Multiple sequence alignment - TraesCS4D01G316400

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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 TraesCS4D01G316400 chr4D 100.000 3071 0 0 1 3071 481546514 481549584 0.000000e+00 5672
1 TraesCS4D01G316400 chr4B 87.675 2353 129 62 1 2296 610561210 610563458 0.000000e+00 2590
2 TraesCS4D01G316400 chr4B 97.436 351 9 0 2370 2720 610564163 610564513 1.580000e-167 599
3 TraesCS4D01G316400 chr4B 89.577 355 20 4 2734 3071 610564498 610564852 4.700000e-118 435
4 TraesCS4D01G316400 chr5A 89.604 1943 73 49 1215 3069 661149379 661147478 0.000000e+00 2350
5 TraesCS4D01G316400 chr5A 84.158 707 44 37 519 1187 661150050 661149374 9.350000e-175 623
6 TraesCS4D01G316400 chr5A 83.184 446 30 18 1 429 661150517 661150100 1.740000e-97 366
7 TraesCS4D01G316400 chr1D 82.482 274 33 9 1498 1768 262475300 262475561 3.080000e-55 226
8 TraesCS4D01G316400 chr1B 82.117 274 34 10 1498 1768 348479121 348479382 1.430000e-53 220
9 TraesCS4D01G316400 chr1A 87.654 162 20 0 1498 1659 336476444 336476605 4.040000e-44 189


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 TraesCS4D01G316400 chr4D 481546514 481549584 3070 False 5672 5672 100.000000 1 3071 1 chr4D.!!$F1 3070
1 TraesCS4D01G316400 chr4B 610561210 610564852 3642 False 1208 2590 91.562667 1 3071 3 chr4B.!!$F1 3070
2 TraesCS4D01G316400 chr5A 661147478 661150517 3039 True 1113 2350 85.648667 1 3069 3 chr5A.!!$R1 3068

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
788 850 0.313043 CCTTTGCCTCTTGTGTGCTG 59.687 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2413 1.070289 GTACATGTACTAGGGCAGGCC 59.93 57.143 25.56 4.33 33.45 5.19 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
18 19 3.516263 CGGCCGAACGTACTAGTAC 57.484 57.895 24.07 21.06 0.00 2.73
19 20 1.009829 CGGCCGAACGTACTAGTACT 58.990 55.000 24.07 12.22 34.04 2.73
20 21 2.201732 CGGCCGAACGTACTAGTACTA 58.798 52.381 24.07 1.89 34.04 1.82
22 23 2.032463 GGCCGAACGTACTAGTACTAGC 60.032 54.545 26.54 20.21 36.66 3.42
114 120 2.107953 GCTAGCTTCCAGCCGGAG 59.892 66.667 5.05 0.00 43.77 4.63
213 223 0.840729 GAGATAAAGCGAGCGTGACG 59.159 55.000 0.00 0.00 0.00 4.35
323 333 2.888834 TCATCCGCGAATCAGAATCA 57.111 45.000 8.23 0.00 0.00 2.57
324 334 3.177997 TCATCCGCGAATCAGAATCAA 57.822 42.857 8.23 0.00 0.00 2.57
325 335 3.732212 TCATCCGCGAATCAGAATCAAT 58.268 40.909 8.23 0.00 0.00 2.57
326 336 3.742882 TCATCCGCGAATCAGAATCAATC 59.257 43.478 8.23 0.00 0.00 2.67
334 348 4.443725 CGAATCAGAATCAATCAGAGGACG 59.556 45.833 0.00 0.00 0.00 4.79
366 380 3.435186 GCAACGGAGGAGGCAAGC 61.435 66.667 0.00 0.00 0.00 4.01
367 381 2.348998 CAACGGAGGAGGCAAGCT 59.651 61.111 0.00 0.00 0.00 3.74
509 532 4.570663 GATCGCCTCGACCCACCG 62.571 72.222 0.00 0.00 39.18 4.94
528 551 2.243957 TGTACTGTGCGCACTGTGC 61.244 57.895 44.13 42.41 42.27 4.57
604 643 1.813192 GCCGGTGAGGAAGAGAGAG 59.187 63.158 1.90 0.00 45.00 3.20
605 644 0.681564 GCCGGTGAGGAAGAGAGAGA 60.682 60.000 1.90 0.00 45.00 3.10
606 645 1.388547 CCGGTGAGGAAGAGAGAGAG 58.611 60.000 0.00 0.00 45.00 3.20
607 646 1.065053 CCGGTGAGGAAGAGAGAGAGA 60.065 57.143 0.00 0.00 45.00 3.10
639 678 8.822855 CCACGTCAGACAGATATAGATAGATAC 58.177 40.741 0.41 0.00 0.00 2.24
642 681 9.594478 CGTCAGACAGATATAGATAGATACAGT 57.406 37.037 0.41 0.00 0.00 3.55
680 721 1.352156 CTTCGCACCAACGCTACCTC 61.352 60.000 0.00 0.00 0.00 3.85
761 823 2.287457 TTTAGGACCACCCGCGATCG 62.287 60.000 11.69 11.69 40.87 3.69
787 849 0.825010 CCCTTTGCCTCTTGTGTGCT 60.825 55.000 0.00 0.00 0.00 4.40
788 850 0.313043 CCTTTGCCTCTTGTGTGCTG 59.687 55.000 0.00 0.00 0.00 4.41
789 851 0.318445 CTTTGCCTCTTGTGTGCTGC 60.318 55.000 0.00 0.00 0.00 5.25
830 892 4.484872 GCCTAACCTCCGCACCCC 62.485 72.222 0.00 0.00 0.00 4.95
831 893 4.157120 CCTAACCTCCGCACCCCG 62.157 72.222 0.00 0.00 0.00 5.73
832 894 3.387947 CTAACCTCCGCACCCCGT 61.388 66.667 0.00 0.00 34.38 5.28
833 895 3.366739 CTAACCTCCGCACCCCGTC 62.367 68.421 0.00 0.00 34.38 4.79
847 909 3.702048 CGTCGGGCCTCTTTCCCA 61.702 66.667 0.84 0.00 44.11 4.37
851 913 2.193248 GGGCCTCTTTCCCATCCG 59.807 66.667 0.84 0.00 43.37 4.18
852 914 2.680370 GGGCCTCTTTCCCATCCGT 61.680 63.158 0.84 0.00 43.37 4.69
915 982 1.480212 CCACACACCCTCACTAGCCA 61.480 60.000 0.00 0.00 0.00 4.75
928 1000 3.391296 TCACTAGCCACTCCCATTATTCC 59.609 47.826 0.00 0.00 0.00 3.01
940 1012 2.423373 CCATTATTCCCACCTGTCCCAG 60.423 54.545 0.00 0.00 0.00 4.45
950 1027 1.630878 ACCTGTCCCAGTTGATCTTCC 59.369 52.381 0.00 0.00 0.00 3.46
1034 1125 1.517242 AGCAAGAAACGCTCCTTCTG 58.483 50.000 0.00 0.00 33.35 3.02
1198 1298 0.031178 CACCTGCACTTTGTTCTGGC 59.969 55.000 0.00 0.00 0.00 4.85
1211 1311 0.172578 TTCTGGCGTCGGTCATACAG 59.827 55.000 0.00 0.00 0.00 2.74
1228 1328 2.126346 GTGCCTGCATCCAAACGC 60.126 61.111 0.00 0.00 0.00 4.84
1258 1358 4.304110 TGCTTCGGACTGTAAACTAACTG 58.696 43.478 0.00 0.00 0.00 3.16
1418 1540 5.301551 TCTCTTCTGTTCTGCTAGATCCATC 59.698 44.000 0.00 0.00 0.00 3.51
1478 1600 0.247185 GCTCTGCTCTGCTCTGTTCT 59.753 55.000 0.00 0.00 0.00 3.01
1481 1603 2.491298 CTCTGCTCTGCTCTGTTCTACA 59.509 50.000 0.00 0.00 0.00 2.74
1496 1618 6.588756 TCTGTTCTACATCGTTTTATTTCGCT 59.411 34.615 0.00 0.00 0.00 4.93
1644 1766 0.107945 CCAAGGAGCCCGAGAAGAAG 60.108 60.000 0.00 0.00 0.00 2.85
1725 1850 3.119096 GGCGACGGCAAGAAGGAC 61.119 66.667 17.49 0.00 42.47 3.85
1731 1856 2.125106 GGCAAGAAGGACGGCGAT 60.125 61.111 16.62 0.00 0.00 4.58
1767 1895 2.184579 GGGAAGAAGGACGGCGAG 59.815 66.667 16.62 0.00 0.00 5.03
1827 1955 0.391597 AGAAGGACGGCGACAAGAAA 59.608 50.000 16.62 0.00 0.00 2.52
2104 2232 2.138844 CTCGATCGCTCGCGTACGTA 62.139 60.000 17.90 4.68 44.65 3.57
2105 2233 2.060394 CGATCGCTCGCGTACGTAC 61.060 63.158 17.90 15.90 38.20 3.67
2279 2413 2.293627 GCGATGCTACGTACTGCCG 61.294 63.158 4.55 3.44 35.59 5.69
2345 2870 6.620678 TCCTTTCAACAACAGAGAACAAAAG 58.379 36.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.849883 ACGTATGATTCGAGCTGTTCTAG 58.150 43.478 0.00 0.00 0.00 2.43
103 109 2.364317 CTCCTCCTCCGGCTGGAA 60.364 66.667 16.91 0.00 45.87 3.53
164 170 3.499737 GATTCCCGGTGCTGTGCG 61.500 66.667 0.00 0.00 0.00 5.34
170 178 2.202892 GAGGTCGATTCCCGGTGC 60.203 66.667 0.00 0.00 39.14 5.01
171 179 1.320344 TGAGAGGTCGATTCCCGGTG 61.320 60.000 0.00 0.00 39.14 4.94
172 180 1.000019 TGAGAGGTCGATTCCCGGT 60.000 57.895 0.00 0.00 39.14 5.28
259 269 2.988549 CTTGTCACGCGTCGAGTGC 61.989 63.158 22.33 17.37 39.31 4.40
311 321 4.443725 CGTCCTCTGATTGATTCTGATTCG 59.556 45.833 0.00 0.00 32.55 3.34
323 333 2.722201 GGTCCGGCGTCCTCTGATT 61.722 63.158 6.01 0.00 0.00 2.57
324 334 3.148279 GGTCCGGCGTCCTCTGAT 61.148 66.667 6.01 0.00 0.00 2.90
348 362 2.747855 CTTGCCTCCTCCGTTGCC 60.748 66.667 0.00 0.00 0.00 4.52
351 365 1.901085 CTAGCTTGCCTCCTCCGTT 59.099 57.895 0.00 0.00 0.00 4.44
352 366 2.726351 GCTAGCTTGCCTCCTCCGT 61.726 63.158 9.15 0.00 0.00 4.69
504 527 3.411351 GCGCACAGTACACGGTGG 61.411 66.667 13.48 5.96 41.34 4.61
509 532 1.564622 CACAGTGCGCACAGTACAC 59.435 57.895 39.21 13.68 37.96 2.90
604 643 1.269723 TGTCTGACGTGGATGTGTCTC 59.730 52.381 0.00 0.00 36.10 3.36
605 644 1.270826 CTGTCTGACGTGGATGTGTCT 59.729 52.381 0.00 0.00 36.10 3.41
606 645 1.269723 TCTGTCTGACGTGGATGTGTC 59.730 52.381 0.00 0.00 35.67 3.67
607 646 1.328279 TCTGTCTGACGTGGATGTGT 58.672 50.000 0.00 0.00 0.00 3.72
639 678 1.992277 AGCCCAGTGCCCTCTACTG 60.992 63.158 0.00 0.00 43.94 2.74
642 681 3.402681 GCAGCCCAGTGCCCTCTA 61.403 66.667 0.00 0.00 42.71 2.43
834 896 2.193248 CGGATGGGAAAGAGGCCC 59.807 66.667 0.00 0.00 46.22 5.80
835 897 1.153147 GACGGATGGGAAAGAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
836 898 1.153147 GGACGGATGGGAAAGAGGC 60.153 63.158 0.00 0.00 0.00 4.70
837 899 0.466124 GAGGACGGATGGGAAAGAGG 59.534 60.000 0.00 0.00 0.00 3.69
838 900 0.466124 GGAGGACGGATGGGAAAGAG 59.534 60.000 0.00 0.00 0.00 2.85
839 901 1.327690 CGGAGGACGGATGGGAAAGA 61.328 60.000 0.00 0.00 39.42 2.52
840 902 1.144057 CGGAGGACGGATGGGAAAG 59.856 63.158 0.00 0.00 39.42 2.62
841 903 3.026431 GCGGAGGACGGATGGGAAA 62.026 63.158 0.00 0.00 44.51 3.13
842 904 3.467226 GCGGAGGACGGATGGGAA 61.467 66.667 0.00 0.00 44.51 3.97
843 905 4.458829 AGCGGAGGACGGATGGGA 62.459 66.667 0.00 0.00 44.51 4.37
885 952 4.980805 TGTGTGGGAACGGCGAGC 62.981 66.667 16.62 4.27 0.00 5.03
886 953 3.041940 GTGTGTGGGAACGGCGAG 61.042 66.667 16.62 0.00 0.00 5.03
887 954 4.612412 GGTGTGTGGGAACGGCGA 62.612 66.667 16.62 0.00 0.00 5.54
889 956 4.265056 AGGGTGTGTGGGAACGGC 62.265 66.667 0.00 0.00 0.00 5.68
890 957 2.032071 GAGGGTGTGTGGGAACGG 59.968 66.667 0.00 0.00 0.00 4.44
891 958 1.597027 GTGAGGGTGTGTGGGAACG 60.597 63.158 0.00 0.00 0.00 3.95
892 959 1.002087 CTAGTGAGGGTGTGTGGGAAC 59.998 57.143 0.00 0.00 0.00 3.62
915 982 2.509964 GACAGGTGGGAATAATGGGAGT 59.490 50.000 0.00 0.00 0.00 3.85
950 1027 4.812476 TGAACGGGCAGGCGATCG 62.812 66.667 11.69 11.69 0.00 3.69
959 1036 0.390472 CAGAGAGAAGGTGAACGGGC 60.390 60.000 0.00 0.00 0.00 6.13
1028 1119 4.701651 TCCATGAACATTACAAGCAGAAGG 59.298 41.667 0.00 0.00 0.00 3.46
1034 1125 7.434307 CAGAATCAATCCATGAACATTACAAGC 59.566 37.037 0.00 0.00 42.54 4.01
1198 1298 1.511305 AGGCACTGTATGACCGACG 59.489 57.895 0.00 0.00 36.75 5.12
1211 1311 2.126346 GCGTTTGGATGCAGGCAC 60.126 61.111 0.00 0.00 37.73 5.01
1228 1328 0.108424 CAGTCCGAAGCAGAGGAAGG 60.108 60.000 0.00 0.00 38.41 3.46
1258 1358 3.818787 CCAGCATCGGCAAGCCAC 61.819 66.667 12.19 0.00 44.61 5.01
1318 1419 1.337703 TGCTTGTCCTTGTTGTCATGC 59.662 47.619 0.00 0.00 0.00 4.06
1397 1498 5.163426 ACTGATGGATCTAGCAGAACAGAAG 60.163 44.000 28.28 3.08 32.86 2.85
1418 1540 1.067846 TCGATCGGTGGTCTTTGACTG 60.068 52.381 16.41 0.00 32.47 3.51
1478 1600 5.110598 TGCCTAGCGAAATAAAACGATGTA 58.889 37.500 0.00 0.00 0.00 2.29
1481 1603 4.084537 CGATGCCTAGCGAAATAAAACGAT 60.085 41.667 0.00 0.00 38.09 3.73
1593 1715 3.078196 TCGATGTAGGCCGCCCAA 61.078 61.111 5.55 0.00 0.00 4.12
1644 1766 1.788229 CCTCCTCCTTCTTCTCCTCC 58.212 60.000 0.00 0.00 0.00 4.30
1715 1840 2.464459 CCATCGCCGTCCTTCTTGC 61.464 63.158 0.00 0.00 0.00 4.01
1725 1850 1.521681 GTCCTTCTTCCCATCGCCG 60.522 63.158 0.00 0.00 0.00 6.46
1731 1856 2.602267 TCGCCGTCCTTCTTCCCA 60.602 61.111 0.00 0.00 0.00 4.37
1767 1895 1.518302 GTCGCCCTCCTCCTTCTTC 59.482 63.158 0.00 0.00 0.00 2.87
2279 2413 1.070289 GTACATGTACTAGGGCAGGCC 59.930 57.143 25.56 4.33 33.45 5.19
2345 2870 3.703921 ACCCACTCTTTCCTCTCTCTAC 58.296 50.000 0.00 0.00 0.00 2.59
2481 3251 7.424227 TTGCAAGAGAAAATGCCAAAAATAG 57.576 32.000 0.00 0.00 41.87 1.73
2570 3340 1.372087 CCAACGGCTGCTGATTCTCC 61.372 60.000 16.72 0.00 0.00 3.71
2749 3527 4.275689 TGAATTCAAACAGCACGTGAATCT 59.724 37.500 22.23 3.67 40.28 2.40
2790 3568 4.937620 ACACTGATTATTCTGACGTGCAAT 59.062 37.500 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.