Multiple sequence alignment - TraesCS3A01G372100

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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 TraesCS3A01G372100 chr3A 100.000 3646 0 0 1 3646 622817349 622820994 0.000000e+00 6734.0
1 TraesCS3A01G372100 chr3A 96.328 3649 129 5 1 3646 622717661 622721307 0.000000e+00 5991.0
2 TraesCS3A01G372100 chr3A 94.733 3664 162 6 1 3646 622898560 622902210 0.000000e+00 5668.0
3 TraesCS3A01G372100 chr3A 94.124 3676 172 10 1 3646 622708948 622712609 0.000000e+00 5552.0
4 TraesCS3A01G372100 chr3A 93.854 1806 89 1 1863 3646 622891720 622893525 0.000000e+00 2700.0
5 TraesCS3A01G372100 chr3A 95.055 1173 56 2 1863 3035 622801595 622802765 0.000000e+00 1844.0
6 TraesCS3A01G372100 chr3A 91.719 640 30 2 3029 3646 622811671 622812309 0.000000e+00 867.0
7 TraesCS3A01G372100 chr3D 90.380 1975 166 3 1695 3646 479451135 479453108 0.000000e+00 2573.0
8 TraesCS3A01G372100 chr3D 90.223 1974 165 7 1695 3646 479894615 479892648 0.000000e+00 2551.0
9 TraesCS3A01G372100 chr3D 90.161 1982 162 6 1695 3646 479914025 479912047 0.000000e+00 2549.0
10 TraesCS3A01G372100 chr3D 90.159 1697 157 10 1 1692 479449399 479451090 0.000000e+00 2200.0
11 TraesCS3A01G372100 chr3D 83.168 2020 245 36 1695 3646 478739261 478741253 0.000000e+00 1759.0
12 TraesCS3A01G372100 chr3D 84.668 1748 204 27 1924 3646 479213666 479215374 0.000000e+00 1685.0
13 TraesCS3A01G372100 chr3D 84.900 1404 150 35 321 1693 478737845 478739217 0.000000e+00 1362.0
14 TraesCS3A01G372100 chr3D 86.379 1182 130 8 2495 3646 479122403 479123583 0.000000e+00 1262.0
15 TraesCS3A01G372100 chr3D 90.200 898 65 16 1 889 479919241 479918358 0.000000e+00 1149.0
16 TraesCS3A01G372100 chr3D 87.192 812 88 8 885 1695 479914863 479914067 0.000000e+00 909.0
17 TraesCS3A01G372100 chr3D 86.598 194 26 0 1502 1695 479894850 479894657 7.930000e-52 215.0
18 TraesCS3A01G372100 chr3B 85.620 1370 145 26 347 1693 639753513 639754853 0.000000e+00 1391.0
19 TraesCS3A01G372100 chr3B 84.286 1400 162 34 321 1693 639148634 639150002 0.000000e+00 1314.0
20 TraesCS3A01G372100 chr3B 83.476 1398 177 31 321 1693 639552861 639554229 0.000000e+00 1253.0
21 TraesCS3A01G372100 chr3B 81.655 1559 221 31 1695 3228 639554273 639555791 0.000000e+00 1234.0
22 TraesCS3A01G372100 chr3B 82.796 1395 176 32 324 1693 639398409 639399764 0.000000e+00 1188.0
23 TraesCS3A01G372100 chr3B 81.142 1559 218 36 1695 3228 639150046 639151553 0.000000e+00 1181.0
24 TraesCS3A01G372100 chr3B 84.024 1183 154 16 1695 2858 639399808 639400974 0.000000e+00 1105.0
25 TraesCS3A01G372100 chr3B 77.778 162 34 2 1538 1698 639007333 639007493 8.330000e-17 99.0
26 TraesCS3A01G372100 chr3B 97.143 35 1 0 1658 1692 639658493 639658527 3.930000e-05 60.2


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 TraesCS3A01G372100 chr3A 622817349 622820994 3645 False 6734.000000 6734 100.000000 1 3646 1 chr3A.!!$F5 3645
1 TraesCS3A01G372100 chr3A 622717661 622721307 3646 False 5991.000000 5991 96.328000 1 3646 1 chr3A.!!$F2 3645
2 TraesCS3A01G372100 chr3A 622898560 622902210 3650 False 5668.000000 5668 94.733000 1 3646 1 chr3A.!!$F7 3645
3 TraesCS3A01G372100 chr3A 622708948 622712609 3661 False 5552.000000 5552 94.124000 1 3646 1 chr3A.!!$F1 3645
4 TraesCS3A01G372100 chr3A 622891720 622893525 1805 False 2700.000000 2700 93.854000 1863 3646 1 chr3A.!!$F6 1783
5 TraesCS3A01G372100 chr3A 622801595 622802765 1170 False 1844.000000 1844 95.055000 1863 3035 1 chr3A.!!$F3 1172
6 TraesCS3A01G372100 chr3A 622811671 622812309 638 False 867.000000 867 91.719000 3029 3646 1 chr3A.!!$F4 617
7 TraesCS3A01G372100 chr3D 479449399 479453108 3709 False 2386.500000 2573 90.269500 1 3646 2 chr3D.!!$F4 3645
8 TraesCS3A01G372100 chr3D 479213666 479215374 1708 False 1685.000000 1685 84.668000 1924 3646 1 chr3D.!!$F2 1722
9 TraesCS3A01G372100 chr3D 478737845 478741253 3408 False 1560.500000 1759 84.034000 321 3646 2 chr3D.!!$F3 3325
10 TraesCS3A01G372100 chr3D 479912047 479919241 7194 True 1535.666667 2549 89.184333 1 3646 3 chr3D.!!$R2 3645
11 TraesCS3A01G372100 chr3D 479892648 479894850 2202 True 1383.000000 2551 88.410500 1502 3646 2 chr3D.!!$R1 2144
12 TraesCS3A01G372100 chr3D 479122403 479123583 1180 False 1262.000000 1262 86.379000 2495 3646 1 chr3D.!!$F1 1151
13 TraesCS3A01G372100 chr3B 639753513 639754853 1340 False 1391.000000 1391 85.620000 347 1693 1 chr3B.!!$F3 1346
14 TraesCS3A01G372100 chr3B 639148634 639151553 2919 False 1247.500000 1314 82.714000 321 3228 2 chr3B.!!$F4 2907
15 TraesCS3A01G372100 chr3B 639552861 639555791 2930 False 1243.500000 1253 82.565500 321 3228 2 chr3B.!!$F6 2907
16 TraesCS3A01G372100 chr3B 639398409 639400974 2565 False 1146.500000 1188 83.410000 324 2858 2 chr3B.!!$F5 2534

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
753 789 0.107410 TGGCAACCATCATCGGGTAC 60.107 55.0 0.00 0.00 37.77 3.34 F
818 855 0.184933 AGGCTTAACTTGTGGCCACA 59.815 50.0 34.74 34.74 46.23 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2607 6257 0.693430 TCTCATCCTCCTGCCAGCAT 60.693 55.000 0.0 0.0 0.0 3.79 R
2831 6497 8.625786 TGCATCACATCATATTAAAGTGCTAT 57.374 30.769 0.0 0.0 0.0 2.97 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
48 49 1.526041 GAGACACGAGATGATGCATGC 59.474 52.381 11.82 11.82 0.00 4.06
82 83 3.400054 GGAAGTGCTAGGGCGGGT 61.400 66.667 0.00 0.00 42.25 5.28
263 267 5.592104 TTGTAGAACACACAAGAGTCAGA 57.408 39.130 0.00 0.00 36.69 3.27
409 419 0.765903 GATGATCCAGGGCTCCAGGA 60.766 60.000 7.62 7.62 43.29 3.86
416 426 0.961753 CAGGGCTCCAGGACAAAAAC 59.038 55.000 0.00 0.00 0.00 2.43
426 437 6.208797 GCTCCAGGACAAAAACTAAAAGGTAT 59.791 38.462 0.00 0.00 0.00 2.73
511 534 6.077838 CGTGTAGAATGACTTTACCTTTTGC 58.922 40.000 0.00 0.00 0.00 3.68
623 648 2.158871 CCATCCCCCGAATTAGAAACGA 60.159 50.000 0.00 0.00 0.00 3.85
753 789 0.107410 TGGCAACCATCATCGGGTAC 60.107 55.000 0.00 0.00 37.77 3.34
818 855 0.184933 AGGCTTAACTTGTGGCCACA 59.815 50.000 34.74 34.74 46.23 4.17
920 4456 8.653338 CACCTTTTTCATCAATGACATGAATTC 58.347 33.333 0.00 0.00 39.46 2.17
1022 4567 0.916086 ACACACCAGAACCCACAAGA 59.084 50.000 0.00 0.00 0.00 3.02
1035 4583 3.714798 ACCCACAAGAAAGAGTAGGTGAA 59.285 43.478 0.00 0.00 0.00 3.18
1068 4616 2.334023 GGCAAGGAGAGATAGGATGGT 58.666 52.381 0.00 0.00 0.00 3.55
1100 4648 2.151202 GCAAGGACGTGAATTTCTCCA 58.849 47.619 0.00 0.00 0.00 3.86
1151 4702 1.587043 CGAAGGTGAGGAGCAGACGA 61.587 60.000 0.00 0.00 0.00 4.20
1189 4740 1.298157 CTTCCATCTTCGCGCCAACA 61.298 55.000 0.00 0.00 0.00 3.33
1386 4937 0.322816 GATGCAGGAGGAAGCAACCA 60.323 55.000 0.00 0.00 44.88 3.67
1555 5106 2.359011 GGGAATGGTGGTGGGGTC 59.641 66.667 0.00 0.00 0.00 4.46
1740 5375 1.993701 ATGGGCGATGGCATGGTGTA 61.994 55.000 3.81 0.00 42.47 2.90
1765 5400 0.762418 CCAACGGGTATGCAGGGATA 59.238 55.000 0.00 0.00 0.00 2.59
1848 5483 1.690219 GACGGGAGGAGCACCATGAT 61.690 60.000 2.07 0.00 38.94 2.45
1881 5516 2.027653 TGATGAACTGTATGGGCGACAA 60.028 45.455 0.00 0.00 0.00 3.18
1894 5529 1.670811 GGCGACAAAACGATGATGGAT 59.329 47.619 0.00 0.00 35.09 3.41
2155 5791 1.064003 TACCAAGGAGCTTGAAGCCA 58.936 50.000 14.45 0.00 43.77 4.75
2280 5916 5.783111 TCCAGTTCTTACCGTTACTAAACC 58.217 41.667 0.00 0.00 31.46 3.27
2284 5920 5.920840 AGTTCTTACCGTTACTAAACCGTTC 59.079 40.000 0.00 0.00 31.01 3.95
2607 6257 3.370846 CCACCATTCAGCTTCCATAGTCA 60.371 47.826 0.00 0.00 0.00 3.41
3058 6750 2.456577 TCCCATGAGACTTGACGATGA 58.543 47.619 0.00 0.00 0.00 2.92
3115 6807 1.142748 CCTCCATCGTGGCTCACTC 59.857 63.158 4.21 0.00 37.47 3.51
3151 6847 1.600636 CCTTGAGTTGCGCTTCCCA 60.601 57.895 9.73 0.00 0.00 4.37
3296 6999 4.257267 GCAAGAACCTAATTGCCAAGTT 57.743 40.909 0.00 0.00 44.76 2.66
3508 7276 5.574830 GTGTGTTTGATGCAACTACAACAAA 59.425 36.000 0.00 0.00 39.21 2.83
3519 7287 4.053469 ACTACAACAAAAATGGTGGTGC 57.947 40.909 0.00 0.00 37.18 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.721231 CACCAACCACCGCACAAG 59.279 61.111 0.00 0.00 0.00 3.16
82 83 7.821359 GCTAGATGATACCAAGATGCATTTCTA 59.179 37.037 0.00 0.00 0.00 2.10
623 648 1.409427 GCCTACTACTGCCAAGATCGT 59.591 52.381 0.00 0.00 0.00 3.73
753 789 3.129287 GTGTGCTGGTTCCATTCAATAGG 59.871 47.826 0.00 0.00 0.00 2.57
818 855 0.243636 GTACTGCCAAAGCGCCAAAT 59.756 50.000 2.29 0.00 44.31 2.32
1022 4567 3.005578 GTGGTCTCGTTCACCTACTCTTT 59.994 47.826 2.63 0.00 34.66 2.52
1035 4583 1.069765 CTTGCCACTGTGGTCTCGT 59.930 57.895 26.48 0.00 40.46 4.18
1068 4616 0.037326 GTCCTTGCTCATGTCCGACA 60.037 55.000 3.10 3.10 0.00 4.35
1100 4648 1.048601 TGCGAGGTGACTTCTTCCTT 58.951 50.000 0.00 0.00 44.43 3.36
1189 4740 2.169352 AGAGTATTGCAGCTCGTCCAAT 59.831 45.455 0.00 0.00 36.88 3.16
1476 5027 2.356278 GAGGCTGGGAATGCACCA 59.644 61.111 0.00 0.00 36.38 4.17
1555 5106 4.851114 CGCTGTTCATTCGCCGCG 62.851 66.667 6.39 6.39 34.50 6.46
1756 5391 1.897423 CACCACGACTATCCCTGCA 59.103 57.895 0.00 0.00 0.00 4.41
1848 5483 3.072915 ACAGTTCATCATGTCAACCTCCA 59.927 43.478 0.00 0.00 0.00 3.86
1881 5516 2.872245 CCGCTGTTATCCATCATCGTTT 59.128 45.455 0.00 0.00 0.00 3.60
2155 5791 4.100279 CCTCCTTGAGGTGGTTTAGTTT 57.900 45.455 9.50 0.00 44.25 2.66
2254 5890 7.388776 GGTTTAGTAACGGTAAGAACTGGAAAT 59.611 37.037 0.00 0.00 36.19 2.17
2280 5916 2.126467 CTGCAACAAAATGGTGGAACG 58.874 47.619 0.00 0.00 34.20 3.95
2284 5920 3.383761 GTCTTCTGCAACAAAATGGTGG 58.616 45.455 0.00 0.00 35.13 4.61
2359 5996 3.958147 TGATGGCGAGTGTAGGAGAATTA 59.042 43.478 0.00 0.00 0.00 1.40
2560 6210 2.632028 ACCTATCACCAGATGCAGCTAG 59.368 50.000 3.06 0.00 35.67 3.42
2607 6257 0.693430 TCTCATCCTCCTGCCAGCAT 60.693 55.000 0.00 0.00 0.00 3.79
2831 6497 8.625786 TGCATCACATCATATTAAAGTGCTAT 57.374 30.769 0.00 0.00 0.00 2.97
3115 6807 1.749033 GCTATCCGGACCCTCAAGG 59.251 63.158 6.12 0.00 43.78 3.61
3171 6867 6.986817 CCGTAAGAGTATGAAGGTTGATGATT 59.013 38.462 0.00 0.00 43.02 2.57
3296 6999 7.371159 TCAACACACACATTAACTGTTTTCAA 58.629 30.769 0.00 0.00 35.29 2.69
3519 7287 5.790495 GCAAAGAAAACGTAACTGCTATCAG 59.210 40.000 0.00 0.00 45.71 2.90


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

AutoCloner maintained by Alex Coulton.