Multiple sequence alignment - TraesCS5A01G035200

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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 TraesCS5A01G035200 chr5A 100.000 4549 0 0 1 4549 32709499 32704951 0.000000e+00 8401
1 TraesCS5A01G035200 chr5A 81.234 762 123 15 2816 3564 33176875 33176121 8.420000e-167 597
2 TraesCS5A01G035200 chr5B 94.733 3835 170 17 1 3820 38161188 38165005 0.000000e+00 5934
3 TraesCS5A01G035200 chr5B 83.314 845 127 14 2715 3553 41255830 41254994 0.000000e+00 767
4 TraesCS5A01G035200 chr5B 86.898 519 49 11 4046 4549 38165369 38165883 8.540000e-157 564
5 TraesCS5A01G035200 chr5B 72.840 1377 297 45 1397 2731 41260190 41258849 2.550000e-107 399
6 TraesCS5A01G035200 chr5B 77.677 663 137 6 2536 3189 38050598 38049938 1.190000e-105 394
7 TraesCS5A01G035200 chr5B 89.333 225 21 2 3818 4042 38165108 38165329 3.470000e-71 279
8 TraesCS5A01G035200 chr5D 95.783 3652 104 20 1 3644 42929427 42925818 0.000000e+00 5845
9 TraesCS5A01G035200 chr5D 95.890 511 11 2 4046 4549 42925206 42924699 0.000000e+00 819
10 TraesCS5A01G035200 chr5D 98.588 425 5 1 3627 4050 42925661 42925237 0.000000e+00 750
11 TraesCS5A01G035200 chr5D 83.877 521 59 12 2628 3134 42948267 42947758 1.480000e-129 473
12 TraesCS5A01G035200 chr6D 96.502 486 17 0 1382 1867 269966351 269966836 0.000000e+00 804
13 TraesCS5A01G035200 chr6D 96.414 474 17 0 1394 1867 269965675 269965202 0.000000e+00 782
14 TraesCS5A01G035200 chr4A 95.983 473 19 0 1395 1867 360414408 360413936 0.000000e+00 769
15 TraesCS5A01G035200 chr3D 96.833 221 7 0 1647 1867 608502017 608501797 2.000000e-98 370


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 TraesCS5A01G035200 chr5A 32704951 32709499 4548 True 8401.000000 8401 100.000000 1 4549 1 chr5A.!!$R1 4548
1 TraesCS5A01G035200 chr5A 33176121 33176875 754 True 597.000000 597 81.234000 2816 3564 1 chr5A.!!$R2 748
2 TraesCS5A01G035200 chr5B 38161188 38165883 4695 False 2259.000000 5934 90.321333 1 4549 3 chr5B.!!$F1 4548
3 TraesCS5A01G035200 chr5B 41254994 41260190 5196 True 583.000000 767 78.077000 1397 3553 2 chr5B.!!$R2 2156
4 TraesCS5A01G035200 chr5B 38049938 38050598 660 True 394.000000 394 77.677000 2536 3189 1 chr5B.!!$R1 653
5 TraesCS5A01G035200 chr5D 42924699 42929427 4728 True 2471.333333 5845 96.753667 1 4549 3 chr5D.!!$R2 4548
6 TraesCS5A01G035200 chr5D 42947758 42948267 509 True 473.000000 473 83.877000 2628 3134 1 chr5D.!!$R1 506

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
112 113 0.511653 CATCTGCGCAAGGATCATCG 59.488 55.000 13.05 0.0 36.74 3.84 F
1046 1054 0.449388 CTCATCGCCTTCAAAGTGGC 59.551 55.000 0.00 0.0 45.25 5.01 F
1413 1421 0.527565 GCAACCGCTTCATGGTCATT 59.472 50.000 0.00 0.0 39.29 2.57 F
1515 1523 1.672356 GGGCATCAACAGCACGTCT 60.672 57.895 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1133 0.033601 TGCCGATGCCAAAAGGGTAT 60.034 50.000 0.00 0.0 45.68 2.73 R
2240 2301 1.732259 GTTAGCACAGGTTGACATCCG 59.268 52.381 0.00 0.0 0.00 4.18 R
3225 6359 3.653344 TCTTCTGGTGAAACGTCATGAG 58.347 45.455 0.00 0.0 38.12 2.90 R
3565 6700 2.917897 TTACCCCAGCAGGCCAAGG 61.918 63.158 5.01 0.0 0.00 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
40 41 3.611530 GCATGCGTGTAAACAGTCCATTT 60.612 43.478 0.00 0.00 0.00 2.32
91 92 1.408822 CCTCCAGGGTATCACTTTGGC 60.409 57.143 0.00 0.00 0.00 4.52
112 113 0.511653 CATCTGCGCAAGGATCATCG 59.488 55.000 13.05 0.00 36.74 3.84
134 136 1.529010 CTCCCTGCCACAACAGCAA 60.529 57.895 0.00 0.00 40.35 3.91
136 138 0.685785 TCCCTGCCACAACAGCAAAA 60.686 50.000 0.00 0.00 40.35 2.44
163 165 1.024271 TGCCTGTGAAAGCTGTGAAC 58.976 50.000 0.00 0.00 0.00 3.18
295 297 8.267894 AGTGCTTCCATCTAGTTTGTTATGTAT 58.732 33.333 0.00 0.00 0.00 2.29
311 317 8.188531 TGTTATGTATAAGTTCCAAACTACGC 57.811 34.615 0.00 0.00 41.91 4.42
362 368 6.811253 TTCACATGTGGGACATTAAACTAC 57.189 37.500 25.16 0.00 44.52 2.73
416 422 6.171213 CCTATAAACCGGTGAAGACTTTTCT 58.829 40.000 8.52 0.00 0.00 2.52
498 504 5.701290 AGAGAAACCTTCAATAGAAACGTGG 59.299 40.000 0.00 0.00 32.35 4.94
517 523 4.142687 CGTGGGAGCGAACTAATCAAAAAT 60.143 41.667 0.00 0.00 0.00 1.82
619 625 6.459923 ACTCTGGTATCACTTTCTTTCACTC 58.540 40.000 0.00 0.00 0.00 3.51
909 917 3.906720 TCAAGCCTAGGGTACACAATC 57.093 47.619 15.26 0.00 0.00 2.67
916 924 4.561734 GCCTAGGGTACACAATCAGATAGC 60.562 50.000 11.72 0.00 0.00 2.97
917 925 4.588951 CCTAGGGTACACAATCAGATAGCA 59.411 45.833 0.00 0.00 0.00 3.49
918 926 5.070446 CCTAGGGTACACAATCAGATAGCAA 59.930 44.000 0.00 0.00 0.00 3.91
919 927 4.770795 AGGGTACACAATCAGATAGCAAC 58.229 43.478 0.00 0.00 0.00 4.17
920 928 3.555956 GGGTACACAATCAGATAGCAACG 59.444 47.826 0.00 0.00 0.00 4.10
931 939 4.635765 TCAGATAGCAACGAAGGAAAATGG 59.364 41.667 0.00 0.00 0.00 3.16
936 944 3.694566 AGCAACGAAGGAAAATGGGATAC 59.305 43.478 0.00 0.00 0.00 2.24
966 974 5.763204 CCTAAGTTGGCAAGTTAGAAAGACA 59.237 40.000 38.21 16.15 43.83 3.41
967 975 5.757850 AAGTTGGCAAGTTAGAAAGACAG 57.242 39.130 18.35 0.00 0.00 3.51
968 976 3.565902 AGTTGGCAAGTTAGAAAGACAGC 59.434 43.478 0.00 0.00 0.00 4.40
969 977 2.143122 TGGCAAGTTAGAAAGACAGCG 58.857 47.619 0.00 0.00 0.00 5.18
970 978 1.135944 GGCAAGTTAGAAAGACAGCGC 60.136 52.381 0.00 0.00 0.00 5.92
971 979 1.135944 GCAAGTTAGAAAGACAGCGCC 60.136 52.381 2.29 0.00 0.00 6.53
972 980 1.126846 CAAGTTAGAAAGACAGCGCCG 59.873 52.381 2.29 0.00 0.00 6.46
973 981 1.014564 AGTTAGAAAGACAGCGCCGC 61.015 55.000 2.29 0.00 0.00 6.53
974 982 1.005512 TTAGAAAGACAGCGCCGCA 60.006 52.632 13.36 0.00 0.00 5.69
993 1001 2.956333 GCAGGAAGTAACCACCAAGTTT 59.044 45.455 0.00 0.00 0.00 2.66
1013 1021 5.070847 AGTTTCCAACCATGAAAGAAGCATT 59.929 36.000 0.00 0.00 32.70 3.56
1039 1047 2.102084 CTCCTGATTCTCATCGCCTTCA 59.898 50.000 0.00 0.00 31.08 3.02
1046 1054 0.449388 CTCATCGCCTTCAAAGTGGC 59.551 55.000 0.00 0.00 45.25 5.01
1063 1071 2.511373 CGGCGCTATCTGCAACCA 60.511 61.111 7.64 0.00 43.06 3.67
1068 1076 2.009042 GCGCTATCTGCAACCACTTCT 61.009 52.381 0.00 0.00 43.06 2.85
1089 1097 0.946221 GGATCTCCATAGCGTTGCCG 60.946 60.000 0.00 0.00 35.64 5.69
1125 1133 1.149401 TGGCAACGTGTCAATCCCA 59.851 52.632 0.00 0.00 42.51 4.37
1131 1139 1.580059 ACGTGTCAATCCCATACCCT 58.420 50.000 0.00 0.00 0.00 4.34
1386 1394 1.683025 TACGCCGTTCATCCCCTCA 60.683 57.895 0.00 0.00 0.00 3.86
1392 1400 1.546773 CCGTTCATCCCCTCAACCAAA 60.547 52.381 0.00 0.00 0.00 3.28
1413 1421 0.527565 GCAACCGCTTCATGGTCATT 59.472 50.000 0.00 0.00 39.29 2.57
1515 1523 1.672356 GGGCATCAACAGCACGTCT 60.672 57.895 0.00 0.00 0.00 4.18
3038 6162 2.012673 GCACTGAAGCCCATAGACAAG 58.987 52.381 0.00 0.00 0.00 3.16
3225 6359 3.248029 CGCTATCGCATGCCTTCC 58.752 61.111 13.15 0.00 35.30 3.46
3565 6700 8.138074 TGCAAGATGACTACTGTATGTATCTTC 58.862 37.037 13.21 10.55 29.35 2.87
3877 7291 3.068732 TGATCTCCAGAATAGTCTTGGCG 59.931 47.826 0.00 0.00 28.78 5.69
3878 7292 2.457598 TCTCCAGAATAGTCTTGGCGT 58.542 47.619 0.00 0.00 28.78 5.68
3879 7293 3.628008 TCTCCAGAATAGTCTTGGCGTA 58.372 45.455 0.00 0.00 28.78 4.42
3880 7294 4.215908 TCTCCAGAATAGTCTTGGCGTAT 58.784 43.478 0.00 0.00 28.78 3.06
4035 7452 1.593296 CTGAGGCCAGCAGGAAAAGC 61.593 60.000 15.73 0.00 36.89 3.51
4043 7460 2.440409 CAGCAGGAAAAGCACATAGGT 58.560 47.619 0.00 0.00 0.00 3.08
4044 7461 4.979258 CCAGCAGGAAAAGCACATAGGTG 61.979 52.174 2.43 2.43 42.29 4.00
4195 7653 1.599542 GGACTTAGTTGATGCGGCATC 59.400 52.381 30.93 30.93 40.88 3.91
4289 7752 5.070981 AGGGAGCTCATCTTTTTCATCGATA 59.929 40.000 17.19 0.00 0.00 2.92
4353 7816 5.411781 CCTAATAAGGCGCCTAATAGACTG 58.588 45.833 33.07 14.68 35.64 3.51
4433 7910 6.377146 TGGACTGAAGGAAATATAACAAAGCC 59.623 38.462 0.00 0.00 0.00 4.35
4438 7915 9.487790 CTGAAGGAAATATAACAAAGCCAAAAA 57.512 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 1.139853 GCAGGGAGAAACGATGATCCT 59.860 52.381 0.00 0.00 32.18 3.24
112 113 0.954452 CTGTTGTGGCAGGGAGAAAC 59.046 55.000 0.00 0.00 33.11 2.78
134 136 4.344968 AGCTTTCACAGGCATTAGGTTTTT 59.655 37.500 0.00 0.00 0.00 1.94
136 138 3.256631 CAGCTTTCACAGGCATTAGGTTT 59.743 43.478 0.00 0.00 0.00 3.27
155 157 1.659098 CCGTTTATCTCCGTTCACAGC 59.341 52.381 0.00 0.00 0.00 4.40
163 165 3.323243 ACTGTTCAACCGTTTATCTCCG 58.677 45.455 0.00 0.00 0.00 4.63
263 265 3.887352 ACTAGATGGAAGCACTAGTCGA 58.113 45.455 0.00 0.00 41.64 4.20
295 297 6.327934 GTCAGATAGCGTAGTTTGGAACTTA 58.672 40.000 0.00 0.00 42.81 2.24
362 368 3.165058 TGCCAGTCAAAGTATAGCTCG 57.835 47.619 0.00 0.00 0.00 5.03
545 551 9.567848 GTCACCCATTTGTATTGTTTAGTATTG 57.432 33.333 0.00 0.00 0.00 1.90
598 604 6.459066 TGAGAGTGAAAGAAAGTGATACCAG 58.541 40.000 0.00 0.00 0.00 4.00
619 625 5.991606 TCCTTTGTATTGACAAGTGTCTGAG 59.008 40.000 12.43 1.34 46.11 3.35
661 667 5.283060 ACGCAGTGCTTATTAAGAAACAG 57.717 39.130 14.33 3.41 42.51 3.16
851 857 3.806521 CAGACTGGTGCTTATGTATGAGC 59.193 47.826 2.03 2.03 39.58 4.26
909 917 4.201950 CCCATTTTCCTTCGTTGCTATCTG 60.202 45.833 0.00 0.00 0.00 2.90
916 924 3.064820 CGGTATCCCATTTTCCTTCGTTG 59.935 47.826 0.00 0.00 0.00 4.10
917 925 3.275999 CGGTATCCCATTTTCCTTCGTT 58.724 45.455 0.00 0.00 0.00 3.85
918 926 2.237893 ACGGTATCCCATTTTCCTTCGT 59.762 45.455 0.00 0.00 0.00 3.85
919 927 2.914059 ACGGTATCCCATTTTCCTTCG 58.086 47.619 0.00 0.00 0.00 3.79
920 928 3.181490 GCAACGGTATCCCATTTTCCTTC 60.181 47.826 0.00 0.00 0.00 3.46
931 939 2.285977 CCAACTTAGGCAACGGTATCC 58.714 52.381 0.00 0.00 46.39 2.59
942 950 5.763204 TGTCTTTCTAACTTGCCAACTTAGG 59.237 40.000 4.65 0.00 0.00 2.69
950 958 1.135944 GCGCTGTCTTTCTAACTTGCC 60.136 52.381 0.00 0.00 0.00 4.52
952 960 1.126846 CGGCGCTGTCTTTCTAACTTG 59.873 52.381 8.45 0.00 0.00 3.16
956 964 1.005512 TGCGGCGCTGTCTTTCTAA 60.006 52.632 33.26 5.11 0.00 2.10
957 965 1.446099 CTGCGGCGCTGTCTTTCTA 60.446 57.895 33.26 8.10 0.00 2.10
960 968 3.825160 TTCCTGCGGCGCTGTCTTT 62.825 57.895 33.26 0.00 0.00 2.52
961 969 4.314440 TTCCTGCGGCGCTGTCTT 62.314 61.111 33.26 0.00 0.00 3.01
962 970 4.749310 CTTCCTGCGGCGCTGTCT 62.749 66.667 33.26 0.00 0.00 3.41
963 971 3.642778 TACTTCCTGCGGCGCTGTC 62.643 63.158 33.26 10.84 0.00 3.51
964 972 3.234630 TTACTTCCTGCGGCGCTGT 62.235 57.895 33.26 22.68 0.00 4.40
966 974 2.434359 GTTACTTCCTGCGGCGCT 60.434 61.111 33.26 14.16 0.00 5.92
967 975 3.497031 GGTTACTTCCTGCGGCGC 61.497 66.667 27.44 27.44 0.00 6.53
968 976 2.047655 TGGTTACTTCCTGCGGCG 60.048 61.111 0.51 0.51 0.00 6.46
969 977 2.038837 GGTGGTTACTTCCTGCGGC 61.039 63.158 0.00 0.00 0.00 6.53
970 978 0.250553 TTGGTGGTTACTTCCTGCGG 60.251 55.000 0.00 0.00 0.00 5.69
971 979 1.156736 CTTGGTGGTTACTTCCTGCG 58.843 55.000 0.00 0.00 0.00 5.18
972 980 2.271944 ACTTGGTGGTTACTTCCTGC 57.728 50.000 0.00 0.00 0.00 4.85
973 981 3.568430 GGAAACTTGGTGGTTACTTCCTG 59.432 47.826 0.00 0.00 0.00 3.86
974 982 3.203487 TGGAAACTTGGTGGTTACTTCCT 59.797 43.478 0.00 0.00 29.73 3.36
993 1001 4.151121 TGAATGCTTCTTTCATGGTTGGA 58.849 39.130 0.00 0.00 0.00 3.53
1026 1034 1.945819 GCCACTTTGAAGGCGATGAGA 60.946 52.381 0.00 0.00 41.70 3.27
1039 1047 1.815421 CAGATAGCGCCGCCACTTT 60.815 57.895 4.98 0.00 0.00 2.66
1125 1133 0.033601 TGCCGATGCCAAAAGGGTAT 60.034 50.000 0.00 0.00 45.68 2.73
1131 1139 1.079266 GCCATTGCCGATGCCAAAA 60.079 52.632 0.00 0.00 36.33 2.44
1413 1421 2.074113 TACCCATGGTGTTGCAGCCA 62.074 55.000 11.73 8.78 36.19 4.75
1958 1976 1.740025 GCAGTGACAGTTGCTTATCCC 59.260 52.381 0.00 0.00 37.35 3.85
2095 2156 4.633126 GCTTGCACTCATCTATGTCTGAAA 59.367 41.667 0.00 0.00 0.00 2.69
2229 2290 3.306019 GGTTGACATCCGGAATTTTTGCT 60.306 43.478 9.01 0.00 0.00 3.91
2240 2301 1.732259 GTTAGCACAGGTTGACATCCG 59.268 52.381 0.00 0.00 0.00 4.18
3225 6359 3.653344 TCTTCTGGTGAAACGTCATGAG 58.347 45.455 0.00 0.00 38.12 2.90
3565 6700 2.917897 TTACCCCAGCAGGCCAAGG 61.918 63.158 5.01 0.00 0.00 3.61
3877 7291 0.661020 GCGGGGCATGTGTGTAATAC 59.339 55.000 0.00 0.00 0.00 1.89
3878 7292 0.253327 TGCGGGGCATGTGTGTAATA 59.747 50.000 0.00 0.00 31.71 0.98
3879 7293 0.610509 TTGCGGGGCATGTGTGTAAT 60.611 50.000 0.00 0.00 38.76 1.89
3880 7294 0.823769 TTTGCGGGGCATGTGTGTAA 60.824 50.000 0.00 0.00 38.76 2.41
4035 7452 2.749621 GGCTTCAACCTTCACCTATGTG 59.250 50.000 0.00 0.00 44.18 3.21
4043 7460 2.282180 GCGGGGCTTCAACCTTCA 60.282 61.111 0.00 0.00 0.00 3.02
4044 7461 1.603739 AAGCGGGGCTTCAACCTTC 60.604 57.895 0.00 0.00 46.77 3.46
4195 7653 6.074516 CGACCCAAAACTGTACGTGATATATG 60.075 42.308 0.00 0.00 0.00 1.78
4196 7654 5.981315 CGACCCAAAACTGTACGTGATATAT 59.019 40.000 0.00 0.00 0.00 0.86
4197 7655 5.125257 TCGACCCAAAACTGTACGTGATATA 59.875 40.000 0.00 0.00 0.00 0.86
4353 7816 2.989196 CTGCAGTCTAGATGGCAGC 58.011 57.895 25.88 13.84 46.00 5.25
4438 7915 8.980481 TGATTCTAGAACCTTTCTCTGTTTTT 57.020 30.769 7.48 0.00 41.14 1.94


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

AutoCloner maintained by Alex Coulton.