Multiple sequence alignment - TraesCS7D01G273900

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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 TraesCS7D01G273900 chr7D 100.000 2714 0 0 1 2714 264033831 264036544 0.000000e+00 5012
1 TraesCS7D01G273900 chr7D 92.368 1284 39 28 818 2074 264054301 264055552 0.000000e+00 1773
2 TraesCS7D01G273900 chr7D 91.979 748 52 5 223 962 264044447 264045194 0.000000e+00 1042
3 TraesCS7D01G273900 chr7D 90.303 330 15 3 2381 2709 264055967 264056280 1.500000e-112 416
4 TraesCS7D01G273900 chr7D 85.404 322 24 11 2072 2378 264055619 264055932 2.030000e-81 313
5 TraesCS7D01G273900 chr7D 87.435 191 21 1 2090 2277 264028067 264028257 1.640000e-52 217
6 TraesCS7D01G273900 chr7D 78.495 279 30 5 2400 2648 264028521 264028799 3.620000e-34 156
7 TraesCS7D01G273900 chr7B 93.158 2163 112 17 574 2714 244404675 244406823 0.000000e+00 3142
8 TraesCS7D01G273900 chr7B 92.545 1489 64 8 550 2007 244409617 244411089 0.000000e+00 2091
9 TraesCS7D01G273900 chr7B 89.089 779 79 4 1001 1777 244394122 244394896 0.000000e+00 963
10 TraesCS7D01G273900 chr7B 83.585 993 144 13 818 1799 244406805 244407789 0.000000e+00 913
11 TraesCS7D01G273900 chr7B 88.657 335 16 4 2381 2709 244411554 244411872 3.280000e-104 388
12 TraesCS7D01G273900 chr7B 86.025 322 24 13 2072 2380 244411208 244411521 2.610000e-85 326
13 TraesCS7D01G273900 chr7B 89.362 188 20 0 223 410 244404477 244404664 1.260000e-58 237
14 TraesCS7D01G273900 chr7B 89.189 148 12 2 2133 2277 244395447 244395593 5.970000e-42 182
15 TraesCS7D01G273900 chr7B 78.521 284 31 5 2395 2648 244395852 244396135 2.800000e-35 159
16 TraesCS7D01G273900 chr7A 93.156 1987 99 9 332 2304 287491477 287493440 0.000000e+00 2881
17 TraesCS7D01G273900 chr7A 93.509 1710 79 12 319 2007 287525754 287527452 0.000000e+00 2514
18 TraesCS7D01G273900 chr7A 92.020 1391 87 16 406 1789 287499157 287500530 0.000000e+00 1932
19 TraesCS7D01G273900 chr7A 85.532 864 120 3 937 1799 287484941 287485800 0.000000e+00 898
20 TraesCS7D01G273900 chr7A 83.895 683 44 25 2072 2709 287527556 287528217 2.330000e-165 592
21 TraesCS7D01G273900 chr7A 90.883 351 16 1 2378 2712 287493806 287494156 8.860000e-125 457
22 TraesCS7D01G273900 chr7A 90.265 226 20 2 1 226 546885 546662 7.350000e-76 294
23 TraesCS7D01G273900 chr7A 87.719 114 13 1 2395 2507 287484501 287484614 6.100000e-27 132
24 TraesCS7D01G273900 chr7A 88.991 109 9 2 253 358 287497762 287497870 6.100000e-27 132
25 TraesCS7D01G273900 chr7A 80.319 188 20 6 2090 2272 287484060 287484235 2.840000e-25 126
26 TraesCS7D01G273900 chr7A 100.000 68 0 0 2313 2380 287493707 287493774 2.840000e-25 126
27 TraesCS7D01G273900 chr6D 98.667 225 3 0 1 225 463066989 463066765 1.510000e-107 399
28 TraesCS7D01G273900 chr6D 98.667 225 3 0 1 225 463070891 463070667 1.510000e-107 399
29 TraesCS7D01G273900 chr1D 98.222 225 4 0 1 225 466360390 466360166 7.040000e-106 394
30 TraesCS7D01G273900 chr3D 97.778 225 5 0 1 225 569377197 569377421 3.280000e-104 388
31 TraesCS7D01G273900 chr5B 92.889 225 14 1 1 225 487490608 487490386 2.610000e-85 326
32 TraesCS7D01G273900 chr3A 90.667 225 19 2 1 225 734464945 734465167 5.680000e-77 298
33 TraesCS7D01G273900 chr2B 88.000 225 14 6 1 225 38227287 38227498 1.250000e-63 254


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 TraesCS7D01G273900 chr7D 264033831 264036544 2713 False 5012.000000 5012 100.000000 1 2714 1 chr7D.!!$F1 2713
1 TraesCS7D01G273900 chr7D 264044447 264045194 747 False 1042.000000 1042 91.979000 223 962 1 chr7D.!!$F2 739
2 TraesCS7D01G273900 chr7D 264054301 264056280 1979 False 834.000000 1773 89.358333 818 2709 3 chr7D.!!$F4 1891
3 TraesCS7D01G273900 chr7B 244404477 244411872 7395 False 1182.833333 3142 88.888667 223 2714 6 chr7B.!!$F2 2491
4 TraesCS7D01G273900 chr7B 244394122 244396135 2013 False 434.666667 963 85.599667 1001 2648 3 chr7B.!!$F1 1647
5 TraesCS7D01G273900 chr7A 287525754 287528217 2463 False 1553.000000 2514 88.702000 319 2709 2 chr7A.!!$F3 2390
6 TraesCS7D01G273900 chr7A 287491477 287500530 9053 False 1105.600000 2881 93.010000 253 2712 5 chr7A.!!$F2 2459
7 TraesCS7D01G273900 chr7A 287484060 287485800 1740 False 385.333333 898 84.523333 937 2507 3 chr7A.!!$F1 1570
8 TraesCS7D01G273900 chr6D 463066765 463070891 4126 True 399.000000 399 98.667000 1 225 2 chr6D.!!$R1 224

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
113 114 1.266178 TGCGAGATCACAGGGAGAAA 58.734 50.0 0.0 0.0 0.0 2.52 F
950 2987 1.981256 TGTCTTGCCAACCTTTCTCC 58.019 50.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 3048 1.21823 GCGCGCTTCCAGATCTTAGG 61.218 60.0 26.67 0.00 0.00 2.69 R
2398 10280 0.79264 GTGCACACAGATTCTGGACG 59.207 55.0 17.66 8.26 35.51 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
60 61 2.746362 CTGGCACTCAATCTGGAGTTTC 59.254 50.000 0.00 0.00 45.59 2.78
113 114 1.266178 TGCGAGATCACAGGGAGAAA 58.734 50.000 0.00 0.00 0.00 2.52
238 239 3.490890 GCTCGGTGCTGATTGGAC 58.509 61.111 0.00 0.00 38.95 4.02
266 267 2.341101 CGACTGGCCAGTAGGTCGT 61.341 63.158 37.87 15.38 44.71 4.34
313 546 9.131791 GGATATTTTCAACCACAGGTATACATT 57.868 33.333 5.01 0.00 33.12 2.71
370 606 2.620115 CCAAGCATGCTTCCATACGAAT 59.380 45.455 29.81 2.28 33.42 3.34
389 625 7.101993 ACGAATAGCGAACGAATATTTAAGG 57.898 36.000 0.00 0.00 44.57 2.69
446 1028 7.043986 GCAATACTGTTAGTGTAGTCGAGAATG 60.044 40.741 0.00 0.00 0.00 2.67
475 1057 3.569701 CACTTACATGGCTGTCCTTTTGT 59.430 43.478 0.00 0.00 36.79 2.83
484 1066 3.153919 GCTGTCCTTTTGTTGTGGGATA 58.846 45.455 0.00 0.00 0.00 2.59
563 1145 4.381411 ACCAGCAGAGAACAAGACTAAAC 58.619 43.478 0.00 0.00 0.00 2.01
950 2987 1.981256 TGTCTTGCCAACCTTTCTCC 58.019 50.000 0.00 0.00 0.00 3.71
1022 3059 2.771943 TGGCTTACCACCTAAGATCTGG 59.228 50.000 0.00 0.00 42.67 3.86
1884 9108 5.764686 TCATTTATGCAAGCTCCACGATATT 59.235 36.000 0.00 0.00 0.00 1.28
2094 9486 1.380785 CATGCCAGCTCCAACCCAT 60.381 57.895 0.00 0.00 0.00 4.00
2097 9489 1.751927 GCCAGCTCCAACCCATGAG 60.752 63.158 0.00 0.00 0.00 2.90
2113 9512 4.395231 CCCATGAGCTAGTGATAATGCATG 59.605 45.833 0.00 0.00 33.55 4.06
2178 9653 1.563924 ATCAGGCCAACACATGCAAT 58.436 45.000 5.01 0.00 0.00 3.56
2187 9665 4.911610 GCCAACACATGCAATCGATAATAC 59.088 41.667 0.00 0.00 0.00 1.89
2188 9666 5.277974 GCCAACACATGCAATCGATAATACT 60.278 40.000 0.00 0.00 0.00 2.12
2189 9667 6.138088 CCAACACATGCAATCGATAATACTG 58.862 40.000 0.00 0.00 0.00 2.74
2190 9668 6.018016 CCAACACATGCAATCGATAATACTGA 60.018 38.462 0.00 0.00 0.00 3.41
2191 9669 6.530913 ACACATGCAATCGATAATACTGAC 57.469 37.500 0.00 0.00 0.00 3.51
2194 9672 5.698089 ACATGCAATCGATAATACTGACCAG 59.302 40.000 0.00 0.00 0.00 4.00
2224 9705 7.688918 ATCCACTGAAGATCCTTTCTTATCT 57.311 36.000 0.00 0.00 44.88 1.98
2230 9711 7.120432 ACTGAAGATCCTTTCTTATCTTGTTGC 59.880 37.037 2.49 0.00 44.88 4.17
2256 9737 4.371681 ACCTTCCCTTCTGCTTCCTAATA 58.628 43.478 0.00 0.00 0.00 0.98
2398 10280 5.063438 TCTCAGAATTATACTTGCGTGTTGC 59.937 40.000 0.00 0.00 46.70 4.17
2494 10378 5.551583 AGGCATAAGACCCCATCATAATGTA 59.448 40.000 0.00 0.00 0.00 2.29
2603 10516 2.093869 ACGAAACACCCGTGCAGTATAT 60.094 45.455 0.00 0.00 38.97 0.86
2671 10589 0.596082 ATGTTTGCCACGCTAACCAC 59.404 50.000 8.15 0.00 41.88 4.16
2712 10630 6.491745 CACTCTCTTATGGAGGTTAGCAGATA 59.508 42.308 0.00 0.00 42.10 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.391405 ACAGCTCCCAAAAGAAAAACAG 57.609 40.909 0.00 0.00 0.00 3.16
266 267 3.550233 CCTGTTGAAGACTCGTCGAAGAA 60.550 47.826 1.95 0.00 39.69 2.52
370 606 5.922544 GGCTACCTTAAATATTCGTTCGCTA 59.077 40.000 0.00 0.00 0.00 4.26
431 1013 3.429547 GGATGCACATTCTCGACTACACT 60.430 47.826 0.00 0.00 0.00 3.55
446 1028 1.755179 AGCCATGTAAGTGGATGCAC 58.245 50.000 9.70 9.70 42.02 4.57
475 1057 3.146066 GTGTGTTTCAGCTATCCCACAA 58.854 45.455 9.26 0.00 34.91 3.33
513 1095 1.135972 CGTTATGGTGAGTTGCACTGC 60.136 52.381 0.00 0.00 46.86 4.40
526 1108 1.737793 GCTGGTTCTCCAACGTTATGG 59.262 52.381 0.00 0.00 43.81 2.74
563 1145 3.745332 TCGTGTTGCTGCAATGATTAG 57.255 42.857 19.11 7.48 0.00 1.73
913 2065 0.746063 CAAGGGCTGCAGTTTGTTGA 59.254 50.000 16.64 0.00 0.00 3.18
950 2987 7.011857 GCTACTTTCTTCAGTATGGAAATGGAG 59.988 40.741 0.00 0.00 36.16 3.86
1011 3048 1.218230 GCGCGCTTCCAGATCTTAGG 61.218 60.000 26.67 0.00 0.00 2.69
1022 3059 3.265636 GGCTAGAAGGCGCGCTTC 61.266 66.667 32.29 28.26 0.00 3.86
2094 9486 6.105397 TGATCATGCATTATCACTAGCTCA 57.895 37.500 17.64 0.00 0.00 4.26
2113 9512 5.941555 AGGTATTCCCCTCGATAATGATC 57.058 43.478 0.00 0.00 0.00 2.92
2178 9653 6.984474 GGATTTGTTCTGGTCAGTATTATCGA 59.016 38.462 0.00 0.00 0.00 3.59
2187 9665 3.743521 TCAGTGGATTTGTTCTGGTCAG 58.256 45.455 0.00 0.00 0.00 3.51
2188 9666 3.855255 TCAGTGGATTTGTTCTGGTCA 57.145 42.857 0.00 0.00 0.00 4.02
2189 9667 4.389374 TCTTCAGTGGATTTGTTCTGGTC 58.611 43.478 0.00 0.00 0.00 4.02
2190 9668 4.437682 TCTTCAGTGGATTTGTTCTGGT 57.562 40.909 0.00 0.00 0.00 4.00
2191 9669 4.397417 GGATCTTCAGTGGATTTGTTCTGG 59.603 45.833 0.00 0.00 0.00 3.86
2194 9672 6.432472 AGAAAGGATCTTCAGTGGATTTGTTC 59.568 38.462 0.00 0.00 33.39 3.18
2224 9705 2.441750 AGAAGGGAAGGTACAGCAACAA 59.558 45.455 0.00 0.00 0.00 2.83
2230 9711 2.355209 GGAAGCAGAAGGGAAGGTACAG 60.355 54.545 0.00 0.00 0.00 2.74
2256 9737 5.763204 ACGGAAACATGAAGTTCATTGTACT 59.237 36.000 15.85 8.52 40.26 2.73
2311 9895 6.767423 TGCATAAAATAGAAGCATGCTACTGA 59.233 34.615 23.00 7.32 41.94 3.41
2398 10280 0.792640 GTGCACACAGATTCTGGACG 59.207 55.000 17.66 8.26 35.51 4.79
2494 10378 2.618241 TGTTGTGCTCGCTGATTTTTCT 59.382 40.909 0.00 0.00 0.00 2.52
2671 10589 4.694509 AGAGAGTGTTGCTTTATCTGCTTG 59.305 41.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.