Multiple sequence alignment - TraesCS5B01G359600

Loading Multiple Alignment...

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 TraesCS5B01G359600 chr5B 100.000 3897 0 0 1 3897 539312646 539308750 0.000000e+00 7197.0
1 TraesCS5B01G359600 chr5B 77.651 613 110 8 2205 2802 102064860 102065460 8.010000e-92 348.0
2 TraesCS5B01G359600 chr5D 94.973 3581 112 21 1 3516 443069801 443066224 0.000000e+00 5553.0
3 TraesCS5B01G359600 chr5D 78.072 529 100 10 2205 2731 95052460 95052974 1.750000e-83 320.0
4 TraesCS5B01G359600 chr5D 95.597 159 7 0 3739 3897 443066050 443065892 5.000000e-64 255.0
5 TraesCS5B01G359600 chr5D 90.244 164 7 2 3504 3667 443066205 443066051 5.100000e-49 206.0
6 TraesCS5B01G359600 chr5A 94.706 3117 105 19 1 3073 559095942 559092842 0.000000e+00 4787.0
7 TraesCS5B01G359600 chr5A 89.038 520 27 10 3066 3557 559092723 559092206 5.530000e-173 617.0
8 TraesCS5B01G359600 chr5A 75.326 920 185 22 1898 2802 89385171 89386063 1.690000e-108 403.0
9 TraesCS5B01G359600 chr5A 92.090 177 12 1 3721 3897 559091986 559091812 8.360000e-62 248.0
10 TraesCS5B01G359600 chr5A 97.826 92 2 0 3627 3718 559092205 559092114 4.030000e-35 159.0
11 TraesCS5B01G359600 chr3A 89.474 76 3 2 3035 3106 696374379 696374305 1.490000e-14 91.6
12 TraesCS5B01G359600 chr3D 87.500 80 5 4 3031 3106 61038278 61038200 1.930000e-13 87.9


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 TraesCS5B01G359600 chr5B 539308750 539312646 3896 True 7197.000000 7197 100.000000 1 3897 1 chr5B.!!$R1 3896
1 TraesCS5B01G359600 chr5B 102064860 102065460 600 False 348.000000 348 77.651000 2205 2802 1 chr5B.!!$F1 597
2 TraesCS5B01G359600 chr5D 443065892 443069801 3909 True 2004.666667 5553 93.604667 1 3897 3 chr5D.!!$R1 3896
3 TraesCS5B01G359600 chr5D 95052460 95052974 514 False 320.000000 320 78.072000 2205 2731 1 chr5D.!!$F1 526
4 TraesCS5B01G359600 chr5A 559091812 559095942 4130 True 1452.750000 4787 93.415000 1 3897 4 chr5A.!!$R1 3896
5 TraesCS5B01G359600 chr5A 89385171 89386063 892 False 403.000000 403 75.326000 1898 2802 1 chr5A.!!$F1 904

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
204 206 1.542492 CTTGTTGATCCTGCCTTGCT 58.458 50.0 0.0 0.0 0.00 3.91 F
1550 1578 0.905357 GCTCCTTCAGGTTCCAGCTA 59.095 55.0 0.0 0.0 36.34 3.32 F
2544 2608 0.037697 TCGTCCACTACACACATGGC 60.038 55.0 0.0 0.0 33.20 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2168 1.300963 GCCATTCTGAGCACTGGGA 59.699 57.895 0.0 0.0 0.0 4.37 R
2827 2915 0.177604 CTGTGCTCTCCCCTGATGTC 59.822 60.000 0.0 0.0 0.0 3.06 R
3612 3885 0.322816 TGAGCCTAGCAAAAGCCTGG 60.323 55.000 0.0 0.0 0.0 4.45 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
24 25 7.622893 GATAAGGTGAGCTGAAAATTCTCTT 57.377 36.000 0.00 0.00 0.00 2.85
159 161 2.197324 GAAAGGTGTGGGGGCACA 59.803 61.111 0.00 0.00 40.89 4.57
204 206 1.542492 CTTGTTGATCCTGCCTTGCT 58.458 50.000 0.00 0.00 0.00 3.91
282 284 3.307199 GGAGGTGAAGGTTCGTGGAATTA 60.307 47.826 0.00 0.00 0.00 1.40
295 297 7.916977 GGTTCGTGGAATTACTTTGTAAAGTTT 59.083 33.333 14.47 4.98 46.52 2.66
512 520 3.242870 GGAATTGATTAAGCCAGCAGACG 60.243 47.826 0.00 0.00 0.00 4.18
595 603 5.177511 TGCTTCACATTCGAGAACTTTGTAG 59.822 40.000 0.00 0.00 0.00 2.74
694 702 4.039852 TGCTGTGGTGTGAAGTCATACTTA 59.960 41.667 7.93 0.00 38.80 2.24
779 787 6.489700 TGAACCATTTTAATGCTCTGACTGAA 59.510 34.615 0.00 0.00 35.08 3.02
780 788 7.177216 TGAACCATTTTAATGCTCTGACTGAAT 59.823 33.333 0.00 0.00 35.08 2.57
946 973 3.272574 TCCAGAATACTCGGTACTCGT 57.727 47.619 0.00 0.00 40.32 4.18
965 992 2.668457 CGTCCACTTGCAGATTGTAGAC 59.332 50.000 0.00 0.00 0.00 2.59
1133 1161 2.781681 ACATTCCGGAAACAGGTAGG 57.218 50.000 23.08 0.00 0.00 3.18
1241 1269 6.601613 TCCATAGGCGTAATTGTTTCTCATTT 59.398 34.615 0.00 0.00 0.00 2.32
1493 1521 1.845809 GCGTGGCTTGAACAGAGTGG 61.846 60.000 0.00 0.00 0.00 4.00
1550 1578 0.905357 GCTCCTTCAGGTTCCAGCTA 59.095 55.000 0.00 0.00 36.34 3.32
1768 1799 4.442192 GGGTCACCTAGCACTATGAAGAAG 60.442 50.000 0.00 0.00 0.00 2.85
2016 2047 2.185004 ACTGTGCATTACCAGTCCAC 57.815 50.000 2.03 0.00 0.00 4.02
2137 2168 3.489738 GGCATTATGCTGACGCTGAATTT 60.490 43.478 17.13 0.00 44.28 1.82
2342 2406 3.146066 TCAAAGGAAATCTTGTGGGACG 58.854 45.455 0.00 0.00 35.55 4.79
2364 2428 3.057946 GGAAAGAAGCTGCGAAACTTGAT 60.058 43.478 0.00 0.00 0.00 2.57
2494 2558 3.000041 TGGTTTCACTATAAGTGCAGCG 59.000 45.455 2.12 0.00 45.54 5.18
2544 2608 0.037697 TCGTCCACTACACACATGGC 60.038 55.000 0.00 0.00 33.20 4.40
2668 2732 0.729116 CACTGCCGTTCATGGATGTC 59.271 55.000 0.00 0.00 0.00 3.06
2669 2733 0.740868 ACTGCCGTTCATGGATGTCG 60.741 55.000 0.00 0.00 0.00 4.35
2677 2741 3.201290 GTTCATGGATGTCGCAGAGATT 58.799 45.455 0.00 0.00 42.02 2.40
2905 2993 0.737804 TGAAGCTTTGACGCTGCAAA 59.262 45.000 0.00 0.00 42.50 3.68
2913 3001 0.234625 TGACGCTGCAAATGTTCGAC 59.765 50.000 0.00 0.00 0.00 4.20
2934 3022 2.099098 CACCAAAGACTGTGTTTCCCAC 59.901 50.000 0.00 0.00 44.78 4.61
2943 3031 1.934589 GTGTTTCCCACAAAGCCAAC 58.065 50.000 0.00 0.00 43.92 3.77
2957 3045 1.086696 GCCAACTCAAGCATAGCGAA 58.913 50.000 0.00 0.00 0.00 4.70
2974 3062 3.067106 GCGAAACCTCAAGAAGACATCA 58.933 45.455 0.00 0.00 0.00 3.07
2986 3074 6.429078 TCAAGAAGACATCAAGAAGGACATTG 59.571 38.462 0.00 0.00 0.00 2.82
3083 3297 7.428282 TGATTTGTACTAAATCAGCGACAAA 57.572 32.000 20.22 3.17 42.79 2.83
3084 3298 7.295201 TGATTTGTACTAAATCAGCGACAAAC 58.705 34.615 20.22 0.33 42.06 2.93
3094 3308 7.807977 AAATCAGCGACAAACTAATATGGAT 57.192 32.000 0.00 0.00 0.00 3.41
3122 3336 5.110598 GGGAGTAAGAAGTTTCGGAGAATC 58.889 45.833 0.00 0.00 45.90 2.52
3154 3368 6.472686 AGTCCCATAGTTCACAACTCTATC 57.527 41.667 0.00 0.00 41.77 2.08
3223 3437 5.827797 ACAGCAAACTCTGTTTCAGGATTTA 59.172 36.000 0.00 0.00 44.26 1.40
3275 3489 0.037326 CGCCTTTGAGTGCTCTGGTA 60.037 55.000 0.00 0.00 0.00 3.25
3283 3497 2.234661 TGAGTGCTCTGGTAGTTCCATG 59.765 50.000 0.00 0.00 46.12 3.66
3285 3499 2.639839 AGTGCTCTGGTAGTTCCATGTT 59.360 45.455 0.00 0.00 46.12 2.71
3287 3501 2.637382 TGCTCTGGTAGTTCCATGTTGA 59.363 45.455 0.00 0.00 46.12 3.18
3288 3502 3.003480 GCTCTGGTAGTTCCATGTTGAC 58.997 50.000 0.00 0.00 46.12 3.18
3289 3503 3.557054 GCTCTGGTAGTTCCATGTTGACA 60.557 47.826 0.00 0.00 46.12 3.58
3290 3504 4.248859 CTCTGGTAGTTCCATGTTGACAG 58.751 47.826 0.00 0.00 46.12 3.51
3291 3505 2.744202 CTGGTAGTTCCATGTTGACAGC 59.256 50.000 0.00 0.00 46.12 4.40
3292 3506 2.105649 TGGTAGTTCCATGTTGACAGCA 59.894 45.455 0.00 0.00 41.93 4.41
3309 3551 6.979465 TGACAGCATGATGTTATGTTTTGAA 58.021 32.000 19.10 0.00 39.69 2.69
3530 3803 9.938280 AAGAAGTATGTTGTAAGTGCAGTATTA 57.062 29.630 0.00 0.00 0.00 0.98
3582 3855 0.466124 GGGTCCTACTGACATCTGGC 59.534 60.000 0.00 0.00 46.38 4.85
3609 3882 1.377856 GACTTGGGCTGGGCTTCTC 60.378 63.158 0.00 0.00 0.00 2.87
3610 3883 2.129555 GACTTGGGCTGGGCTTCTCA 62.130 60.000 0.00 0.00 0.00 3.27
3611 3884 1.378250 CTTGGGCTGGGCTTCTCAG 60.378 63.158 0.00 0.00 35.49 3.35
3718 3991 2.108362 GTCCGGCCCTATCCAACG 59.892 66.667 0.00 0.00 0.00 4.10
3719 3992 3.158648 TCCGGCCCTATCCAACGG 61.159 66.667 0.00 0.00 45.52 4.44
3737 4135 5.295152 CAACGGACCTTACAAACTAGACTT 58.705 41.667 0.00 0.00 0.00 3.01
3892 4290 4.467198 AACCTACGGATGACCAAGTTAG 57.533 45.455 0.00 0.00 35.59 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.740115 GAGCTAAACTCCCAAGAACACA 58.260 45.455 0.00 0.00 39.75 3.72
159 161 6.302026 AGGAAGAATAGAGGTAATCTCCCT 57.698 41.667 0.00 0.00 43.44 4.20
204 206 1.416401 GGAGACACACAACAAGAGGGA 59.584 52.381 0.00 0.00 0.00 4.20
512 520 8.041323 TCCTTAGATCACAAGAAACTGGATTAC 58.959 37.037 8.29 0.00 0.00 1.89
595 603 3.421844 ACAAGAAAGGATGCCTTGTACC 58.578 45.455 5.72 0.00 43.92 3.34
694 702 0.769247 AAGGCGTTAGGAACCCAACT 59.231 50.000 0.00 0.00 0.00 3.16
946 973 5.738619 TTAGTCTACAATCTGCAAGTGGA 57.261 39.130 0.00 0.00 33.76 4.02
965 992 5.600696 ACCACCAATTGCTTTCAAGTTTAG 58.399 37.500 0.00 0.00 35.37 1.85
1133 1161 7.878127 AGCACATAGTATGGGTAATGTCATAAC 59.122 37.037 13.89 0.00 35.65 1.89
1207 1235 8.547967 ACAATTACGCCTATGGACAAATATAG 57.452 34.615 0.00 0.00 0.00 1.31
1241 1269 8.851541 AAATAAAGGTGTCAAAACCGTATAGA 57.148 30.769 0.00 0.00 45.53 1.98
1282 1310 3.056821 TCTGAACCTTGTACAGACGATGG 60.057 47.826 0.00 0.00 36.04 3.51
1478 1506 2.012673 CATAGCCACTCTGTTCAAGCC 58.987 52.381 0.00 0.00 0.00 4.35
1550 1578 7.119846 CACATCATCATCACTATCATCTGCATT 59.880 37.037 0.00 0.00 0.00 3.56
1751 1782 6.402222 AGTTTGTCTTCTTCATAGTGCTAGG 58.598 40.000 0.00 0.00 0.00 3.02
1768 1799 2.351726 ACTCACACTTGCGAAGTTTGTC 59.648 45.455 12.03 0.00 40.46 3.18
2016 2047 3.581770 TCCTGGATTGATGATGCTAGAGG 59.418 47.826 0.00 0.00 0.00 3.69
2137 2168 1.300963 GCCATTCTGAGCACTGGGA 59.699 57.895 0.00 0.00 0.00 4.37
2342 2406 2.290641 TCAAGTTTCGCAGCTTCTTTCC 59.709 45.455 0.00 0.00 0.00 3.13
2364 2428 8.084073 GTGATTTCTTCATGGTGATTTTCTTCA 58.916 33.333 0.00 0.00 36.54 3.02
2431 2495 2.922955 TGAATAACCCATGGAACCAGGA 59.077 45.455 15.22 0.00 0.00 3.86
2544 2608 1.302033 GAGGGTGTGCTGTCTGTGG 60.302 63.158 0.00 0.00 0.00 4.17
2668 2732 2.890109 GCGGGCATCAATCTCTGCG 61.890 63.158 0.00 0.00 39.30 5.18
2669 2733 2.550101 GGCGGGCATCAATCTCTGC 61.550 63.158 0.00 0.00 37.66 4.26
2677 2741 2.526450 CTTCTGACTGGCGGGCATCA 62.526 60.000 0.18 10.10 29.39 3.07
2827 2915 0.177604 CTGTGCTCTCCCCTGATGTC 59.822 60.000 0.00 0.00 0.00 3.06
2905 2993 2.872245 CACAGTCTTTGGTGTCGAACAT 59.128 45.455 0.00 0.00 0.00 2.71
2913 3001 2.374184 TGGGAAACACAGTCTTTGGTG 58.626 47.619 0.00 0.00 40.78 4.17
2934 3022 2.730090 CGCTATGCTTGAGTTGGCTTTG 60.730 50.000 0.00 0.00 0.00 2.77
2943 3031 2.621338 TGAGGTTTCGCTATGCTTGAG 58.379 47.619 0.00 0.00 0.00 3.02
2957 3045 5.072329 TCCTTCTTGATGTCTTCTTGAGGTT 59.928 40.000 0.00 0.00 0.00 3.50
2974 3062 5.071788 TCTGAACCTACACAATGTCCTTCTT 59.928 40.000 0.00 0.00 0.00 2.52
3115 3329 2.624364 GGGACTAGTTCCTCGATTCTCC 59.376 54.545 13.55 0.00 45.09 3.71
3122 3336 4.571372 GAACTATGGGACTAGTTCCTCG 57.429 50.000 21.31 11.34 46.23 4.63
3154 3368 3.255379 GCGTTTCTAGAGCCCGCG 61.255 66.667 14.26 0.00 34.66 6.46
3233 3447 6.291060 GCGGTGATATTAAAACAAAGCATTCG 60.291 38.462 0.00 0.00 0.00 3.34
3275 3489 3.144657 TCATGCTGTCAACATGGAACT 57.855 42.857 14.68 0.00 44.09 3.01
3283 3497 6.862608 TCAAAACATAACATCATGCTGTCAAC 59.137 34.615 2.07 0.00 0.00 3.18
3285 3499 6.572167 TCAAAACATAACATCATGCTGTCA 57.428 33.333 2.07 0.00 0.00 3.58
3287 3501 7.148540 GCAATTCAAAACATAACATCATGCTGT 60.149 33.333 0.00 0.00 0.00 4.40
3288 3502 7.064134 AGCAATTCAAAACATAACATCATGCTG 59.936 33.333 0.00 0.00 36.62 4.41
3289 3503 7.064134 CAGCAATTCAAAACATAACATCATGCT 59.936 33.333 0.00 0.00 38.31 3.79
3290 3504 7.177407 CAGCAATTCAAAACATAACATCATGC 58.823 34.615 0.00 0.00 0.00 4.06
3291 3505 7.546316 TCCAGCAATTCAAAACATAACATCATG 59.454 33.333 0.00 0.00 0.00 3.07
3292 3506 7.613585 TCCAGCAATTCAAAACATAACATCAT 58.386 30.769 0.00 0.00 0.00 2.45
3309 3551 2.875094 AAGCTCTGTTCTCCAGCAAT 57.125 45.000 0.00 0.00 41.25 3.56
3347 3589 6.312487 CACAAATGACAGCTTGAGATAACAG 58.688 40.000 6.98 0.00 0.00 3.16
3474 3716 6.623486 TCAAAATTGCTCAAGTGATACATGG 58.377 36.000 0.00 0.00 0.00 3.66
3543 3816 3.054802 CCCCAGCAGAGTGTTCTAGATTT 60.055 47.826 0.00 0.00 30.73 2.17
3544 3817 2.503356 CCCCAGCAGAGTGTTCTAGATT 59.497 50.000 0.00 0.00 30.73 2.40
3592 3865 2.134630 CTGAGAAGCCCAGCCCAAGT 62.135 60.000 0.00 0.00 0.00 3.16
3609 3882 1.941999 GCCTAGCAAAAGCCTGGCTG 61.942 60.000 24.16 12.22 39.62 4.85
3610 3883 1.680314 GCCTAGCAAAAGCCTGGCT 60.680 57.895 17.22 17.22 42.56 4.75
3611 3884 1.661498 GAGCCTAGCAAAAGCCTGGC 61.661 60.000 11.65 11.65 40.54 4.85
3612 3885 0.322816 TGAGCCTAGCAAAAGCCTGG 60.323 55.000 0.00 0.00 0.00 4.45
3613 3886 1.674962 GATGAGCCTAGCAAAAGCCTG 59.325 52.381 0.00 0.00 0.00 4.85
3614 3887 1.563410 AGATGAGCCTAGCAAAAGCCT 59.437 47.619 0.00 0.00 0.00 4.58
3615 3888 2.049888 AGATGAGCCTAGCAAAAGCC 57.950 50.000 0.00 0.00 0.00 4.35
3718 3991 5.100943 CGCTAAGTCTAGTTTGTAAGGTCC 58.899 45.833 0.00 0.00 0.00 4.46
3719 3992 5.947443 TCGCTAAGTCTAGTTTGTAAGGTC 58.053 41.667 0.00 0.00 0.00 3.85
3769 4167 4.702131 CCCATCAGAGGAGTTTTTACCTTG 59.298 45.833 0.00 0.00 36.57 3.61
3799 4197 2.095567 CCAAAGCTCCTTGATGACAACG 60.096 50.000 0.00 0.00 32.27 4.10
3804 4202 2.877300 GCTCACCAAAGCTCCTTGATGA 60.877 50.000 0.00 0.00 39.27 2.92
3815 4213 4.553323 CAGATGGAAAAAGCTCACCAAAG 58.447 43.478 0.00 0.00 36.00 2.77


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

AutoCloner maintained by Alex Coulton.