Multiple sequence alignment - TraesCS4B01G004100

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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 TraesCS4B01G004100 chr4B 100.000 3139 0 0 1 3139 2691191 2694329 0.000000e+00 5797.0
1 TraesCS4B01G004100 chr4B 95.729 3067 111 7 76 3139 2702780 2705829 0.000000e+00 4920.0
2 TraesCS4B01G004100 chrUn 96.403 3086 102 6 58 3139 51907456 51910536 0.000000e+00 5075.0
3 TraesCS4B01G004100 chrUn 96.403 3086 102 6 58 3139 290968642 290971722 0.000000e+00 5075.0
4 TraesCS4B01G004100 chrUn 87.048 1328 170 2 58 1385 51924288 51922963 0.000000e+00 1498.0
5 TraesCS4B01G004100 chrUn 85.434 865 72 27 1990 2822 412749000 412748158 0.000000e+00 850.0
6 TraesCS4B01G004100 chrUn 87.013 308 35 4 1685 1991 412749328 412749025 3.000000e-90 342.0
7 TraesCS4B01G004100 chrUn 88.031 259 29 2 1425 1683 51921912 51921656 3.930000e-79 305.0
8 TraesCS4B01G004100 chr4A 89.590 2315 152 37 14 2280 602379478 602381751 0.000000e+00 2857.0
9 TraesCS4B01G004100 chr4A 86.338 1442 169 12 1 1428 602370986 602372413 0.000000e+00 1546.0
10 TraesCS4B01G004100 chr4A 85.371 1456 141 35 1425 2846 602373379 602374796 0.000000e+00 1443.0
11 TraesCS4B01G004100 chr4A 93.878 343 15 2 2797 3139 602374797 602375133 2.160000e-141 512.0
12 TraesCS4B01G004100 chr4A 83.254 418 50 14 2464 2879 602381744 602382143 1.780000e-97 366.0
13 TraesCS4B01G004100 chr4A 84.422 199 22 4 2924 3119 602382272 602382464 1.490000e-43 187.0
14 TraesCS4B01G004100 chr4D 93.993 1365 81 1 83 1446 3225380 3224016 0.000000e+00 2065.0
15 TraesCS4B01G004100 chr4D 86.441 1770 146 45 1425 3138 3227866 3226135 0.000000e+00 1853.0
16 TraesCS4B01G004100 chr4D 84.171 1453 143 43 1479 2889 3224016 3222609 0.000000e+00 1328.0
17 TraesCS4B01G004100 chr4D 96.610 59 2 0 1 59 3228959 3228901 7.160000e-17 99.0
18 TraesCS4B01G004100 chr6B 76.228 1140 226 34 520 1628 7823907 7822782 2.110000e-156 562.0
19 TraesCS4B01G004100 chr6B 76.190 147 29 6 2030 2174 30403488 30403346 4.340000e-09 73.1
20 TraesCS4B01G004100 chr6D 75.486 1028 227 19 269 1280 432876384 432877402 2.190000e-131 479.0
21 TraesCS4B01G004100 chr7D 81.057 227 37 3 184 404 633374079 633373853 3.220000e-40 176.0
22 TraesCS4B01G004100 chr7B 78.804 184 29 4 222 405 749408471 749408298 7.110000e-22 115.0


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 TraesCS4B01G004100 chr4B 2691191 2694329 3138 False 5797.000000 5797 100.000000 1 3139 1 chr4B.!!$F1 3138
1 TraesCS4B01G004100 chr4B 2702780 2705829 3049 False 4920.000000 4920 95.729000 76 3139 1 chr4B.!!$F2 3063
2 TraesCS4B01G004100 chrUn 51907456 51910536 3080 False 5075.000000 5075 96.403000 58 3139 1 chrUn.!!$F1 3081
3 TraesCS4B01G004100 chrUn 290968642 290971722 3080 False 5075.000000 5075 96.403000 58 3139 1 chrUn.!!$F2 3081
4 TraesCS4B01G004100 chrUn 51921656 51924288 2632 True 901.500000 1498 87.539500 58 1683 2 chrUn.!!$R1 1625
5 TraesCS4B01G004100 chrUn 412748158 412749328 1170 True 596.000000 850 86.223500 1685 2822 2 chrUn.!!$R2 1137
6 TraesCS4B01G004100 chr4A 602370986 602375133 4147 False 1167.000000 1546 88.529000 1 3139 3 chr4A.!!$F1 3138
7 TraesCS4B01G004100 chr4A 602379478 602382464 2986 False 1136.666667 2857 85.755333 14 3119 3 chr4A.!!$F2 3105
8 TraesCS4B01G004100 chr4D 3222609 3228959 6350 True 1336.250000 2065 90.303750 1 3138 4 chr4D.!!$R1 3137
9 TraesCS4B01G004100 chr6B 7822782 7823907 1125 True 562.000000 562 76.228000 520 1628 1 chr6B.!!$R1 1108
10 TraesCS4B01G004100 chr6D 432876384 432877402 1018 False 479.000000 479 75.486000 269 1280 1 chr6D.!!$F1 1011

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
72 100 0.669625 GGCGCTAGAAGAAACGGTGT 60.670 55.000 7.64 0.0 0.0 4.16 F
640 4166 2.259204 CGGGGCTTCACGACGTTA 59.741 61.111 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 7421 4.922206 TCCATTGTCAAGAAAGCCAGTAT 58.078 39.130 0.0 0.0 0.0 2.12 R
2612 8214 5.895636 TTTCTGCATGATTTCAACGGTAT 57.104 34.783 0.0 0.0 0.0 2.73 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
30 31 2.769602 TACCCTAACCCTAGCTCCTG 57.230 55.000 0.00 0.00 0.00 3.86
72 100 0.669625 GGCGCTAGAAGAAACGGTGT 60.670 55.000 7.64 0.00 0.00 4.16
99 3610 4.345547 CCCCTGGTTTCTATTACTCCTCTC 59.654 50.000 0.00 0.00 0.00 3.20
149 3669 8.871686 ATTTGGTTTTAACAGTCTTGATTGAC 57.128 30.769 0.20 0.00 37.23 3.18
150 3670 7.397892 TTGGTTTTAACAGTCTTGATTGACA 57.602 32.000 0.20 0.00 39.27 3.58
167 3687 6.314648 TGATTGACAATTCTCTTCCGATCTTG 59.685 38.462 1.39 0.00 0.00 3.02
265 3785 3.642977 CTTCTCCAGGAGATCCCCA 57.357 57.895 20.59 3.74 38.56 4.96
306 3826 4.361971 TCCCTCCCTCGTGCGTCT 62.362 66.667 0.00 0.00 0.00 4.18
640 4166 2.259204 CGGGGCTTCACGACGTTA 59.741 61.111 0.00 0.00 0.00 3.18
819 4348 3.117888 GTGCTTGGGGAGATATTTCCTCA 60.118 47.826 10.82 10.82 46.00 3.86
922 4451 4.218417 GTGATGCCCTTGTGTTTGATACTT 59.782 41.667 0.00 0.00 0.00 2.24
927 4456 8.588290 ATGCCCTTGTGTTTGATACTTAAATA 57.412 30.769 0.00 0.00 0.00 1.40
953 4482 3.072944 GTCTTGCTGTGATTGAGAAGCT 58.927 45.455 0.00 0.00 36.60 3.74
1491 7012 4.808895 GCCTGTGATGTATCGTGATGTAAA 59.191 41.667 0.00 0.00 0.00 2.01
1645 7175 8.255905 GGAAACTGGCTATAACTACACTAAGAA 58.744 37.037 0.00 0.00 0.00 2.52
1885 7421 5.781210 TTTTGCACACTGGTCATAAATGA 57.219 34.783 0.00 0.00 0.00 2.57
1908 7444 3.565307 ACTGGCTTTCTTGACAATGGAA 58.435 40.909 0.00 0.00 0.00 3.53
2653 8255 6.675987 CAGAAATTTGAGTTCTTCTGGGAAG 58.324 40.000 0.00 1.28 40.61 3.46
2654 8256 6.264067 CAGAAATTTGAGTTCTTCTGGGAAGT 59.736 38.462 0.00 0.00 40.61 3.01
2661 8263 5.477291 TGAGTTCTTCTGGGAAGTAGTAGTG 59.523 44.000 7.09 0.00 0.00 2.74
2685 8287 4.082787 CCAATTGGGTTACTCACATGACAC 60.083 45.833 17.36 0.00 0.00 3.67
2828 8430 6.153000 ACCTCTGTAGTATGTAGGTTGTTCTG 59.847 42.308 0.00 0.00 37.25 3.02
2848 8500 3.741249 TGCTTTTATGTACGGTTGTCCA 58.259 40.909 0.00 0.00 0.00 4.02
2943 8679 7.095187 GGGTTAATAGTCTTTGTGAAGTCAGTG 60.095 40.741 0.00 0.00 34.41 3.66
2986 8723 7.776618 TCTGAGTCTTCCTAGTGATTTAACA 57.223 36.000 0.00 0.00 0.00 2.41
3042 8779 2.005451 GCAGCAGGGATAGATAATGCG 58.995 52.381 0.00 0.00 41.69 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.813346 TTTTTGCCTCGACCCTCC 57.187 55.556 0.00 0.00 0.00 4.30
72 100 2.916934 AGTAATAGAAACCAGGGGCACA 59.083 45.455 0.00 0.00 0.00 4.57
99 3610 0.991920 TTGGGAAAGCAGGAGGTAGG 59.008 55.000 0.00 0.00 0.00 3.18
263 3783 2.203126 GAGGAGGAAGGCGCATGG 60.203 66.667 10.83 0.00 0.00 3.66
265 3785 2.906458 CTGAGGAGGAAGGCGCAT 59.094 61.111 10.83 0.00 0.00 4.73
640 4166 4.495422 CAGGCATAGAAACTACTCGTTGT 58.505 43.478 0.00 0.00 35.61 3.32
922 4451 7.386059 TCAATCACAGCAAGACTCTGTATTTA 58.614 34.615 0.00 0.00 42.38 1.40
927 4456 3.323115 TCTCAATCACAGCAAGACTCTGT 59.677 43.478 0.00 0.00 44.87 3.41
953 4482 1.275010 TGATAGCGTTCTTGTCTGCCA 59.725 47.619 0.00 0.00 0.00 4.92
1275 4808 9.707957 AAATTATGGTAGGGATAAAACATGTCA 57.292 29.630 0.00 0.00 0.00 3.58
1512 7033 8.394121 GCAATAGATATCCGAAATCCATCTTTC 58.606 37.037 0.00 0.00 32.84 2.62
1645 7175 9.927081 ACATAGGAGATTGTTTCCTCATATTTT 57.073 29.630 0.00 0.00 43.90 1.82
1885 7421 4.922206 TCCATTGTCAAGAAAGCCAGTAT 58.078 39.130 0.00 0.00 0.00 2.12
2612 8214 5.895636 TTTCTGCATGATTTCAACGGTAT 57.104 34.783 0.00 0.00 0.00 2.73
2616 8218 6.364165 ACTCAAATTTCTGCATGATTTCAACG 59.636 34.615 0.00 0.00 0.00 4.10
2653 8255 4.840271 AGTAACCCAATTGGCACTACTAC 58.160 43.478 19.75 11.94 37.83 2.73
2654 8256 4.532916 TGAGTAACCCAATTGGCACTACTA 59.467 41.667 19.75 8.47 37.83 1.82
2661 8263 3.088532 TCATGTGAGTAACCCAATTGGC 58.911 45.455 19.75 5.31 37.83 4.52
2685 8287 3.265791 GAGGTACCTGCAGAACAATCAG 58.734 50.000 22.10 0.00 0.00 2.90
2828 8430 3.126343 CCTGGACAACCGTACATAAAAGC 59.874 47.826 0.00 0.00 34.66 3.51
2848 8500 7.610580 TTAAATCCAACAAATTCCACTTCCT 57.389 32.000 0.00 0.00 0.00 3.36
2986 8723 4.408270 AGTGATGTGAGCTCCATTATCACT 59.592 41.667 28.13 28.13 46.22 3.41


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

AutoCloner maintained by Alex Coulton.