Multiple sequence alignment - TraesCS1B01G435200

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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 TraesCS1B01G435200 chr1B 100.000 2267 0 0 1 2267 659293726 659295992 0.000000e+00 4187
1 TraesCS1B01G435200 chr1B 94.063 1617 48 14 670 2267 659033498 659035085 0.000000e+00 2410
2 TraesCS1B01G435200 chr1B 90.802 1609 74 28 670 2267 658968866 658970411 0.000000e+00 2084
3 TraesCS1B01G435200 chr1B 92.691 1464 50 16 837 2267 659002555 659003994 0.000000e+00 2058
4 TraesCS1B01G435200 chr1B 94.461 1354 37 8 837 2187 659285896 659287214 0.000000e+00 2050
5 TraesCS1B01G435200 chr1B 95.785 1210 37 5 978 2180 659073582 659074784 0.000000e+00 1940
6 TraesCS1B01G435200 chr1B 92.941 680 29 11 4 670 659285059 659285732 0.000000e+00 972
7 TraesCS1B01G435200 chr1B 92.920 678 31 9 4 670 659181518 659182189 0.000000e+00 970
8 TraesCS1B01G435200 chr1B 93.123 538 32 2 837 1373 659182353 659182886 0.000000e+00 784
9 TraesCS1B01G435200 chr1B 80.585 1025 88 55 3 937 659072567 659073570 0.000000e+00 688
10 TraesCS1B01G435200 chr1B 84.006 619 60 13 1652 2261 659327172 659327760 1.970000e-155 558
11 TraesCS1B01G435200 chr1B 86.728 437 31 15 248 668 658968395 658968820 5.710000e-126 460
12 TraesCS1B01G435200 chr1B 89.167 240 11 3 2028 2267 659190872 659191096 3.690000e-73 285
13 TraesCS1B01G435200 chr1B 88.750 240 12 3 2028 2267 659083060 659083284 1.710000e-71 279
14 TraesCS1B01G435200 chr1B 96.774 124 3 1 670 792 659182233 659182356 2.950000e-49 206
15 TraesCS1B01G435200 chr1B 96.774 124 3 1 670 792 659285776 659285899 2.950000e-49 206
16 TraesCS1B01G435200 chr1B 91.071 56 3 2 3 58 658968319 658968372 8.680000e-10 75
17 TraesCS1B01G435200 chr1D 87.165 1644 62 43 670 2261 473960918 473962464 0.000000e+00 1729
18 TraesCS1B01G435200 chr1D 85.100 698 48 23 938 1598 473879765 473880443 0.000000e+00 662
19 TraesCS1B01G435200 chr1D 83.542 638 55 23 1652 2261 473993105 473993720 3.290000e-153 551
20 TraesCS1B01G435200 chr1D 86.166 253 15 11 1652 1904 473997879 473998111 2.890000e-64 255
21 TraesCS1B01G435200 chr1A 94.024 753 33 2 839 1579 568265903 568266655 0.000000e+00 1131
22 TraesCS1B01G435200 chr1A 87.789 778 69 23 670 1433 568327695 568328460 0.000000e+00 887
23 TraesCS1B01G435200 chr1A 88.508 583 39 13 98 670 568327020 568327584 0.000000e+00 680
24 TraesCS1B01G435200 chr1A 93.919 444 20 2 1624 2067 568266926 568267362 0.000000e+00 664
25 TraesCS1B01G435200 chr1A 84.628 618 55 14 1654 2261 568399455 568400042 1.510000e-161 579
26 TraesCS1B01G435200 chr1A 84.174 575 50 11 1652 2205 568377871 568378425 9.280000e-144 520
27 TraesCS1B01G435200 chr1A 93.827 324 17 2 1789 2110 568334079 568334401 3.390000e-133 484
28 TraesCS1B01G435200 chr1A 79.180 610 63 34 86 668 568265148 568265720 4.600000e-97 364
29 TraesCS1B01G435200 chr1A 94.776 134 6 1 670 802 568265766 568265899 8.210000e-50 207
30 TraesCS1B01G435200 chr1A 86.275 153 12 5 1447 1598 568122507 568122651 8.380000e-35 158
31 TraesCS1B01G435200 chr1A 86.577 149 12 2 1447 1595 568383884 568384024 8.380000e-35 158
32 TraesCS1B01G435200 chr7B 82.266 203 16 5 1405 1595 65395670 65395864 8.380000e-35 158


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 TraesCS1B01G435200 chr1B 659293726 659295992 2266 False 4187.000000 4187 100.000000 1 2267 1 chr1B.!!$F5 2266
1 TraesCS1B01G435200 chr1B 659033498 659035085 1587 False 2410.000000 2410 94.063000 670 2267 1 chr1B.!!$F2 1597
2 TraesCS1B01G435200 chr1B 659002555 659003994 1439 False 2058.000000 2058 92.691000 837 2267 1 chr1B.!!$F1 1430
3 TraesCS1B01G435200 chr1B 659072567 659074784 2217 False 1314.000000 1940 88.185000 3 2180 2 chr1B.!!$F8 2177
4 TraesCS1B01G435200 chr1B 659285059 659287214 2155 False 1076.000000 2050 94.725333 4 2187 3 chr1B.!!$F10 2183
5 TraesCS1B01G435200 chr1B 658968319 658970411 2092 False 873.000000 2084 89.533667 3 2267 3 chr1B.!!$F7 2264
6 TraesCS1B01G435200 chr1B 659181518 659182886 1368 False 653.333333 970 94.272333 4 1373 3 chr1B.!!$F9 1369
7 TraesCS1B01G435200 chr1B 659327172 659327760 588 False 558.000000 558 84.006000 1652 2261 1 chr1B.!!$F6 609
8 TraesCS1B01G435200 chr1D 473960918 473962464 1546 False 1729.000000 1729 87.165000 670 2261 1 chr1D.!!$F2 1591
9 TraesCS1B01G435200 chr1D 473879765 473880443 678 False 662.000000 662 85.100000 938 1598 1 chr1D.!!$F1 660
10 TraesCS1B01G435200 chr1D 473993105 473993720 615 False 551.000000 551 83.542000 1652 2261 1 chr1D.!!$F3 609
11 TraesCS1B01G435200 chr1A 568327020 568328460 1440 False 783.500000 887 88.148500 98 1433 2 chr1A.!!$F7 1335
12 TraesCS1B01G435200 chr1A 568265148 568267362 2214 False 591.500000 1131 90.474750 86 2067 4 chr1A.!!$F6 1981
13 TraesCS1B01G435200 chr1A 568399455 568400042 587 False 579.000000 579 84.628000 1654 2261 1 chr1A.!!$F5 607
14 TraesCS1B01G435200 chr1A 568377871 568378425 554 False 520.000000 520 84.174000 1652 2205 1 chr1A.!!$F3 553

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
816 1048 0.531657 CCACAGCCACAGAGAGAGAG 59.468 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 2337 0.394192 CACTGTCCACTGGAGCTTCA 59.606 55.0 0.0 0.0 29.39 3.02 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
184 213 3.747010 GTCAAATGCATGCAAACCATTGA 59.253 39.130 26.68 23.41 38.94 2.57
187 216 3.965379 ATGCATGCAAACCATTGAAGA 57.035 38.095 26.68 0.00 38.94 2.87
191 220 4.060205 GCATGCAAACCATTGAAGAAAGT 58.940 39.130 14.21 0.00 38.94 2.66
192 221 4.151157 GCATGCAAACCATTGAAGAAAGTC 59.849 41.667 14.21 0.00 38.94 3.01
195 224 3.975035 GCAAACCATTGAAGAAAGTCGAC 59.025 43.478 7.70 7.70 38.94 4.20
209 239 1.300311 TCGACGTCGCACCACATTT 60.300 52.632 32.19 0.00 39.60 2.32
221 251 2.751259 CACCACATTTCCATCTGTCAGG 59.249 50.000 0.00 0.00 0.00 3.86
244 289 2.436646 CGGTGCCACCCTGACATC 60.437 66.667 8.62 0.00 33.75 3.06
349 408 8.845413 AGAATTATAGGATGTTGAAGAGATGC 57.155 34.615 0.00 0.00 0.00 3.91
429 490 4.186856 AGGCATGGGAAAAACAAATACG 57.813 40.909 0.00 0.00 0.00 3.06
476 557 2.404215 ACTCAGAATACGCACACACAC 58.596 47.619 0.00 0.00 0.00 3.82
477 558 2.223947 ACTCAGAATACGCACACACACA 60.224 45.455 0.00 0.00 0.00 3.72
525 609 8.315220 AGATTTAATTTCCCTTTGAGATGCAT 57.685 30.769 0.00 0.00 0.00 3.96
527 611 7.722949 TTTAATTTCCCTTTGAGATGCATCT 57.277 32.000 29.09 29.09 40.50 2.90
528 612 7.722949 TTAATTTCCCTTTGAGATGCATCTT 57.277 32.000 29.26 13.91 37.25 2.40
529 613 8.821686 TTAATTTCCCTTTGAGATGCATCTTA 57.178 30.769 29.26 23.00 37.25 2.10
559 646 8.564574 GCCAGGAAATTACATCGAACAATTATA 58.435 33.333 0.00 0.00 0.00 0.98
636 735 7.648112 CAGATTTAGATACGACGGATTCAAGAA 59.352 37.037 0.00 0.00 0.00 2.52
744 965 9.539825 AATTGTTCATGTCTGATACTGATACTC 57.460 33.333 0.00 0.00 0.00 2.59
788 1020 0.979665 TTTGTCCTCTCCTCAGCCAG 59.020 55.000 0.00 0.00 0.00 4.85
791 1023 1.381056 TCCTCTCCTCAGCCAGCTC 60.381 63.158 0.00 0.00 0.00 4.09
814 1046 1.190833 ACCCACAGCCACAGAGAGAG 61.191 60.000 0.00 0.00 0.00 3.20
816 1048 0.531657 CCACAGCCACAGAGAGAGAG 59.468 60.000 0.00 0.00 0.00 3.20
817 1049 1.543607 CACAGCCACAGAGAGAGAGA 58.456 55.000 0.00 0.00 0.00 3.10
818 1050 1.473677 CACAGCCACAGAGAGAGAGAG 59.526 57.143 0.00 0.00 0.00 3.20
889 1129 2.242043 CAAAGAGAGCCACCAAACCAT 58.758 47.619 0.00 0.00 0.00 3.55
973 1222 7.011109 GCACAAGAAAGTAGTGTTCTTAGTTCA 59.989 37.037 0.00 0.00 42.15 3.18
1297 1557 8.643324 AGGTATAATTCTCAACAGACATAGGAC 58.357 37.037 0.00 0.00 0.00 3.85
1477 1839 3.490759 GCATGACGACTGGCACCG 61.491 66.667 0.00 3.37 0.00 4.94
1499 1861 5.206299 CGTGAACTAACTCTCTATAAGCCG 58.794 45.833 0.00 0.00 0.00 5.52
1559 1928 6.092122 TCAGTGGTTTAATCTTAGCACAATCG 59.908 38.462 9.25 0.00 43.31 3.34
1704 2311 2.412065 GCGCAAGTGTCTTCTCATGTTC 60.412 50.000 0.30 0.00 41.68 3.18
1726 2333 3.023832 TCAGGATCGATGAAGCAGTGTA 58.976 45.455 0.54 0.00 0.00 2.90
1727 2334 3.447229 TCAGGATCGATGAAGCAGTGTAA 59.553 43.478 0.54 0.00 0.00 2.41
1728 2335 3.801050 CAGGATCGATGAAGCAGTGTAAG 59.199 47.826 0.54 0.00 0.00 2.34
1729 2336 2.541762 GGATCGATGAAGCAGTGTAAGC 59.458 50.000 0.54 0.00 0.00 3.09
1730 2337 3.452474 GATCGATGAAGCAGTGTAAGCT 58.548 45.455 0.54 0.00 45.97 3.74
1731 2338 2.610433 TCGATGAAGCAGTGTAAGCTG 58.390 47.619 0.00 0.00 42.53 4.24
2153 2799 6.951971 TCCTCCTTCCTAAAAGAGAATTCAG 58.048 40.000 8.44 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.323178 AGCCATTGGTTCCAGCTCTG 60.323 55.000 4.26 0.00 0.00 3.35
1 2 0.407139 AAGCCATTGGTTCCAGCTCT 59.593 50.000 4.26 0.00 32.19 4.09
184 213 0.938168 GGTGCGACGTCGACTTTCTT 60.938 55.000 39.74 0.00 43.02 2.52
187 216 1.947642 GTGGTGCGACGTCGACTTT 60.948 57.895 39.74 0.00 43.02 2.66
191 220 1.279527 GAAATGTGGTGCGACGTCGA 61.280 55.000 39.74 22.22 43.02 4.20
192 221 1.129809 GAAATGTGGTGCGACGTCG 59.870 57.895 32.57 32.57 43.27 5.12
195 224 0.096976 GATGGAAATGTGGTGCGACG 59.903 55.000 0.00 0.00 0.00 5.12
209 239 2.673200 GCAGCCCCTGACAGATGGA 61.673 63.158 13.42 0.00 32.44 3.41
349 408 7.919690 TGAAATTCTACATGGCTATCGAAAAG 58.080 34.615 0.00 0.00 0.00 2.27
429 490 4.974399 ACCCTAGCTTGCTATTCATTACC 58.026 43.478 2.59 0.00 0.00 2.85
525 609 7.732025 TCGATGTAATTTCCTGGCTAATAAGA 58.268 34.615 0.00 0.00 0.00 2.10
527 611 7.771361 TGTTCGATGTAATTTCCTGGCTAATAA 59.229 33.333 0.00 0.00 0.00 1.40
528 612 7.276658 TGTTCGATGTAATTTCCTGGCTAATA 58.723 34.615 0.00 0.00 0.00 0.98
529 613 6.119536 TGTTCGATGTAATTTCCTGGCTAAT 58.880 36.000 0.00 0.00 0.00 1.73
584 681 6.621316 TTAGTGCTTCGGTTTGATGTAAAA 57.379 33.333 0.00 0.00 0.00 1.52
744 965 0.795085 CTCGCAGGTTTTCTGAGCTG 59.205 55.000 0.00 0.07 46.18 4.24
788 1020 0.250727 TGTGGCTGTGGGTTAAGAGC 60.251 55.000 0.00 0.00 0.00 4.09
791 1023 1.347707 TCTCTGTGGCTGTGGGTTAAG 59.652 52.381 0.00 0.00 0.00 1.85
814 1046 2.358898 GTGCCATGTCTCTCTCTCTCTC 59.641 54.545 0.00 0.00 0.00 3.20
816 1048 1.065401 CGTGCCATGTCTCTCTCTCTC 59.935 57.143 0.00 0.00 0.00 3.20
817 1049 1.102154 CGTGCCATGTCTCTCTCTCT 58.898 55.000 0.00 0.00 0.00 3.10
818 1050 0.527385 GCGTGCCATGTCTCTCTCTC 60.527 60.000 0.00 0.00 0.00 3.20
889 1129 1.476845 TTGGAGAAGCGCTGGTGGTA 61.477 55.000 12.58 0.00 0.00 3.25
973 1222 5.481824 TCAGGTGAGATGTGATGTTCTACTT 59.518 40.000 0.00 0.00 0.00 2.24
1221 1471 2.441901 TTGGGGAATGGGATGCGC 60.442 61.111 0.00 0.00 0.00 6.09
1297 1557 5.034152 TGAAAACTTGTTAGAAGCAAAGCG 58.966 37.500 0.00 0.00 0.00 4.68
1477 1839 6.374565 TCGGCTTATAGAGAGTTAGTTCAC 57.625 41.667 0.00 0.00 0.00 3.18
1559 1928 4.830600 TGGAAGTAGGGAATTTGTTTGTCC 59.169 41.667 0.00 0.00 0.00 4.02
1704 2311 2.159128 ACACTGCTTCATCGATCCTGAG 60.159 50.000 0.00 0.00 0.00 3.35
1728 2335 0.673022 CTGTCCACTGGAGCTTCAGC 60.673 60.000 22.62 6.16 38.26 4.26
1729 2336 0.683973 ACTGTCCACTGGAGCTTCAG 59.316 55.000 21.11 21.11 40.40 3.02
1730 2337 0.394192 CACTGTCCACTGGAGCTTCA 59.606 55.000 0.00 0.00 29.39 3.02
1731 2338 0.681733 TCACTGTCCACTGGAGCTTC 59.318 55.000 0.00 0.00 29.39 3.86
2153 2799 7.764331 TCCTGTGGTTCTTTAACAAAGTTTAC 58.236 34.615 0.00 0.00 39.52 2.01


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

AutoCloner maintained by Alex Coulton.