Multiple sequence alignment - TraesCS5D01G158100

Loading Multiple Alignment...

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 TraesCS5D01G158100 chr5D 100.000 3551 0 0 1 3551 246014470 246010920 0.000000e+00 6558
1 TraesCS5D01G158100 chr5D 98.073 467 9 0 1 467 480488306 480488772 0.000000e+00 813
2 TraesCS5D01G158100 chr5D 97.002 467 14 0 1 467 421146667 421146201 0.000000e+00 785
3 TraesCS5D01G158100 chr5D 96.788 467 15 0 1 467 467446646 467447112 0.000000e+00 780
4 TraesCS5D01G158100 chr5D 76.213 1463 308 29 2102 3546 485060050 485058610 0.000000e+00 737
5 TraesCS5D01G158100 chr5D 94.332 247 10 3 463 708 421145771 421145528 3.350000e-100 375
6 TraesCS5D01G158100 chr5D 94.332 247 10 3 463 708 480483879 480484122 3.350000e-100 375
7 TraesCS5D01G158100 chr5D 76.809 677 131 21 2878 3544 77017243 77016583 1.210000e-94 357
8 TraesCS5D01G158100 chr5A 93.892 2865 149 13 709 3551 329996220 329993360 0.000000e+00 4298
9 TraesCS5D01G158100 chr5A 77.375 1463 301 23 2102 3548 606352873 606351425 0.000000e+00 841
10 TraesCS5D01G158100 chr5A 75.605 1488 320 36 2081 3544 73828610 73827142 0.000000e+00 697
11 TraesCS5D01G158100 chr5B 92.725 2859 176 17 713 3551 280651515 280648669 0.000000e+00 4098
12 TraesCS5D01G158100 chr5B 76.876 1466 310 19 2102 3548 596824493 596823038 0.000000e+00 802
13 TraesCS5D01G158100 chr5B 76.765 1459 317 16 2102 3548 596224155 596225603 0.000000e+00 797
14 TraesCS5D01G158100 chr5B 76.112 1461 313 27 2102 3548 596393863 596395301 0.000000e+00 732
15 TraesCS5D01G158100 chr5B 78.411 491 82 13 1100 1569 280606565 280606078 7.450000e-77 298
16 TraesCS5D01G158100 chr7D 76.975 1468 310 25 2099 3551 19050923 19052377 0.000000e+00 813
17 TraesCS5D01G158100 chr7D 95.436 241 7 3 469 708 423695284 423695521 7.190000e-102 381
18 TraesCS5D01G158100 chr7D 94.378 249 11 2 463 708 593954227 593954475 2.590000e-101 379
19 TraesCS5D01G158100 chr3D 97.645 467 11 0 1 467 48970811 48971277 0.000000e+00 802
20 TraesCS5D01G158100 chr3D 96.146 467 18 0 1 467 569835601 569836067 0.000000e+00 763
21 TraesCS5D01G158100 chr4A 76.755 1467 309 27 2102 3551 713505173 713503722 0.000000e+00 791
22 TraesCS5D01G158100 chr4A 77.620 706 126 27 2082 2767 739780907 739781600 1.990000e-107 399
23 TraesCS5D01G158100 chr7A 76.615 1471 310 31 2099 3551 19517134 19518588 0.000000e+00 780
24 TraesCS5D01G158100 chr1D 96.788 467 15 0 1 467 412795762 412796228 0.000000e+00 780
25 TraesCS5D01G158100 chr1D 94.048 252 11 3 463 713 462019315 462019067 2.590000e-101 379
26 TraesCS5D01G158100 chr1D 93.976 249 12 2 463 708 107141856 107141608 1.200000e-99 374
27 TraesCS5D01G158100 chr6D 96.767 464 15 0 4 467 97232534 97232071 0.000000e+00 774
28 TraesCS5D01G158100 chr6D 93.976 249 12 2 463 708 379032385 379032633 1.200000e-99 374
29 TraesCS5D01G158100 chr2D 96.360 467 17 0 1 467 586127506 586127972 0.000000e+00 769
30 TraesCS5D01G158100 chr2D 96.154 468 16 2 1 467 593405873 593406339 0.000000e+00 763
31 TraesCS5D01G158100 chr2D 95.062 243 8 3 469 710 60081111 60080872 2.590000e-101 379
32 TraesCS5D01G158100 chr2D 94.378 249 11 2 463 708 552737663 552737911 2.590000e-101 379


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 TraesCS5D01G158100 chr5D 246010920 246014470 3550 True 6558 6558 100.000 1 3551 1 chr5D.!!$R2 3550
1 TraesCS5D01G158100 chr5D 485058610 485060050 1440 True 737 737 76.213 2102 3546 1 chr5D.!!$R3 1444
2 TraesCS5D01G158100 chr5D 421145528 421146667 1139 True 580 785 95.667 1 708 2 chr5D.!!$R4 707
3 TraesCS5D01G158100 chr5D 77016583 77017243 660 True 357 357 76.809 2878 3544 1 chr5D.!!$R1 666
4 TraesCS5D01G158100 chr5A 329993360 329996220 2860 True 4298 4298 93.892 709 3551 1 chr5A.!!$R2 2842
5 TraesCS5D01G158100 chr5A 606351425 606352873 1448 True 841 841 77.375 2102 3548 1 chr5A.!!$R3 1446
6 TraesCS5D01G158100 chr5A 73827142 73828610 1468 True 697 697 75.605 2081 3544 1 chr5A.!!$R1 1463
7 TraesCS5D01G158100 chr5B 280648669 280651515 2846 True 4098 4098 92.725 713 3551 1 chr5B.!!$R2 2838
8 TraesCS5D01G158100 chr5B 596823038 596824493 1455 True 802 802 76.876 2102 3548 1 chr5B.!!$R3 1446
9 TraesCS5D01G158100 chr5B 596224155 596225603 1448 False 797 797 76.765 2102 3548 1 chr5B.!!$F1 1446
10 TraesCS5D01G158100 chr5B 596393863 596395301 1438 False 732 732 76.112 2102 3548 1 chr5B.!!$F2 1446
11 TraesCS5D01G158100 chr7D 19050923 19052377 1454 False 813 813 76.975 2099 3551 1 chr7D.!!$F1 1452
12 TraesCS5D01G158100 chr4A 713503722 713505173 1451 True 791 791 76.755 2102 3551 1 chr4A.!!$R1 1449
13 TraesCS5D01G158100 chr4A 739780907 739781600 693 False 399 399 77.620 2082 2767 1 chr4A.!!$F1 685
14 TraesCS5D01G158100 chr7A 19517134 19518588 1454 False 780 780 76.615 2099 3551 1 chr7A.!!$F1 1452

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
824 1261 0.179215 GCGCGTGTTCAGATTTCAGG 60.179 55.0 8.43 0.00 0.00 3.86 F
1325 1795 0.724549 CTGACGAGTCTCGACCTCTG 59.275 60.0 28.33 14.87 43.74 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2105 0.110486 TGGCTGGACAGAAGGAAACC 59.890 55.0 3.00 0.0 0.00 3.27 R
2773 3253 0.178992 TCCCCTGAGCAAGTTGTTGG 60.179 55.0 4.48 0.0 33.87 3.77 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
47 48 0.803740 GTCGACTAGCTTGTCTCCGT 59.196 55.000 22.89 0.00 35.00 4.69
164 165 1.069022 CCCAGAACACGTTCATTGCTG 60.069 52.381 12.21 1.64 41.84 4.41
267 268 4.380444 GCCATGAGTCGAAAAATGCCTAAA 60.380 41.667 0.00 0.00 0.00 1.85
300 301 9.956640 TTTTTGGATTGTTGGAAATATTAGCAT 57.043 25.926 0.00 0.00 0.00 3.79
342 343 5.186215 TCCACGAGTAAACAGTAATCATGGA 59.814 40.000 0.00 0.00 0.00 3.41
350 351 9.661563 AGTAAACAGTAATCATGGAAAATACGA 57.338 29.630 0.00 0.00 0.00 3.43
351 352 9.916397 GTAAACAGTAATCATGGAAAATACGAG 57.084 33.333 0.00 0.00 0.00 4.18
392 393 1.877637 AAGCATGTGAGCACGTACAA 58.122 45.000 0.00 0.00 36.85 2.41
440 441 4.112634 CAACATATATACGGCTAGCGCAT 58.887 43.478 11.47 4.17 38.10 4.73
470 890 0.469331 ATAGGGGATGAACGAGGCGA 60.469 55.000 0.00 0.00 0.00 5.54
472 892 2.107141 GGGATGAACGAGGCGAGG 59.893 66.667 0.00 0.00 0.00 4.63
475 895 3.411418 GATGAACGAGGCGAGGCGA 62.411 63.158 0.00 0.00 0.00 5.54
477 897 4.856607 GAACGAGGCGAGGCGAGG 62.857 72.222 0.00 0.00 0.00 4.63
553 985 2.576191 AGCTCCCAATAGCAAGTGGTAA 59.424 45.455 0.00 0.00 45.30 2.85
569 1001 5.576128 AGTGGTAAAGCAGCCCTTATAAAA 58.424 37.500 0.00 0.00 32.20 1.52
665 1098 4.892198 TGGGCCTTAGAGATTAACTAGGT 58.108 43.478 4.53 0.00 0.00 3.08
728 1161 6.109156 TCACAGAGTTTAAGCTGACCATAA 57.891 37.500 0.00 0.00 36.07 1.90
765 1199 5.579511 CCATCAAGCACTCAAATTCAAATCC 59.420 40.000 0.00 0.00 0.00 3.01
818 1255 1.635844 TTAATCGCGCGTGTTCAGAT 58.364 45.000 30.98 11.21 0.00 2.90
824 1261 0.179215 GCGCGTGTTCAGATTTCAGG 60.179 55.000 8.43 0.00 0.00 3.86
902 1354 2.726821 CGGTAGGTACAGTACAGGGAA 58.273 52.381 12.89 0.00 0.00 3.97
971 1423 3.307674 GAGCTCTCATTCATAGTCAGCG 58.692 50.000 6.43 0.00 0.00 5.18
974 1426 3.243367 GCTCTCATTCATAGTCAGCGACT 60.243 47.826 14.10 14.10 45.54 4.18
1314 1784 2.681778 CTGAGGGCCCTGACGAGT 60.682 66.667 34.59 1.71 0.00 4.18
1325 1795 0.724549 CTGACGAGTCTCGACCTCTG 59.275 60.000 28.33 14.87 43.74 3.35
1338 1808 3.429141 CTCTGGCGCAACAGGCTG 61.429 66.667 14.16 14.16 41.67 4.85
1495 1965 2.561569 ACCAAATCTCCGGCGAAATAG 58.438 47.619 9.30 0.00 0.00 1.73
1563 2033 1.614317 GGCAATCAGCTGGTTGGTAGT 60.614 52.381 34.61 3.33 44.79 2.73
1635 2105 1.264288 GACAACAAGCTTTCAGGTCCG 59.736 52.381 0.00 0.00 0.00 4.79
1653 2123 0.955919 CGGTTTCCTTCTGTCCAGCC 60.956 60.000 0.00 0.00 0.00 4.85
1764 2234 1.204146 TATCCAGCCTCCAACACCTC 58.796 55.000 0.00 0.00 0.00 3.85
1782 2252 4.079253 ACCTCGACATAAGCCAAAACAAT 58.921 39.130 0.00 0.00 0.00 2.71
1788 2258 6.422400 TCGACATAAGCCAAAACAATTTTTCC 59.578 34.615 0.00 0.00 32.27 3.13
1793 2263 2.616376 GCCAAAACAATTTTTCCGGCTT 59.384 40.909 0.00 0.00 39.26 4.35
1865 2335 3.134458 CAGATAATCAGCTTTCGGGACC 58.866 50.000 0.00 0.00 0.00 4.46
1866 2336 2.135933 GATAATCAGCTTTCGGGACCG 58.864 52.381 3.96 3.96 41.35 4.79
1975 2445 9.712359 GTTTAGGAAACTTAACACAGTTAACAG 57.288 33.333 8.61 1.86 46.47 3.16
2078 2548 2.490991 AGGACAGAACAAACTTACGGC 58.509 47.619 0.00 0.00 0.00 5.68
2331 2801 9.189723 CAAGAAATTGGAAACTTGAGAAATCTC 57.810 33.333 3.43 3.43 41.16 2.75
2343 2813 4.703897 TGAGAAATCTCGTTTGGTTGACT 58.296 39.130 5.99 0.00 45.72 3.41
2368 2838 4.254402 AGTTCTAACAAACTCTCCGGTC 57.746 45.455 0.00 0.00 34.37 4.79
2391 2861 0.608035 TGCCATCCGGTCTTTGTTCC 60.608 55.000 0.00 0.00 33.28 3.62
2415 2885 1.544246 GGCCGGCTACAAAATTTCACT 59.456 47.619 28.56 0.00 0.00 3.41
2640 3120 2.076100 TGCGTGCCTCAGAAAATAGTG 58.924 47.619 0.00 0.00 0.00 2.74
2773 3253 4.060205 ACATTGTTCAATTTGAGCCTTGC 58.940 39.130 10.28 0.00 0.00 4.01
3062 3550 3.928727 TGCTTGAAGCCTTGAATCTTG 57.071 42.857 15.43 0.00 41.51 3.02
3157 3645 5.821470 GTCTTATAACAAACTAGAAGGGCCC 59.179 44.000 16.46 16.46 0.00 5.80
3245 3733 3.214328 GGTGATGGTGTGAAAAGTCTGT 58.786 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.689813 TGGAGCCGTTCTTACTGTGAA 59.310 47.619 0.00 0.00 0.00 3.18
62 63 1.620822 ACCACCATCTTTGTTGGAGC 58.379 50.000 0.00 0.00 37.69 4.70
164 165 0.977395 AGGACTACCTTGTGGCTCAC 59.023 55.000 0.00 0.00 45.36 3.51
217 218 2.803956 CGCTACTCTGAAACCGGAAAAA 59.196 45.455 9.46 0.00 0.00 1.94
259 260 8.382405 ACAATCCAAAAACCTTATTTTAGGCAT 58.618 29.630 0.00 0.00 38.99 4.40
300 301 6.632909 TCGTGGATTAGATTAGTCGGAAAAA 58.367 36.000 0.00 0.00 0.00 1.94
350 351 7.469870 GCTTAGATATCGGTATGAGATGCATCT 60.470 40.741 29.09 29.09 40.50 2.90
351 352 6.640499 GCTTAGATATCGGTATGAGATGCATC 59.360 42.308 19.37 19.37 38.44 3.91
371 372 2.606108 TGTACGTGCTCACATGCTTAG 58.394 47.619 4.97 0.00 36.15 2.18
392 393 9.477484 GTTCATAGATGTTTCGGTTCTATGTAT 57.523 33.333 15.15 0.00 44.88 2.29
420 421 3.380320 TCATGCGCTAGCCGTATATATGT 59.620 43.478 9.73 0.00 40.37 2.29
440 441 2.503765 TCATCCCCTATTTGCTCGTTCA 59.496 45.455 0.00 0.00 0.00 3.18
569 1001 6.267928 TGCTAAAGTAAGAAGAGTGAGACCTT 59.732 38.462 0.00 0.00 0.00 3.50
665 1098 7.878127 GGCTTAGGCTCATGTAAGACAATAATA 59.122 37.037 0.00 0.00 34.79 0.98
682 1115 2.310052 GGATTATGGATGGGCTTAGGCT 59.690 50.000 5.62 0.00 38.73 4.58
728 1161 3.245016 TGCTTGATGGAGATGGTCAAAGT 60.245 43.478 0.00 0.00 32.08 2.66
765 1199 1.355210 GCGGCGTGGAATTGTATGG 59.645 57.895 9.37 0.00 0.00 2.74
789 1225 1.973137 GCGCGATTAAAAGGACGCCA 61.973 55.000 12.10 0.00 46.69 5.69
818 1255 1.952990 TGAATGAACAAGCGCCTGAAA 59.047 42.857 14.09 0.00 0.00 2.69
824 1261 3.542712 TTCTTCTGAATGAACAAGCGC 57.457 42.857 0.00 0.00 0.00 5.92
902 1354 0.036388 TGCGGCGGATTTCTTCTTCT 60.036 50.000 9.78 0.00 0.00 2.85
971 1423 4.167268 GTGTAGTTCCACGATTCTGAGTC 58.833 47.826 0.00 0.00 0.00 3.36
974 1426 2.232941 GGGTGTAGTTCCACGATTCTGA 59.767 50.000 0.00 0.00 36.16 3.27
1161 1631 1.189524 TCGACGTGTTTCCCCAGGAT 61.190 55.000 0.00 0.00 0.00 3.24
1275 1745 3.379445 GCGAAGTCGAGGGACCCA 61.379 66.667 14.60 0.00 44.54 4.51
1314 1784 2.989253 TTGCGCCAGAGGTCGAGA 60.989 61.111 4.18 0.00 0.00 4.04
1338 1808 4.570874 GGAGGAATGCTCCCGGCC 62.571 72.222 9.91 0.00 43.64 6.13
1346 1816 2.602322 GCGATGCTCGGAGGAATGC 61.602 63.158 2.54 6.94 40.84 3.56
1495 1965 1.340889 CAGCTCTCCTATCTGTCCTGC 59.659 57.143 0.00 0.00 0.00 4.85
1563 2033 2.441750 GTGGCCTATTTCACAGGGGATA 59.558 50.000 3.32 0.00 33.44 2.59
1635 2105 0.110486 TGGCTGGACAGAAGGAAACC 59.890 55.000 3.00 0.00 0.00 3.27
1764 2234 6.589454 GGAAAAATTGTTTTGGCTTATGTCG 58.411 36.000 0.00 0.00 37.07 4.35
1782 2252 2.562125 CGGGATCAAGCCGGAAAAA 58.438 52.632 5.05 0.00 0.00 1.94
1793 2263 3.151710 CTACACCGCCCGGGATCA 61.152 66.667 29.31 0.46 39.97 2.92
2007 2477 5.061721 TCCTTATTTCTTTAGGGATGGGC 57.938 43.478 0.00 0.00 0.00 5.36
2078 2548 1.806542 CCAGACTGTTTGGAATGGACG 59.193 52.381 11.74 0.00 37.96 4.79
2331 2801 6.477688 TGTTAGAACTTAGAGTCAACCAAACG 59.522 38.462 0.00 0.00 0.00 3.60
2343 2813 5.537674 ACCGGAGAGTTTGTTAGAACTTAGA 59.462 40.000 9.46 0.00 39.84 2.10
2368 2838 2.983879 AAAGACCGGATGGCAGGGG 61.984 63.158 9.46 3.72 39.70 4.79
2415 2885 5.536538 TCCAACCAACATGTTGTTATAAGCA 59.463 36.000 31.20 9.46 43.22 3.91
2640 3120 1.899814 TGGTGGTATGACTCCAGTGAC 59.100 52.381 0.00 0.00 35.49 3.67
2773 3253 0.178992 TCCCCTGAGCAAGTTGTTGG 60.179 55.000 4.48 0.00 33.87 3.77
3245 3733 2.035237 GACGTGTGGTCACAAGGGGA 62.035 60.000 18.15 0.00 45.36 4.81
3262 3750 7.941919 ACTTCCTTCCTTTTTGATAACTTGAC 58.058 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.