Multiple sequence alignment - TraesCS3A01G368200

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 TraesCS3A01G368200 chr3A 100.000 3647 0 0 1 3647 617072374 617076020 0.000000e+00 6735.0
1 TraesCS3A01G368200 chr3A 76.151 239 42 8 23 261 580594197 580594420 1.070000e-20 111.0
2 TraesCS3A01G368200 chr3D 93.333 3420 149 29 272 3647 474653946 474657330 0.000000e+00 4979.0
3 TraesCS3A01G368200 chr3D 90.400 250 16 3 14 263 474651926 474652167 4.540000e-84 322.0
4 TraesCS3A01G368200 chr3B 96.060 2843 90 11 14 2849 631047267 631050094 0.000000e+00 4610.0
5 TraesCS3A01G368200 chr3B 90.086 817 62 12 2842 3647 631051391 631052199 0.000000e+00 1042.0
6 TraesCS3A01G368200 chr2D 79.167 624 116 14 1922 2538 518970139 518970755 1.570000e-113 420.0
7 TraesCS3A01G368200 chr2D 76.824 699 122 32 1079 1760 518969290 518969965 1.250000e-94 357.0
8 TraesCS3A01G368200 chr2A 79.167 624 116 14 1922 2538 663145884 663145268 1.570000e-113 420.0
9 TraesCS3A01G368200 chr2A 77.188 697 123 30 1079 1760 663146733 663146058 1.240000e-99 374.0
10 TraesCS3A01G368200 chr6B 78.744 621 108 21 1079 1690 505683150 505682545 9.490000e-106 394.0
11 TraesCS3A01G368200 chr2B 78.205 624 122 14 1922 2538 611193117 611193733 1.590000e-103 387.0
12 TraesCS3A01G368200 chr2B 76.858 713 135 24 1060 1760 611192240 611192934 3.440000e-100 375.0
13 TraesCS3A01G368200 chr6D 76.912 693 132 25 1079 1760 318453749 318454424 5.750000e-98 368.0
14 TraesCS3A01G368200 chr6A 76.879 692 134 23 1079 1760 456011608 456012283 5.750000e-98 368.0
15 TraesCS3A01G368200 chr5D 91.111 45 4 0 136 180 152788611 152788655 1.090000e-05 62.1


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 TraesCS3A01G368200 chr3A 617072374 617076020 3646 False 6735.0 6735 100.0000 1 3647 1 chr3A.!!$F2 3646
1 TraesCS3A01G368200 chr3D 474651926 474657330 5404 False 2650.5 4979 91.8665 14 3647 2 chr3D.!!$F1 3633
2 TraesCS3A01G368200 chr3B 631047267 631052199 4932 False 2826.0 4610 93.0730 14 3647 2 chr3B.!!$F1 3633
3 TraesCS3A01G368200 chr2D 518969290 518970755 1465 False 388.5 420 77.9955 1079 2538 2 chr2D.!!$F1 1459
4 TraesCS3A01G368200 chr2A 663145268 663146733 1465 True 397.0 420 78.1775 1079 2538 2 chr2A.!!$R1 1459
5 TraesCS3A01G368200 chr6B 505682545 505683150 605 True 394.0 394 78.7440 1079 1690 1 chr6B.!!$R1 611
6 TraesCS3A01G368200 chr2B 611192240 611193733 1493 False 381.0 387 77.5315 1060 2538 2 chr2B.!!$F1 1478
7 TraesCS3A01G368200 chr6D 318453749 318454424 675 False 368.0 368 76.9120 1079 1760 1 chr6D.!!$F1 681
8 TraesCS3A01G368200 chr6A 456011608 456012283 675 False 368.0 368 76.8790 1079 1760 1 chr6A.!!$F1 681

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
189 190 0.036164 AATGCTCACCTGTAACCGCA 59.964 50.0 0.00 0.0 0.00 5.69 F
953 2752 0.106894 CGAGGCCTAAATCCACCTCC 59.893 60.0 4.42 0.0 44.89 4.30 F
954 2753 0.474614 GAGGCCTAAATCCACCTCCC 59.525 60.0 4.42 0.0 42.44 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 3395 0.100682 TATCGAAGGTGAGACGCAGC 59.899 55.000 0.0 0.0 45.24 5.25 R
2608 4464 0.673644 GTGGTTGGGATCACGACTGG 60.674 60.000 15.1 0.0 0.00 4.00 R
2757 4613 4.062293 CCTCATCAAAAGTACACAACCGA 58.938 43.478 0.0 0.0 0.00 4.69 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
28 29 4.082081 GCCCATTTTGTGATGATCAGTTCA 60.082 41.667 0.09 0.00 39.12 3.18
75 76 5.506483 CGATACATCCAAACACCAAACAACA 60.506 40.000 0.00 0.00 0.00 3.33
102 103 3.552875 TGGAAACACCGAACCAAACATA 58.447 40.909 0.00 0.00 42.61 2.29
103 104 4.145807 TGGAAACACCGAACCAAACATAT 58.854 39.130 0.00 0.00 42.61 1.78
151 152 4.993029 TCAACTCAATTCGGTTTGGTTT 57.007 36.364 0.00 0.00 0.00 3.27
181 182 2.811431 TCGGTGTAAAAATGCTCACCTG 59.189 45.455 10.66 5.53 45.44 4.00
188 189 1.165270 AAATGCTCACCTGTAACCGC 58.835 50.000 0.00 0.00 0.00 5.68
189 190 0.036164 AATGCTCACCTGTAACCGCA 59.964 50.000 0.00 0.00 0.00 5.69
267 269 0.532115 GCAAAGTGCCCATTACCCTG 59.468 55.000 0.00 0.00 37.42 4.45
278 2050 3.431766 CCCATTACCCTGTAGTGTAGTGC 60.432 52.174 0.00 0.00 0.00 4.40
344 2116 3.818961 CAAGCATACACTTGTCCTGTG 57.181 47.619 0.00 0.00 41.74 3.66
406 2192 4.156556 CAGTTGGTTGTATGATGGTTGGAG 59.843 45.833 0.00 0.00 0.00 3.86
562 2348 1.989165 CAAGAGAGGAAAACGAGAGCG 59.011 52.381 0.00 0.00 44.79 5.03
597 2383 5.578776 ACGAACAAACACTCTGAATTTTCC 58.421 37.500 0.00 0.00 0.00 3.13
623 2409 2.214920 AACACCCTCCGACACCTCC 61.215 63.158 0.00 0.00 0.00 4.30
827 2625 5.350633 TGAATTCAAAACCTTGCAAGACTG 58.649 37.500 28.05 17.06 32.14 3.51
855 2653 1.009335 GAAACGTTTCCACACGGCC 60.009 57.895 27.01 2.44 44.82 6.13
880 2679 4.682787 TGTGCAGAGCATATATATACGCC 58.317 43.478 7.16 0.08 41.91 5.68
953 2752 0.106894 CGAGGCCTAAATCCACCTCC 59.893 60.000 4.42 0.00 44.89 4.30
954 2753 0.474614 GAGGCCTAAATCCACCTCCC 59.525 60.000 4.42 0.00 42.44 4.30
955 2754 1.148498 GGCCTAAATCCACCTCCCG 59.852 63.158 0.00 0.00 0.00 5.14
982 2781 7.012327 TGGTTAATTATATCAGCTGTCACAAGC 59.988 37.037 14.67 8.34 43.88 4.01
1596 3413 1.153745 GCTGCGTCTCACCTTCGAT 60.154 57.895 0.00 0.00 0.00 3.59
1788 3605 4.441695 CTCCGCAAGAGCCTCGCA 62.442 66.667 0.00 0.00 43.02 5.10
2049 3902 4.373116 GCGTCCGTGCTCAGGGAA 62.373 66.667 12.29 0.00 45.69 3.97
2193 4049 1.369692 CTCCAAGTACGTGGTGGCA 59.630 57.895 24.53 7.18 39.88 4.92
2780 4636 3.364964 CGGTTGTGTACTTTTGATGAGGC 60.365 47.826 0.00 0.00 0.00 4.70
2872 6030 5.650543 ACATTATTTTCTTCCGGTGCATTC 58.349 37.500 0.00 0.00 0.00 2.67
2930 6090 1.683441 GAAGGACCGGGTTCCACAT 59.317 57.895 13.28 0.00 38.25 3.21
2962 6122 8.961634 TGATGATAACCGAACAAAATTATCCAA 58.038 29.630 0.00 0.00 34.50 3.53
2975 6135 8.084073 ACAAAATTATCCAATATCCGATGCAAG 58.916 33.333 0.00 0.00 0.00 4.01
3009 6179 3.251571 AGACAGAAAGAATAACGCGGTC 58.748 45.455 12.47 3.13 0.00 4.79
3013 6183 1.664151 GAAAGAATAACGCGGTCAGGG 59.336 52.381 12.47 0.00 38.93 4.45
3058 6229 7.615365 TGGTTAATCCATCTTAATCAACTTGCT 59.385 33.333 0.00 0.00 41.93 3.91
3095 6267 0.340558 TATTCGGGAGGGGGTTCTCA 59.659 55.000 0.00 0.00 35.58 3.27
3100 6272 1.562475 CGGGAGGGGGTTCTCATTTTA 59.438 52.381 0.00 0.00 35.58 1.52
3125 6297 2.651382 AGTTAAGGCCAAAAGTCGGT 57.349 45.000 5.01 0.00 0.00 4.69
3130 6302 3.733960 GCCAAAAGTCGGTCGGGC 61.734 66.667 0.00 0.00 0.00 6.13
3152 6324 4.375988 GCGTTTTTCTTAAGCTTGACTTCG 59.624 41.667 9.86 5.15 39.97 3.79
3156 6328 7.569591 CGTTTTTCTTAAGCTTGACTTCGAGAT 60.570 37.037 9.86 0.00 39.97 2.75
3193 6365 2.161410 CGAATGGCATTTCCTTCGTTGA 59.839 45.455 14.93 0.00 38.98 3.18
3238 6410 6.721668 TCGACTATAGATGGATCAGTTGGATT 59.278 38.462 6.78 0.00 36.00 3.01
3243 6415 4.321718 AGATGGATCAGTTGGATTATGCG 58.678 43.478 0.00 0.00 36.00 4.73
3264 6436 3.731264 CGGTTGGTCTCTAGCGAAAGTAG 60.731 52.174 0.00 0.00 40.82 2.57
3310 6482 2.930950 TGCCCCTATTTCAAATCCTCG 58.069 47.619 0.00 0.00 0.00 4.63
3436 6628 2.959030 CTCCAGTGATTGTCGAGGGATA 59.041 50.000 0.00 0.00 0.00 2.59
3475 6667 3.744940 ATCCTCATCCTTTGCTTGGAA 57.255 42.857 0.00 0.00 37.13 3.53
3540 6732 7.607991 GGTTGTAGTGATGGGATATCTAATTGG 59.392 40.741 2.05 0.00 0.00 3.16
3548 6740 6.241223 TGGGATATCTAATTGGGGAGTAGA 57.759 41.667 2.05 0.00 39.09 2.59
3589 6781 5.248477 TCTGAACCACAAGCTATAGTCCTTT 59.752 40.000 0.84 0.00 0.00 3.11
3590 6782 5.876357 TGAACCACAAGCTATAGTCCTTTT 58.124 37.500 0.84 0.00 0.00 2.27
3592 6784 4.504858 ACCACAAGCTATAGTCCTTTTCG 58.495 43.478 0.84 0.00 0.00 3.46
3593 6785 4.222145 ACCACAAGCTATAGTCCTTTTCGA 59.778 41.667 0.84 0.00 0.00 3.71
3594 6786 5.175859 CCACAAGCTATAGTCCTTTTCGAA 58.824 41.667 0.84 0.00 0.00 3.71
3595 6787 5.642063 CCACAAGCTATAGTCCTTTTCGAAA 59.358 40.000 6.47 6.47 0.00 3.46
3596 6788 6.148811 CCACAAGCTATAGTCCTTTTCGAAAA 59.851 38.462 21.35 21.35 0.00 2.29
3609 6801 6.207221 TCCTTTTCGAAAAATTACCCACCTAC 59.793 38.462 22.67 0.00 0.00 3.18
3628 6820 1.444553 GGTTCCTCGTGAGCGACAG 60.445 63.158 0.00 0.00 42.81 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.891422 TCATCACAAAATGGGCATTCC 57.109 42.857 0.00 0.00 0.00 3.01
1 2 5.013568 TGATCATCACAAAATGGGCATTC 57.986 39.130 0.00 0.00 0.00 2.67
2 3 4.468510 ACTGATCATCACAAAATGGGCATT 59.531 37.500 0.00 0.00 0.00 3.56
3 4 4.028131 ACTGATCATCACAAAATGGGCAT 58.972 39.130 0.00 0.00 0.00 4.40
4 5 3.433343 ACTGATCATCACAAAATGGGCA 58.567 40.909 0.00 0.00 0.00 5.36
5 6 4.082081 TGAACTGATCATCACAAAATGGGC 60.082 41.667 0.00 0.00 31.50 5.36
6 7 5.184479 ACTGAACTGATCATCACAAAATGGG 59.816 40.000 0.00 0.00 37.44 4.00
7 8 6.263516 ACTGAACTGATCATCACAAAATGG 57.736 37.500 0.00 0.00 37.44 3.16
8 9 9.850628 ATAAACTGAACTGATCATCACAAAATG 57.149 29.630 0.00 0.00 37.44 2.32
9 10 9.850628 CATAAACTGAACTGATCATCACAAAAT 57.149 29.630 0.00 0.00 37.44 1.82
10 11 8.849168 ACATAAACTGAACTGATCATCACAAAA 58.151 29.630 0.00 0.00 37.44 2.44
11 12 8.394971 ACATAAACTGAACTGATCATCACAAA 57.605 30.769 0.00 0.00 37.44 2.83
12 13 7.984422 ACATAAACTGAACTGATCATCACAA 57.016 32.000 0.00 0.00 37.44 3.33
28 29 8.827177 TCGTCAGTTTTCATCTTACATAAACT 57.173 30.769 0.00 0.00 39.03 2.66
75 76 0.872388 GTTCGGTGTTTCCATCGCTT 59.128 50.000 0.00 0.00 44.90 4.68
123 124 5.968387 AACCGAATTGAGTTGATCGATAC 57.032 39.130 0.00 0.00 37.48 2.24
151 152 5.875359 AGCATTTTTACACCGAAAACCAAAA 59.125 32.000 0.00 0.00 0.00 2.44
214 215 7.399634 TCCTCGGTCCTGAGTTAAATATTTTT 58.600 34.615 5.91 0.00 34.04 1.94
215 216 6.954232 TCCTCGGTCCTGAGTTAAATATTTT 58.046 36.000 5.91 0.00 34.04 1.82
216 217 6.555463 TCCTCGGTCCTGAGTTAAATATTT 57.445 37.500 5.89 5.89 34.04 1.40
217 218 6.070424 TGTTCCTCGGTCCTGAGTTAAATATT 60.070 38.462 9.08 0.00 34.04 1.28
218 219 5.424252 TGTTCCTCGGTCCTGAGTTAAATAT 59.576 40.000 9.08 0.00 34.04 1.28
219 220 4.773674 TGTTCCTCGGTCCTGAGTTAAATA 59.226 41.667 9.08 0.00 34.04 1.40
267 269 4.655762 TGATCCATCTGCACTACACTAC 57.344 45.455 0.00 0.00 0.00 2.73
278 2050 3.200483 TGTTCGCTCATTGATCCATCTG 58.800 45.455 0.00 0.00 0.00 2.90
344 2116 8.144478 ACATATCAGACACATGTAGATTGGTAC 58.856 37.037 0.00 0.00 31.26 3.34
562 2348 1.764180 TTGTTCGTTTGCCGTCGACC 61.764 55.000 10.58 0.00 37.94 4.79
597 2383 3.357079 GGAGGGTGTTGTGCTGCG 61.357 66.667 0.00 0.00 0.00 5.18
623 2409 0.324285 AGAGTGCAGCAGAAAGGGAG 59.676 55.000 0.00 0.00 0.00 4.30
696 2494 2.164624 GTCGCTCACTCTAATCCAGTGT 59.835 50.000 0.02 0.00 41.82 3.55
827 2625 0.317854 GAAACGTTTCACCTGGCTGC 60.318 55.000 30.99 4.85 37.15 5.25
828 2626 0.310854 GGAAACGTTTCACCTGGCTG 59.689 55.000 34.79 0.00 38.92 4.85
829 2627 0.106918 TGGAAACGTTTCACCTGGCT 60.107 50.000 34.79 3.11 38.92 4.75
855 2653 6.292542 GGCGTATATATATGCTCTGCACATTG 60.293 42.308 27.88 0.00 43.04 2.82
880 2679 0.667184 GAAATGTGTTTGGCGCCCTG 60.667 55.000 26.77 0.00 0.00 4.45
953 2752 5.989168 TGACAGCTGATATAATTAACCACGG 59.011 40.000 23.35 0.00 0.00 4.94
954 2753 6.478673 TGTGACAGCTGATATAATTAACCACG 59.521 38.462 23.35 0.00 0.00 4.94
955 2754 7.786178 TGTGACAGCTGATATAATTAACCAC 57.214 36.000 23.35 9.99 0.00 4.16
1578 3395 0.100682 TATCGAAGGTGAGACGCAGC 59.899 55.000 0.00 0.00 45.24 5.25
1584 3401 3.489229 CGCAGATGTTATCGAAGGTGAGA 60.489 47.826 0.00 0.00 0.00 3.27
1596 3413 1.220749 GGTCAGCCCGCAGATGTTA 59.779 57.895 0.00 0.00 0.00 2.41
1788 3605 1.072331 GTCATGAACTGGTCCACCACT 59.928 52.381 0.00 0.00 42.01 4.00
2608 4464 0.673644 GTGGTTGGGATCACGACTGG 60.674 60.000 15.10 0.00 0.00 4.00
2757 4613 4.062293 CCTCATCAAAAGTACACAACCGA 58.938 43.478 0.00 0.00 0.00 4.69
2780 4636 4.700268 TTCATTTGACGATCCACCAATG 57.300 40.909 0.00 0.00 0.00 2.82
2838 4694 9.124807 CGGAAGAAAATAATGTTTTACCTTCAC 57.875 33.333 14.03 6.85 34.04 3.18
2946 6106 7.271223 GCATCGGATATTGGATAATTTTGTTCG 59.729 37.037 0.00 0.00 0.00 3.95
2991 6161 2.348666 CCTGACCGCGTTATTCTTTCTG 59.651 50.000 4.92 0.00 0.00 3.02
3009 6179 3.221771 TCCACAATCAGAAAACACCCTG 58.778 45.455 0.00 0.00 0.00 4.45
3013 6183 5.200368 ACCAATCCACAATCAGAAAACAC 57.800 39.130 0.00 0.00 0.00 3.32
3014 6184 5.867903 AACCAATCCACAATCAGAAAACA 57.132 34.783 0.00 0.00 0.00 2.83
3053 6224 3.637432 TGCGACCATTTGTTAAAGCAAG 58.363 40.909 0.00 0.00 0.00 4.01
3058 6229 6.030849 CCGAATATTGCGACCATTTGTTAAA 58.969 36.000 0.00 0.00 0.00 1.52
3061 6232 3.181491 CCCGAATATTGCGACCATTTGTT 60.181 43.478 0.00 0.00 0.00 2.83
3095 6267 8.428852 ACTTTTGGCCTTAACTTCATGTAAAAT 58.571 29.630 3.32 0.00 0.00 1.82
3100 6272 4.023193 CGACTTTTGGCCTTAACTTCATGT 60.023 41.667 3.32 0.00 0.00 3.21
3125 6297 1.886886 AGCTTAAGAAAAACGCCCGA 58.113 45.000 6.67 0.00 0.00 5.14
3130 6302 5.734311 TCGAAGTCAAGCTTAAGAAAAACG 58.266 37.500 6.67 0.00 37.59 3.60
3152 6324 4.318332 TCGAATTGGTCATATGCCATCTC 58.682 43.478 16.40 14.33 35.71 2.75
3156 6328 3.569277 CCATTCGAATTGGTCATATGCCA 59.431 43.478 8.21 12.98 0.00 4.92
3193 6365 1.306568 GCCTCTCCCCTCCAGAACT 60.307 63.158 0.00 0.00 0.00 3.01
3238 6410 0.384309 CGCTAGAGACCAACCGCATA 59.616 55.000 0.00 0.00 0.00 3.14
3243 6415 2.745515 ACTTTCGCTAGAGACCAACC 57.254 50.000 0.00 0.00 0.00 3.77
3264 6436 5.316987 CCTCCCCATAAATGTTGATAGTCC 58.683 45.833 0.00 0.00 0.00 3.85
3317 6489 0.036010 ACAACAGGATCAAGGCCTCG 60.036 55.000 5.23 0.00 32.12 4.63
3325 6498 3.190327 CGCATGGTTAAACAACAGGATCA 59.810 43.478 0.00 0.00 0.00 2.92
3436 6628 6.385176 TGAGGATTTGATGATGTCTAGTTCCT 59.615 38.462 0.00 0.00 32.67 3.36
3475 6667 3.118992 TGATCTTTAGCACTGACATCGCT 60.119 43.478 4.37 4.37 39.80 4.93
3484 6676 6.767902 TCTTTGTGAAGTTGATCTTTAGCACT 59.232 34.615 0.00 0.00 36.40 4.40
3520 6712 5.424068 TCCCCAATTAGATATCCCATCACT 58.576 41.667 0.00 0.00 0.00 3.41
3540 6732 3.814005 TGGTAATTCGCTTCTACTCCC 57.186 47.619 0.00 0.00 0.00 4.30
3548 6740 6.601613 TGGTTCAGATTATTGGTAATTCGCTT 59.398 34.615 0.00 0.00 30.75 4.68


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

AutoCloner maintained by Alex Coulton.