Multiple sequence alignment - TraesCS5B01G218600

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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 TraesCS5B01G218600 chr5B 100.000 2495 0 0 1 2495 392117876 392120370 0.000000e+00 4608.0
1 TraesCS5B01G218600 chr5B 99.104 781 5 2 1715 2495 392079552 392080330 0.000000e+00 1402.0
2 TraesCS5B01G218600 chr5B 99.828 581 1 0 1 581 392070556 392071136 0.000000e+00 1068.0
3 TraesCS5B01G218600 chr5B 86.882 991 79 12 666 1615 391826810 391825830 0.000000e+00 1062.0
4 TraesCS5B01G218600 chr5B 100.000 464 0 0 118 581 392077971 392078434 0.000000e+00 857.0
5 TraesCS5B01G218600 chr5B 83.653 887 84 21 701 1552 391866545 391867405 0.000000e+00 778.0
6 TraesCS5B01G218600 chr5B 84.964 552 69 12 1956 2495 278243655 278243106 4.690000e-152 547.0
7 TraesCS5B01G218600 chr5B 81.381 478 55 22 666 1125 392048318 392048779 2.360000e-95 359.0
8 TraesCS5B01G218600 chr5B 81.381 478 55 22 666 1125 392063303 392063764 2.360000e-95 359.0
9 TraesCS5B01G218600 chr5B 81.381 478 55 22 666 1125 392107058 392107519 2.360000e-95 359.0
10 TraesCS5B01G218600 chr5D 91.773 1410 66 9 582 1965 335121050 335122435 0.000000e+00 1916.0
11 TraesCS5B01G218600 chr5D 88.652 987 75 7 666 1615 334970102 334969116 0.000000e+00 1168.0
12 TraesCS5B01G218600 chr5D 85.633 1058 78 33 582 1607 335086928 335087943 0.000000e+00 1044.0
13 TraesCS5B01G218600 chr5D 85.469 991 65 37 667 1604 334991102 334990138 0.000000e+00 959.0
14 TraesCS5B01G218600 chr5D 87.326 576 54 11 3 561 335120493 335121066 2.090000e-180 641.0
15 TraesCS5B01G218600 chr5D 87.591 137 13 3 425 561 335086812 335086944 3.320000e-34 156.0
16 TraesCS5B01G218600 chr5D 81.746 126 15 6 111 231 487645799 487645677 5.680000e-17 99.0
17 TraesCS5B01G218600 chr5A 91.505 824 40 9 1148 1965 436614004 436614803 0.000000e+00 1107.0
18 TraesCS5B01G218600 chr5A 86.526 898 74 22 736 1601 436329417 436328535 0.000000e+00 944.0
19 TraesCS5B01G218600 chr5A 84.751 905 80 21 746 1616 436548621 436549501 0.000000e+00 854.0
20 TraesCS5B01G218600 chr5A 92.795 458 23 5 1169 1616 436381890 436382347 0.000000e+00 654.0
21 TraesCS5B01G218600 chr5A 92.560 457 25 4 1169 1616 436590841 436591297 0.000000e+00 647.0
22 TraesCS5B01G218600 chr5A 87.209 86 4 1 582 667 436590748 436590826 9.500000e-15 91.6
23 TraesCS5B01G218600 chr5A 86.047 86 5 1 582 667 436381797 436381875 4.420000e-13 86.1
24 TraesCS5B01G218600 chr7B 90.018 541 40 12 1955 2486 639285568 639286103 0.000000e+00 688.0
25 TraesCS5B01G218600 chr7B 86.022 558 42 14 582 1128 141009156 141008624 1.300000e-157 566.0
26 TraesCS5B01G218600 chr4A 87.612 557 51 14 1954 2495 733776537 733775984 4.530000e-177 630.0
27 TraesCS5B01G218600 chr4A 85.326 552 71 9 1950 2493 714815671 714816220 1.680000e-156 562.0
28 TraesCS5B01G218600 chr1B 85.872 545 67 10 1955 2493 676738005 676737465 2.780000e-159 571.0
29 TraesCS5B01G218600 chr1B 80.368 163 15 13 143 302 422723700 422723848 9.440000e-20 108.0
30 TraesCS5B01G218600 chr1B 74.874 199 37 10 126 316 21381154 21381347 7.400000e-11 78.7
31 TraesCS5B01G218600 chr1B 74.874 199 36 11 126 316 21388138 21388330 7.400000e-11 78.7
32 TraesCS5B01G218600 chr4B 85.507 552 68 11 1954 2495 245775435 245775984 1.300000e-157 566.0
33 TraesCS5B01G218600 chr7D 87.449 486 44 2 647 1128 175662257 175661785 6.070000e-151 544.0
34 TraesCS5B01G218600 chr7D 78.109 201 23 17 111 304 127077685 127077871 9.440000e-20 108.0
35 TraesCS5B01G218600 chr7D 77.679 112 15 9 197 304 376936133 376936238 2.680000e-05 60.2
36 TraesCS5B01G218600 chr6B 84.239 552 74 11 1956 2495 47229885 47229335 2.200000e-145 525.0
37 TraesCS5B01G218600 chr6B 84.034 119 12 4 97 209 477064619 477064736 9.440000e-20 108.0
38 TraesCS5B01G218600 chr6A 84.144 555 74 13 1954 2495 212166238 212165685 2.200000e-145 525.0
39 TraesCS5B01G218600 chr7A 87.158 475 40 7 672 1127 177344802 177344330 1.020000e-143 520.0
40 TraesCS5B01G218600 chrUn 81.381 478 55 22 666 1125 341236332 341236793 2.360000e-95 359.0
41 TraesCS5B01G218600 chr3B 88.841 233 25 1 2264 2495 177914169 177914401 4.060000e-73 285.0
42 TraesCS5B01G218600 chr3B 84.615 117 12 5 119 231 208757040 208756926 7.290000e-21 111.0
43 TraesCS5B01G218600 chr4D 78.109 201 23 16 111 304 182547778 182547964 9.440000e-20 108.0
44 TraesCS5B01G218600 chr6D 77.315 216 26 16 97 304 232700157 232699957 3.390000e-19 106.0


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 TraesCS5B01G218600 chr5B 392117876 392120370 2494 False 4608.00 4608 100.0000 1 2495 1 chr5B.!!$F6 2494
1 TraesCS5B01G218600 chr5B 392077971 392080330 2359 False 1129.50 1402 99.5520 118 2495 2 chr5B.!!$F7 2377
2 TraesCS5B01G218600 chr5B 392070556 392071136 580 False 1068.00 1068 99.8280 1 581 1 chr5B.!!$F4 580
3 TraesCS5B01G218600 chr5B 391825830 391826810 980 True 1062.00 1062 86.8820 666 1615 1 chr5B.!!$R2 949
4 TraesCS5B01G218600 chr5B 391866545 391867405 860 False 778.00 778 83.6530 701 1552 1 chr5B.!!$F1 851
5 TraesCS5B01G218600 chr5B 278243106 278243655 549 True 547.00 547 84.9640 1956 2495 1 chr5B.!!$R1 539
6 TraesCS5B01G218600 chr5D 335120493 335122435 1942 False 1278.50 1916 89.5495 3 1965 2 chr5D.!!$F2 1962
7 TraesCS5B01G218600 chr5D 334969116 334970102 986 True 1168.00 1168 88.6520 666 1615 1 chr5D.!!$R1 949
8 TraesCS5B01G218600 chr5D 334990138 334991102 964 True 959.00 959 85.4690 667 1604 1 chr5D.!!$R2 937
9 TraesCS5B01G218600 chr5D 335086812 335087943 1131 False 600.00 1044 86.6120 425 1607 2 chr5D.!!$F1 1182
10 TraesCS5B01G218600 chr5A 436614004 436614803 799 False 1107.00 1107 91.5050 1148 1965 1 chr5A.!!$F2 817
11 TraesCS5B01G218600 chr5A 436328535 436329417 882 True 944.00 944 86.5260 736 1601 1 chr5A.!!$R1 865
12 TraesCS5B01G218600 chr5A 436548621 436549501 880 False 854.00 854 84.7510 746 1616 1 chr5A.!!$F1 870
13 TraesCS5B01G218600 chr5A 436381797 436382347 550 False 370.05 654 89.4210 582 1616 2 chr5A.!!$F3 1034
14 TraesCS5B01G218600 chr5A 436590748 436591297 549 False 369.30 647 89.8845 582 1616 2 chr5A.!!$F4 1034
15 TraesCS5B01G218600 chr7B 639285568 639286103 535 False 688.00 688 90.0180 1955 2486 1 chr7B.!!$F1 531
16 TraesCS5B01G218600 chr7B 141008624 141009156 532 True 566.00 566 86.0220 582 1128 1 chr7B.!!$R1 546
17 TraesCS5B01G218600 chr4A 733775984 733776537 553 True 630.00 630 87.6120 1954 2495 1 chr4A.!!$R1 541
18 TraesCS5B01G218600 chr4A 714815671 714816220 549 False 562.00 562 85.3260 1950 2493 1 chr4A.!!$F1 543
19 TraesCS5B01G218600 chr1B 676737465 676738005 540 True 571.00 571 85.8720 1955 2493 1 chr1B.!!$R1 538
20 TraesCS5B01G218600 chr4B 245775435 245775984 549 False 566.00 566 85.5070 1954 2495 1 chr4B.!!$F1 541
21 TraesCS5B01G218600 chr6B 47229335 47229885 550 True 525.00 525 84.2390 1956 2495 1 chr6B.!!$R1 539
22 TraesCS5B01G218600 chr6A 212165685 212166238 553 True 525.00 525 84.1440 1954 2495 1 chr6A.!!$R1 541

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
625 643 2.23565 ACATCACATAGTGCTGACTGCT 59.764 45.455 7.85 0.0 43.37 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2222 0.600255 GTGGGTTATCTCGATGGCGG 60.6 60.0 0.0 0.0 38.28 6.13 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
620 638 5.088680 TGAATCACATCACATAGTGCTGA 57.911 39.130 7.85 2.26 33.95 4.26
621 639 4.872124 TGAATCACATCACATAGTGCTGAC 59.128 41.667 7.85 0.00 33.95 3.51
622 640 4.750021 ATCACATCACATAGTGCTGACT 57.250 40.909 7.85 0.00 33.95 3.41
623 641 3.853475 TCACATCACATAGTGCTGACTG 58.147 45.455 7.85 0.00 33.95 3.51
624 642 2.350804 CACATCACATAGTGCTGACTGC 59.649 50.000 7.85 0.00 43.25 4.40
625 643 2.235650 ACATCACATAGTGCTGACTGCT 59.764 45.455 7.85 0.00 43.37 4.24
626 644 2.375173 TCACATAGTGCTGACTGCTG 57.625 50.000 5.87 0.00 43.37 4.41
837 886 2.599281 TCACGGGTTGGCTCTCGA 60.599 61.111 9.18 0.00 0.00 4.04
927 992 5.238583 ACAACAATCAGAACTGTACTAGCC 58.761 41.667 1.73 0.00 0.00 3.93
1021 1105 2.475466 GCGACTGTGATGGCCATGG 61.475 63.158 26.56 7.63 0.00 3.66
1152 1266 1.407656 AACCCAAGACGAGCACCTCA 61.408 55.000 0.00 0.00 0.00 3.86
1159 1273 0.532573 GACGAGCACCTCAATCTGGA 59.467 55.000 0.00 0.00 0.00 3.86
1338 1456 4.961511 GTGCTGTCCGTGGCGTCA 62.962 66.667 0.00 0.00 0.00 4.35
1630 1765 9.520515 AGACTGTTCATAAAAATGGTGATAGTT 57.479 29.630 0.00 0.00 0.00 2.24
1635 1770 9.573133 GTTCATAAAAATGGTGATAGTTCAAGG 57.427 33.333 0.00 0.00 32.48 3.61
1656 1791 2.819608 GCATTGGTGGAAGAGTTTGCTA 59.180 45.455 0.00 0.00 0.00 3.49
1677 1812 4.577246 CGGCTAGCAGGGACTCGC 62.577 72.222 18.24 0.00 34.60 5.03
2068 2208 1.175983 TTCAAGCACCGCCGGAAAAT 61.176 50.000 11.71 0.00 0.00 1.82
2082 2222 3.621715 CCGGAAAATCTACTGTAAGCACC 59.378 47.826 0.00 0.00 37.60 5.01
2450 2614 6.341316 AGAAAAGCGCATATAGAGAAACAGA 58.659 36.000 11.47 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
591 609 7.267857 CACTATGTGATGTGATTCAGGTCTTA 58.732 38.462 0.00 0.00 35.23 2.10
594 612 4.272018 GCACTATGTGATGTGATTCAGGTC 59.728 45.833 1.52 0.00 35.23 3.85
620 638 2.049985 GTGTCGACGCTCAGCAGT 60.050 61.111 21.55 0.00 0.00 4.40
621 639 1.612469 CTTGTGTCGACGCTCAGCAG 61.612 60.000 27.76 12.90 0.00 4.24
622 640 1.661509 CTTGTGTCGACGCTCAGCA 60.662 57.895 27.76 6.33 0.00 4.41
623 641 3.004734 GCTTGTGTCGACGCTCAGC 62.005 63.158 27.01 27.01 0.00 4.26
624 642 0.941463 AAGCTTGTGTCGACGCTCAG 60.941 55.000 27.76 22.83 31.30 3.35
625 643 0.939577 GAAGCTTGTGTCGACGCTCA 60.940 55.000 27.76 15.70 31.30 4.26
626 644 0.664767 AGAAGCTTGTGTCGACGCTC 60.665 55.000 27.76 17.11 31.30 5.03
837 886 2.172717 ACAATTTATAGGCCGTGCTCCT 59.827 45.455 0.00 0.00 37.72 3.69
1152 1266 3.127533 GCCAGCGCGTTCCAGATT 61.128 61.111 8.43 0.00 0.00 2.40
1194 1308 3.747976 GCAAGGCGCCCGTTGATT 61.748 61.111 27.37 11.30 38.72 2.57
1630 1765 1.425066 ACTCTTCCACCAATGCCTTGA 59.575 47.619 2.97 0.00 34.04 3.02
1635 1770 1.615392 AGCAAACTCTTCCACCAATGC 59.385 47.619 0.00 0.00 0.00 3.56
1656 1791 1.551452 GAGTCCCTGCTAGCCGATAT 58.449 55.000 13.29 0.00 0.00 1.63
1677 1812 3.953712 TGCACCCCATATATACACGAG 57.046 47.619 0.00 0.00 0.00 4.18
2068 2208 0.901114 TGGCGGGTGCTTACAGTAGA 60.901 55.000 0.00 0.00 42.25 2.59
2082 2222 0.600255 GTGGGTTATCTCGATGGCGG 60.600 60.000 0.00 0.00 38.28 6.13
2450 2614 4.319549 GCGTCTGAAAACTCCTTTCGAATT 60.320 41.667 0.00 0.00 45.59 2.17


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

AutoCloner maintained by Alex Coulton.