Multiple sequence alignment - TraesCS5D01G217700

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 TraesCS5D01G217700 chr5D 100.000 4637 0 0 1 4637 326737468 326732832 0.000000e+00 8564.0
1 TraesCS5D01G217700 chr5D 93.333 240 14 1 1633 1870 524590476 524590237 2.050000e-93 353.0
2 TraesCS5D01G217700 chr5D 79.054 148 27 2 1635 1780 369295537 369295682 1.060000e-16 99.0
3 TraesCS5D01G217700 chr5B 95.341 3992 111 18 1 3967 379337338 379333397 0.000000e+00 6272.0
4 TraesCS5D01G217700 chr5B 83.230 483 54 14 4086 4549 576219662 576220136 7.180000e-113 418.0
5 TraesCS5D01G217700 chr5A 94.411 3328 123 28 640 3964 429753880 429757147 0.000000e+00 5057.0
6 TraesCS5D01G217700 chr5A 95.469 309 6 3 1 301 429753310 429753618 1.940000e-133 486.0
7 TraesCS5D01G217700 chr5A 92.164 268 13 4 354 614 429753626 429753892 5.670000e-99 372.0
8 TraesCS5D01G217700 chr5A 78.378 148 28 2 1635 1780 471692696 471692841 4.940000e-15 93.5
9 TraesCS5D01G217700 chr5A 86.154 65 8 1 3967 4030 282465846 282465782 8.330000e-08 69.4
10 TraesCS5D01G217700 chr4D 97.198 678 12 3 3967 4637 214998676 214999353 0.000000e+00 1140.0
11 TraesCS5D01G217700 chr4D 73.371 706 155 28 1402 2095 50641669 50642353 1.000000e-56 231.0
12 TraesCS5D01G217700 chr4D 78.195 133 24 4 1652 1780 443512321 443512190 3.850000e-11 80.5
13 TraesCS5D01G217700 chr2D 96.608 678 16 3 3967 4637 474738668 474739345 0.000000e+00 1118.0
14 TraesCS5D01G217700 chr2D 91.900 679 25 10 3967 4637 6967365 6968021 0.000000e+00 922.0
15 TraesCS5D01G217700 chr2D 81.928 332 40 9 2210 2539 605094330 605094017 3.560000e-66 263.0
16 TraesCS5D01G217700 chr2D 85.965 114 15 1 2254 2367 451646589 451646477 2.270000e-23 121.0
17 TraesCS5D01G217700 chr1A 94.993 679 22 5 3967 4637 504585577 504584903 0.000000e+00 1055.0
18 TraesCS5D01G217700 chr6B 94.591 684 20 9 3967 4637 562545513 562546192 0.000000e+00 1042.0
19 TraesCS5D01G217700 chr1B 94.067 691 22 12 3965 4637 325802634 325801945 0.000000e+00 1031.0
20 TraesCS5D01G217700 chr1B 91.362 301 21 4 2033 2331 26338126 26337829 1.550000e-109 407.0
21 TraesCS5D01G217700 chr1B 93.436 259 17 0 1776 2034 26360608 26360350 7.280000e-103 385.0
22 TraesCS5D01G217700 chr1B 85.942 313 18 10 1814 2126 4177949 4177663 1.250000e-80 311.0
23 TraesCS5D01G217700 chr1B 91.981 212 16 1 2121 2331 4156070 4155859 3.510000e-76 296.0
24 TraesCS5D01G217700 chr1B 85.448 268 17 7 1438 1695 26360862 26360607 4.600000e-65 259.0
25 TraesCS5D01G217700 chr1B 94.444 54 3 0 1333 1386 4178247 4178194 2.970000e-12 84.2
26 TraesCS5D01G217700 chr1B 92.593 54 4 0 1333 1386 26360914 26360861 1.380000e-10 78.7
27 TraesCS5D01G217700 chr1B 86.364 66 8 1 3966 4030 26284217 26284282 2.310000e-08 71.3
28 TraesCS5D01G217700 chr3B 82.570 677 72 27 3967 4611 819312705 819312043 5.240000e-154 555.0
29 TraesCS5D01G217700 chr3B 87.445 454 36 3 4057 4510 438406199 438406631 1.930000e-138 503.0
30 TraesCS5D01G217700 chr3D 92.140 229 17 1 1643 1870 47139046 47138818 5.790000e-84 322.0
31 TraesCS5D01G217700 chr4A 74.085 710 143 33 1402 2095 546298467 546297783 2.140000e-63 254.0
32 TraesCS5D01G217700 chr2A 82.051 312 34 8 2254 2559 736256887 736256592 3.580000e-61 246.0
33 TraesCS5D01G217700 chr2B 74.292 459 97 14 1402 1854 596410843 596411286 1.720000e-39 174.0
34 TraesCS5D01G217700 chr1D 95.745 47 2 0 2026 2072 475248863 475248909 4.980000e-10 76.8
35 TraesCS5D01G217700 chr4B 76.190 147 30 4 1638 1780 552831830 552831685 6.440000e-09 73.1


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 TraesCS5D01G217700 chr5D 326732832 326737468 4636 True 8564.000000 8564 100.000000 1 4637 1 chr5D.!!$R1 4636
1 TraesCS5D01G217700 chr5B 379333397 379337338 3941 True 6272.000000 6272 95.341000 1 3967 1 chr5B.!!$R1 3966
2 TraesCS5D01G217700 chr5A 429753310 429757147 3837 False 1971.666667 5057 94.014667 1 3964 3 chr5A.!!$F2 3963
3 TraesCS5D01G217700 chr4D 214998676 214999353 677 False 1140.000000 1140 97.198000 3967 4637 1 chr4D.!!$F2 670
4 TraesCS5D01G217700 chr4D 50641669 50642353 684 False 231.000000 231 73.371000 1402 2095 1 chr4D.!!$F1 693
5 TraesCS5D01G217700 chr2D 474738668 474739345 677 False 1118.000000 1118 96.608000 3967 4637 1 chr2D.!!$F2 670
6 TraesCS5D01G217700 chr2D 6967365 6968021 656 False 922.000000 922 91.900000 3967 4637 1 chr2D.!!$F1 670
7 TraesCS5D01G217700 chr1A 504584903 504585577 674 True 1055.000000 1055 94.993000 3967 4637 1 chr1A.!!$R1 670
8 TraesCS5D01G217700 chr6B 562545513 562546192 679 False 1042.000000 1042 94.591000 3967 4637 1 chr6B.!!$F1 670
9 TraesCS5D01G217700 chr1B 325801945 325802634 689 True 1031.000000 1031 94.067000 3965 4637 1 chr1B.!!$R3 672
10 TraesCS5D01G217700 chr1B 26360350 26360914 564 True 240.900000 385 90.492333 1333 2034 3 chr1B.!!$R5 701
11 TraesCS5D01G217700 chr3B 819312043 819312705 662 True 555.000000 555 82.570000 3967 4611 1 chr3B.!!$R1 644
12 TraesCS5D01G217700 chr4A 546297783 546298467 684 True 254.000000 254 74.085000 1402 2095 1 chr4A.!!$R1 693

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
493 512 0.249955 TGCTTGATGCCTGATCGTCA 59.750 50.0 0.00 0.0 42.0 4.35 F
1036 1081 0.622154 TCTCCTCGTCCTCCTCCTCT 60.622 60.0 0.00 0.0 0.0 3.69 F
2883 2942 0.604243 TTAGGCACGCGTTTGGTGAT 60.604 50.0 10.22 0.0 37.6 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2443 0.173935 CCACGTACGTCCTTATGGCA 59.826 55.0 19.94 0.0 0.00 4.92 R
2958 3017 0.392998 GAGGGCACGACATGGATGTT 60.393 55.0 0.00 0.0 41.95 2.71 R
3800 3859 0.981183 TAATGTGCTGTTCCCGTCCT 59.019 50.0 0.00 0.0 0.00 3.85 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
351 362 1.006220 AGCGACGCAGACATGAACA 60.006 52.632 23.70 0.00 0.00 3.18
386 397 2.267642 GTGCACGGCCATGGAGTA 59.732 61.111 18.40 0.00 0.00 2.59
485 504 1.228063 CGGGCTATGCTTGATGCCT 60.228 57.895 0.00 0.00 44.36 4.75
488 507 1.547223 GGGCTATGCTTGATGCCTGAT 60.547 52.381 0.00 0.00 44.36 2.90
489 508 1.811359 GGCTATGCTTGATGCCTGATC 59.189 52.381 0.00 0.00 41.92 2.92
490 509 1.463831 GCTATGCTTGATGCCTGATCG 59.536 52.381 0.00 0.00 42.00 3.69
493 512 0.249955 TGCTTGATGCCTGATCGTCA 59.750 50.000 0.00 0.00 42.00 4.35
507 526 1.225745 CGTCAATCGGTGCGCTTTC 60.226 57.895 9.73 0.00 35.71 2.62
621 647 3.763897 CCAACGGAATTCCATCTTCCTTT 59.236 43.478 24.09 0.00 40.07 3.11
622 648 4.220602 CCAACGGAATTCCATCTTCCTTTT 59.779 41.667 24.09 0.33 40.07 2.27
624 650 5.644977 ACGGAATTCCATCTTCCTTTTTC 57.355 39.130 24.09 0.00 40.07 2.29
797 837 5.761234 ACTGCAGAATTAGGTTTACGACAAA 59.239 36.000 23.35 0.00 0.00 2.83
798 838 6.430000 ACTGCAGAATTAGGTTTACGACAAAT 59.570 34.615 23.35 0.00 0.00 2.32
799 839 7.040686 ACTGCAGAATTAGGTTTACGACAAATT 60.041 33.333 23.35 0.00 31.74 1.82
800 840 7.653647 TGCAGAATTAGGTTTACGACAAATTT 58.346 30.769 0.00 0.00 30.21 1.82
801 841 8.138712 TGCAGAATTAGGTTTACGACAAATTTT 58.861 29.630 0.00 0.00 30.21 1.82
802 842 8.974408 GCAGAATTAGGTTTACGACAAATTTTT 58.026 29.630 0.00 0.00 30.21 1.94
861 901 4.410099 TGCACAGGGAAATCAAGATCTTT 58.590 39.130 4.86 0.00 0.00 2.52
911 951 5.610398 TGCTGGCTCTATATTTGAATCGAA 58.390 37.500 0.00 0.00 0.00 3.71
930 970 1.736645 CGCCTCGACGGATTGTTGT 60.737 57.895 5.24 0.00 33.33 3.32
934 974 1.068474 CTCGACGGATTGTTGTCACC 58.932 55.000 0.00 0.00 34.78 4.02
981 1022 4.690719 CCCCCACGTACGCTGCAA 62.691 66.667 16.72 0.00 0.00 4.08
982 1023 3.118454 CCCCACGTACGCTGCAAG 61.118 66.667 16.72 4.85 0.00 4.01
983 1024 3.118454 CCCACGTACGCTGCAAGG 61.118 66.667 16.72 7.74 0.00 3.61
1024 1069 2.995574 AACCACCCCGTCTCCTCG 60.996 66.667 0.00 0.00 0.00 4.63
1036 1081 0.622154 TCTCCTCGTCCTCCTCCTCT 60.622 60.000 0.00 0.00 0.00 3.69
1042 1090 1.813192 GTCCTCCTCCTCTTCTGCG 59.187 63.158 0.00 0.00 0.00 5.18
1044 1092 0.624254 TCCTCCTCCTCTTCTGCGTA 59.376 55.000 0.00 0.00 0.00 4.42
1046 1094 1.028905 CTCCTCCTCTTCTGCGTAGG 58.971 60.000 0.00 0.00 0.00 3.18
1048 1096 1.040339 CCTCCTCTTCTGCGTAGGCT 61.040 60.000 9.11 0.00 40.82 4.58
1620 1678 1.913762 CTCCTCCCACGGAACCACT 60.914 63.158 0.00 0.00 31.44 4.00
1812 1870 0.748367 TCAGCTCGGACATACTCGCT 60.748 55.000 0.00 0.00 0.00 4.93
2808 2866 5.130311 TCTTTAGGTGCTAGCCATCATGTTA 59.870 40.000 13.29 0.00 0.00 2.41
2883 2942 0.604243 TTAGGCACGCGTTTGGTGAT 60.604 50.000 10.22 0.00 37.60 3.06
2903 2962 6.071051 GGTGATTTCTCTTTCTCTCCAGTAGT 60.071 42.308 0.00 0.00 0.00 2.73
2946 3005 6.542852 TCGAGCTGCAAATAATTCAGTTTAC 58.457 36.000 1.02 0.00 0.00 2.01
2958 3017 3.885724 TCAGTTTACGATGATGCAGGA 57.114 42.857 0.00 0.00 0.00 3.86
3205 3264 1.058438 CTCGTCTACGACACGTCCG 59.942 63.158 0.14 5.44 44.22 4.79
3228 3287 4.787999 GACTACGTCGCCTTCCTG 57.212 61.111 0.00 0.00 0.00 3.86
3438 3497 2.667199 GTGTACGCGGCCAAGGTT 60.667 61.111 12.47 0.00 0.00 3.50
3644 3703 0.834612 TGGGGGATGTAACACCGATC 59.165 55.000 0.00 0.00 33.50 3.69
3749 3808 1.283029 TGGAAGAATTCTGGCTCCTGG 59.717 52.381 20.39 0.00 46.56 4.45
3800 3859 5.295787 GGCGATTGTTGGAGTACATTTCATA 59.704 40.000 0.00 0.00 0.00 2.15
3804 3863 7.254455 CGATTGTTGGAGTACATTTCATAGGAC 60.254 40.741 0.00 0.00 0.00 3.85
3948 4007 9.360093 CACTTCAAATAAACACAAAACTAACCA 57.640 29.630 0.00 0.00 0.00 3.67
3956 4015 5.731957 ACACAAAACTAACCACTGGTTTT 57.268 34.783 18.75 5.46 44.33 2.43
4359 4448 8.887264 AAGAGAGATAGAGAAAGAGTGGTTAA 57.113 34.615 0.00 0.00 0.00 2.01
4454 4553 7.222180 TCTCCTATACCTCAAAAGACCTCTA 57.778 40.000 0.00 0.00 0.00 2.43
4505 4605 9.213799 ACACTGTAAAACACAACAATCAAATTT 57.786 25.926 0.00 0.00 36.48 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
386 397 3.041940 CGTCTTTCCAAGCGGCGT 61.042 61.111 9.37 0.00 0.00 5.68
485 504 2.164663 GCGCACCGATTGACGATCA 61.165 57.895 0.30 0.00 45.77 2.92
488 507 1.623081 GAAAGCGCACCGATTGACGA 61.623 55.000 11.47 0.00 45.77 4.20
489 508 1.225745 GAAAGCGCACCGATTGACG 60.226 57.895 11.47 0.00 35.13 4.35
490 509 1.225745 CGAAAGCGCACCGATTGAC 60.226 57.895 11.47 0.00 35.13 3.18
493 512 2.860293 CACGAAAGCGCACCGATT 59.140 55.556 19.78 3.01 42.48 3.34
507 526 3.632080 TACTGTGGTGGGGGCACG 61.632 66.667 0.00 0.00 0.00 5.34
633 659 4.032900 CACAGATGGAACTCCGTTTATTCG 59.967 45.833 0.00 0.00 39.43 3.34
645 671 1.303561 TGGCCTGCACAGATGGAAC 60.304 57.895 3.32 0.00 0.00 3.62
810 850 6.515002 CACATCAACAACAATAGTCGTAAACG 59.485 38.462 0.00 0.00 41.45 3.60
811 851 7.320324 CACACATCAACAACAATAGTCGTAAAC 59.680 37.037 0.00 0.00 0.00 2.01
812 852 7.348956 CACACATCAACAACAATAGTCGTAAA 58.651 34.615 0.00 0.00 0.00 2.01
813 853 6.565060 GCACACATCAACAACAATAGTCGTAA 60.565 38.462 0.00 0.00 0.00 3.18
814 854 5.107259 GCACACATCAACAACAATAGTCGTA 60.107 40.000 0.00 0.00 0.00 3.43
815 855 4.319477 GCACACATCAACAACAATAGTCGT 60.319 41.667 0.00 0.00 0.00 4.34
816 856 4.083855 AGCACACATCAACAACAATAGTCG 60.084 41.667 0.00 0.00 0.00 4.18
817 857 5.149273 CAGCACACATCAACAACAATAGTC 58.851 41.667 0.00 0.00 0.00 2.59
818 858 4.557296 GCAGCACACATCAACAACAATAGT 60.557 41.667 0.00 0.00 0.00 2.12
819 859 3.916172 GCAGCACACATCAACAACAATAG 59.084 43.478 0.00 0.00 0.00 1.73
820 860 3.317430 TGCAGCACACATCAACAACAATA 59.683 39.130 0.00 0.00 0.00 1.90
823 863 1.101331 TGCAGCACACATCAACAACA 58.899 45.000 0.00 0.00 0.00 3.33
846 886 6.433766 CCGCTAATGAAAGATCTTGATTTCC 58.566 40.000 9.17 4.86 35.08 3.13
861 901 2.478370 CGTACGAACTTCCCGCTAATGA 60.478 50.000 10.44 0.00 0.00 2.57
911 951 1.736645 CAACAATCCGTCGAGGCGT 60.737 57.895 0.00 0.00 40.77 5.68
934 974 2.042843 AGTAGAGGGAGTGGGCGG 60.043 66.667 0.00 0.00 0.00 6.13
948 989 1.390926 GGGAGTGGGAGTGGGAGTA 59.609 63.158 0.00 0.00 0.00 2.59
980 1021 2.570181 CGCGTTCGTACCTCCCTT 59.430 61.111 0.00 0.00 0.00 3.95
981 1022 4.125695 GCGCGTTCGTACCTCCCT 62.126 66.667 8.43 0.00 38.14 4.20
983 1024 3.711541 ATGGCGCGTTCGTACCTCC 62.712 63.158 8.43 0.00 38.14 4.30
1024 1069 0.968393 ACGCAGAAGAGGAGGAGGAC 60.968 60.000 0.00 0.00 0.00 3.85
1036 1081 1.654954 GACGAGGAGCCTACGCAGAA 61.655 60.000 0.00 0.00 37.52 3.02
1042 1090 4.253257 CGCGGACGAGGAGCCTAC 62.253 72.222 0.00 0.00 43.93 3.18
2385 2443 0.173935 CCACGTACGTCCTTATGGCA 59.826 55.000 19.94 0.00 0.00 4.92
2665 2723 8.429641 AGTACAATCCTCAAGAGTTTTTCTACA 58.570 33.333 0.00 0.00 34.14 2.74
2808 2866 2.678336 GCGAACTGCACCTAAAGCTAAT 59.322 45.455 0.00 0.00 45.45 1.73
2883 2942 7.891183 AGTCATACTACTGGAGAGAAAGAGAAA 59.109 37.037 0.00 0.00 0.00 2.52
2903 2962 5.638596 TCGAGTTTGTAAGCTCAGTCATA 57.361 39.130 8.78 0.00 36.21 2.15
2946 3005 1.957668 TGGATGTTCCTGCATCATCG 58.042 50.000 8.11 0.00 45.11 3.84
2958 3017 0.392998 GAGGGCACGACATGGATGTT 60.393 55.000 0.00 0.00 41.95 2.71
3370 3429 1.909781 GGTGGTACCTGACGGTGGA 60.910 63.158 14.36 0.00 45.18 4.02
3380 3439 3.755628 TCAGCTCGCGGTGGTACC 61.756 66.667 6.13 4.43 39.09 3.34
3644 3703 2.014128 ACGAATTTTACTCGCCCATGG 58.986 47.619 4.14 4.14 39.97 3.66
3695 3754 4.240103 CATCGATCTGCCCCGCCA 62.240 66.667 0.00 0.00 0.00 5.69
3703 3762 2.349590 TGCAACACTTCCATCGATCTG 58.650 47.619 0.00 0.00 0.00 2.90
3774 3833 2.093306 TGTACTCCAACAATCGCCTG 57.907 50.000 0.00 0.00 0.00 4.85
3800 3859 0.981183 TAATGTGCTGTTCCCGTCCT 59.019 50.000 0.00 0.00 0.00 3.85
3804 3863 5.339990 CCTTTTATTAATGTGCTGTTCCCG 58.660 41.667 0.00 0.00 0.00 5.14
3876 3935 8.062065 TGGAAGATGAACTAAAACTGTTTTGT 57.938 30.769 24.59 17.75 34.70 2.83
3948 4007 8.873144 TGGTCTAGTACTTTGTATAAAACCAGT 58.127 33.333 0.00 0.00 0.00 4.00
3956 4015 9.150028 TGCCATTATGGTCTAGTACTTTGTATA 57.850 33.333 13.28 0.00 40.46 1.47
4305 4390 4.234550 TGCCCACATCTTCTGGTATAGAT 58.765 43.478 0.00 0.00 34.80 1.98
4359 4448 4.591321 TTTTCAATCAGAGTATGGGGCT 57.409 40.909 0.00 0.00 0.00 5.19
4454 4553 1.005805 TGGTGTGCCCTTATGCTTGAT 59.994 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.