Multiple sequence alignment - TraesCS5D01G155300

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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 TraesCS5D01G155300 chr5D 100.000 4732 0 0 1 4732 243821524 243816793 0.000000e+00 8739.0
1 TraesCS5D01G155300 chr5D 96.167 287 11 0 2 288 542479842 542480128 1.990000e-128 470.0
2 TraesCS5D01G155300 chr5D 95.848 289 12 0 3 291 450700377 450700665 7.170000e-128 468.0
3 TraesCS5D01G155300 chr5D 94.881 293 15 0 1 293 441797600 441797308 4.320000e-125 459.0
4 TraesCS5D01G155300 chr5D 89.655 174 17 1 3250 3422 150835564 150835737 2.220000e-53 220.0
5 TraesCS5D01G155300 chr5D 83.000 100 14 2 1640 1736 243829164 243829065 2.350000e-13 87.9
6 TraesCS5D01G155300 chr5B 95.857 3862 109 23 1 3838 276912476 276908642 0.000000e+00 6198.0
7 TraesCS5D01G155300 chr5B 95.862 290 12 0 1 290 425872147 425871858 1.990000e-128 470.0
8 TraesCS5D01G155300 chr5B 83.178 107 14 3 1586 1692 276949571 276949469 1.400000e-15 95.3
9 TraesCS5D01G155300 chr5A 96.275 3570 95 25 290 3838 327922861 327919309 0.000000e+00 5821.0
10 TraesCS5D01G155300 chr5A 82.243 107 15 3 1586 1692 328003795 328003693 6.520000e-14 89.8
11 TraesCS5D01G155300 chr2D 95.022 904 34 6 3836 4732 57275852 57274953 0.000000e+00 1410.0
12 TraesCS5D01G155300 chr2D 94.549 899 38 9 3837 4732 61228975 61228085 0.000000e+00 1378.0
13 TraesCS5D01G155300 chr1D 95.006 901 32 9 3838 4732 56171134 56172027 0.000000e+00 1402.0
14 TraesCS5D01G155300 chrUn 94.772 899 40 6 3837 4732 115838517 115837623 0.000000e+00 1393.0
15 TraesCS5D01G155300 chrUn 93.348 902 41 8 3839 4732 10729901 10729011 0.000000e+00 1315.0
16 TraesCS5D01G155300 chrUn 90.588 170 14 2 3250 3418 81477803 81477635 1.710000e-54 224.0
17 TraesCS5D01G155300 chr7D 94.784 901 30 12 3838 4732 74562330 74563219 0.000000e+00 1387.0
18 TraesCS5D01G155300 chr7D 96.246 293 10 1 1 292 150764312 150764604 3.310000e-131 479.0
19 TraesCS5D01G155300 chr7D 95.189 291 14 0 1 291 204100083 204099793 1.200000e-125 460.0
20 TraesCS5D01G155300 chr3D 94.216 899 41 11 3837 4731 436263056 436263947 0.000000e+00 1362.0
21 TraesCS5D01G155300 chr3D 93.764 898 40 10 3840 4732 62355343 62356229 0.000000e+00 1334.0
22 TraesCS5D01G155300 chr3D 97.232 289 8 0 1 289 30751969 30751681 1.530000e-134 490.0
23 TraesCS5D01G155300 chr6D 93.771 899 39 14 3837 4732 260067395 260066511 0.000000e+00 1334.0
24 TraesCS5D01G155300 chr6D 95.517 290 13 0 1 290 423443470 423443759 9.280000e-127 464.0
25 TraesCS5D01G155300 chr3B 92.593 162 11 1 3254 3414 552226568 552226407 1.020000e-56 231.0
26 TraesCS5D01G155300 chr6B 91.071 168 13 2 3249 3414 232734813 232734980 4.760000e-55 226.0
27 TraesCS5D01G155300 chr2A 91.071 168 13 2 3249 3414 676177801 676177968 4.760000e-55 226.0
28 TraesCS5D01G155300 chr3A 90.909 165 13 2 3251 3414 726768965 726769128 2.220000e-53 220.0
29 TraesCS5D01G155300 chr7A 88.043 184 17 5 3254 3433 677696409 677696227 3.710000e-51 213.0


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 TraesCS5D01G155300 chr5D 243816793 243821524 4731 True 8739 8739 100.000 1 4732 1 chr5D.!!$R1 4731
1 TraesCS5D01G155300 chr5B 276908642 276912476 3834 True 6198 6198 95.857 1 3838 1 chr5B.!!$R1 3837
2 TraesCS5D01G155300 chr5A 327919309 327922861 3552 True 5821 5821 96.275 290 3838 1 chr5A.!!$R1 3548
3 TraesCS5D01G155300 chr2D 57274953 57275852 899 True 1410 1410 95.022 3836 4732 1 chr2D.!!$R1 896
4 TraesCS5D01G155300 chr2D 61228085 61228975 890 True 1378 1378 94.549 3837 4732 1 chr2D.!!$R2 895
5 TraesCS5D01G155300 chr1D 56171134 56172027 893 False 1402 1402 95.006 3838 4732 1 chr1D.!!$F1 894
6 TraesCS5D01G155300 chrUn 115837623 115838517 894 True 1393 1393 94.772 3837 4732 1 chrUn.!!$R3 895
7 TraesCS5D01G155300 chrUn 10729011 10729901 890 True 1315 1315 93.348 3839 4732 1 chrUn.!!$R1 893
8 TraesCS5D01G155300 chr7D 74562330 74563219 889 False 1387 1387 94.784 3838 4732 1 chr7D.!!$F1 894
9 TraesCS5D01G155300 chr3D 436263056 436263947 891 False 1362 1362 94.216 3837 4731 1 chr3D.!!$F2 894
10 TraesCS5D01G155300 chr3D 62355343 62356229 886 False 1334 1334 93.764 3840 4732 1 chr3D.!!$F1 892
11 TraesCS5D01G155300 chr6D 260066511 260067395 884 True 1334 1334 93.771 3837 4732 1 chr6D.!!$R1 895

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
180 181 1.271871 TGATGCCAAGACGGTGGATTT 60.272 47.619 6.26 0.0 41.65 2.17 F
1117 1124 4.137543 TCCAAAGGCTTGTTTCTCTCTTC 58.862 43.478 0.00 0.0 0.00 2.87 F
1409 1432 0.831711 ACAATGTTTGTCCCCAGGGC 60.832 55.000 0.00 0.0 40.56 5.19 F
3164 3197 0.671796 ACTTTTTGGCCTGGTAACGC 59.328 50.000 3.32 0.0 42.51 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1273 0.035317 AGCATCACGACAAGGCTGAA 59.965 50.000 0.0 0.0 32.76 3.02 R
2487 2519 3.245514 CCCATATTGCATTCCCATCTCCT 60.246 47.826 0.0 0.0 0.00 3.69 R
3240 3273 4.597507 TGGAGGGAGTAATTGGGACATATC 59.402 45.833 0.0 0.0 39.30 1.63 R
4667 4741 0.169009 GAAATGCCCTTCTGTGTCGC 59.831 55.000 0.0 0.0 0.00 5.19 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
41 42 1.676014 GCGTCAGACCAGTTTATGCCT 60.676 52.381 0.00 0.00 0.00 4.75
48 49 1.282157 ACCAGTTTATGCCTCAGACCC 59.718 52.381 0.00 0.00 0.00 4.46
75 76 4.479993 CTCGGCTGGGGCTTCTGG 62.480 72.222 0.00 0.00 38.73 3.86
113 114 2.188817 AGGTGAGTGGACTGGGTATTC 58.811 52.381 0.00 0.00 0.00 1.75
147 148 3.432749 CGCCCCTTCATCATATGGATAGG 60.433 52.174 2.13 5.20 33.95 2.57
148 149 3.782523 GCCCCTTCATCATATGGATAGGA 59.217 47.826 2.13 0.00 33.95 2.94
149 150 4.141528 GCCCCTTCATCATATGGATAGGAG 60.142 50.000 2.13 0.00 33.95 3.69
180 181 1.271871 TGATGCCAAGACGGTGGATTT 60.272 47.619 6.26 0.00 41.65 2.17
189 190 4.273148 AGACGGTGGATTTAGGCATATC 57.727 45.455 0.00 0.00 0.00 1.63
208 209 9.037737 GGCATATCGTTGTAATACTTTGTAAGA 57.962 33.333 0.00 0.00 0.00 2.10
214 215 8.525316 TCGTTGTAATACTTTGTAAGATCCTCA 58.475 33.333 0.00 0.00 0.00 3.86
1086 1092 8.402472 CAGAACATAGAGAGACCTACTAGTTTG 58.598 40.741 0.00 0.00 0.00 2.93
1117 1124 4.137543 TCCAAAGGCTTGTTTCTCTCTTC 58.862 43.478 0.00 0.00 0.00 2.87
1277 1288 2.612972 GGAAGATTCAGCCTTGTCGTGA 60.613 50.000 0.00 0.00 0.00 4.35
1297 1316 6.093357 TCGTGATGCTATAATGTTCTGCAAAA 59.907 34.615 0.00 0.00 37.20 2.44
1299 1318 7.044510 CGTGATGCTATAATGTTCTGCAAAAAG 60.045 37.037 0.00 0.00 37.20 2.27
1302 1321 9.357652 GATGCTATAATGTTCTGCAAAAAGAAA 57.642 29.630 0.00 0.00 37.90 2.52
1335 1358 4.026968 CAGTTGCATTGTTTTGTTACCACG 60.027 41.667 0.00 0.00 0.00 4.94
1336 1359 3.784701 TGCATTGTTTTGTTACCACGT 57.215 38.095 0.00 0.00 0.00 4.49
1337 1360 4.895224 TGCATTGTTTTGTTACCACGTA 57.105 36.364 0.00 0.00 0.00 3.57
1338 1361 4.599047 TGCATTGTTTTGTTACCACGTAC 58.401 39.130 0.00 0.00 0.00 3.67
1339 1362 3.976306 GCATTGTTTTGTTACCACGTACC 59.024 43.478 0.00 0.00 0.00 3.34
1340 1363 4.497674 GCATTGTTTTGTTACCACGTACCA 60.498 41.667 0.00 0.00 0.00 3.25
1341 1364 4.612932 TTGTTTTGTTACCACGTACCAC 57.387 40.909 0.00 0.00 0.00 4.16
1371 1394 9.826574 AAGTTAGAAGTGACACTATGTTTGTTA 57.173 29.630 8.91 0.00 0.00 2.41
1373 1396 9.859692 GTTAGAAGTGACACTATGTTTGTTAAC 57.140 33.333 8.91 0.00 34.75 2.01
1409 1432 0.831711 ACAATGTTTGTCCCCAGGGC 60.832 55.000 0.00 0.00 40.56 5.19
1708 1735 1.537202 GTTGACACAGCAGATCCAACC 59.463 52.381 0.00 0.00 0.00 3.77
1810 1837 7.787725 ACAGAAAAGTGTACTCCAAAGTAAG 57.212 36.000 0.00 0.00 39.66 2.34
2167 2199 7.984002 TGCAAATTGATTATGTATTTCCACG 57.016 32.000 0.00 0.00 0.00 4.94
2412 2444 5.406780 CCGCTTCAGATTGAGGTATACATTC 59.593 44.000 5.01 2.63 0.00 2.67
2647 2679 4.984295 TCATCCAGGTGAAACAGAAATGA 58.016 39.130 0.00 0.00 39.98 2.57
2764 2796 5.299028 TGCATGGCATTACAAGATTTACGAT 59.701 36.000 0.00 0.00 31.71 3.73
2768 2800 9.897744 CATGGCATTACAAGATTTACGATAAAT 57.102 29.630 0.00 0.00 0.00 1.40
2892 2924 4.157656 TGGCATGCTTACAAACTATTGGTC 59.842 41.667 18.92 0.00 41.01 4.02
2930 2962 4.344938 AGAGGGCATATCTACCAGCTAT 57.655 45.455 0.00 0.00 0.00 2.97
2973 3005 1.273327 CCCATGAAAAGCACTTGGGTC 59.727 52.381 0.00 0.00 43.38 4.46
3164 3197 0.671796 ACTTTTTGGCCTGGTAACGC 59.328 50.000 3.32 0.00 42.51 4.84
3181 3214 6.597672 TGGTAACGCATGAGTTTAAATCTGAT 59.402 34.615 20.11 0.00 42.51 2.90
3240 3273 6.319658 AGCTAATGATTTGTAATGGTCACCAG 59.680 38.462 1.19 0.00 36.75 4.00
3372 3405 5.020795 TGTACATCCGTATGTAGCCCATAT 58.979 41.667 0.46 0.00 46.68 1.78
3599 3633 1.757118 TCTGATAACCCTGAGAAGCCG 59.243 52.381 0.00 0.00 0.00 5.52
3636 3670 2.146342 AGCACAACGTGAGAAATGAGG 58.854 47.619 0.00 0.00 35.23 3.86
3866 3900 7.889178 ACAATTCCATTTATCCCCCTAACTTA 58.111 34.615 0.00 0.00 0.00 2.24
3875 3909 1.569072 CCCCCTAACTTAAGCCACCAT 59.431 52.381 1.29 0.00 0.00 3.55
3924 3958 4.657814 TGCTCAAAAATACCCCTCTTCT 57.342 40.909 0.00 0.00 0.00 2.85
3997 4032 5.006153 CCGTCTGGTGAATAGTAACATGA 57.994 43.478 0.00 0.00 0.00 3.07
3999 4034 5.163550 CCGTCTGGTGAATAGTAACATGAGA 60.164 44.000 0.00 0.00 0.00 3.27
4259 4310 1.608109 GGGGCTTGCAAATTTTTGTGG 59.392 47.619 0.00 0.00 40.24 4.17
4285 4341 2.243264 GCATGCGAGGTGCTCTAGC 61.243 63.158 0.00 0.00 46.63 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.775344 CACTCACATGTGTCGTCGC 59.225 57.895 24.63 0.00 33.61 5.19
41 42 1.305802 AGCCACATACCGGGTCTGA 60.306 57.895 18.30 0.00 0.00 3.27
48 49 2.586079 CAGCCGAGCCACATACCG 60.586 66.667 0.00 0.00 0.00 4.02
75 76 5.126067 TCACCTAAGCCTATCATCAAAAGC 58.874 41.667 0.00 0.00 0.00 3.51
120 121 0.321671 TATGATGAAGGGGCGCTAGC 59.678 55.000 7.64 4.06 44.18 3.42
171 172 3.040147 ACGATATGCCTAAATCCACCG 57.960 47.619 0.00 0.00 0.00 4.94
174 175 8.372459 AGTATTACAACGATATGCCTAAATCCA 58.628 33.333 0.00 0.00 0.00 3.41
189 190 8.697846 TGAGGATCTTACAAAGTATTACAACG 57.302 34.615 0.00 0.00 34.92 4.10
208 209 8.854117 GCCACTTTATTGATTATTCTTGAGGAT 58.146 33.333 0.00 0.00 0.00 3.24
214 215 8.567948 CATACGGCCACTTTATTGATTATTCTT 58.432 33.333 2.24 0.00 0.00 2.52
290 291 4.898861 AGCAAGTTACCCCTCAAAAATGAA 59.101 37.500 0.00 0.00 0.00 2.57
823 827 4.332828 ACTAACACCAATGTAAAGAGGGC 58.667 43.478 0.00 0.00 38.45 5.19
1096 1103 4.140536 AGAAGAGAGAAACAAGCCTTTGG 58.859 43.478 0.00 0.00 38.66 3.28
1117 1124 9.535878 GTGGGAGTACTAATTAGAATCTGAAAG 57.464 37.037 19.38 0.00 0.00 2.62
1256 1267 1.734465 CACGACAAGGCTGAATCTTCC 59.266 52.381 0.00 0.00 0.00 3.46
1262 1273 0.035317 AGCATCACGACAAGGCTGAA 59.965 50.000 0.00 0.00 32.76 3.02
1277 1288 9.709495 TTTTCTTTTTGCAGAACATTATAGCAT 57.291 25.926 0.00 0.00 34.87 3.79
1302 1321 7.174080 ACAAAACAATGCAACTGGTAACTTTTT 59.826 29.630 0.00 0.00 37.61 1.94
1335 1358 7.040548 AGTGTCACTTCTAACTTCTAGTGGTAC 60.041 40.741 0.00 0.00 38.75 3.34
1336 1359 7.002879 AGTGTCACTTCTAACTTCTAGTGGTA 58.997 38.462 0.00 0.00 38.75 3.25
1337 1360 5.834204 AGTGTCACTTCTAACTTCTAGTGGT 59.166 40.000 0.00 0.00 38.75 4.16
1338 1361 6.334102 AGTGTCACTTCTAACTTCTAGTGG 57.666 41.667 0.00 0.00 38.75 4.00
1339 1362 8.516234 ACATAGTGTCACTTCTAACTTCTAGTG 58.484 37.037 11.54 0.00 39.41 2.74
1340 1363 8.638629 ACATAGTGTCACTTCTAACTTCTAGT 57.361 34.615 11.54 0.00 0.00 2.57
1341 1364 9.915629 AAACATAGTGTCACTTCTAACTTCTAG 57.084 33.333 11.54 0.00 0.00 2.43
1371 1394 6.721208 ACATTGTTTCCATGAGTAATGAGGTT 59.279 34.615 0.00 0.00 38.72 3.50
1373 1396 6.764308 ACATTGTTTCCATGAGTAATGAGG 57.236 37.500 0.00 0.00 38.72 3.86
1810 1837 4.010349 ACCTATAACCAGCTTTGTTCAGC 58.990 43.478 1.76 0.00 40.44 4.26
2167 2199 5.173774 TGTCAGTCTTGATTTGAAGTTGC 57.826 39.130 0.00 0.00 35.39 4.17
2231 2263 7.476667 TCAACCACGCATAACCAAAATTATAG 58.523 34.615 0.00 0.00 0.00 1.31
2487 2519 3.245514 CCCATATTGCATTCCCATCTCCT 60.246 47.826 0.00 0.00 0.00 3.69
2674 2706 9.902196 TGATAATGCACAATCACAATTATCATC 57.098 29.630 8.38 0.00 35.73 2.92
2911 2943 8.487028 GTTTAATATAGCTGGTAGATATGCCCT 58.513 37.037 0.00 0.00 28.68 5.19
2930 2962 7.397476 TGGGTGCACTTAATTCATGGTTTAATA 59.603 33.333 17.98 0.00 0.00 0.98
3181 3214 7.336931 GCTATCATCCAAACCTCTTCACTAAAA 59.663 37.037 0.00 0.00 0.00 1.52
3219 3252 8.853126 CATATCTGGTGACCATTACAAATCATT 58.147 33.333 4.03 0.00 30.82 2.57
3240 3273 4.597507 TGGAGGGAGTAATTGGGACATATC 59.402 45.833 0.00 0.00 39.30 1.63
3563 3597 2.272146 GATGCCCAAAGCCCTCGA 59.728 61.111 0.00 0.00 42.71 4.04
3599 3633 2.029020 GTGCTTCCTTTTCCAATCCCAC 60.029 50.000 0.00 0.00 0.00 4.61
3636 3670 7.094890 CCATGTCTTATCAAGGTTATCAGATGC 60.095 40.741 0.00 0.00 0.00 3.91
4210 4261 1.829222 CCAAGCCTCTTTGATGCCAAT 59.171 47.619 0.00 0.00 31.46 3.16
4259 4310 0.179156 CACCTCGCATGCCATTTGAC 60.179 55.000 13.15 0.00 0.00 3.18
4460 4533 5.319140 TGTACGCTCTGAGCAGTAAATTA 57.681 39.130 27.46 14.09 42.58 1.40
4474 4547 7.599054 ACGAAAAACTTTAAAATGTACGCTC 57.401 32.000 0.00 0.00 0.00 5.03
4659 4733 2.615493 CCCTTCTGTGTCGCTACCATTT 60.615 50.000 0.00 0.00 0.00 2.32
4660 4734 1.066143 CCCTTCTGTGTCGCTACCATT 60.066 52.381 0.00 0.00 0.00 3.16
4662 4736 1.972198 CCCTTCTGTGTCGCTACCA 59.028 57.895 0.00 0.00 0.00 3.25
4667 4741 0.169009 GAAATGCCCTTCTGTGTCGC 59.831 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.