Multiple sequence alignment - TraesCS3D01G232100

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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 TraesCS3D01G232100 chr3D 100.000 5054 0 0 1 5054 318576020 318570967 0.000000e+00 9334
1 TraesCS3D01G232100 chr3D 91.489 94 8 0 4465 4558 318571471 318571378 4.110000e-26 130
2 TraesCS3D01G232100 chr3D 91.489 94 8 0 4550 4643 318571556 318571463 4.110000e-26 130
3 TraesCS3D01G232100 chr3B 94.671 5123 182 41 1 5054 401026945 401032045 0.000000e+00 7864
4 TraesCS3D01G232100 chr3B 93.617 94 6 0 4550 4643 401031436 401031529 1.900000e-29 141
5 TraesCS3D01G232100 chr3B 92.553 94 7 0 4465 4558 401031521 401031614 8.830000e-28 135
6 TraesCS3D01G232100 chr3A 96.300 3892 112 16 686 4558 407423144 407427022 0.000000e+00 6360
7 TraesCS3D01G232100 chr3A 89.226 594 55 3 72 657 407422235 407422827 0.000000e+00 734
8 TraesCS3D01G232100 chr3A 89.962 528 22 14 4550 5054 407426929 407427448 0.000000e+00 652


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 TraesCS3D01G232100 chr3D 318570967 318576020 5053 True 9334.000000 9334 100.000000 1 5054 1 chr3D.!!$R1 5053
1 TraesCS3D01G232100 chr3B 401026945 401032045 5100 False 2713.333333 7864 93.613667 1 5054 3 chr3B.!!$F1 5053
2 TraesCS3D01G232100 chr3A 407422235 407427448 5213 False 2582.000000 6360 91.829333 72 5054 3 chr3A.!!$F1 4982

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
675 980 0.457035 GTGGTTACCGCGGTGATAGA 59.543 55.000 40.02 18.25 0.00 1.98 F
700 1014 0.565674 GAGAGGGAGAGGGGAGGATT 59.434 60.000 0.00 0.00 0.00 3.01 F
931 1256 0.926293 GATCCCTCCCAAATCACCCA 59.074 55.000 0.00 0.00 0.00 4.51 F
1548 1874 1.800586 CAGCCGCGTCATTGCTTATAT 59.199 47.619 4.92 0.00 31.77 0.86 F
3124 3455 1.464997 GAAGCTGAACTAAAGGCACGG 59.535 52.381 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1941 4.361783 TGGTCTGAGGAGTGGATTAATCA 58.638 43.478 17.07 1.07 0.00 2.57 R
2479 2810 5.659463 TCCAAATTACAGGCAACATAATGC 58.341 37.500 0.00 0.00 45.67 3.56 R
2991 3322 9.539194 AATTCATTTCTCCTGGAATAAGAAGTT 57.461 29.630 0.00 0.00 33.53 2.66 R
3135 3466 0.188587 ATGCTACTCCCTCCGATCCA 59.811 55.000 0.00 0.00 0.00 3.41 R
5011 5372 0.536260 CTTCACCCCTCTCTCAGCTG 59.464 60.000 7.63 7.63 0.00 4.24 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
40 41 5.180271 ACAAACACCTCACTCGTCTTTTTA 58.820 37.500 0.00 0.00 0.00 1.52
41 42 5.820947 ACAAACACCTCACTCGTCTTTTTAT 59.179 36.000 0.00 0.00 0.00 1.40
42 43 6.987992 ACAAACACCTCACTCGTCTTTTTATA 59.012 34.615 0.00 0.00 0.00 0.98
43 44 7.042254 ACAAACACCTCACTCGTCTTTTTATAC 60.042 37.037 0.00 0.00 0.00 1.47
44 45 6.092955 ACACCTCACTCGTCTTTTTATACA 57.907 37.500 0.00 0.00 0.00 2.29
45 46 6.698380 ACACCTCACTCGTCTTTTTATACAT 58.302 36.000 0.00 0.00 0.00 2.29
60 62 4.864334 CATCTGGTCCTGGCGCCC 62.864 72.222 26.77 8.13 0.00 6.13
82 84 1.571773 GGGCTTGGACCACCCATACT 61.572 60.000 14.16 0.00 46.10 2.12
83 85 1.209621 GGCTTGGACCACCCATACTA 58.790 55.000 0.00 0.00 46.10 1.82
145 147 5.357257 TCACTTTAATCCATACCTTCTCGC 58.643 41.667 0.00 0.00 0.00 5.03
206 208 1.992834 TCCTTGCCGAGGTATGCCA 60.993 57.895 1.54 0.00 46.39 4.92
211 213 1.227380 GCCGAGGTATGCCACTCTG 60.227 63.158 1.54 0.00 37.19 3.35
269 271 3.309582 CACGCTGGGGTGTAGGAT 58.690 61.111 9.21 0.00 34.50 3.24
279 281 2.090999 GGGGTGTAGGATCTTCTCTCCT 60.091 54.545 0.00 0.00 45.22 3.69
337 340 1.189524 ATCGGGTTGACCTCACGGAA 61.190 55.000 0.00 0.00 36.97 4.30
340 343 1.003718 GGTTGACCTCACGGAAGGG 60.004 63.158 9.81 0.00 41.04 3.95
416 426 2.573167 CGATTTTTGCGACGGCGG 60.573 61.111 15.06 0.00 44.10 6.13
418 428 4.413800 ATTTTTGCGACGGCGGGC 62.414 61.111 15.06 15.28 44.10 6.13
443 453 1.376543 CTGCTTCAATGGCGACTGAT 58.623 50.000 0.00 0.00 0.00 2.90
509 519 2.429236 AGCAAGACAGTCGACGCG 60.429 61.111 10.46 3.53 0.00 6.01
576 587 1.174712 ATTTGTGAGGCGTGCTGCTT 61.175 50.000 0.00 0.00 45.43 3.91
606 617 2.949106 CAAGCGGCAGTGGTGAAG 59.051 61.111 1.45 0.00 0.00 3.02
616 627 3.164977 TGGTGAAGTGCGGTGGGA 61.165 61.111 0.00 0.00 0.00 4.37
665 970 1.792993 CGTCGAGCTAAGTGGTTACCG 60.793 57.143 0.00 0.00 0.00 4.02
675 980 0.457035 GTGGTTACCGCGGTGATAGA 59.543 55.000 40.02 18.25 0.00 1.98
685 990 1.655329 GGTGATAGACGCGGGAGAG 59.345 63.158 12.47 0.00 0.00 3.20
688 993 1.228184 GATAGACGCGGGAGAGGGA 60.228 63.158 12.47 0.00 0.00 4.20
700 1014 0.565674 GAGAGGGAGAGGGGAGGATT 59.434 60.000 0.00 0.00 0.00 3.01
708 1022 1.807495 GAGGGGAGGATTAGACGGCG 61.807 65.000 4.80 4.80 0.00 6.46
725 1048 1.735376 GCGCCCTCTCATCTAACGGA 61.735 60.000 0.00 0.00 0.00 4.69
764 1087 3.283684 CTGGCGCCGGTTGACAAA 61.284 61.111 27.83 1.51 0.00 2.83
831 1154 1.217689 CCTCAGTCTCTCCCCTCTCAT 59.782 57.143 0.00 0.00 0.00 2.90
931 1256 0.926293 GATCCCTCCCAAATCACCCA 59.074 55.000 0.00 0.00 0.00 4.51
1390 1715 2.680577 CAGGCCTTGTTTCAGCATTTC 58.319 47.619 0.00 0.00 0.00 2.17
1404 1729 5.049167 TCAGCATTTCTTTTTCGCATTTGT 58.951 33.333 0.00 0.00 0.00 2.83
1548 1874 1.800586 CAGCCGCGTCATTGCTTATAT 59.199 47.619 4.92 0.00 31.77 0.86
1615 1941 3.360740 TCATGGACTACCCCACCATAT 57.639 47.619 0.00 0.00 41.68 1.78
1763 2089 2.356125 GCCAGCAAGGGAGAAGAATGTA 60.356 50.000 0.00 0.00 38.09 2.29
1845 2171 3.592059 TGTAGCGTTTGTAATCCTGACC 58.408 45.455 0.00 0.00 0.00 4.02
2184 2510 2.143925 ACTGCTGAGTTTAGCCGTTTC 58.856 47.619 0.00 0.00 43.02 2.78
2702 3033 4.644234 TCAGAACTTTGAATGCACTTCCAA 59.356 37.500 0.00 0.00 32.49 3.53
2721 3052 8.882736 ACTTCCAATTGACAAAAATGTTTCTTC 58.117 29.630 7.12 0.00 0.00 2.87
3124 3455 1.464997 GAAGCTGAACTAAAGGCACGG 59.535 52.381 0.00 0.00 0.00 4.94
3228 3561 1.134521 TCTGTGTGCAACCTCGTTTCT 60.135 47.619 0.00 0.00 34.36 2.52
3258 3591 4.992951 GCATGGGATTTATTGAATTGGAGC 59.007 41.667 0.00 0.00 0.00 4.70
3273 3606 8.585471 TGAATTGGAGCAATCTTCTTATCTTT 57.415 30.769 0.00 0.00 32.43 2.52
3351 3684 8.385491 AGAACATCATATACCCTTGCATATTCA 58.615 33.333 0.00 0.00 0.00 2.57
3395 3728 4.149046 GCTGTCACGTAAGAACTTGAGAAG 59.851 45.833 0.00 0.00 34.83 2.85
3463 3796 4.681483 GTGGCAAAATGAGTTGACTAAAGC 59.319 41.667 0.00 0.00 37.42 3.51
3904 4237 3.730761 CAACCAGCCGCAGCAGAC 61.731 66.667 0.00 0.00 43.56 3.51
4268 4608 4.637387 AGAGCCAGATCCTATCCAATTG 57.363 45.455 0.00 0.00 0.00 2.32
4331 4671 5.864418 AACATCATCCCAGATTGGAAATG 57.136 39.130 0.00 1.10 40.96 2.32
4418 4762 9.231297 TCTTGAGTAAGTATTTCCAGGAATTTG 57.769 33.333 1.58 0.00 35.38 2.32
4527 4872 2.450476 CTTGGGAAACTTCTGATGGGG 58.550 52.381 0.00 0.00 0.00 4.96
4532 4877 3.610911 GGAAACTTCTGATGGGGTAGTG 58.389 50.000 0.00 0.00 0.00 2.74
4561 4906 8.707938 TCTCATCATACATATAAATTCCAGCG 57.292 34.615 0.00 0.00 0.00 5.18
4631 4976 8.829746 TGATGGGCTAGTAAAATCTCATCATAT 58.170 33.333 4.72 0.00 36.06 1.78
4813 5174 7.686434 ACCCTGTCAAGTAGCTAGAAAAATAA 58.314 34.615 0.00 0.00 0.00 1.40
4834 5195 8.854614 AATAATCTTATGCCTAATCCTGTCAC 57.145 34.615 0.00 0.00 0.00 3.67
4863 5224 4.927049 TCCAGAGCCATTTGAAGATCTTT 58.073 39.130 9.87 0.00 0.00 2.52
4879 5240 2.297701 TCTTTTGTGCTTCCACTCCAC 58.702 47.619 0.00 0.00 42.54 4.02
5011 5372 4.863491 TCATTCAGTTGAGCAAAAGCTTC 58.137 39.130 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.447643 GCGCCAGGACCAGATGTAT 59.552 57.895 0.00 0.00 0.00 2.29
41 42 2.731571 GGCGCCAGGACCAGATGTA 61.732 63.158 24.80 0.00 0.00 2.29
42 43 4.101448 GGCGCCAGGACCAGATGT 62.101 66.667 24.80 0.00 0.00 3.06
43 44 4.864334 GGGCGCCAGGACCAGATG 62.864 72.222 30.85 0.00 46.58 2.90
60 62 4.410400 GGGTGGTCCAAGCCCTCG 62.410 72.222 9.89 0.00 39.31 4.63
82 84 8.027189 GGTAAATATGTAGCTGTCGATGTCATA 58.973 37.037 0.00 0.00 0.00 2.15
83 85 6.868864 GGTAAATATGTAGCTGTCGATGTCAT 59.131 38.462 0.00 0.00 0.00 3.06
145 147 2.203070 GGCATGTACCGCCCTCTG 60.203 66.667 11.49 0.00 44.22 3.35
211 213 5.221601 TGGCTAGGAAAGATGATCTGACATC 60.222 44.000 0.00 10.37 44.65 3.06
377 380 1.189524 ACCGACGGGATCAGGACAAA 61.190 55.000 20.00 0.00 36.97 2.83
378 381 1.608336 ACCGACGGGATCAGGACAA 60.608 57.895 20.00 0.00 36.97 3.18
379 382 2.036731 ACCGACGGGATCAGGACA 59.963 61.111 20.00 0.00 36.97 4.02
416 426 0.102481 CCATTGAAGCAGCATCAGCC 59.898 55.000 0.00 0.00 43.56 4.85
418 428 0.248498 CGCCATTGAAGCAGCATCAG 60.248 55.000 0.00 0.00 0.00 2.90
449 459 4.227134 CGCGGGTCCTGATGAGGG 62.227 72.222 0.31 0.00 40.25 4.30
509 519 2.757868 ACCAGTCTCAGCTACACTCATC 59.242 50.000 0.00 0.00 0.00 2.92
553 564 0.602638 AGCACGCCTCACAAATTCGA 60.603 50.000 0.00 0.00 0.00 3.71
602 613 0.893270 CCAAATCCCACCGCACTTCA 60.893 55.000 0.00 0.00 0.00 3.02
606 617 4.114997 CGCCAAATCCCACCGCAC 62.115 66.667 0.00 0.00 0.00 5.34
616 627 3.118454 CGTCGACTGCCGCCAAAT 61.118 61.111 14.70 0.00 38.37 2.32
665 970 3.825833 CTCCCGCGTCTATCACCGC 62.826 68.421 4.92 0.00 46.10 5.68
675 980 4.824515 CCTCTCCCTCTCCCGCGT 62.825 72.222 4.92 0.00 0.00 6.01
685 990 1.824045 CGTCTAATCCTCCCCTCTCCC 60.824 61.905 0.00 0.00 0.00 4.30
688 993 0.470268 GCCGTCTAATCCTCCCCTCT 60.470 60.000 0.00 0.00 0.00 3.69
700 1014 2.123854 ATGAGAGGGCGCCGTCTA 60.124 61.111 42.44 31.03 40.67 2.59
708 1022 1.067821 CTGTCCGTTAGATGAGAGGGC 59.932 57.143 0.00 0.00 0.00 5.19
758 1081 2.682856 GTGTTGAGAGTTGGCTTTGTCA 59.317 45.455 0.00 0.00 0.00 3.58
764 1087 1.202818 GGAAGGTGTTGAGAGTTGGCT 60.203 52.381 0.00 0.00 0.00 4.75
831 1154 0.479589 AGGGATCCTTTGTTGGGGGA 60.480 55.000 12.58 0.00 0.00 4.81
931 1256 4.814294 GGAGCGAATCGGGTGCGT 62.814 66.667 4.35 0.00 0.00 5.24
1338 1663 5.460646 AGCTAATTGTGATTTTCGTGGTTG 58.539 37.500 0.00 0.00 0.00 3.77
1390 1715 7.318674 GCAATCAAGTTTACAAATGCGAAAAAG 59.681 33.333 0.00 0.00 0.00 2.27
1456 1782 1.011333 CGAACCGAACACCACAAAGT 58.989 50.000 0.00 0.00 0.00 2.66
1615 1941 4.361783 TGGTCTGAGGAGTGGATTAATCA 58.638 43.478 17.07 1.07 0.00 2.57
1667 1993 7.291182 AGCCCTAGATGTCACTAATGTTAGATT 59.709 37.037 6.78 0.00 34.84 2.40
1763 2089 6.593382 GTGCTCTTGTCTTCTAGTTTGATGAT 59.407 38.462 0.00 0.00 0.00 2.45
1845 2171 9.837525 CCTGAAATGAACAAGAGAAATTAAGAG 57.162 33.333 0.00 0.00 0.00 2.85
2184 2510 9.946165 TCGACACTAAGTATCAAATACTATGTG 57.054 33.333 19.49 19.49 44.94 3.21
2479 2810 5.659463 TCCAAATTACAGGCAACATAATGC 58.341 37.500 0.00 0.00 45.67 3.56
2991 3322 9.539194 AATTCATTTCTCCTGGAATAAGAAGTT 57.461 29.630 0.00 0.00 33.53 2.66
3135 3466 0.188587 ATGCTACTCCCTCCGATCCA 59.811 55.000 0.00 0.00 0.00 3.41
3176 3507 9.733556 TGTGCATCTTAAAGAGGAAAATACTAA 57.266 29.630 0.00 0.00 0.00 2.24
3228 3561 4.544683 TCAATAAATCCCATGCATGACCA 58.455 39.130 28.31 11.20 0.00 4.02
3273 3606 5.537295 TGCACTAGACTGTGTTTTCTAGGTA 59.463 40.000 9.77 0.00 43.90 3.08
3351 3684 4.596643 AGCAGCTCAAACTGATATATCCCT 59.403 41.667 10.25 0.00 40.25 4.20
3395 3728 9.872721 AACTATAGCTTAGTAAGGTTCAGTTTC 57.127 33.333 22.60 3.85 37.98 2.78
3441 3774 4.556501 CGCTTTAGTCAACTCATTTTGCCA 60.557 41.667 0.00 0.00 0.00 4.92
3868 4201 1.137086 TGATTACGAGGAGCAGCTTCC 59.863 52.381 0.00 0.00 37.52 3.46
3904 4237 1.334869 ACGCTTCCTTGTTTGCTCTTG 59.665 47.619 0.00 0.00 0.00 3.02
4018 4351 5.184096 GGGAGATCCAAGAAAAAGAAAGGAC 59.816 44.000 0.47 0.00 37.91 3.85
4062 4395 1.746322 TACAACAACTCGGGTGGCGA 61.746 55.000 0.00 0.00 0.00 5.54
4386 4726 7.311092 TGGAAATACTTACTCAAGACCTGAA 57.689 36.000 0.00 0.00 35.60 3.02
4439 4783 6.544931 TGGATTCTAAGAAATGGCAAGATCTG 59.455 38.462 0.00 0.00 0.00 2.90
4440 4784 6.666678 TGGATTCTAAGAAATGGCAAGATCT 58.333 36.000 0.00 0.00 0.00 2.75
4441 4785 6.949352 TGGATTCTAAGAAATGGCAAGATC 57.051 37.500 0.00 0.00 0.00 2.75
4561 4906 8.494433 TGGACATGGATATAATTATTCTAGGGC 58.506 37.037 2.68 3.68 0.00 5.19
4601 4946 6.349300 TGAGATTTTACTAGCCCATCAGAAC 58.651 40.000 0.00 0.00 0.00 3.01
4631 4976 9.839185 ACCTATAGGCAAAGAGGAACTTATATA 57.161 33.333 19.25 0.00 37.56 0.86
4748 5094 4.851639 AGAGGAAAACCATGCTATGACT 57.148 40.909 0.00 0.00 0.00 3.41
4749 5095 6.823689 TCTTAAGAGGAAAACCATGCTATGAC 59.176 38.462 0.00 0.00 0.00 3.06
4750 5096 6.957631 TCTTAAGAGGAAAACCATGCTATGA 58.042 36.000 0.00 0.00 0.00 2.15
4751 5097 6.825721 ACTCTTAAGAGGAAAACCATGCTATG 59.174 38.462 30.98 6.22 46.13 2.23
4753 5099 6.374417 ACTCTTAAGAGGAAAACCATGCTA 57.626 37.500 30.98 0.00 46.13 3.49
4754 5100 5.248380 ACTCTTAAGAGGAAAACCATGCT 57.752 39.130 30.98 7.58 46.13 3.79
4755 5101 5.966742 AACTCTTAAGAGGAAAACCATGC 57.033 39.130 30.98 0.00 46.13 4.06
4813 5174 4.660303 TGGTGACAGGATTAGGCATAAGAT 59.340 41.667 0.00 0.00 35.01 2.40
4834 5195 1.068333 CAAATGGCTCTGGAAACGTGG 60.068 52.381 0.00 0.00 0.00 4.94
4863 5224 1.429930 TAGGTGGAGTGGAAGCACAA 58.570 50.000 0.00 0.00 0.00 3.33
5011 5372 0.536260 CTTCACCCCTCTCTCAGCTG 59.464 60.000 7.63 7.63 0.00 4.24


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

AutoCloner maintained by Alex Coulton.