Multiple sequence alignment - TraesCS1B01G074700

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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 TraesCS1B01G074700 chr1B 100.000 4043 0 0 1 4043 58029819 58033861 0.000000e+00 7467.0
1 TraesCS1B01G074700 chr1B 99.070 1290 10 1 2756 4043 58108338 58109627 0.000000e+00 2314.0
2 TraesCS1B01G074700 chr1B 99.145 1287 8 3 936 2221 58107061 58108345 0.000000e+00 2313.0
3 TraesCS1B01G074700 chr1B 99.164 1196 7 3 936 2130 58079621 58080814 0.000000e+00 2150.0
4 TraesCS1B01G074700 chr1B 90.560 1483 123 10 1518 2986 57782511 57783990 0.000000e+00 1947.0
5 TraesCS1B01G074700 chr1B 99.321 884 6 0 3160 4043 58082593 58083476 0.000000e+00 1600.0
6 TraesCS1B01G074700 chr1B 80.470 1234 207 19 1671 2893 58752943 58754153 0.000000e+00 913.0
7 TraesCS1B01G074700 chr1B 78.636 1334 226 40 1648 2955 58540111 58541411 0.000000e+00 830.0
8 TraesCS1B01G074700 chr1B 99.221 385 3 0 1837 2221 58081873 58082257 0.000000e+00 695.0
9 TraesCS1B01G074700 chr1B 98.851 348 3 1 2756 3102 58082250 58082597 1.600000e-173 619.0
10 TraesCS1B01G074700 chr1B 81.400 543 66 25 416 936 31373034 31372505 1.050000e-110 411.0
11 TraesCS1B01G074700 chr1B 82.773 476 56 17 3011 3480 58753975 58754430 6.290000e-108 401.0
12 TraesCS1B01G074700 chr1A 89.929 1549 136 12 1481 3014 37466438 37467981 0.000000e+00 1978.0
13 TraesCS1B01G074700 chr1D 90.162 1484 133 7 1515 2986 38293935 38295417 0.000000e+00 1919.0
14 TraesCS1B01G074700 chr1D 88.629 941 93 8 1515 2443 38250175 38251113 0.000000e+00 1133.0
15 TraesCS1B01G074700 chr1D 79.401 1335 221 37 1648 2955 38655206 38656513 0.000000e+00 893.0
16 TraesCS1B01G074700 chr1D 79.426 1254 227 19 1745 2983 39651489 39652726 0.000000e+00 857.0
17 TraesCS1B01G074700 chr1D 92.131 521 36 3 2471 2986 38251110 38251630 0.000000e+00 730.0
18 TraesCS1B01G074700 chr1D 82.812 256 39 5 3766 4020 38561124 38561375 1.460000e-54 224.0
19 TraesCS1B01G074700 chr1D 91.566 83 7 0 1671 1753 39649301 39649383 9.180000e-22 115.0
20 TraesCS1B01G074700 chr1D 86.111 72 7 3 1390 1460 38250036 38250105 1.560000e-09 75.0
21 TraesCS1B01G074700 chr1D 84.932 73 8 3 1390 1460 38293794 38293865 2.020000e-08 71.3
22 TraesCS1B01G074700 chr2B 99.359 936 6 0 1 936 20341346 20340411 0.000000e+00 1696.0
23 TraesCS1B01G074700 chr2A 96.460 565 17 2 372 936 9827895 9828456 0.000000e+00 929.0
24 TraesCS1B01G074700 chr2A 97.706 523 8 2 1 523 9827489 9828007 0.000000e+00 896.0
25 TraesCS1B01G074700 chr4A 95.745 564 19 3 372 935 742904675 742904117 0.000000e+00 904.0
26 TraesCS1B01G074700 chr4A 95.567 564 22 2 372 935 710054971 710054411 0.000000e+00 900.0
27 TraesCS1B01G074700 chr4A 97.706 523 7 3 1 523 742905080 742904563 0.000000e+00 894.0
28 TraesCS1B01G074700 chr4A 97.323 523 10 2 1 523 710055377 710054859 0.000000e+00 885.0
29 TraesCS1B01G074700 chr4A 95.029 523 18 6 1 521 512421706 512422222 0.000000e+00 815.0
30 TraesCS1B01G074700 chr4A 89.219 538 32 9 393 929 512422127 512422639 0.000000e+00 649.0
31 TraesCS1B01G074700 chr6D 93.300 403 24 3 936 1336 410210615 410210214 3.480000e-165 592.0
32 TraesCS1B01G074700 chr4B 93.671 395 25 0 936 1330 233336975 233336581 3.480000e-165 592.0
33 TraesCS1B01G074700 chr7B 92.424 396 26 4 936 1330 336716483 336716875 2.730000e-156 562.0
34 TraesCS1B01G074700 chr7B 79.566 553 74 29 407 935 648176206 648176743 3.840000e-95 359.0
35 TraesCS1B01G074700 chr6B 91.832 404 28 4 936 1334 251104200 251104603 3.530000e-155 558.0
36 TraesCS1B01G074700 chr5D 91.687 409 23 9 936 1337 47329198 47328794 1.270000e-154 556.0
37 TraesCS1B01G074700 chr3D 92.746 386 26 2 948 1331 558557866 558558251 1.270000e-154 556.0
38 TraesCS1B01G074700 chr3D 79.581 573 61 29 385 938 578866307 578866842 3.840000e-95 359.0
39 TraesCS1B01G074700 chr3B 91.980 399 28 4 936 1330 383474046 383474444 1.270000e-154 556.0
40 TraesCS1B01G074700 chrUn 100.000 222 0 0 3822 4043 263386415 263386194 1.050000e-110 411.0
41 TraesCS1B01G074700 chrUn 100.000 222 0 0 3822 4043 344445221 344445000 1.050000e-110 411.0
42 TraesCS1B01G074700 chr7D 79.468 526 86 18 420 936 24315476 24315988 1.790000e-93 353.0


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 TraesCS1B01G074700 chr1B 58029819 58033861 4042 False 7467.00 7467 100.00000 1 4043 1 chr1B.!!$F2 4042
1 TraesCS1B01G074700 chr1B 58107061 58109627 2566 False 2313.50 2314 99.10750 936 4043 2 chr1B.!!$F5 3107
2 TraesCS1B01G074700 chr1B 57782511 57783990 1479 False 1947.00 1947 90.56000 1518 2986 1 chr1B.!!$F1 1468
3 TraesCS1B01G074700 chr1B 58079621 58083476 3855 False 1266.00 2150 99.13925 936 4043 4 chr1B.!!$F4 3107
4 TraesCS1B01G074700 chr1B 58540111 58541411 1300 False 830.00 830 78.63600 1648 2955 1 chr1B.!!$F3 1307
5 TraesCS1B01G074700 chr1B 58752943 58754430 1487 False 657.00 913 81.62150 1671 3480 2 chr1B.!!$F6 1809
6 TraesCS1B01G074700 chr1B 31372505 31373034 529 True 411.00 411 81.40000 416 936 1 chr1B.!!$R1 520
7 TraesCS1B01G074700 chr1A 37466438 37467981 1543 False 1978.00 1978 89.92900 1481 3014 1 chr1A.!!$F1 1533
8 TraesCS1B01G074700 chr1D 38293794 38295417 1623 False 995.15 1919 87.54700 1390 2986 2 chr1D.!!$F4 1596
9 TraesCS1B01G074700 chr1D 38655206 38656513 1307 False 893.00 893 79.40100 1648 2955 1 chr1D.!!$F2 1307
10 TraesCS1B01G074700 chr1D 38250036 38251630 1594 False 646.00 1133 88.95700 1390 2986 3 chr1D.!!$F3 1596
11 TraesCS1B01G074700 chr1D 39649301 39652726 3425 False 486.00 857 85.49600 1671 2983 2 chr1D.!!$F5 1312
12 TraesCS1B01G074700 chr2B 20340411 20341346 935 True 1696.00 1696 99.35900 1 936 1 chr2B.!!$R1 935
13 TraesCS1B01G074700 chr2A 9827489 9828456 967 False 912.50 929 97.08300 1 936 2 chr2A.!!$F1 935
14 TraesCS1B01G074700 chr4A 742904117 742905080 963 True 899.00 904 96.72550 1 935 2 chr4A.!!$R2 934
15 TraesCS1B01G074700 chr4A 710054411 710055377 966 True 892.50 900 96.44500 1 935 2 chr4A.!!$R1 934
16 TraesCS1B01G074700 chr4A 512421706 512422639 933 False 732.00 815 92.12400 1 929 2 chr4A.!!$F1 928
17 TraesCS1B01G074700 chr7B 648176206 648176743 537 False 359.00 359 79.56600 407 935 1 chr7B.!!$F2 528
18 TraesCS1B01G074700 chr3D 578866307 578866842 535 False 359.00 359 79.58100 385 938 1 chr3D.!!$F2 553
19 TraesCS1B01G074700 chr7D 24315476 24315988 512 False 353.00 353 79.46800 420 936 1 chr7D.!!$F1 516

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
658 773 4.321230 GCCCAAACACACAGGAAAATAGAG 60.321 45.833 0.0 0.0 0.00 2.43 F
2523 6163 2.093869 GCATTGCCACATGAGAATGGTT 60.094 45.455 0.0 0.0 38.34 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 6282 1.444895 ATCGCCACCAACGTCGTAC 60.445 57.895 0.0 0.0 0.0 3.67 R
3549 7214 2.501602 GCCCACTGCCCCATAATGC 61.502 63.158 0.0 0.0 0.0 3.56 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
658 773 4.321230 GCCCAAACACACAGGAAAATAGAG 60.321 45.833 0.00 0.00 0.00 2.43
1289 1407 9.951866 AGGGGTTTTTCTATAAAATGGTATGAT 57.048 29.630 0.00 0.00 34.62 2.45
1435 1553 9.470399 TCCAAATAATTTACTAGGAAAACCTCC 57.530 33.333 3.73 0.00 45.81 4.30
2355 5995 5.106555 GGAATGTTGTATGTGACTGTTGGAG 60.107 44.000 0.00 0.00 0.00 3.86
2523 6163 2.093869 GCATTGCCACATGAGAATGGTT 60.094 45.455 0.00 0.00 38.34 3.67
2633 6282 5.772825 TTGGAAAGGATGAGTTTGTTCAG 57.227 39.130 0.00 0.00 0.00 3.02
2641 6290 3.425577 TGAGTTTGTTCAGTACGACGT 57.574 42.857 5.52 5.52 0.00 4.34
2666 6315 1.072331 GGCGATGGTGGTGAGGATAAT 59.928 52.381 0.00 0.00 0.00 1.28
2719 6368 1.671901 CTCGACTTGGAGAGAGGGCC 61.672 65.000 0.00 0.00 36.65 5.80
3089 6751 1.064060 CCGGGAAATTCAACGAGATGC 59.936 52.381 10.15 0.00 0.00 3.91
3137 6799 3.495629 CCATGTCTATGTGCCATGCTACT 60.496 47.826 0.00 0.00 35.70 2.57
3240 6902 3.788227 TTAGATGCTCAACCACCTTGT 57.212 42.857 0.00 0.00 0.00 3.16
3371 7034 5.985911 TCCCAGATTACTACCTTGCTTAAC 58.014 41.667 0.00 0.00 0.00 2.01
3549 7214 4.853924 AATGTACTTGCACAGGAAAAGG 57.146 40.909 0.00 0.00 0.00 3.11
3686 7351 1.325640 CATCATTCAGTGCGAACCTCG 59.674 52.381 0.00 0.00 43.89 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 271 3.386237 GGTCTCTGCCTCGCCACT 61.386 66.667 0.00 0.00 0.00 4.00
658 773 2.037367 GGGAGGCCCACCCTTTTC 59.963 66.667 23.66 2.25 46.60 2.29
973 1091 4.787598 ACGAAATTGAAGATCACTTGCAC 58.212 39.130 0.00 0.00 36.39 4.57
1221 1339 4.272504 CCCGCAGTACATATCGAATGTTTT 59.727 41.667 15.21 5.31 33.76 2.43
1434 1552 9.730420 AATTTTTACGAGAATAAAATCCATCGG 57.270 29.630 0.00 0.00 34.75 4.18
2130 5764 3.142951 ACGCCAAAATAGTTACACAGCA 58.857 40.909 0.00 0.00 0.00 4.41
2355 5995 4.537015 CCTTCGAACACCAAAACTTCATC 58.463 43.478 0.00 0.00 0.00 2.92
2523 6163 5.583854 CCAATGTCCAAACAACAATTGAACA 59.416 36.000 13.59 3.77 39.30 3.18
2633 6282 1.444895 ATCGCCACCAACGTCGTAC 60.445 57.895 0.00 0.00 0.00 3.67
2641 6290 2.282110 CACCACCATCGCCACCAA 60.282 61.111 0.00 0.00 0.00 3.67
2666 6315 4.378978 CGATAATCGCAGTTCCAAAACCAA 60.379 41.667 0.00 0.00 32.19 3.67
2719 6368 3.423539 TCTGGTCATGGAGGAAAACAG 57.576 47.619 0.00 0.00 0.00 3.16
3089 6751 2.578178 CTGCTCGAAGCCGTCTCG 60.578 66.667 4.73 0.00 41.51 4.04
3137 6799 2.968574 ACTCTTGAGCTGGAACTTCTGA 59.031 45.455 0.00 0.00 0.00 3.27
3240 6902 7.356089 AGATAACACCGACAACCAGAATATA 57.644 36.000 0.00 0.00 0.00 0.86
3503 7168 5.126869 TGCTTGTCTGATTTTGAGGTTTCAA 59.873 36.000 0.00 0.00 41.44 2.69
3549 7214 2.501602 GCCCACTGCCCCATAATGC 61.502 63.158 0.00 0.00 0.00 3.56
3686 7351 4.228912 ACAAGCTGTTGACATTGTTAGC 57.771 40.909 0.00 0.00 37.10 3.09


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

AutoCloner maintained by Alex Coulton.