Multiple sequence alignment - TraesCS1B01G097600

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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 TraesCS1B01G097600 chr1B 100.000 3185 0 0 1 3185 104347150 104350334 0.000000e+00 5882
1 TraesCS1B01G097600 chr1D 95.697 2417 84 15 723 3125 63607335 63609745 0.000000e+00 3869
2 TraesCS1B01G097600 chr1A 95.021 1908 82 9 729 2629 62575432 62577333 0.000000e+00 2985
3 TraesCS1B01G097600 chr1A 93.772 562 23 5 2632 3185 62577393 62577950 0.000000e+00 833
4 TraesCS1B01G097600 chr5B 96.203 711 26 1 1 711 237825581 237824872 0.000000e+00 1162
5 TraesCS1B01G097600 chr5B 95.537 717 30 1 1 715 63252305 63251589 0.000000e+00 1146
6 TraesCS1B01G097600 chr5B 95.537 717 29 3 1 715 98843894 98844609 0.000000e+00 1144
7 TraesCS1B01G097600 chr5B 78.652 267 48 8 2475 2736 328374012 328373750 5.460000e-38 169
8 TraesCS1B01G097600 chr5A 95.933 713 26 1 1 710 664389576 664388864 0.000000e+00 1153
9 TraesCS1B01G097600 chr4B 95.816 717 25 4 1 714 28682222 28681508 0.000000e+00 1153
10 TraesCS1B01G097600 chr4A 96.045 708 24 3 1 707 666278163 666278867 0.000000e+00 1149
11 TraesCS1B01G097600 chr3B 95.910 709 28 1 1 708 300556035 300555327 0.000000e+00 1147
12 TraesCS1B01G097600 chr3A 95.910 709 27 2 1 708 522043505 522044212 0.000000e+00 1147
13 TraesCS1B01G097600 chr7B 95.664 715 28 2 1 713 664047495 664046782 0.000000e+00 1146
14 TraesCS1B01G097600 chr5D 84.496 258 35 3 2480 2733 315935973 315936229 1.900000e-62 250
15 TraesCS1B01G097600 chr4D 83.402 241 40 0 2478 2718 373205847 373205607 1.150000e-54 224
16 TraesCS1B01G097600 chr3D 83.475 236 36 2 2484 2718 558290549 558290316 1.920000e-52 217
17 TraesCS1B01G097600 chr2A 82.379 227 36 4 2478 2703 743564759 743564982 9.010000e-46 195
18 TraesCS1B01G097600 chr6D 80.303 264 43 7 2473 2733 132312144 132312401 1.170000e-44 191
19 TraesCS1B01G097600 chr6A 80.303 264 43 7 2473 2733 171459270 171459527 1.170000e-44 191


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 TraesCS1B01G097600 chr1B 104347150 104350334 3184 False 5882 5882 100.0000 1 3185 1 chr1B.!!$F1 3184
1 TraesCS1B01G097600 chr1D 63607335 63609745 2410 False 3869 3869 95.6970 723 3125 1 chr1D.!!$F1 2402
2 TraesCS1B01G097600 chr1A 62575432 62577950 2518 False 1909 2985 94.3965 729 3185 2 chr1A.!!$F1 2456
3 TraesCS1B01G097600 chr5B 237824872 237825581 709 True 1162 1162 96.2030 1 711 1 chr5B.!!$R2 710
4 TraesCS1B01G097600 chr5B 63251589 63252305 716 True 1146 1146 95.5370 1 715 1 chr5B.!!$R1 714
5 TraesCS1B01G097600 chr5B 98843894 98844609 715 False 1144 1144 95.5370 1 715 1 chr5B.!!$F1 714
6 TraesCS1B01G097600 chr5A 664388864 664389576 712 True 1153 1153 95.9330 1 710 1 chr5A.!!$R1 709
7 TraesCS1B01G097600 chr4B 28681508 28682222 714 True 1153 1153 95.8160 1 714 1 chr4B.!!$R1 713
8 TraesCS1B01G097600 chr4A 666278163 666278867 704 False 1149 1149 96.0450 1 707 1 chr4A.!!$F1 706
9 TraesCS1B01G097600 chr3B 300555327 300556035 708 True 1147 1147 95.9100 1 708 1 chr3B.!!$R1 707
10 TraesCS1B01G097600 chr3A 522043505 522044212 707 False 1147 1147 95.9100 1 708 1 chr3A.!!$F1 707
11 TraesCS1B01G097600 chr7B 664046782 664047495 713 True 1146 1146 95.6640 1 713 1 chr7B.!!$R1 712

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
933 942 0.040646 TTCTTCTCGGCCTCCCAGTA 59.959 55.0 0.00 0.00 0.0 2.74 F
1104 1113 0.438830 CGCTGGTTAACGTGAAGCTC 59.561 55.0 15.63 6.94 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1839 0.892358 CCAATGTGAGGTGCAGCAGT 60.892 55.000 19.63 0.0 0.00 4.40 R
2714 2786 1.133915 TGCTCCCTCCGTTTCAAAACT 60.134 47.619 4.28 0.0 36.77 2.66 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
313 314 3.056962 ACATGCACGTAAAATTGCCATGA 60.057 39.130 0.00 0.00 38.00 3.07
380 381 8.259411 TGCCATCATCAAAATACTAAAATTGCT 58.741 29.630 0.00 0.00 0.00 3.91
686 694 4.622456 GTGCAAACGCCCACACGG 62.622 66.667 0.00 0.00 37.37 4.94
715 723 8.127954 GGGCGTTAACATTTCCGTATATTTTTA 58.872 33.333 6.39 0.00 0.00 1.52
716 724 9.500864 GGCGTTAACATTTCCGTATATTTTTAA 57.499 29.630 6.39 0.00 0.00 1.52
762 770 5.964958 TGCCTTTGGATGTCTTTTCTTAG 57.035 39.130 0.00 0.00 0.00 2.18
764 772 6.068010 TGCCTTTGGATGTCTTTTCTTAGAA 58.932 36.000 0.00 0.00 0.00 2.10
765 773 6.207417 TGCCTTTGGATGTCTTTTCTTAGAAG 59.793 38.462 0.00 0.00 0.00 2.85
929 938 1.222113 CCTTTCTTCTCGGCCTCCC 59.778 63.158 0.00 0.00 0.00 4.30
933 942 0.040646 TTCTTCTCGGCCTCCCAGTA 59.959 55.000 0.00 0.00 0.00 2.74
1104 1113 0.438830 CGCTGGTTAACGTGAAGCTC 59.561 55.000 15.63 6.94 0.00 4.09
1268 1277 2.435938 GATGTTTGGCTCCGCGGA 60.436 61.111 29.03 29.03 0.00 5.54
1310 1319 1.275291 CAGATACCACACCCTGTTCGT 59.725 52.381 0.00 0.00 0.00 3.85
1447 1456 1.270414 CCTCCTCATGCTCACCCTGT 61.270 60.000 0.00 0.00 0.00 4.00
1536 1545 1.358402 CTCGATCCTCAGTCGCCAG 59.642 63.158 0.00 0.00 38.88 4.85
1554 1563 2.266055 CCTGACCACTTCGCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
1739 1748 1.376466 GGCTGAAGGAGTGGCAGAA 59.624 57.895 0.00 0.00 0.00 3.02
1758 1767 3.844211 AGAAGCTTCCATACACTAACCCA 59.156 43.478 22.81 0.00 0.00 4.51
1762 1771 4.719773 AGCTTCCATACACTAACCCATACA 59.280 41.667 0.00 0.00 0.00 2.29
1815 1824 1.728971 GTGTCAGAGAAGCGGAATGTG 59.271 52.381 0.00 0.00 0.00 3.21
1830 1839 3.420893 GAATGTGGGAGTGTTCCATGAA 58.579 45.455 0.00 0.00 45.98 2.57
2111 2120 1.655372 AGGAGGAGCAGAGAAAGCTT 58.345 50.000 0.00 0.00 43.58 3.74
2115 2124 3.406764 GAGGAGCAGAGAAAGCTTCAAA 58.593 45.455 0.00 0.00 43.58 2.69
2271 2282 2.571202 TGATGGTTCAGCAGGTATGTGA 59.429 45.455 0.00 0.00 0.00 3.58
2273 2284 3.500448 TGGTTCAGCAGGTATGTGAAA 57.500 42.857 0.00 0.00 32.23 2.69
2289 2300 4.869215 TGTGAAAATTGATGCATCGTGTT 58.131 34.783 21.34 13.63 0.00 3.32
2313 2324 3.016736 ACGCACATTCCAGAATTTAGGG 58.983 45.455 0.00 0.00 0.00 3.53
2336 2347 9.875708 AGGGAATTACAATGCCTACATTATTAA 57.124 29.630 0.00 0.00 44.83 1.40
2372 2383 5.234466 ACCAAGATCTTTACACAGCTCTT 57.766 39.130 4.86 0.00 30.84 2.85
2403 2414 3.866703 TTGTCACCCCACAGAACAATA 57.133 42.857 0.00 0.00 0.00 1.90
2412 2423 7.554835 TCACCCCACAGAACAATATGTTTATAC 59.445 37.037 0.00 0.00 41.28 1.47
2454 2465 3.334583 TCTTTTTCCTGCAGCTACGAT 57.665 42.857 8.66 0.00 0.00 3.73
2713 2785 6.231211 TCACTTAGGACAATCCTTGAACTTC 58.769 40.000 1.99 0.00 46.91 3.01
2714 2786 5.997746 CACTTAGGACAATCCTTGAACTTCA 59.002 40.000 1.99 0.00 46.91 3.02
2715 2787 6.148480 CACTTAGGACAATCCTTGAACTTCAG 59.852 42.308 1.99 0.00 46.91 3.02
2747 2823 0.322008 GGGAGCAGCTAACAGCAAGT 60.322 55.000 0.00 0.00 45.56 3.16
2816 2892 0.543277 CTTAGCAGACTGGGATGCCA 59.457 55.000 5.57 5.57 43.60 4.92
2874 2950 7.379797 GGATGTTTGTCTCTGTTTTTCTAAAGC 59.620 37.037 0.00 0.00 0.00 3.51
2878 2954 7.807977 TTGTCTCTGTTTTTCTAAAGCTGAT 57.192 32.000 0.00 0.00 0.00 2.90
2908 2984 5.249780 TCCCTGTTATGCAGTCCTAAAAA 57.750 39.130 0.00 0.00 43.55 1.94
3076 3152 3.234234 AGGAAATCATATGGTGGGCTG 57.766 47.619 2.13 0.00 0.00 4.85
3126 3202 3.815401 ACAAGGTGATGTTCAGCAGTAAC 59.185 43.478 9.14 0.00 46.52 2.50
3127 3203 2.688507 AGGTGATGTTCAGCAGTAACG 58.311 47.619 9.14 0.00 46.52 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 381 7.880713 TGTGGCAGTTTTAGTTTGTAGATCATA 59.119 33.333 0.00 0.00 0.00 2.15
480 487 3.527253 AGACCCCATGTTGATATGTTCCA 59.473 43.478 0.00 0.00 0.00 3.53
482 489 5.930135 ACTAGACCCCATGTTGATATGTTC 58.070 41.667 0.00 0.00 0.00 3.18
533 540 5.972382 CGAACTAAAAATCCGTTTTCACCAA 59.028 36.000 0.00 0.00 40.07 3.67
627 635 3.687212 CACCACTCATTTTGCCACGTATA 59.313 43.478 0.00 0.00 0.00 1.47
686 694 0.169451 CGGAAATGTTAACGCCCACC 59.831 55.000 0.26 0.50 0.00 4.61
716 724 8.897752 GCATTTTGTCTGATAATTACTCCTCTT 58.102 33.333 0.00 0.00 0.00 2.85
717 725 7.500559 GGCATTTTGTCTGATAATTACTCCTCT 59.499 37.037 0.00 0.00 0.00 3.69
718 726 7.500559 AGGCATTTTGTCTGATAATTACTCCTC 59.499 37.037 0.00 0.00 26.79 3.71
719 727 7.349598 AGGCATTTTGTCTGATAATTACTCCT 58.650 34.615 0.00 0.00 26.79 3.69
720 728 7.573968 AGGCATTTTGTCTGATAATTACTCC 57.426 36.000 0.00 0.00 26.79 3.85
721 729 9.294030 CAAAGGCATTTTGTCTGATAATTACTC 57.706 33.333 0.00 0.00 41.02 2.59
726 734 6.855763 TCCAAAGGCATTTTGTCTGATAAT 57.144 33.333 0.00 0.00 43.78 1.28
727 735 6.211184 ACATCCAAAGGCATTTTGTCTGATAA 59.789 34.615 0.00 0.00 43.78 1.75
800 808 3.151022 CCTCTGTCTCTCGGGGGC 61.151 72.222 0.00 0.00 36.11 5.80
871 880 1.397343 GAAACCTAGCAGCGTAAAGGC 59.603 52.381 6.17 0.00 31.98 4.35
929 938 4.789075 CCCGCCGTCACCGTACTG 62.789 72.222 0.00 0.00 0.00 2.74
1104 1113 0.745845 CCGGATCCTTGACCAGCTTG 60.746 60.000 10.75 0.00 0.00 4.01
1518 1527 1.358402 CTGGCGACTGAGGATCGAG 59.642 63.158 0.00 0.00 42.25 4.04
1528 1537 4.008933 GTGGTCAGGCTGGCGACT 62.009 66.667 24.42 0.00 27.81 4.18
1536 1545 3.959991 GAGGGCGAAGTGGTCAGGC 62.960 68.421 0.00 0.00 0.00 4.85
1554 1563 4.020617 TCACCCTCGGGCTGCTTG 62.021 66.667 0.82 0.00 39.32 4.01
1739 1748 4.719773 TGTATGGGTTAGTGTATGGAAGCT 59.280 41.667 0.00 0.00 0.00 3.74
1758 1767 3.524606 CCGGAGGCGTCGGTGTAT 61.525 66.667 12.23 0.00 46.14 2.29
1830 1839 0.892358 CCAATGTGAGGTGCAGCAGT 60.892 55.000 19.63 0.00 0.00 4.40
2111 2120 6.828273 CCTCATCCAGTTACCACAATATTTGA 59.172 38.462 0.00 0.00 0.00 2.69
2115 2124 6.575244 TTCCTCATCCAGTTACCACAATAT 57.425 37.500 0.00 0.00 0.00 1.28
2271 2282 5.827568 GTTCAACACGATGCATCAATTTT 57.172 34.783 25.70 10.06 0.00 1.82
2289 2300 4.155826 CCTAAATTCTGGAATGTGCGTTCA 59.844 41.667 6.49 0.00 0.00 3.18
2336 2347 8.470657 AAAGATCTTGGTAAAAGAAAGCTTCT 57.529 30.769 9.17 0.00 43.15 2.85
2350 2361 4.899352 AGAGCTGTGTAAAGATCTTGGT 57.101 40.909 9.17 0.31 39.91 3.67
2372 2383 4.895889 TGTGGGGTGACAAAATGACATAAA 59.104 37.500 0.00 0.00 0.00 1.40
2412 2423 8.782339 AAGAAAAGCAAAATATGAGGAAATGG 57.218 30.769 0.00 0.00 0.00 3.16
2417 2428 8.650490 AGGAAAAAGAAAAGCAAAATATGAGGA 58.350 29.630 0.00 0.00 0.00 3.71
2706 2778 4.095782 CCTCCGTTTCAAAACTGAAGTTCA 59.904 41.667 5.25 5.25 37.25 3.18
2713 2785 1.266989 GCTCCCTCCGTTTCAAAACTG 59.733 52.381 4.28 0.00 36.77 3.16
2714 2786 1.133915 TGCTCCCTCCGTTTCAAAACT 60.134 47.619 4.28 0.00 36.77 2.66
2715 2787 1.266989 CTGCTCCCTCCGTTTCAAAAC 59.733 52.381 0.00 0.00 35.59 2.43
2816 2892 3.099141 CTGTTTGGCCCCATACTCAAAT 58.901 45.455 0.00 0.00 32.73 2.32
2874 2950 5.649395 TGCATAACAGGGAAGAAAAGATCAG 59.351 40.000 0.00 0.00 0.00 2.90
2908 2984 3.960571 ACTATGCTTGAAGACATTGGCT 58.039 40.909 0.00 0.00 0.00 4.75
3076 3152 9.740710 ATAGGCAAGTATAATTGGTAATTCTCC 57.259 33.333 14.26 4.77 32.38 3.71
3105 3181 3.120546 CGTTACTGCTGAACATCACCTTG 60.121 47.826 0.00 0.00 0.00 3.61
3126 3202 5.292765 ACAGGAATGCTCAGTACATATTCG 58.707 41.667 0.00 0.00 0.00 3.34
3127 3203 8.662781 TTAACAGGAATGCTCAGTACATATTC 57.337 34.615 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.