Multiple sequence alignment - TraesCS5D01G088600

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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 TraesCS5D01G088600 chr5D 100.000 4696 0 0 1 4696 95049592 95054287 0.000000e+00 8672
1 TraesCS5D01G088600 chr5D 83.118 1937 256 37 4 1908 74217382 74215485 0.000000e+00 1700
2 TraesCS5D01G088600 chr5D 83.247 1743 228 33 2809 4506 74214667 74212944 0.000000e+00 1543
3 TraesCS5D01G088600 chr5D 85.652 1143 159 4 1664 2806 74215849 74214712 0.000000e+00 1197
4 TraesCS5D01G088600 chr5D 80.658 243 45 2 1790 2031 74215849 74215608 2.230000e-43 187
5 TraesCS5D01G088600 chr5D 79.675 246 45 4 1790 2031 95051132 95051376 6.250000e-39 172
6 TraesCS5D01G088600 chr5D 87.121 132 15 2 2286 2416 443068087 443067957 1.050000e-31 148
7 TraesCS5D01G088600 chr5B 94.630 4711 198 21 1 4696 102062026 102066696 0.000000e+00 7247
8 TraesCS5D01G088600 chr5B 82.778 1742 248 24 2807 4511 78135411 78137137 0.000000e+00 1507
9 TraesCS5D01G088600 chr5B 82.787 1679 217 40 1 1655 78133288 78134918 0.000000e+00 1434
10 TraesCS5D01G088600 chr5B 85.491 448 63 1 2359 2806 78134923 78135368 2.560000e-127 466
11 TraesCS5D01G088600 chr5B 78.072 529 100 10 2869 3383 539310442 539309916 2.110000e-83 320
12 TraesCS5D01G088600 chr5B 79.012 243 49 2 1790 2031 102063545 102063786 1.050000e-36 165
13 TraesCS5D01G088600 chr5A 94.089 4737 219 17 1 4693 89382581 89387300 0.000000e+00 7140
14 TraesCS5D01G088600 chr5A 84.539 2723 342 48 99 2806 69365395 69362737 0.000000e+00 2623
15 TraesCS5D01G088600 chr5A 83.634 2823 359 53 4 2806 69341242 69338503 0.000000e+00 2558
16 TraesCS5D01G088600 chr5A 82.114 1750 246 43 2807 4511 69338460 69336733 0.000000e+00 1435
17 TraesCS5D01G088600 chr5A 81.943 1750 253 35 2805 4511 69362695 69360966 0.000000e+00 1423
18 TraesCS5D01G088600 chr5A 74.517 1656 309 67 60 1659 559095882 559094284 2.400000e-172 616
19 TraesCS5D01G088600 chr5A 77.297 370 62 15 1664 2031 69339753 69339404 1.030000e-46 198
20 TraesCS5D01G088600 chr5A 87.121 132 15 2 2286 2416 559094239 559094109 1.050000e-31 148
21 TraesCS5D01G088600 chr5A 77.406 239 50 4 1790 2026 89384118 89384354 6.340000e-29 139


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 TraesCS5D01G088600 chr5D 95049592 95054287 4695 False 4422.000000 8672 89.837500 1 4696 2 chr5D.!!$F1 4695
1 TraesCS5D01G088600 chr5D 74212944 74217382 4438 True 1156.750000 1700 83.168750 4 4506 4 chr5D.!!$R2 4502
2 TraesCS5D01G088600 chr5B 102062026 102066696 4670 False 3706.000000 7247 86.821000 1 4696 2 chr5B.!!$F2 4695
3 TraesCS5D01G088600 chr5B 78133288 78137137 3849 False 1135.666667 1507 83.685333 1 4511 3 chr5B.!!$F1 4510
4 TraesCS5D01G088600 chr5B 539309916 539310442 526 True 320.000000 320 78.072000 2869 3383 1 chr5B.!!$R1 514
5 TraesCS5D01G088600 chr5A 89382581 89387300 4719 False 3639.500000 7140 85.747500 1 4693 2 chr5A.!!$F1 4692
6 TraesCS5D01G088600 chr5A 69360966 69365395 4429 True 2023.000000 2623 83.241000 99 4511 2 chr5A.!!$R2 4412
7 TraesCS5D01G088600 chr5A 69336733 69341242 4509 True 1397.000000 2558 81.015000 4 4511 3 chr5A.!!$R1 4507
8 TraesCS5D01G088600 chr5A 559094109 559095882 1773 True 382.000000 616 80.819000 60 2416 2 chr5A.!!$R3 2356

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
325 345 3.751175 TCGTTCTCCCATCACAATTTGTC 59.249 43.478 0.0 0.0 0.00 3.18 F
1028 1101 0.321919 AAGCCAAGCGAGCATCTCAA 60.322 50.000 0.0 0.0 0.00 3.02 F
2232 2318 0.838122 AGTGACCCTGAACCTCCCAG 60.838 60.000 0.0 0.0 0.00 4.45 F
3047 3209 3.851976 TGAGGAAGGGAATCTCCATGAAA 59.148 43.478 0.0 0.0 38.64 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2304 0.254178 CACATCTGGGAGGTTCAGGG 59.746 60.000 0.00 0.00 33.36 4.45 R
2462 2548 1.152589 TGCACCCACATGCTTTCCA 60.153 52.632 0.00 0.00 46.28 3.53 R
3212 3383 1.404748 GCTACACCCTTACTCGAGGAC 59.595 57.143 18.41 0.00 39.25 3.85 R
4655 4902 0.380733 TGACGCATGCTAGTAGGTCG 59.619 55.000 17.13 7.48 0.00 4.79 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
89 92 8.339344 TGCTTGATTTGTTCATGAGAAATCTA 57.661 30.769 26.62 22.06 37.12 1.98
325 345 3.751175 TCGTTCTCCCATCACAATTTGTC 59.249 43.478 0.00 0.00 0.00 3.18
1028 1101 0.321919 AAGCCAAGCGAGCATCTCAA 60.322 50.000 0.00 0.00 0.00 3.02
1099 1172 7.931407 ACAATGATACGATAAAGCAGACCATAA 59.069 33.333 0.00 0.00 0.00 1.90
1169 1250 5.543507 ATGCTTTGAGTAGTCTATGGAGG 57.456 43.478 0.00 0.00 0.00 4.30
1289 1375 8.082852 TCTTTATAGGTCATAGAACTTCATCGC 58.917 37.037 0.00 0.00 29.72 4.58
1349 1435 6.817765 TGCCAAAGAGGTGAATTAAGTAAG 57.182 37.500 0.00 0.00 40.61 2.34
1386 1472 6.594788 AAATGTATTCATCACCATATGGGC 57.405 37.500 25.55 5.00 34.72 5.36
1401 1487 5.510690 CCATATGGGCGTATAAGAACAGTCA 60.511 44.000 14.52 0.00 0.00 3.41
1445 1531 6.064060 TGGACATGATATGAAGAAACCATCC 58.936 40.000 0.00 0.00 0.00 3.51
1573 1659 6.072342 TCAGATGATGCACATGCCAATAATAC 60.072 38.462 0.49 0.00 39.56 1.89
1698 1784 3.064271 TGATGCACATGACGATGACAATG 59.936 43.478 0.00 0.00 33.36 2.82
1699 1785 2.697654 TGCACATGACGATGACAATGA 58.302 42.857 0.00 0.00 33.36 2.57
1700 1786 3.272581 TGCACATGACGATGACAATGAT 58.727 40.909 0.00 0.00 33.36 2.45
1855 1941 8.695456 TGATGTAGTAATATTGTCAGAGAAGCA 58.305 33.333 0.00 0.00 0.00 3.91
1926 2012 5.384336 TGAAGAACATTCTGGTTCCAATCA 58.616 37.500 2.68 3.43 46.52 2.57
2064 2150 1.560923 CTCCTCACGCGTGAATAAGG 58.439 55.000 38.11 33.43 39.39 2.69
2071 2157 1.278238 CGCGTGAATAAGGAGTGGAC 58.722 55.000 0.00 0.00 0.00 4.02
2218 2304 3.799420 GTCTATTCATTCGCAGGAGTGAC 59.201 47.826 0.00 0.00 38.47 3.67
2232 2318 0.838122 AGTGACCCTGAACCTCCCAG 60.838 60.000 0.00 0.00 0.00 4.45
2462 2548 6.158695 TCCCAAGCTTAGAAGATACCTTGAAT 59.841 38.462 0.00 0.00 33.40 2.57
2899 3061 4.499696 GGGTCAATATCAAAAGCAATCCCG 60.500 45.833 0.00 0.00 0.00 5.14
2900 3062 4.499696 GGTCAATATCAAAAGCAATCCCGG 60.500 45.833 0.00 0.00 0.00 5.73
3047 3209 3.851976 TGAGGAAGGGAATCTCCATGAAA 59.148 43.478 0.00 0.00 38.64 2.69
3142 3304 9.416284 AGAAGGTAGTTCAAAAATTCTTGGTTA 57.584 29.630 0.00 0.00 37.67 2.85
3187 3349 4.774660 AAGATCCTCAACTCTCATGCAT 57.225 40.909 0.00 0.00 0.00 3.96
3211 3382 0.603707 CACAAGGGCACAGACGACAT 60.604 55.000 0.00 0.00 0.00 3.06
3212 3383 0.603707 ACAAGGGCACAGACGACATG 60.604 55.000 0.00 0.00 0.00 3.21
3283 3457 1.106285 GACACCAATGCCAGGAATCC 58.894 55.000 0.00 0.00 0.00 3.01
3308 3482 2.105649 TGACCTGAATGTTGCACTACCA 59.894 45.455 0.00 0.00 0.00 3.25
3494 3668 7.281098 ACAATGATGATGACTCTGAAGCTATT 58.719 34.615 0.00 0.00 0.00 1.73
3495 3669 7.226918 ACAATGATGATGACTCTGAAGCTATTG 59.773 37.037 0.00 0.00 0.00 1.90
3503 3677 6.233434 TGACTCTGAAGCTATTGAACAACAT 58.767 36.000 0.00 0.00 0.00 2.71
3803 3995 2.888594 AGGAACATCGTGTATGGTTCG 58.111 47.619 0.00 0.00 35.70 3.95
4005 4233 3.761218 TGTTTGAGAACAAAGGTCAGCAA 59.239 39.130 0.00 0.00 44.97 3.91
4144 4373 7.394359 TCATGGGATAGCTAATTTTAGAATGGC 59.606 37.037 0.00 0.00 32.47 4.40
4260 4497 1.870055 GCCAACCACCTGAGCACATG 61.870 60.000 0.00 0.00 0.00 3.21
4261 4498 1.582968 CAACCACCTGAGCACATGC 59.417 57.895 0.00 0.00 42.49 4.06
4281 4518 1.762460 CCACGATAGGCTCACCCCT 60.762 63.158 0.00 0.00 43.77 4.79
4378 4615 7.582667 TCTTCATCATAGAGATACGGTTTGA 57.417 36.000 0.00 0.00 34.43 2.69
4385 4623 4.303086 AGAGATACGGTTTGATACACGG 57.697 45.455 0.00 0.00 0.00 4.94
4386 4624 3.949754 AGAGATACGGTTTGATACACGGA 59.050 43.478 0.00 0.00 0.00 4.69
4392 4630 0.325602 GTTTGATACACGGACCCCCA 59.674 55.000 0.00 0.00 0.00 4.96
4405 4646 3.192633 CGGACCCCCATTAGAAAAGTTTG 59.807 47.826 0.00 0.00 0.00 2.93
4463 4708 5.825593 ACTTACATCTCACTTCAAAGGGA 57.174 39.130 0.00 0.00 35.74 4.20
4524 4771 1.503542 GCAACAAGCGCTGCTATGT 59.496 52.632 12.58 9.05 38.25 2.29
4542 4789 5.276584 GCTATGTAGACGATGTTTTGCTGAG 60.277 44.000 0.00 0.00 0.00 3.35
4553 4800 6.345250 CGATGTTTTGCTGAGAATTTGTGAAC 60.345 38.462 0.00 0.00 0.00 3.18
4584 4831 0.392998 ATCCAAGCAACTGTAGCCCG 60.393 55.000 0.00 0.00 0.00 6.13
4606 4853 1.906966 CGCAATGTCACAGAAATTCGC 59.093 47.619 0.00 0.00 0.00 4.70
4647 4894 3.390521 CTGGGCGTGCTGGGAGTA 61.391 66.667 0.00 0.00 0.00 2.59
4655 4902 0.811281 GTGCTGGGAGTAAATGCCAC 59.189 55.000 0.00 0.00 45.95 5.01
4667 4914 1.191535 AATGCCACGACCTACTAGCA 58.808 50.000 0.00 0.00 34.28 3.49
4668 4915 1.414158 ATGCCACGACCTACTAGCAT 58.586 50.000 0.00 0.00 36.18 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.572290 ACTTCCAAGAACAAAGTCCCG 58.428 47.619 0.00 0.00 0.00 5.14
226 236 4.994852 TCTTCACCTCCATAAACAAACTCG 59.005 41.667 0.00 0.00 0.00 4.18
305 325 4.761739 TCTGACAAATTGTGATGGGAGAAC 59.238 41.667 2.20 0.00 0.00 3.01
325 345 5.240891 TGGTAAACAAGATCAAGAGCTCTG 58.759 41.667 19.06 11.72 0.00 3.35
441 478 6.590292 CCTCTTTATCTAAAGCAGACAAACGA 59.410 38.462 5.06 0.00 41.77 3.85
903 968 2.632512 GCCTTCAACTTCCATTCCCAAA 59.367 45.455 0.00 0.00 0.00 3.28
1028 1101 8.815565 TGTGGGTGTTATTGTGAATATGTTAT 57.184 30.769 0.00 0.00 0.00 1.89
1099 1172 3.127548 CGGAATGTAGCTTCTTGTGCAAT 59.872 43.478 0.00 0.00 0.00 3.56
1349 1435 9.448294 GATGAATACATTTTCTCTTGAGAATGC 57.552 33.333 13.04 0.00 44.07 3.56
1386 1472 4.495422 ACTTGCCTGACTGTTCTTATACG 58.505 43.478 0.00 0.00 0.00 3.06
1573 1659 6.750963 CGATAGTATCACCACATCATCATCAG 59.249 42.308 10.71 0.00 0.00 2.90
1637 1723 4.536090 TCCTTCACATTTGTACCAGGAGAT 59.464 41.667 0.00 0.00 0.00 2.75
1700 1786 9.312904 TCTAATAGTATCACCACATCATCATCA 57.687 33.333 0.00 0.00 0.00 3.07
1855 1941 4.201940 GCTTTCTTGGCAAACTTTTTGCAT 60.202 37.500 21.67 0.00 46.58 3.96
1926 2012 5.963176 TCACAATCATAAACATGTGCACT 57.037 34.783 19.41 0.00 42.16 4.40
2020 2106 5.705441 CCCTCACTGTTAAGCTTCACATTTA 59.295 40.000 13.63 0.02 0.00 1.40
2064 2150 5.944007 ATGGTTGTAAACTATTGGTCCACTC 59.056 40.000 0.00 0.00 46.51 3.51
2071 2157 7.630242 ACATCTGATGGTTGTAAACTATTGG 57.370 36.000 20.83 0.00 46.51 3.16
2218 2304 0.254178 CACATCTGGGAGGTTCAGGG 59.746 60.000 0.00 0.00 33.36 4.45
2232 2318 4.171754 GGCTCAATTTCAAGCTTCACATC 58.828 43.478 0.00 0.00 38.58 3.06
2462 2548 1.152589 TGCACCCACATGCTTTCCA 60.153 52.632 0.00 0.00 46.28 3.53
2899 3061 8.421784 TCATGTCCTCTACACAATTATAGAACC 58.578 37.037 0.00 0.00 42.09 3.62
2900 3062 9.817809 TTCATGTCCTCTACACAATTATAGAAC 57.182 33.333 0.00 0.00 42.09 3.01
3047 3209 4.942761 ATTTGATGGCACTTGTGACTTT 57.057 36.364 8.17 0.00 0.00 2.66
3142 3304 7.504926 TTCTCAGTGGTTGTATTAATAGGGT 57.495 36.000 0.00 0.00 0.00 4.34
3187 3349 1.533625 GTCTGTGCCCTTGTGCATAA 58.466 50.000 0.00 0.00 44.30 1.90
3211 3382 2.719739 CTACACCCTTACTCGAGGACA 58.280 52.381 18.41 0.00 39.25 4.02
3212 3383 1.404748 GCTACACCCTTACTCGAGGAC 59.595 57.143 18.41 0.00 39.25 3.85
3257 3428 2.173519 CTGGCATTGGTGTCATCCTTT 58.826 47.619 0.00 0.00 39.63 3.11
3283 3457 2.559668 AGTGCAACATTCAGGTCAATGG 59.440 45.455 0.00 0.00 41.43 3.16
3308 3482 7.339721 GCATCTATCTCCATTTCATCCATGAAT 59.660 37.037 2.83 0.00 45.30 2.57
3351 3525 5.825593 TCTGGTTCTTGAGGAATAGTGTT 57.174 39.130 0.00 0.00 36.24 3.32
3460 3634 8.986847 CAGAGTCATCATCATTGTTATTACCTC 58.013 37.037 0.00 0.00 0.00 3.85
3803 3995 9.315525 GGTTTGTAGAGACCATATTAGAGTTTC 57.684 37.037 0.00 0.00 35.95 2.78
3861 4053 6.948353 TCTCAAACAAGAGTTCGATTTGAAG 58.052 36.000 8.84 4.87 38.45 3.02
4005 4233 9.182214 ACATCATCAGTGAGTTAAAATAGCATT 57.818 29.630 0.00 0.00 37.87 3.56
4068 4297 4.153411 CCTCCAGTAGACCTTACCTATGG 58.847 52.174 0.00 0.00 0.00 2.74
4144 4373 1.672356 CCACACCCTTTCTCGCCAG 60.672 63.158 0.00 0.00 0.00 4.85
4260 4497 1.521681 GGTGAGCCTATCGTGGTGC 60.522 63.158 0.00 0.00 0.00 5.01
4261 4498 1.144057 GGGTGAGCCTATCGTGGTG 59.856 63.158 0.00 0.00 34.45 4.17
4281 4518 5.874810 CGATTGGAGTTTTCTACTTGATCCA 59.125 40.000 0.00 0.00 37.17 3.41
4315 4552 4.406456 TGGAAACTTGGCATCATTAGTGT 58.594 39.130 0.00 0.00 0.00 3.55
4371 4608 0.741927 GGGGTCCGTGTATCAAACCG 60.742 60.000 0.00 0.00 0.00 4.44
4378 4615 2.482414 TCTAATGGGGGTCCGTGTAT 57.518 50.000 0.00 0.00 35.24 2.29
4385 4623 6.008331 ACTACAAACTTTTCTAATGGGGGTC 58.992 40.000 0.00 0.00 0.00 4.46
4386 4624 5.960704 ACTACAAACTTTTCTAATGGGGGT 58.039 37.500 0.00 0.00 0.00 4.95
4392 4630 9.201127 GTCTCGGTTACTACAAACTTTTCTAAT 57.799 33.333 0.00 0.00 0.00 1.73
4405 4646 5.764192 ACCATAGATCTGTCTCGGTTACTAC 59.236 44.000 5.18 0.00 37.17 2.73
4524 4771 6.204688 ACAAATTCTCAGCAAAACATCGTCTA 59.795 34.615 0.00 0.00 0.00 2.59
4542 4789 2.793278 AGTTGCCGGTTCACAAATTC 57.207 45.000 1.90 0.00 0.00 2.17
4553 4800 1.017387 GCTTGGATCTAAGTTGCCGG 58.983 55.000 18.80 0.00 0.00 6.13
4584 4831 3.155998 CGAATTTCTGTGACATTGCGTC 58.844 45.455 0.00 0.00 45.61 5.19
4606 4853 1.597027 GGACAAGGACCACCACACG 60.597 63.158 0.00 0.00 38.94 4.49
4647 4894 1.553248 TGCTAGTAGGTCGTGGCATTT 59.447 47.619 0.00 0.00 0.00 2.32
4655 4902 0.380733 TGACGCATGCTAGTAGGTCG 59.619 55.000 17.13 7.48 0.00 4.79
4667 4914 3.090037 AGTAGGTTGTCTAGTGACGCAT 58.910 45.455 0.00 0.00 45.70 4.73
4668 4915 2.511659 AGTAGGTTGTCTAGTGACGCA 58.488 47.619 0.00 0.00 45.70 5.24


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

AutoCloner maintained by Alex Coulton.