Multiple sequence alignment - TraesCS6B01G348300

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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 TraesCS6B01G348300 chr6B 100.000 4478 0 0 1 4478 613111135 613115612 0.000000e+00 8270
1 TraesCS6B01G348300 chr6D 95.258 4471 116 31 1 4425 408650525 408654945 0.000000e+00 6994
2 TraesCS6B01G348300 chr6D 81.703 634 68 24 5 621 450820674 450820072 6.730000e-133 484
3 TraesCS6B01G348300 chr6A 96.063 3708 88 18 502 4190 554459214 554462882 0.000000e+00 5986
4 TraesCS6B01G348300 chr6A 93.204 412 21 5 1 410 554458817 554459223 2.310000e-167 599
5 TraesCS6B01G348300 chr6A 94.792 288 11 2 4191 4478 554462950 554463233 3.180000e-121 446
6 TraesCS6B01G348300 chr6A 78.636 557 60 24 202 742 596341119 596340606 9.350000e-82 315
7 TraesCS6B01G348300 chr3D 82.451 359 39 20 7 358 335628950 335628609 4.380000e-75 292
8 TraesCS6B01G348300 chr3B 82.173 359 40 20 7 358 434048839 434048498 2.040000e-73 287
9 TraesCS6B01G348300 chr3B 89.024 82 5 2 3837 3918 22056104 22056027 1.030000e-16 99
10 TraesCS6B01G348300 chr3A 82.173 359 40 19 7 358 453601924 453601583 2.040000e-73 287
11 TraesCS6B01G348300 chr1D 88.350 103 6 4 3829 3931 320590034 320589938 7.870000e-23 119
12 TraesCS6B01G348300 chr1D 87.234 94 9 1 3831 3924 319515834 319515744 2.200000e-18 104
13 TraesCS6B01G348300 chr2B 92.683 82 3 1 3837 3918 754008455 754008533 1.020000e-21 115
14 TraesCS6B01G348300 chr2B 89.286 84 6 1 3837 3920 139078987 139078907 7.920000e-18 102
15 TraesCS6B01G348300 chr7A 88.095 84 8 1 3835 3918 679894568 679894487 1.030000e-16 99
16 TraesCS6B01G348300 chr4A 88.235 85 6 2 3835 3918 567678338 567678257 1.030000e-16 99


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 TraesCS6B01G348300 chr6B 613111135 613115612 4477 False 8270.000000 8270 100.000000 1 4478 1 chr6B.!!$F1 4477
1 TraesCS6B01G348300 chr6D 408650525 408654945 4420 False 6994.000000 6994 95.258000 1 4425 1 chr6D.!!$F1 4424
2 TraesCS6B01G348300 chr6D 450820072 450820674 602 True 484.000000 484 81.703000 5 621 1 chr6D.!!$R1 616
3 TraesCS6B01G348300 chr6A 554458817 554463233 4416 False 2343.666667 5986 94.686333 1 4478 3 chr6A.!!$F1 4477
4 TraesCS6B01G348300 chr6A 596340606 596341119 513 True 315.000000 315 78.636000 202 742 1 chr6A.!!$R1 540

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
411 426 0.544357 CATCGGGGGATGGCCTAGTA 60.544 60.0 3.32 0.0 0.00 1.82 F
1503 1663 0.179056 CCGCCGTCATCCCACTTATT 60.179 55.0 0.00 0.0 0.00 1.40 F
1536 1696 0.322816 AGGCCAACTACCTCGTCGTA 60.323 55.0 5.01 0.0 28.76 3.43 F
1800 1960 0.391661 CTGCACGCCACCTTATGTCT 60.392 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2217 0.250901 AAAGGCAGCCTCAACACGAT 60.251 50.0 16.53 0.0 30.89 3.73 R
2920 3080 0.323629 TCATCACCGGAAGACCCAAC 59.676 55.0 9.46 0.0 34.14 3.77 R
3405 3565 0.324552 CCAAGCCATCCAATCCCACA 60.325 55.0 0.00 0.0 0.00 4.17 R
3779 3968 2.907910 GCAAGTGCTACATCACCAAG 57.092 50.0 0.00 0.0 37.68 3.61 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
114 116 3.495193 CCTGTGCAATTTCAGAATGTCG 58.505 45.455 3.73 0.00 37.40 4.35
188 190 5.878116 TCAACATAACCGGTCTTAATCAAGG 59.122 40.000 8.04 0.00 32.22 3.61
220 225 4.378774 ACTATAGCAAAGCATGAGCAGAG 58.621 43.478 0.00 0.00 45.49 3.35
368 383 2.879002 ACAGGACTGCATAGTGATCG 57.121 50.000 0.00 0.00 37.25 3.69
383 398 3.376935 ATCGGTGGCCTCAAGCTCG 62.377 63.158 3.32 0.00 43.05 5.03
396 411 3.918220 GCTCGGAAGCGCACATCG 61.918 66.667 11.47 8.20 42.44 3.84
411 426 0.544357 CATCGGGGGATGGCCTAGTA 60.544 60.000 3.32 0.00 0.00 1.82
418 433 3.850173 GGGGGATGGCCTAGTAATGATAA 59.150 47.826 3.32 0.00 0.00 1.75
419 434 4.478686 GGGGGATGGCCTAGTAATGATAAT 59.521 45.833 3.32 0.00 0.00 1.28
421 436 6.332901 GGGGGATGGCCTAGTAATGATAATAT 59.667 42.308 3.32 0.00 0.00 1.28
422 437 7.227156 GGGGATGGCCTAGTAATGATAATATG 58.773 42.308 3.32 0.00 0.00 1.78
425 440 8.486210 GGATGGCCTAGTAATGATAATATGACA 58.514 37.037 3.32 0.00 0.00 3.58
426 441 9.890629 GATGGCCTAGTAATGATAATATGACAA 57.109 33.333 3.32 0.00 0.00 3.18
427 442 9.672673 ATGGCCTAGTAATGATAATATGACAAC 57.327 33.333 3.32 0.00 0.00 3.32
428 443 8.655901 TGGCCTAGTAATGATAATATGACAACA 58.344 33.333 3.32 0.00 0.00 3.33
429 444 9.502091 GGCCTAGTAATGATAATATGACAACAA 57.498 33.333 0.00 0.00 0.00 2.83
441 456 3.793797 TGACAACAAAGAGAGACACGA 57.206 42.857 0.00 0.00 0.00 4.35
494 509 1.673665 GTGCAGTTCAGGAGCCAGG 60.674 63.158 0.00 0.00 0.00 4.45
495 510 1.842920 TGCAGTTCAGGAGCCAGGA 60.843 57.895 0.00 0.00 0.00 3.86
496 511 1.078567 GCAGTTCAGGAGCCAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
497 512 1.078567 CAGTTCAGGAGCCAGGAGC 60.079 63.158 0.00 0.00 44.25 4.70
689 817 2.492090 CTGAGCTTCGGGGAGACG 59.508 66.667 0.00 0.00 0.00 4.18
713 845 4.704833 CAGTGCCGTGGGAGTGGG 62.705 72.222 7.31 0.00 33.98 4.61
743 875 5.012561 AGGTGAAGCTTCTATGTTCAGAGTT 59.987 40.000 26.09 0.00 30.94 3.01
744 876 5.703130 GGTGAAGCTTCTATGTTCAGAGTTT 59.297 40.000 26.09 0.00 30.94 2.66
745 877 6.205658 GGTGAAGCTTCTATGTTCAGAGTTTT 59.794 38.462 26.09 0.00 30.94 2.43
746 878 7.255277 GGTGAAGCTTCTATGTTCAGAGTTTTT 60.255 37.037 26.09 0.00 30.94 1.94
747 879 7.800847 GTGAAGCTTCTATGTTCAGAGTTTTTC 59.199 37.037 26.09 0.00 30.94 2.29
748 880 7.716998 TGAAGCTTCTATGTTCAGAGTTTTTCT 59.283 33.333 26.09 0.00 36.25 2.52
749 881 8.457238 AAGCTTCTATGTTCAGAGTTTTTCTT 57.543 30.769 0.00 0.00 32.41 2.52
750 882 8.457238 AGCTTCTATGTTCAGAGTTTTTCTTT 57.543 30.769 0.00 0.00 32.41 2.52
840 972 1.812571 AGGCAAAGTACGCTTTCATGG 59.187 47.619 0.00 0.00 42.54 3.66
842 974 2.414161 GGCAAAGTACGCTTTCATGGAC 60.414 50.000 0.00 0.00 42.54 4.02
872 1013 3.517500 GGAAAAACATTCCATAGGGCCAA 59.482 43.478 6.18 0.00 38.45 4.52
873 1014 4.383010 GGAAAAACATTCCATAGGGCCAAG 60.383 45.833 6.18 0.00 38.45 3.61
885 1030 2.361737 GCCAAGCCACCTCTTCCC 60.362 66.667 0.00 0.00 0.00 3.97
903 1050 1.378778 CTCCCGACTCTCCCTTCGT 60.379 63.158 0.00 0.00 33.23 3.85
990 1137 4.161295 CTCGCCGCATCCTTCCCA 62.161 66.667 0.00 0.00 0.00 4.37
991 1138 3.466791 CTCGCCGCATCCTTCCCAT 62.467 63.158 0.00 0.00 0.00 4.00
1008 1156 1.421646 CCATAGACCCCAATGGAGGAC 59.578 57.143 12.74 7.33 44.62 3.85
1096 1244 2.687200 TCCCCATGGACCAGGACG 60.687 66.667 15.22 0.00 35.03 4.79
1097 1245 2.687200 CCCCATGGACCAGGACGA 60.687 66.667 15.22 0.00 0.00 4.20
1098 1246 2.735772 CCCCATGGACCAGGACGAG 61.736 68.421 15.22 0.00 0.00 4.18
1099 1247 2.735772 CCCATGGACCAGGACGAGG 61.736 68.421 15.22 0.00 0.00 4.63
1100 1248 1.685765 CCATGGACCAGGACGAGGA 60.686 63.158 5.56 0.00 0.00 3.71
1101 1249 1.517832 CATGGACCAGGACGAGGAC 59.482 63.158 0.00 0.00 0.00 3.85
1102 1250 1.686110 ATGGACCAGGACGAGGACC 60.686 63.158 0.00 0.00 40.71 4.46
1103 1251 2.283676 GGACCAGGACGAGGACCA 60.284 66.667 0.00 0.00 40.15 4.02
1104 1252 2.352032 GGACCAGGACGAGGACCAG 61.352 68.421 0.00 0.00 40.15 4.00
1105 1253 2.283966 ACCAGGACGAGGACCAGG 60.284 66.667 0.00 0.00 39.50 4.45
1106 1254 3.775654 CCAGGACGAGGACCAGGC 61.776 72.222 0.00 0.00 0.00 4.85
1503 1663 0.179056 CCGCCGTCATCCCACTTATT 60.179 55.000 0.00 0.00 0.00 1.40
1536 1696 0.322816 AGGCCAACTACCTCGTCGTA 60.323 55.000 5.01 0.00 28.76 3.43
1800 1960 0.391661 CTGCACGCCACCTTATGTCT 60.392 55.000 0.00 0.00 0.00 3.41
2057 2217 1.688884 TCGACCCTGGCATGGATGA 60.689 57.895 16.19 9.39 0.00 2.92
2067 2227 1.600957 GGCATGGATGATCGTGTTGAG 59.399 52.381 0.00 0.00 0.00 3.02
2130 2290 3.458189 GCAGGTTATCGCAGATAGTGTT 58.542 45.455 0.00 0.00 45.12 3.32
2457 2617 4.994852 GTGTTGGTCTACACTGATAAGCAA 59.005 41.667 8.09 0.00 43.92 3.91
2520 2680 2.026262 TGTGCTTAAGAAGGGGGACATC 60.026 50.000 6.67 0.00 0.00 3.06
2640 2800 3.832490 TCTGGGATGGTAGGATTGATACG 59.168 47.826 0.00 0.00 0.00 3.06
2712 2872 7.866729 TGTTCTATAGCTATTCTTCAGTCTCG 58.133 38.462 12.39 0.00 0.00 4.04
2920 3080 3.087031 GGATCATATTCCCATGTGGCTG 58.913 50.000 0.00 0.00 0.00 4.85
3229 3389 2.014857 CAGTTCTGCATGACCCATCTG 58.985 52.381 0.00 0.00 0.00 2.90
3405 3565 7.360029 TGTACCGAGATTTTGGGACAAAACTT 61.360 38.462 5.03 1.69 46.91 2.66
3768 3957 3.946606 TCTGTGATGACATTGTGATGCT 58.053 40.909 0.00 0.00 36.72 3.79
3858 4047 5.546499 TCCCTCTGTACCAAAATGTAAGACT 59.454 40.000 0.00 0.00 0.00 3.24
3859 4048 6.043938 TCCCTCTGTACCAAAATGTAAGACTT 59.956 38.462 0.00 0.00 0.00 3.01
3860 4049 6.715264 CCCTCTGTACCAAAATGTAAGACTTT 59.285 38.462 0.00 0.00 0.00 2.66
3861 4050 7.230712 CCCTCTGTACCAAAATGTAAGACTTTT 59.769 37.037 0.00 0.00 0.00 2.27
3930 4119 4.168101 TGGAGGGAGTTGTTATGACTCTT 58.832 43.478 4.49 0.00 42.44 2.85
3944 4133 9.166173 TGTTATGACTCTTGATATTGTTTGGAG 57.834 33.333 0.00 0.00 0.00 3.86
4024 4213 7.451501 TTCAGTCTCATTGATTAATTGTGCA 57.548 32.000 0.00 0.00 0.00 4.57
4115 4305 1.827969 CAGCAAGCTGTAGGTAGAGGT 59.172 52.381 13.72 0.00 39.10 3.85
4140 4330 4.727507 TCTAGGTGACAGCTCAAGAATC 57.272 45.455 11.11 0.00 0.00 2.52
4152 4342 5.411977 CAGCTCAAGAATCTGTTTGATCAGT 59.588 40.000 0.00 0.00 36.85 3.41
4164 4354 2.549064 TGATCAGTTGGTCAGTGTGG 57.451 50.000 0.00 0.00 0.00 4.17
4208 4465 7.051623 ACAACCTTTAGTTTGACTATGTGTGA 58.948 34.615 0.00 0.00 36.18 3.58
4250 4507 6.954102 AGGAAATGCTGGAAACCTATAACTTT 59.046 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.491342 AGAAGGTCTCCTTTCTTTTGCC 58.509 45.455 2.48 0.00 44.82 4.52
114 116 1.186200 GGGAGGTGAAAAATGAGGGC 58.814 55.000 0.00 0.00 0.00 5.19
216 221 3.932089 GCTAGAGCAGGTTTTCTTCTCTG 59.068 47.826 0.00 0.00 41.59 3.35
368 383 3.254024 TTCCGAGCTTGAGGCCACC 62.254 63.158 5.01 0.00 43.05 4.61
396 411 1.742308 TCATTACTAGGCCATCCCCC 58.258 55.000 5.01 0.00 0.00 5.40
418 433 6.025749 TCGTGTCTCTCTTTGTTGTCATAT 57.974 37.500 0.00 0.00 0.00 1.78
419 434 5.447624 TCGTGTCTCTCTTTGTTGTCATA 57.552 39.130 0.00 0.00 0.00 2.15
421 436 3.793797 TCGTGTCTCTCTTTGTTGTCA 57.206 42.857 0.00 0.00 0.00 3.58
422 437 5.610552 CGAATTCGTGTCTCTCTTTGTTGTC 60.611 44.000 19.67 0.00 34.11 3.18
425 440 4.974103 CGAATTCGTGTCTCTCTTTGTT 57.026 40.909 19.67 0.00 34.11 2.83
441 456 4.487714 TCTCCATTCCTGCTTACGAATT 57.512 40.909 0.00 0.00 0.00 2.17
457 472 0.535553 CCCCCGTTCGTTTTTCTCCA 60.536 55.000 0.00 0.00 0.00 3.86
497 512 0.897863 CTCGATCTAGGCCTCCTGGG 60.898 65.000 9.68 0.00 34.61 4.45
708 840 1.484444 GCTTCACCTGGAGTCCCACT 61.484 60.000 6.74 0.00 37.58 4.00
709 841 1.003233 GCTTCACCTGGAGTCCCAC 60.003 63.158 6.74 0.00 37.58 4.61
710 842 0.768221 AAGCTTCACCTGGAGTCCCA 60.768 55.000 6.74 0.00 40.95 4.37
711 843 0.035915 GAAGCTTCACCTGGAGTCCC 60.036 60.000 21.67 0.00 0.00 4.46
712 844 0.980423 AGAAGCTTCACCTGGAGTCC 59.020 55.000 27.57 0.73 0.00 3.85
713 845 3.196685 ACATAGAAGCTTCACCTGGAGTC 59.803 47.826 27.57 0.00 0.00 3.36
769 901 2.169352 CCGTTCCCTCATCTCTGAACAT 59.831 50.000 0.00 0.00 37.53 2.71
823 955 2.478894 ACGTCCATGAAAGCGTACTTTG 59.521 45.455 0.00 0.00 46.20 2.77
855 987 1.689258 GGCTTGGCCCTATGGAATGTT 60.689 52.381 0.00 0.00 44.06 2.71
872 1013 2.285743 GGGAGGGAAGAGGTGGCT 60.286 66.667 0.00 0.00 0.00 4.75
873 1014 3.787001 CGGGAGGGAAGAGGTGGC 61.787 72.222 0.00 0.00 0.00 5.01
875 1016 1.305381 AGTCGGGAGGGAAGAGGTG 60.305 63.158 0.00 0.00 0.00 4.00
876 1017 1.000612 GAGTCGGGAGGGAAGAGGT 59.999 63.158 0.00 0.00 0.00 3.85
878 1019 0.753848 GGAGAGTCGGGAGGGAAGAG 60.754 65.000 0.00 0.00 0.00 2.85
879 1020 1.306970 GGAGAGTCGGGAGGGAAGA 59.693 63.158 0.00 0.00 0.00 2.87
882 1027 2.226149 GAAGGGAGAGTCGGGAGGGA 62.226 65.000 0.00 0.00 0.00 4.20
885 1030 1.378124 GACGAAGGGAGAGTCGGGAG 61.378 65.000 0.00 0.00 41.56 4.30
903 1050 4.329545 GGCCAGAACTGTGCGGGA 62.330 66.667 9.35 0.00 0.00 5.14
990 1137 1.424638 CGTCCTCCATTGGGGTCTAT 58.575 55.000 0.96 0.00 38.11 1.98
991 1138 0.689745 CCGTCCTCCATTGGGGTCTA 60.690 60.000 0.96 0.00 38.11 2.59
1071 1219 2.764128 TCCATGGGGACGAGAGCC 60.764 66.667 13.02 0.00 38.64 4.70
1497 1657 1.743995 GTCGGCGCCACCAATAAGT 60.744 57.895 28.98 0.00 39.03 2.24
1536 1696 1.762222 GCGCGAGAATATGGTTGCGT 61.762 55.000 12.10 0.00 46.55 5.24
1782 1942 0.391130 GAGACATAAGGTGGCGTGCA 60.391 55.000 0.00 0.00 42.34 4.57
2048 2208 1.600957 CCTCAACACGATCATCCATGC 59.399 52.381 0.00 0.00 0.00 4.06
2057 2217 0.250901 AAAGGCAGCCTCAACACGAT 60.251 50.000 16.53 0.00 30.89 3.73
2067 2227 0.528017 GAAGCTGGTTAAAGGCAGCC 59.472 55.000 1.84 1.84 41.21 4.85
2310 2470 2.839836 TGGTCGCCACCCATTTCA 59.160 55.556 0.00 0.00 42.99 2.69
2457 2617 2.297701 GCCATATCACCACGGAATGTT 58.702 47.619 0.00 0.00 0.00 2.71
2490 2650 0.404040 TCTTAAGCACACCAAGGGGG 59.596 55.000 0.00 0.00 44.81 5.40
2520 2680 1.135315 CAGCTCCGGCACAAAATCG 59.865 57.895 0.00 0.00 41.70 3.34
2640 2800 2.029918 GTCCTCAGTCAAATGCCCAAAC 60.030 50.000 0.00 0.00 0.00 2.93
2712 2872 2.584391 AACGAGCAGTGGACCTCCC 61.584 63.158 0.00 0.00 34.29 4.30
2920 3080 0.323629 TCATCACCGGAAGACCCAAC 59.676 55.000 9.46 0.00 34.14 3.77
3405 3565 0.324552 CCAAGCCATCCAATCCCACA 60.325 55.000 0.00 0.00 0.00 4.17
3484 3644 4.473444 AGTCAACCATCCAACATCTTGTT 58.527 39.130 0.00 0.00 42.08 2.83
3485 3645 4.074970 GAGTCAACCATCCAACATCTTGT 58.925 43.478 0.00 0.00 0.00 3.16
3774 3963 5.455392 CAAGTGCTACATCACCAAGAAAAG 58.545 41.667 0.00 0.00 37.68 2.27
3779 3968 2.907910 GCAAGTGCTACATCACCAAG 57.092 50.000 0.00 0.00 37.68 3.61
3908 4097 3.791320 AGAGTCATAACAACTCCCTCCA 58.209 45.455 0.00 0.00 43.41 3.86
3944 4133 6.272822 AGAAATGGCAACTTGGAGAAATAC 57.727 37.500 0.00 0.00 37.61 1.89
4024 4213 4.463891 CCACCTTCCAGAATAAGCAACAAT 59.536 41.667 0.00 0.00 0.00 2.71
4115 4305 4.152647 TCTTGAGCTGTCACCTAGAAGAA 58.847 43.478 0.00 0.00 30.10 2.52
4140 4330 3.879295 ACACTGACCAACTGATCAAACAG 59.121 43.478 0.00 3.37 42.78 3.16
4152 4342 3.587061 AGAATGGATACCACACTGACCAA 59.413 43.478 0.00 0.00 35.80 3.67
4164 4354 6.884836 AGGTTGTAAGGTGAAAGAATGGATAC 59.115 38.462 0.00 0.00 0.00 2.24
4250 4507 3.586470 TTGGTTACCTGCTTCTTGGAA 57.414 42.857 2.07 0.00 0.00 3.53
4454 4711 6.824305 CAGGTCTTGTGTTCCAAATCTAAT 57.176 37.500 0.00 0.00 31.20 1.73


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

AutoCloner maintained by Alex Coulton.