Multiple sequence alignment - TraesCS1B01G481400

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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 TraesCS1B01G481400 chr1B 100.000 3457 0 0 1 3457 689686235 689682779 0.000000e+00 6384
1 TraesCS1B01G481400 chr1B 98.536 3143 29 5 327 3457 689809520 689806383 0.000000e+00 5533
2 TraesCS1B01G481400 chr1B 96.088 2326 33 10 857 3161 689491667 689489379 0.000000e+00 3738
3 TraesCS1B01G481400 chr1B 95.947 1974 55 13 857 2817 689556688 689554727 0.000000e+00 3179
4 TraesCS1B01G481400 chr1B 97.213 1579 25 5 857 2424 689505606 689504036 0.000000e+00 2654
5 TraesCS1B01G481400 chr1B 94.297 789 9 8 1 777 689557579 689556815 0.000000e+00 1175
6 TraesCS1B01G481400 chr1B 95.969 521 9 5 268 777 689492313 689491794 0.000000e+00 835
7 TraesCS1B01G481400 chr1B 95.777 521 10 2 268 777 689506252 689505733 0.000000e+00 830
8 TraesCS1B01G481400 chr1B 92.366 131 7 3 1 130 46961075 46961203 2.120000e-42 183
9 TraesCS1B01G481400 chr1B 81.651 218 13 8 1 217 41968749 41968558 4.620000e-34 156
10 TraesCS1B01G481400 chr1B 80.702 228 18 11 1 227 585820384 585820586 1.660000e-33 154
11 TraesCS1B01G481400 chrUn 95.824 1844 40 7 859 2690 306396761 306394943 0.000000e+00 2944
12 TraesCS1B01G481400 chrUn 96.082 1608 32 5 1221 2817 371634626 371636213 0.000000e+00 2591
13 TraesCS1B01G481400 chrUn 95.753 1554 47 12 1221 2771 391042968 391044505 0.000000e+00 2486
14 TraesCS1B01G481400 chrUn 94.175 1133 41 14 2337 3457 308753333 308754452 0.000000e+00 1703
15 TraesCS1B01G481400 chrUn 96.759 864 21 7 2300 3161 393512209 393511351 0.000000e+00 1434
16 TraesCS1B01G481400 chrUn 96.528 864 23 7 2300 3161 439928072 439928930 0.000000e+00 1423
17 TraesCS1B01G481400 chrUn 98.353 668 11 0 1113 1780 470694217 470694884 0.000000e+00 1173
18 TraesCS1B01G481400 chrUn 93.598 781 24 3 2047 2817 455436247 455435483 0.000000e+00 1142
19 TraesCS1B01G481400 chrUn 99.302 573 4 0 1108 1680 403564557 403565129 0.000000e+00 1037
20 TraesCS1B01G481400 chrUn 96.290 620 10 2 169 777 306397507 306396890 0.000000e+00 1005
21 TraesCS1B01G481400 chrUn 97.398 538 4 2 857 1384 440306996 440306459 0.000000e+00 907
22 TraesCS1B01G481400 chrUn 97.143 525 4 2 871 1384 339963085 339963609 0.000000e+00 876
23 TraesCS1B01G481400 chrUn 95.969 521 9 5 268 777 411718395 411718914 0.000000e+00 835
24 TraesCS1B01G481400 chrUn 94.238 538 4 3 857 1384 411719041 411719561 0.000000e+00 797
25 TraesCS1B01G481400 chrUn 94.444 522 16 3 268 777 457236917 457237437 0.000000e+00 791
26 TraesCS1B01G481400 chrUn 92.692 520 32 6 2300 2817 260327527 260328042 0.000000e+00 745
27 TraesCS1B01G481400 chrUn 94.919 433 10 2 356 777 440307554 440307123 0.000000e+00 667
28 TraesCS1B01G481400 chrUn 91.562 320 10 6 787 1096 457237558 457237870 3.190000e-115 425
29 TraesCS1B01G481400 chrUn 98.578 211 3 0 268 478 339962874 339963084 1.170000e-99 374
30 TraesCS1B01G481400 chrUn 99.451 182 1 0 212 393 339962759 339962940 7.150000e-87 331
31 TraesCS1B01G481400 chrUn 98.352 182 3 0 212 393 411718280 411718461 1.550000e-83 320
32 TraesCS1B01G481400 chrUn 99.275 138 1 0 212 349 403564421 403564558 2.060000e-62 250
33 TraesCS1B01G481400 chrUn 100.000 67 0 0 268 334 339962933 339962999 1.300000e-24 124
34 TraesCS1B01G481400 chrUn 98.507 67 1 0 327 393 339962815 339962881 6.060000e-23 119
35 TraesCS1B01G481400 chr3B 93.365 211 12 2 1 211 131834683 131834891 9.320000e-81 311
36 TraesCS1B01G481400 chr3B 89.573 211 20 2 1 211 65391614 65391406 2.050000e-67 267
37 TraesCS1B01G481400 chr7D 86.973 261 33 1 3198 3457 35013629 35013369 3.370000e-75 292
38 TraesCS1B01G481400 chr4B 92.500 200 11 3 1 197 2542349 2542547 2.030000e-72 283
39 TraesCS1B01G481400 chr7B 90.952 210 17 2 2 211 545395240 545395033 7.300000e-72 281
40 TraesCS1B01G481400 chr7B 90.610 213 17 3 1 211 503123557 503123346 2.630000e-71 279
41 TraesCS1B01G481400 chr7B 84.332 217 8 8 1 217 611535177 611534987 4.550000e-44 189
42 TraesCS1B01G481400 chr5B 90.610 213 18 2 1 212 618314803 618315014 7.300000e-72 281
43 TraesCS1B01G481400 chr5B 88.479 217 22 3 1 216 697707675 697707889 3.420000e-65 259
44 TraesCS1B01G481400 chr5B 93.103 174 7 3 1 174 702101532 702101364 2.060000e-62 250
45 TraesCS1B01G481400 chr3D 85.824 261 36 1 3198 3457 516643526 516643786 3.400000e-70 276
46 TraesCS1B01G481400 chr4A 90.047 211 18 2 1 211 647720924 647721131 1.580000e-68 270
47 TraesCS1B01G481400 chr6B 89.671 213 18 3 1 212 41295569 41295778 5.690000e-68 268
48 TraesCS1B01G481400 chr2B 82.222 225 14 8 1 223 650024676 650024476 1.650000e-38 171


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 TraesCS1B01G481400 chr1B 689682779 689686235 3456 True 6384.000000 6384 100.000000 1 3457 1 chr1B.!!$R2 3456
1 TraesCS1B01G481400 chr1B 689806383 689809520 3137 True 5533.000000 5533 98.536000 327 3457 1 chr1B.!!$R3 3130
2 TraesCS1B01G481400 chr1B 689489379 689492313 2934 True 2286.500000 3738 96.028500 268 3161 2 chr1B.!!$R4 2893
3 TraesCS1B01G481400 chr1B 689554727 689557579 2852 True 2177.000000 3179 95.122000 1 2817 2 chr1B.!!$R6 2816
4 TraesCS1B01G481400 chr1B 689504036 689506252 2216 True 1742.000000 2654 96.495000 268 2424 2 chr1B.!!$R5 2156
5 TraesCS1B01G481400 chrUn 371634626 371636213 1587 False 2591.000000 2591 96.082000 1221 2817 1 chrUn.!!$F3 1596
6 TraesCS1B01G481400 chrUn 391042968 391044505 1537 False 2486.000000 2486 95.753000 1221 2771 1 chrUn.!!$F4 1550
7 TraesCS1B01G481400 chrUn 306394943 306397507 2564 True 1974.500000 2944 96.057000 169 2690 2 chrUn.!!$R3 2521
8 TraesCS1B01G481400 chrUn 308753333 308754452 1119 False 1703.000000 1703 94.175000 2337 3457 1 chrUn.!!$F2 1120
9 TraesCS1B01G481400 chrUn 393511351 393512209 858 True 1434.000000 1434 96.759000 2300 3161 1 chrUn.!!$R1 861
10 TraesCS1B01G481400 chrUn 439928072 439928930 858 False 1423.000000 1423 96.528000 2300 3161 1 chrUn.!!$F5 861
11 TraesCS1B01G481400 chrUn 470694217 470694884 667 False 1173.000000 1173 98.353000 1113 1780 1 chrUn.!!$F6 667
12 TraesCS1B01G481400 chrUn 455435483 455436247 764 True 1142.000000 1142 93.598000 2047 2817 1 chrUn.!!$R2 770
13 TraesCS1B01G481400 chrUn 440306459 440307554 1095 True 787.000000 907 96.158500 356 1384 2 chrUn.!!$R4 1028
14 TraesCS1B01G481400 chrUn 260327527 260328042 515 False 745.000000 745 92.692000 2300 2817 1 chrUn.!!$F1 517
15 TraesCS1B01G481400 chrUn 411718280 411719561 1281 False 650.666667 835 96.186333 212 1384 3 chrUn.!!$F9 1172
16 TraesCS1B01G481400 chrUn 403564421 403565129 708 False 643.500000 1037 99.288500 212 1680 2 chrUn.!!$F8 1468
17 TraesCS1B01G481400 chrUn 457236917 457237870 953 False 608.000000 791 93.003000 268 1096 2 chrUn.!!$F10 828
18 TraesCS1B01G481400 chrUn 339962759 339963609 850 False 364.800000 876 98.735800 212 1384 5 chrUn.!!$F7 1172

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
685 816 1.202758 TGCACGGACTTCAGAACCATT 60.203 47.619 0.00 0.0 0.00 3.16 F
702 833 2.356125 CCATTGGTCCAAACGAGGATCT 60.356 50.000 8.75 0.0 39.63 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2464 2.038426 TCGGAGAAAATCAAGCTCCACA 59.962 45.455 0.0 0.0 46.74 4.17 R
3207 3497 1.838077 GTATTGACTACTGGTGGGGCT 59.162 52.381 0.0 0.0 0.00 5.19 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 3.449737 TGACAAACCGATACTAAGGAGGG 59.550 47.826 0.00 0.00 0.00 4.30
123 125 7.930332 GACCTTTAGTCCCCACTCTTTAGTGT 61.930 46.154 4.94 0.00 44.31 3.55
133 135 5.117355 CACTCTTTAGTGTCGGTTGTAGA 57.883 43.478 0.00 0.00 46.76 2.59
134 136 5.526115 CACTCTTTAGTGTCGGTTGTAGAA 58.474 41.667 0.00 0.00 46.76 2.10
135 137 5.401674 CACTCTTTAGTGTCGGTTGTAGAAC 59.598 44.000 0.00 0.00 46.76 3.01
136 138 5.508657 ACTCTTTAGTGTCGGTTGTAGAACC 60.509 44.000 11.77 11.77 40.61 3.62
144 146 2.460757 GGTTGTAGAACCGGCACTAA 57.539 50.000 5.96 0.00 42.47 2.24
145 147 2.769893 GGTTGTAGAACCGGCACTAAA 58.230 47.619 5.96 0.00 42.47 1.85
146 148 2.740447 GGTTGTAGAACCGGCACTAAAG 59.260 50.000 5.96 0.00 42.47 1.85
147 149 2.740447 GTTGTAGAACCGGCACTAAAGG 59.260 50.000 0.00 0.00 0.00 3.11
148 150 1.338389 TGTAGAACCGGCACTAAAGGC 60.338 52.381 0.00 0.00 0.00 4.35
685 816 1.202758 TGCACGGACTTCAGAACCATT 60.203 47.619 0.00 0.00 0.00 3.16
702 833 2.356125 CCATTGGTCCAAACGAGGATCT 60.356 50.000 8.75 0.00 39.63 2.75
2194 2464 0.608640 ATGGAGCGAGAGGAAAACGT 59.391 50.000 0.00 0.00 0.00 3.99
3207 3497 3.732212 CCATCTCTGCATTCGATAACCA 58.268 45.455 0.00 0.00 0.00 3.67
3314 3604 3.302344 GTTGCACACCGCCCCAAT 61.302 61.111 0.00 0.00 41.33 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 134 3.587095 GGCCTTTAGTGCCGGTTC 58.413 61.111 1.90 0.0 39.48 3.62
137 139 0.390209 TCGTAACGGCCTTTAGTGCC 60.390 55.000 1.13 0.0 45.70 5.01
138 140 1.127397 GTTCGTAACGGCCTTTAGTGC 59.873 52.381 1.13 0.0 0.00 4.40
139 141 1.728425 GGTTCGTAACGGCCTTTAGTG 59.272 52.381 1.13 0.0 0.00 2.74
140 142 1.669795 CGGTTCGTAACGGCCTTTAGT 60.670 52.381 1.13 0.0 0.00 2.24
141 143 0.994263 CGGTTCGTAACGGCCTTTAG 59.006 55.000 1.13 0.0 0.00 1.85
142 144 0.389687 CCGGTTCGTAACGGCCTTTA 60.390 55.000 5.32 0.0 43.96 1.85
143 145 1.668793 CCGGTTCGTAACGGCCTTT 60.669 57.895 5.32 0.0 43.96 3.11
144 146 2.047939 CCGGTTCGTAACGGCCTT 60.048 61.111 5.32 0.0 43.96 4.35
149 151 1.387756 CTTTAGTGCCGGTTCGTAACG 59.612 52.381 1.90 0.0 0.00 3.18
150 152 1.728425 CCTTTAGTGCCGGTTCGTAAC 59.272 52.381 1.90 0.0 0.00 2.50
151 153 1.940752 GCCTTTAGTGCCGGTTCGTAA 60.941 52.381 1.90 0.0 0.00 3.18
152 154 0.390209 GCCTTTAGTGCCGGTTCGTA 60.390 55.000 1.90 0.0 0.00 3.43
153 155 1.670083 GCCTTTAGTGCCGGTTCGT 60.670 57.895 1.90 0.0 0.00 3.85
154 156 2.396157 GGCCTTTAGTGCCGGTTCG 61.396 63.158 1.90 0.0 39.48 3.95
410 530 0.886490 GCACCCGAATAGCATCCCTG 60.886 60.000 0.00 0.0 0.00 4.45
553 684 5.517904 GCTACGTGTCCAGGTTTAGTATAG 58.482 45.833 0.00 0.0 0.00 1.31
685 816 3.502123 AAAAGATCCTCGTTTGGACCA 57.498 42.857 0.00 0.0 39.17 4.02
2194 2464 2.038426 TCGGAGAAAATCAAGCTCCACA 59.962 45.455 0.00 0.0 46.74 4.17
3207 3497 1.838077 GTATTGACTACTGGTGGGGCT 59.162 52.381 0.00 0.0 0.00 5.19
3314 3604 0.396139 GGCTGAGGATCCCAATGCAA 60.396 55.000 8.55 0.0 0.00 4.08


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

AutoCloner maintained by Alex Coulton.