Multiple sequence alignment - TraesCS3A01G372000

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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 TraesCS3A01G372000 chr3A 100.000 3515 0 0 1 3515 622717728 622721242 0.000000e+00 6492.0
1 TraesCS3A01G372000 chr3A 96.275 3517 126 5 1 3515 622817416 622820929 0.000000e+00 5764.0
2 TraesCS3A01G372000 chr3A 94.566 3533 160 8 1 3515 622898627 622902145 0.000000e+00 5432.0
3 TraesCS3A01G372000 chr3A 93.907 3545 171 10 1 3515 622709015 622712544 0.000000e+00 5308.0
4 TraesCS3A01G372000 chr3A 93.685 1742 84 5 1799 3515 622891720 622893460 0.000000e+00 2584.0
5 TraesCS3A01G372000 chr3A 94.118 1173 65 4 1799 2969 622801595 622802765 0.000000e+00 1781.0
6 TraesCS3A01G372000 chr3A 92.348 575 21 2 2963 3515 622811671 622812244 0.000000e+00 797.0
7 TraesCS3A01G372000 chr3D 90.728 1909 151 5 1632 3515 479451136 479453043 0.000000e+00 2521.0
8 TraesCS3A01G372000 chr3D 90.461 1908 152 9 1632 3515 479894614 479892713 0.000000e+00 2488.0
9 TraesCS3A01G372000 chr3D 90.188 1916 153 8 1632 3515 479914024 479912112 0.000000e+00 2464.0
10 TraesCS3A01G372000 chr3D 89.810 1629 161 5 1 1628 479449466 479451090 0.000000e+00 2084.0
11 TraesCS3A01G372000 chr3D 83.308 1953 231 42 1632 3515 478739262 478741188 0.000000e+00 1712.0
12 TraesCS3A01G372000 chr3D 85.282 1685 178 33 1860 3515 479213666 479215309 0.000000e+00 1674.0
13 TraesCS3A01G372000 chr3D 84.544 1404 157 30 255 1629 478737845 478739217 0.000000e+00 1336.0
14 TraesCS3A01G372000 chr3D 86.482 1117 119 7 2430 3515 479122403 479123518 0.000000e+00 1197.0
15 TraesCS3A01G372000 chr3D 88.782 829 76 10 1 824 479919174 479918358 0.000000e+00 1000.0
16 TraesCS3A01G372000 chr3D 87.546 811 86 7 820 1630 479914863 479914068 0.000000e+00 924.0
17 TraesCS3A01G372000 chr3B 85.412 1371 148 24 281 1629 639753513 639754853 0.000000e+00 1376.0
18 TraesCS3A01G372000 chr3B 83.440 1401 179 24 255 1629 638959708 638961081 0.000000e+00 1253.0
19 TraesCS3A01G372000 chr3B 83.262 1398 182 28 255 1629 639552861 639554229 0.000000e+00 1238.0
20 TraesCS3A01G372000 chr3B 81.386 1558 212 38 1632 3162 639150047 639151553 0.000000e+00 1199.0
21 TraesCS3A01G372000 chr3B 82.581 1395 181 29 258 1629 639398409 639399764 0.000000e+00 1173.0
22 TraesCS3A01G372000 chr3B 84.920 1061 119 22 1632 2691 639754898 639755918 0.000000e+00 1035.0
23 TraesCS3A01G372000 chr3B 80.488 861 90 38 2688 3515 639756000 639756815 3.910000e-164 588.0
24 TraesCS3A01G372000 chr3B 80.189 212 35 5 2296 2507 639463932 639464136 6.080000e-33 152.0
25 TraesCS3A01G372000 chr3B 84.507 142 14 6 1 136 639140894 639141033 2.200000e-27 134.0
26 TraesCS3A01G372000 chr3B 83.099 142 15 6 1 136 639745831 639745969 1.710000e-23 121.0
27 TraesCS3A01G372000 chr3B 79.618 157 30 2 1474 1629 639007333 639007488 1.030000e-20 111.0
28 TraesCS3A01G372000 chr3B 97.143 35 1 0 1594 1628 639658493 639658527 3.790000e-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 TraesCS3A01G372000 chr3A 622717728 622721242 3514 False 6492.000000 6492 100.000000 1 3515 1 chr3A.!!$F2 3514
1 TraesCS3A01G372000 chr3A 622817416 622820929 3513 False 5764.000000 5764 96.275000 1 3515 1 chr3A.!!$F5 3514
2 TraesCS3A01G372000 chr3A 622898627 622902145 3518 False 5432.000000 5432 94.566000 1 3515 1 chr3A.!!$F7 3514
3 TraesCS3A01G372000 chr3A 622709015 622712544 3529 False 5308.000000 5308 93.907000 1 3515 1 chr3A.!!$F1 3514
4 TraesCS3A01G372000 chr3A 622891720 622893460 1740 False 2584.000000 2584 93.685000 1799 3515 1 chr3A.!!$F6 1716
5 TraesCS3A01G372000 chr3A 622801595 622802765 1170 False 1781.000000 1781 94.118000 1799 2969 1 chr3A.!!$F3 1170
6 TraesCS3A01G372000 chr3A 622811671 622812244 573 False 797.000000 797 92.348000 2963 3515 1 chr3A.!!$F4 552
7 TraesCS3A01G372000 chr3D 479892713 479894614 1901 True 2488.000000 2488 90.461000 1632 3515 1 chr3D.!!$R1 1883
8 TraesCS3A01G372000 chr3D 479449466 479453043 3577 False 2302.500000 2521 90.269000 1 3515 2 chr3D.!!$F4 3514
9 TraesCS3A01G372000 chr3D 479213666 479215309 1643 False 1674.000000 1674 85.282000 1860 3515 1 chr3D.!!$F2 1655
10 TraesCS3A01G372000 chr3D 478737845 478741188 3343 False 1524.000000 1712 83.926000 255 3515 2 chr3D.!!$F3 3260
11 TraesCS3A01G372000 chr3D 479912112 479919174 7062 True 1462.666667 2464 88.838667 1 3515 3 chr3D.!!$R2 3514
12 TraesCS3A01G372000 chr3D 479122403 479123518 1115 False 1197.000000 1197 86.482000 2430 3515 1 chr3D.!!$F1 1085
13 TraesCS3A01G372000 chr3B 638959708 638961081 1373 False 1253.000000 1253 83.440000 255 1629 1 chr3B.!!$F1 1374
14 TraesCS3A01G372000 chr3B 639552861 639554229 1368 False 1238.000000 1238 83.262000 255 1629 1 chr3B.!!$F7 1374
15 TraesCS3A01G372000 chr3B 639150047 639151553 1506 False 1199.000000 1199 81.386000 1632 3162 1 chr3B.!!$F4 1530
16 TraesCS3A01G372000 chr3B 639398409 639399764 1355 False 1173.000000 1173 82.581000 258 1629 1 chr3B.!!$F5 1371
17 TraesCS3A01G372000 chr3B 639753513 639756815 3302 False 999.666667 1376 83.606667 281 3515 3 chr3B.!!$F10 3234

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
169 171 1.068474 ACACGCAAGAGTTCGTATGC 58.932 50.000 0.00 0.0 38.22 3.14 F
726 759 1.071071 CACAACCCCCGAGTTTGTCTA 59.929 52.381 0.00 0.0 0.00 2.59 F
1093 4653 0.622136 TGAGGAGCAGATGGTTGCAT 59.378 50.000 0.52 0.0 46.47 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1072 4626 0.321919 GCAACCATCTGCTCCTCACA 60.322 55.0 0.0 0.0 39.34 3.58 R
1821 5465 1.091771 CGCCGCTGTTCTCCATCATT 61.092 55.0 0.0 0.0 0.00 2.57 R
2997 6808 1.225376 CTACCCAAGCGTTGCGAACA 61.225 55.0 0.0 0.0 0.00 3.18 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
92 93 6.040209 TGACCGCCTACAGTTTTTCTAATA 57.960 37.500 0.00 0.00 0.00 0.98
169 171 1.068474 ACACGCAAGAGTTCGTATGC 58.932 50.000 0.00 0.00 38.22 3.14
459 478 9.668497 ACTTTACCTTTTGTCACCTATCTATTC 57.332 33.333 0.00 0.00 0.00 1.75
544 565 4.631234 ACTCCTTGTACTAATCCATCCCA 58.369 43.478 0.00 0.00 0.00 4.37
631 662 7.331026 GCATATACTTATCTCCCATGCTAACA 58.669 38.462 0.00 0.00 35.56 2.41
665 697 1.445582 CGTTGGTACTGAGGCGTCC 60.446 63.158 3.56 0.00 0.00 4.79
710 743 3.193267 GCTATTGAATGGAACCAGCACAA 59.807 43.478 0.00 6.23 0.00 3.33
726 759 1.071071 CACAACCCCCGAGTTTGTCTA 59.929 52.381 0.00 0.00 0.00 2.59
734 767 4.553323 CCCCGAGTTTGTCTAATATACCG 58.447 47.826 0.00 0.00 0.00 4.02
793 835 5.782677 ACCCTATCTATCCAGTACGAGAT 57.217 43.478 6.04 6.04 33.32 2.75
1004 4558 1.272203 GGCGAGGAGAGATAGGATGGA 60.272 57.143 0.00 0.00 0.00 3.41
1072 4626 4.430765 ACCCGCGCGTTCTCGAAT 62.431 61.111 29.95 1.46 39.71 3.34
1085 4639 2.382882 TCTCGAATGTGAGGAGCAGAT 58.617 47.619 0.00 0.00 36.61 2.90
1093 4653 0.622136 TGAGGAGCAGATGGTTGCAT 59.378 50.000 0.52 0.00 46.47 3.96
1154 4714 4.302455 GAGATGCAATACTCTATGTGCGT 58.698 43.478 10.32 0.00 39.92 5.24
1267 4827 3.267233 TGGGCATGGAGGTGGCTT 61.267 61.111 0.00 0.00 43.55 4.35
1282 4842 2.358737 CTTCGGTGGTGGGTGCTC 60.359 66.667 0.00 0.00 0.00 4.26
1754 5398 2.064581 GGGTGGGTATCGTGAGCCT 61.065 63.158 8.60 0.00 37.88 4.58
1805 5449 3.513912 ACGGAGGTTGACATGATGAACTA 59.486 43.478 0.00 0.00 0.00 2.24
1821 5465 3.449377 TGAACTATATGGGCGACAGAACA 59.551 43.478 0.00 0.00 0.00 3.18
2046 5692 3.454812 AGGTTGGTGACACTTACACTCTT 59.545 43.478 5.39 0.00 42.67 2.85
2146 5792 4.710375 TCTGAAAGCTAAGGAGGTACGAAT 59.290 41.667 0.00 0.00 31.56 3.34
2265 5912 7.121020 ACAATTTTGCTGACCAAGAAACAAATT 59.879 29.630 0.00 0.00 34.34 1.82
2347 6000 5.450592 TTGCTTGTGACAATCTAAATGCA 57.549 34.783 0.00 0.00 0.00 3.96
2617 6287 7.447594 CGGGGTGGTATCATAATTTACTAGTT 58.552 38.462 0.00 0.00 0.00 2.24
2646 6317 2.159179 ACCCATAAGGACCCAAATGC 57.841 50.000 0.00 0.00 39.89 3.56
2873 6657 5.503662 TGACACACGAGTTGAGTTTAGTA 57.496 39.130 0.00 0.00 0.00 1.82
2879 6663 5.909610 ACACGAGTTGAGTTTAGTAACGTAC 59.090 40.000 0.00 0.00 39.31 3.67
2997 6808 1.187087 GAGACTTGACGATGGTCCCT 58.813 55.000 5.33 0.00 42.73 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 7.916914 TTGGAGTATTAGAAAAACTGTAGGC 57.083 36.000 0.00 0.00 0.00 3.93
177 180 7.230712 TCTCATACTGACTCTTGTGTGTTCTAA 59.769 37.037 0.00 0.00 0.00 2.10
250 256 6.882678 GGACCACAACTACACCAATATAGTTT 59.117 38.462 0.00 0.00 39.15 2.66
368 378 7.362401 GGAGAAAGTGAGACATGCATGTTAAAT 60.362 37.037 31.82 18.51 41.95 1.40
459 478 5.599732 TGTGGTGTCATCAAAAATGGAAAG 58.400 37.500 0.00 0.00 0.00 2.62
544 565 3.160777 AGATCGCCGTTTCTAATTCGT 57.839 42.857 0.00 0.00 0.00 3.85
606 637 7.331026 TGTTAGCATGGGAGATAAGTATATGC 58.669 38.462 0.00 0.00 39.61 3.14
665 697 2.827051 CGATGATGGTTGCCGCTGG 61.827 63.158 0.00 0.00 0.00 4.85
710 743 4.346127 GGTATATTAGACAAACTCGGGGGT 59.654 45.833 0.00 0.00 0.00 4.95
726 759 4.457466 CCACAAGTTAAGCCCGGTATATT 58.543 43.478 0.00 0.00 0.00 1.28
734 767 1.862602 CGTGGCCACAAGTTAAGCCC 61.863 60.000 34.16 3.99 45.14 5.19
1004 4558 1.740380 CGTCCTTGCTCATGTCCGATT 60.740 52.381 0.00 0.00 0.00 3.34
1072 4626 0.321919 GCAACCATCTGCTCCTCACA 60.322 55.000 0.00 0.00 39.34 3.58
1093 4653 4.373116 GGAAGACTGCCGTGCCGA 62.373 66.667 0.00 0.00 0.00 5.54
1135 4695 3.133691 CCACGCACATAGAGTATTGCAT 58.866 45.455 0.00 0.00 34.49 3.96
1154 4714 2.132996 CCAAAGTTGTGCCCTGCCA 61.133 57.895 0.00 0.00 0.00 4.92
1267 4827 2.927856 ATGAGCACCCACCACCGA 60.928 61.111 0.00 0.00 0.00 4.69
1300 4860 2.165998 GTTGCTTCCTCCTGCATCTTT 58.834 47.619 0.00 0.00 39.07 2.52
1754 5398 3.687321 CTCCCGTCCGACGACCCTA 62.687 68.421 22.40 2.06 46.05 3.53
1805 5449 3.558931 TCATTGTTCTGTCGCCCATAT 57.441 42.857 0.00 0.00 0.00 1.78
1821 5465 1.091771 CGCCGCTGTTCTCCATCATT 61.092 55.000 0.00 0.00 0.00 2.57
2046 5692 3.735591 CCTGTCCGGTTAAGAAAGACAA 58.264 45.455 0.00 0.00 37.04 3.18
2146 5792 5.538053 TCTCATGGTTTCATTGGTAAGCAAA 59.462 36.000 0.00 1.77 35.81 3.68
2214 5861 5.021033 TCTGCAACAAAATGGTGAAACAT 57.979 34.783 0.00 0.00 37.20 2.71
2265 5912 5.821097 TGATGGTGGGAAAATGTACATACA 58.179 37.500 9.21 1.24 40.98 2.29
2347 6000 4.949856 ACACATTGACTGTTTGAAGACCTT 59.050 37.500 0.00 0.00 35.29 3.50
2494 6152 2.255406 CTATCCCCAGATGCAGCTACT 58.745 52.381 3.06 0.00 33.67 2.57
2617 6287 4.227982 GGGTCCTTATGGGTTTTAGGTACA 59.772 45.833 0.00 0.00 36.25 2.90
2873 6657 2.415857 TGTGAAAAAGTGTGCGTACGTT 59.584 40.909 17.90 0.00 0.00 3.99
2879 6663 2.535166 CACCAATGTGAAAAAGTGTGCG 59.465 45.455 0.00 0.00 45.76 5.34
2997 6808 1.225376 CTACCCAAGCGTTGCGAACA 61.225 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.