Multiple sequence alignment - TraesCS3B01G594400

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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 TraesCS3B01G594400 chr3B 100.000 3974 0 0 756 4729 817710255 817714228 0.000000e+00 7339
1 TraesCS3B01G594400 chr3B 98.641 3974 54 0 756 4729 817687100 817691073 0.000000e+00 7040
2 TraesCS3B01G594400 chr3B 96.706 3309 105 3 761 4066 745188 748495 0.000000e+00 5504
3 TraesCS3B01G594400 chr3B 100.000 399 0 0 1 399 817709500 817709898 0.000000e+00 737
4 TraesCS3B01G594400 chr3B 97.494 399 10 0 1 399 817686689 817687087 0.000000e+00 682
5 TraesCS3B01G594400 chr3B 96.250 400 13 2 1 399 784352165 784351767 0.000000e+00 654
6 TraesCS3B01G594400 chr7B 96.553 3975 136 1 756 4729 695575422 695571448 0.000000e+00 6580
7 TraesCS3B01G594400 chr7B 96.688 3955 116 4 756 4709 681953779 681957719 0.000000e+00 6564
8 TraesCS3B01G594400 chr7B 95.750 400 16 1 1 399 695575834 695575435 1.110000e-180 643
9 TraesCS3B01G594400 chr7B 95.489 399 15 3 1 398 681953369 681953765 6.680000e-178 634
10 TraesCS3B01G594400 chr7A 96.553 3974 136 1 756 4728 395514280 395518253 0.000000e+00 6578
11 TraesCS3B01G594400 chr7A 93.485 307 20 0 756 1062 75693646 75693952 1.550000e-124 457
12 TraesCS3B01G594400 chr7A 92.430 251 19 0 812 1062 557427111 557426861 4.500000e-95 359
13 TraesCS3B01G594400 chr7A 83.122 237 27 9 1522 1753 125840533 125840305 2.230000e-48 204
14 TraesCS3B01G594400 chr6B 96.428 3975 141 1 756 4729 83866800 83870774 0.000000e+00 6553
15 TraesCS3B01G594400 chr6B 97.243 399 10 1 1 398 83866388 83866786 0.000000e+00 675
16 TraesCS3B01G594400 chr5A 96.586 3954 134 1 776 4728 631069218 631065265 0.000000e+00 6553
17 TraesCS3B01G594400 chr5A 96.000 400 14 2 1 399 213047103 213047501 0.000000e+00 649
18 TraesCS3B01G594400 chr6A 96.428 3975 139 3 756 4728 307921892 307917919 0.000000e+00 6551
19 TraesCS3B01G594400 chr1A 96.409 3982 132 4 757 4728 236391760 236395740 0.000000e+00 6551
20 TraesCS3B01G594400 chr4B 97.500 400 9 1 1 399 552795956 552796355 0.000000e+00 682
21 TraesCS3B01G594400 chrUn 95.750 400 15 2 1 399 87505960 87505562 1.110000e-180 643
22 TraesCS3B01G594400 chr2A 95.250 400 16 3 1 399 290318696 290319093 8.640000e-177 630


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 TraesCS3B01G594400 chr3B 817709500 817714228 4728 False 4038.0 7339 100.0000 1 4729 2 chr3B.!!$F3 4728
1 TraesCS3B01G594400 chr3B 745188 748495 3307 False 5504.0 5504 96.7060 761 4066 1 chr3B.!!$F1 3305
2 TraesCS3B01G594400 chr3B 817686689 817691073 4384 False 3861.0 7040 98.0675 1 4729 2 chr3B.!!$F2 4728
3 TraesCS3B01G594400 chr7B 695571448 695575834 4386 True 3611.5 6580 96.1515 1 4729 2 chr7B.!!$R1 4728
4 TraesCS3B01G594400 chr7B 681953369 681957719 4350 False 3599.0 6564 96.0885 1 4709 2 chr7B.!!$F1 4708
5 TraesCS3B01G594400 chr7A 395514280 395518253 3973 False 6578.0 6578 96.5530 756 4728 1 chr7A.!!$F2 3972
6 TraesCS3B01G594400 chr6B 83866388 83870774 4386 False 3614.0 6553 96.8355 1 4729 2 chr6B.!!$F1 4728
7 TraesCS3B01G594400 chr5A 631065265 631069218 3953 True 6553.0 6553 96.5860 776 4728 1 chr5A.!!$R1 3952
8 TraesCS3B01G594400 chr6A 307917919 307921892 3973 True 6551.0 6551 96.4280 756 4728 1 chr6A.!!$R1 3972
9 TraesCS3B01G594400 chr1A 236391760 236395740 3980 False 6551.0 6551 96.4090 757 4728 1 chr1A.!!$F1 3971

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
891 894 2.060383 CAGAGGTGGCCGGATCTGA 61.060 63.158 20.6 0.0 41.35 3.27 F
1102 1114 1.456518 CGCCTCCTCCAGATCCTCA 60.457 63.158 0.0 0.0 0.00 3.86 F
2057 2069 0.389948 GTCGGACCAATCGCTCAACT 60.390 55.000 0.0 0.0 0.00 3.16 F
2665 2679 0.684479 TGATGGAGCGCTAGGACTGT 60.684 55.000 11.5 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2069 0.520404 GAGACGTGCGTACCTGAAGA 59.480 55.000 0.00 0.0 0.00 2.87 R
2299 2313 1.747355 ACACATATTCTGCAAGCTGCC 59.253 47.619 0.00 0.0 44.23 4.85 R
3374 3388 2.159226 CGGACTCATCTGGTACAAGGAC 60.159 54.545 0.00 0.0 38.70 3.85 R
4037 4051 9.761504 AGCTATATTTGCTACATATCAGCTATG 57.238 33.333 7.24 0.0 39.21 2.23 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
857 860 2.281539 TCGTCGGGATCTGCCTAATA 57.718 50.000 0.00 0.00 36.66 0.98
858 861 2.803956 TCGTCGGGATCTGCCTAATAT 58.196 47.619 0.00 0.00 36.66 1.28
891 894 2.060383 CAGAGGTGGCCGGATCTGA 61.060 63.158 20.60 0.00 41.35 3.27
1102 1114 1.456518 CGCCTCCTCCAGATCCTCA 60.457 63.158 0.00 0.00 0.00 3.86
1177 1189 3.374402 CGACCCACTCGGCTGTCT 61.374 66.667 0.00 0.00 38.87 3.41
1387 1399 4.105754 AGCTTCTGCCCTCTTTTTAGTT 57.894 40.909 0.00 0.00 40.80 2.24
1693 1705 6.839124 ATTGATTCTTGTTCATGCCACTTA 57.161 33.333 0.00 0.00 0.00 2.24
2057 2069 0.389948 GTCGGACCAATCGCTCAACT 60.390 55.000 0.00 0.00 0.00 3.16
2165 2178 6.872920 TGCTTCTGATACATGTATGTGTGTA 58.127 36.000 22.93 6.21 41.89 2.90
2299 2313 6.888797 CGTTCATTTGTATTTGCAAATTAGCG 59.111 34.615 28.45 15.46 43.97 4.26
2506 2520 2.867975 ACCACGCACTAACTACAACAAC 59.132 45.455 0.00 0.00 0.00 3.32
2586 2600 2.897326 AGGTACACCCCTGAATTTTTGC 59.103 45.455 0.00 0.00 36.42 3.68
2659 2673 3.461061 TGATTCTTTGATGGAGCGCTAG 58.539 45.455 11.50 1.36 0.00 3.42
2665 2679 0.684479 TGATGGAGCGCTAGGACTGT 60.684 55.000 11.50 0.00 0.00 3.55
3162 3176 1.156322 TCCACCTCCCTCTCCCTCTT 61.156 60.000 0.00 0.00 0.00 2.85
3374 3388 5.646606 TGAGTGTGATGCATTTTGATGATG 58.353 37.500 0.00 0.00 0.00 3.07
4037 4051 9.687210 TGTATGGTGTACATAAATATCGAGTTC 57.313 33.333 0.00 0.00 43.36 3.01
4678 4693 2.363795 CTACGTGGCCTGGGGAGA 60.364 66.667 3.32 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
807 810 2.595655 GGCCGAAACCCTAGCCAT 59.404 61.111 0.00 0.0 45.07 4.40
837 840 1.633774 ATTAGGCAGATCCCGACGAT 58.366 50.000 0.00 0.0 34.51 3.73
891 894 3.007323 GGAGGGGCTTACCGGTGT 61.007 66.667 19.93 0.0 41.60 4.16
1177 1189 1.163420 GGGTCGTTGACACATGCACA 61.163 55.000 0.00 0.0 35.79 4.57
1387 1399 3.091545 CCCAAATGCAAGAAGCTAAGGA 58.908 45.455 0.00 0.0 45.94 3.36
1593 1605 3.335579 ACAACGGACTAAAAGATGCCTC 58.664 45.455 0.00 0.0 0.00 4.70
2057 2069 0.520404 GAGACGTGCGTACCTGAAGA 59.480 55.000 0.00 0.0 0.00 2.87
2119 2132 2.936919 TCAGTCAACACTCTTGGCAT 57.063 45.000 0.00 0.0 0.00 4.40
2299 2313 1.747355 ACACATATTCTGCAAGCTGCC 59.253 47.619 0.00 0.0 44.23 4.85
2586 2600 5.943416 TGTACATTGATCAGGTTGTAAAGGG 59.057 40.000 13.57 0.0 0.00 3.95
2659 2673 5.767816 AAAACTACCATTTCACACAGTCC 57.232 39.130 0.00 0.0 0.00 3.85
2807 2821 3.676646 CAGAAAAGCATAAGCAGCAAACC 59.323 43.478 0.00 0.0 45.49 3.27
3374 3388 2.159226 CGGACTCATCTGGTACAAGGAC 60.159 54.545 0.00 0.0 38.70 3.85
4037 4051 9.761504 AGCTATATTTGCTACATATCAGCTATG 57.238 33.333 7.24 0.0 39.21 2.23
4678 4693 1.539827 GGCGTTTTGGTCACTAGCAAT 59.460 47.619 0.00 0.0 42.37 3.56


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

AutoCloner maintained by Alex Coulton.