Multiple sequence alignment - TraesCS7D01G195500

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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 TraesCS7D01G195500 chr7D 100.000 3090 0 0 1 3090 151930020 151933109 0.000000e+00 5707.0
1 TraesCS7D01G195500 chr7D 98.676 2493 30 1 1 2490 151823836 151826328 0.000000e+00 4418.0
2 TraesCS7D01G195500 chr7D 85.699 1888 181 53 489 2346 151770659 151768831 0.000000e+00 1908.0
3 TraesCS7D01G195500 chr7D 87.617 1389 127 25 974 2346 152086959 152088318 0.000000e+00 1570.0
4 TraesCS7D01G195500 chr7D 87.249 1145 104 22 941 2074 151791512 151790399 0.000000e+00 1267.0
5 TraesCS7D01G195500 chr7D 96.886 578 18 0 2513 3090 151837322 151837899 0.000000e+00 968.0
6 TraesCS7D01G195500 chr7D 87.838 740 50 18 591 1309 151779937 151779217 0.000000e+00 832.0
7 TraesCS7D01G195500 chr7D 100.000 55 0 0 2459 2513 151826329 151826383 5.450000e-18 102.0
8 TraesCS7D01G195500 chr7B 89.118 2426 197 36 1 2406 113803830 113801452 0.000000e+00 2955.0
9 TraesCS7D01G195500 chr7B 89.470 1624 132 21 502 2115 113540318 113538724 0.000000e+00 2015.0
10 TraesCS7D01G195500 chr7B 85.645 1651 166 49 499 2111 113528987 113527370 0.000000e+00 1670.0
11 TraesCS7D01G195500 chr7B 86.311 1388 156 24 974 2346 113627001 113625633 0.000000e+00 1480.0
12 TraesCS7D01G195500 chr7A 88.367 1960 136 44 741 2643 152084214 152086138 0.000000e+00 2272.0
13 TraesCS7D01G195500 chr7A 87.794 1614 135 26 499 2077 151862242 151863828 0.000000e+00 1832.0
14 TraesCS7D01G195500 chr7A 88.619 1151 104 17 941 2075 151961618 151960479 0.000000e+00 1375.0
15 TraesCS7D01G195500 chr7A 93.617 423 25 2 320 740 152083665 152084087 5.620000e-177 630.0
16 TraesCS7D01G195500 chr7A 85.849 318 23 8 593 893 151872810 151873122 4.970000e-83 318.0
17 TraesCS7D01G195500 chr7A 86.466 133 8 3 149 271 692125720 692125852 1.490000e-28 137.0
18 TraesCS7D01G195500 chrUn 86.311 1388 156 24 974 2346 185555853 185554485 0.000000e+00 1480.0
19 TraesCS7D01G195500 chr2B 85.768 267 36 2 3 268 39791023 39790758 6.520000e-72 281.0
20 TraesCS7D01G195500 chr3A 78.104 443 78 13 2624 3061 575006365 575005937 2.360000e-66 263.0
21 TraesCS7D01G195500 chr3A 82.759 203 27 4 47 248 624427527 624427332 1.140000e-39 174.0
22 TraesCS7D01G195500 chr2D 77.586 464 77 22 2569 3022 479206619 479207065 3.950000e-64 255.0
23 TraesCS7D01G195500 chr2A 76.258 497 93 21 2570 3061 621929261 621929737 1.110000e-59 241.0
24 TraesCS7D01G195500 chr6B 79.730 296 56 4 2764 3059 350014833 350014542 8.680000e-51 211.0
25 TraesCS7D01G195500 chr5A 84.615 169 24 2 102 269 604755339 604755172 1.910000e-37 167.0
26 TraesCS7D01G195500 chr6A 75.676 296 69 3 2764 3059 326619098 326618806 8.930000e-31 145.0
27 TraesCS7D01G195500 chr5D 90.385 52 4 1 2841 2891 564843122 564843071 1.990000e-07 67.6
28 TraesCS7D01G195500 chr5D 100.000 33 0 0 2859 2891 47868527 47868495 9.250000e-06 62.1
29 TraesCS7D01G195500 chr5B 88.000 50 6 0 2961 3010 499688466 499688515 3.330000e-05 60.2


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 TraesCS7D01G195500 chr7D 151930020 151933109 3089 False 5707 5707 100.000 1 3090 1 chr7D.!!$F2 3089
1 TraesCS7D01G195500 chr7D 151823836 151826383 2547 False 2260 4418 99.338 1 2513 2 chr7D.!!$F4 2512
2 TraesCS7D01G195500 chr7D 151768831 151770659 1828 True 1908 1908 85.699 489 2346 1 chr7D.!!$R1 1857
3 TraesCS7D01G195500 chr7D 152086959 152088318 1359 False 1570 1570 87.617 974 2346 1 chr7D.!!$F3 1372
4 TraesCS7D01G195500 chr7D 151790399 151791512 1113 True 1267 1267 87.249 941 2074 1 chr7D.!!$R3 1133
5 TraesCS7D01G195500 chr7D 151837322 151837899 577 False 968 968 96.886 2513 3090 1 chr7D.!!$F1 577
6 TraesCS7D01G195500 chr7D 151779217 151779937 720 True 832 832 87.838 591 1309 1 chr7D.!!$R2 718
7 TraesCS7D01G195500 chr7B 113801452 113803830 2378 True 2955 2955 89.118 1 2406 1 chr7B.!!$R4 2405
8 TraesCS7D01G195500 chr7B 113538724 113540318 1594 True 2015 2015 89.470 502 2115 1 chr7B.!!$R2 1613
9 TraesCS7D01G195500 chr7B 113527370 113528987 1617 True 1670 1670 85.645 499 2111 1 chr7B.!!$R1 1612
10 TraesCS7D01G195500 chr7B 113625633 113627001 1368 True 1480 1480 86.311 974 2346 1 chr7B.!!$R3 1372
11 TraesCS7D01G195500 chr7A 151862242 151863828 1586 False 1832 1832 87.794 499 2077 1 chr7A.!!$F1 1578
12 TraesCS7D01G195500 chr7A 152083665 152086138 2473 False 1451 2272 90.992 320 2643 2 chr7A.!!$F4 2323
13 TraesCS7D01G195500 chr7A 151960479 151961618 1139 True 1375 1375 88.619 941 2075 1 chr7A.!!$R1 1134
14 TraesCS7D01G195500 chrUn 185554485 185555853 1368 True 1480 1480 86.311 974 2346 1 chrUn.!!$R1 1372

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
811 992 0.252197 GAGGCGGTTGTATGGAGGTT 59.748 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2757 3102 0.809241 GGAGAAGCAGCCTCACGATG 60.809 60.0 0.0 0.0 32.48 3.84 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
323 328 1.879380 TGACATTTCCTGAGCGTTTGG 59.121 47.619 0.00 0.00 0.00 3.28
683 714 7.399478 AGAGACAGATGATAGATTGATGGCATA 59.601 37.037 0.00 0.00 0.00 3.14
811 992 0.252197 GAGGCGGTTGTATGGAGGTT 59.748 55.000 0.00 0.00 0.00 3.50
2092 2338 1.359475 CTACGCTCCGAACTAGGGC 59.641 63.158 0.00 0.00 0.00 5.19
2362 2666 5.963586 GTCCACTTTTCAACTCAACTTAACG 59.036 40.000 0.00 0.00 0.00 3.18
2429 2735 7.263901 TCCTCTACTATTTATCCATTCCCCAT 58.736 38.462 0.00 0.00 0.00 4.00
2519 2859 1.958288 AGATGACTAGCCCCACAGTT 58.042 50.000 0.00 0.00 0.00 3.16
2727 3072 2.142292 ATCTCAGGTGCGCCCCTTTT 62.142 55.000 9.40 0.00 34.57 2.27
2728 3073 2.282180 TCAGGTGCGCCCCTTTTC 60.282 61.111 9.40 0.00 34.57 2.29
2757 3102 5.844004 TCTACTCCAGAAAAAGTGTGAGAC 58.156 41.667 0.00 0.00 0.00 3.36
2813 3158 2.711922 AACGCCTAGCTCTGGACGG 61.712 63.158 18.62 8.06 0.00 4.79
2980 3325 9.307121 CTCGAAGTTTGTAACAATGAGATCTAT 57.693 33.333 0.00 0.00 31.04 1.98
2984 3329 8.798859 AGTTTGTAACAATGAGATCTATGCTT 57.201 30.769 0.00 0.00 0.00 3.91
3020 3365 2.076863 GTGGTCCTGGTTCTTGATTCG 58.923 52.381 0.00 0.00 0.00 3.34
3027 3372 1.202879 TGGTTCTTGATTCGTTGGGCT 60.203 47.619 0.00 0.00 0.00 5.19
3028 3373 1.886542 GGTTCTTGATTCGTTGGGCTT 59.113 47.619 0.00 0.00 0.00 4.35
3036 3381 5.560966 TGATTCGTTGGGCTTATCTTTTC 57.439 39.130 0.00 0.00 0.00 2.29
3062 3407 6.263617 TGTTTTCTACTACAATTCCCAACACC 59.736 38.462 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
308 313 1.228429 CCCCCAAACGCTCAGGAAA 60.228 57.895 0.00 0.00 0.00 3.13
683 714 2.354704 CCAGTGTGTCGTCCATGGTAAT 60.355 50.000 12.58 0.00 0.00 1.89
1642 1882 2.943690 CGAGAGGACAACGAGATCCTTA 59.056 50.000 7.39 0.00 45.74 2.69
2092 2338 7.123830 CCTTACAACAACTAAGAAACAACGAG 58.876 38.462 0.00 0.00 0.00 4.18
2362 2666 2.793278 AACTGGTTTCGAAACATGGC 57.207 45.000 34.79 21.38 40.63 4.40
2514 2854 4.228824 TCTAAGTAAGGGTGGACAACTGT 58.771 43.478 0.00 0.00 0.00 3.55
2519 2859 5.046591 CACAATCTCTAAGTAAGGGTGGACA 60.047 44.000 0.00 0.00 0.00 4.02
2605 2946 4.101448 CCTCCCTCCCTTGCGGTG 62.101 72.222 0.00 0.00 0.00 4.94
2682 3027 2.034053 CGAGAACATCTGTCTCTAGGGC 59.966 54.545 0.00 0.00 0.00 5.19
2683 3028 3.066064 CACGAGAACATCTGTCTCTAGGG 59.934 52.174 0.00 0.00 0.00 3.53
2727 3072 6.553852 ACACTTTTTCTGGAGTAGAACTAGGA 59.446 38.462 0.00 0.00 44.84 2.94
2728 3073 6.647067 CACACTTTTTCTGGAGTAGAACTAGG 59.353 42.308 0.00 0.00 44.84 3.02
2757 3102 0.809241 GGAGAAGCAGCCTCACGATG 60.809 60.000 0.00 0.00 32.48 3.84
2813 3158 5.907197 CCAACGATATGGTAGTGATTCAC 57.093 43.478 8.82 8.82 35.65 3.18
2984 3329 6.070596 CCAGGACCACTATGAAGATGCATATA 60.071 42.308 0.00 0.00 30.90 0.86
3003 3348 2.484264 CCAACGAATCAAGAACCAGGAC 59.516 50.000 0.00 0.00 0.00 3.85
3020 3365 6.749139 AGAAAACAGAAAAGATAAGCCCAAC 58.251 36.000 0.00 0.00 0.00 3.77
3036 3381 7.360361 GTGTTGGGAATTGTAGTAGAAAACAG 58.640 38.462 0.00 0.00 0.00 3.16
3062 3407 0.099791 AGTTTTTGCCGACAACACCG 59.900 50.000 0.00 0.00 34.87 4.94


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

AutoCloner maintained by Alex Coulton.