Multiple sequence alignment - TraesCS3A01G372200

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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 TraesCS3A01G372200 chr3A 100.000 3633 0 0 1 3633 622898568 622902200 0.000000e+00 6709.0
1 TraesCS3A01G372200 chr3A 94.734 3646 161 6 1 3633 622817357 622820984 0.000000e+00 5640.0
2 TraesCS3A01G372200 chr3A 94.681 3647 162 8 1 3633 622717669 622721297 0.000000e+00 5631.0
3 TraesCS3A01G372200 chr3A 93.822 3658 187 7 1 3633 622708956 622712599 0.000000e+00 5467.0
4 TraesCS3A01G372200 chr3A 93.430 1796 95 2 1861 3633 622891720 622893515 0.000000e+00 2641.0
5 TraesCS3A01G372200 chr3A 94.373 1173 63 3 1861 3032 622801595 622802765 0.000000e+00 1797.0
6 TraesCS3A01G372200 chr3A 83.488 1399 167 36 312 1691 622276815 622278168 0.000000e+00 1245.0
7 TraesCS3A01G372200 chr3A 92.063 630 27 2 3026 3633 622811671 622812299 0.000000e+00 865.0
8 TraesCS3A01G372200 chr3D 90.474 1963 160 6 1696 3633 479451138 479453098 0.000000e+00 2564.0
9 TraesCS3A01G372200 chr3D 89.903 1961 169 8 1696 3633 479894612 479892658 0.000000e+00 2497.0
10 TraesCS3A01G372200 chr3D 89.843 1969 166 7 1696 3633 479914022 479912057 0.000000e+00 2497.0
11 TraesCS3A01G372200 chr3D 89.202 1704 150 11 1 1690 479449407 479451090 0.000000e+00 2097.0
12 TraesCS3A01G372200 chr3D 82.802 2006 251 40 1696 3633 478739264 478741243 0.000000e+00 1707.0
13 TraesCS3A01G372200 chr3D 84.744 1737 202 26 1922 3633 479213666 479215364 0.000000e+00 1681.0
14 TraesCS3A01G372200 chr3D 86.986 1168 121 8 2496 3633 479122407 479123573 0.000000e+00 1286.0
15 TraesCS3A01G372200 chr3D 83.855 1406 166 29 314 1691 478737845 478739217 0.000000e+00 1282.0
16 TraesCS3A01G372200 chr3D 89.527 888 63 12 1 870 479919233 479918358 0.000000e+00 1098.0
17 TraesCS3A01G372200 chr3D 87.423 811 87 7 882 1692 479914863 479914068 0.000000e+00 918.0
18 TraesCS3A01G372200 chr3D 82.075 636 94 16 860 1491 478757873 478758492 3.210000e-145 525.0
19 TraesCS3A01G372200 chr3D 87.047 193 25 0 1500 1692 479894850 479894658 6.110000e-53 219.0
20 TraesCS3A01G372200 chr3D 85.294 68 10 0 1622 1689 478751509 478751576 1.810000e-08 71.3
21 TraesCS3A01G372200 chr3B 84.526 1383 141 31 340 1691 639753513 639754853 0.000000e+00 1301.0
22 TraesCS3A01G372200 chr3B 83.298 1413 157 36 314 1691 639148634 639150002 0.000000e+00 1229.0
23 TraesCS3A01G372200 chr3B 82.790 1412 166 38 314 1691 639552861 639554229 0.000000e+00 1190.0
24 TraesCS3A01G372200 chr3B 81.234 1556 215 39 1696 3225 639150049 639151553 0.000000e+00 1184.0
25 TraesCS3A01G372200 chr3B 82.498 1417 166 35 314 1691 638959708 638961081 0.000000e+00 1168.0
26 TraesCS3A01G372200 chr3B 82.031 1408 168 37 317 1691 639398409 639399764 0.000000e+00 1120.0
27 TraesCS3A01G372200 chr3B 84.608 1059 122 16 1696 2753 639754900 639755918 0.000000e+00 1014.0
28 TraesCS3A01G372200 chr3B 87.065 201 18 7 1 195 639140835 639141033 1.700000e-53 220.0
29 TraesCS3A01G372200 chr3B 86.000 200 20 6 1 195 638952476 638952672 1.320000e-49 207.0
30 TraesCS3A01G372200 chr3B 85.572 201 20 6 1 195 639745772 639745969 6.150000e-48 202.0
31 TraesCS3A01G372200 chr3B 84.080 201 23 6 1 195 639385442 639385639 6.190000e-43 185.0


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 TraesCS3A01G372200 chr3A 622898568 622902200 3632 False 6709.000000 6709 100.0000 1 3633 1 chr3A.!!$F8 3632
1 TraesCS3A01G372200 chr3A 622817357 622820984 3627 False 5640.000000 5640 94.7340 1 3633 1 chr3A.!!$F6 3632
2 TraesCS3A01G372200 chr3A 622717669 622721297 3628 False 5631.000000 5631 94.6810 1 3633 1 chr3A.!!$F3 3632
3 TraesCS3A01G372200 chr3A 622708956 622712599 3643 False 5467.000000 5467 93.8220 1 3633 1 chr3A.!!$F2 3632
4 TraesCS3A01G372200 chr3A 622891720 622893515 1795 False 2641.000000 2641 93.4300 1861 3633 1 chr3A.!!$F7 1772
5 TraesCS3A01G372200 chr3A 622801595 622802765 1170 False 1797.000000 1797 94.3730 1861 3032 1 chr3A.!!$F4 1171
6 TraesCS3A01G372200 chr3A 622276815 622278168 1353 False 1245.000000 1245 83.4880 312 1691 1 chr3A.!!$F1 1379
7 TraesCS3A01G372200 chr3A 622811671 622812299 628 False 865.000000 865 92.0630 3026 3633 1 chr3A.!!$F5 607
8 TraesCS3A01G372200 chr3D 479449407 479453098 3691 False 2330.500000 2564 89.8380 1 3633 2 chr3D.!!$F6 3632
9 TraesCS3A01G372200 chr3D 479213666 479215364 1698 False 1681.000000 1681 84.7440 1922 3633 1 chr3D.!!$F4 1711
10 TraesCS3A01G372200 chr3D 479912057 479919233 7176 True 1504.333333 2497 88.9310 1 3633 3 chr3D.!!$R2 3632
11 TraesCS3A01G372200 chr3D 478737845 478741243 3398 False 1494.500000 1707 83.3285 314 3633 2 chr3D.!!$F5 3319
12 TraesCS3A01G372200 chr3D 479892658 479894850 2192 True 1358.000000 2497 88.4750 1500 3633 2 chr3D.!!$R1 2133
13 TraesCS3A01G372200 chr3D 479122407 479123573 1166 False 1286.000000 1286 86.9860 2496 3633 1 chr3D.!!$F3 1137
14 TraesCS3A01G372200 chr3D 478757873 478758492 619 False 525.000000 525 82.0750 860 1491 1 chr3D.!!$F2 631
15 TraesCS3A01G372200 chr3B 639148634 639151553 2919 False 1206.500000 1229 82.2660 314 3225 2 chr3B.!!$F8 2911
16 TraesCS3A01G372200 chr3B 639552861 639554229 1368 False 1190.000000 1190 82.7900 314 1691 1 chr3B.!!$F6 1377
17 TraesCS3A01G372200 chr3B 638959708 638961081 1373 False 1168.000000 1168 82.4980 314 1691 1 chr3B.!!$F2 1377
18 TraesCS3A01G372200 chr3B 639753513 639755918 2405 False 1157.500000 1301 84.5670 340 2753 2 chr3B.!!$F9 2413
19 TraesCS3A01G372200 chr3B 639398409 639399764 1355 False 1120.000000 1120 82.0310 317 1691 1 chr3B.!!$F5 1374

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
988 4538 1.145571 ATAAATAGGGGGAGCGGCAA 58.854 50.0 1.45 0.0 0.0 4.52 F
1179 4761 0.250513 ACGGCAGTCTTCCATCTTCC 59.749 55.0 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 5860 0.674895 GCAACTTCGCACCTCCTCAT 60.675 55.0 0.00 0.0 0.00 2.90 R
3113 6835 0.326238 AGGCTATCCGGACCCTCAAA 60.326 55.0 6.12 0.0 37.47 2.69 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
27 28 4.588951 AGAGTTAGTGGAACATGAGACACA 59.411 41.667 16.36 0.39 44.52 3.72
123 124 5.458215 GCCATTATTTCTATCTGAACCCCCT 60.458 44.000 0.00 0.00 33.88 4.79
212 214 8.253113 GGACAATATGACATTTTTCTGGAACAT 58.747 33.333 0.00 0.00 38.20 2.71
400 409 2.090550 TCTAGATGATCCAGGGCTCCAA 60.091 50.000 0.00 0.00 0.00 3.53
583 619 8.239314 CGTGTTGTAAGACTCCTTGTACTAATA 58.761 37.037 0.00 0.00 33.94 0.98
756 794 3.382546 GCTATTGAATGGAACCAGCACAT 59.617 43.478 0.00 0.00 0.00 3.21
789 827 5.196341 TGTCTCATATACCAGGCTTAACG 57.804 43.478 0.00 0.00 0.00 3.18
827 866 3.729966 GCTTTGGCAGTACCCTATCTAC 58.270 50.000 0.00 0.00 37.83 2.59
962 4509 4.964593 TGATGCTTATCTCTTGCATGCTA 58.035 39.130 20.33 10.88 45.90 3.49
988 4538 1.145571 ATAAATAGGGGGAGCGGCAA 58.854 50.000 1.45 0.00 0.00 4.52
1054 4630 2.048127 GACCACAGTGGCGAGGAC 60.048 66.667 20.48 1.00 42.67 3.85
1071 4647 1.412710 GGACAGATAGGATGGCGTCAA 59.587 52.381 9.27 0.00 0.00 3.18
1179 4761 0.250513 ACGGCAGTCTTCCATCTTCC 59.749 55.000 0.00 0.00 0.00 3.46
1221 4803 3.457234 CAATACTCTATGTGCGAGGCAA 58.543 45.455 0.00 0.00 41.47 4.52
1299 4881 3.591254 GAGTTCCAAGCGGCGACCT 62.591 63.158 12.98 0.00 0.00 3.85
1300 4882 2.221906 GAGTTCCAAGCGGCGACCTA 62.222 60.000 12.98 0.00 0.00 3.08
1361 4943 3.083997 GATGGAGGCCGAGGTGGT 61.084 66.667 0.00 0.00 41.21 4.16
1626 5208 0.916086 TGTCAAGGTTGGTGTGGTCT 59.084 50.000 0.00 0.00 0.00 3.85
1694 5360 2.158755 CCATGGACAGATGAACCCTACC 60.159 54.545 5.56 0.00 0.00 3.18
1827 5493 4.988716 TGAGCCCAGGGTCGTCGT 62.989 66.667 7.55 0.00 44.68 4.34
1904 5570 1.375908 GATGGAGAACAGCGGCACA 60.376 57.895 1.45 0.00 0.00 4.57
2007 5673 3.049674 CCACACAATCGCGTGGCT 61.050 61.111 5.77 0.00 45.77 4.75
2044 5711 1.126488 TGGCTGCCAAAATTGTTGGA 58.874 45.000 21.08 0.00 42.06 3.53
2056 5723 7.575343 GCCAAAATTGTTGGATTTATGCAATGT 60.575 33.333 9.95 0.00 42.06 2.71
2139 5807 0.621609 ACCGGCAGGCTTATACCAAA 59.378 50.000 0.00 0.00 42.76 3.28
2192 5860 5.913137 GAGGAGAACTCTCATCTGAAAGA 57.087 43.478 12.88 0.00 46.73 2.52
2213 5881 1.004440 AGGAGGTGCGAAGTTGCTC 60.004 57.895 0.00 0.00 35.36 4.26
2414 6088 6.538742 GCTTGTGACAATCTAAATGCTAGGTA 59.461 38.462 0.00 0.00 0.00 3.08
2458 6134 2.622942 GCTGATGAAAACACCTTGTGGA 59.377 45.455 0.00 0.00 37.94 4.02
2493 6169 5.407407 TTTCTTACAGCTAGTGGAGAAGG 57.593 43.478 0.00 0.00 36.08 3.46
2505 6181 0.463474 GGAGAAGGTGATGGAGCAGC 60.463 60.000 0.00 0.00 36.57 5.25
2604 6280 3.209410 CACCATTCAGCTTCCATAGTCC 58.791 50.000 0.00 0.00 0.00 3.85
2710 6401 4.675063 ACCCATAAGAACCCAAATGTCT 57.325 40.909 0.00 0.00 0.00 3.41
2818 6509 6.868339 GGAACAAAAGCAAGTTAGCAATATGT 59.132 34.615 0.00 0.00 36.85 2.29
3077 6799 2.504681 CGTTCGCAATGCTTGGGC 60.505 61.111 2.94 0.00 42.68 5.36
3113 6835 1.593787 CTCCATCGTGGCTCACTGT 59.406 57.895 4.21 0.00 37.47 3.55
3333 7074 6.482308 GTGTGTGTTGATGGTAATACCCTATC 59.518 42.308 7.03 5.01 37.50 2.08
3334 7075 6.157123 TGTGTGTTGATGGTAATACCCTATCA 59.843 38.462 7.03 7.60 37.50 2.15
3486 7281 2.618241 TGAATCTGGTTGTCTTGTGTGC 59.382 45.455 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.416296 CCGCACAAACATGCATCATCTT 60.416 45.455 0.00 0.00 46.47 2.40
123 124 1.080638 AACCATAGGGGGTCAGCAAA 58.919 50.000 0.00 0.00 41.32 3.68
162 163 5.278660 CCTTCAAGGAGTGGAAAATCAACAG 60.279 44.000 0.00 0.00 37.67 3.16
212 214 8.165239 ACAAAAATGTCATACTAACTCTTGCA 57.835 30.769 0.00 0.00 0.00 4.08
527 562 8.868522 TCTTCAATTCATAGAGGTGACAAATT 57.131 30.769 0.00 0.00 0.00 1.82
583 619 2.420967 CCGTTTCTAATTCGGGGGATGT 60.421 50.000 0.00 0.00 40.49 3.06
827 866 3.204526 AGATAGTTCGTCTCGTACTGGG 58.795 50.000 10.62 0.00 37.94 4.45
869 922 9.418361 AGGTGGGCTATAGATAGATAGATAGAT 57.582 37.037 3.21 0.00 32.00 1.98
870 923 8.822246 AGGTGGGCTATAGATAGATAGATAGA 57.178 38.462 3.21 0.00 32.00 1.98
871 924 9.875708 AAAGGTGGGCTATAGATAGATAGATAG 57.124 37.037 3.21 0.00 32.00 2.08
873 926 9.567702 AAAAAGGTGGGCTATAGATAGATAGAT 57.432 33.333 3.21 0.00 32.00 1.98
874 927 8.974292 AAAAAGGTGGGCTATAGATAGATAGA 57.026 34.615 3.21 0.00 32.00 1.98
875 928 8.816894 TGAAAAAGGTGGGCTATAGATAGATAG 58.183 37.037 3.21 0.00 32.05 2.08
876 929 8.736097 TGAAAAAGGTGGGCTATAGATAGATA 57.264 34.615 3.21 0.00 32.05 1.98
962 4509 3.055094 CGCTCCCCCTATTTATAGCATGT 60.055 47.826 0.00 0.00 0.00 3.21
988 4538 0.916086 TGGTGTGTGGTCCAGTCTTT 59.084 50.000 0.00 0.00 0.00 2.52
1054 4630 3.459232 TCTTTGACGCCATCCTATCTG 57.541 47.619 0.00 0.00 0.00 2.90
1071 4647 2.839486 TTCACGTCCTTGCTCATCTT 57.161 45.000 0.00 0.00 0.00 2.40
1130 4706 1.254284 CCGTCTGCTCCTCACCTTCT 61.254 60.000 0.00 0.00 0.00 2.85
1221 4803 0.188342 ATGGACCCAAAGTTGTGCCT 59.812 50.000 0.00 0.00 0.00 4.75
1299 4881 0.998928 ATGCCCACCAAGACACCATA 59.001 50.000 0.00 0.00 0.00 2.74
1300 4882 0.612732 CATGCCCACCAAGACACCAT 60.613 55.000 0.00 0.00 0.00 3.55
1339 4921 1.153289 CCTCGGCCTCCATCAACAG 60.153 63.158 0.00 0.00 0.00 3.16
1342 4924 2.669133 CCACCTCGGCCTCCATCAA 61.669 63.158 0.00 0.00 0.00 2.57
1361 4943 0.986527 TGCTTCCTCCTGCATCTTCA 59.013 50.000 0.00 0.00 33.94 3.02
1755 5421 1.696097 GGCACCACGACCATCCCTAT 61.696 60.000 0.00 0.00 0.00 2.57
1827 5493 1.001120 TCATGGTGCTCCTCCCGTA 59.999 57.895 6.34 0.00 34.23 4.02
2007 5673 2.290071 GCCAAGTAAGTACCTGCTTCCA 60.290 50.000 0.00 0.00 0.00 3.53
2093 5760 6.613233 AGAAAGACATAGAGTGTAAGTGTCG 58.387 40.000 0.00 0.00 42.36 4.35
2139 5807 3.067833 GTTTAGTTCGGCTTCAAGCTCT 58.932 45.455 9.83 5.86 41.99 4.09
2192 5860 0.674895 GCAACTTCGCACCTCCTCAT 60.675 55.000 0.00 0.00 0.00 2.90
2202 5870 0.874390 TCATTGGTGAGCAACTTCGC 59.126 50.000 0.00 0.00 0.00 4.70
2213 5881 7.441760 TGAATTTTCTCATGGTTTTCATTGGTG 59.558 33.333 0.00 0.00 32.92 4.17
2414 6088 5.342433 CACACACACATTGACTGTTTGAAT 58.658 37.500 0.00 0.00 37.68 2.57
2493 6169 1.751927 CCTTGGGCTGCTCCATCAC 60.752 63.158 10.07 0.00 36.58 3.06
2505 6181 2.697751 TGGTGTTCACATTTTCCTTGGG 59.302 45.455 5.32 0.00 0.00 4.12
2604 6280 1.146485 CTCATCCTCCTGCCAGCAG 59.854 63.158 12.78 12.78 43.26 4.24
2710 6401 3.509575 ACTTGCTTGACCAGAAAAACACA 59.490 39.130 0.00 0.00 0.00 3.72
2778 6469 4.320608 TTGTTCCATTTGCCTGAAGTTC 57.679 40.909 0.00 0.00 0.00 3.01
3077 6799 0.912486 AGGGGAAAGGGAATCGACTG 59.088 55.000 0.00 0.00 0.00 3.51
3113 6835 0.326238 AGGCTATCCGGACCCTCAAA 60.326 55.000 6.12 0.00 37.47 2.69
3333 7074 6.761242 TCACCATCTGTAAAAATATCTCGGTG 59.239 38.462 0.00 0.00 40.25 4.94
3334 7075 6.884832 TCACCATCTGTAAAAATATCTCGGT 58.115 36.000 0.00 0.00 0.00 4.69
3486 7281 5.403166 CCATTGTTGTTGTAGTTGCATCAAG 59.597 40.000 0.00 0.00 31.29 3.02


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

AutoCloner maintained by Alex Coulton.