Multiple sequence alignment - TraesCS4A01G493600

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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 TraesCS4A01G493600 chr4A 100.000 3934 0 0 971 4904 742036061 742032128 0.000000e+00 7265.0
1 TraesCS4A01G493600 chr4A 97.634 3761 58 11 974 4729 739630468 739626734 0.000000e+00 6423.0
2 TraesCS4A01G493600 chr4A 96.124 3947 85 22 974 4904 740541138 740537244 0.000000e+00 6379.0
3 TraesCS4A01G493600 chr4A 80.980 2571 422 46 1890 4440 740209447 740206924 0.000000e+00 1977.0
4 TraesCS4A01G493600 chr4A 97.372 647 17 0 979 1625 739844222 739843576 0.000000e+00 1101.0
5 TraesCS4A01G493600 chr4A 100.000 516 0 0 1 516 739630994 739630479 0.000000e+00 953.0
6 TraesCS4A01G493600 chr4A 100.000 516 0 0 1 516 742037031 742036516 0.000000e+00 953.0
7 TraesCS4A01G493600 chr4A 99.806 516 1 0 1 516 740541664 740541149 0.000000e+00 948.0
8 TraesCS4A01G493600 chr4A 98.062 516 8 2 1 516 739844740 739844227 0.000000e+00 896.0
9 TraesCS4A01G493600 chr4A 88.075 587 36 11 3989 4572 740161408 740161963 0.000000e+00 665.0
10 TraesCS4A01G493600 chr4A 89.552 134 10 3 4767 4896 741177374 741177241 3.040000e-37 167.0
11 TraesCS4A01G493600 chr4A 95.960 99 4 0 4568 4666 741177864 741177766 1.410000e-35 161.0
12 TraesCS4A01G493600 chr4A 100.000 41 0 0 3221 3261 742123535 742123495 5.260000e-10 76.8
13 TraesCS4A01G493600 chr7A 93.073 3479 213 13 980 4443 2827338 2830803 0.000000e+00 5064.0
14 TraesCS4A01G493600 chr7A 92.185 3442 238 16 981 4405 2093388 2096815 0.000000e+00 4837.0
15 TraesCS4A01G493600 chr7A 88.952 2453 234 26 1904 4334 3780565 3783002 0.000000e+00 2994.0
16 TraesCS4A01G493600 chr7A 92.759 511 31 2 4400 4904 2096948 2097458 0.000000e+00 734.0
17 TraesCS4A01G493600 chr7A 93.396 424 21 3 4488 4904 2830813 2831236 5.390000e-174 621.0
18 TraesCS4A01G493600 chr7A 92.564 390 21 5 1 387 2826652 2827036 1.990000e-153 553.0
19 TraesCS4A01G493600 chr7A 87.202 461 28 6 20 453 2092705 2093161 3.410000e-136 496.0
20 TraesCS4A01G493600 chr7A 77.122 813 154 16 971 1773 3273207 3273997 4.510000e-120 442.0
21 TraesCS4A01G493600 chr7A 96.183 131 5 0 4381 4511 3783005 3783135 1.070000e-51 215.0
22 TraesCS4A01G493600 chr7A 98.333 60 1 0 386 445 2827061 2827120 6.710000e-19 106.0
23 TraesCS4A01G493600 chr7D 86.871 3976 429 32 977 4904 3858739 3854809 0.000000e+00 4364.0
24 TraesCS4A01G493600 chr7D 86.434 3435 370 54 971 4358 2408347 2411732 0.000000e+00 3674.0
25 TraesCS4A01G493600 chr7D 87.310 2829 298 27 1899 4690 2651653 2654457 0.000000e+00 3179.0
26 TraesCS4A01G493600 chr7D 80.954 2620 416 53 1857 4440 3688296 3690868 0.000000e+00 1997.0
27 TraesCS4A01G493600 chr7D 78.894 796 135 20 987 1773 3685928 3686699 4.380000e-140 508.0
28 TraesCS4A01G493600 chr7D 77.242 747 140 14 975 1715 2650048 2650770 1.270000e-110 411.0
29 TraesCS4A01G493600 chr7D 93.407 182 12 0 4723 4904 2654452 2654633 2.250000e-68 270.0
30 TraesCS4A01G493600 chr7D 97.895 95 2 0 4568 4662 2411920 2412014 1.090000e-36 165.0
31 TraesCS4A01G493600 chr7D 83.168 101 13 4 4568 4668 2437915 2438011 6.760000e-14 89.8
32 TraesCS4A01G493600 chrUn 100.000 516 0 0 1 516 444984903 444985418 0.000000e+00 953.0
33 TraesCS4A01G493600 chr5D 71.902 1178 233 65 2598 3744 422947517 422946407 8.150000e-63 252.0
34 TraesCS4A01G493600 chr4D 100.000 29 0 0 288 316 98936073 98936101 2.000000e-03 54.7
35 TraesCS4A01G493600 chr1B 96.875 32 1 0 1242 1273 658353068 658353099 2.000000e-03 54.7
36 TraesCS4A01G493600 chr1B 94.286 35 2 0 1242 1276 660532121 660532087 2.000000e-03 54.7
37 TraesCS4A01G493600 chr1A 94.286 35 2 0 1242 1276 570864726 570864692 2.000000e-03 54.7


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 TraesCS4A01G493600 chr4A 742032128 742037031 4903 True 4109.000000 7265 100.000000 1 4904 2 chr4A.!!$R7 4903
1 TraesCS4A01G493600 chr4A 739626734 739630994 4260 True 3688.000000 6423 98.817000 1 4729 2 chr4A.!!$R3 4728
2 TraesCS4A01G493600 chr4A 740537244 740541664 4420 True 3663.500000 6379 97.965000 1 4904 2 chr4A.!!$R5 4903
3 TraesCS4A01G493600 chr4A 740206924 740209447 2523 True 1977.000000 1977 80.980000 1890 4440 1 chr4A.!!$R1 2550
4 TraesCS4A01G493600 chr4A 739843576 739844740 1164 True 998.500000 1101 97.717000 1 1625 2 chr4A.!!$R4 1624
5 TraesCS4A01G493600 chr4A 740161408 740161963 555 False 665.000000 665 88.075000 3989 4572 1 chr4A.!!$F1 583
6 TraesCS4A01G493600 chr7A 2092705 2097458 4753 False 2022.333333 4837 90.715333 20 4904 3 chr7A.!!$F2 4884
7 TraesCS4A01G493600 chr7A 3780565 3783135 2570 False 1604.500000 2994 92.567500 1904 4511 2 chr7A.!!$F4 2607
8 TraesCS4A01G493600 chr7A 2826652 2831236 4584 False 1586.000000 5064 94.341500 1 4904 4 chr7A.!!$F3 4903
9 TraesCS4A01G493600 chr7A 3273207 3273997 790 False 442.000000 442 77.122000 971 1773 1 chr7A.!!$F1 802
10 TraesCS4A01G493600 chr7D 3854809 3858739 3930 True 4364.000000 4364 86.871000 977 4904 1 chr7D.!!$R1 3927
11 TraesCS4A01G493600 chr7D 2408347 2412014 3667 False 1919.500000 3674 92.164500 971 4662 2 chr7D.!!$F2 3691
12 TraesCS4A01G493600 chr7D 2650048 2654633 4585 False 1286.666667 3179 85.986333 975 4904 3 chr7D.!!$F3 3929
13 TraesCS4A01G493600 chr7D 3685928 3690868 4940 False 1252.500000 1997 79.924000 987 4440 2 chr7D.!!$F4 3453
14 TraesCS4A01G493600 chrUn 444984903 444985418 515 False 953.000000 953 100.000000 1 516 1 chrUn.!!$F1 515
15 TraesCS4A01G493600 chr5D 422946407 422947517 1110 True 252.000000 252 71.902000 2598 3744 1 chr5D.!!$R1 1146

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
1113 1142 6.472887 TCGGAAGAACCTAAAGAATGACATT 58.527 36.000 0.00 0.0 37.03 2.71 F
3318 5025 4.012374 GTCATCTCTCAAAGGCCATCAAA 58.988 43.478 5.01 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3318 5025 2.172293 GGTGCTTCTCTCAATGATCCCT 59.828 50.0 0.0 0.0 0.0 4.20 R
4720 6754 0.537188 CTGTCATTAGCGTGAGGGGT 59.463 55.0 0.0 0.0 0.0 4.95 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
1113 1142 6.472887 TCGGAAGAACCTAAAGAATGACATT 58.527 36.000 0.00 0.00 37.03 2.71
3318 5025 4.012374 GTCATCTCTCAAAGGCCATCAAA 58.988 43.478 5.01 0.00 0.00 2.69
3978 5713 0.040351 TCCTCCTCACCTCTCCACAG 59.960 60.000 0.00 0.00 0.00 3.66
3979 5714 0.252012 CCTCCTCACCTCTCCACAGT 60.252 60.000 0.00 0.00 0.00 3.55
3980 5715 0.894141 CTCCTCACCTCTCCACAGTG 59.106 60.000 0.00 0.00 0.00 3.66
3981 5716 0.542938 TCCTCACCTCTCCACAGTGG 60.543 60.000 14.19 14.19 38.99 4.00
3982 5717 1.294780 CTCACCTCTCCACAGTGGC 59.705 63.158 15.64 0.00 37.47 5.01
3983 5718 1.459348 TCACCTCTCCACAGTGGCA 60.459 57.895 15.64 2.72 37.47 4.92
3984 5719 1.302033 CACCTCTCCACAGTGGCAC 60.302 63.158 15.64 10.29 37.47 5.01
3985 5720 1.460305 ACCTCTCCACAGTGGCACT 60.460 57.895 15.88 15.88 37.47 4.40
4011 5746 5.630121 TCACATCCTGGTAATGACACTTTT 58.370 37.500 2.65 0.00 0.00 2.27
4113 5869 3.867493 TCATCAAGATGATCAAGTGCGTC 59.133 43.478 8.61 0.00 42.42 5.19
4344 6131 5.687166 TGGTTATTTCGGTCCTAGTCAAT 57.313 39.130 0.00 0.00 0.00 2.57
4426 6358 6.993079 ACTTGTTTGGGATAAATTCTGGAAC 58.007 36.000 0.00 0.00 0.00 3.62
4695 6729 3.438434 GCAATCTTTCTCCTTCAGACCAC 59.562 47.826 0.00 0.00 0.00 4.16
4720 6754 1.319541 GTAGACGGAGATGCTGCCTA 58.680 55.000 0.00 0.00 0.00 3.93
4765 6809 3.511477 TCTACCCTCTCTTTCTGTGCTT 58.489 45.455 0.00 0.00 0.00 3.91
4808 6852 5.300286 ACCAATCCAATCCGATCAATCTTTC 59.700 40.000 0.00 0.00 0.00 2.62
4874 6918 3.244976 GTTGGAAATTTGATGGCTGTCG 58.755 45.455 0.00 0.00 0.00 4.35
4897 6941 4.952262 TGCTGCTGCTTTAGTTTAGATG 57.048 40.909 17.00 0.00 40.48 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1113 1142 6.609237 GCAAACTCATGCTTGATGTAGATA 57.391 37.500 2.33 0.00 43.06 1.98
3318 5025 2.172293 GGTGCTTCTCTCAATGATCCCT 59.828 50.000 0.00 0.00 0.00 4.20
3956 5682 1.010795 TGGAGAGGTGAGGAGGATGA 58.989 55.000 0.00 0.00 0.00 2.92
3978 5713 0.877071 CAGGATGTGAACAGTGCCAC 59.123 55.000 8.77 8.77 0.00 5.01
3979 5714 0.250858 CCAGGATGTGAACAGTGCCA 60.251 55.000 0.00 0.00 0.00 4.92
3980 5715 0.250901 ACCAGGATGTGAACAGTGCC 60.251 55.000 0.00 0.00 0.00 5.01
3981 5716 2.472695 TACCAGGATGTGAACAGTGC 57.527 50.000 0.00 0.00 0.00 4.40
3982 5717 4.393062 GTCATTACCAGGATGTGAACAGTG 59.607 45.833 0.00 0.00 0.00 3.66
3983 5718 4.041567 TGTCATTACCAGGATGTGAACAGT 59.958 41.667 0.00 0.00 0.00 3.55
3984 5719 4.393062 GTGTCATTACCAGGATGTGAACAG 59.607 45.833 0.00 0.00 0.00 3.16
3985 5720 4.041567 AGTGTCATTACCAGGATGTGAACA 59.958 41.667 0.00 0.00 0.00 3.18
4011 5746 5.221641 ACCTGTACTGTCTGCACAATAGAAA 60.222 40.000 0.00 0.00 29.82 2.52
4025 5764 1.865865 CAAGTCGCAACCTGTACTGT 58.134 50.000 0.00 0.00 0.00 3.55
4113 5869 7.306283 CGAGAGCAAAGAGGACTAAATTATTCG 60.306 40.741 0.00 0.00 0.00 3.34
4344 6131 2.790433 ACTCCGCAGAAGCCAATTAAA 58.210 42.857 0.00 0.00 37.52 1.52
4358 6145 9.651718 CTAAATTTGTGAGAAATAATACTCCGC 57.348 33.333 0.00 0.00 32.84 5.54
4426 6358 5.801947 GCACTGCACATCAAGTAAATAAAGG 59.198 40.000 0.00 0.00 0.00 3.11
4695 6729 3.858877 GCAGCATCTCCGTCTACCATTAG 60.859 52.174 0.00 0.00 0.00 1.73
4703 6737 1.395826 GGTAGGCAGCATCTCCGTCT 61.396 60.000 0.00 0.00 0.00 4.18
4720 6754 0.537188 CTGTCATTAGCGTGAGGGGT 59.463 55.000 0.00 0.00 0.00 4.95
4765 6809 4.464947 TGGTGTGTCATTGTCAACCAATA 58.535 39.130 12.03 0.00 41.93 1.90
4779 6823 2.107950 TCGGATTGGATTGGTGTGTC 57.892 50.000 0.00 0.00 0.00 3.67
4808 6852 4.637534 CCAACTACACAGATCATTCCCTTG 59.362 45.833 0.00 0.00 0.00 3.61
4848 6892 4.020839 CAGCCATCAAATTTCCAACCTCTT 60.021 41.667 0.00 0.00 0.00 2.85
4874 6918 4.749245 TCTAAACTAAAGCAGCAGCAAC 57.251 40.909 3.17 0.00 45.49 4.17


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

AutoCloner maintained by Alex Coulton.