Multiple sequence alignment - TraesCS7A01G174600

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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 TraesCS7A01G174600 chr7A 100.000 3309 0 0 1 3309 128454642 128457950 0.000000e+00 6111
1 TraesCS7A01G174600 chr7A 95.710 606 21 2 2704 3309 192766421 192765821 0.000000e+00 970
2 TraesCS7A01G174600 chr5A 97.381 2711 58 6 1 2706 39635364 39632662 0.000000e+00 4601
3 TraesCS7A01G174600 chr7B 95.753 2708 94 5 1 2706 85050566 85047878 0.000000e+00 4344
4 TraesCS7A01G174600 chr7B 84.211 513 61 12 2195 2703 724445445 724445941 6.420000e-132 481
5 TraesCS7A01G174600 chr2D 93.594 2716 122 20 1 2706 560672906 560675579 0.000000e+00 4004
6 TraesCS7A01G174600 chr2D 91.262 103 9 0 2605 2707 181489364 181489262 1.240000e-29 141
7 TraesCS7A01G174600 chr5B 93.559 2717 122 25 1 2706 129493225 129490551 0.000000e+00 3999
8 TraesCS7A01G174600 chr3B 92.654 1198 85 3 1 1197 233675292 233674097 0.000000e+00 1722
9 TraesCS7A01G174600 chr3B 86.228 1503 145 28 1235 2707 233674103 233672633 0.000000e+00 1572
10 TraesCS7A01G174600 chr3B 91.176 102 9 0 2605 2706 167248767 167248666 4.450000e-29 139
11 TraesCS7A01G174600 chr4A 96.370 606 18 3 2704 3309 151053183 151053784 0.000000e+00 994
12 TraesCS7A01G174600 chr4A 95.710 606 22 3 2704 3309 71392698 71392097 0.000000e+00 972
13 TraesCS7A01G174600 chr4A 91.176 408 36 0 1702 2109 557038737 557038330 3.730000e-154 555
14 TraesCS7A01G174600 chr2A 96.358 604 19 2 2704 3307 511397314 511397914 0.000000e+00 990
15 TraesCS7A01G174600 chr2A 95.875 606 21 3 2704 3309 661528654 661528053 0.000000e+00 977
16 TraesCS7A01G174600 chr1A 96.198 605 20 2 2704 3307 358998136 358998738 0.000000e+00 987
17 TraesCS7A01G174600 chr1A 91.262 103 9 0 2605 2707 572026153 572026051 1.240000e-29 141
18 TraesCS7A01G174600 chr6A 95.875 606 19 4 2704 3309 96969237 96969836 0.000000e+00 976
19 TraesCS7A01G174600 chr3A 95.875 606 20 3 2704 3309 728920191 728919591 0.000000e+00 976
20 TraesCS7A01G174600 chr3A 95.717 607 20 4 2704 3309 61275099 61275700 0.000000e+00 972
21 TraesCS7A01G174600 chr1B 85.496 524 48 16 2195 2706 576756391 576756898 3.780000e-144 521
22 TraesCS7A01G174600 chr6B 83.237 519 46 22 2205 2706 133750496 133750990 3.920000e-119 438
23 TraesCS7A01G174600 chr3D 83.012 518 53 15 2195 2706 345758611 345759099 1.410000e-118 436
24 TraesCS7A01G174600 chrUn 82.648 438 40 16 2214 2632 158034218 158034638 4.060000e-94 355
25 TraesCS7A01G174600 chr6D 91.235 251 22 0 2456 2706 435850469 435850719 3.160000e-90 342
26 TraesCS7A01G174600 chr5D 86.719 256 8 9 2201 2456 444786576 444786347 9.110000e-66 261


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 TraesCS7A01G174600 chr7A 128454642 128457950 3308 False 6111 6111 100.000 1 3309 1 chr7A.!!$F1 3308
1 TraesCS7A01G174600 chr7A 192765821 192766421 600 True 970 970 95.710 2704 3309 1 chr7A.!!$R1 605
2 TraesCS7A01G174600 chr5A 39632662 39635364 2702 True 4601 4601 97.381 1 2706 1 chr5A.!!$R1 2705
3 TraesCS7A01G174600 chr7B 85047878 85050566 2688 True 4344 4344 95.753 1 2706 1 chr7B.!!$R1 2705
4 TraesCS7A01G174600 chr2D 560672906 560675579 2673 False 4004 4004 93.594 1 2706 1 chr2D.!!$F1 2705
5 TraesCS7A01G174600 chr5B 129490551 129493225 2674 True 3999 3999 93.559 1 2706 1 chr5B.!!$R1 2705
6 TraesCS7A01G174600 chr3B 233672633 233675292 2659 True 1647 1722 89.441 1 2707 2 chr3B.!!$R2 2706
7 TraesCS7A01G174600 chr4A 151053183 151053784 601 False 994 994 96.370 2704 3309 1 chr4A.!!$F1 605
8 TraesCS7A01G174600 chr4A 71392097 71392698 601 True 972 972 95.710 2704 3309 1 chr4A.!!$R1 605
9 TraesCS7A01G174600 chr2A 511397314 511397914 600 False 990 990 96.358 2704 3307 1 chr2A.!!$F1 603
10 TraesCS7A01G174600 chr2A 661528053 661528654 601 True 977 977 95.875 2704 3309 1 chr2A.!!$R1 605
11 TraesCS7A01G174600 chr1A 358998136 358998738 602 False 987 987 96.198 2704 3307 1 chr1A.!!$F1 603
12 TraesCS7A01G174600 chr6A 96969237 96969836 599 False 976 976 95.875 2704 3309 1 chr6A.!!$F1 605
13 TraesCS7A01G174600 chr3A 728919591 728920191 600 True 976 976 95.875 2704 3309 1 chr3A.!!$R1 605
14 TraesCS7A01G174600 chr3A 61275099 61275700 601 False 972 972 95.717 2704 3309 1 chr3A.!!$F1 605
15 TraesCS7A01G174600 chr1B 576756391 576756898 507 False 521 521 85.496 2195 2706 1 chr1B.!!$F1 511

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
789 794 0.378257 CTTGTGCGGCACATACCATC 59.622 55.0 33.66 6.32 44.16 3.51 F
959 964 0.463116 ACGACTCGGTTTGCCACTTT 60.463 50.0 2.98 0.00 34.09 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2140 0.531974 TGCTCGACGAACCTTTGCTT 60.532 50.0 0.0 0.0 0.0 3.91 R
2897 2941 0.400670 GCCCTCCTCCACTTATCCCT 60.401 60.0 0.0 0.0 0.0 4.20 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
136 137 4.260661 CGATGAGCAAGATCAATCAACCAG 60.261 45.833 0.00 0.00 31.76 4.00
221 226 5.828328 AGAAACTCGTGGAAAAGGAAAGAAT 59.172 36.000 0.00 0.00 0.00 2.40
283 288 5.934781 ACAAGTTGAAGGAGAAACAGAGAT 58.065 37.500 10.54 0.00 0.00 2.75
305 310 8.693120 AGATCTCATGAATACATTGCAGATTT 57.307 30.769 0.00 0.00 34.15 2.17
504 509 1.675714 GCATGGTCGTTGACTGGATGA 60.676 52.381 0.00 0.00 32.47 2.92
579 584 3.576118 TGGTATCTCATTCTGCTAGAGGC 59.424 47.826 0.00 0.00 42.22 4.70
777 782 2.987413 TATTTTGGACTGCTTGTGCG 57.013 45.000 0.00 0.00 43.34 5.34
789 794 0.378257 CTTGTGCGGCACATACCATC 59.622 55.000 33.66 6.32 44.16 3.51
828 833 4.202441 ACATTGGTAAGAAGCCTGCTATG 58.798 43.478 0.00 0.00 0.00 2.23
902 907 5.654497 CACTAGAGTGTTGTCTATGATGCA 58.346 41.667 0.00 0.00 40.96 3.96
920 925 5.945191 TGATGCATTCTTTTACTGGTGATCA 59.055 36.000 0.00 0.00 0.00 2.92
959 964 0.463116 ACGACTCGGTTTGCCACTTT 60.463 50.000 2.98 0.00 34.09 2.66
1041 1047 2.515854 ACAAAGTGGAGCGACTCTAGA 58.484 47.619 6.78 0.00 0.00 2.43
1214 1220 7.277098 CCTTTATGGTGATCTTGAAAATGCAAG 59.723 37.037 0.00 0.00 45.10 4.01
1501 1507 3.244875 TGGCACTGATTCTTTTGGCTCTA 60.245 43.478 0.00 0.00 35.63 2.43
1728 1739 3.005554 CTCATCTGCGTGTGAAAGGAAT 58.994 45.455 0.00 0.00 0.00 3.01
1998 2013 1.153147 GGATTGAAGGGGAGGCGAC 60.153 63.158 0.00 0.00 0.00 5.19
1999 2014 1.153147 GATTGAAGGGGAGGCGACC 60.153 63.158 0.00 0.00 0.00 4.79
2050 2065 4.982241 TGAAGAACAAGATGGAGAAGGT 57.018 40.909 0.00 0.00 0.00 3.50
2125 2140 6.556212 CGTAAATGAGAAGAAGAGAGCACTA 58.444 40.000 0.00 0.00 0.00 2.74
2266 2284 7.199167 TGATGGAGAGAATGAGGACAATTTA 57.801 36.000 0.00 0.00 0.00 1.40
2750 2794 6.553100 ACAAAAACTAATTGGACCAATGGAGA 59.447 34.615 25.71 11.66 34.04 3.71
2866 2910 1.868109 GCTTGAGTTGGTTTTTCGGGC 60.868 52.381 0.00 0.00 0.00 6.13
2897 2941 1.661463 AGAGGAAGAAGATGGGTGCA 58.339 50.000 0.00 0.00 0.00 4.57
3107 3154 6.582677 TGGGATATTTTTATATTGCACGGG 57.417 37.500 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 4.510340 TCAAAGACCTCTTTCGCACTAAAC 59.490 41.667 0.00 0.0 43.72 2.01
201 206 5.828328 AGAAATTCTTTCCTTTTCCACGAGT 59.172 36.000 0.00 0.0 40.54 4.18
221 226 3.554337 GGTTTGAGTGCTAGTCCGAGAAA 60.554 47.826 0.00 0.0 0.00 2.52
283 288 7.634671 ACAAATCTGCAATGTATTCATGAGA 57.365 32.000 0.00 0.0 34.19 3.27
305 310 4.219115 TGGAATTCCAGCTTGGTAAAACA 58.781 39.130 23.63 0.0 42.01 2.83
504 509 4.699257 GTCCAAGCATCTGTCAAAAGAGAT 59.301 41.667 0.00 0.0 35.98 2.75
579 584 0.242825 TAGCTCGGAGAAACCACACG 59.757 55.000 9.69 0.0 38.90 4.49
777 782 3.372206 GCATTAGATCGATGGTATGTGCC 59.628 47.826 0.54 0.0 0.00 5.01
789 794 4.212847 CCAATGTCCTCAAGCATTAGATCG 59.787 45.833 0.00 0.0 34.01 3.69
828 833 8.748380 ACTTTGCTTTCTTAATTGTATTCTGC 57.252 30.769 0.00 0.0 0.00 4.26
920 925 3.865745 CGTTCCAGCTCGAACTAAATCAT 59.134 43.478 19.91 0.0 40.03 2.45
1214 1220 3.643159 AACGGACAGCAATTTCCTTTC 57.357 42.857 0.00 0.0 0.00 2.62
1501 1507 3.950397 TCCTTTGTCGAATAGCCATTGT 58.050 40.909 0.00 0.0 0.00 2.71
1728 1739 1.425066 ACCCTCTCAAATGCACTCCAA 59.575 47.619 0.00 0.0 0.00 3.53
1877 1892 8.230486 CCTCTTGTTAAACATGACATAGACAAC 58.770 37.037 0.00 0.0 30.47 3.32
1998 2013 3.741476 GCTGCTGCCCTTCAACGG 61.741 66.667 3.85 0.0 0.00 4.44
1999 2014 2.467946 CTTGCTGCTGCCCTTCAACG 62.468 60.000 13.47 0.0 38.71 4.10
2050 2065 7.285858 TCACCATCATAATCAGATGCATTTTCA 59.714 33.333 0.00 0.0 41.13 2.69
2125 2140 0.531974 TGCTCGACGAACCTTTGCTT 60.532 50.000 0.00 0.0 0.00 3.91
2715 2759 7.803659 GTCCAATTAGTTTTTGTTCTAGTGCTC 59.196 37.037 0.00 0.0 0.00 4.26
2750 2794 5.880901 AGATTGTTCCTTGGTATGTGACTT 58.119 37.500 0.00 0.0 0.00 3.01
2866 2910 6.522625 TCTTCTTCCTCTATCTCACACAAG 57.477 41.667 0.00 0.0 0.00 3.16
2897 2941 0.400670 GCCCTCCTCCACTTATCCCT 60.401 60.000 0.00 0.0 0.00 4.20
3107 3154 6.920569 TTTTCTGTCTGTTTCCTGACTTAC 57.079 37.500 0.00 0.0 39.52 2.34


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

AutoCloner maintained by Alex Coulton.