Multiple sequence alignment - TraesCS3D01G415000

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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 TraesCS3D01G415000 chr3D 100.000 3485 0 0 1 3485 526973931 526977415 0.000000e+00 6436
1 TraesCS3D01G415000 chr3B 94.073 3003 124 13 2 2979 696327537 696330510 0.000000e+00 4510
2 TraesCS3D01G415000 chr3B 93.933 511 21 8 2976 3484 696330567 696331069 0.000000e+00 763
3 TraesCS3D01G415000 chr3A 93.493 3012 125 22 1 2979 661472693 661475666 0.000000e+00 4410
4 TraesCS3D01G415000 chr3A 95.108 511 16 7 2976 3485 661475723 661476225 0.000000e+00 797
5 TraesCS3D01G415000 chr7D 91.362 1065 84 4 952 2013 496314134 496315193 0.000000e+00 1450
6 TraesCS3D01G415000 chr7B 91.406 128 5 1 465 586 312023750 312023623 1.660000e-38 171
7 TraesCS3D01G415000 chr7B 90.625 128 6 2 465 586 311927075 311926948 7.740000e-37 165


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 TraesCS3D01G415000 chr3D 526973931 526977415 3484 False 6436.0 6436 100.0000 1 3485 1 chr3D.!!$F1 3484
1 TraesCS3D01G415000 chr3B 696327537 696331069 3532 False 2636.5 4510 94.0030 2 3484 2 chr3B.!!$F1 3482
2 TraesCS3D01G415000 chr3A 661472693 661476225 3532 False 2603.5 4410 94.3005 1 3485 2 chr3A.!!$F1 3484
3 TraesCS3D01G415000 chr7D 496314134 496315193 1059 False 1450.0 1450 91.3620 952 2013 1 chr7D.!!$F1 1061

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
993 1025 0.536460 GCCGGGGAACTTTGTCTGAA 60.536 55.0 2.18 0.0 0.0 3.02 F
995 1027 0.875059 CGGGGAACTTTGTCTGAAGC 59.125 55.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2171 1.079612 GGGCCTTCATTGCTTGCAC 60.080 57.895 0.84 0.0 0.0 4.57 R
2979 3017 1.506309 CTATTGCGCGGCTGCCAATA 61.506 55.000 26.30 26.3 40.3 1.90 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
122 123 2.213499 GGCAGATGGATACGAAGTTGG 58.787 52.381 0.00 0.00 37.78 3.77
135 136 1.740025 GAAGTTGGGATCAAGGAAGCG 59.260 52.381 0.00 0.00 32.92 4.68
157 159 4.029809 GGTGAGGGGAACGGTGGG 62.030 72.222 0.00 0.00 0.00 4.61
255 257 3.858247 TCCTGCATCGATCATCATCATC 58.142 45.455 0.00 0.00 0.00 2.92
258 260 4.495422 CTGCATCGATCATCATCATCAGA 58.505 43.478 0.00 0.00 0.00 3.27
302 307 8.279970 TGGACGAATCAATTCAACTAATCAAT 57.720 30.769 3.81 0.00 36.61 2.57
306 311 6.141211 CGAATCAATTCAACTAATCAATGCCG 59.859 38.462 3.81 0.00 36.61 5.69
324 329 1.064060 CCGGATTTCAGTTTCATCGGC 59.936 52.381 0.00 0.00 0.00 5.54
353 358 6.721208 AGCATTGAAGAAAGTTTCCCAGAATA 59.279 34.615 12.05 0.00 0.00 1.75
717 747 4.615121 CGCTCTCTATCTTTTATGCTCGAC 59.385 45.833 0.00 0.00 0.00 4.20
952 984 4.048470 GGGGGAGTGGGTGGAAGC 62.048 72.222 0.00 0.00 0.00 3.86
953 985 2.936032 GGGGAGTGGGTGGAAGCT 60.936 66.667 0.00 0.00 0.00 3.74
954 986 2.539081 GGGGAGTGGGTGGAAGCTT 61.539 63.158 0.00 0.00 0.00 3.74
955 987 1.303643 GGGAGTGGGTGGAAGCTTG 60.304 63.158 2.10 0.00 0.00 4.01
956 988 1.303643 GGAGTGGGTGGAAGCTTGG 60.304 63.158 2.10 0.00 0.00 3.61
960 992 1.150536 TGGGTGGAAGCTTGGTGTC 59.849 57.895 2.10 0.00 0.00 3.67
988 1020 2.203437 GTGGCCGGGGAACTTTGT 60.203 61.111 2.18 0.00 0.00 2.83
989 1021 2.114411 TGGCCGGGGAACTTTGTC 59.886 61.111 2.18 0.00 0.00 3.18
990 1022 2.434774 GGCCGGGGAACTTTGTCT 59.565 61.111 2.18 0.00 0.00 3.41
991 1023 1.971695 GGCCGGGGAACTTTGTCTG 60.972 63.158 2.18 0.00 0.00 3.51
992 1024 1.072505 GCCGGGGAACTTTGTCTGA 59.927 57.895 2.18 0.00 0.00 3.27
993 1025 0.536460 GCCGGGGAACTTTGTCTGAA 60.536 55.000 2.18 0.00 0.00 3.02
995 1027 0.875059 CGGGGAACTTTGTCTGAAGC 59.125 55.000 0.00 0.00 0.00 3.86
996 1028 1.543429 CGGGGAACTTTGTCTGAAGCT 60.543 52.381 0.00 0.00 0.00 3.74
1272 1306 4.514577 CTCCTCGCCGCGTCCATT 62.515 66.667 13.39 0.00 0.00 3.16
1282 1316 2.264480 CGTCCATTCCGCACCTCA 59.736 61.111 0.00 0.00 0.00 3.86
1555 1589 3.089284 TCTAATCAGTGTCTTGAGCCGA 58.911 45.455 0.00 0.00 0.00 5.54
1701 1735 4.572571 TTCCGGGCGTTGCTGGTT 62.573 61.111 0.00 0.00 0.00 3.67
1833 1867 1.804372 GCTGTGCTTACCATCGAGGAG 60.804 57.143 0.00 0.00 41.22 3.69
1836 1870 1.300233 GCTTACCATCGAGGAGGCG 60.300 63.158 0.00 0.00 41.22 5.52
1941 1975 2.106683 GGGACGGTTGAATGAGGCG 61.107 63.158 0.00 0.00 0.00 5.52
2048 2082 3.550437 ACAGAGGGTAGATGATGCAAC 57.450 47.619 0.00 0.00 0.00 4.17
2137 2171 0.449388 GAAGGGTCTTTGCGATGCTG 59.551 55.000 0.00 0.00 0.00 4.41
2237 2271 5.016051 TCTATCTTGATCAGTGGCTTGTC 57.984 43.478 0.00 0.00 0.00 3.18
2238 2272 2.479566 TCTTGATCAGTGGCTTGTCC 57.520 50.000 0.00 0.00 0.00 4.02
2240 2274 2.373169 TCTTGATCAGTGGCTTGTCCTT 59.627 45.455 0.00 0.00 35.26 3.36
2263 2297 3.194968 AGAAGGAAAGTTTATCGAGGCGA 59.805 43.478 0.00 0.00 41.13 5.54
2267 2301 3.434299 GGAAAGTTTATCGAGGCGACAAA 59.566 43.478 0.00 0.00 39.18 2.83
2321 2355 3.493129 CGTCCTGACAGAAACGATTTCAA 59.507 43.478 19.51 0.00 42.10 2.69
2459 2493 6.985653 TTCATCATCTTTAGGAGTAGGAGG 57.014 41.667 0.00 0.00 0.00 4.30
2470 2504 2.957006 GGAGTAGGAGGAAGCGTTATGA 59.043 50.000 0.00 0.00 0.00 2.15
2538 2572 1.135546 CACACCAAAGACAACGCAACA 60.136 47.619 0.00 0.00 0.00 3.33
2642 2680 4.074799 TCAGTATGAAGAGGAGGGGAAA 57.925 45.455 0.00 0.00 45.97 3.13
2643 2681 4.635473 TCAGTATGAAGAGGAGGGGAAAT 58.365 43.478 0.00 0.00 45.97 2.17
2644 2682 4.410228 TCAGTATGAAGAGGAGGGGAAATG 59.590 45.833 0.00 0.00 45.97 2.32
2645 2683 3.718956 AGTATGAAGAGGAGGGGAAATGG 59.281 47.826 0.00 0.00 0.00 3.16
2646 2684 1.298953 TGAAGAGGAGGGGAAATGGG 58.701 55.000 0.00 0.00 0.00 4.00
2647 2685 0.553333 GAAGAGGAGGGGAAATGGGG 59.447 60.000 0.00 0.00 0.00 4.96
2648 2686 0.123266 AAGAGGAGGGGAAATGGGGA 59.877 55.000 0.00 0.00 0.00 4.81
2649 2687 0.123266 AGAGGAGGGGAAATGGGGAA 59.877 55.000 0.00 0.00 0.00 3.97
2662 2700 3.778954 ATGGGGAATTGAGCTAGCTAC 57.221 47.619 19.38 11.96 0.00 3.58
2663 2701 2.477245 TGGGGAATTGAGCTAGCTACA 58.523 47.619 19.38 14.51 0.00 2.74
2691 2729 2.086869 CGCAAACATGAGGAGGTTCAT 58.913 47.619 0.00 0.00 38.30 2.57
2692 2730 2.489329 CGCAAACATGAGGAGGTTCATT 59.511 45.455 0.00 0.00 35.67 2.57
2710 2748 2.549064 TTGAGTGCTGCTTGCTTCTA 57.451 45.000 0.00 0.00 43.37 2.10
2806 2844 2.154462 GTGGTGACAGGTTGGAATCTG 58.846 52.381 0.00 0.00 44.46 2.90
2901 2939 3.049674 CGCGAAGGAGCAGCCAAA 61.050 61.111 0.00 0.00 40.02 3.28
2911 2949 1.335145 AGCAGCCAAAAAGCTCACAT 58.665 45.000 0.00 0.00 42.61 3.21
2979 3017 2.307768 TCTTGAGAGTGAACACGGACT 58.692 47.619 0.00 1.63 36.20 3.85
2980 3018 3.483421 TCTTGAGAGTGAACACGGACTA 58.517 45.455 0.00 0.00 36.20 2.59
3066 3165 5.184864 TGTTTGGTTCTTTCATATGCCGATT 59.815 36.000 0.00 0.00 0.00 3.34
3178 3277 4.204012 TCCCAGACTTTGTTTTGTGTAGG 58.796 43.478 0.00 0.00 0.00 3.18
3179 3278 3.317993 CCCAGACTTTGTTTTGTGTAGGG 59.682 47.826 0.00 0.00 0.00 3.53
3203 3302 7.312899 GGCTATTTAGTTTTTGAGCAAGCTTA 58.687 34.615 0.00 0.00 0.00 3.09
3377 3477 1.644786 GCTACCGGCGCACTTGATTT 61.645 55.000 10.83 0.00 0.00 2.17
3378 3478 1.647346 CTACCGGCGCACTTGATTTA 58.353 50.000 10.83 0.00 0.00 1.40
3379 3479 1.326548 CTACCGGCGCACTTGATTTAC 59.673 52.381 10.83 0.00 0.00 2.01
3380 3480 0.321298 ACCGGCGCACTTGATTTACT 60.321 50.000 10.83 0.00 0.00 2.24
3381 3481 0.373716 CCGGCGCACTTGATTTACTC 59.626 55.000 10.83 0.00 0.00 2.59
3382 3482 1.359848 CGGCGCACTTGATTTACTCT 58.640 50.000 10.83 0.00 0.00 3.24
3455 3555 3.903876 GCATCATGCGTCGTTTCAT 57.096 47.368 0.00 0.00 31.71 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 2.897350 CGCCCGCTTCCTTGATCC 60.897 66.667 0.00 0.00 0.00 3.36
157 159 1.207329 AGCTCGGAGGTTAACATCACC 59.793 52.381 20.75 5.35 34.06 4.02
255 257 6.316140 TCCATATGATCCTCGTTTGTTTTCTG 59.684 38.462 3.65 0.00 0.00 3.02
258 260 5.064707 CGTCCATATGATCCTCGTTTGTTTT 59.935 40.000 3.65 0.00 0.00 2.43
302 307 1.737236 CGATGAAACTGAAATCCGGCA 59.263 47.619 0.00 0.00 0.00 5.69
306 311 3.378112 TGATGCCGATGAAACTGAAATCC 59.622 43.478 0.00 0.00 0.00 3.01
324 329 5.166398 GGGAAACTTTCTTCAATGCTGATG 58.834 41.667 1.57 0.00 0.00 3.07
353 358 2.524306 TCGTTTCCTTCCATGCCATTT 58.476 42.857 0.00 0.00 0.00 2.32
479 495 1.454295 GGTCGAGGAGGAGGAGGAC 60.454 68.421 0.00 0.00 0.00 3.85
717 747 2.333701 AATAGTTAAGGCGGGCGGGG 62.334 60.000 0.00 0.00 0.00 5.73
937 969 1.303643 CAAGCTTCCACCCACTCCC 60.304 63.158 0.00 0.00 0.00 4.30
938 970 1.303643 CCAAGCTTCCACCCACTCC 60.304 63.158 0.00 0.00 0.00 3.85
939 971 0.890996 CACCAAGCTTCCACCCACTC 60.891 60.000 0.00 0.00 0.00 3.51
944 976 1.227853 ACGACACCAAGCTTCCACC 60.228 57.895 0.00 0.00 0.00 4.61
985 1017 1.675714 CGCCATACCAGCTTCAGACAA 60.676 52.381 0.00 0.00 0.00 3.18
988 1020 0.461548 CTCGCCATACCAGCTTCAGA 59.538 55.000 0.00 0.00 0.00 3.27
989 1021 0.531532 CCTCGCCATACCAGCTTCAG 60.532 60.000 0.00 0.00 0.00 3.02
990 1022 1.522092 CCTCGCCATACCAGCTTCA 59.478 57.895 0.00 0.00 0.00 3.02
991 1023 1.227674 CCCTCGCCATACCAGCTTC 60.228 63.158 0.00 0.00 0.00 3.86
992 1024 2.746375 CCCCTCGCCATACCAGCTT 61.746 63.158 0.00 0.00 0.00 3.74
993 1025 3.164269 CCCCTCGCCATACCAGCT 61.164 66.667 0.00 0.00 0.00 4.24
995 1027 4.609018 CGCCCCTCGCCATACCAG 62.609 72.222 0.00 0.00 0.00 4.00
1408 1442 1.227292 GGAATTCGTCGAGGAGCCC 60.227 63.158 7.98 7.23 0.00 5.19
1555 1589 4.452733 GCGGTAGGCGCCTCTGTT 62.453 66.667 36.73 12.19 0.00 3.16
1836 1870 3.508840 CGGTCAATGGCTTCCCGC 61.509 66.667 0.00 0.00 38.13 6.13
1941 1975 4.559153 CCATGTCCTGAAACAAATTGTCC 58.441 43.478 0.00 0.00 31.81 4.02
2137 2171 1.079612 GGGCCTTCATTGCTTGCAC 60.080 57.895 0.84 0.00 0.00 4.57
2238 2272 5.232414 CGCCTCGATAAACTTTCCTTCTAAG 59.768 44.000 0.00 0.00 0.00 2.18
2240 2274 4.400251 TCGCCTCGATAAACTTTCCTTCTA 59.600 41.667 0.00 0.00 0.00 2.10
2254 2288 2.550978 CATAACCTTTGTCGCCTCGAT 58.449 47.619 0.00 0.00 38.42 3.59
2263 2297 3.852578 ACCATCCTCTCCATAACCTTTGT 59.147 43.478 0.00 0.00 0.00 2.83
2267 2301 3.421394 TCACCATCCTCTCCATAACCT 57.579 47.619 0.00 0.00 0.00 3.50
2316 2350 9.239002 CATAAACCTTCAATAACGTTGTTGAAA 57.761 29.630 36.36 27.45 44.10 2.69
2321 2355 8.073768 CAGAACATAAACCTTCAATAACGTTGT 58.926 33.333 11.99 0.00 0.00 3.32
2459 2493 4.024556 ACATAGCTGCAATCATAACGCTTC 60.025 41.667 1.02 0.00 0.00 3.86
2470 2504 5.933617 TCCTAATTCTCACATAGCTGCAAT 58.066 37.500 1.02 0.00 0.00 3.56
2642 2680 3.048600 TGTAGCTAGCTCAATTCCCCAT 58.951 45.455 23.26 0.00 0.00 4.00
2643 2681 2.477245 TGTAGCTAGCTCAATTCCCCA 58.523 47.619 23.26 0.00 0.00 4.96
2644 2682 3.778954 ATGTAGCTAGCTCAATTCCCC 57.221 47.619 23.26 0.91 0.00 4.81
2645 2683 4.274459 CACAATGTAGCTAGCTCAATTCCC 59.726 45.833 23.26 2.33 0.00 3.97
2646 2684 4.878397 ACACAATGTAGCTAGCTCAATTCC 59.122 41.667 23.26 4.12 0.00 3.01
2647 2685 5.007136 GGACACAATGTAGCTAGCTCAATTC 59.993 44.000 23.26 9.92 0.00 2.17
2648 2686 4.878397 GGACACAATGTAGCTAGCTCAATT 59.122 41.667 23.26 18.53 0.00 2.32
2649 2687 4.446371 GGACACAATGTAGCTAGCTCAAT 58.554 43.478 23.26 13.34 0.00 2.57
2662 2700 2.587956 CTCATGTTTGCGGACACAATG 58.412 47.619 0.00 0.24 31.30 2.82
2663 2701 1.541147 CCTCATGTTTGCGGACACAAT 59.459 47.619 0.00 0.00 28.45 2.71
2710 2748 2.489329 CAAACATGTCTCAGGCCGAAAT 59.511 45.455 0.00 0.00 0.00 2.17
2749 2787 4.811908 CAGCATGGTTTTCATTGTGATGA 58.188 39.130 0.00 0.00 40.46 2.92
2806 2844 4.175787 TCTCTTTCCTTCAGCGTTACTC 57.824 45.455 0.00 0.00 0.00 2.59
2911 2949 8.750515 TGCCATCAGAAATAAGAATTGATACA 57.249 30.769 0.00 0.00 0.00 2.29
2979 3017 1.506309 CTATTGCGCGGCTGCCAATA 61.506 55.000 26.30 26.30 40.30 1.90
2980 3018 2.828095 TATTGCGCGGCTGCCAAT 60.828 55.556 26.72 26.72 41.61 3.16
3091 3190 0.245539 GCTTAGCCCGACAGTGTGTA 59.754 55.000 0.00 0.00 0.00 2.90
3092 3191 1.004918 GCTTAGCCCGACAGTGTGT 60.005 57.895 0.00 0.00 0.00 3.72
3094 3193 1.191535 TATGCTTAGCCCGACAGTGT 58.808 50.000 0.29 0.00 0.00 3.55
3143 3242 1.134670 GTCTGGGATTTGGTCTCTCCG 60.135 57.143 0.00 0.00 39.52 4.63
3178 3277 5.714047 AGCTTGCTCAAAAACTAAATAGCC 58.286 37.500 0.00 0.00 0.00 3.93
3179 3278 8.742554 TTAAGCTTGCTCAAAAACTAAATAGC 57.257 30.769 9.86 0.00 0.00 2.97
3272 3372 2.618053 GACGTCCGGAAATCATTCTGT 58.382 47.619 5.23 0.00 39.83 3.41
3326 3426 4.671766 GCAAACCACGAACAACAGGATATC 60.672 45.833 0.00 0.00 0.00 1.63
3364 3464 3.831715 AAAGAGTAAATCAAGTGCGCC 57.168 42.857 4.18 0.00 0.00 6.53
3446 3546 4.989168 ACTCCACACTCTAAATGAAACGAC 59.011 41.667 0.00 0.00 0.00 4.34
3455 3555 5.353394 AACAACTGACTCCACACTCTAAA 57.647 39.130 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.