Multiple sequence alignment - TraesCS2D01G367500

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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 TraesCS2D01G367500 chr2D 100.000 2618 0 0 1 2618 472193454 472190837 0.000000e+00 4835
1 TraesCS2D01G367500 chr2D 95.541 785 33 2 1 785 406870523 406871305 0.000000e+00 1254
2 TraesCS2D01G367500 chr3D 97.243 1850 30 5 779 2618 134599603 134597765 0.000000e+00 3114
3 TraesCS2D01G367500 chr3D 96.748 1845 39 5 784 2618 365842307 365840474 0.000000e+00 3055
4 TraesCS2D01G367500 chr3D 96.490 1852 37 8 784 2618 593933534 593935374 0.000000e+00 3035
5 TraesCS2D01G367500 chr3D 98.002 1602 30 2 1018 2618 535654891 535656491 0.000000e+00 2780
6 TraesCS2D01G367500 chr3D 93.384 786 49 3 2 786 299399288 299400071 0.000000e+00 1160
7 TraesCS2D01G367500 chr3D 93.478 782 49 2 1 781 475356342 475357122 0.000000e+00 1160
8 TraesCS2D01G367500 chr5D 95.720 1846 37 9 783 2618 498267537 498269350 0.000000e+00 2933
9 TraesCS2D01G367500 chr5D 98.275 1507 24 2 1112 2618 100988722 100990226 0.000000e+00 2638
10 TraesCS2D01G367500 chr5D 91.765 340 6 6 784 1114 100987849 100988175 1.100000e-123 453
11 TraesCS2D01G367500 chr4B 94.742 1864 71 14 775 2618 592155485 592153629 0.000000e+00 2874
12 TraesCS2D01G367500 chr4B 96.195 1498 54 2 1121 2618 592031412 592029918 0.000000e+00 2447
13 TraesCS2D01G367500 chr4B 91.484 364 17 11 775 1126 592032082 592031721 3.030000e-134 488
14 TraesCS2D01G367500 chr6D 98.210 1564 27 1 1055 2618 466182370 466183932 0.000000e+00 2732
15 TraesCS2D01G367500 chr6D 98.422 1458 22 1 1161 2618 47793110 47794566 0.000000e+00 2564
16 TraesCS2D01G367500 chr7A 93.339 1156 51 14 777 1923 597554158 597553020 0.000000e+00 1685
17 TraesCS2D01G367500 chr7D 93.367 784 46 6 1 782 110831721 110830942 0.000000e+00 1155
18 TraesCS2D01G367500 chr2A 93.038 790 50 2 1 786 338987855 338987067 0.000000e+00 1149
19 TraesCS2D01G367500 chr2A 92.214 411 21 8 855 1257 659088670 659088263 2.920000e-159 571
20 TraesCS2D01G367500 chr3B 92.630 787 52 6 1 786 441616133 441616914 0.000000e+00 1127
21 TraesCS2D01G367500 chr3B 90.986 355 18 10 784 1126 13052271 13052623 1.420000e-127 466
22 TraesCS2D01G367500 chr3B 90.968 155 6 6 784 932 104276003 104276155 4.420000e-48 202
23 TraesCS2D01G367500 chr6A 92.503 787 58 1 1 786 34616734 34615948 0.000000e+00 1125
24 TraesCS2D01G367500 chr1B 92.611 785 54 4 2 786 407888977 407889757 0.000000e+00 1125
25 TraesCS2D01G367500 chr7B 92.503 787 53 6 1 786 3353960 3354741 0.000000e+00 1122
26 TraesCS2D01G367500 chr7B 91.443 818 42 13 784 1576 255252763 255251949 0.000000e+00 1098
27 TraesCS2D01G367500 chr1D 92.379 433 19 9 892 1316 59966 59540 2.880000e-169 604


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 TraesCS2D01G367500 chr2D 472190837 472193454 2617 True 4835.0 4835 100.0000 1 2618 1 chr2D.!!$R1 2617
1 TraesCS2D01G367500 chr2D 406870523 406871305 782 False 1254.0 1254 95.5410 1 785 1 chr2D.!!$F1 784
2 TraesCS2D01G367500 chr3D 134597765 134599603 1838 True 3114.0 3114 97.2430 779 2618 1 chr3D.!!$R1 1839
3 TraesCS2D01G367500 chr3D 365840474 365842307 1833 True 3055.0 3055 96.7480 784 2618 1 chr3D.!!$R2 1834
4 TraesCS2D01G367500 chr3D 593933534 593935374 1840 False 3035.0 3035 96.4900 784 2618 1 chr3D.!!$F4 1834
5 TraesCS2D01G367500 chr3D 535654891 535656491 1600 False 2780.0 2780 98.0020 1018 2618 1 chr3D.!!$F3 1600
6 TraesCS2D01G367500 chr3D 299399288 299400071 783 False 1160.0 1160 93.3840 2 786 1 chr3D.!!$F1 784
7 TraesCS2D01G367500 chr3D 475356342 475357122 780 False 1160.0 1160 93.4780 1 781 1 chr3D.!!$F2 780
8 TraesCS2D01G367500 chr5D 498267537 498269350 1813 False 2933.0 2933 95.7200 783 2618 1 chr5D.!!$F1 1835
9 TraesCS2D01G367500 chr5D 100987849 100990226 2377 False 1545.5 2638 95.0200 784 2618 2 chr5D.!!$F2 1834
10 TraesCS2D01G367500 chr4B 592153629 592155485 1856 True 2874.0 2874 94.7420 775 2618 1 chr4B.!!$R1 1843
11 TraesCS2D01G367500 chr4B 592029918 592032082 2164 True 1467.5 2447 93.8395 775 2618 2 chr4B.!!$R2 1843
12 TraesCS2D01G367500 chr6D 466182370 466183932 1562 False 2732.0 2732 98.2100 1055 2618 1 chr6D.!!$F2 1563
13 TraesCS2D01G367500 chr6D 47793110 47794566 1456 False 2564.0 2564 98.4220 1161 2618 1 chr6D.!!$F1 1457
14 TraesCS2D01G367500 chr7A 597553020 597554158 1138 True 1685.0 1685 93.3390 777 1923 1 chr7A.!!$R1 1146
15 TraesCS2D01G367500 chr7D 110830942 110831721 779 True 1155.0 1155 93.3670 1 782 1 chr7D.!!$R1 781
16 TraesCS2D01G367500 chr2A 338987067 338987855 788 True 1149.0 1149 93.0380 1 786 1 chr2A.!!$R1 785
17 TraesCS2D01G367500 chr3B 441616133 441616914 781 False 1127.0 1127 92.6300 1 786 1 chr3B.!!$F3 785
18 TraesCS2D01G367500 chr6A 34615948 34616734 786 True 1125.0 1125 92.5030 1 786 1 chr6A.!!$R1 785
19 TraesCS2D01G367500 chr1B 407888977 407889757 780 False 1125.0 1125 92.6110 2 786 1 chr1B.!!$F1 784
20 TraesCS2D01G367500 chr7B 3353960 3354741 781 False 1122.0 1122 92.5030 1 786 1 chr7B.!!$F1 785
21 TraesCS2D01G367500 chr7B 255251949 255252763 814 True 1098.0 1098 91.4430 784 1576 1 chr7B.!!$R1 792

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
205 207 0.108329 GTCGGCATCCTTTCTTCGGA 60.108 55.0 0.0 0.0 34.52 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2794 0.460109 CAGCGGTTGTCGGATCATGA 60.46 55.0 0.0 0.0 39.69 3.07 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
23 24 2.106683 CGGGCGTCACAATTCTCCC 61.107 63.158 0.00 0.00 0.00 4.30
58 59 2.865343 TCGTCCCGAGATTTAAGAGC 57.135 50.000 0.00 0.00 0.00 4.09
92 94 5.942236 GGGGAAAGGTCTAGTTACGAAATTT 59.058 40.000 0.00 0.00 0.00 1.82
181 183 8.632679 TCATTTTTCTGCTTCAAGTCATTAAGT 58.367 29.630 0.00 0.00 0.00 2.24
205 207 0.108329 GTCGGCATCCTTTCTTCGGA 60.108 55.000 0.00 0.00 34.52 4.55
306 314 1.915078 ATCGGGGAAGGTGGCAGAAG 61.915 60.000 0.00 0.00 0.00 2.85
311 319 1.340114 GGGAAGGTGGCAGAAGGTAAG 60.340 57.143 0.00 0.00 0.00 2.34
326 334 6.423905 CAGAAGGTAAGTCTCGAATTGAAACA 59.576 38.462 0.00 0.00 0.00 2.83
695 706 3.605634 CAACAACATCGATACCAAGGGA 58.394 45.455 0.00 0.00 0.00 4.20
766 778 1.671850 GGCAAAGTTCTCGTCCATCGA 60.672 52.381 0.00 0.00 46.83 3.59
1289 2207 4.402528 CATCGACAACCCCGCCCA 62.403 66.667 0.00 0.00 0.00 5.36
1571 2490 2.579873 GGTGCCGTATGAGTACTCCTA 58.420 52.381 20.11 11.87 0.00 2.94
1690 2609 6.141685 GTGGTTGCTATAAAACTTGTGTTTCG 59.858 38.462 0.00 0.00 44.70 3.46
2345 3267 1.136891 CTCAGGCATACACGGTCATCA 59.863 52.381 0.00 0.00 0.00 3.07
2444 3366 4.386867 TGAACTAGAAGGCCAAGATACG 57.613 45.455 5.01 0.00 0.00 3.06
2565 3487 2.473891 TAGGACTCGAGTGGGCGACA 62.474 60.000 25.58 0.00 36.17 4.35
2566 3488 2.649034 GACTCGAGTGGGCGACAA 59.351 61.111 25.58 0.00 36.17 3.18
2584 3506 4.081862 CGACAACAAGAATGGGTACTCCTA 60.082 45.833 0.00 0.00 36.20 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.522553 GGACGAGATTTCTTGTAGTGGG 58.477 50.000 0.37 0.0 40.54 4.61
92 94 3.119245 CCAAGACCGAGAAGATCCGTTAA 60.119 47.826 0.00 0.0 0.00 2.01
181 183 2.859165 AGAAAGGATGCCGACTTCAA 57.141 45.000 0.00 0.0 0.00 2.69
306 314 8.475331 TCTTATGTTTCAATTCGAGACTTACC 57.525 34.615 0.00 0.0 30.03 2.85
337 345 3.963428 ACCTCATTACTTTGCTCTCGT 57.037 42.857 0.00 0.0 0.00 4.18
531 539 1.152030 TTGACTCTCCTGCACCCCT 60.152 57.895 0.00 0.0 0.00 4.79
695 706 2.239681 ATGGTTCTCTTCGTCCCTCT 57.760 50.000 0.00 0.0 0.00 3.69
766 778 3.389329 AGAGATGACATTTCGGTAGCCAT 59.611 43.478 0.62 0.0 0.00 4.40
825 839 5.092781 CGAAAATGGTGGGACGAAAATAAG 58.907 41.667 0.00 0.0 0.00 1.73
863 878 1.158007 AAACCAGTGGAAGGTGGGAT 58.842 50.000 18.40 0.0 39.86 3.85
1273 2191 3.400599 GATGGGCGGGGTTGTCGAT 62.401 63.158 0.00 0.0 0.00 3.59
1289 2207 2.750637 AGTCGACCGCACCGAGAT 60.751 61.111 13.01 0.0 36.66 2.75
1399 2318 1.545875 GCCCTCCTCGAGCTCATACTA 60.546 57.143 15.40 0.0 0.00 1.82
1400 2319 0.825840 GCCCTCCTCGAGCTCATACT 60.826 60.000 15.40 0.0 0.00 2.12
1435 2354 0.941542 GTCTCGTCGAGCTCTAGCAT 59.058 55.000 17.61 0.0 45.16 3.79
1571 2490 0.721718 GCACGCGAACTTATTGCTCT 59.278 50.000 15.93 0.0 0.00 4.09
1646 2565 5.013547 ACCACGGTTTAATCATCATTTGGA 58.986 37.500 0.00 0.0 0.00 3.53
1874 2794 0.460109 CAGCGGTTGTCGGATCATGA 60.460 55.000 0.00 0.0 39.69 3.07
2345 3267 4.227300 TCAGGTGGCAACTTAGATACCAAT 59.773 41.667 0.00 0.0 37.61 3.16
2444 3366 9.728025 TCAAGCTATGAACTCAGGCATACCTTC 62.728 44.444 9.19 0.0 38.81 3.46
2565 3487 6.849151 AGTTTTAGGAGTACCCATTCTTGTT 58.151 36.000 3.60 0.0 37.41 2.83
2566 3488 6.449830 AGTTTTAGGAGTACCCATTCTTGT 57.550 37.500 3.60 0.0 37.41 3.16


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

AutoCloner maintained by Alex Coulton.