Multiple sequence alignment - TraesCS7A01G397300

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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 TraesCS7A01G397300 chr7A 100.000 4045 0 0 1 4045 576086846 576090890 0.000000e+00 7470.0
1 TraesCS7A01G397300 chr7A 96.281 4060 78 19 13 4045 39479353 39483366 0.000000e+00 6593.0
2 TraesCS7A01G397300 chr4B 97.710 4061 61 8 13 4045 475802128 475798072 0.000000e+00 6955.0
3 TraesCS7A01G397300 chr4B 89.674 184 16 3 1998 2180 446508575 446508756 8.740000e-57 231.0
4 TraesCS7A01G397300 chr3B 97.390 4061 67 11 13 4045 491826131 491822082 0.000000e+00 6876.0
5 TraesCS7A01G397300 chr3B 91.685 445 25 5 88 522 115400763 115401205 1.240000e-169 606.0
6 TraesCS7A01G397300 chr3B 95.982 224 8 1 24 247 43404822 43404600 2.970000e-96 363.0
7 TraesCS7A01G397300 chr2B 97.107 3560 74 4 13 3547 88852993 88856548 0.000000e+00 5976.0
8 TraesCS7A01G397300 chr2B 86.808 1084 57 36 535 1566 774768688 774769737 0.000000e+00 1131.0
9 TraesCS7A01G397300 chr2B 86.905 1008 45 33 538 1503 744374756 744373794 0.000000e+00 1050.0
10 TraesCS7A01G397300 chr2B 92.645 707 40 6 1669 2370 38263232 38262533 0.000000e+00 1007.0
11 TraesCS7A01G397300 chr2B 94.717 265 14 0 2654 2918 38260475 38260211 2.910000e-111 412.0
12 TraesCS7A01G397300 chr2B 83.673 98 14 2 1566 1663 406249167 406249072 1.550000e-14 91.6
13 TraesCS7A01G397300 chrUn 98.164 2015 29 3 2032 4045 309099466 309101473 0.000000e+00 3509.0
14 TraesCS7A01G397300 chrUn 98.114 2015 30 3 2032 4045 309113731 309111724 0.000000e+00 3504.0
15 TraesCS7A01G397300 chrUn 97.500 800 11 1 1205 2004 309098549 309099339 0.000000e+00 1358.0
16 TraesCS7A01G397300 chrUn 97.500 800 11 1 1205 2004 309114648 309113858 0.000000e+00 1358.0
17 TraesCS7A01G397300 chrUn 93.005 629 11 3 732 1345 472255659 472256269 0.000000e+00 887.0
18 TraesCS7A01G397300 chr3A 98.114 2015 30 3 2032 4045 35092071 35090064 0.000000e+00 3504.0
19 TraesCS7A01G397300 chr3A 95.533 2015 35 6 15 2004 35094182 35092198 0.000000e+00 3171.0
20 TraesCS7A01G397300 chr3A 98.258 1033 16 2 3014 4045 35148932 35147901 0.000000e+00 1807.0
21 TraesCS7A01G397300 chr3A 97.500 800 11 1 1205 2004 35150393 35149603 0.000000e+00 1358.0
22 TraesCS7A01G397300 chr3A 96.281 726 17 1 15 730 35152312 35151587 0.000000e+00 1182.0
23 TraesCS7A01G397300 chr5A 97.708 1440 21 2 2607 4045 637185501 637184073 0.000000e+00 2466.0
24 TraesCS7A01G397300 chr5A 95.241 1429 24 5 15 1417 637188221 637186811 0.000000e+00 2222.0
25 TraesCS7A01G397300 chr5A 88.584 473 41 6 2190 2652 249850533 249850064 2.730000e-156 562.0
26 TraesCS7A01G397300 chr5A 85.513 497 55 12 1685 2176 249851274 249850790 1.680000e-138 503.0
27 TraesCS7A01G397300 chr1D 93.069 707 27 7 538 1226 432637428 432636726 0.000000e+00 1014.0
28 TraesCS7A01G397300 chr1D 94.426 305 8 3 1273 1568 432636729 432636425 1.020000e-125 460.0
29 TraesCS7A01G397300 chr2D 95.455 462 11 1 14 465 14792015 14792476 0.000000e+00 728.0
30 TraesCS7A01G397300 chr2D 95.897 390 12 2 535 920 631285769 631286158 2.650000e-176 628.0
31 TraesCS7A01G397300 chr2D 88.824 170 19 0 2007 2176 547878606 547878437 4.100000e-50 209.0
32 TraesCS7A01G397300 chr5D 90.580 552 38 8 3412 3959 537912131 537911590 0.000000e+00 719.0
33 TraesCS7A01G397300 chr5D 89.773 88 8 1 3959 4045 537911518 537911431 1.190000e-20 111.0
34 TraesCS7A01G397300 chr7B 91.910 445 24 5 88 522 388872399 388872841 2.670000e-171 612.0
35 TraesCS7A01G397300 chr1A 89.301 458 35 7 2190 2637 90167642 90167189 2.730000e-156 562.0
36 TraesCS7A01G397300 chr1A 83.807 352 45 8 1829 2176 90168239 90167896 1.400000e-84 324.0
37 TraesCS7A01G397300 chr1A 88.710 186 18 3 1998 2182 367001353 367001170 1.460000e-54 224.0


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 TraesCS7A01G397300 chr7A 576086846 576090890 4044 False 7470.0 7470 100.000000 1 4045 1 chr7A.!!$F2 4044
1 TraesCS7A01G397300 chr7A 39479353 39483366 4013 False 6593.0 6593 96.281000 13 4045 1 chr7A.!!$F1 4032
2 TraesCS7A01G397300 chr4B 475798072 475802128 4056 True 6955.0 6955 97.710000 13 4045 1 chr4B.!!$R1 4032
3 TraesCS7A01G397300 chr3B 491822082 491826131 4049 True 6876.0 6876 97.390000 13 4045 1 chr3B.!!$R2 4032
4 TraesCS7A01G397300 chr2B 88852993 88856548 3555 False 5976.0 5976 97.107000 13 3547 1 chr2B.!!$F1 3534
5 TraesCS7A01G397300 chr2B 774768688 774769737 1049 False 1131.0 1131 86.808000 535 1566 1 chr2B.!!$F2 1031
6 TraesCS7A01G397300 chr2B 744373794 744374756 962 True 1050.0 1050 86.905000 538 1503 1 chr2B.!!$R2 965
7 TraesCS7A01G397300 chr2B 38260211 38263232 3021 True 709.5 1007 93.681000 1669 2918 2 chr2B.!!$R3 1249
8 TraesCS7A01G397300 chrUn 309098549 309101473 2924 False 2433.5 3509 97.832000 1205 4045 2 chrUn.!!$F2 2840
9 TraesCS7A01G397300 chrUn 309111724 309114648 2924 True 2431.0 3504 97.807000 1205 4045 2 chrUn.!!$R1 2840
10 TraesCS7A01G397300 chrUn 472255659 472256269 610 False 887.0 887 93.005000 732 1345 1 chrUn.!!$F1 613
11 TraesCS7A01G397300 chr3A 35090064 35094182 4118 True 3337.5 3504 96.823500 15 4045 2 chr3A.!!$R1 4030
12 TraesCS7A01G397300 chr3A 35147901 35152312 4411 True 1449.0 1807 97.346333 15 4045 3 chr3A.!!$R2 4030
13 TraesCS7A01G397300 chr5A 637184073 637188221 4148 True 2344.0 2466 96.474500 15 4045 2 chr5A.!!$R2 4030
14 TraesCS7A01G397300 chr5A 249850064 249851274 1210 True 532.5 562 87.048500 1685 2652 2 chr5A.!!$R1 967
15 TraesCS7A01G397300 chr1D 432636425 432637428 1003 True 737.0 1014 93.747500 538 1568 2 chr1D.!!$R1 1030
16 TraesCS7A01G397300 chr5D 537911431 537912131 700 True 415.0 719 90.176500 3412 4045 2 chr5D.!!$R1 633
17 TraesCS7A01G397300 chr1A 90167189 90168239 1050 True 443.0 562 86.554000 1829 2637 2 chr1A.!!$R2 808

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
536 550 1.229082 AGAGGCGGGACACCAACTA 60.229 57.895 0.0 0.0 36.13 2.24 F
1448 2833 1.893137 TGTAGACTCCACGTTCAGCAT 59.107 47.619 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 3219 2.747460 GCGAGCCCTCACATGCAA 60.747 61.111 0.0 0.0 0.0 4.08 R
3136 6692 2.024414 GCAAACACACCTCCTTCAAGT 58.976 47.619 0.0 0.0 0.0 3.16 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
258 271 2.850833 TGGAAGGGATCTGATTGGAGT 58.149 47.619 0.00 0.00 0.00 3.85
426 440 1.403687 ATCTTCTCCCCGTAGCCTGC 61.404 60.000 0.00 0.00 0.00 4.85
536 550 1.229082 AGAGGCGGGACACCAACTA 60.229 57.895 0.00 0.00 36.13 2.24
1011 1060 2.125147 GACGCTATGCCCAGCACA 60.125 61.111 7.35 0.00 43.04 4.57
1268 2002 7.866393 GCGAGCTAGATAGGTTAACTGAAATTA 59.134 37.037 5.42 0.00 33.58 1.40
1448 2833 1.893137 TGTAGACTCCACGTTCAGCAT 59.107 47.619 0.00 0.00 0.00 3.79
1516 2904 6.042638 TGGAGCAATAATCCTACAGCTATC 57.957 41.667 0.00 0.00 37.74 2.08
1773 3165 2.513204 CTCCGGGATGCTGCAGTG 60.513 66.667 16.64 0.00 0.00 3.66
2066 3589 7.700656 GGTTGTGATTTTGTTATTATCCCGAAG 59.299 37.037 0.00 0.00 0.00 3.79
2670 6226 9.357652 GATTTCTTTTGTGATGCTTATTTGCTA 57.642 29.630 0.00 0.00 0.00 3.49
2955 6511 1.588824 TACGAACATGGGACGCTCGT 61.589 55.000 9.03 9.03 44.32 4.18
3106 6662 5.780984 TGCAGCACATCAATTGTTGAATTA 58.219 33.333 20.66 0.00 43.95 1.40
3136 6692 4.828939 AGGAGCTGTCAATTGTTGAATTCA 59.171 37.500 3.38 3.38 42.15 2.57
3591 7148 0.407528 TGCCACATTTTGAGGGCCTA 59.592 50.000 5.73 0.00 39.40 3.93
3705 7262 7.562454 TGGAGATTTTCTGCATCTTTTATGGAT 59.438 33.333 0.00 0.00 39.98 3.41
3989 7622 8.831550 GGAGTATGTTCCAATAGAAATCTTCAC 58.168 37.037 0.00 0.00 35.85 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.268539 CGCACGGGATTATTTTCAGGC 60.269 52.381 0.00 0.00 0.00 4.85
1 2 2.014128 ACGCACGGGATTATTTTCAGG 58.986 47.619 0.00 0.00 0.00 3.86
2 3 3.425404 CAACGCACGGGATTATTTTCAG 58.575 45.455 0.00 0.00 0.00 3.02
3 4 2.414824 GCAACGCACGGGATTATTTTCA 60.415 45.455 0.00 0.00 0.00 2.69
4 5 2.182014 GCAACGCACGGGATTATTTTC 58.818 47.619 0.00 0.00 0.00 2.29
5 6 1.466697 CGCAACGCACGGGATTATTTT 60.467 47.619 0.00 0.00 0.00 1.82
6 7 0.098025 CGCAACGCACGGGATTATTT 59.902 50.000 0.00 0.00 0.00 1.40
7 8 0.741574 TCGCAACGCACGGGATTATT 60.742 50.000 0.00 0.00 0.00 1.40
8 9 0.741574 TTCGCAACGCACGGGATTAT 60.742 50.000 0.00 0.00 0.00 1.28
9 10 1.374378 TTCGCAACGCACGGGATTA 60.374 52.632 0.00 0.00 0.00 1.75
10 11 2.666862 TTCGCAACGCACGGGATT 60.667 55.556 0.00 0.00 0.00 3.01
11 12 3.419759 GTTCGCAACGCACGGGAT 61.420 61.111 0.00 0.00 0.00 3.85
51 52 4.662961 CTGGTGTGGCGTCGCTCA 62.663 66.667 18.11 13.67 0.00 4.26
258 271 3.329889 AAGGGCGCAGATCCACCA 61.330 61.111 10.83 0.00 0.00 4.17
706 721 3.487764 TTGCCGCTGTACACGTCGT 62.488 57.895 13.98 0.00 0.00 4.34
821 840 4.227073 AGATTCAGAAAGAAGGGGAGAAGG 59.773 45.833 0.00 0.00 40.15 3.46
1287 2021 1.138464 TGACTGATGGCAGCTGATCTC 59.862 52.381 20.43 10.28 46.26 2.75
1329 2067 4.944619 TCCAGTTATCAGAGTAGCATGG 57.055 45.455 0.00 0.00 0.00 3.66
1516 2904 3.184541 CACGGACTGTAAATCTTACCCG 58.815 50.000 0.00 0.00 41.24 5.28
1773 3165 2.896443 CTCCTGCTCGACCCTTCC 59.104 66.667 0.00 0.00 0.00 3.46
1827 3219 2.747460 GCGAGCCCTCACATGCAA 60.747 61.111 0.00 0.00 0.00 4.08
2182 3710 4.866486 ACTGGTTCATTTATTACGACGACC 59.134 41.667 0.00 0.00 0.00 4.79
3106 6662 4.210331 ACAATTGACAGCTCCTTCAAACT 58.790 39.130 13.59 0.00 35.42 2.66
3136 6692 2.024414 GCAAACACACCTCCTTCAAGT 58.976 47.619 0.00 0.00 0.00 3.16
3591 7148 8.450578 TCTCAAGTGTTGTATTCTTCAATTGT 57.549 30.769 5.13 0.00 37.24 2.71
3978 7611 4.703897 TCAAGGTGTTCGTGAAGATTTCT 58.296 39.130 0.00 0.00 31.17 2.52


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

AutoCloner maintained by Alex Coulton.