Multiple sequence alignment - TraesCS5D01G127700

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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 TraesCS5D01G127700 chr5D 100.000 2903 0 0 1 2903 198458872 198461774 0.000000e+00 5361.0
1 TraesCS5D01G127700 chr5D 99.421 518 3 0 2386 2903 198392426 198392943 0.000000e+00 941.0
2 TraesCS5D01G127700 chr5D 94.357 443 14 5 1 434 198391981 198392421 0.000000e+00 669.0
3 TraesCS5D01G127700 chr5D 83.178 107 12 6 49 152 325926271 325926374 3.080000e-15 93.5
4 TraesCS5D01G127700 chr5A 95.623 1965 69 14 613 2568 398676737 398674781 0.000000e+00 3136.0
5 TraesCS5D01G127700 chr5A 96.296 1323 46 3 1168 2490 219433792 219435111 0.000000e+00 2169.0
6 TraesCS5D01G127700 chr5A 86.129 930 75 23 2016 2903 492835915 492834998 0.000000e+00 953.0
7 TraesCS5D01G127700 chr5A 86.866 868 75 19 1070 1927 492836834 492835996 0.000000e+00 935.0
8 TraesCS5D01G127700 chr5A 92.042 377 11 2 2545 2903 219435111 219435486 2.000000e-141 512.0
9 TraesCS5D01G127700 chr5A 82.500 560 59 17 2372 2896 46484057 46484612 3.410000e-124 455.0
10 TraesCS5D01G127700 chr5A 91.916 334 9 1 2588 2903 398674792 398674459 4.410000e-123 451.0
11 TraesCS5D01G127700 chr5A 77.858 551 74 21 290 824 705536256 705535738 6.080000e-77 298.0
12 TraesCS5D01G127700 chr5A 88.235 187 21 1 670 856 18724039 18723854 3.770000e-54 222.0
13 TraesCS5D01G127700 chr5A 100.000 32 0 0 1483 1514 492836529 492836498 3.120000e-05 60.2
14 TraesCS5D01G127700 chr2A 96.026 1661 45 4 1262 2903 191920789 191922447 0.000000e+00 2682.0
15 TraesCS5D01G127700 chr2A 93.729 303 19 0 538 840 409143295 409143597 3.410000e-124 455.0
16 TraesCS5D01G127700 chr2A 93.617 188 12 0 880 1067 409143595 409143782 6.120000e-72 281.0
17 TraesCS5D01G127700 chr2A 85.714 105 10 4 54 155 730021618 730021516 3.960000e-19 106.0
18 TraesCS5D01G127700 chr3A 92.873 1838 97 12 240 2063 89361006 89362823 0.000000e+00 2638.0
19 TraesCS5D01G127700 chr3A 93.774 530 33 0 538 1067 575765575 575766104 0.000000e+00 797.0
20 TraesCS5D01G127700 chr3A 79.941 683 79 28 2256 2903 610779783 610779124 1.590000e-122 449.0
21 TraesCS5D01G127700 chr3A 86.667 90 9 3 231 319 235835095 235835182 2.380000e-16 97.1
22 TraesCS5D01G127700 chr4A 96.221 1323 47 3 1168 2490 60353801 60352482 0.000000e+00 2163.0
23 TraesCS5D01G127700 chr4A 91.512 377 13 2 2545 2903 60352482 60352107 4.320000e-138 501.0
24 TraesCS5D01G127700 chr4A 82.321 560 60 17 2372 2896 627001968 627002523 1.590000e-122 449.0
25 TraesCS5D01G127700 chr4A 87.500 144 14 4 1186 1327 174993274 174993415 2.310000e-36 163.0
26 TraesCS5D01G127700 chr4A 81.818 121 16 5 59 175 271537272 271537154 2.380000e-16 97.1
27 TraesCS5D01G127700 chr4A 87.654 81 9 1 77 156 309258996 309258916 3.080000e-15 93.5
28 TraesCS5D01G127700 chr7B 94.802 1212 59 3 1041 2251 83104661 83103453 0.000000e+00 1886.0
29 TraesCS5D01G127700 chr7B 93.208 795 52 2 253 1045 83107711 83106917 0.000000e+00 1168.0
30 TraesCS5D01G127700 chr7B 93.012 415 24 2 2246 2660 83060558 83060149 4.140000e-168 601.0
31 TraesCS5D01G127700 chr7B 90.566 265 7 6 2657 2903 83049298 83049034 4.640000e-88 335.0
32 TraesCS5D01G127700 chr3D 86.906 1474 135 16 1070 2496 418327420 418325958 0.000000e+00 1600.0
33 TraesCS5D01G127700 chr3D 89.840 187 19 0 670 856 113998202 113998016 1.040000e-59 241.0
34 TraesCS5D01G127700 chr1B 94.883 899 42 4 238 1135 684140634 684141529 0.000000e+00 1402.0
35 TraesCS5D01G127700 chr1B 94.764 783 31 5 1709 2490 684141841 684142614 0.000000e+00 1210.0
36 TraesCS5D01G127700 chr1B 97.115 312 8 1 1287 1598 684141526 684141836 2.560000e-145 525.0
37 TraesCS5D01G127700 chr1B 92.042 377 11 5 2545 2903 684142614 684142989 2.000000e-141 512.0
38 TraesCS5D01G127700 chr7A 77.979 663 87 26 2256 2891 114280742 114281372 7.650000e-96 361.0
39 TraesCS5D01G127700 chr7A 89.051 137 15 0 932 1068 919346 919210 1.380000e-38 171.0
40 TraesCS5D01G127700 chr6A 91.262 206 18 0 538 743 523550159 523550364 6.120000e-72 281.0
41 TraesCS5D01G127700 chr6A 86.598 97 13 0 240 336 317811344 317811248 1.100000e-19 108.0
42 TraesCS5D01G127700 chr6A 86.000 100 12 2 238 336 287307362 287307264 3.960000e-19 106.0
43 TraesCS5D01G127700 chr6A 83.333 108 11 6 52 156 456679898 456680001 3.080000e-15 93.5
44 TraesCS5D01G127700 chr4D 87.413 143 16 2 1186 1327 304302194 304302053 2.310000e-36 163.0
45 TraesCS5D01G127700 chr5B 92.553 94 7 0 238 331 573575056 573575149 5.050000e-28 135.0
46 TraesCS5D01G127700 chr5B 82.569 109 12 5 228 333 182432129 182432025 3.980000e-14 89.8
47 TraesCS5D01G127700 chr5B 84.946 93 8 5 50 139 620325280 620325369 3.980000e-14 89.8
48 TraesCS5D01G127700 chr7D 97.222 72 2 0 166 237 264962151 264962080 3.930000e-24 122.0
49 TraesCS5D01G127700 chr6B 91.250 80 6 1 77 155 350661336 350661257 1.100000e-19 108.0
50 TraesCS5D01G127700 chr3B 84.821 112 4 3 499 606 188243462 188243360 1.840000e-17 100.0
51 TraesCS5D01G127700 chr1A 87.654 81 5 4 57 135 449792593 449792516 3.980000e-14 89.8


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 TraesCS5D01G127700 chr5D 198458872 198461774 2902 False 5361.00 5361 100.000000 1 2903 1 chr5D.!!$F1 2902
1 TraesCS5D01G127700 chr5D 198391981 198392943 962 False 805.00 941 96.889000 1 2903 2 chr5D.!!$F3 2902
2 TraesCS5D01G127700 chr5A 398674459 398676737 2278 True 1793.50 3136 93.769500 613 2903 2 chr5A.!!$R3 2290
3 TraesCS5D01G127700 chr5A 219433792 219435486 1694 False 1340.50 2169 94.169000 1168 2903 2 chr5A.!!$F2 1735
4 TraesCS5D01G127700 chr5A 492834998 492836834 1836 True 649.40 953 90.998333 1070 2903 3 chr5A.!!$R4 1833
5 TraesCS5D01G127700 chr5A 46484057 46484612 555 False 455.00 455 82.500000 2372 2896 1 chr5A.!!$F1 524
6 TraesCS5D01G127700 chr5A 705535738 705536256 518 True 298.00 298 77.858000 290 824 1 chr5A.!!$R2 534
7 TraesCS5D01G127700 chr2A 191920789 191922447 1658 False 2682.00 2682 96.026000 1262 2903 1 chr2A.!!$F1 1641
8 TraesCS5D01G127700 chr3A 89361006 89362823 1817 False 2638.00 2638 92.873000 240 2063 1 chr3A.!!$F1 1823
9 TraesCS5D01G127700 chr3A 575765575 575766104 529 False 797.00 797 93.774000 538 1067 1 chr3A.!!$F3 529
10 TraesCS5D01G127700 chr3A 610779124 610779783 659 True 449.00 449 79.941000 2256 2903 1 chr3A.!!$R1 647
11 TraesCS5D01G127700 chr4A 60352107 60353801 1694 True 1332.00 2163 93.866500 1168 2903 2 chr4A.!!$R3 1735
12 TraesCS5D01G127700 chr4A 627001968 627002523 555 False 449.00 449 82.321000 2372 2896 1 chr4A.!!$F2 524
13 TraesCS5D01G127700 chr7B 83103453 83107711 4258 True 1527.00 1886 94.005000 253 2251 2 chr7B.!!$R3 1998
14 TraesCS5D01G127700 chr3D 418325958 418327420 1462 True 1600.00 1600 86.906000 1070 2496 1 chr3D.!!$R2 1426
15 TraesCS5D01G127700 chr1B 684140634 684142989 2355 False 912.25 1402 94.701000 238 2903 4 chr1B.!!$F1 2665
16 TraesCS5D01G127700 chr7A 114280742 114281372 630 False 361.00 361 77.979000 2256 2891 1 chr7A.!!$F1 635

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
279 289 0.109226 GGTTGAGTCTCTCGGGTTCG 60.109 60.0 0.65 0.0 32.35 3.95 F
1068 3374 0.102844 GCAAGAAGGCAAGCAACACA 59.897 50.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 4090 0.906066 GGAGGAGGACCAAAGTCTCC 59.094 60.000 0.0 0.0 43.05 3.71 R
2190 4567 1.139058 AGTCGCTGGTTCTTGTCTTGT 59.861 47.619 0.0 0.0 0.00 3.16 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
17 18 3.741325 AGGGAAGTTGGGATCGGG 58.259 61.111 0.00 0.00 0.00 5.14
115 116 6.715464 CACGGTGTGATCCAAATAACTATTC 58.285 40.000 0.00 0.00 35.23 1.75
143 144 6.867519 TCCAGGATTAGAATAGTGTTGTCA 57.132 37.500 0.00 0.00 0.00 3.58
144 145 7.437713 TCCAGGATTAGAATAGTGTTGTCAT 57.562 36.000 0.00 0.00 0.00 3.06
209 219 2.035155 TCTCGAGCCCGTTCCTGA 59.965 61.111 7.81 0.00 37.05 3.86
236 246 6.428385 CCGAACCGGTATAGGTATTACTAG 57.572 45.833 8.00 0.00 45.21 2.57
279 289 0.109226 GGTTGAGTCTCTCGGGTTCG 60.109 60.000 0.65 0.00 32.35 3.95
758 804 3.064324 GCGGGTGCCAGCAAGATT 61.064 61.111 8.42 0.00 33.98 2.40
930 976 3.181520 GCAGTACATTGTTCTTGCGGTAG 60.182 47.826 0.00 0.00 0.00 3.18
1068 3374 0.102844 GCAAGAAGGCAAGCAACACA 59.897 50.000 0.00 0.00 0.00 3.72
1183 3489 4.408821 GGGTGGCATCGCTGGTCA 62.409 66.667 0.00 0.00 0.00 4.02
1235 3541 5.111293 CCATTGAACAACACTCTTGCTTTT 58.889 37.500 0.00 0.00 0.00 2.27
1236 3542 5.581874 CCATTGAACAACACTCTTGCTTTTT 59.418 36.000 0.00 0.00 0.00 1.94
1387 3695 7.042797 TCTCTGCAAAATAAGTCTTGCTTTT 57.957 32.000 8.13 0.00 46.49 2.27
1779 4090 9.950680 ATTTTAATAGACCAGCAATATTGTTCG 57.049 29.630 16.61 6.35 0.00 3.95
2071 4441 1.412343 AGGTTTGAAAATTGCGCAGGT 59.588 42.857 11.31 0.00 0.00 4.00
2190 4567 5.473846 CAGTAATAGCATCGACTAGGAGGAA 59.526 44.000 0.00 0.00 0.00 3.36
2202 4579 5.216614 ACTAGGAGGAACAAGACAAGAAC 57.783 43.478 0.00 0.00 0.00 3.01
2210 4587 1.139058 ACAAGACAAGAACCAGCGACT 59.861 47.619 0.00 0.00 0.00 4.18
2367 4780 6.913673 GCAGTTTAGAAGAATCGGTAGTAGAG 59.086 42.308 0.00 0.00 0.00 2.43
2808 5315 3.454587 TTGCGCCTCTGGAACACGT 62.455 57.895 4.18 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.677228 CATGACCACCACCTCCCC 59.323 66.667 0.00 0.00 0.00 4.81
115 116 9.838339 ACAACACTATTCTAATCCTGGAATTAG 57.162 33.333 0.00 9.55 39.54 1.73
120 121 6.867519 TGACAACACTATTCTAATCCTGGA 57.132 37.500 0.00 0.00 0.00 3.86
236 246 5.522824 CCGTGCTTTACTATTAGGGAAAGAC 59.477 44.000 17.80 13.23 31.83 3.01
536 568 3.319198 GGAGGGGAGCCGTGAACA 61.319 66.667 0.00 0.00 0.00 3.18
758 804 4.088351 TCTCCATCCCCGGCCTCA 62.088 66.667 0.00 0.00 0.00 3.86
930 976 0.994263 GCAAATCAAATGCGTCAGCC 59.006 50.000 0.00 0.00 44.33 4.85
1136 3442 1.754803 TGTCCTGGTTCTCGCGATAAT 59.245 47.619 10.36 0.00 0.00 1.28
1166 3472 4.408821 TGACCAGCGATGCCACCC 62.409 66.667 0.00 0.00 0.00 4.61
1183 3489 5.679382 GCCAAGTTTAAACCCGTTTTACACT 60.679 40.000 14.72 1.60 40.80 3.55
1235 3541 9.581289 TGATTGATAAAAGGTCCTAACAGAAAA 57.419 29.630 0.00 0.00 0.00 2.29
1236 3542 9.753674 ATGATTGATAAAAGGTCCTAACAGAAA 57.246 29.630 0.00 0.00 0.00 2.52
1387 3695 7.339212 TGAAAAGAAACAGTTCAATCTTCTGGA 59.661 33.333 0.15 0.00 36.09 3.86
1577 3887 5.185454 CCTGCAGACTTGTCCATATACAAA 58.815 41.667 17.39 0.00 38.81 2.83
1673 3983 3.119814 CGGGATACATACCAGTCATCTCG 60.120 52.174 0.00 0.00 33.74 4.04
1779 4090 0.906066 GGAGGAGGACCAAAGTCTCC 59.094 60.000 0.00 0.00 43.05 3.71
2190 4567 1.139058 AGTCGCTGGTTCTTGTCTTGT 59.861 47.619 0.00 0.00 0.00 3.16
2210 4587 2.042686 CTTAGCCAGCAATGGTAGCA 57.957 50.000 5.59 0.00 0.00 3.49
2317 4730 1.896660 CCACAACCCGTCCCAAGTG 60.897 63.158 0.00 0.00 0.00 3.16
2367 4780 4.165779 CCATTGGCTTTAACATTCACGTC 58.834 43.478 0.00 0.00 0.00 4.34
2808 5315 2.010145 CTGCTCTTTGTTAGCGGCTA 57.990 50.000 5.42 5.42 43.11 3.93


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

AutoCloner maintained by Alex Coulton.