Multiple sequence alignment - TraesCS5D01G452800

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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 TraesCS5D01G452800 chr5D 100.000 4382 0 0 1 4382 500677123 500672742 0.000000e+00 8093.0
1 TraesCS5D01G452800 chr5B 97.351 4039 73 10 1 4013 622069513 622065483 0.000000e+00 6835.0
2 TraesCS5D01G452800 chr5B 98.663 374 3 1 4011 4382 622065379 622065006 0.000000e+00 662.0
3 TraesCS5D01G452800 chr5B 78.065 310 45 14 3550 3839 622380902 622380596 1.620000e-39 174.0
4 TraesCS5D01G452800 chr5A 79.310 232 27 14 4153 4371 624801567 624801790 4.570000e-30 143.0
5 TraesCS5D01G452800 chr7A 71.520 625 142 21 2155 2748 320060 320679 7.640000e-28 135.0
6 TraesCS5D01G452800 chr1D 93.617 47 3 0 1601 1647 192569780 192569826 2.190000e-08 71.3
7 TraesCS5D01G452800 chr1A 93.617 47 3 0 1601 1647 238678433 238678479 2.190000e-08 71.3


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 TraesCS5D01G452800 chr5D 500672742 500677123 4381 True 8093.0 8093 100.000 1 4382 1 chr5D.!!$R1 4381
1 TraesCS5D01G452800 chr5B 622065006 622069513 4507 True 3748.5 6835 98.007 1 4382 2 chr5B.!!$R2 4381

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
190 191 0.309922 TCCGTCAACACTCGTCTCAC 59.690 55.0 0.00 0.00 0.00 3.51 F
969 984 0.473755 TCATGTAGGCGCCCATCAAT 59.526 50.0 26.15 5.68 0.00 2.57 F
2073 2096 0.676184 CAGCAGGAGCGCTAATCCTA 59.324 55.0 11.50 0.00 45.67 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1559 0.821301 TTGCCATGCCGTTGTTCTGA 60.821 50.0 0.00 0.0 0.0 3.27 R
2583 2606 0.098200 CATCGTCGAGGAGCACGTTA 59.902 55.0 13.85 0.0 37.3 3.18 R
4009 4036 0.547471 TCCTGGGTGCTCTTGGATCA 60.547 55.0 0.00 0.0 0.0 2.92 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
152 153 3.609853 CATTGGAGAAATGGTTCCTCGA 58.390 45.455 0.00 0.00 41.80 4.04
183 184 0.321653 AGGCCATTCCGTCAACACTC 60.322 55.000 5.01 0.00 40.77 3.51
190 191 0.309922 TCCGTCAACACTCGTCTCAC 59.690 55.000 0.00 0.00 0.00 3.51
223 224 1.144969 GATGCCGAACACGAAAGACA 58.855 50.000 0.00 0.00 0.00 3.41
234 235 3.053455 CACGAAAGACACAGAGAAGGAC 58.947 50.000 0.00 0.00 0.00 3.85
240 241 1.374758 CACAGAGAAGGACCGCACC 60.375 63.158 0.00 0.00 0.00 5.01
347 348 2.994995 TCCGTCCGCTGTGACCAT 60.995 61.111 0.00 0.00 31.35 3.55
457 458 2.472029 CCAAGCTAAGGAAGAGGAGGA 58.528 52.381 0.00 0.00 0.00 3.71
646 661 1.869767 GATATGCCTGCCGAAGACTTG 59.130 52.381 0.00 0.00 0.00 3.16
659 674 3.362237 CGAAGACTTGTTCTGAAGTAGCG 59.638 47.826 0.00 0.00 36.27 4.26
758 773 2.587522 GGCATAAATCTTCTGGTCCCC 58.412 52.381 0.00 0.00 0.00 4.81
798 813 6.719370 TCATAATACCAAGGGCCACATAATTC 59.281 38.462 6.18 0.00 0.00 2.17
939 954 4.686191 AATTGGGTGCACAATTGAAGAA 57.314 36.364 20.43 0.00 46.23 2.52
969 984 0.473755 TCATGTAGGCGCCCATCAAT 59.526 50.000 26.15 5.68 0.00 2.57
993 1008 5.652744 AATGTCGTTTCTGTTGTCACTAC 57.347 39.130 0.00 0.00 0.00 2.73
1010 1025 1.732259 CTACCGTTGAATGGCACTCAC 59.268 52.381 0.00 0.00 0.00 3.51
1033 1053 3.133003 GCCTAGACTAAGATGCTTGTGGA 59.867 47.826 0.00 0.00 0.00 4.02
1038 1058 5.241662 AGACTAAGATGCTTGTGGAAAGAC 58.758 41.667 0.00 0.00 0.00 3.01
1183 1203 3.854669 CTCTGCCCTGGCCCGTAG 61.855 72.222 5.57 0.00 41.09 3.51
1216 1236 5.337788 TCCTTGGCCTTAACCAACAAATAT 58.662 37.500 3.32 0.00 44.80 1.28
1258 1278 3.443037 CAGTTCATCTACTCTGGCTTCG 58.557 50.000 0.00 0.00 0.00 3.79
1284 1304 1.084370 CCAATCTGGTTCTCGACGGC 61.084 60.000 0.00 0.00 31.35 5.68
1334 1354 1.383523 GACCTAACCAATGGCTCTGC 58.616 55.000 0.00 0.00 0.00 4.26
1499 1522 3.134623 TCACCAAGCAAGAACTTCTCAGA 59.865 43.478 0.00 0.00 0.00 3.27
1511 1534 2.835431 CTCAGACGCCCTCCCGAT 60.835 66.667 0.00 0.00 0.00 4.18
1536 1559 1.056700 ACATGGGCCTCCTTAGCGAT 61.057 55.000 4.53 0.00 0.00 4.58
1700 1723 7.052873 GGCTTCTATGATGATAAGCATGGTAT 58.947 38.462 0.00 0.00 44.81 2.73
1874 1897 4.408270 AGTCCTCACAGAATCAGCATATGT 59.592 41.667 4.29 0.00 0.00 2.29
1884 1907 6.485648 CAGAATCAGCATATGTTGGATTCTCA 59.514 38.462 27.35 10.00 34.49 3.27
2040 2063 6.201806 CCAAGTTTCTAGAGATAATTCTGCCG 59.798 42.308 0.00 0.00 30.30 5.69
2073 2096 0.676184 CAGCAGGAGCGCTAATCCTA 59.324 55.000 11.50 0.00 45.67 2.94
2091 2114 2.480419 CCTAGTGGTTTTTCTGCTCGTG 59.520 50.000 0.00 0.00 0.00 4.35
2259 2282 3.486263 GGATTGCTTCCGGTGTCG 58.514 61.111 0.00 0.00 33.93 4.35
2320 2343 3.498774 ATCAGGGGATGAAGGAATTCG 57.501 47.619 0.00 0.00 42.53 3.34
2375 2398 1.750778 CCGCAATCTTGTGCCCTTAAT 59.249 47.619 0.00 0.00 41.73 1.40
2395 2418 3.849953 GCTACTGCCGGCGAAACG 61.850 66.667 23.90 10.07 0.00 3.60
2426 2449 8.200792 ACTCCTTCTAGTGTATGAATTCATGTC 58.799 37.037 27.59 20.17 37.15 3.06
2583 2606 3.005554 CCATCGAGACATCAAAGCAAGT 58.994 45.455 0.00 0.00 0.00 3.16
2742 2765 1.682257 GAAGGCAAGCCCTCTCACT 59.318 57.895 7.62 0.00 45.62 3.41
2767 2790 3.560481 TGTATTTTCTTTCGGCGTGTTCA 59.440 39.130 6.85 0.00 0.00 3.18
2910 2933 1.212688 AGGCTGCATGGCAACTATGTA 59.787 47.619 0.50 0.00 44.55 2.29
2961 2984 3.321039 AGGATTGATATGCTCTCACCCA 58.679 45.455 0.00 0.00 0.00 4.51
3129 3152 3.756963 CCTCGTATCCTTCATCGATGGTA 59.243 47.826 24.61 12.44 0.00 3.25
3138 3161 4.262635 CCTTCATCGATGGTAAGCTATGGT 60.263 45.833 24.61 0.00 0.00 3.55
3142 3165 4.746535 TCGATGGTAAGCTATGGTTCAA 57.253 40.909 0.00 0.00 0.00 2.69
3394 3419 8.602424 CCTCTAGAGAATGAGATAGAACTAGGA 58.398 40.741 21.76 0.00 32.44 2.94
3395 3420 9.658799 CTCTAGAGAATGAGATAGAACTAGGAG 57.341 40.741 15.05 0.00 32.44 3.69
3396 3421 8.602424 TCTAGAGAATGAGATAGAACTAGGAGG 58.398 40.741 0.00 0.00 0.00 4.30
3400 3425 4.456662 TGAGATAGAACTAGGAGGTCCC 57.543 50.000 0.00 0.00 30.45 4.46
3475 3500 4.849383 GGGTTCATGAACAAATAAACGACG 59.151 41.667 33.42 0.00 42.85 5.12
3484 3509 2.396590 AATAAACGACGAGGGCATGT 57.603 45.000 0.00 0.00 0.00 3.21
3493 3518 1.093972 CGAGGGCATGTTTATGTGCA 58.906 50.000 0.00 0.00 43.00 4.57
3506 3531 5.974158 TGTTTATGTGCACACAATGTTGTAC 59.026 36.000 24.37 11.35 45.41 2.90
3507 3532 6.183360 TGTTTATGTGCACACAATGTTGTACT 60.183 34.615 24.37 3.83 45.41 2.73
3508 3533 4.916983 ATGTGCACACAATGTTGTACTT 57.083 36.364 24.37 0.00 45.41 2.24
3509 3534 7.497925 TTATGTGCACACAATGTTGTACTTA 57.502 32.000 24.37 2.49 45.41 2.24
3598 3623 3.657727 TGAAGAAGGGGGAGTTCTTTCAT 59.342 43.478 0.00 0.00 42.95 2.57
3780 3805 3.054878 GCCTCAAAGTCATGCTGTTTTG 58.945 45.455 0.00 0.00 33.09 2.44
3825 3850 4.141041 TCCCTCAGGAATTTTTCTTCCACA 60.141 41.667 0.00 0.00 46.02 4.17
3948 3973 5.419471 GCTCCTACAGTAATCCCCATACTAG 59.581 48.000 0.00 0.00 32.47 2.57
4004 4031 6.463995 AGTACAACACAACACAATTCCAAT 57.536 33.333 0.00 0.00 0.00 3.16
4005 4032 6.503524 AGTACAACACAACACAATTCCAATC 58.496 36.000 0.00 0.00 0.00 2.67
4008 4035 6.169094 ACAACACAACACAATTCCAATCAAA 58.831 32.000 0.00 0.00 0.00 2.69
4009 4036 6.822676 ACAACACAACACAATTCCAATCAAAT 59.177 30.769 0.00 0.00 0.00 2.32
4112 4244 5.335661 GCGTTTACTGGGATTCAAGAACAAT 60.336 40.000 0.00 0.00 0.00 2.71
4208 4340 0.693622 ATCCCGCTATCTCCTCTCGA 59.306 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.745975 TGAAGGACATCAACGACAATCAC 59.254 43.478 0.00 0.00 0.00 3.06
152 153 2.174424 GGAATGGCCTTCTTCATCTCCT 59.826 50.000 3.32 0.00 34.08 3.69
190 191 1.665448 CGGCATCAGCTCTGTCTATCG 60.665 57.143 0.00 0.00 41.70 2.92
223 224 2.584391 GGGTGCGGTCCTTCTCTGT 61.584 63.158 0.00 0.00 0.00 3.41
234 235 2.124320 CCCAATGGTAGGGTGCGG 60.124 66.667 0.00 0.00 41.61 5.69
240 241 1.376609 GCAAGTCGCCCAATGGTAGG 61.377 60.000 0.00 0.00 32.94 3.18
251 252 1.439365 CTGCGTTTCTGCAAGTCGC 60.439 57.895 14.94 14.94 45.74 5.19
286 287 1.296727 GTTAACCTCTACGGCCATGC 58.703 55.000 2.24 0.00 35.61 4.06
364 365 2.222027 CTTCACTGGGACAAACCTCAC 58.778 52.381 0.00 0.00 38.70 3.51
457 458 4.287067 AGGTGTGTCATTCCTTCTACATGT 59.713 41.667 2.69 2.69 0.00 3.21
615 619 1.942657 CAGGCATATCCACAAACCTCG 59.057 52.381 0.00 0.00 37.29 4.63
646 661 1.000506 TGTGACCCGCTACTTCAGAAC 59.999 52.381 0.00 0.00 0.00 3.01
758 773 9.961265 TTGGTATTATGAAGATACTTGTCTACG 57.039 33.333 0.00 0.00 32.02 3.51
844 859 2.867472 CAACAATGCCCGGACGTC 59.133 61.111 7.13 7.13 0.00 4.34
939 954 3.371097 CTACATGACGGGCACGCCT 62.371 63.158 9.12 0.00 46.04 5.52
969 984 6.201425 GGTAGTGACAACAGAAACGACATTTA 59.799 38.462 0.00 0.00 0.00 1.40
993 1008 1.497278 CGTGAGTGCCATTCAACGG 59.503 57.895 0.00 0.00 0.00 4.44
1010 1025 3.119291 CACAAGCATCTTAGTCTAGGCG 58.881 50.000 0.00 0.00 0.00 5.52
1033 1053 1.701847 AGTCATGCCAGTCCTGTCTTT 59.298 47.619 0.00 0.00 0.00 2.52
1178 1198 1.134965 CAAGGAAGAGGAGCACTACGG 60.135 57.143 0.00 0.00 0.00 4.02
1183 1203 1.377856 GGCCAAGGAAGAGGAGCAC 60.378 63.158 0.00 0.00 0.00 4.40
1216 1236 3.455177 TGGTCACCAGTACCAGTAACAAA 59.545 43.478 0.00 0.00 42.10 2.83
1511 1534 1.207488 AAGGAGGCCCATGTACTGCA 61.207 55.000 0.00 0.00 33.88 4.41
1536 1559 0.821301 TTGCCATGCCGTTGTTCTGA 60.821 50.000 0.00 0.00 0.00 3.27
1700 1723 5.986501 AACAAGGGTCAAGTTGTTAAACA 57.013 34.783 2.11 0.00 43.45 2.83
1784 1807 1.858739 AAGGTTTAGCGGGGCCATGA 61.859 55.000 4.39 0.00 0.00 3.07
1820 1843 1.452025 CGTGCTTGGTCGATATTAGCG 59.548 52.381 0.00 0.00 34.65 4.26
1821 1844 2.471743 GTCGTGCTTGGTCGATATTAGC 59.528 50.000 0.00 0.00 38.32 3.09
1874 1897 2.640184 CTGCTGCTGATGAGAATCCAA 58.360 47.619 0.00 0.00 0.00 3.53
1884 1907 2.754658 GCCTTGCCTGCTGCTGAT 60.755 61.111 8.20 0.00 42.00 2.90
2010 2033 9.261035 AGAATTATCTCTAGAAACTTGGACAGA 57.739 33.333 0.00 0.00 0.00 3.41
2073 2096 2.158957 TCTCACGAGCAGAAAAACCACT 60.159 45.455 0.00 0.00 0.00 4.00
2091 2114 2.765122 GCATACCTCAGATGCCTTCTC 58.235 52.381 0.00 0.00 43.24 2.87
2304 2327 3.877508 CTGTTACGAATTCCTTCATCCCC 59.122 47.826 0.00 0.00 0.00 4.81
2395 2418 5.916661 TCATACACTAGAAGGAGTTCACC 57.083 43.478 0.00 0.00 34.82 4.02
2583 2606 0.098200 CATCGTCGAGGAGCACGTTA 59.902 55.000 13.85 0.00 37.30 3.18
2742 2765 3.749088 ACACGCCGAAAGAAAATACATCA 59.251 39.130 0.00 0.00 0.00 3.07
2767 2790 1.208052 CCCACATGTGACCTCGAGAAT 59.792 52.381 27.46 0.49 0.00 2.40
2910 2933 3.087031 CACCAAACATGCCTCTTGATCT 58.913 45.455 0.00 0.00 0.00 2.75
2961 2984 2.124151 GGCCTTGCGTCCATGGAT 60.124 61.111 19.62 0.00 38.26 3.41
3059 3082 0.747283 CTGCATCAAGGCCAGAGTCC 60.747 60.000 5.01 0.00 0.00 3.85
3138 3161 5.342017 TCTCCTGAGAAGGAAGGTATTGAA 58.658 41.667 0.00 0.00 37.55 2.69
3142 3165 5.594777 TCTTTCTCCTGAGAAGGAAGGTAT 58.405 41.667 16.55 0.00 46.23 2.73
3396 3421 4.366684 CCTGGCCAGGTTGGGGAC 62.367 72.222 39.52 0.00 43.61 4.46
3411 3436 1.421268 TCAAGTGACAATGCAGACCCT 59.579 47.619 0.00 0.00 0.00 4.34
3475 3500 1.818060 TGTGCACATAAACATGCCCTC 59.182 47.619 17.42 0.00 0.00 4.30
3484 3509 6.384258 AGTACAACATTGTGTGCACATAAA 57.616 33.333 29.18 22.86 42.31 1.40
3507 3532 9.167311 GGAGAGAGTGAATGCTTATTTTTCTAA 57.833 33.333 0.00 0.00 0.00 2.10
3508 3533 8.543774 AGGAGAGAGTGAATGCTTATTTTTCTA 58.456 33.333 0.00 0.00 0.00 2.10
3509 3534 7.401246 AGGAGAGAGTGAATGCTTATTTTTCT 58.599 34.615 0.00 0.00 0.00 2.52
3598 3623 9.392506 TGAGATATAATGGATGGAGAAACCTTA 57.607 33.333 0.00 0.00 39.86 2.69
3711 3736 8.421249 TGAAAATACAGGTGGATGAAGAAAAT 57.579 30.769 0.00 0.00 0.00 1.82
3753 3778 3.698040 CAGCATGACTTTGAGGCCTAATT 59.302 43.478 4.42 0.00 39.69 1.40
3767 3792 1.135689 CCCTACGCAAAACAGCATGAC 60.136 52.381 0.00 0.00 39.69 3.06
3948 3973 8.984764 TGTGTAGTTATGGCGATATATGTTTTC 58.015 33.333 0.00 0.00 0.00 2.29
3972 3999 7.618502 TGTGTTGTGTTGTACTTAAATCTGT 57.381 32.000 0.00 0.00 0.00 3.41
4004 4031 2.041485 TGGGTGCTCTTGGATCATTTGA 59.959 45.455 0.00 0.00 0.00 2.69
4005 4032 2.426024 CTGGGTGCTCTTGGATCATTTG 59.574 50.000 0.00 0.00 0.00 2.32
4008 4035 0.549950 CCTGGGTGCTCTTGGATCAT 59.450 55.000 0.00 0.00 0.00 2.45
4009 4036 0.547471 TCCTGGGTGCTCTTGGATCA 60.547 55.000 0.00 0.00 0.00 2.92
4097 4229 4.344104 TCCTCCAATTGTTCTTGAATCCC 58.656 43.478 4.43 0.00 0.00 3.85
4112 4244 5.188948 TGATCCTCTCGTTAATTTCCTCCAA 59.811 40.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.