Multiple sequence alignment - TraesCS5D01G204700

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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 TraesCS5D01G204700 chr5D 100.000 4106 0 0 1 4106 310033042 310037147 0.000000e+00 7583.0
1 TraesCS5D01G204700 chr5A 91.822 4182 192 65 31 4106 403700311 403704448 0.000000e+00 5690.0
2 TraesCS5D01G204700 chr5A 92.727 55 4 0 3816 3870 28061119 28061065 3.400000e-11 80.5
3 TraesCS5D01G204700 chr5A 87.879 66 8 0 3816 3881 400473943 400473878 1.220000e-10 78.7
4 TraesCS5D01G204700 chr5B 94.961 2818 106 19 693 3483 355902136 355904944 0.000000e+00 4385.0
5 TraesCS5D01G204700 chr5B 90.174 631 44 13 3485 4106 355910206 355910827 0.000000e+00 806.0
6 TraesCS5D01G204700 chr5B 89.984 629 32 11 58 657 355901419 355902045 0.000000e+00 784.0
7 TraesCS5D01G204700 chrUn 86.709 158 21 0 1271 1428 377579916 377579759 4.220000e-40 176.0
8 TraesCS5D01G204700 chrUn 86.076 158 22 0 1271 1428 11818654 11818811 1.960000e-38 171.0
9 TraesCS5D01G204700 chrUn 86.076 158 22 0 1271 1428 11821200 11821357 1.960000e-38 171.0
10 TraesCS5D01G204700 chrUn 86.076 158 22 0 1271 1428 385071643 385071800 1.960000e-38 171.0
11 TraesCS5D01G204700 chr3B 88.312 77 9 0 3800 3876 790632563 790632639 4.370000e-15 93.5
12 TraesCS5D01G204700 chr1A 91.935 62 5 0 3816 3877 334680284 334680345 2.030000e-13 87.9
13 TraesCS5D01G204700 chr1A 92.593 54 4 0 3817 3870 356132200 356132253 1.220000e-10 78.7
14 TraesCS5D01G204700 chr4A 90.164 61 6 0 3816 3876 259990622 259990682 3.400000e-11 80.5
15 TraesCS5D01G204700 chr4A 90.909 55 5 0 3816 3870 97523340 97523394 1.580000e-09 75.0


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 TraesCS5D01G204700 chr5D 310033042 310037147 4105 False 7583.0 7583 100.0000 1 4106 1 chr5D.!!$F1 4105
1 TraesCS5D01G204700 chr5A 403700311 403704448 4137 False 5690.0 5690 91.8220 31 4106 1 chr5A.!!$F1 4075
2 TraesCS5D01G204700 chr5B 355901419 355904944 3525 False 2584.5 4385 92.4725 58 3483 2 chr5B.!!$F2 3425
3 TraesCS5D01G204700 chr5B 355910206 355910827 621 False 806.0 806 90.1740 3485 4106 1 chr5B.!!$F1 621

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
390 419 0.603439 TTCTTCTGCTGCATGCGTCA 60.603 50.000 14.09 12.08 46.63 4.35 F
632 699 1.004918 CCCCGTCGGCAATCTATCC 60.005 63.158 5.50 0.00 0.00 2.59 F
1369 1521 0.320683 CCTGTGGATGCTCGTGAACA 60.321 55.000 0.00 0.00 0.00 3.18 F
2326 2478 0.979709 CCTCCTCTCCTGCATGGACA 60.980 60.000 0.00 0.00 40.56 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1376 0.179043 CGTCCTGGATCTCCTCGAGA 60.179 60.000 15.71 0.0 43.20 4.04 R
1839 1991 0.396417 CCTCCGGTCTGATCCACTCT 60.396 60.000 0.00 0.0 0.00 3.24 R
2529 2681 2.829592 GGTATGGCCTCCGGGAAG 59.170 66.667 3.32 0.0 33.58 3.46 R
3896 4071 0.759346 AAAACAGGAGACGAGCCAGT 59.241 50.000 0.00 0.0 0.00 4.00 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
26 27 7.460751 GGATTACTACCGATCAACAACTTAC 57.539 40.000 0.00 0.00 0.00 2.34
27 28 7.263496 GGATTACTACCGATCAACAACTTACT 58.737 38.462 0.00 0.00 0.00 2.24
28 29 7.763071 GGATTACTACCGATCAACAACTTACTT 59.237 37.037 0.00 0.00 0.00 2.24
29 30 9.793252 GATTACTACCGATCAACAACTTACTTA 57.207 33.333 0.00 0.00 0.00 2.24
35 36 1.794116 TCAACAACTTACTTACGCGCC 59.206 47.619 5.73 0.00 0.00 6.53
390 419 0.603439 TTCTTCTGCTGCATGCGTCA 60.603 50.000 14.09 12.08 46.63 4.35
475 510 7.201741 GGTTTGCTTCTAAGTTTCAACTCTTCT 60.202 37.037 0.00 0.00 38.57 2.85
484 519 4.571176 AGTTTCAACTCTTCTTCGTTCACC 59.429 41.667 0.00 0.00 32.86 4.02
493 531 1.968493 TCTTCGTTCACCAAGCTAGGT 59.032 47.619 0.00 0.00 44.48 3.08
494 532 2.367567 TCTTCGTTCACCAAGCTAGGTT 59.632 45.455 0.12 0.12 40.77 3.50
495 533 3.575256 TCTTCGTTCACCAAGCTAGGTTA 59.425 43.478 6.90 0.00 40.77 2.85
496 534 3.308438 TCGTTCACCAAGCTAGGTTAC 57.692 47.619 6.90 0.66 40.77 2.50
507 545 7.658575 CACCAAGCTAGGTTACTTACTTGTAAA 59.341 37.037 6.90 0.00 40.77 2.01
632 699 1.004918 CCCCGTCGGCAATCTATCC 60.005 63.158 5.50 0.00 0.00 2.59
669 747 3.724374 CATCAAAGCCATAGCCCAAATG 58.276 45.455 0.00 0.00 41.25 2.32
792 911 1.469251 CGTTCCTATCCACTGGTGTCG 60.469 57.143 0.00 0.00 0.00 4.35
866 1000 2.482316 CCTGTCTGGTAACACGTGTTCA 60.482 50.000 35.40 25.90 46.17 3.18
867 1001 2.538449 CTGTCTGGTAACACGTGTTCAC 59.462 50.000 35.40 27.44 46.17 3.18
868 1002 1.519758 GTCTGGTAACACGTGTTCACG 59.480 52.381 35.40 21.55 46.17 4.35
883 1017 5.277876 CGTGTTCACGCTCCTCTATAAGTAT 60.278 44.000 12.19 0.00 0.00 2.12
887 1021 2.488545 ACGCTCCTCTATAAGTATGCGG 59.511 50.000 0.00 0.00 45.26 5.69
908 1042 2.809696 GCTCTCGGTATCCTCTCACTAC 59.190 54.545 0.00 0.00 0.00 2.73
927 1065 1.628846 ACGAATTACAGCCCACCTCTT 59.371 47.619 0.00 0.00 0.00 2.85
947 1085 7.398904 ACCTCTTAATCTCTCTTGAGCTTACTT 59.601 37.037 0.00 0.00 40.03 2.24
1032 1184 4.263572 CCACCACGGAGCCAACCA 62.264 66.667 0.00 0.00 36.56 3.67
1224 1376 4.416738 GGCCTCCTGCTCGCCTTT 62.417 66.667 0.00 0.00 39.70 3.11
1248 1400 2.415608 GGAGATCCAGGACGCGACA 61.416 63.158 15.93 0.00 35.64 4.35
1369 1521 0.320683 CCTGTGGATGCTCGTGAACA 60.321 55.000 0.00 0.00 0.00 3.18
1434 1586 2.203195 GCGGCCATGGATGTGCTA 60.203 61.111 18.40 0.00 0.00 3.49
1691 1843 1.152943 TAGATGGCGAGCTCTCCGT 60.153 57.895 17.42 17.42 0.00 4.69
1892 2044 3.431346 CCGATCACACTGGAACTCATGAT 60.431 47.826 0.00 0.00 0.00 2.45
2326 2478 0.979709 CCTCCTCTCCTGCATGGACA 60.980 60.000 0.00 0.00 40.56 4.02
2523 2675 1.570475 CGAGTACGCCGAGGAGATC 59.430 63.158 0.00 0.00 0.00 2.75
2571 2723 0.175760 TAGTGCGGCTCATCAAGGAC 59.824 55.000 0.00 0.00 0.00 3.85
2879 3031 1.449726 CTGCTTGTCTTGCTGTGCCA 61.450 55.000 0.00 0.00 0.00 4.92
3261 3413 3.763897 AGATTGAATTTTGTTCCTCCCCG 59.236 43.478 0.00 0.00 0.00 5.73
3409 3579 4.906618 TGGAAGAAGATAGTTGTGGGAAC 58.093 43.478 0.00 0.00 0.00 3.62
3432 3603 2.795329 AGATTTGGTGGCGACTGAAAT 58.205 42.857 0.00 4.19 0.00 2.17
3476 3647 9.787435 AAAACCTTGACTGTACTTACATGATTA 57.213 29.630 0.00 0.00 35.36 1.75
3591 3762 2.738846 CAGTCGTTCTGATTGGAACAGG 59.261 50.000 7.87 0.00 46.27 4.00
3682 3853 6.588756 TGACTTTCGTGCGAATCTAAATAGTT 59.411 34.615 7.87 0.00 33.79 2.24
3743 3914 0.395448 ACTCTACTCCGTAGTGGGCC 60.395 60.000 0.00 0.00 37.41 5.80
3746 3917 0.395311 CTACTCCGTAGTGGGCCTGA 60.395 60.000 4.53 0.00 36.36 3.86
3749 3920 3.390521 CCGTAGTGGGCCTGAGCA 61.391 66.667 4.53 0.00 42.56 4.26
3764 3935 1.417517 TGAGCAAGAGAGTGAAGGCAA 59.582 47.619 0.00 0.00 0.00 4.52
3802 3973 6.993902 AGAACAAGAAATTCCATTTTGCACAT 59.006 30.769 0.00 0.00 31.47 3.21
3824 3999 0.612174 AGCCCGTCTAGCTCAGTTGA 60.612 55.000 0.00 0.00 34.91 3.18
3852 4027 2.586648 AAGGCTCTTAACCTTGTGGG 57.413 50.000 0.00 0.00 45.88 4.61
3911 4086 1.388065 CCCTACTGGCTCGTCTCCTG 61.388 65.000 0.00 0.00 0.00 3.86
3916 4091 1.270358 ACTGGCTCGTCTCCTGTTTTC 60.270 52.381 0.00 0.00 32.79 2.29
3917 4092 1.001406 CTGGCTCGTCTCCTGTTTTCT 59.999 52.381 0.00 0.00 0.00 2.52
3922 4097 3.921630 GCTCGTCTCCTGTTTTCTACTTC 59.078 47.826 0.00 0.00 0.00 3.01
3923 4098 4.487019 CTCGTCTCCTGTTTTCTACTTCC 58.513 47.826 0.00 0.00 0.00 3.46
3934 4109 6.966021 TGTTTTCTACTTCCCTTTTCATTCG 58.034 36.000 0.00 0.00 0.00 3.34
3936 4111 7.716123 TGTTTTCTACTTCCCTTTTCATTCGTA 59.284 33.333 0.00 0.00 0.00 3.43
4031 4206 8.501580 CGGACTAATCATTCTACTACAACGATA 58.498 37.037 0.00 0.00 0.00 2.92
4070 4245 2.935201 GCTGAGCAGATGGTTTGAGTAG 59.065 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.088194 TGTTGATCGGTAGTAATCCGC 57.912 47.619 0.00 0.00 46.49 5.54
2 3 7.263496 AGTAAGTTGTTGATCGGTAGTAATCC 58.737 38.462 0.00 0.00 0.00 3.01
3 4 8.699283 AAGTAAGTTGTTGATCGGTAGTAATC 57.301 34.615 0.00 0.00 0.00 1.75
4 5 9.578439 GTAAGTAAGTTGTTGATCGGTAGTAAT 57.422 33.333 0.00 0.00 0.00 1.89
5 6 7.750458 CGTAAGTAAGTTGTTGATCGGTAGTAA 59.250 37.037 0.00 0.00 0.00 2.24
6 7 7.243487 CGTAAGTAAGTTGTTGATCGGTAGTA 58.757 38.462 0.00 0.00 0.00 1.82
7 8 6.088824 CGTAAGTAAGTTGTTGATCGGTAGT 58.911 40.000 0.00 0.00 0.00 2.73
8 9 5.004156 GCGTAAGTAAGTTGTTGATCGGTAG 59.996 44.000 0.00 0.00 41.68 3.18
9 10 4.858692 GCGTAAGTAAGTTGTTGATCGGTA 59.141 41.667 0.00 0.00 41.68 4.02
10 11 3.676646 GCGTAAGTAAGTTGTTGATCGGT 59.323 43.478 0.00 0.00 41.68 4.69
11 12 3.241552 CGCGTAAGTAAGTTGTTGATCGG 60.242 47.826 0.00 0.00 41.68 4.18
12 13 3.776795 GCGCGTAAGTAAGTTGTTGATCG 60.777 47.826 8.43 0.00 41.68 3.69
13 14 3.483085 GGCGCGTAAGTAAGTTGTTGATC 60.483 47.826 8.43 0.00 41.68 2.92
14 15 2.414138 GGCGCGTAAGTAAGTTGTTGAT 59.586 45.455 8.43 0.00 41.68 2.57
15 16 1.794116 GGCGCGTAAGTAAGTTGTTGA 59.206 47.619 8.43 0.00 41.68 3.18
16 17 1.796459 AGGCGCGTAAGTAAGTTGTTG 59.204 47.619 8.43 0.00 41.68 3.33
17 18 2.064014 GAGGCGCGTAAGTAAGTTGTT 58.936 47.619 8.43 0.00 41.68 2.83
18 19 1.670967 GGAGGCGCGTAAGTAAGTTGT 60.671 52.381 8.43 0.00 41.68 3.32
19 20 0.997196 GGAGGCGCGTAAGTAAGTTG 59.003 55.000 8.43 0.00 41.68 3.16
20 21 0.893447 AGGAGGCGCGTAAGTAAGTT 59.107 50.000 8.43 0.00 41.68 2.66
21 22 0.893447 AAGGAGGCGCGTAAGTAAGT 59.107 50.000 8.43 0.00 41.68 2.24
22 23 1.557651 GAAGGAGGCGCGTAAGTAAG 58.442 55.000 8.43 0.00 41.68 2.34
23 24 0.174162 GGAAGGAGGCGCGTAAGTAA 59.826 55.000 8.43 0.00 41.68 2.24
24 25 1.669999 GGGAAGGAGGCGCGTAAGTA 61.670 60.000 8.43 0.00 41.68 2.24
25 26 2.577593 GGAAGGAGGCGCGTAAGT 59.422 61.111 8.43 0.00 41.68 2.24
26 27 2.202892 GGGAAGGAGGCGCGTAAG 60.203 66.667 8.43 0.00 43.44 2.34
27 28 4.137872 CGGGAAGGAGGCGCGTAA 62.138 66.667 8.43 0.00 37.00 3.18
35 36 0.175989 GCCTACTGAACGGGAAGGAG 59.824 60.000 8.00 0.00 0.00 3.69
46 47 0.538584 TCTACTCCGTCGCCTACTGA 59.461 55.000 0.00 0.00 0.00 3.41
93 95 3.554342 CTCATCCCCTGGCCTCCG 61.554 72.222 3.32 0.00 0.00 4.63
181 187 2.986728 AGGGGATATACTTTGGGCGATT 59.013 45.455 0.00 0.00 0.00 3.34
223 236 4.075910 CGTGCGACGCATTGCAGT 62.076 61.111 27.23 7.60 46.32 4.40
390 419 2.038557 ACCTCATTTGGTCTACGCAACT 59.961 45.455 0.00 0.00 34.86 3.16
475 510 2.922740 AACCTAGCTTGGTGAACGAA 57.077 45.000 20.90 0.00 40.73 3.85
484 519 8.597662 TGTTTACAAGTAAGTAACCTAGCTTG 57.402 34.615 0.00 0.00 37.98 4.01
507 545 7.259088 AGTAAGATGGATTCCTTGTACTTGT 57.741 36.000 3.95 0.00 0.00 3.16
513 551 6.012745 AGCAAAAGTAAGATGGATTCCTTGT 58.987 36.000 3.95 0.00 0.00 3.16
632 699 0.240145 GATGCATGCATGTCCGGATG 59.760 55.000 36.73 3.49 36.70 3.51
866 1000 2.488545 CCGCATACTTATAGAGGAGCGT 59.511 50.000 0.00 0.00 40.20 5.07
867 1001 2.732597 GCCGCATACTTATAGAGGAGCG 60.733 54.545 0.00 0.00 40.93 5.03
868 1002 2.494073 AGCCGCATACTTATAGAGGAGC 59.506 50.000 0.00 0.00 0.00 4.70
883 1017 2.123854 AGGATACCGAGAGCCGCA 60.124 61.111 0.00 0.00 36.84 5.69
887 1021 1.975660 AGTGAGAGGATACCGAGAGC 58.024 55.000 0.00 0.00 37.17 4.09
908 1042 2.403252 AAGAGGTGGGCTGTAATTCG 57.597 50.000 0.00 0.00 0.00 3.34
947 1085 4.431378 TGGATTAAGGGAAGTAGTGTGGA 58.569 43.478 0.00 0.00 0.00 4.02
991 1143 2.801162 CGCCGGCATCGTAGATCG 60.801 66.667 28.98 0.98 45.12 3.69
992 1144 3.106407 GCGCCGGCATCGTAGATC 61.106 66.667 28.98 0.00 45.12 2.75
1179 1331 4.873810 ACTGCTTGGTGCGTGCCA 62.874 61.111 0.00 0.00 46.63 4.92
1221 1373 2.360801 GTCCTGGATCTCCTCGAGAAAG 59.639 54.545 15.71 11.14 42.27 2.62
1224 1376 0.179043 CGTCCTGGATCTCCTCGAGA 60.179 60.000 15.71 0.00 43.20 4.04
1357 1509 2.224042 TGAGTTCAGTGTTCACGAGCAT 60.224 45.455 0.00 0.00 0.00 3.79
1369 1521 2.159310 GCTCAGACGCTATGAGTTCAGT 60.159 50.000 12.14 0.00 44.92 3.41
1839 1991 0.396417 CCTCCGGTCTGATCCACTCT 60.396 60.000 0.00 0.00 0.00 3.24
1863 2015 2.665000 AGTGTGATCGGGCACTGG 59.335 61.111 14.05 0.00 43.45 4.00
2529 2681 2.829592 GGTATGGCCTCCGGGAAG 59.170 66.667 3.32 0.00 33.58 3.46
3025 3177 2.969238 CGATGATGACGGCCTGGC 60.969 66.667 11.05 11.05 0.00 4.85
3261 3413 4.025145 GCGTAGTATAACACAAGGAATGGC 60.025 45.833 0.00 0.00 0.00 4.40
3409 3579 1.879380 TCAGTCGCCACCAAATCTTTG 59.121 47.619 0.00 0.00 37.90 2.77
3484 3655 7.234988 ACCTCTACCAAACTATTCTGTAACTGT 59.765 37.037 0.00 0.00 0.00 3.55
3485 3656 7.612677 ACCTCTACCAAACTATTCTGTAACTG 58.387 38.462 0.00 0.00 0.00 3.16
3486 3657 7.793948 ACCTCTACCAAACTATTCTGTAACT 57.206 36.000 0.00 0.00 0.00 2.24
3487 3658 8.843885 AAACCTCTACCAAACTATTCTGTAAC 57.156 34.615 0.00 0.00 0.00 2.50
3488 3659 9.280174 CAAAACCTCTACCAAACTATTCTGTAA 57.720 33.333 0.00 0.00 0.00 2.41
3489 3660 8.653191 TCAAAACCTCTACCAAACTATTCTGTA 58.347 33.333 0.00 0.00 0.00 2.74
3591 3762 5.405269 ACAAAGAACTTTTTGTGTGCTTGAC 59.595 36.000 3.57 0.00 46.44 3.18
3642 3813 4.579340 CGAAAGTCATAGCTACTACAGGGA 59.421 45.833 0.00 0.00 0.00 4.20
3682 3853 3.438781 GTCCATACTTCATTTCGCCACAA 59.561 43.478 0.00 0.00 0.00 3.33
3743 3914 1.001746 TGCCTTCACTCTCTTGCTCAG 59.998 52.381 0.00 0.00 0.00 3.35
3746 3917 2.875094 ATTGCCTTCACTCTCTTGCT 57.125 45.000 0.00 0.00 0.00 3.91
3802 3973 1.754621 CTGAGCTAGACGGGCTGGA 60.755 63.158 0.00 0.00 40.40 3.86
3896 4071 0.759346 AAAACAGGAGACGAGCCAGT 59.241 50.000 0.00 0.00 0.00 4.00
3901 4076 4.487019 GGAAGTAGAAAACAGGAGACGAG 58.513 47.826 0.00 0.00 0.00 4.18
3911 4086 6.967135 ACGAATGAAAAGGGAAGTAGAAAAC 58.033 36.000 0.00 0.00 0.00 2.43
3916 4091 7.603024 AGAAACTACGAATGAAAAGGGAAGTAG 59.397 37.037 0.00 0.00 37.09 2.57
3917 4092 7.386848 CAGAAACTACGAATGAAAAGGGAAGTA 59.613 37.037 0.00 0.00 0.00 2.24
3922 4097 5.941948 ACAGAAACTACGAATGAAAAGGG 57.058 39.130 0.00 0.00 0.00 3.95
3923 4098 8.628882 AAAAACAGAAACTACGAATGAAAAGG 57.371 30.769 0.00 0.00 0.00 3.11
3966 4141 3.479370 GCGATGTGCACAGAGGAC 58.521 61.111 25.84 12.17 45.45 3.85
3990 4165 1.453745 TCCGCAGAAATGGGGCATC 60.454 57.895 6.47 0.00 41.13 3.91
3995 4170 2.917933 TGATTAGTCCGCAGAAATGGG 58.082 47.619 0.00 0.00 0.00 4.00
4031 4206 5.749109 GCTCAGCTGTAACGATACTGTAAAT 59.251 40.000 14.67 0.00 34.47 1.40
4049 4224 1.818642 ACTCAAACCATCTGCTCAGC 58.181 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.