Multiple sequence alignment - TraesCS3B01G430700

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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 TraesCS3B01G430700 chr3B 100.000 2475 0 0 1 2475 669817678 669815204 0.000000e+00 4571
1 TraesCS3B01G430700 chr3B 98.405 627 8 1 1849 2475 669840575 669839951 0.000000e+00 1101
2 TraesCS3B01G430700 chr3B 96.338 628 23 0 1846 2473 483376379 483377006 0.000000e+00 1033
3 TraesCS3B01G430700 chr3B 98.907 183 2 0 1743 1925 669840717 669840535 6.600000e-86 327
4 TraesCS3B01G430700 chr3B 93.491 169 10 1 1758 1925 483376254 483376422 1.470000e-62 250
5 TraesCS3B01G430700 chr2D 92.553 2511 121 28 1 2475 604414183 604411703 0.000000e+00 3541
6 TraesCS3B01G430700 chr2D 96.667 630 21 0 1846 2475 189921747 189922376 0.000000e+00 1048
7 TraesCS3B01G430700 chr3A 97.064 1737 46 2 1 1736 633121765 633123497 0.000000e+00 2920
8 TraesCS3B01G430700 chr3A 96.384 719 23 3 1758 2475 633123605 633124321 0.000000e+00 1181
9 TraesCS3B01G430700 chr6A 96.893 1738 43 4 1 1736 64687532 64685804 0.000000e+00 2900
10 TraesCS3B01G430700 chrUn 96.835 1738 44 4 1 1736 86467991 86466263 0.000000e+00 2894
11 TraesCS3B01G430700 chr1B 96.433 1738 51 4 1 1736 672580351 672578623 0.000000e+00 2856
12 TraesCS3B01G430700 chr1B 95.833 720 28 2 1758 2475 672578514 672577795 0.000000e+00 1162
13 TraesCS3B01G430700 chr7A 96.373 1737 54 3 1 1736 60253099 60254827 0.000000e+00 2850
14 TraesCS3B01G430700 chr7A 96.974 727 21 1 1750 2475 120865557 120864831 0.000000e+00 1219
15 TraesCS3B01G430700 chr4B 96.203 1738 55 4 1 1736 209133146 209134874 0.000000e+00 2833
16 TraesCS3B01G430700 chr4B 96.667 720 22 2 1758 2475 209284034 209284753 0.000000e+00 1195
17 TraesCS3B01G430700 chr4B 95.972 720 27 2 1758 2475 209062372 209061653 0.000000e+00 1168
18 TraesCS3B01G430700 chr6B 95.975 1739 66 4 1 1736 297446823 297448560 0.000000e+00 2820
19 TraesCS3B01G430700 chr6B 94.675 169 8 1 1758 1925 625627569 625627401 6.790000e-66 261
20 TraesCS3B01G430700 chr6B 93.491 169 10 1 1758 1925 215778819 215778987 1.470000e-62 250
21 TraesCS3B01G430700 chr3D 95.912 1737 55 8 2 1736 523715695 523713973 0.000000e+00 2800
22 TraesCS3B01G430700 chr7B 93.733 718 27 9 1758 2475 52969794 52969095 0.000000e+00 1061


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 TraesCS3B01G430700 chr3B 669815204 669817678 2474 True 4571.0 4571 100.0000 1 2475 1 chr3B.!!$R1 2474
1 TraesCS3B01G430700 chr3B 669839951 669840717 766 True 714.0 1101 98.6560 1743 2475 2 chr3B.!!$R2 732
2 TraesCS3B01G430700 chr3B 483376254 483377006 752 False 641.5 1033 94.9145 1758 2473 2 chr3B.!!$F1 715
3 TraesCS3B01G430700 chr2D 604411703 604414183 2480 True 3541.0 3541 92.5530 1 2475 1 chr2D.!!$R1 2474
4 TraesCS3B01G430700 chr2D 189921747 189922376 629 False 1048.0 1048 96.6670 1846 2475 1 chr2D.!!$F1 629
5 TraesCS3B01G430700 chr3A 633121765 633124321 2556 False 2050.5 2920 96.7240 1 2475 2 chr3A.!!$F1 2474
6 TraesCS3B01G430700 chr6A 64685804 64687532 1728 True 2900.0 2900 96.8930 1 1736 1 chr6A.!!$R1 1735
7 TraesCS3B01G430700 chrUn 86466263 86467991 1728 True 2894.0 2894 96.8350 1 1736 1 chrUn.!!$R1 1735
8 TraesCS3B01G430700 chr1B 672577795 672580351 2556 True 2009.0 2856 96.1330 1 2475 2 chr1B.!!$R1 2474
9 TraesCS3B01G430700 chr7A 60253099 60254827 1728 False 2850.0 2850 96.3730 1 1736 1 chr7A.!!$F1 1735
10 TraesCS3B01G430700 chr7A 120864831 120865557 726 True 1219.0 1219 96.9740 1750 2475 1 chr7A.!!$R1 725
11 TraesCS3B01G430700 chr4B 209133146 209134874 1728 False 2833.0 2833 96.2030 1 1736 1 chr4B.!!$F1 1735
12 TraesCS3B01G430700 chr4B 209284034 209284753 719 False 1195.0 1195 96.6670 1758 2475 1 chr4B.!!$F2 717
13 TraesCS3B01G430700 chr4B 209061653 209062372 719 True 1168.0 1168 95.9720 1758 2475 1 chr4B.!!$R1 717
14 TraesCS3B01G430700 chr6B 297446823 297448560 1737 False 2820.0 2820 95.9750 1 1736 1 chr6B.!!$F2 1735
15 TraesCS3B01G430700 chr3D 523713973 523715695 1722 True 2800.0 2800 95.9120 2 1736 1 chr3D.!!$R1 1734
16 TraesCS3B01G430700 chr7B 52969095 52969794 699 True 1061.0 1061 93.7330 1758 2475 1 chr7B.!!$R1 717

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
265 266 0.912486 ACATAAGCCGCCTTTCTCCT 59.088 50.0 0.0 0.0 32.47 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2387 1.146041 GGGACATATGAGCGTGGCA 59.854 57.895 10.38 0.0 0.0 4.92 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
143 144 1.281867 GGTCCCCACTCATCACAATCA 59.718 52.381 0.00 0.00 0.00 2.57
172 173 2.165167 CATCCCGCATTGGAGCATAAT 58.835 47.619 0.00 0.00 42.00 1.28
254 255 4.280929 ACAAGGGAAGTTTTCACATAAGCC 59.719 41.667 0.00 0.00 34.83 4.35
265 266 0.912486 ACATAAGCCGCCTTTCTCCT 59.088 50.000 0.00 0.00 32.47 3.69
302 303 8.071235 AGTACCTATACCTAAATCCTTCTCCT 57.929 38.462 0.00 0.00 30.88 3.69
429 430 7.817418 AAACAAGTTCATAGTAACATGTGGT 57.183 32.000 0.00 0.00 39.59 4.16
540 541 5.815581 AGAAATAGAGCAACACCCATTGTA 58.184 37.500 0.00 0.00 37.51 2.41
630 631 4.405358 TGATGGTTGAGCCTTTGTTCTTTT 59.595 37.500 0.00 0.00 38.35 2.27
634 635 4.439563 GGTTGAGCCTTTGTTCTTTTCGAA 60.440 41.667 0.00 0.00 0.00 3.71
728 729 3.416156 CTTTCTTCCTTCCACCTTCCTG 58.584 50.000 0.00 0.00 0.00 3.86
742 743 2.414293 CCTTCCTGTTGTACTCGACTCG 60.414 54.545 0.00 0.00 0.00 4.18
778 779 0.947244 AACAAAGGCTTGCTCGTCTG 59.053 50.000 0.00 0.00 35.84 3.51
801 802 4.691216 GCGTCATAGTCCAAACTCTTTCTT 59.309 41.667 0.00 0.00 36.92 2.52
966 967 4.196971 AGCAAAAGTACGGTTCAAAGTCT 58.803 39.130 0.00 0.00 0.00 3.24
967 968 4.638865 AGCAAAAGTACGGTTCAAAGTCTT 59.361 37.500 0.00 0.00 0.00 3.01
968 969 5.124936 AGCAAAAGTACGGTTCAAAGTCTTT 59.875 36.000 0.00 0.00 0.00 2.52
969 970 5.803461 GCAAAAGTACGGTTCAAAGTCTTTT 59.197 36.000 0.00 0.00 35.14 2.27
1131 1135 7.705325 GGCATTAGTAGAATTCTCAAACTACGA 59.295 37.037 12.24 1.43 39.75 3.43
1323 1334 6.584488 AGGAAAATCACTCTGATCTCTGATG 58.416 40.000 0.00 0.00 35.76 3.07
1584 1596 1.172180 TGAGCTTTTGGGGAGCAACG 61.172 55.000 0.00 0.00 42.56 4.10
1659 1671 0.178961 GGCTTTGGGGTGGTTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
1736 1751 7.979115 TGTTCTTCCTTTTGATTTAAACGTG 57.021 32.000 0.00 0.00 0.00 4.49
1737 1752 6.975772 TGTTCTTCCTTTTGATTTAAACGTGG 59.024 34.615 0.00 0.00 0.00 4.94
1738 1753 6.945938 TCTTCCTTTTGATTTAAACGTGGA 57.054 33.333 0.00 0.00 0.00 4.02
1739 1754 6.966021 TCTTCCTTTTGATTTAAACGTGGAG 58.034 36.000 0.00 0.00 0.00 3.86
1740 1755 6.768861 TCTTCCTTTTGATTTAAACGTGGAGA 59.231 34.615 0.00 0.00 0.00 3.71
1741 1756 6.554334 TCCTTTTGATTTAAACGTGGAGAG 57.446 37.500 0.00 0.00 0.00 3.20
2195 2387 9.389755 GCTTCTATCAAAAGAGGAAAAGATACT 57.610 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.969894 GGGCTGGCTATGTACGAGAT 59.030 55.000 0.00 0.00 0.00 2.75
96 97 4.003648 AGCTGAAAACCTACATACAGTGC 58.996 43.478 0.00 0.00 0.00 4.40
143 144 2.302517 AATGCGGGATGAGGGCCAAT 62.303 55.000 6.18 0.00 0.00 3.16
172 173 8.058667 TCTTGATACACCGAAAGATACTAACA 57.941 34.615 0.00 0.00 0.00 2.41
254 255 3.831715 CCTTTTAACAGGAGAAAGGCG 57.168 47.619 1.00 0.00 41.90 5.52
277 278 7.951245 CAGGAGAAGGATTTAGGTATAGGTACT 59.049 40.741 0.00 0.00 46.37 2.73
284 285 4.721776 TGCACAGGAGAAGGATTTAGGTAT 59.278 41.667 0.00 0.00 0.00 2.73
286 287 2.912956 TGCACAGGAGAAGGATTTAGGT 59.087 45.455 0.00 0.00 0.00 3.08
302 303 3.273434 GAACAGGAGAATAGCATGCACA 58.727 45.455 21.98 7.55 0.00 4.57
355 356 4.246458 AGACCACTTTGATAACGAGCTTC 58.754 43.478 0.00 0.00 0.00 3.86
424 425 0.888619 CTAGGAGCTCAACGACCACA 59.111 55.000 17.19 0.00 0.00 4.17
429 430 2.891580 AGTCAAACTAGGAGCTCAACGA 59.108 45.455 17.19 0.00 0.00 3.85
540 541 8.715190 ACTCTCTCTAGTAAAAGAAAGGAAGT 57.285 34.615 0.00 0.00 0.00 3.01
630 631 2.930826 AAGAGAAAGGCAAGGTTCGA 57.069 45.000 0.00 0.00 0.00 3.71
657 658 3.087031 CCATCAAAGAACTCCACAGCAT 58.913 45.455 0.00 0.00 0.00 3.79
728 729 0.169894 GGGGACGAGTCGAGTACAAC 59.830 60.000 21.50 1.82 0.00 3.32
742 743 1.993391 TTGGGGAGTGATCGGGGAC 60.993 63.158 0.00 0.00 0.00 4.46
778 779 4.246458 AGAAAGAGTTTGGACTATGACGC 58.754 43.478 0.00 0.00 35.88 5.19
801 802 1.065491 AGAAAGCACCACAGTCACACA 60.065 47.619 0.00 0.00 0.00 3.72
1323 1334 2.930682 GTGAGCCACTTATTTCTCCGAC 59.069 50.000 0.00 0.00 0.00 4.79
1480 1492 6.316390 ACAATTCTTCCGAGTATTCCATTCAC 59.684 38.462 0.00 0.00 0.00 3.18
1609 1621 7.607223 CACTATGGTATCTCCTACTACTGGTAC 59.393 44.444 0.00 0.00 37.07 3.34
1736 1751 3.999663 CACTCTCCACATTTTCACTCTCC 59.000 47.826 0.00 0.00 0.00 3.71
1737 1752 4.887748 TCACTCTCCACATTTTCACTCTC 58.112 43.478 0.00 0.00 0.00 3.20
1738 1753 4.963318 TCACTCTCCACATTTTCACTCT 57.037 40.909 0.00 0.00 0.00 3.24
1739 1754 5.240891 TCATCACTCTCCACATTTTCACTC 58.759 41.667 0.00 0.00 0.00 3.51
1740 1755 5.233083 TCATCACTCTCCACATTTTCACT 57.767 39.130 0.00 0.00 0.00 3.41
1741 1756 6.149973 TGAATCATCACTCTCCACATTTTCAC 59.850 38.462 0.00 0.00 0.00 3.18
1901 2055 5.705397 TCATCAGATGAACTCCCTGATTT 57.295 39.130 10.93 0.00 42.97 2.17
2034 2226 7.902403 GCTTCTTTGAATCTCGAAATAACAGAG 59.098 37.037 0.00 0.00 0.00 3.35
2195 2387 1.146041 GGGACATATGAGCGTGGCA 59.854 57.895 10.38 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.