Multiple sequence alignment - TraesCS2D01G591800

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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 TraesCS2D01G591800 chr2D 100.000 3553 0 0 1 3553 646999362 647002914 0.000000e+00 6562
1 TraesCS2D01G591800 chr2D 97.715 2582 53 3 474 3055 646849899 646852474 0.000000e+00 4436
2 TraesCS2D01G591800 chr2D 96.870 2620 73 5 383 2998 646970360 646972974 0.000000e+00 4375
3 TraesCS2D01G591800 chr2D 96.369 2616 83 7 383 2998 646892393 646894996 0.000000e+00 4294
4 TraesCS2D01G591800 chr2D 96.790 2523 72 4 476 2998 646808504 646811017 0.000000e+00 4202
5 TraesCS2D01G591800 chr2D 96.573 2247 61 4 478 2724 646870233 646872463 0.000000e+00 3709
6 TraesCS2D01G591800 chr2D 96.958 1808 49 3 1248 3055 646948500 646950301 0.000000e+00 3029
7 TraesCS2D01G591800 chr2D 96.057 1750 39 13 1308 3055 646916138 646917859 0.000000e+00 2822
8 TraesCS2D01G591800 chr2D 97.447 1606 38 2 1450 3055 646787328 646788930 0.000000e+00 2736
9 TraesCS2D01G591800 chr2D 96.338 1338 44 2 490 1826 647101389 647102722 0.000000e+00 2194
10 TraesCS2D01G591800 chr2D 89.827 1386 123 12 1676 3055 646633797 646632424 0.000000e+00 1762
11 TraesCS2D01G591800 chr2D 94.725 872 27 4 383 1252 646935215 646936069 0.000000e+00 1338
12 TraesCS2D01G591800 chr2D 96.173 810 23 2 476 1285 646786526 646787327 0.000000e+00 1317
13 TraesCS2D01G591800 chr2D 93.349 842 34 5 521 1347 646736956 646736122 0.000000e+00 1225
14 TraesCS2D01G591800 chr2D 97.735 618 12 1 484 1101 646831539 646832154 0.000000e+00 1062
15 TraesCS2D01G591800 chr2D 87.079 890 65 26 1251 2124 646765238 646766093 0.000000e+00 961
16 TraesCS2D01G591800 chr2D 97.551 490 10 1 3066 3553 646872756 646873245 0.000000e+00 837
17 TraesCS2D01G591800 chr2D 97.551 490 9 2 3066 3553 646917902 646918390 0.000000e+00 835
18 TraesCS2D01G591800 chr2D 97.347 490 11 1 3066 3553 646950344 646950833 0.000000e+00 832
19 TraesCS2D01G591800 chr2D 97.143 490 12 1 3066 3553 646852517 646853006 0.000000e+00 826
20 TraesCS2D01G591800 chr2D 97.143 490 11 2 3066 3553 646788973 646789461 0.000000e+00 824
21 TraesCS2D01G591800 chr2D 96.735 490 14 1 3066 3553 646811255 646811744 0.000000e+00 815
22 TraesCS2D01G591800 chr2D 97.474 475 10 1 1 475 646849456 646849928 0.000000e+00 809
23 TraesCS2D01G591800 chr2D 96.531 490 15 1 3066 3553 646973212 646973701 0.000000e+00 809
24 TraesCS2D01G591800 chr2D 97.204 465 11 1 1 465 646831096 646831558 0.000000e+00 785
25 TraesCS2D01G591800 chr2D 95.102 490 16 2 3066 3553 646895234 646895717 0.000000e+00 765
26 TraesCS2D01G591800 chr2D 94.286 490 26 1 3066 3553 646632381 646631892 0.000000e+00 749
27 TraesCS2D01G591800 chr2D 97.638 381 7 1 1 381 646891749 646892127 0.000000e+00 652
28 TraesCS2D01G591800 chr2D 97.375 381 8 1 1 381 646934570 646934948 0.000000e+00 647
29 TraesCS2D01G591800 chr2D 97.113 381 9 1 1 381 646869525 646869903 2.990000e-180 641
30 TraesCS2D01G591800 chr2D 96.850 381 9 2 1 381 646807799 646808176 5.000000e-178 634
31 TraesCS2D01G591800 chr2D 96.588 381 11 1 1 381 646969716 646970094 6.470000e-177 630
32 TraesCS2D01G591800 chr2D 95.065 385 13 2 1 381 647100689 647101071 5.080000e-168 601
33 TraesCS2D01G591800 chr2D 91.495 388 24 5 1 381 646737714 646737329 3.140000e-145 525
34 TraesCS2D01G591800 chr2D 97.849 93 2 0 387 479 646786467 646786559 1.020000e-35 161
35 TraesCS2D01G591800 chr2D 96.552 87 3 0 383 469 646808441 646808527 1.030000e-30 145
36 TraesCS2D01G591800 chr2D 96.386 83 3 0 383 465 646758772 646758854 1.720000e-28 137
37 TraesCS2D01G591800 chr2B 84.200 981 146 7 1693 2669 788797155 788798130 0.000000e+00 944
38 TraesCS2D01G591800 chr7D 86.822 258 25 5 2686 2943 204017342 204017590 2.700000e-71 279


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 TraesCS2D01G591800 chr2D 646999362 647002914 3552 False 6562.000000 6562 100.000000 1 3553 1 chr2D.!!$F3 3552
1 TraesCS2D01G591800 chr2D 646849456 646853006 3550 False 2023.666667 4436 97.444000 1 3553 3 chr2D.!!$F7 3552
2 TraesCS2D01G591800 chr2D 646969716 646973701 3985 False 1938.000000 4375 96.663000 1 3553 3 chr2D.!!$F13 3552
3 TraesCS2D01G591800 chr2D 646948500 646950833 2333 False 1930.500000 3029 97.152500 1248 3553 2 chr2D.!!$F12 2305
4 TraesCS2D01G591800 chr2D 646891749 646895717 3968 False 1903.666667 4294 96.369667 1 3553 3 chr2D.!!$F9 3552
5 TraesCS2D01G591800 chr2D 646916138 646918390 2252 False 1828.500000 2822 96.804000 1308 3553 2 chr2D.!!$F10 2245
6 TraesCS2D01G591800 chr2D 646869525 646873245 3720 False 1729.000000 3709 97.079000 1 3553 3 chr2D.!!$F8 3552
7 TraesCS2D01G591800 chr2D 646807799 646811744 3945 False 1449.000000 4202 96.731750 1 3553 4 chr2D.!!$F5 3552
8 TraesCS2D01G591800 chr2D 647100689 647102722 2033 False 1397.500000 2194 95.701500 1 1826 2 chr2D.!!$F14 1825
9 TraesCS2D01G591800 chr2D 646786467 646789461 2994 False 1259.500000 2736 97.153000 387 3553 4 chr2D.!!$F4 3166
10 TraesCS2D01G591800 chr2D 646631892 646633797 1905 True 1255.500000 1762 92.056500 1676 3553 2 chr2D.!!$R1 1877
11 TraesCS2D01G591800 chr2D 646934570 646936069 1499 False 992.500000 1338 96.050000 1 1252 2 chr2D.!!$F11 1251
12 TraesCS2D01G591800 chr2D 646765238 646766093 855 False 961.000000 961 87.079000 1251 2124 1 chr2D.!!$F2 873
13 TraesCS2D01G591800 chr2D 646831096 646832154 1058 False 923.500000 1062 97.469500 1 1101 2 chr2D.!!$F6 1100
14 TraesCS2D01G591800 chr2D 646736122 646737714 1592 True 875.000000 1225 92.422000 1 1347 2 chr2D.!!$R2 1346
15 TraesCS2D01G591800 chr2B 788797155 788798130 975 False 944.000000 944 84.200000 1693 2669 1 chr2B.!!$F1 976

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
399 674 4.868268 TCCACAGTACTAGTATGAGCCTT 58.132 43.478 5.75 0.0 0.00 4.35 F
1841 2192 0.752054 GGAGAGCATGGAGACCTCTG 59.248 60.000 4.73 0.0 36.16 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2505 0.45460 GTCAATAGCTGGACCGACGA 59.545 55.000 0.0 0.0 0.0 4.20 R
2708 3093 1.67782 GGTTTGTACATCCACTCCCCG 60.678 57.143 0.0 0.0 0.0 5.73 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
399 674 4.868268 TCCACAGTACTAGTATGAGCCTT 58.132 43.478 5.75 0.00 0.00 4.35
639 952 8.472413 ACATTATTTCATCTCCAGTTTTGATGG 58.528 33.333 0.00 0.00 38.38 3.51
946 1261 5.446741 GCAGACACGTTAGAAACAGACAAAA 60.447 40.000 0.00 0.00 0.00 2.44
1062 1392 1.079819 GCTCACACGCAGGCTTCTA 60.080 57.895 0.00 0.00 0.00 2.10
1182 1512 8.726870 TGTAGCTTGTTAACTTAAGAAACTGT 57.273 30.769 10.09 3.15 0.00 3.55
1365 1698 2.810852 GCTCTGAAACTGAAGACCAAGG 59.189 50.000 0.00 0.00 0.00 3.61
1398 1740 3.366374 CCCCATCAGCTTTTCGAAAAGTC 60.366 47.826 37.54 30.86 45.48 3.01
1423 1765 1.064240 TCCCCATCAGTACGCTCACTA 60.064 52.381 0.00 0.00 0.00 2.74
1442 1784 4.764823 CACTACTTCACTCTCCAACTCTCT 59.235 45.833 0.00 0.00 0.00 3.10
1443 1785 5.007682 ACTACTTCACTCTCCAACTCTCTC 58.992 45.833 0.00 0.00 0.00 3.20
1841 2192 0.752054 GGAGAGCATGGAGACCTCTG 59.248 60.000 4.73 0.00 36.16 3.35
2111 2462 1.002430 GCATCAAGGAGGTCAGTGACA 59.998 52.381 24.20 2.60 33.68 3.58
2429 2808 1.508808 GCGGCCTTTGTTTCCGTGTA 61.509 55.000 0.00 0.00 44.58 2.90
2641 3025 7.195374 AGGAAATTACAATAGTGCAGACCTA 57.805 36.000 0.00 0.00 0.00 3.08
2708 3093 3.944015 AGTCAGCATAGCTCAAATGGTTC 59.056 43.478 0.00 0.00 36.40 3.62
2765 3151 2.089854 CCTCACGGAGGCGAATTTG 58.910 57.895 6.97 0.00 43.29 2.32
2801 3187 2.496899 TGAGGACCATGCTTTCCTTC 57.503 50.000 9.45 5.15 42.68 3.46
3118 3674 6.328641 AGTAGAGTAATCACAACAACTCGT 57.671 37.500 0.00 0.00 42.51 4.18
3257 3819 9.533831 AACCTAATCAATTGGTTGAAGTATCTT 57.466 29.630 14.35 0.00 46.67 2.40
3416 3978 8.392372 AGACAATAATCATGATGATGTGAAGG 57.608 34.615 19.95 0.30 37.15 3.46
3418 3980 8.392372 ACAATAATCATGATGATGTGAAGGAG 57.608 34.615 9.46 0.00 37.15 3.69
3547 4109 3.855668 ACTGATTTGGAAATGGGTTGGA 58.144 40.909 0.00 0.00 0.00 3.53
3548 4110 4.230455 ACTGATTTGGAAATGGGTTGGAA 58.770 39.130 0.00 0.00 0.00 3.53
3549 4111 4.284234 ACTGATTTGGAAATGGGTTGGAAG 59.716 41.667 0.00 0.00 0.00 3.46
3550 4112 3.582208 TGATTTGGAAATGGGTTGGAAGG 59.418 43.478 0.00 0.00 0.00 3.46
3551 4113 2.785357 TTGGAAATGGGTTGGAAGGT 57.215 45.000 0.00 0.00 0.00 3.50
3552 4114 2.785357 TGGAAATGGGTTGGAAGGTT 57.215 45.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.500783 CCTTCTCCCCAAGCCTGGAA 61.501 60.000 1.80 0.00 46.92 3.53
302 307 5.589855 TGATTTCACTATGGACGATGCAATT 59.410 36.000 0.00 0.00 0.00 2.32
399 674 2.108168 CAGAACCCAAGGTCCGATCTA 58.892 52.381 0.00 0.00 33.12 1.98
658 971 2.026729 TGCCACATCACCTCCGATTTTA 60.027 45.455 0.00 0.00 0.00 1.52
946 1261 4.755266 AAGTATGCGGGAATCTTACTGT 57.245 40.909 0.00 0.00 0.00 3.55
1062 1392 4.965200 GGTGATTACCTAGAGCATCCTT 57.035 45.455 0.00 0.00 43.97 3.36
1182 1512 1.979855 TTAAGAAGCAGCAGCCACAA 58.020 45.000 0.00 0.00 43.56 3.33
1365 1698 3.837355 AGCTGATGGGGAAATTATGGAC 58.163 45.455 0.00 0.00 0.00 4.02
1398 1740 2.614057 GAGCGTACTGATGGGGAAATTG 59.386 50.000 0.00 0.00 0.00 2.32
1423 1765 4.079253 GAGAGAGAGTTGGAGAGTGAAGT 58.921 47.826 0.00 0.00 0.00 3.01
1442 1784 5.083122 ACCTGTCTTGAATTGAGAGAGAGA 58.917 41.667 11.91 0.00 36.84 3.10
1443 1785 5.185635 AGACCTGTCTTGAATTGAGAGAGAG 59.814 44.000 11.91 6.76 36.84 3.20
2111 2462 1.861982 ACCTTGTACCTATCACGCCT 58.138 50.000 0.00 0.00 0.00 5.52
2154 2505 0.454600 GTCAATAGCTGGACCGACGA 59.545 55.000 0.00 0.00 0.00 4.20
2208 2585 2.210013 TCAGTGCCAACGAGCTCCT 61.210 57.895 8.47 0.00 0.00 3.69
2404 2783 1.271102 GGAAACAAAGGCCGCACAATA 59.729 47.619 0.00 0.00 0.00 1.90
2708 3093 1.677820 GGTTTGTACATCCACTCCCCG 60.678 57.143 0.00 0.00 0.00 5.73
2765 3151 4.700692 GTCCTCAAGAACAAATAGGAACCC 59.299 45.833 0.00 0.00 38.06 4.11
2801 3187 6.528321 TCCTCAAGGATAAATGCATGAGTAG 58.472 40.000 13.33 2.73 40.72 2.57
2945 3331 3.493503 AGCTTACCAACTTTTCTTCGACG 59.506 43.478 0.00 0.00 0.00 5.12
3055 3579 5.227569 TCAATGCATACTTCCGTATCCAT 57.772 39.130 0.00 0.00 36.32 3.41
3057 3581 5.700832 TCAATCAATGCATACTTCCGTATCC 59.299 40.000 0.00 0.00 34.14 2.59
3058 3582 6.646653 TCTCAATCAATGCATACTTCCGTATC 59.353 38.462 0.00 0.00 34.14 2.24
3059 3583 6.524734 TCTCAATCAATGCATACTTCCGTAT 58.475 36.000 0.00 0.00 36.79 3.06
3061 3585 4.769688 TCTCAATCAATGCATACTTCCGT 58.230 39.130 0.00 0.00 0.00 4.69
3062 3586 5.739752 TTCTCAATCAATGCATACTTCCG 57.260 39.130 0.00 0.00 0.00 4.30
3063 3587 6.263842 TCCATTCTCAATCAATGCATACTTCC 59.736 38.462 0.00 0.00 30.94 3.46
3092 3648 7.085116 CGAGTTGTTGTGATTACTCTACTTCT 58.915 38.462 0.00 0.00 35.89 2.85
3118 3674 2.942804 TGCAGGGAAACATCAAGAACA 58.057 42.857 0.00 0.00 0.00 3.18
3257 3819 8.174085 TCCCCCACATCTTTTTAAAATTCTCTA 58.826 33.333 0.55 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.