Multiple sequence alignment - TraesCS2D01G333200

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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 TraesCS2D01G333200 chr2D 100.000 3185 0 0 1 3185 426940792 426937608 0.000000e+00 5882
1 TraesCS2D01G333200 chr2D 99.342 152 0 1 2413 2563 426933239 426933088 1.130000e-69 274
2 TraesCS2D01G333200 chr2B 95.098 2387 97 9 40 2417 503760759 503758384 0.000000e+00 3742
3 TraesCS2D01G333200 chr2A 92.744 1516 78 14 926 2416 561852795 561854303 0.000000e+00 2161
4 TraesCS2D01G333200 chr2A 92.976 1438 86 10 988 2417 562092802 562094232 0.000000e+00 2082
5 TraesCS2D01G333200 chr2A 91.228 1482 99 21 963 2417 561843518 561844995 0.000000e+00 1988
6 TraesCS2D01G333200 chr2A 98.314 771 12 1 2416 3185 739700992 739700222 0.000000e+00 1351
7 TraesCS2D01G333200 chr2A 98.684 152 1 1 2413 2563 739695856 739695705 5.240000e-68 268
8 TraesCS2D01G333200 chr7D 99.352 772 4 1 2415 3185 92598228 92597457 0.000000e+00 1397
9 TraesCS2D01G333200 chr7D 88.796 598 53 13 335 921 532629250 532629844 0.000000e+00 721
10 TraesCS2D01G333200 chr7D 88.442 597 59 5 335 923 552304141 552304735 0.000000e+00 712
11 TraesCS2D01G333200 chr7D 88.423 596 57 8 335 921 135438691 135439283 0.000000e+00 708
12 TraesCS2D01G333200 chr7D 97.500 160 1 2 2413 2569 92593089 92592930 1.460000e-68 270
13 TraesCS2D01G333200 chr6D 99.222 771 5 1 2416 3185 6505055 6504285 0.000000e+00 1389
14 TraesCS2D01G333200 chr6D 96.471 340 10 1 1 338 16177805 16178144 7.720000e-156 560
15 TraesCS2D01G333200 chr6D 98.026 152 2 1 2413 2563 6499920 6499769 2.440000e-66 263
16 TraesCS2D01G333200 chr3A 97.063 783 20 3 2405 3185 644828741 644827960 0.000000e+00 1315
17 TraesCS2D01G333200 chr3A 91.317 334 13 3 2552 2869 10254864 10255197 2.920000e-120 442
18 TraesCS2D01G333200 chr3A 96.711 152 4 1 2413 2563 644823595 644823444 5.270000e-63 252
19 TraesCS2D01G333200 chr3D 89.517 601 53 7 335 927 577412548 577411950 0.000000e+00 752
20 TraesCS2D01G333200 chr3D 94.721 341 15 2 1 338 589431906 589431566 7.830000e-146 527
21 TraesCS2D01G333200 chr3D 93.548 341 13 3 1 338 549376687 549377021 1.710000e-137 499
22 TraesCS2D01G333200 chr4A 89.430 596 53 5 335 921 727414720 727415314 0.000000e+00 743
23 TraesCS2D01G333200 chr4A 93.529 340 20 2 1 338 24117574 24117913 3.670000e-139 505
24 TraesCS2D01G333200 chr1D 88.591 596 57 8 335 922 58512343 58512935 0.000000e+00 713
25 TraesCS2D01G333200 chr5D 88.552 594 58 6 335 921 305778815 305779405 0.000000e+00 712
26 TraesCS2D01G333200 chr5D 95.858 338 11 2 4 338 539037183 539036846 7.770000e-151 544
27 TraesCS2D01G333200 chr4D 88.403 595 59 6 335 921 25384458 25383866 0.000000e+00 708
28 TraesCS2D01G333200 chr1B 95.300 383 15 1 2806 3185 34514326 34514708 3.510000e-169 604
29 TraesCS2D01G333200 chr5A 95.601 341 12 2 1 338 73805068 73804728 7.770000e-151 544
30 TraesCS2D01G333200 chr5A 93.275 342 19 2 1 338 480478076 480478417 4.740000e-138 501
31 TraesCS2D01G333200 chr6B 94.970 338 13 2 5 338 27918354 27918691 7.830000e-146 527


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 TraesCS2D01G333200 chr2D 426937608 426940792 3184 True 5882 5882 100.000 1 3185 1 chr2D.!!$R2 3184
1 TraesCS2D01G333200 chr2B 503758384 503760759 2375 True 3742 3742 95.098 40 2417 1 chr2B.!!$R1 2377
2 TraesCS2D01G333200 chr2A 561852795 561854303 1508 False 2161 2161 92.744 926 2416 1 chr2A.!!$F2 1490
3 TraesCS2D01G333200 chr2A 562092802 562094232 1430 False 2082 2082 92.976 988 2417 1 chr2A.!!$F3 1429
4 TraesCS2D01G333200 chr2A 561843518 561844995 1477 False 1988 1988 91.228 963 2417 1 chr2A.!!$F1 1454
5 TraesCS2D01G333200 chr2A 739700222 739700992 770 True 1351 1351 98.314 2416 3185 1 chr2A.!!$R2 769
6 TraesCS2D01G333200 chr7D 92597457 92598228 771 True 1397 1397 99.352 2415 3185 1 chr7D.!!$R2 770
7 TraesCS2D01G333200 chr7D 532629250 532629844 594 False 721 721 88.796 335 921 1 chr7D.!!$F2 586
8 TraesCS2D01G333200 chr7D 552304141 552304735 594 False 712 712 88.442 335 923 1 chr7D.!!$F3 588
9 TraesCS2D01G333200 chr7D 135438691 135439283 592 False 708 708 88.423 335 921 1 chr7D.!!$F1 586
10 TraesCS2D01G333200 chr6D 6504285 6505055 770 True 1389 1389 99.222 2416 3185 1 chr6D.!!$R2 769
11 TraesCS2D01G333200 chr3A 644827960 644828741 781 True 1315 1315 97.063 2405 3185 1 chr3A.!!$R2 780
12 TraesCS2D01G333200 chr3D 577411950 577412548 598 True 752 752 89.517 335 927 1 chr3D.!!$R1 592
13 TraesCS2D01G333200 chr4A 727414720 727415314 594 False 743 743 89.430 335 921 1 chr4A.!!$F2 586
14 TraesCS2D01G333200 chr1D 58512343 58512935 592 False 713 713 88.591 335 922 1 chr1D.!!$F1 587
15 TraesCS2D01G333200 chr5D 305778815 305779405 590 False 712 712 88.552 335 921 1 chr5D.!!$F1 586
16 TraesCS2D01G333200 chr4D 25383866 25384458 592 True 708 708 88.403 335 921 1 chr4D.!!$R1 586

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
996 1024 0.040425 GTTCGTCACCAAAGCGCAAT 60.04 50.0 11.47 0.0 0.00 3.56 F
1518 1561 0.250424 TCGACCTGGTCTACGACACA 60.25 55.0 23.49 0.0 33.68 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1945 0.615331 GGACATCCTCAGCTTGGACA 59.385 55.0 7.32 0.0 36.3 4.02 R
2566 2625 0.755698 GGAGACGGGTGGCTCTGATA 60.756 60.0 0.00 0.0 0.0 2.15 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
32 33 4.598894 CTCCAGCAGGCGCGCTAT 62.599 66.667 32.29 17.65 45.49 2.97
33 34 3.212906 CTCCAGCAGGCGCGCTATA 62.213 63.158 32.29 8.72 45.49 1.31
34 35 2.047844 CCAGCAGGCGCGCTATAT 60.048 61.111 32.29 12.41 45.49 0.86
35 36 1.669115 CCAGCAGGCGCGCTATATT 60.669 57.895 32.29 10.43 45.49 1.28
36 37 1.230635 CCAGCAGGCGCGCTATATTT 61.231 55.000 32.29 9.28 45.49 1.40
37 38 0.164647 CAGCAGGCGCGCTATATTTC 59.835 55.000 32.29 12.47 45.49 2.17
38 39 0.249868 AGCAGGCGCGCTATATTTCA 60.250 50.000 32.29 0.00 45.49 2.69
39 40 0.798776 GCAGGCGCGCTATATTTCAT 59.201 50.000 32.29 2.84 0.00 2.57
40 41 1.197721 GCAGGCGCGCTATATTTCATT 59.802 47.619 32.29 0.93 0.00 2.57
41 42 2.350772 GCAGGCGCGCTATATTTCATTT 60.351 45.455 32.29 0.00 0.00 2.32
42 43 3.853307 GCAGGCGCGCTATATTTCATTTT 60.853 43.478 32.29 0.00 0.00 1.82
43 44 4.290155 CAGGCGCGCTATATTTCATTTTT 58.710 39.130 32.29 0.00 0.00 1.94
68 69 4.945543 TCTTGACGCCTACTATGTGAACTA 59.054 41.667 0.00 0.00 0.00 2.24
70 71 4.011698 TGACGCCTACTATGTGAACTACA 58.988 43.478 0.00 0.00 44.87 2.74
95 96 5.265350 TCGATACACATTTGGTTCCGATA 57.735 39.130 0.00 0.00 0.00 2.92
99 100 6.866770 CGATACACATTTGGTTCCGATAGTAT 59.133 38.462 0.00 0.00 0.00 2.12
103 104 8.974060 ACACATTTGGTTCCGATAGTATAAAT 57.026 30.769 0.00 0.00 0.00 1.40
104 105 8.836413 ACACATTTGGTTCCGATAGTATAAATG 58.164 33.333 0.00 0.00 39.12 2.32
257 258 1.433879 GTGATGTCCTCCTCCGACG 59.566 63.158 0.00 0.00 32.68 5.12
497 498 1.340248 ACGTCCGTGAAGTTCATGTCT 59.660 47.619 20.91 0.95 31.62 3.41
510 511 2.283529 ATGTCTCAACGGGACCGCT 61.284 57.895 11.21 0.00 44.19 5.52
511 512 0.968901 ATGTCTCAACGGGACCGCTA 60.969 55.000 11.21 0.00 44.19 4.26
600 612 4.832608 GCCGCCCGACCGAATCTT 62.833 66.667 0.00 0.00 0.00 2.40
697 709 4.602259 CAGTGGTGGCGTGTCGGT 62.602 66.667 0.00 0.00 0.00 4.69
718 730 0.172803 GCGAGGAGAGAAAGCGGTAA 59.827 55.000 0.00 0.00 0.00 2.85
811 825 2.743928 CGAGCTGCCGCCTTTTCT 60.744 61.111 0.00 0.00 36.60 2.52
907 927 2.513666 CATCCTTTGGCGCGGCTA 60.514 61.111 33.23 24.13 0.00 3.93
924 944 2.402305 GCTATTGGAGATGCTCTCACG 58.598 52.381 13.06 0.00 45.12 4.35
996 1024 0.040425 GTTCGTCACCAAAGCGCAAT 60.040 50.000 11.47 0.00 0.00 3.56
1518 1561 0.250424 TCGACCTGGTCTACGACACA 60.250 55.000 23.49 0.00 33.68 3.72
1832 1875 4.157120 GTACGACCCTGGGCGCAT 62.157 66.667 23.35 11.81 0.00 4.73
1833 1876 4.155733 TACGACCCTGGGCGCATG 62.156 66.667 23.35 0.59 0.00 4.06
1938 1981 3.350163 CCTGGGGTGAGGGCCAAT 61.350 66.667 6.18 0.00 0.00 3.16
1970 2013 1.459455 ATCGATGAGCGGTGGAGAGG 61.459 60.000 0.00 0.00 41.33 3.69
2036 2079 1.980765 TGTTCTTCCCTCTGCTGACAT 59.019 47.619 0.00 0.00 0.00 3.06
2138 2181 0.037882 CAGCACATGAGTGGAGACGT 60.038 55.000 0.00 0.00 45.98 4.34
2142 2185 1.000843 CACATGAGTGGAGACGTGGAA 59.999 52.381 0.00 0.00 42.13 3.53
2157 2200 2.928757 CGTGGAAAGATCTCAAGAGCAG 59.071 50.000 0.00 0.00 31.88 4.24
2245 2290 6.223852 CCTTAGCTGAGTTCTGTTAGTTTCA 58.776 40.000 4.63 0.00 0.00 2.69
2246 2291 6.146347 CCTTAGCTGAGTTCTGTTAGTTTCAC 59.854 42.308 4.63 0.00 0.00 3.18
2566 2625 4.946157 CCTTCTTGAGCTAATCAACATGGT 59.054 41.667 0.00 0.00 43.09 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.498291 ATATAGCGCGCCTGCTGGAG 62.498 60.000 30.33 11.77 46.70 3.86
16 17 2.099652 AATATAGCGCGCCTGCTGGA 62.100 55.000 30.33 6.69 46.70 3.86
17 18 1.230635 AAATATAGCGCGCCTGCTGG 61.231 55.000 30.33 5.03 46.70 4.85
18 19 0.164647 GAAATATAGCGCGCCTGCTG 59.835 55.000 30.33 0.00 46.70 4.41
20 21 0.798776 ATGAAATATAGCGCGCCTGC 59.201 50.000 30.33 11.01 37.91 4.85
21 22 3.542712 AAATGAAATATAGCGCGCCTG 57.457 42.857 30.33 0.00 0.00 4.85
22 23 4.568152 AAAAATGAAATATAGCGCGCCT 57.432 36.364 30.33 18.68 0.00 5.52
41 42 5.543714 TCACATAGTAGGCGTCAAGAAAAA 58.456 37.500 0.00 0.00 0.00 1.94
42 43 5.142061 TCACATAGTAGGCGTCAAGAAAA 57.858 39.130 0.00 0.00 0.00 2.29
43 44 4.794278 TCACATAGTAGGCGTCAAGAAA 57.206 40.909 0.00 0.00 0.00 2.52
44 45 4.219944 AGTTCACATAGTAGGCGTCAAGAA 59.780 41.667 0.00 0.00 0.00 2.52
45 46 3.762288 AGTTCACATAGTAGGCGTCAAGA 59.238 43.478 0.00 0.00 0.00 3.02
68 69 5.391523 CGGAACCAAATGTGTATCGAATTGT 60.392 40.000 0.00 0.00 0.00 2.71
70 71 4.938832 TCGGAACCAAATGTGTATCGAATT 59.061 37.500 0.00 0.00 0.00 2.17
95 96 8.683615 TGTGACGAACTATCTCACATTTATACT 58.316 33.333 0.00 0.00 38.07 2.12
99 100 7.648112 GCTATGTGACGAACTATCTCACATTTA 59.352 37.037 17.34 3.98 43.74 1.40
103 104 4.202020 GGCTATGTGACGAACTATCTCACA 60.202 45.833 5.39 5.39 42.46 3.58
104 105 4.036971 AGGCTATGTGACGAACTATCTCAC 59.963 45.833 0.00 0.00 35.79 3.51
231 232 1.142748 GAGGACATCACCGAGGCAG 59.857 63.158 0.00 0.00 34.73 4.85
257 258 0.798771 CTTGACGCCTACGCTCAGAC 60.799 60.000 0.00 0.00 45.53 3.51
497 498 2.050350 CCTCTAGCGGTCCCGTTGA 61.050 63.158 7.66 2.96 42.09 3.18
600 612 3.066190 CCGACACCTACTCCGCCA 61.066 66.667 0.00 0.00 0.00 5.69
697 709 2.573869 CGCTTTCTCTCCTCGCCA 59.426 61.111 0.00 0.00 0.00 5.69
718 730 2.411504 GCTCTCTCGTCGCTCCCTT 61.412 63.158 0.00 0.00 0.00 3.95
894 914 2.051804 CTCCAATAGCCGCGCCAAAG 62.052 60.000 0.00 0.00 0.00 2.77
924 944 2.747989 GACGAGGGGTGGAGAATTTTTC 59.252 50.000 0.00 0.00 0.00 2.29
996 1024 1.301087 CCCGAACGGCGCCATTATA 60.301 57.895 28.98 0.00 39.11 0.98
1518 1561 0.542232 AGTAGACCTTGCCACCGTCT 60.542 55.000 0.00 0.00 40.00 4.18
1679 1722 2.787994 AGATCTGCTTGAACCTTGTGG 58.212 47.619 0.00 0.00 39.83 4.17
1784 1827 1.544246 AGATGTCGTTGTCGGACATGA 59.456 47.619 12.26 10.29 37.66 3.07
1892 1935 3.365265 CTTGGACAACCGCTGGGC 61.365 66.667 0.00 0.00 39.42 5.36
1902 1945 0.615331 GGACATCCTCAGCTTGGACA 59.385 55.000 7.32 0.00 36.30 4.02
1923 1966 2.444696 CAATTGGCCCTCACCCCA 59.555 61.111 0.00 0.00 0.00 4.96
1938 1981 3.676049 GCTCATCGATCCAGTACACACAA 60.676 47.826 0.00 0.00 0.00 3.33
1970 2013 1.447140 TCGAACACCATAGGCACGC 60.447 57.895 0.00 0.00 0.00 5.34
2036 2079 1.555967 GCATAGGGGGCTTTGAACAA 58.444 50.000 0.00 0.00 0.00 2.83
2138 2181 2.303890 TGCTGCTCTTGAGATCTTTCCA 59.696 45.455 0.00 0.00 0.00 3.53
2142 2185 2.186243 TCCTGCTGCTCTTGAGATCTT 58.814 47.619 0.00 0.00 0.00 2.40
2157 2200 6.993786 AACTTAGATCTTTTAGCTTCCTGC 57.006 37.500 0.00 0.00 43.29 4.85
2217 2262 3.492102 ACAGAACTCAGCTAAGGCAAA 57.508 42.857 0.00 0.00 41.70 3.68
2245 2290 7.564793 TCTAAATAACCTGCACAGTCATATGT 58.435 34.615 1.90 0.00 0.00 2.29
2246 2291 8.501580 CATCTAAATAACCTGCACAGTCATATG 58.498 37.037 0.00 0.00 0.00 1.78
2399 2457 6.293626 CCTCTCAACACTCATTAACACCAAAG 60.294 42.308 0.00 0.00 0.00 2.77
2566 2625 0.755698 GGAGACGGGTGGCTCTGATA 60.756 60.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.