Multiple sequence alignment - TraesCS1B01G387300

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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 TraesCS1B01G387300 chr1B 100.000 4015 0 0 1 4015 621587414 621583400 0.000000e+00 7415
1 TraesCS1B01G387300 chr7B 97.071 4028 91 19 1 4015 733218692 733214679 0.000000e+00 6759
2 TraesCS1B01G387300 chr7B 92.326 4105 193 66 1 4015 712607067 712611139 0.000000e+00 5723
3 TraesCS1B01G387300 chr4B 92.627 4096 175 67 8 4015 638494325 638490269 0.000000e+00 5773
4 TraesCS1B01G387300 chr3B 97.262 2593 52 11 4 2588 18008678 18006097 0.000000e+00 4377
5 TraesCS1B01G387300 chr7D 85.304 2681 273 73 1174 3801 21681045 21678433 0.000000e+00 2656
6 TraesCS1B01G387300 chr7D 85.170 2677 286 71 1174 3801 108301243 108298629 0.000000e+00 2641
7 TraesCS1B01G387300 chr7D 84.942 2683 286 71 1174 3801 108264318 108261699 0.000000e+00 2608
8 TraesCS1B01G387300 chr7D 87.805 205 23 2 3812 4015 108298577 108298374 5.190000e-59 239
9 TraesCS1B01G387300 chr7D 86.829 205 25 2 3812 4015 108261647 108261444 1.120000e-55 228
10 TraesCS1B01G387300 chr5D 85.177 2685 278 74 1174 3801 30633318 30630697 0.000000e+00 2643
11 TraesCS1B01G387300 chr5D 80.614 521 59 24 2 486 420310595 420310081 8.200000e-97 364
12 TraesCS1B01G387300 chr5D 87.864 206 22 3 3812 4015 420306810 420306606 5.190000e-59 239
13 TraesCS1B01G387300 chr5D 88.235 187 20 2 3830 4015 30630627 30630442 5.220000e-54 222
14 TraesCS1B01G387300 chr2D 84.650 2684 291 78 1174 3801 343142477 343139859 0.000000e+00 2562
15 TraesCS1B01G387300 chr2D 87.805 205 23 2 3812 4015 343139807 343139604 5.190000e-59 239
16 TraesCS1B01G387300 chr6A 84.830 2472 266 64 1177 3589 615412314 615409893 0.000000e+00 2386
17 TraesCS1B01G387300 chr6A 79.070 516 64 25 10 486 615413526 615413016 8.380000e-82 315
18 TraesCS1B01G387300 chr1D 85.384 2292 244 60 1174 3425 66199547 66197307 0.000000e+00 2292
19 TraesCS1B01G387300 chr1D 88.293 205 22 2 3812 4015 66196826 66196623 1.110000e-60 244
20 TraesCS1B01G387300 chr3A 85.362 1380 164 26 1174 2540 735465574 735466928 0.000000e+00 1395
21 TraesCS1B01G387300 chr3A 86.193 1014 83 33 2613 3589 735466924 735467917 0.000000e+00 1044
22 TraesCS1B01G387300 chr3A 80.891 539 56 30 2 504 735464347 735464874 8.140000e-102 381


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 TraesCS1B01G387300 chr1B 621583400 621587414 4014 True 7415.0 7415 100.000000 1 4015 1 chr1B.!!$R1 4014
1 TraesCS1B01G387300 chr7B 733214679 733218692 4013 True 6759.0 6759 97.071000 1 4015 1 chr7B.!!$R1 4014
2 TraesCS1B01G387300 chr7B 712607067 712611139 4072 False 5723.0 5723 92.326000 1 4015 1 chr7B.!!$F1 4014
3 TraesCS1B01G387300 chr4B 638490269 638494325 4056 True 5773.0 5773 92.627000 8 4015 1 chr4B.!!$R1 4007
4 TraesCS1B01G387300 chr3B 18006097 18008678 2581 True 4377.0 4377 97.262000 4 2588 1 chr3B.!!$R1 2584
5 TraesCS1B01G387300 chr7D 21678433 21681045 2612 True 2656.0 2656 85.304000 1174 3801 1 chr7D.!!$R1 2627
6 TraesCS1B01G387300 chr7D 108298374 108301243 2869 True 1440.0 2641 86.487500 1174 4015 2 chr7D.!!$R3 2841
7 TraesCS1B01G387300 chr7D 108261444 108264318 2874 True 1418.0 2608 85.885500 1174 4015 2 chr7D.!!$R2 2841
8 TraesCS1B01G387300 chr5D 30630442 30633318 2876 True 1432.5 2643 86.706000 1174 4015 2 chr5D.!!$R1 2841
9 TraesCS1B01G387300 chr5D 420306606 420310595 3989 True 301.5 364 84.239000 2 4015 2 chr5D.!!$R2 4013
10 TraesCS1B01G387300 chr2D 343139604 343142477 2873 True 1400.5 2562 86.227500 1174 4015 2 chr2D.!!$R1 2841
11 TraesCS1B01G387300 chr6A 615409893 615413526 3633 True 1350.5 2386 81.950000 10 3589 2 chr6A.!!$R1 3579
12 TraesCS1B01G387300 chr1D 66196623 66199547 2924 True 1268.0 2292 86.838500 1174 4015 2 chr1D.!!$R1 2841
13 TraesCS1B01G387300 chr3A 735464347 735467917 3570 False 940.0 1395 84.148667 2 3589 3 chr3A.!!$F1 3587

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
143 158 2.366266 TCAAACGGTACTGCCTACACTT 59.634 45.455 0.23 0.0 34.25 3.16 F
1016 1158 0.603707 CGCATGTCACACTCTTGGGT 60.604 55.000 0.00 0.0 0.00 4.51 F
1321 1518 4.043435 AGGCACTAAAGAGAAACCAATCCT 59.957 41.667 0.00 0.0 36.02 3.24 F
2252 2502 2.778299 AGCATTGCCTCTACACGAAAA 58.222 42.857 4.70 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1796 3.255642 TCCTTTTTGGAGGCAAATTCTCG 59.744 43.478 0.00 0.0 40.56 4.04 R
2252 2502 2.158841 GCAATCAACCGTACACGTTCAT 59.841 45.455 0.58 0.0 37.74 2.57 R
2386 2649 2.815503 CAATGCTCACCATGAACTGACA 59.184 45.455 0.00 0.0 33.49 3.58 R
3746 4160 2.053747 TCCTGTTGGGGTAGGAACAT 57.946 50.000 0.00 0.0 40.03 2.71 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
143 158 2.366266 TCAAACGGTACTGCCTACACTT 59.634 45.455 0.23 0.00 34.25 3.16
302 405 2.819608 ACACATTGCACCCATTAGACAC 59.180 45.455 0.00 0.00 0.00 3.67
856 979 6.429385 CTAGTTCATAGAAAAGGATGGCATCC 59.571 42.308 34.42 34.42 40.80 3.51
1016 1158 0.603707 CGCATGTCACACTCTTGGGT 60.604 55.000 0.00 0.00 0.00 4.51
1117 1296 7.775561 GGAAGGTATCATCAAAATTCTACCTGT 59.224 37.037 0.00 0.00 39.05 4.00
1218 1413 6.095432 TGTCCCTTTCAACATTATTTGTGG 57.905 37.500 0.00 0.00 38.99 4.17
1311 1508 6.942005 TGATGATCAAAAAGGCACTAAAGAGA 59.058 34.615 0.00 0.00 38.49 3.10
1321 1518 4.043435 AGGCACTAAAGAGAAACCAATCCT 59.957 41.667 0.00 0.00 36.02 3.24
1354 1551 8.514594 TGACTACCTTCATGAAAATTTGATGAC 58.485 33.333 9.88 0.00 0.00 3.06
1413 1610 6.404074 CCCTTTCTTTTGTGTAGCATCATCTC 60.404 42.308 0.00 0.00 0.00 2.75
1414 1611 6.373774 CCTTTCTTTTGTGTAGCATCATCTCT 59.626 38.462 0.00 0.00 0.00 3.10
1415 1612 7.550551 CCTTTCTTTTGTGTAGCATCATCTCTA 59.449 37.037 0.00 0.00 0.00 2.43
1568 1771 9.116067 AGACAACTTATACAACACAAAGCTTTA 57.884 29.630 12.25 0.00 0.00 1.85
1593 1796 4.429854 AGGCTCTTCATCAAGGGATAAC 57.570 45.455 0.00 0.00 30.51 1.89
1633 1836 4.170468 AGGATAATACACCCAAGCAAGG 57.830 45.455 0.00 0.00 0.00 3.61
1939 2152 6.922957 GTCATGTGGAAGCTTATGTTTTCAAA 59.077 34.615 0.00 0.00 0.00 2.69
1989 2203 6.940430 AAATCATCCAAGGAGGTCAAAAAT 57.060 33.333 0.25 0.00 39.02 1.82
2252 2502 2.778299 AGCATTGCCTCTACACGAAAA 58.222 42.857 4.70 0.00 0.00 2.29
2417 2680 4.213564 TGGTGAGCATTGGTTTTTGTTT 57.786 36.364 0.00 0.00 0.00 2.83
2576 2849 0.814010 GCTGCTAATACCCACACCCG 60.814 60.000 0.00 0.00 0.00 5.28
2933 3235 0.324943 ACGTAGCAGATGCAAGGGTT 59.675 50.000 7.68 0.00 45.16 4.11
3161 3473 4.521130 TTTTGTGTTTGCCACTGTAACA 57.479 36.364 0.00 0.00 44.81 2.41
3164 3476 4.103365 TGTGTTTGCCACTGTAACAAAG 57.897 40.909 7.43 0.00 44.81 2.77
3165 3477 3.508012 TGTGTTTGCCACTGTAACAAAGT 59.492 39.130 7.43 0.00 44.81 2.66
3196 3514 4.514816 TGTGATTGTCTGCGATTTTTGAGA 59.485 37.500 0.00 0.00 0.00 3.27
3712 4126 3.068590 AGCACAAGTGAAAAAGTGGATGG 59.931 43.478 4.04 0.00 32.80 3.51
3746 4160 4.595781 AGGGACATACTGTGTTAAGGTCAA 59.404 41.667 0.00 0.00 42.36 3.18
3816 4271 9.616156 TGTCTACCAGTACTCAAATTTAAACAA 57.384 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 56 6.772605 TGACATCCATAGTATTTCCATCTGG 58.227 40.000 0.00 0.00 0.00 3.86
302 405 4.574599 AAGAAGTACTTTTGCCTTGCAG 57.425 40.909 10.02 0.00 40.61 4.41
352 455 5.882000 CACAATCATCATGGTCTGGAAGTAA 59.118 40.000 0.00 0.00 33.76 2.24
529 633 1.402325 GGGTGAATTTTGTAGCACGGC 60.402 52.381 0.00 0.00 32.24 5.68
600 705 2.611292 CCTTCGATGACATCCTTGCTTC 59.389 50.000 9.87 0.00 0.00 3.86
1321 1518 8.918202 ATTTTCATGAAGGTAGTCACTTACAA 57.082 30.769 8.41 0.00 0.00 2.41
1568 1771 5.659849 ATCCCTTGATGAAGAGCCTAAAT 57.340 39.130 0.00 0.00 0.00 1.40
1593 1796 3.255642 TCCTTTTTGGAGGCAAATTCTCG 59.744 43.478 0.00 0.00 40.56 4.04
1633 1836 5.221402 TGTGATCATATGGAGAGCAGAGAAC 60.221 44.000 0.00 0.00 31.29 3.01
1989 2203 7.389884 CACCTAGTGTAGTGAAGAAGTAGTGTA 59.610 40.741 0.00 0.00 36.01 2.90
2083 2330 4.515567 CACCCAAGAAGTCCAGTAAAGTTC 59.484 45.833 0.00 0.00 0.00 3.01
2252 2502 2.158841 GCAATCAACCGTACACGTTCAT 59.841 45.455 0.58 0.00 37.74 2.57
2386 2649 2.815503 CAATGCTCACCATGAACTGACA 59.184 45.455 0.00 0.00 33.49 3.58
2417 2680 7.428282 TTTTCTTGCTATAATGTCGACAACA 57.572 32.000 24.13 13.61 43.51 3.33
2576 2849 5.544136 AGCAACACAACAAAAATGGAAAC 57.456 34.783 0.00 0.00 0.00 2.78
3145 3457 4.792521 AACTTTGTTACAGTGGCAAACA 57.207 36.364 0.00 0.00 0.00 2.83
3160 3472 6.737750 GCAGACAATCACAAAAACAAACTTTG 59.262 34.615 0.00 0.00 39.26 2.77
3161 3473 6.400940 CGCAGACAATCACAAAAACAAACTTT 60.401 34.615 0.00 0.00 0.00 2.66
3164 3476 4.560819 TCGCAGACAATCACAAAAACAAAC 59.439 37.500 0.00 0.00 0.00 2.93
3165 3477 4.738124 TCGCAGACAATCACAAAAACAAA 58.262 34.783 0.00 0.00 0.00 2.83
3746 4160 2.053747 TCCTGTTGGGGTAGGAACAT 57.946 50.000 0.00 0.00 40.03 2.71
3816 4271 8.725148 GTTCATGGATGATATCGCTTTTTCTAT 58.275 33.333 0.00 0.00 36.56 1.98


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

AutoCloner maintained by Alex Coulton.