGAGCATGTTGTCA 58.743 50.000 7.46 0.00 0.00 3.58
2775 4347 2.200067 CATCTCCGAGAGCATGTTGTC 58.800 52.381 4.07 0.00 0.00 3.18
2820 4395 2.401583 TGTCTGATGATGTTTCCCGG 57.598 50.000 0.00 0.00 0.00 5.73
2920 4516 7.815840 TTCATGTACAAGTTCTTCAATTCCA 57.184 32.000 0.00 0.00 0.00 3.53
2983 4585 6.357367 AGGTCAAGAGTTTTCACACTTGTAT 58.643 36.000 10.91 0.00 46.29 2.29
3068 4673 0.894141 GTGCCCATACAATTGTGCCA 59.106 50.000 21.42 1.21 0.00 4.92
3163 4780 5.164158 GCTGATGTTAATGTTGTTCGCAAAG 60.164 40.000 0.00 0.00 39.04 2.77
3500 5178 3.450904 TGTAACTATCTTGGGGCACTCT 58.549 45.455 0.00 0.00 0.00 3.24
3567 5272 3.904717 TCTCCAAAAGTTTGTTGCCCTA 58.095 40.909 3.26 0.00 36.45 3.53
3962 7317 5.940617 TCTAGGGTAATCAAATGGGTCATG 58.059 41.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.