Multiple sequence alignment - TraesCS4A01G052800

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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 TraesCS4A01G052800 chr4A 100.000 2871 0 0 1 2871 44650095 44652965 0.000000e+00 5302
1 TraesCS4A01G052800 chr4A 97.443 2894 50 4 1 2871 44781569 44784461 0.000000e+00 4913
2 TraesCS4A01G052800 chr4A 98.081 1459 22 5 1208 2664 44645359 44643905 0.000000e+00 2534
3 TraesCS4A01G052800 chr4A 98.240 1023 16 1 1 1021 44646372 44645350 0.000000e+00 1788
4 TraesCS4A01G052800 chr4A 93.274 565 33 5 2108 2670 730679902 730679341 0.000000e+00 828
5 TraesCS4A01G052800 chr4A 95.652 230 6 3 2642 2871 44306794 44307019 1.630000e-97 366
6 TraesCS4A01G052800 chr4A 94.348 230 10 2 2642 2871 45017014 45017240 1.640000e-92 350
7 TraesCS4A01G052800 chr3A 97.544 2687 36 5 1 2660 688613456 688610773 0.000000e+00 4569
8 TraesCS4A01G052800 chr3A 95.874 1745 36 6 587 2317 264036093 264037815 0.000000e+00 2791
9 TraesCS4A01G052800 chr6A 92.514 2084 124 17 1 2055 85351398 85353478 0.000000e+00 2955
10 TraesCS4A01G052800 chr3D 92.242 2101 109 21 1 2055 50895023 50897115 0.000000e+00 2928
11 TraesCS4A01G052800 chr3D 91.702 470 33 5 2190 2657 50897143 50897608 0.000000e+00 647
12 TraesCS4A01G052800 chr3D 85.253 217 30 1 2657 2871 395016727 395016511 3.720000e-54 222
13 TraesCS4A01G052800 chr7B 91.108 2103 135 21 1 2055 471226805 471224707 0.000000e+00 2800
14 TraesCS4A01G052800 chr6B 95.018 1706 64 10 1 1705 708191210 708192895 0.000000e+00 2660
15 TraesCS4A01G052800 chr6B 94.197 741 34 7 1700 2437 708205279 708206013 0.000000e+00 1122
16 TraesCS4A01G052800 chr6B 85.648 216 30 1 2657 2871 712413895 712413680 2.880000e-55 226
17 TraesCS4A01G052800 chr1D 95.214 1567 60 11 1099 2660 202978686 202980242 0.000000e+00 2464
18 TraesCS4A01G052800 chr1D 92.484 1530 75 14 1 1493 456809804 456811330 0.000000e+00 2152
19 TraesCS4A01G052800 chr2B 90.985 1431 87 23 1 1412 730525745 730527152 0.000000e+00 1890
20 TraesCS4A01G052800 chr2B 90.826 218 15 3 2657 2871 107082079 107082294 1.300000e-73 287
21 TraesCS4A01G052800 chr1A 92.182 1164 82 7 895 2055 516653145 516651988 0.000000e+00 1637
22 TraesCS4A01G052800 chr1A 89.978 459 40 5 2206 2662 516651982 516651528 3.190000e-164 588
23 TraesCS4A01G052800 chr6D 91.314 472 35 5 2190 2659 28691039 28690572 8.670000e-180 640
24 TraesCS4A01G052800 chrUn 82.845 478 63 14 1715 2188 108609209 108609671 7.400000e-111 411
25 TraesCS4A01G052800 chr4D 94.348 230 10 2 2642 2871 419986287 419986061 1.640000e-92 350
26 TraesCS4A01G052800 chr5B 91.304 230 16 3 2642 2871 646624241 646624466 7.720000e-81 311
27 TraesCS4A01G052800 chr2D 86.175 217 28 1 2657 2871 60091890 60092106 1.720000e-57 233


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 TraesCS4A01G052800 chr4A 44650095 44652965 2870 False 5302.0 5302 100.0000 1 2871 1 chr4A.!!$F2 2870
1 TraesCS4A01G052800 chr4A 44781569 44784461 2892 False 4913.0 4913 97.4430 1 2871 1 chr4A.!!$F3 2870
2 TraesCS4A01G052800 chr4A 44643905 44646372 2467 True 2161.0 2534 98.1605 1 2664 2 chr4A.!!$R2 2663
3 TraesCS4A01G052800 chr4A 730679341 730679902 561 True 828.0 828 93.2740 2108 2670 1 chr4A.!!$R1 562
4 TraesCS4A01G052800 chr3A 688610773 688613456 2683 True 4569.0 4569 97.5440 1 2660 1 chr3A.!!$R1 2659
5 TraesCS4A01G052800 chr3A 264036093 264037815 1722 False 2791.0 2791 95.8740 587 2317 1 chr3A.!!$F1 1730
6 TraesCS4A01G052800 chr6A 85351398 85353478 2080 False 2955.0 2955 92.5140 1 2055 1 chr6A.!!$F1 2054
7 TraesCS4A01G052800 chr3D 50895023 50897608 2585 False 1787.5 2928 91.9720 1 2657 2 chr3D.!!$F1 2656
8 TraesCS4A01G052800 chr7B 471224707 471226805 2098 True 2800.0 2800 91.1080 1 2055 1 chr7B.!!$R1 2054
9 TraesCS4A01G052800 chr6B 708191210 708192895 1685 False 2660.0 2660 95.0180 1 1705 1 chr6B.!!$F1 1704
10 TraesCS4A01G052800 chr6B 708205279 708206013 734 False 1122.0 1122 94.1970 1700 2437 1 chr6B.!!$F2 737
11 TraesCS4A01G052800 chr1D 202978686 202980242 1556 False 2464.0 2464 95.2140 1099 2660 1 chr1D.!!$F1 1561
12 TraesCS4A01G052800 chr1D 456809804 456811330 1526 False 2152.0 2152 92.4840 1 1493 1 chr1D.!!$F2 1492
13 TraesCS4A01G052800 chr2B 730525745 730527152 1407 False 1890.0 1890 90.9850 1 1412 1 chr2B.!!$F2 1411
14 TraesCS4A01G052800 chr1A 516651528 516653145 1617 True 1112.5 1637 91.0800 895 2662 2 chr1A.!!$R1 1767

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
540 542 2.603075 TTTTGCAAGGGATAGGCAGT 57.397 45.000 0.0 0.0 38.97 4.40 F
733 735 3.764972 GCTGAACTAGAGTTGGAGTAGGT 59.235 47.826 0.0 0.0 38.56 3.08 F
1741 1831 4.471904 AATCCTTGCGACACTTGAGATA 57.528 40.909 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1713 0.038744 CCCAAGAAGGCACAGGATGT 59.961 55.000 0.00 0.0 43.3 3.06 R
1741 1831 1.967066 CCACGAGCTAGATCAGGGATT 59.033 52.381 8.99 0.0 0.0 3.01 R
2618 2711 7.016153 TGTAGACATTCAAGACCTGGTATTT 57.984 36.000 3.50 0.0 0.0 1.40 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
311 312 4.457834 AAGAGCTGTATAACTTGCGTCT 57.542 40.909 0.00 0.00 0.00 4.18
333 334 6.470877 GTCTTTCTCGAGCTAGAAATGTAGTG 59.529 42.308 7.81 1.17 42.87 2.74
540 542 2.603075 TTTTGCAAGGGATAGGCAGT 57.397 45.000 0.00 0.00 38.97 4.40
623 625 7.609097 TGATCCTCTAGATGATGCTAACTTT 57.391 36.000 14.45 0.00 34.42 2.66
733 735 3.764972 GCTGAACTAGAGTTGGAGTAGGT 59.235 47.826 0.00 0.00 38.56 3.08
1741 1831 4.471904 AATCCTTGCGACACTTGAGATA 57.528 40.909 0.00 0.00 0.00 1.98
1787 1877 6.161855 ACATCTTGCGATCTTATGGTAAGA 57.838 37.500 5.28 5.28 41.92 2.10
1816 1906 1.495951 CGAACGCTTGTACCAAGCC 59.504 57.895 19.94 8.10 40.02 4.35
2089 2181 8.206189 AGTTTTTGGACAAATTGATGTTCTCAT 58.794 29.630 0.00 0.00 36.95 2.90
2254 2346 2.526304 TGAGGAGTTGGAACTTGTCG 57.474 50.000 0.00 0.00 39.88 4.35
2323 2415 7.465379 GCCAGTTTTTCTTGTATTTTGGACAAC 60.465 37.037 0.00 0.00 33.35 3.32
2515 2608 4.020839 CCAAACAAGATTTGGCATTCCTCT 60.021 41.667 5.53 0.00 41.95 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
311 312 5.417894 TCCACTACATTTCTAGCTCGAGAAA 59.582 40.000 18.75 12.85 46.63 2.52
333 334 2.558359 CCACAACCCAAATGTTCTCTCC 59.442 50.000 0.00 0.00 0.00 3.71
521 523 2.603075 ACTGCCTATCCCTTGCAAAA 57.397 45.000 0.00 0.00 34.06 2.44
540 542 5.007921 CGAGCAACAAATCATCCATCACATA 59.992 40.000 0.00 0.00 0.00 2.29
623 625 5.246203 AGTGCTGACTTGAACACTCCTAATA 59.754 40.000 0.00 0.00 39.04 0.98
733 735 1.753930 TATCTAGTCGACCCGCACAA 58.246 50.000 13.01 0.00 0.00 3.33
1623 1713 0.038744 CCCAAGAAGGCACAGGATGT 59.961 55.000 0.00 0.00 43.30 3.06
1741 1831 1.967066 CCACGAGCTAGATCAGGGATT 59.033 52.381 8.99 0.00 0.00 3.01
1787 1877 2.205074 CAAGCGTTCGCTAAGGATCAT 58.795 47.619 19.67 0.00 41.04 2.45
1816 1906 2.751806 GTTCATGGGAAGCTCAAGAAGG 59.248 50.000 0.00 0.00 32.62 3.46
2089 2181 4.784177 ACAGCCACATATCATGATGAACA 58.216 39.130 18.72 0.00 0.00 3.18
2125 2217 9.823647 TGTTCAAAAACATGAAAAATTAGGCTA 57.176 25.926 0.00 0.00 40.45 3.93
2235 2327 2.035961 CTCGACAAGTTCCAACTCCTCA 59.964 50.000 0.00 0.00 38.57 3.86
2323 2415 3.928727 AATTGGCACAGACAACATCAG 57.071 42.857 0.00 0.00 42.39 2.90
2397 2490 9.140286 GAAATTAAATCTGATCATCATGCCATG 57.860 33.333 0.00 0.00 0.00 3.66
2618 2711 7.016153 TGTAGACATTCAAGACCTGGTATTT 57.984 36.000 3.50 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.