Multiple sequence alignment - TraesCS1B01G370700

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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 TraesCS1B01G370700 chr1B 100.000 2330 0 0 1 2330 600337912 600335583 0.000000e+00 4303.0
1 TraesCS1B01G370700 chr1B 94.175 1545 61 6 750 2288 6182273 6183794 0.000000e+00 2327.0
2 TraesCS1B01G370700 chr1B 97.561 41 1 0 2290 2330 95296118 95296158 1.160000e-08 71.3
3 TraesCS1B01G370700 chr2B 95.367 2180 77 16 1 2169 51008889 51011055 0.000000e+00 3445.0
4 TraesCS1B01G370700 chr2B 90.281 1173 46 29 1146 2289 731071249 731072382 0.000000e+00 1472.0
5 TraesCS1B01G370700 chr2B 92.035 791 46 15 1508 2288 750617912 750618695 0.000000e+00 1096.0
6 TraesCS1B01G370700 chr5B 93.313 2333 81 25 1 2288 209176257 209173955 0.000000e+00 3374.0
7 TraesCS1B01G370700 chr5B 91.173 2345 119 26 1 2288 265537613 265535300 0.000000e+00 3103.0
8 TraesCS1B01G370700 chr5B 83.652 575 46 24 958 1521 61820048 61820585 4.470000e-137 497.0
9 TraesCS1B01G370700 chr5B 86.364 110 2 7 1422 1521 62356802 62356696 8.800000e-20 108.0
10 TraesCS1B01G370700 chr5B 95.238 42 2 0 2289 2330 19701141 19701100 1.490000e-07 67.6
11 TraesCS1B01G370700 chr5B 92.857 42 3 0 2289 2330 682824604 682824645 6.950000e-06 62.1
12 TraesCS1B01G370700 chr3B 93.239 2337 80 21 1 2288 228481146 228478839 0.000000e+00 3369.0
13 TraesCS1B01G370700 chr3B 92.136 2327 92 26 1 2288 517874505 517872231 0.000000e+00 3199.0
14 TraesCS1B01G370700 chr3B 90.789 912 44 20 1392 2288 557722494 557723380 0.000000e+00 1182.0
15 TraesCS1B01G370700 chr3B 89.414 888 58 26 750 1630 177462377 177461519 0.000000e+00 1086.0
16 TraesCS1B01G370700 chr3B 89.247 93 5 2 1542 1630 761521878 761521787 6.810000e-21 111.0
17 TraesCS1B01G370700 chr3B 97.619 42 1 0 2289 2330 29581037 29581078 3.210000e-09 73.1
18 TraesCS1B01G370700 chr3B 95.238 42 2 0 2289 2330 191161002 191161043 1.490000e-07 67.6
19 TraesCS1B01G370700 chr3B 95.238 42 2 0 2289 2330 745596312 745596353 1.490000e-07 67.6
20 TraesCS1B01G370700 chr6A 91.770 2345 103 27 1 2288 11912181 11909870 0.000000e+00 3179.0
21 TraesCS1B01G370700 chr1A 91.258 2345 120 27 1 2288 54871239 54868923 0.000000e+00 3116.0
22 TraesCS1B01G370700 chr1A 84.914 696 45 24 958 1630 443864323 443864981 0.000000e+00 649.0
23 TraesCS1B01G370700 chr5A 91.045 2345 124 22 1 2287 596914402 596916718 0.000000e+00 3088.0
24 TraesCS1B01G370700 chr5A 94.286 175 10 0 4 178 178860589 178860415 3.820000e-68 268.0
25 TraesCS1B01G370700 chr6B 90.769 2329 146 38 1 2290 208208934 208211232 0.000000e+00 3046.0
26 TraesCS1B01G370700 chr4B 93.790 1546 72 14 750 2288 263059083 263057555 0.000000e+00 2302.0
27 TraesCS1B01G370700 chr4B 87.033 1365 102 37 958 2288 113846167 113847490 0.000000e+00 1471.0
28 TraesCS1B01G370700 chr4B 95.238 42 2 0 2289 2330 510858269 510858228 1.490000e-07 67.6
29 TraesCS1B01G370700 chr3A 91.872 1661 79 17 1 1630 153244941 153243306 0.000000e+00 2268.0
30 TraesCS1B01G370700 chr3A 89.810 844 39 18 809 1630 233452484 233451666 0.000000e+00 1038.0
31 TraesCS1B01G370700 chr3A 84.783 138 15 5 1506 1640 733878333 733878199 1.450000e-27 134.0
32 TraesCS1B01G370700 chr4A 93.032 1550 68 10 750 2288 660550133 660551653 0.000000e+00 2228.0
33 TraesCS1B01G370700 chr7B 92.820 1546 76 10 750 2289 749274417 749275933 0.000000e+00 2207.0
34 TraesCS1B01G370700 chr2A 92.637 421 30 1 958 1377 610790198 610790618 2.560000e-169 604.0
35 TraesCS1B01G370700 chr2A 86.331 139 12 5 1506 1640 605787789 605787924 6.710000e-31 145.0
36 TraesCS1B01G370700 chr5D 92.857 42 3 0 2289 2330 232844162 232844203 6.950000e-06 62.1
37 TraesCS1B01G370700 chr3D 92.857 42 3 0 2289 2330 380487641 380487600 6.950000e-06 62.1


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 TraesCS1B01G370700 chr1B 600335583 600337912 2329 True 4303 4303 100.000 1 2330 1 chr1B.!!$R1 2329
1 TraesCS1B01G370700 chr1B 6182273 6183794 1521 False 2327 2327 94.175 750 2288 1 chr1B.!!$F1 1538
2 TraesCS1B01G370700 chr2B 51008889 51011055 2166 False 3445 3445 95.367 1 2169 1 chr2B.!!$F1 2168
3 TraesCS1B01G370700 chr2B 731071249 731072382 1133 False 1472 1472 90.281 1146 2289 1 chr2B.!!$F2 1143
4 TraesCS1B01G370700 chr2B 750617912 750618695 783 False 1096 1096 92.035 1508 2288 1 chr2B.!!$F3 780
5 TraesCS1B01G370700 chr5B 209173955 209176257 2302 True 3374 3374 93.313 1 2288 1 chr5B.!!$R3 2287
6 TraesCS1B01G370700 chr5B 265535300 265537613 2313 True 3103 3103 91.173 1 2288 1 chr5B.!!$R4 2287
7 TraesCS1B01G370700 chr5B 61820048 61820585 537 False 497 497 83.652 958 1521 1 chr5B.!!$F1 563
8 TraesCS1B01G370700 chr3B 228478839 228481146 2307 True 3369 3369 93.239 1 2288 1 chr3B.!!$R2 2287
9 TraesCS1B01G370700 chr3B 517872231 517874505 2274 True 3199 3199 92.136 1 2288 1 chr3B.!!$R3 2287
10 TraesCS1B01G370700 chr3B 557722494 557723380 886 False 1182 1182 90.789 1392 2288 1 chr3B.!!$F3 896
11 TraesCS1B01G370700 chr3B 177461519 177462377 858 True 1086 1086 89.414 750 1630 1 chr3B.!!$R1 880
12 TraesCS1B01G370700 chr6A 11909870 11912181 2311 True 3179 3179 91.770 1 2288 1 chr6A.!!$R1 2287
13 TraesCS1B01G370700 chr1A 54868923 54871239 2316 True 3116 3116 91.258 1 2288 1 chr1A.!!$R1 2287
14 TraesCS1B01G370700 chr1A 443864323 443864981 658 False 649 649 84.914 958 1630 1 chr1A.!!$F1 672
15 TraesCS1B01G370700 chr5A 596914402 596916718 2316 False 3088 3088 91.045 1 2287 1 chr5A.!!$F1 2286
16 TraesCS1B01G370700 chr6B 208208934 208211232 2298 False 3046 3046 90.769 1 2290 1 chr6B.!!$F1 2289
17 TraesCS1B01G370700 chr4B 263057555 263059083 1528 True 2302 2302 93.790 750 2288 1 chr4B.!!$R1 1538
18 TraesCS1B01G370700 chr4B 113846167 113847490 1323 False 1471 1471 87.033 958 2288 1 chr4B.!!$F1 1330
19 TraesCS1B01G370700 chr3A 153243306 153244941 1635 True 2268 2268 91.872 1 1630 1 chr3A.!!$R1 1629
20 TraesCS1B01G370700 chr3A 233451666 233452484 818 True 1038 1038 89.810 809 1630 1 chr3A.!!$R2 821
21 TraesCS1B01G370700 chr4A 660550133 660551653 1520 False 2228 2228 93.032 750 2288 1 chr4A.!!$F1 1538
22 TraesCS1B01G370700 chr7B 749274417 749275933 1516 False 2207 2207 92.820 750 2289 1 chr7B.!!$F1 1539

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
506 508 1.685803 CCATGCTTTGTCCATGCCCTA 60.686 52.381 0.0 0.0 38.93 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2289 0.877071 AAGCTGACGTGGCAGAATTG 59.123 50.0 6.96 0.0 38.14 2.32 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
271 273 1.862201 CACAGCACACATTTTTGCCAG 59.138 47.619 0.00 0.00 39.75 4.85
285 287 5.906113 TTTTGCCAGTGTGAGAACTTTTA 57.094 34.783 0.00 0.00 0.00 1.52
352 354 8.746922 TGATTCTTGCTGAATAACATTTTGAC 57.253 30.769 5.70 0.00 44.70 3.18
385 387 3.820777 ACATTTCAGAAAGAAGAGCGC 57.179 42.857 0.00 0.00 37.57 5.92
420 422 4.702392 CTGTCTGCGATTGACTTGTTTAC 58.298 43.478 0.00 0.00 35.63 2.01
506 508 1.685803 CCATGCTTTGTCCATGCCCTA 60.686 52.381 0.00 0.00 38.93 3.53
713 715 3.983344 GTGTTCCATGCTTTGATGTTGTC 59.017 43.478 0.00 0.00 0.00 3.18
1028 1030 4.424566 GAAGGACGCGCCGGTACA 62.425 66.667 5.73 0.00 43.43 2.90
1054 1056 4.417437 AGGTGAAGAGCCAAAGTCTACTA 58.583 43.478 0.00 0.00 0.00 1.82
1114 1116 3.612479 GCAAAGCACATTCCTCACGAATT 60.612 43.478 0.00 0.00 39.28 2.17
1327 1335 4.276926 GCAAGAAGTGTCAAGAACAGGAAT 59.723 41.667 0.00 0.00 38.97 3.01
1488 1561 5.942396 GCTGAGAGCTGTTGCATTTTGCA 62.942 47.826 0.00 0.00 44.76 4.08
1540 1687 6.992123 TGTGAAGTTATGTGATCTTGTGAACT 59.008 34.615 0.00 0.00 0.00 3.01
1884 2144 7.124298 GGTTCCATTCCTAGAAAATAAAAGGCT 59.876 37.037 0.00 0.00 0.00 4.58
1996 2260 1.379527 CTAAAATGGACCGGGCTGAC 58.620 55.000 7.57 0.00 0.00 3.51
2006 2270 3.071167 GGACCGGGCTGACTCTATTTTAT 59.929 47.826 7.57 0.00 0.00 1.40
2176 2444 7.553334 AGAAAGGTCGCTATAGTCAATTAACA 58.447 34.615 0.84 0.00 0.00 2.41
2196 2464 1.286880 CGGCCAGCTTTTGACCTTG 59.713 57.895 2.24 0.00 0.00 3.61
2245 2513 7.710475 ACAAATTGAAAACAGTGACCATTTAGG 59.290 33.333 0.00 0.00 45.67 2.69
2290 2558 5.634020 AGTTGACGTATTTCTTGTAGTGCTC 59.366 40.000 0.00 0.00 0.00 4.26
2291 2559 4.491676 TGACGTATTTCTTGTAGTGCTCC 58.508 43.478 0.00 0.00 0.00 4.70
2292 2560 4.219944 TGACGTATTTCTTGTAGTGCTCCT 59.780 41.667 0.00 0.00 0.00 3.69
2293 2561 4.745649 ACGTATTTCTTGTAGTGCTCCTC 58.254 43.478 0.00 0.00 0.00 3.71
2294 2562 4.463186 ACGTATTTCTTGTAGTGCTCCTCT 59.537 41.667 0.00 0.00 0.00 3.69
2295 2563 5.047235 ACGTATTTCTTGTAGTGCTCCTCTT 60.047 40.000 0.00 0.00 0.00 2.85
2296 2564 5.517054 CGTATTTCTTGTAGTGCTCCTCTTC 59.483 44.000 0.00 0.00 0.00 2.87
2297 2565 5.753721 ATTTCTTGTAGTGCTCCTCTTCT 57.246 39.130 0.00 0.00 0.00 2.85
2298 2566 4.527509 TTCTTGTAGTGCTCCTCTTCTG 57.472 45.455 0.00 0.00 0.00 3.02
2299 2567 3.767711 TCTTGTAGTGCTCCTCTTCTGA 58.232 45.455 0.00 0.00 0.00 3.27
2300 2568 3.508012 TCTTGTAGTGCTCCTCTTCTGAC 59.492 47.826 0.00 0.00 0.00 3.51
2301 2569 3.162147 TGTAGTGCTCCTCTTCTGACT 57.838 47.619 0.00 0.00 0.00 3.41
2302 2570 3.085533 TGTAGTGCTCCTCTTCTGACTC 58.914 50.000 0.00 0.00 0.00 3.36
2303 2571 2.300956 AGTGCTCCTCTTCTGACTCA 57.699 50.000 0.00 0.00 0.00 3.41
2304 2572 2.170166 AGTGCTCCTCTTCTGACTCAG 58.830 52.381 0.00 0.00 0.00 3.35
2305 2573 1.204467 GTGCTCCTCTTCTGACTCAGG 59.796 57.143 6.20 0.00 31.51 3.86
2306 2574 1.203112 TGCTCCTCTTCTGACTCAGGT 60.203 52.381 6.20 0.00 31.51 4.00
2307 2575 2.041755 TGCTCCTCTTCTGACTCAGGTA 59.958 50.000 6.20 0.00 31.51 3.08
2308 2576 3.295973 GCTCCTCTTCTGACTCAGGTAT 58.704 50.000 6.20 0.00 31.51 2.73
2309 2577 3.068024 GCTCCTCTTCTGACTCAGGTATG 59.932 52.174 6.20 0.00 31.51 2.39
2310 2578 3.636300 CTCCTCTTCTGACTCAGGTATGG 59.364 52.174 6.20 4.87 31.51 2.74
2311 2579 2.697751 CCTCTTCTGACTCAGGTATGGG 59.302 54.545 6.20 0.15 31.51 4.00
2312 2580 3.628513 CCTCTTCTGACTCAGGTATGGGA 60.629 52.174 6.20 0.00 31.51 4.37
2313 2581 3.636300 CTCTTCTGACTCAGGTATGGGAG 59.364 52.174 6.20 0.00 37.18 4.30
2314 2582 2.461300 TCTGACTCAGGTATGGGAGG 57.539 55.000 6.20 0.00 35.45 4.30
2315 2583 1.930204 TCTGACTCAGGTATGGGAGGA 59.070 52.381 6.20 0.00 35.45 3.71
2316 2584 2.314852 TCTGACTCAGGTATGGGAGGAA 59.685 50.000 6.20 0.00 35.45 3.36
2317 2585 3.051803 TCTGACTCAGGTATGGGAGGAAT 60.052 47.826 6.20 0.00 35.45 3.01
2318 2586 4.170053 TCTGACTCAGGTATGGGAGGAATA 59.830 45.833 6.20 0.00 35.45 1.75
2319 2587 4.890988 TGACTCAGGTATGGGAGGAATAA 58.109 43.478 0.00 0.00 35.45 1.40
2320 2588 4.901849 TGACTCAGGTATGGGAGGAATAAG 59.098 45.833 0.00 0.00 35.45 1.73
2321 2589 5.148502 GACTCAGGTATGGGAGGAATAAGA 58.851 45.833 0.00 0.00 35.45 2.10
2322 2590 5.731924 ACTCAGGTATGGGAGGAATAAGAT 58.268 41.667 0.00 0.00 35.45 2.40
2323 2591 5.782845 ACTCAGGTATGGGAGGAATAAGATC 59.217 44.000 0.00 0.00 35.45 2.75
2324 2592 5.094387 TCAGGTATGGGAGGAATAAGATCC 58.906 45.833 0.00 0.00 39.96 3.36
2325 2593 4.081420 CAGGTATGGGAGGAATAAGATCCG 60.081 50.000 0.00 0.00 44.60 4.18
2326 2594 3.369576 GGTATGGGAGGAATAAGATCCGC 60.370 52.174 0.00 0.00 44.60 5.54
2327 2595 1.801242 TGGGAGGAATAAGATCCGCA 58.199 50.000 0.00 0.00 44.60 5.69
2328 2596 1.416401 TGGGAGGAATAAGATCCGCAC 59.584 52.381 0.00 0.00 44.60 5.34
2329 2597 1.416401 GGGAGGAATAAGATCCGCACA 59.584 52.381 0.00 0.00 41.80 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 5.749588 TGTACACGACTTTTTCTCGATTCAA 59.250 36.000 0.00 0.00 35.08 2.69
271 273 7.832769 AGGTCTCTAGATAAAAGTTCTCACAC 58.167 38.462 0.00 0.00 0.00 3.82
285 287 7.079048 AGGATCAAATGGTAAGGTCTCTAGAT 58.921 38.462 0.00 0.00 0.00 1.98
385 387 0.036577 CAGACAGCTCCTCACCCTTG 60.037 60.000 0.00 0.00 0.00 3.61
474 476 4.718961 ACAAAGCATGGAGTGACTTACTT 58.281 39.130 0.00 0.00 40.53 2.24
506 508 3.575256 TCAAAGCTGGCTGTGAATCAAAT 59.425 39.130 12.47 0.00 37.36 2.32
658 660 5.065090 TGAATCAAACAGCATGGAACTATCG 59.935 40.000 0.00 0.00 43.62 2.92
1028 1030 4.281657 AGACTTTGGCTCTTCACCTTTTT 58.718 39.130 0.00 0.00 0.00 1.94
1054 1056 6.795399 ACAACACTTCTTCGACAATTTGAAT 58.205 32.000 2.79 0.00 0.00 2.57
1114 1116 1.839994 CCTAGATGACTGGAGCCCAAA 59.160 52.381 0.00 0.00 30.80 3.28
1313 1321 6.314152 GGCTAACTTCTATTCCTGTTCTTGAC 59.686 42.308 0.00 0.00 0.00 3.18
1327 1335 4.487714 CCATCAAGTGGGCTAACTTCTA 57.512 45.455 3.59 0.00 44.79 2.10
1488 1561 2.895404 ACAGGTGCTCTGAATGCAAAAT 59.105 40.909 13.18 0.00 46.18 1.82
1489 1562 2.034939 CACAGGTGCTCTGAATGCAAAA 59.965 45.455 13.18 0.00 46.18 2.44
1494 1577 1.808945 GGTTCACAGGTGCTCTGAATG 59.191 52.381 13.18 4.03 46.18 2.67
1496 1579 1.131638 AGGTTCACAGGTGCTCTGAA 58.868 50.000 13.18 0.57 46.18 3.02
1540 1687 7.717436 TCCACATAACTTCACATAACTTCACAA 59.283 33.333 0.00 0.00 0.00 3.33
1595 1742 6.149973 CACAAGTGATCCACATAACTTCACAT 59.850 38.462 0.00 0.00 39.27 3.21
1860 2120 9.762381 TTAGCCTTTTATTTTCTAGGAATGGAA 57.238 29.630 0.00 0.00 0.00 3.53
1930 2192 3.352554 TTCGGCCCGTTTAAGTTTTTC 57.647 42.857 1.63 0.00 0.00 2.29
2025 2289 0.877071 AAGCTGACGTGGCAGAATTG 59.123 50.000 6.96 0.00 38.14 2.32
2176 2444 3.443588 GGTCAAAAGCTGGCCGTT 58.556 55.556 0.00 0.00 40.90 4.44
2273 2541 6.533367 CAGAAGAGGAGCACTACAAGAAATAC 59.467 42.308 0.00 0.00 0.00 1.89
2290 2558 2.697751 CCCATACCTGAGTCAGAAGAGG 59.302 54.545 22.09 16.12 32.44 3.69
2291 2559 3.636300 CTCCCATACCTGAGTCAGAAGAG 59.364 52.174 22.09 12.60 32.44 2.85
2292 2560 3.628513 CCTCCCATACCTGAGTCAGAAGA 60.629 52.174 22.09 6.40 32.44 2.87
2293 2561 2.697751 CCTCCCATACCTGAGTCAGAAG 59.302 54.545 22.09 8.25 32.44 2.85
2294 2562 2.314852 TCCTCCCATACCTGAGTCAGAA 59.685 50.000 22.09 9.53 32.44 3.02
2295 2563 1.930204 TCCTCCCATACCTGAGTCAGA 59.070 52.381 22.09 2.54 32.44 3.27
2296 2564 2.461300 TCCTCCCATACCTGAGTCAG 57.539 55.000 13.56 13.56 0.00 3.51
2297 2565 2.940514 TTCCTCCCATACCTGAGTCA 57.059 50.000 0.00 0.00 0.00 3.41
2298 2566 5.148502 TCTTATTCCTCCCATACCTGAGTC 58.851 45.833 0.00 0.00 0.00 3.36
2299 2567 5.157770 TCTTATTCCTCCCATACCTGAGT 57.842 43.478 0.00 0.00 0.00 3.41
2300 2568 5.188751 GGATCTTATTCCTCCCATACCTGAG 59.811 48.000 0.00 0.00 32.68 3.35
2301 2569 5.094387 GGATCTTATTCCTCCCATACCTGA 58.906 45.833 0.00 0.00 32.68 3.86
2302 2570 4.081420 CGGATCTTATTCCTCCCATACCTG 60.081 50.000 0.00 0.00 33.30 4.00
2303 2571 4.097418 CGGATCTTATTCCTCCCATACCT 58.903 47.826 0.00 0.00 33.30 3.08
2304 2572 3.369576 GCGGATCTTATTCCTCCCATACC 60.370 52.174 0.00 0.00 33.30 2.73
2305 2573 3.260884 TGCGGATCTTATTCCTCCCATAC 59.739 47.826 0.00 0.00 33.30 2.39
2306 2574 3.260884 GTGCGGATCTTATTCCTCCCATA 59.739 47.826 0.00 0.00 33.30 2.74
2307 2575 2.039084 GTGCGGATCTTATTCCTCCCAT 59.961 50.000 0.00 0.00 33.30 4.00
2308 2576 1.416401 GTGCGGATCTTATTCCTCCCA 59.584 52.381 0.00 0.00 33.30 4.37
2309 2577 1.416401 TGTGCGGATCTTATTCCTCCC 59.584 52.381 0.00 0.00 33.30 4.30
2310 2578 2.910688 TGTGCGGATCTTATTCCTCC 57.089 50.000 0.00 0.00 33.30 4.30


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

AutoCloner maintained by Alex Coulton.