Multiple sequence alignment - TraesCS2D01G050800

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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 TraesCS2D01G050800 chr2D 100.000 2961 0 0 1 2961 19044356 19047316 0.000000e+00 5469.0
1 TraesCS2D01G050800 chr2D 86.909 1291 149 14 1324 2598 18763315 18762029 0.000000e+00 1430.0
2 TraesCS2D01G050800 chr2D 100.000 686 0 0 3062 3747 19047417 19048102 0.000000e+00 1267.0
3 TraesCS2D01G050800 chr2D 99.085 328 3 0 3419 3746 593430918 593431245 1.160000e-164 590.0
4 TraesCS2D01G050800 chr2D 96.639 357 4 1 3062 3418 593430540 593430888 1.500000e-163 586.0
5 TraesCS2D01G050800 chr2D 96.073 331 10 1 3419 3746 116830405 116830735 1.530000e-148 536.0
6 TraesCS2D01G050800 chr2D 96.266 241 8 1 3110 3350 116830015 116830254 9.750000e-106 394.0
7 TraesCS2D01G050800 chr2D 96.078 51 2 0 3370 3420 116830315 116830365 2.400000e-12 84.2
8 TraesCS2D01G050800 chrUn 100.000 1729 0 0 1 1729 322649696 322647968 0.000000e+00 3193.0
9 TraesCS2D01G050800 chrUn 100.000 686 0 0 3062 3747 317332110 317332795 0.000000e+00 1267.0
10 TraesCS2D01G050800 chrUn 100.000 686 0 0 3062 3747 374513932 374514617 0.000000e+00 1267.0
11 TraesCS2D01G050800 chrUn 96.657 359 4 1 3062 3420 24772568 24772918 1.160000e-164 590.0
12 TraesCS2D01G050800 chrUn 99.085 328 3 0 3419 3746 24772946 24773273 1.160000e-164 590.0
13 TraesCS2D01G050800 chrUn 81.548 168 27 4 798 963 34210911 34210746 6.530000e-28 135.0
14 TraesCS2D01G050800 chr2A 91.637 1973 113 17 1010 2954 19949399 19947451 0.000000e+00 2682.0
15 TraesCS2D01G050800 chr2A 87.500 688 71 6 1 679 19950960 19950279 0.000000e+00 780.0
16 TraesCS2D01G050800 chr2A 88.235 85 10 0 1 85 19952138 19952054 6.620000e-18 102.0
17 TraesCS2D01G050800 chr2A 88.235 85 9 1 1 85 19951390 19951307 2.380000e-17 100.0
18 TraesCS2D01G050800 chr1D 87.237 1332 153 12 1289 2607 329669838 329668511 0.000000e+00 1502.0
19 TraesCS2D01G050800 chr1B 86.472 1338 157 13 1288 2607 444671172 444669841 0.000000e+00 1447.0
20 TraesCS2D01G050800 chr1B 81.928 166 29 1 795 959 658353852 658354017 5.050000e-29 139.0
21 TraesCS2D01G050800 chr1A 86.692 1300 153 14 1313 2598 426876645 426875352 0.000000e+00 1424.0
22 TraesCS2D01G050800 chr1A 94.774 287 10 3 3064 3350 552470909 552470628 3.430000e-120 442.0
23 TraesCS2D01G050800 chr1A 87.879 231 9 6 3119 3332 47727986 47727758 1.730000e-63 254.0
24 TraesCS2D01G050800 chr1A 83.333 150 22 3 809 956 71070743 71070595 6.530000e-28 135.0
25 TraesCS2D01G050800 chr1A 97.143 70 2 0 3351 3420 552470580 552470511 6.570000e-23 119.0
26 TraesCS2D01G050800 chr4A 85.308 1266 163 8 1325 2589 589787466 589788709 0.000000e+00 1286.0
27 TraesCS2D01G050800 chr4A 85.133 1278 165 15 1320 2592 589842598 589843855 0.000000e+00 1284.0
28 TraesCS2D01G050800 chr4A 85.696 769 97 6 1825 2592 589781454 589780698 0.000000e+00 798.0
29 TraesCS2D01G050800 chr4A 81.765 170 28 3 788 955 75320413 75320581 5.050000e-29 139.0
30 TraesCS2D01G050800 chr4A 90.476 63 5 1 3351 3412 587824 587886 8.630000e-12 82.4
31 TraesCS2D01G050800 chr7D 100.000 686 0 0 3062 3747 521349553 521350238 0.000000e+00 1267.0
32 TraesCS2D01G050800 chr7D 82.716 162 26 2 798 958 128144049 128143889 3.900000e-30 143.0
33 TraesCS2D01G050800 chr4D 84.891 1284 157 18 1320 2592 12662114 12660857 0.000000e+00 1262.0
34 TraesCS2D01G050800 chr4D 84.822 1265 169 11 1326 2589 12653099 12654341 0.000000e+00 1251.0
35 TraesCS2D01G050800 chr4D 85.366 164 22 2 794 956 386984667 386984829 6.440000e-38 169.0
36 TraesCS2D01G050800 chr4B 84.458 1274 178 8 1320 2592 23354410 23355664 0.000000e+00 1238.0
37 TraesCS2D01G050800 chr6D 95.758 330 11 2 3419 3746 39089643 39089315 2.560000e-146 529.0
38 TraesCS2D01G050800 chr6D 96.653 239 7 1 3112 3350 39090031 39089794 2.710000e-106 396.0
39 TraesCS2D01G050800 chr6D 98.039 51 1 0 3370 3420 39089733 39089683 5.150000e-14 89.8
40 TraesCS2D01G050800 chr7A 92.049 327 20 5 3421 3746 650697419 650697740 4.410000e-124 455.0
41 TraesCS2D01G050800 chr7A 90.826 327 21 5 3423 3746 636536940 636537260 2.670000e-116 429.0
42 TraesCS2D01G050800 chr5D 84.076 157 22 3 795 950 538664379 538664533 8.390000e-32 148.0
43 TraesCS2D01G050800 chr2B 81.065 169 30 2 792 959 453265445 453265612 2.350000e-27 134.0
44 TraesCS2D01G050800 chr7B 93.421 76 3 2 3119 3193 692350311 692350237 1.100000e-20 111.0


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 TraesCS2D01G050800 chr2D 19044356 19048102 3746 False 3368.000000 5469 100.000000 1 3747 2 chr2D.!!$F1 3746
1 TraesCS2D01G050800 chr2D 18762029 18763315 1286 True 1430.000000 1430 86.909000 1324 2598 1 chr2D.!!$R1 1274
2 TraesCS2D01G050800 chr2D 593430540 593431245 705 False 588.000000 590 97.862000 3062 3746 2 chr2D.!!$F3 684
3 TraesCS2D01G050800 chr2D 116830015 116830735 720 False 338.066667 536 96.139000 3110 3746 3 chr2D.!!$F2 636
4 TraesCS2D01G050800 chrUn 322647968 322649696 1728 True 3193.000000 3193 100.000000 1 1729 1 chrUn.!!$R2 1728
5 TraesCS2D01G050800 chrUn 317332110 317332795 685 False 1267.000000 1267 100.000000 3062 3747 1 chrUn.!!$F1 685
6 TraesCS2D01G050800 chrUn 374513932 374514617 685 False 1267.000000 1267 100.000000 3062 3747 1 chrUn.!!$F2 685
7 TraesCS2D01G050800 chrUn 24772568 24773273 705 False 590.000000 590 97.871000 3062 3746 2 chrUn.!!$F3 684
8 TraesCS2D01G050800 chr2A 19947451 19952138 4687 True 916.000000 2682 88.901750 1 2954 4 chr2A.!!$R1 2953
9 TraesCS2D01G050800 chr1D 329668511 329669838 1327 True 1502.000000 1502 87.237000 1289 2607 1 chr1D.!!$R1 1318
10 TraesCS2D01G050800 chr1B 444669841 444671172 1331 True 1447.000000 1447 86.472000 1288 2607 1 chr1B.!!$R1 1319
11 TraesCS2D01G050800 chr1A 426875352 426876645 1293 True 1424.000000 1424 86.692000 1313 2598 1 chr1A.!!$R3 1285
12 TraesCS2D01G050800 chr4A 589787466 589788709 1243 False 1286.000000 1286 85.308000 1325 2589 1 chr4A.!!$F3 1264
13 TraesCS2D01G050800 chr4A 589842598 589843855 1257 False 1284.000000 1284 85.133000 1320 2592 1 chr4A.!!$F4 1272
14 TraesCS2D01G050800 chr4A 589780698 589781454 756 True 798.000000 798 85.696000 1825 2592 1 chr4A.!!$R1 767
15 TraesCS2D01G050800 chr7D 521349553 521350238 685 False 1267.000000 1267 100.000000 3062 3747 1 chr7D.!!$F1 685
16 TraesCS2D01G050800 chr4D 12660857 12662114 1257 True 1262.000000 1262 84.891000 1320 2592 1 chr4D.!!$R1 1272
17 TraesCS2D01G050800 chr4D 12653099 12654341 1242 False 1251.000000 1251 84.822000 1326 2589 1 chr4D.!!$F1 1263
18 TraesCS2D01G050800 chr4B 23354410 23355664 1254 False 1238.000000 1238 84.458000 1320 2592 1 chr4B.!!$F1 1272
19 TraesCS2D01G050800 chr6D 39089315 39090031 716 True 338.266667 529 96.816667 3112 3746 3 chr6D.!!$R1 634

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
1941 3913 2.723719 GCGCAAGACGTACCGAACC 61.724 63.158 0.3 0.0 46.11 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2760 4747 1.940613 CGCCTACTCAATAGCAAACCC 59.059 52.381 0.0 0.0 0.0 4.11 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
1941 3913 2.723719 GCGCAAGACGTACCGAACC 61.724 63.158 0.30 0.00 46.11 3.62
2020 3992 0.249573 GTTCGAGTTCCGGTTCACCA 60.250 55.000 0.00 0.00 39.14 4.17
2026 3998 0.748729 GTTCCGGTTCACCAACACCA 60.749 55.000 0.00 0.00 33.70 4.17
2048 4020 1.163554 GACGAGGTCTCCTACGTGTT 58.836 55.000 14.23 0.00 37.45 3.32
2340 4315 4.954970 CAGTGCGGCTTGGGTGGT 62.955 66.667 0.00 0.00 0.00 4.16
2463 4450 4.908687 AACTGCTCGTGCACGGCA 62.909 61.111 35.92 35.92 45.31 5.69
2493 4480 2.523440 GGATATCCGTGGTGGTGGA 58.477 57.895 5.86 0.00 39.52 4.02
2608 4595 6.258947 GTCTGACCTAGGTAAATCAAATGCTC 59.741 42.308 16.29 0.00 0.00 4.26
2637 4624 7.654963 CAACGTTACTTTGCATAGATCAATG 57.345 36.000 11.39 9.12 0.00 2.82
2674 4661 6.171213 AGAGTTAGTTAAGTTCCAATTCCCG 58.829 40.000 0.00 0.00 0.00 5.14
2724 4711 4.477302 AACGGTAGAACCAAACATTTCG 57.523 40.909 0.00 0.00 38.47 3.46
2829 4816 0.248702 CGGTAGAGAAGAGGAAGCGC 60.249 60.000 0.00 0.00 0.00 5.92
2906 4893 1.958205 GAGGGATGATGCCGAAGCG 60.958 63.158 0.00 0.00 44.31 4.68
2954 4941 0.326264 CTGGTGTGGGAAAGGAGAGG 59.674 60.000 0.00 0.00 0.00 3.69
2955 4942 1.133809 TGGTGTGGGAAAGGAGAGGG 61.134 60.000 0.00 0.00 0.00 4.30
2956 4943 1.685820 GTGTGGGAAAGGAGAGGGG 59.314 63.158 0.00 0.00 0.00 4.79
2957 4944 0.840722 GTGTGGGAAAGGAGAGGGGA 60.841 60.000 0.00 0.00 0.00 4.81
2958 4945 0.547712 TGTGGGAAAGGAGAGGGGAG 60.548 60.000 0.00 0.00 0.00 4.30
2959 4946 0.252742 GTGGGAAAGGAGAGGGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
2960 4947 0.496382 TGGGAAAGGAGAGGGGAGAA 59.504 55.000 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1787 3759 2.683933 TCCTCAGGTCCTTCCCGC 60.684 66.667 0.0 0.0 36.75 6.13
1860 3832 0.527817 CCATCACGTAGCGGAAGTCC 60.528 60.000 0.0 0.0 0.00 3.85
1957 3929 3.204827 GATGCCGCTGAACCGCAT 61.205 61.111 0.0 0.0 0.00 4.73
2332 4307 3.879885 CCCGTCACCACCACCCAA 61.880 66.667 0.0 0.0 0.00 4.12
2334 4309 3.837570 GAACCCGTCACCACCACCC 62.838 68.421 0.0 0.0 0.00 4.61
2340 4315 1.600107 GGCATAGAACCCGTCACCA 59.400 57.895 0.0 0.0 0.00 4.17
2478 4465 2.363975 GCCTCCACCACCACGGATA 61.364 63.158 0.0 0.0 38.63 2.59
2505 4492 1.647545 CGCCGAACCACTGAATGCAT 61.648 55.000 0.0 0.0 0.00 3.96
2637 4624 5.993106 AACTAACTCTCAAACTGACAAGC 57.007 39.130 0.0 0.0 0.00 4.01
2724 4711 2.614983 TGCGACAAACCTTACTTTGGTC 59.385 45.455 0.0 0.0 36.69 4.02
2760 4747 1.940613 CGCCTACTCAATAGCAAACCC 59.059 52.381 0.0 0.0 0.00 4.11
2835 4822 2.283173 TGCTCTGTCTCCGCCTCA 60.283 61.111 0.0 0.0 0.00 3.86
2883 4870 2.031768 GGCATCATCCCTCGCTCC 59.968 66.667 0.0 0.0 0.00 4.70
2887 4874 1.958205 GCTTCGGCATCATCCCTCG 60.958 63.158 0.0 0.0 41.33 4.63


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

AutoCloner maintained by Alex Coulton.