Multiple sequence alignment - TraesCS5D01G132100

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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 TraesCS5D01G132100 chr5D 100.000 3329 0 0 1 3329 210058858 210055530 0.000000e+00 6148
1 TraesCS5D01G132100 chr5D 94.118 102 5 1 880 981 49290837 49290737 1.600000e-33 154
2 TraesCS5D01G132100 chr5B 96.667 1980 52 4 977 2956 223648276 223646311 0.000000e+00 3278
3 TraesCS5D01G132100 chr5B 93.764 882 44 5 11 882 223649174 223648294 0.000000e+00 1314
4 TraesCS5D01G132100 chr5B 91.623 382 25 4 2950 3329 223557664 223557288 3.810000e-144 521
5 TraesCS5D01G132100 chr5B 96.842 95 3 0 873 967 417442269 417442175 3.440000e-35 159
6 TraesCS5D01G132100 chr5B 95.833 96 3 1 880 974 345770293 345770198 1.600000e-33 154
7 TraesCS5D01G132100 chr5B 94.898 98 5 0 877 974 705462717 705462620 1.600000e-33 154
8 TraesCS5D01G132100 chr5A 97.236 1845 48 3 977 2819 271496613 271494770 0.000000e+00 3121
9 TraesCS5D01G132100 chr5A 96.271 885 27 5 1 882 271497512 271496631 0.000000e+00 1447
10 TraesCS5D01G132100 chr5A 93.989 549 27 6 2786 3329 271494763 271494216 0.000000e+00 826
11 TraesCS5D01G132100 chr1B 77.512 1085 224 16 992 2066 679749273 679748199 4.690000e-178 634
12 TraesCS5D01G132100 chr1A 79.036 892 177 8 992 1875 586954097 586953208 1.320000e-168 603
13 TraesCS5D01G132100 chr1A 94.059 101 5 1 874 974 409786911 409787010 5.750000e-33 152
14 TraesCS5D01G132100 chr1D 83.333 624 102 2 1253 1875 487953006 487952384 2.880000e-160 575
15 TraesCS5D01G132100 chr3D 96.842 95 3 0 880 974 224304752 224304658 3.440000e-35 159
16 TraesCS5D01G132100 chr3A 94.949 99 3 2 880 976 686127536 686127438 1.600000e-33 154
17 TraesCS5D01G132100 chrUn 93.939 99 6 0 874 972 359670005 359670103 2.070000e-32 150
18 TraesCS5D01G132100 chr7B 92.381 105 8 0 862 966 446149469 446149573 2.070000e-32 150


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 TraesCS5D01G132100 chr5D 210055530 210058858 3328 True 6148 6148 100.0000 1 3329 1 chr5D.!!$R2 3328
1 TraesCS5D01G132100 chr5B 223646311 223649174 2863 True 2296 3278 95.2155 11 2956 2 chr5B.!!$R5 2945
2 TraesCS5D01G132100 chr5A 271494216 271497512 3296 True 1798 3121 95.8320 1 3329 3 chr5A.!!$R1 3328
3 TraesCS5D01G132100 chr1B 679748199 679749273 1074 True 634 634 77.5120 992 2066 1 chr1B.!!$R1 1074
4 TraesCS5D01G132100 chr1A 586953208 586954097 889 True 603 603 79.0360 992 1875 1 chr1A.!!$R1 883
5 TraesCS5D01G132100 chr1D 487952384 487953006 622 True 575 575 83.3330 1253 1875 1 chr1D.!!$R1 622

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
160 167 0.616111 AACCACGCCTGGAGATCTCT 60.616 55.000 21.81 0.0 40.55 3.10 F
337 344 1.918957 CTTTCTCCCTGACCCCATTCT 59.081 52.381 0.00 0.0 0.00 2.40 F
1247 1271 0.252197 GTCCACCACCACCACTATCC 59.748 60.000 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1130 0.671781 CTGAGAGTGGTTGAAGCCCG 60.672 60.0 0.00 0.00 0.00 6.13 R
2260 2288 0.109723 TTGCGCCTTACCTCCAGTTT 59.890 50.0 4.18 0.00 0.00 2.66 R
3211 3285 0.679002 TCCTGGCAGCTGCATCTTTC 60.679 55.0 37.63 20.78 44.36 2.62 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
160 167 0.616111 AACCACGCCTGGAGATCTCT 60.616 55.000 21.81 0.00 40.55 3.10
289 296 2.026729 GGCCTTCACTAGCCTTCTCTTT 60.027 50.000 0.00 0.00 46.14 2.52
313 320 5.640783 TGATCTGATTATTCTATTGCAGCCG 59.359 40.000 0.00 0.00 0.00 5.52
337 344 1.918957 CTTTCTCCCTGACCCCATTCT 59.081 52.381 0.00 0.00 0.00 2.40
535 548 5.895636 TTGATGCCGTTCAACTGATTAAT 57.104 34.783 0.00 0.00 30.82 1.40
649 664 2.948979 TGTTGAACTGTGCCGAAGAAAT 59.051 40.909 0.00 0.00 0.00 2.17
879 894 6.472163 GTGCCAAATTCTACATTCGTATTTGG 59.528 38.462 16.59 16.59 42.77 3.28
880 895 6.151985 TGCCAAATTCTACATTCGTATTTGGT 59.848 34.615 19.99 0.00 42.33 3.67
881 896 7.337184 TGCCAAATTCTACATTCGTATTTGGTA 59.663 33.333 19.99 15.43 42.33 3.25
882 897 7.642586 GCCAAATTCTACATTCGTATTTGGTAC 59.357 37.037 19.99 6.71 42.33 3.34
883 898 8.889717 CCAAATTCTACATTCGTATTTGGTACT 58.110 33.333 13.90 0.00 38.91 2.73
884 899 9.916397 CAAATTCTACATTCGTATTTGGTACTC 57.084 33.333 0.00 0.00 28.22 2.59
885 900 8.658499 AATTCTACATTCGTATTTGGTACTCC 57.342 34.615 0.00 0.00 0.00 3.85
886 901 6.152932 TCTACATTCGTATTTGGTACTCCC 57.847 41.667 0.00 0.00 0.00 4.30
887 902 5.895534 TCTACATTCGTATTTGGTACTCCCT 59.104 40.000 0.00 0.00 0.00 4.20
888 903 5.019785 ACATTCGTATTTGGTACTCCCTC 57.980 43.478 0.00 0.00 0.00 4.30
889 904 4.715297 ACATTCGTATTTGGTACTCCCTCT 59.285 41.667 0.00 0.00 0.00 3.69
890 905 4.730949 TTCGTATTTGGTACTCCCTCTG 57.269 45.455 0.00 0.00 0.00 3.35
891 906 3.705051 TCGTATTTGGTACTCCCTCTGT 58.295 45.455 0.00 0.00 0.00 3.41
892 907 4.858850 TCGTATTTGGTACTCCCTCTGTA 58.141 43.478 0.00 0.00 0.00 2.74
893 908 5.263599 TCGTATTTGGTACTCCCTCTGTAA 58.736 41.667 0.00 0.00 0.00 2.41
894 909 5.716228 TCGTATTTGGTACTCCCTCTGTAAA 59.284 40.000 0.00 0.00 0.00 2.01
895 910 5.809051 CGTATTTGGTACTCCCTCTGTAAAC 59.191 44.000 0.00 0.00 0.00 2.01
896 911 6.350780 CGTATTTGGTACTCCCTCTGTAAACT 60.351 42.308 0.00 0.00 0.00 2.66
897 912 7.148018 CGTATTTGGTACTCCCTCTGTAAACTA 60.148 40.741 0.00 0.00 0.00 2.24
898 913 6.999705 TTTGGTACTCCCTCTGTAAACTAA 57.000 37.500 0.00 0.00 0.00 2.24
899 914 7.563724 TTTGGTACTCCCTCTGTAAACTAAT 57.436 36.000 0.00 0.00 0.00 1.73
900 915 8.669055 TTTGGTACTCCCTCTGTAAACTAATA 57.331 34.615 0.00 0.00 0.00 0.98
901 916 8.849543 TTGGTACTCCCTCTGTAAACTAATAT 57.150 34.615 0.00 0.00 0.00 1.28
902 917 9.940974 TTGGTACTCCCTCTGTAAACTAATATA 57.059 33.333 0.00 0.00 0.00 0.86
903 918 9.940974 TGGTACTCCCTCTGTAAACTAATATAA 57.059 33.333 0.00 0.00 0.00 0.98
907 922 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
908 923 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
909 924 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
910 925 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
911 926 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
959 974 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
960 975 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
961 976 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
1109 1130 2.171341 GGTCCAAGCTCCGATAATCC 57.829 55.000 0.00 0.00 0.00 3.01
1169 1190 2.289565 GCCTATGAACCAGGTTACAGC 58.710 52.381 4.25 0.67 35.45 4.40
1247 1271 0.252197 GTCCACCACCACCACTATCC 59.748 60.000 0.00 0.00 0.00 2.59
2029 2057 1.425066 GGTCTAATCCCCATGGCATCA 59.575 52.381 6.09 0.00 0.00 3.07
2313 2341 4.900635 TGAACTCAAGCTGAAAGGAAAC 57.099 40.909 0.00 0.00 0.00 2.78
2634 2662 7.441017 TGCATCATTAGTTTTTAGCAAGGTTT 58.559 30.769 0.00 0.00 0.00 3.27
2782 2810 2.109126 GTAAGGCCGCCTTGCTCTG 61.109 63.158 31.30 0.00 44.44 3.35
2800 2828 2.571202 TCTGTGCTCTCTCTCTCTCTCA 59.429 50.000 0.00 0.00 0.00 3.27
2802 2830 2.017049 GTGCTCTCTCTCTCTCTCACC 58.983 57.143 0.00 0.00 0.00 4.02
2804 2832 1.750682 GCTCTCTCTCTCTCTCACCCC 60.751 61.905 0.00 0.00 0.00 4.95
2805 2833 1.563879 CTCTCTCTCTCTCTCACCCCA 59.436 57.143 0.00 0.00 0.00 4.96
2806 2834 1.283613 TCTCTCTCTCTCTCACCCCAC 59.716 57.143 0.00 0.00 0.00 4.61
2807 2835 1.284785 CTCTCTCTCTCTCACCCCACT 59.715 57.143 0.00 0.00 0.00 4.00
2808 2836 1.283613 TCTCTCTCTCTCACCCCACTC 59.716 57.143 0.00 0.00 0.00 3.51
2809 2837 1.284785 CTCTCTCTCTCACCCCACTCT 59.715 57.143 0.00 0.00 0.00 3.24
2810 2838 1.283613 TCTCTCTCTCACCCCACTCTC 59.716 57.143 0.00 0.00 0.00 3.20
2853 2927 3.399305 ACATCCCTTTCCCTCTCTTTTGT 59.601 43.478 0.00 0.00 0.00 2.83
2888 2962 0.543749 GCTCCTACCTGCATGTCCTT 59.456 55.000 0.00 0.00 0.00 3.36
3003 3077 0.109723 TCAGCGCTAACCCCAAAAGT 59.890 50.000 10.99 0.00 0.00 2.66
3008 3082 1.068541 CGCTAACCCCAAAAGTGAAGC 60.069 52.381 0.00 0.00 0.00 3.86
3009 3083 1.960689 GCTAACCCCAAAAGTGAAGCA 59.039 47.619 0.00 0.00 30.98 3.91
3019 3093 0.615850 AAGTGAAGCAGTAGGCCTCC 59.384 55.000 9.68 0.00 46.50 4.30
3060 3134 2.894307 AGGCGTACGCTCAATTTTTC 57.106 45.000 36.24 18.27 41.60 2.29
3101 3175 1.410004 AATGCTTGCTGCCATATGCT 58.590 45.000 0.00 0.00 42.00 3.79
3172 3246 1.536766 TGAGCGATTTGTTCAGCCTTG 59.463 47.619 0.00 0.00 32.32 3.61
3211 3285 8.572828 TTGGCAATAAAATTATAGTTGCATCG 57.427 30.769 15.20 0.00 45.07 3.84
3299 3374 6.532657 GTGCATTGGATCACTAATTTGGAAAG 59.467 38.462 0.00 0.00 0.00 2.62
3303 3378 7.391148 TTGGATCACTAATTTGGAAAGCTAC 57.609 36.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.317936 ACAACATTCCATTTCTTTCTTTCTTTC 57.682 29.630 0.00 0.00 0.00 2.62
32 33 7.555087 TGTCAACAACATTCCATTTCTTTCTT 58.445 30.769 0.00 0.00 31.20 2.52
160 167 1.404181 CGAGAAAGAATGCCCACGAGA 60.404 52.381 0.00 0.00 0.00 4.04
289 296 5.640783 CGGCTGCAATAGAATAATCAGATCA 59.359 40.000 0.50 0.00 0.00 2.92
313 320 0.840617 GGGGTCAGGGAGAAAGATCC 59.159 60.000 0.00 0.00 38.76 3.36
337 344 0.764369 AGGGTGCTCTCCTGTCAACA 60.764 55.000 0.00 0.00 32.53 3.33
535 548 5.523552 CGACCAGCAACATGATGTAAAGATA 59.476 40.000 0.00 0.00 30.62 1.98
649 664 0.107263 TGTGCAAGCAGTGAGTTGGA 60.107 50.000 0.00 0.00 0.00 3.53
881 896 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
882 897 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
883 898 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
884 899 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
885 900 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
933 948 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
934 949 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
935 950 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
936 951 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
937 952 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
953 968 9.669887 CTACGTCTTATATAATACTCCCTCTGT 57.330 37.037 0.00 1.92 0.00 3.41
954 969 9.669887 ACTACGTCTTATATAATACTCCCTCTG 57.330 37.037 0.00 0.00 0.00 3.35
955 970 9.669887 CACTACGTCTTATATAATACTCCCTCT 57.330 37.037 0.00 0.00 0.00 3.69
956 971 8.891720 CCACTACGTCTTATATAATACTCCCTC 58.108 40.741 0.00 0.00 0.00 4.30
957 972 8.609483 TCCACTACGTCTTATATAATACTCCCT 58.391 37.037 0.00 0.00 0.00 4.20
958 973 8.798859 TCCACTACGTCTTATATAATACTCCC 57.201 38.462 0.00 0.00 0.00 4.30
1103 1124 1.564348 AGTGGTTGAAGCCCGGATTAT 59.436 47.619 0.73 0.00 0.00 1.28
1109 1130 0.671781 CTGAGAGTGGTTGAAGCCCG 60.672 60.000 0.00 0.00 0.00 6.13
1169 1190 3.045601 ATTCCGACAAGTGGTCAGAAG 57.954 47.619 2.83 0.00 43.99 2.85
1247 1271 1.741732 CGCTCATGGAGTCCTTCTTGG 60.742 57.143 11.33 0.00 31.39 3.61
1896 1924 1.001378 CCTTTATTGCTATGCGCCACC 60.001 52.381 4.18 0.00 38.05 4.61
2260 2288 0.109723 TTGCGCCTTACCTCCAGTTT 59.890 50.000 4.18 0.00 0.00 2.66
2782 2810 2.017049 GGTGAGAGAGAGAGAGAGCAC 58.983 57.143 0.00 0.00 0.00 4.40
2800 2828 1.383963 TAGACAGAGGAGAGTGGGGT 58.616 55.000 0.00 0.00 0.00 4.95
2802 2830 2.104170 GGTTAGACAGAGGAGAGTGGG 58.896 57.143 0.00 0.00 0.00 4.61
2804 2832 3.094484 AGGGTTAGACAGAGGAGAGTG 57.906 52.381 0.00 0.00 0.00 3.51
2805 2833 3.372241 GCTAGGGTTAGACAGAGGAGAGT 60.372 52.174 0.00 0.00 0.00 3.24
2806 2834 3.219281 GCTAGGGTTAGACAGAGGAGAG 58.781 54.545 0.00 0.00 0.00 3.20
2807 2835 2.091775 GGCTAGGGTTAGACAGAGGAGA 60.092 54.545 0.00 0.00 34.83 3.71
2808 2836 2.312390 GGCTAGGGTTAGACAGAGGAG 58.688 57.143 0.00 0.00 34.83 3.69
2809 2837 1.409802 CGGCTAGGGTTAGACAGAGGA 60.410 57.143 0.00 0.00 34.31 3.71
2810 2838 1.033574 CGGCTAGGGTTAGACAGAGG 58.966 60.000 0.00 0.00 34.31 3.69
2853 2927 2.994417 GCGGCACCAATTTGGGGA 60.994 61.111 22.06 0.00 46.22 4.81
2988 3062 1.068541 GCTTCACTTTTGGGGTTAGCG 60.069 52.381 0.00 0.00 0.00 4.26
2994 3068 2.162681 CCTACTGCTTCACTTTTGGGG 58.837 52.381 0.00 0.00 0.00 4.96
2995 3069 1.541588 GCCTACTGCTTCACTTTTGGG 59.458 52.381 0.00 0.00 36.87 4.12
3008 3082 2.811101 CTGAGCGGAGGCCTACTG 59.189 66.667 14.69 7.99 41.24 2.74
3009 3083 3.151022 GCTGAGCGGAGGCCTACT 61.151 66.667 14.69 7.87 41.24 2.57
3037 3111 0.822164 AATTGAGCGTACGCCTAGGT 59.178 50.000 34.88 17.82 43.17 3.08
3060 3134 7.323656 GCATTAGTACAGTTGCTAAAAACAGTG 59.676 37.037 0.00 0.00 34.08 3.66
3211 3285 0.679002 TCCTGGCAGCTGCATCTTTC 60.679 55.000 37.63 20.78 44.36 2.62
3238 3312 5.350504 TGCCATGTTCTTTTCAAGGAAAA 57.649 34.783 4.31 4.31 38.90 2.29
3251 3325 3.623060 AGACACACGAATATGCCATGTTC 59.377 43.478 4.25 4.25 0.00 3.18
3299 3374 3.936453 TCATGAATTACAACCACCGTAGC 59.064 43.478 0.00 0.00 0.00 3.58
3303 3378 8.925161 ATAAAATTCATGAATTACAACCACCG 57.075 30.769 29.16 0.00 39.88 4.94


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

AutoCloner maintained by Alex Coulton.