Multiple sequence alignment - TraesCS2D01G257300

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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 TraesCS2D01G257300 chr2D 100.000 2483 0 0 1 2483 313026818 313029300 0.000000e+00 4586
1 TraesCS2D01G257300 chr2B 89.610 2512 166 50 16 2483 380307336 380309796 0.000000e+00 3105
2 TraesCS2D01G257300 chr2B 93.358 271 16 2 2215 2483 380312397 380312667 1.380000e-107 399
3 TraesCS2D01G257300 chr2A 93.079 968 29 14 631 1586 424165020 424164079 0.000000e+00 1382
4 TraesCS2D01G257300 chr2A 93.920 625 31 5 1 623 424167731 424167112 0.000000e+00 937
5 TraesCS2D01G257300 chr2A 96.429 84 3 0 1616 1699 424164083 424164000 3.330000e-29 139
6 TraesCS2D01G257300 chr5A 92.963 270 17 2 2215 2483 399609886 399610154 2.320000e-105 392
7 TraesCS2D01G257300 chr5A 92.222 270 19 2 2215 2483 400010726 400010994 5.010000e-102 381
8 TraesCS2D01G257300 chr4D 92.937 269 17 2 2215 2482 229401665 229401932 8.330000e-105 390
9 TraesCS2D01G257300 chr4D 91.697 277 20 3 2209 2483 248953457 248953182 5.010000e-102 381
10 TraesCS2D01G257300 chr4D 91.336 277 20 4 2209 2483 176134410 176134136 2.330000e-100 375
11 TraesCS2D01G257300 chr5D 92.565 269 18 2 2216 2483 377906174 377905907 3.870000e-103 385
12 TraesCS2D01G257300 chr1D 91.667 276 20 3 2209 2483 146004734 146004461 1.800000e-101 379


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 TraesCS2D01G257300 chr2D 313026818 313029300 2482 False 4586.000000 4586 100.000 1 2483 1 chr2D.!!$F1 2482
1 TraesCS2D01G257300 chr2B 380307336 380312667 5331 False 1752.000000 3105 91.484 16 2483 2 chr2B.!!$F1 2467
2 TraesCS2D01G257300 chr2A 424164000 424167731 3731 True 819.333333 1382 94.476 1 1699 3 chr2A.!!$R1 1698

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
915 3055 1.032657 TCTCTTCTCTTCTCCCCGCG 61.033 60.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 4585 0.392336 TGCAAAATGACAAGGGGCAC 59.608 50.0 0.0 0.0 0.0 5.01 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
92 94 5.950883 TGAAGTATTAGTCAGAGACAACCG 58.049 41.667 0.00 0.00 34.60 4.44
255 267 1.405105 GGCGCCATTTGCATCTTTCTA 59.595 47.619 24.80 0.00 41.33 2.10
315 327 2.104451 AGAGGGAGATGTGATGTGATGC 59.896 50.000 0.00 0.00 0.00 3.91
379 391 5.232838 GCACAAAGAAAGTTTGGATCAACTG 59.767 40.000 0.00 0.00 33.92 3.16
520 534 7.919091 TCGTAAGGTATCTACACAACATCAATC 59.081 37.037 0.00 0.00 38.47 2.67
745 2873 9.948964 AAAAATACCATACTCGTATTATACCCC 57.051 33.333 0.00 0.00 35.78 4.95
781 2909 9.939047 CAATTATTATCGCGTTGAATAGTACTC 57.061 33.333 5.77 0.00 0.00 2.59
783 2911 2.463553 TCGCGTTGAATAGTACTCCG 57.536 50.000 5.77 0.00 0.00 4.63
784 2912 1.739466 TCGCGTTGAATAGTACTCCGT 59.261 47.619 5.77 0.00 0.00 4.69
785 2913 2.935849 TCGCGTTGAATAGTACTCCGTA 59.064 45.455 5.77 0.00 0.00 4.02
786 2914 3.031812 CGCGTTGAATAGTACTCCGTAC 58.968 50.000 0.00 0.00 39.10 3.67
853 2983 1.299773 CATTCGCTCGCTCTCTCCC 60.300 63.158 0.00 0.00 0.00 4.30
854 2984 2.494530 ATTCGCTCGCTCTCTCCCC 61.495 63.158 0.00 0.00 0.00 4.81
874 3014 6.674573 TCCCCCTCTCTCTATATATAAGCAC 58.325 44.000 0.00 0.00 0.00 4.40
914 3054 1.068434 CATCTCTTCTCTTCTCCCCGC 59.932 57.143 0.00 0.00 0.00 6.13
915 3055 1.032657 TCTCTTCTCTTCTCCCCGCG 61.033 60.000 0.00 0.00 0.00 6.46
925 3065 3.144120 CTCCCCGCGTCCATCTCTG 62.144 68.421 4.92 0.00 0.00 3.35
972 3112 9.947669 AGTAGTATTAACAGTGTAATTAGCGAG 57.052 33.333 0.00 0.00 0.00 5.03
975 3115 2.981859 ACAGTGTAATTAGCGAGGGG 57.018 50.000 0.00 0.00 0.00 4.79
978 3118 2.696707 CAGTGTAATTAGCGAGGGGGTA 59.303 50.000 0.00 0.00 0.00 3.69
1362 3508 1.298488 GAAGATCGACGAGGACGGC 60.298 63.158 3.01 0.00 45.02 5.68
1560 3708 1.656095 CGACTTCGAGTGCAGAAATCC 59.344 52.381 0.00 0.00 43.02 3.01
1593 3742 9.367444 GTGCTGTAAATCTAGTTAAGAAAGCTA 57.633 33.333 0.00 0.00 37.89 3.32
1594 3743 9.367444 TGCTGTAAATCTAGTTAAGAAAGCTAC 57.633 33.333 0.00 0.00 37.89 3.58
1595 3744 9.367444 GCTGTAAATCTAGTTAAGAAAGCTACA 57.633 33.333 0.00 0.00 37.89 2.74
1620 3770 3.502211 AGTATGCCTTGTGCTGTGTTAAC 59.498 43.478 0.00 0.00 42.00 2.01
1796 3952 2.091541 CACGGTTGCATCTAACCCATT 58.908 47.619 0.00 0.00 45.84 3.16
1797 3953 2.097466 CACGGTTGCATCTAACCCATTC 59.903 50.000 0.00 0.00 45.84 2.67
1800 3956 3.192422 CGGTTGCATCTAACCCATTCAAA 59.808 43.478 0.00 0.00 45.84 2.69
1801 3957 4.321601 CGGTTGCATCTAACCCATTCAAAA 60.322 41.667 0.00 0.00 45.84 2.44
1802 3958 5.546526 GGTTGCATCTAACCCATTCAAAAA 58.453 37.500 0.00 0.00 43.44 1.94
1829 3985 4.965200 ATCCCATCTAAGAGGTGCTAAC 57.035 45.455 0.00 0.00 0.00 2.34
1834 3990 6.098409 TCCCATCTAAGAGGTGCTAACTAAAG 59.902 42.308 0.00 0.00 0.00 1.85
1841 3997 5.968254 AGAGGTGCTAACTAAAGCTAGTTC 58.032 41.667 5.14 0.00 43.55 3.01
1843 3999 6.211785 AGAGGTGCTAACTAAAGCTAGTTCTT 59.788 38.462 5.14 0.00 43.55 2.52
1892 4048 5.212194 CCTGTTATTCAAACAACACTTCGG 58.788 41.667 0.00 0.00 31.61 4.30
1985 4141 0.182537 TCCCCTATTTGCATCCCACG 59.817 55.000 0.00 0.00 0.00 4.94
1986 4142 0.182537 CCCCTATTTGCATCCCACGA 59.817 55.000 0.00 0.00 0.00 4.35
1987 4143 1.308998 CCCTATTTGCATCCCACGAC 58.691 55.000 0.00 0.00 0.00 4.34
1991 4147 1.392589 ATTTGCATCCCACGACATCC 58.607 50.000 0.00 0.00 0.00 3.51
2026 4182 2.529780 TTTTTAGCTCGTTCCGTCCA 57.470 45.000 0.00 0.00 0.00 4.02
2048 4204 1.655959 GCTTCCGCTCGTCTCGATC 60.656 63.158 0.00 0.00 34.61 3.69
2049 4205 1.722082 CTTCCGCTCGTCTCGATCA 59.278 57.895 0.00 0.00 34.61 2.92
2062 4218 2.030091 TCTCGATCAGTACGCTGTTACG 59.970 50.000 0.00 0.00 43.05 3.18
2092 4248 2.234913 AAACCGAACTCGATCCCCCG 62.235 60.000 0.00 0.00 43.02 5.73
2103 4259 1.382695 ATCCCCCGTCTGGTTCGAT 60.383 57.895 0.00 0.00 0.00 3.59
2108 4264 2.511600 CGTCTGGTTCGATGCCCC 60.512 66.667 4.38 0.00 0.00 5.80
2113 4269 4.090588 GGTTCGATGCCCCACGGA 62.091 66.667 0.00 0.00 0.00 4.69
2122 4278 4.722700 CCCCACGGACAGCCAAGG 62.723 72.222 0.00 0.00 0.00 3.61
2220 4376 3.244665 TGGACAATGTGAGAGCTTGTGAT 60.245 43.478 0.00 0.00 33.46 3.06
2230 4386 2.109126 GCTTGTGATGCCCCGAGAC 61.109 63.158 0.00 0.00 0.00 3.36
2245 4401 1.402259 CGAGACCGATGCTCTAGTTGT 59.598 52.381 0.00 0.00 38.22 3.32
2249 4405 3.129638 AGACCGATGCTCTAGTTGTCTTC 59.870 47.826 0.00 0.00 0.00 2.87
2255 4411 5.006165 CGATGCTCTAGTTGTCTTCCATTTC 59.994 44.000 0.00 0.00 0.00 2.17
2269 4425 7.973388 TGTCTTCCATTTCTTTTAGTTGTTGTG 59.027 33.333 0.00 0.00 0.00 3.33
2293 4449 5.293079 GGTGTGTTTATTGTGTTTGTTGCAT 59.707 36.000 0.00 0.00 0.00 3.96
2352 4508 7.328493 GTGTTTATGCCATGATCATGATGAATG 59.672 37.037 32.71 17.75 41.20 2.67
2357 4513 4.747810 CCATGATCATGATGAATGCCATG 58.252 43.478 32.71 17.32 41.56 3.66
2358 4514 3.934457 TGATCATGATGAATGCCATGC 57.066 42.857 14.30 0.00 39.82 4.06
2359 4515 3.496331 TGATCATGATGAATGCCATGCT 58.504 40.909 14.30 0.00 39.82 3.79
2360 4516 4.658063 TGATCATGATGAATGCCATGCTA 58.342 39.130 14.30 0.00 39.82 3.49
2361 4517 5.261216 TGATCATGATGAATGCCATGCTAT 58.739 37.500 14.30 0.00 39.82 2.97
2362 4518 5.125417 TGATCATGATGAATGCCATGCTATG 59.875 40.000 14.30 0.00 39.82 2.23
2428 4585 4.912766 GTGCCATTTCATTTTGTTGCATTG 59.087 37.500 0.00 0.00 0.00 2.82
2433 4590 2.492012 TCATTTTGTTGCATTGTGCCC 58.508 42.857 0.00 0.00 44.23 5.36
2466 7494 2.288640 GCATTATGCCATCCTTTGCCTC 60.289 50.000 5.80 0.00 37.42 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 94 3.859411 TGAAACACAACACTTGGAACC 57.141 42.857 0.00 0.00 34.12 3.62
255 267 4.662179 ACATCACATCCAATCTGGGACTAT 59.338 41.667 0.00 0.00 40.44 2.12
315 327 2.604046 AGCTAGCCAAACCATAGTCG 57.396 50.000 12.13 0.00 0.00 4.18
401 413 2.872038 GCATCCCCTGTCAATATCGACC 60.872 54.545 0.00 0.00 34.88 4.79
520 534 6.407475 TGACAATCGTATGAAGAACATGTG 57.593 37.500 0.00 0.00 39.77 3.21
726 2854 9.595823 CAAAATAGGGGTATAATACGAGTATGG 57.404 37.037 0.00 0.00 0.00 2.74
741 2869 8.789762 GCGATAATAATTGTACAAAATAGGGGT 58.210 33.333 13.23 0.00 0.00 4.95
742 2870 7.960738 CGCGATAATAATTGTACAAAATAGGGG 59.039 37.037 13.23 2.76 0.00 4.79
743 2871 8.500773 ACGCGATAATAATTGTACAAAATAGGG 58.499 33.333 15.93 11.42 0.00 3.53
744 2872 9.872757 AACGCGATAATAATTGTACAAAATAGG 57.127 29.630 15.93 0.00 0.00 2.57
779 2907 6.482641 TGCTTTCTATGAGTACTAGTACGGAG 59.517 42.308 23.87 18.78 40.80 4.63
781 2909 6.615264 TGCTTTCTATGAGTACTAGTACGG 57.385 41.667 23.87 14.12 40.80 4.02
831 2961 1.266718 GAGAGAGCGAGCGAATGATCT 59.733 52.381 0.00 0.00 0.00 2.75
853 2983 5.836358 GGGGTGCTTATATATAGAGAGAGGG 59.164 48.000 0.00 0.00 0.00 4.30
854 2984 5.836358 GGGGGTGCTTATATATAGAGAGAGG 59.164 48.000 0.00 0.00 0.00 3.69
855 2985 6.969993 GGGGGTGCTTATATATAGAGAGAG 57.030 45.833 0.00 0.00 0.00 3.20
914 3054 2.586258 ATTCGAACCAGAGATGGACG 57.414 50.000 0.00 6.76 35.29 4.79
915 3055 5.263968 TCTAATTCGAACCAGAGATGGAC 57.736 43.478 0.00 0.00 0.00 4.02
925 3065 7.975058 ACTACTAGCTTTCTTCTAATTCGAACC 59.025 37.037 0.00 0.00 0.00 3.62
970 3110 0.030399 TTAAGCCCCTCTACCCCCTC 60.030 60.000 0.00 0.00 0.00 4.30
972 3112 1.351080 GGTTAAGCCCCTCTACCCCC 61.351 65.000 0.00 0.00 0.00 5.40
1342 3488 0.450583 CCGTCCTCGTCGATCTTCAA 59.549 55.000 0.00 0.00 35.01 2.69
1343 3489 1.989966 GCCGTCCTCGTCGATCTTCA 61.990 60.000 0.00 0.00 35.01 3.02
1613 3763 1.154197 GGTGCGAGAAGGGTTAACAC 58.846 55.000 8.10 3.22 0.00 3.32
1620 3770 0.036010 ACAGAATGGTGCGAGAAGGG 60.036 55.000 0.00 0.00 43.62 3.95
1779 3935 4.799564 TTTGAATGGGTTAGATGCAACC 57.200 40.909 0.00 0.00 46.15 3.77
1801 3957 6.069381 AGCACCTCTTAGATGGGATAGTTTTT 60.069 38.462 0.00 0.00 0.00 1.94
1802 3958 5.430089 AGCACCTCTTAGATGGGATAGTTTT 59.570 40.000 0.00 0.00 0.00 2.43
1803 3959 4.971924 AGCACCTCTTAGATGGGATAGTTT 59.028 41.667 0.00 0.00 0.00 2.66
1804 3960 4.561752 AGCACCTCTTAGATGGGATAGTT 58.438 43.478 0.00 0.00 0.00 2.24
1805 3961 4.206244 AGCACCTCTTAGATGGGATAGT 57.794 45.455 0.00 0.00 0.00 2.12
1806 3962 5.777732 AGTTAGCACCTCTTAGATGGGATAG 59.222 44.000 0.00 0.00 0.00 2.08
1807 3963 5.716979 AGTTAGCACCTCTTAGATGGGATA 58.283 41.667 0.00 0.00 0.00 2.59
1808 3964 4.561752 AGTTAGCACCTCTTAGATGGGAT 58.438 43.478 0.00 0.00 0.00 3.85
1809 3965 3.995636 AGTTAGCACCTCTTAGATGGGA 58.004 45.455 0.00 0.00 0.00 4.37
1810 3966 5.871396 TTAGTTAGCACCTCTTAGATGGG 57.129 43.478 0.00 0.00 0.00 4.00
1811 3967 5.755861 GCTTTAGTTAGCACCTCTTAGATGG 59.244 44.000 0.00 0.00 40.89 3.51
1812 3968 6.578023 AGCTTTAGTTAGCACCTCTTAGATG 58.422 40.000 0.00 0.00 43.68 2.90
1813 3969 6.800072 AGCTTTAGTTAGCACCTCTTAGAT 57.200 37.500 0.00 0.00 43.68 1.98
1814 3970 6.890814 ACTAGCTTTAGTTAGCACCTCTTAGA 59.109 38.462 0.00 0.00 43.68 2.10
1815 3971 7.102847 ACTAGCTTTAGTTAGCACCTCTTAG 57.897 40.000 0.00 0.00 43.68 2.18
1816 3972 7.396623 AGAACTAGCTTTAGTTAGCACCTCTTA 59.603 37.037 1.81 0.00 43.68 2.10
1817 3973 6.211785 AGAACTAGCTTTAGTTAGCACCTCTT 59.788 38.462 1.81 0.00 43.68 2.85
1818 3974 5.717654 AGAACTAGCTTTAGTTAGCACCTCT 59.282 40.000 1.81 0.00 43.68 3.69
1819 3975 5.968254 AGAACTAGCTTTAGTTAGCACCTC 58.032 41.667 1.81 0.00 43.68 3.85
1864 4020 7.833285 AGTGTTGTTTGAATAACAGGGTTAT 57.167 32.000 6.33 0.00 40.03 1.89
1907 4063 2.074547 TCGTGGAGACGGTTTTCATC 57.925 50.000 0.00 0.00 46.11 2.92
1911 4067 1.346722 AGGATTCGTGGAGACGGTTTT 59.653 47.619 0.00 0.00 46.11 2.43
2049 4205 1.154150 GCCGACGTAACAGCGTACT 60.154 57.895 0.00 0.00 45.79 2.73
2092 4248 1.745489 GTGGGGCATCGAACCAGAC 60.745 63.158 9.79 2.34 34.39 3.51
2197 4353 2.225019 CACAAGCTCTCACATTGTCCAC 59.775 50.000 0.00 0.00 35.04 4.02
2230 4386 2.166459 TGGAAGACAACTAGAGCATCGG 59.834 50.000 0.00 0.00 42.67 4.18
2245 4401 7.123547 ACCACAACAACTAAAAGAAATGGAAGA 59.876 33.333 0.00 0.00 0.00 2.87
2249 4405 6.255453 CACACCACAACAACTAAAAGAAATGG 59.745 38.462 0.00 0.00 0.00 3.16
2255 4411 8.591312 CAATAAACACACCACAACAACTAAAAG 58.409 33.333 0.00 0.00 0.00 2.27
2269 4425 4.627467 TGCAACAAACACAATAAACACACC 59.373 37.500 0.00 0.00 0.00 4.16
2352 4508 5.350914 TGCAATAAACAAAACATAGCATGGC 59.649 36.000 0.00 0.00 33.60 4.40
2357 4513 8.188531 ACATGATGCAATAAACAAAACATAGC 57.811 30.769 0.00 0.00 0.00 2.97
2359 4515 9.702494 TGAACATGATGCAATAAACAAAACATA 57.298 25.926 0.00 0.00 0.00 2.29
2360 4516 8.604640 TGAACATGATGCAATAAACAAAACAT 57.395 26.923 0.00 0.00 0.00 2.71
2361 4517 8.604640 ATGAACATGATGCAATAAACAAAACA 57.395 26.923 0.00 0.00 0.00 2.83
2362 4518 8.928733 AGATGAACATGATGCAATAAACAAAAC 58.071 29.630 0.00 0.00 0.00 2.43
2428 4585 0.392336 TGCAAAATGACAAGGGGCAC 59.608 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.