Multiple sequence alignment - TraesCS2A01G132000

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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 TraesCS2A01G132000 chr2A 100.000 3069 0 0 1 3069 79273048 79269980 0.000000e+00 5668
1 TraesCS2A01G132000 chr3B 93.995 2831 122 21 1 2804 39884862 39882053 0.000000e+00 4242
2 TraesCS2A01G132000 chr3B 94.665 2493 118 4 1 2480 176165694 176168184 0.000000e+00 3853
3 TraesCS2A01G132000 chr1A 96.024 2490 91 3 1 2489 88195995 88198477 0.000000e+00 4043
4 TraesCS2A01G132000 chr2B 95.548 2493 98 6 1 2480 697736224 697733732 0.000000e+00 3976
5 TraesCS2A01G132000 chr2B 94.876 1366 57 2 1128 2480 38158073 38159438 0.000000e+00 2122
6 TraesCS2A01G132000 chr2B 94.726 986 39 2 1508 2480 38111217 38112202 0.000000e+00 1520
7 TraesCS2A01G132000 chr5A 94.676 2517 99 6 1 2495 595563984 595561481 0.000000e+00 3873
8 TraesCS2A01G132000 chr5A 90.492 589 55 1 2481 3069 244747545 244748132 0.000000e+00 776
9 TraesCS2A01G132000 chr6D 96.747 2121 68 1 1 2120 431077564 431075444 0.000000e+00 3533
10 TraesCS2A01G132000 chr6D 96.275 2121 78 1 1 2120 419417555 419419675 0.000000e+00 3478
11 TraesCS2A01G132000 chr6D 96.132 2120 78 2 1 2120 327573643 327571528 0.000000e+00 3458
12 TraesCS2A01G132000 chr6D 96.087 2121 82 1 1 2120 12091235 12093355 0.000000e+00 3456
13 TraesCS2A01G132000 chr6D 94.848 330 5 1 2163 2480 12093356 12093685 3.530000e-139 505
14 TraesCS2A01G132000 chr1D 96.173 1803 66 1 1 1800 490865547 490867349 0.000000e+00 2944
15 TraesCS2A01G132000 chr1D 94.864 701 21 2 1795 2480 490872665 490873365 0.000000e+00 1081
16 TraesCS2A01G132000 chr1D 90.598 585 51 3 2481 3065 451355245 451354665 0.000000e+00 773
17 TraesCS2A01G132000 chr7D 91.525 590 49 1 2481 3069 269447015 269447604 0.000000e+00 811
18 TraesCS2A01G132000 chr3D 90.460 587 52 4 2481 3065 573491441 573490857 0.000000e+00 771
19 TraesCS2A01G132000 chr7A 90.323 589 51 5 2481 3069 424527547 424528129 0.000000e+00 767
20 TraesCS2A01G132000 chr5D 90.101 596 52 3 2481 3069 59754097 59753502 0.000000e+00 767
21 TraesCS2A01G132000 chr5D 90.290 587 52 5 2481 3065 412911558 412912141 0.000000e+00 763
22 TraesCS2A01G132000 chr2D 90.153 589 57 1 2481 3069 120383485 120382898 0.000000e+00 765
23 TraesCS2A01G132000 chr7B 90.102 586 49 5 2481 3065 221056768 221056191 0.000000e+00 752


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 TraesCS2A01G132000 chr2A 79269980 79273048 3068 True 5668.0 5668 100.0000 1 3069 1 chr2A.!!$R1 3068
1 TraesCS2A01G132000 chr3B 39882053 39884862 2809 True 4242.0 4242 93.9950 1 2804 1 chr3B.!!$R1 2803
2 TraesCS2A01G132000 chr3B 176165694 176168184 2490 False 3853.0 3853 94.6650 1 2480 1 chr3B.!!$F1 2479
3 TraesCS2A01G132000 chr1A 88195995 88198477 2482 False 4043.0 4043 96.0240 1 2489 1 chr1A.!!$F1 2488
4 TraesCS2A01G132000 chr2B 697733732 697736224 2492 True 3976.0 3976 95.5480 1 2480 1 chr2B.!!$R1 2479
5 TraesCS2A01G132000 chr2B 38158073 38159438 1365 False 2122.0 2122 94.8760 1128 2480 1 chr2B.!!$F2 1352
6 TraesCS2A01G132000 chr2B 38111217 38112202 985 False 1520.0 1520 94.7260 1508 2480 1 chr2B.!!$F1 972
7 TraesCS2A01G132000 chr5A 595561481 595563984 2503 True 3873.0 3873 94.6760 1 2495 1 chr5A.!!$R1 2494
8 TraesCS2A01G132000 chr5A 244747545 244748132 587 False 776.0 776 90.4920 2481 3069 1 chr5A.!!$F1 588
9 TraesCS2A01G132000 chr6D 431075444 431077564 2120 True 3533.0 3533 96.7470 1 2120 1 chr6D.!!$R2 2119
10 TraesCS2A01G132000 chr6D 419417555 419419675 2120 False 3478.0 3478 96.2750 1 2120 1 chr6D.!!$F1 2119
11 TraesCS2A01G132000 chr6D 327571528 327573643 2115 True 3458.0 3458 96.1320 1 2120 1 chr6D.!!$R1 2119
12 TraesCS2A01G132000 chr6D 12091235 12093685 2450 False 1980.5 3456 95.4675 1 2480 2 chr6D.!!$F2 2479
13 TraesCS2A01G132000 chr1D 490865547 490867349 1802 False 2944.0 2944 96.1730 1 1800 1 chr1D.!!$F1 1799
14 TraesCS2A01G132000 chr1D 490872665 490873365 700 False 1081.0 1081 94.8640 1795 2480 1 chr1D.!!$F2 685
15 TraesCS2A01G132000 chr1D 451354665 451355245 580 True 773.0 773 90.5980 2481 3065 1 chr1D.!!$R1 584
16 TraesCS2A01G132000 chr7D 269447015 269447604 589 False 811.0 811 91.5250 2481 3069 1 chr7D.!!$F1 588
17 TraesCS2A01G132000 chr3D 573490857 573491441 584 True 771.0 771 90.4600 2481 3065 1 chr3D.!!$R1 584
18 TraesCS2A01G132000 chr7A 424527547 424528129 582 False 767.0 767 90.3230 2481 3069 1 chr7A.!!$F1 588
19 TraesCS2A01G132000 chr5D 59753502 59754097 595 True 767.0 767 90.1010 2481 3069 1 chr5D.!!$R1 588
20 TraesCS2A01G132000 chr5D 412911558 412912141 583 False 763.0 763 90.2900 2481 3065 1 chr5D.!!$F1 584
21 TraesCS2A01G132000 chr2D 120382898 120383485 587 True 765.0 765 90.1530 2481 3069 1 chr2D.!!$R1 588
22 TraesCS2A01G132000 chr7B 221056191 221056768 577 True 752.0 752 90.1020 2481 3065 1 chr7B.!!$R1 584

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
178 179 0.036388 TCAACCTCCCTAGCTTTGCG 60.036 55.000 0.0 0.0 0.00 4.85 F
438 439 0.176680 GTGGACTGCTCCGATGACAT 59.823 55.000 0.0 0.0 39.88 3.06 F
601 605 0.896923 TTTGGAATGGATGTGCTGCC 59.103 50.000 0.0 0.0 0.00 4.85 F
774 778 1.202830 TGGTGTTACTCGGTTTGCCAT 60.203 47.619 0.0 0.0 34.09 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1883 0.111253 CCCTGTTTGGTGCCTCTTCT 59.889 55.000 0.00 0.00 0.00 2.85 R
1971 1978 0.179045 ACGCATAGCCATCAAGGACC 60.179 55.000 0.00 0.00 41.22 4.46 R
2012 2019 6.493115 TCAGACTCTGATTCAGAAGAAGAAGT 59.507 38.462 16.79 9.51 40.18 3.01 R
2764 2824 3.167485 TCCAAGAAGAATGGCAAGCAAT 58.833 40.909 0.00 0.00 37.88 3.56 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
178 179 0.036388 TCAACCTCCCTAGCTTTGCG 60.036 55.000 0.00 0.00 0.00 4.85
256 257 7.255381 CCATATGAGATGAGTGGACCATTTTTC 60.255 40.741 3.65 0.00 31.59 2.29
327 328 1.001641 GGGAGCTCACAGGTTGCAT 60.002 57.895 17.19 0.00 0.00 3.96
418 419 4.933505 TGGTGTTTGCTTCATTGATTCA 57.066 36.364 0.00 0.00 0.00 2.57
438 439 0.176680 GTGGACTGCTCCGATGACAT 59.823 55.000 0.00 0.00 39.88 3.06
556 557 6.703607 GTGTGAATGTATCAGCAGCTAGTATT 59.296 38.462 0.00 0.00 39.19 1.89
568 569 6.259608 CAGCAGCTAGTATTCTAACAGCAAAT 59.740 38.462 0.00 0.00 30.64 2.32
601 605 0.896923 TTTGGAATGGATGTGCTGCC 59.103 50.000 0.00 0.00 0.00 4.85
642 646 1.283321 GGAGGATCTTGGGAAGCTTGT 59.717 52.381 2.10 0.00 33.73 3.16
655 659 3.005791 GGAAGCTTGTACCAGTTGCAAAT 59.994 43.478 2.10 0.00 0.00 2.32
774 778 1.202830 TGGTGTTACTCGGTTTGCCAT 60.203 47.619 0.00 0.00 34.09 4.40
995 1001 3.341823 GCAGAATGGACAGTGATGTTCT 58.658 45.455 0.00 0.00 35.86 3.01
1030 1036 5.759059 TCTTCCATGGATTAATGCTTGAGT 58.241 37.500 17.06 0.00 0.00 3.41
1041 1047 7.327032 GGATTAATGCTTGAGTCAAAGAAACAC 59.673 37.037 7.06 0.00 0.00 3.32
1083 1089 6.734104 AATGATGAGAGCAAGTACAAAGTC 57.266 37.500 0.00 0.00 0.00 3.01
1214 1220 6.429521 TGAGCATGATGGATCATTTAGAGA 57.570 37.500 0.00 0.00 44.70 3.10
1218 1224 5.163642 GCATGATGGATCATTTAGAGATGCC 60.164 44.000 0.00 0.00 44.70 4.40
1524 1530 8.806429 TCTAGGATTCTTAATTTGACATGCAA 57.194 30.769 0.00 0.00 33.88 4.08
1570 1576 2.662156 GTCAGCTTTCGAAGAGGTAACG 59.338 50.000 0.00 0.00 46.39 3.18
1679 1686 1.470098 CAAAGAAGCGCAATAGGCTGT 59.530 47.619 11.47 0.00 41.39 4.40
1768 1775 9.838339 GAGAACAAAAATAGAGATCCCATAGAA 57.162 33.333 0.00 0.00 0.00 2.10
1800 1807 6.879276 AGATGATGTTCTTGCTGATTATGG 57.121 37.500 0.00 0.00 0.00 2.74
1838 1845 4.457466 TGGGAAAGAACCAACTACAGAAC 58.543 43.478 0.00 0.00 34.44 3.01
1876 1883 4.524053 AGAAAGCTCATGAAGATGCATCA 58.476 39.130 27.81 10.34 0.00 3.07
1971 1978 2.842394 ATCAAGACCGTGAGCCTGCG 62.842 60.000 0.00 0.00 0.00 5.18
2012 2019 1.242989 TGAAACAATGCCGCAAGCTA 58.757 45.000 0.00 0.00 44.23 3.32
2096 2106 6.194235 AGAATGCACCATTACCTTTATGGAA 58.806 36.000 8.75 0.00 44.36 3.53
2516 2557 0.608640 CACCTCGCCCTCAACTAGTT 59.391 55.000 1.12 1.12 0.00 2.24
2524 2565 2.737252 GCCCTCAACTAGTTTCTGTTCG 59.263 50.000 5.07 0.00 0.00 3.95
2567 2609 9.371136 TCAAGTTACTAATCATAGCAACTGAAG 57.629 33.333 3.01 0.00 42.40 3.02
2601 2643 3.009805 ACCCTTGGGTTACTATGAACACC 59.990 47.826 5.34 0.00 31.25 4.16
2709 2751 2.649312 TCCACTTCCAATGACCATTCCT 59.351 45.455 0.00 0.00 0.00 3.36
2761 2820 0.620556 GGCTTCTTCATGGGAGTGGA 59.379 55.000 0.00 0.00 0.00 4.02
2764 2824 3.157087 GCTTCTTCATGGGAGTGGAAAA 58.843 45.455 0.00 0.00 0.00 2.29
2784 2844 3.604875 ATTGCTTGCCATTCTTCTTGG 57.395 42.857 0.00 0.00 37.31 3.61
2813 2874 4.346709 CCTTTCTTTCCCTTGCCCTTTTAA 59.653 41.667 0.00 0.00 0.00 1.52
2831 2892 8.638873 CCCTTTTAATTGAAACTAGTGGTCTTT 58.361 33.333 0.00 0.00 0.00 2.52
2882 2943 6.655003 TCTTGATTTCTACCTTCGCTGATTTT 59.345 34.615 0.00 0.00 0.00 1.82
2956 3018 6.388278 AGTTCATCACGAAGTTCTAGTAACC 58.612 40.000 0.56 0.00 41.61 2.85
2964 3026 5.103000 CGAAGTTCTAGTAACCTGGTGATG 58.897 45.833 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 1.802960 CCGATGGACTCAAGCATATGC 59.197 52.381 20.36 20.36 42.49 3.14
256 257 3.406764 CACCTTCTGTTTCCTCTTCTGG 58.593 50.000 0.00 0.00 0.00 3.86
327 328 3.054508 TGTCCATGCATCAGTCATAACCA 60.055 43.478 0.00 0.00 0.00 3.67
418 419 0.900182 TGTCATCGGAGCAGTCCACT 60.900 55.000 0.00 0.00 44.18 4.00
556 557 5.692115 TGGATGGTCTATTTGCTGTTAGA 57.308 39.130 0.00 0.00 0.00 2.10
601 605 1.693062 AGCATGAGATCTAGGCAGTGG 59.307 52.381 13.32 0.00 0.00 4.00
642 646 8.511321 CACTTGAAATAGTATTTGCAACTGGTA 58.489 33.333 12.86 0.00 0.00 3.25
655 659 7.385205 GTCACTTCTCTTGCACTTGAAATAGTA 59.615 37.037 0.00 0.00 0.00 1.82
774 778 9.030301 GCAAACTTTTCAGATTTAAGTAAGCAA 57.970 29.630 0.00 0.00 34.58 3.91
939 945 4.342772 CCATTGGCTCGAAGAAATTAACG 58.657 43.478 0.00 0.00 34.09 3.18
995 1001 2.767394 CCATGGAAGAATCCCATTGCAA 59.233 45.455 5.56 0.00 45.95 4.08
1030 1036 4.202040 CCTCACAGCAATGTGTTTCTTTGA 60.202 41.667 8.13 0.00 40.45 2.69
1041 1047 6.198650 TCATTATCAAACCTCACAGCAATG 57.801 37.500 0.00 0.00 0.00 2.82
1083 1089 4.898829 TTTATCAATGATGTCCCAAGCG 57.101 40.909 5.91 0.00 0.00 4.68
1214 1220 4.050553 GCAAATGCATGTAATAACGGCAT 58.949 39.130 0.00 0.00 45.61 4.40
1430 1436 6.535865 CACCATTTTGCTGCACATTATACAAT 59.464 34.615 0.00 0.00 0.00 2.71
1524 1530 2.533916 TCCTCTCACAAGCTGATGAGT 58.466 47.619 21.12 0.00 42.52 3.41
1679 1686 1.288188 TCCCTCATCCTGTCATGCAA 58.712 50.000 0.00 0.00 0.00 4.08
1768 1775 7.663081 TCAGCAAGAACATCATCTACTTCTTTT 59.337 33.333 0.00 0.00 31.91 2.27
1800 1807 2.715046 TCCCAGTGATGAACTCATTGC 58.285 47.619 0.00 0.00 39.58 3.56
1838 1845 3.750652 GCTTTCTCTTGTTCTTCCTCAGG 59.249 47.826 0.00 0.00 0.00 3.86
1876 1883 0.111253 CCCTGTTTGGTGCCTCTTCT 59.889 55.000 0.00 0.00 0.00 2.85
1971 1978 0.179045 ACGCATAGCCATCAAGGACC 60.179 55.000 0.00 0.00 41.22 4.46
2012 2019 6.493115 TCAGACTCTGATTCAGAAGAAGAAGT 59.507 38.462 16.79 9.51 40.18 3.01
2516 2557 8.441312 AAATAGGAGTTACAAAACGAACAGAA 57.559 30.769 0.00 0.00 40.73 3.02
2709 2751 7.045416 TGAAACTGAGTGCTTCTACTACAAAA 58.955 34.615 0.00 0.00 0.00 2.44
2761 2820 4.758165 CCAAGAAGAATGGCAAGCAATTTT 59.242 37.500 0.00 0.00 0.00 1.82
2764 2824 3.167485 TCCAAGAAGAATGGCAAGCAAT 58.833 40.909 0.00 0.00 37.88 3.56
2784 2844 2.558795 GCAAGGGAAAGAAAGGGAACTC 59.441 50.000 0.00 0.00 42.68 3.01
2813 2874 8.528044 TGGTTAAAAAGACCACTAGTTTCAAT 57.472 30.769 0.00 0.00 42.06 2.57
2882 2943 1.066422 CAAGCTCTCCGCGATGCTA 59.934 57.895 8.23 0.00 45.59 3.49
2956 3018 3.766591 AGTTCTCTAGTCACCATCACCAG 59.233 47.826 0.00 0.00 0.00 4.00
2964 3026 5.184096 TGATTGACAGAGTTCTCTAGTCACC 59.816 44.000 21.99 18.61 38.01 4.02


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

AutoCloner maintained by Alex Coulton.