Multiple sequence alignment - TraesCS1D01G304300

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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 TraesCS1D01G304300 chr1D 100.000 2978 0 0 1 2978 402007499 402004522 0.000000e+00 5500.0
1 TraesCS1D01G304300 chr1D 99.027 2979 28 1 1 2978 402109062 402106084 0.000000e+00 5339.0
2 TraesCS1D01G304300 chr1D 98.770 2358 24 4 48 2400 402052499 402050142 0.000000e+00 4189.0
3 TraesCS1D01G304300 chr1D 99.464 2240 10 2 1 2238 401922283 401920044 0.000000e+00 4069.0
4 TraesCS1D01G304300 chr1D 94.055 1413 70 5 830 2241 401775169 401773770 0.000000e+00 2132.0
5 TraesCS1D01G304300 chr1D 88.214 280 13 9 899 1158 401700044 401699765 1.720000e-82 316.0
6 TraesCS1D01G304300 chr1D 79.851 402 56 18 2582 2972 452115465 452115852 1.360000e-68 270.0
7 TraesCS1D01G304300 chr1D 95.918 98 4 0 2192 2289 401920052 401919955 3.070000e-35 159.0
8 TraesCS1D01G304300 chr1B 90.575 2175 135 31 14 2154 539590535 539588397 0.000000e+00 2817.0
9 TraesCS1D01G304300 chr1B 80.549 401 65 8 2585 2978 185545951 185545557 2.240000e-76 296.0
10 TraesCS1D01G304300 chr1B 91.667 84 6 1 2495 2578 264766952 264766870 6.750000e-22 115.0
11 TraesCS1D01G304300 chr1A 92.879 1924 95 12 605 2521 497585842 497583954 0.000000e+00 2756.0
12 TraesCS1D01G304300 chr1A 93.033 1421 64 13 830 2241 497580598 497579204 0.000000e+00 2043.0
13 TraesCS1D01G304300 chr1A 89.091 275 14 6 899 1158 497537649 497537376 7.960000e-86 327.0
14 TraesCS1D01G304300 chr1A 89.103 156 8 5 356 503 497580965 497580811 5.070000e-43 185.0
15 TraesCS1D01G304300 chr7B 87.611 1122 124 11 997 2115 535506115 535507224 0.000000e+00 1288.0
16 TraesCS1D01G304300 chr7B 82.266 406 55 14 2582 2978 601930269 601930666 4.760000e-88 335.0
17 TraesCS1D01G304300 chr7B 80.712 337 58 5 2243 2578 526872456 526872126 3.810000e-64 255.0
18 TraesCS1D01G304300 chr7B 83.895 267 42 1 12 278 517606963 517607228 1.370000e-63 254.0
19 TraesCS1D01G304300 chr7B 79.525 337 61 6 2243 2578 526880415 526880086 1.780000e-57 233.0
20 TraesCS1D01G304300 chr7D 87.055 1151 124 19 983 2127 506882674 506883805 0.000000e+00 1277.0
21 TraesCS1D01G304300 chr7D 86.567 268 31 4 12 277 94741828 94741564 1.040000e-74 291.0
22 TraesCS1D01G304300 chr4D 83.333 408 53 11 2582 2978 301503134 301502731 2.180000e-96 363.0
23 TraesCS1D01G304300 chr4D 83.140 344 48 8 2637 2973 333756504 333756164 3.730000e-79 305.0
24 TraesCS1D01G304300 chr4D 79.899 398 59 17 2582 2972 101062355 101062738 3.780000e-69 272.0
25 TraesCS1D01G304300 chr4D 81.915 94 14 1 269 359 28834860 28834767 3.180000e-10 76.8
26 TraesCS1D01G304300 chr5A 83.085 402 54 11 2582 2978 595157800 595158192 1.310000e-93 353.0
27 TraesCS1D01G304300 chr5A 95.652 46 2 0 552 597 47964341 47964386 1.140000e-09 75.0
28 TraesCS1D01G304300 chr5A 90.196 51 4 1 554 603 693652410 693652360 6.890000e-07 65.8
29 TraesCS1D01G304300 chr7A 87.313 268 34 0 12 279 680339068 680338801 1.040000e-79 307.0
30 TraesCS1D01G304300 chr6A 80.788 406 64 10 2582 2978 2840768 2840368 3.730000e-79 305.0
31 TraesCS1D01G304300 chr2A 83.019 265 43 2 12 276 775275980 775275718 3.840000e-59 239.0
32 TraesCS1D01G304300 chr3B 80.635 315 52 8 23 335 390456168 390456475 4.960000e-58 235.0
33 TraesCS1D01G304300 chr3B 85.161 155 13 6 2430 2578 19097585 19097435 1.850000e-32 150.0
34 TraesCS1D01G304300 chr3D 79.180 317 61 5 14 329 336543371 336543683 6.470000e-52 215.0
35 TraesCS1D01G304300 chr3D 83.486 218 33 3 2363 2578 481520568 481520352 1.810000e-47 200.0
36 TraesCS1D01G304300 chr3D 87.671 73 6 3 293 362 509686276 509686348 6.840000e-12 82.4
37 TraesCS1D01G304300 chr3A 90.588 85 7 1 2495 2578 700941069 700941153 8.730000e-21 111.0
38 TraesCS1D01G304300 chr3A 92.157 51 3 1 555 604 681348477 681348527 1.480000e-08 71.3
39 TraesCS1D01G304300 chr6B 86.905 84 11 0 2495 2578 693984486 693984403 8.790000e-16 95.3
40 TraesCS1D01G304300 chr6B 86.905 84 10 1 2495 2578 693955728 693955646 3.160000e-15 93.5
41 TraesCS1D01G304300 chr2B 81.250 96 15 2 269 361 508409675 508409580 1.140000e-09 75.0
42 TraesCS1D01G304300 chr2B 88.889 54 4 2 555 606 67548881 67548934 6.890000e-07 65.8
43 TraesCS1D01G304300 chr5D 95.556 45 2 0 554 598 30554223 30554179 4.120000e-09 73.1
44 TraesCS1D01G304300 chr4B 90.909 55 2 2 305 356 527553878 527553824 1.480000e-08 71.3


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 TraesCS1D01G304300 chr1D 402004522 402007499 2977 True 5500.000000 5500 100.000000 1 2978 1 chr1D.!!$R3 2977
1 TraesCS1D01G304300 chr1D 402106084 402109062 2978 True 5339.000000 5339 99.027000 1 2978 1 chr1D.!!$R5 2977
2 TraesCS1D01G304300 chr1D 402050142 402052499 2357 True 4189.000000 4189 98.770000 48 2400 1 chr1D.!!$R4 2352
3 TraesCS1D01G304300 chr1D 401773770 401775169 1399 True 2132.000000 2132 94.055000 830 2241 1 chr1D.!!$R2 1411
4 TraesCS1D01G304300 chr1D 401919955 401922283 2328 True 2114.000000 4069 97.691000 1 2289 2 chr1D.!!$R6 2288
5 TraesCS1D01G304300 chr1B 539588397 539590535 2138 True 2817.000000 2817 90.575000 14 2154 1 chr1B.!!$R3 2140
6 TraesCS1D01G304300 chr1A 497579204 497585842 6638 True 1661.333333 2756 91.671667 356 2521 3 chr1A.!!$R2 2165
7 TraesCS1D01G304300 chr7B 535506115 535507224 1109 False 1288.000000 1288 87.611000 997 2115 1 chr7B.!!$F2 1118
8 TraesCS1D01G304300 chr7D 506882674 506883805 1131 False 1277.000000 1277 87.055000 983 2127 1 chr7D.!!$F1 1144

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
526 540 2.493675 ACTCATCACGCACACATACTCT 59.506 45.455 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2781 3941 9.158233 TGGTACTCTTTTTATTATGCACTGTAC 57.842 33.333 0.0 0.0 0.0 2.9 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
165 168 3.745799 TGCCCGTTTCAACTAGATTTCA 58.254 40.909 0.00 0.00 0.00 2.69
289 292 3.050275 GTGCCCGACCTGTGCTTC 61.050 66.667 0.00 0.00 0.00 3.86
526 540 2.493675 ACTCATCACGCACACATACTCT 59.506 45.455 0.00 0.00 0.00 3.24
610 635 3.977326 GGGGAGGGATAAATGAAGAGAGT 59.023 47.826 0.00 0.00 0.00 3.24
775 807 8.204160 CACACATCCATCTAACTAACTATTGGA 58.796 37.037 0.00 0.00 36.32 3.53
2579 2981 1.965643 ACCTTCAAACACATGCATGCT 59.034 42.857 26.53 11.04 0.00 3.79
2580 2982 3.156293 ACCTTCAAACACATGCATGCTA 58.844 40.909 26.53 5.73 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 168 3.568538 ACGTAAATCAACGAACTAGCGT 58.431 40.909 3.10 0.0 45.68 5.07
289 292 4.025401 GCGTTTGGCCACGTCAGG 62.025 66.667 3.88 0.0 42.43 3.86
526 540 4.962362 TGTATGATCTTCTGGTTGCTCCTA 59.038 41.667 0.00 0.0 37.07 2.94
784 817 7.228507 AGCAACTTGACATTGACATTGTTAGTA 59.771 33.333 14.37 0.0 0.00 1.82
2781 3941 9.158233 TGGTACTCTTTTTATTATGCACTGTAC 57.842 33.333 0.00 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.