Multiple sequence alignment - TraesCS2D01G141700

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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 TraesCS2D01G141700 chr2D 100.000 3668 0 0 1 3668 83223892 83227559 0.000000e+00 6774.0
1 TraesCS2D01G141700 chr2D 95.903 2685 78 16 1005 3668 83188077 83190750 0.000000e+00 4320.0
2 TraesCS2D01G141700 chr2D 91.878 1970 97 28 1235 3176 83529823 83531757 0.000000e+00 2693.0
3 TraesCS2D01G141700 chr2D 87.802 2279 162 48 1005 3251 127821683 127819489 0.000000e+00 2562.0
4 TraesCS2D01G141700 chr2D 94.215 363 17 3 2 363 83187726 83188085 5.350000e-153 551.0
5 TraesCS2D01G141700 chr2B 95.522 2367 59 17 1180 3517 135197899 135200247 0.000000e+00 3740.0
6 TraesCS2D01G141700 chr2B 92.712 2511 112 28 1180 3656 182153466 182150993 0.000000e+00 3557.0
7 TraesCS2D01G141700 chr2B 93.178 2448 114 24 1161 3580 135357799 135360221 0.000000e+00 3546.0
8 TraesCS2D01G141700 chr2B 93.780 2283 76 34 1019 3268 135463364 135465613 0.000000e+00 3369.0
9 TraesCS2D01G141700 chr2B 91.637 2212 93 47 1083 3270 135126478 135128621 0.000000e+00 2976.0
10 TraesCS2D01G141700 chr2B 89.486 1750 136 19 1300 3034 137814521 137812805 0.000000e+00 2169.0
11 TraesCS2D01G141700 chr2B 90.000 1710 124 24 1340 3034 137349321 137347644 0.000000e+00 2167.0
12 TraesCS2D01G141700 chr2B 93.436 259 17 0 3325 3583 135515489 135515747 5.750000e-103 385.0
13 TraesCS2D01G141700 chr2B 93.333 120 7 1 2 120 135463199 135463318 3.760000e-40 176.0
14 TraesCS2D01G141700 chr2B 97.059 102 2 1 3567 3668 135360240 135360340 1.750000e-38 171.0
15 TraesCS2D01G141700 chr2B 95.506 89 3 1 3580 3668 135215106 135215193 1.370000e-29 141.0
16 TraesCS2D01G141700 chr2B 95.506 89 3 1 3580 3668 135515931 135516018 1.370000e-29 141.0
17 TraesCS2D01G141700 chr2B 82.781 151 17 3 1083 1233 135238829 135238970 3.850000e-25 126.0
18 TraesCS2D01G141700 chr2A 91.987 2371 99 27 1007 3357 83984703 83987002 0.000000e+00 3241.0
19 TraesCS2D01G141700 chr2A 87.240 2359 193 54 1005 3328 134867797 134865512 0.000000e+00 2590.0
20 TraesCS2D01G141700 chr2A 87.654 2195 157 49 1098 3270 83989925 83992027 0.000000e+00 2447.0
21 TraesCS2D01G141700 chr2A 87.150 2140 139 51 1166 3268 84143486 84145526 0.000000e+00 2303.0
22 TraesCS2D01G141700 chr2A 92.012 651 46 2 362 1008 451547151 451547799 0.000000e+00 909.0
23 TraesCS2D01G141700 chr2A 93.798 258 16 0 3309 3566 83992267 83992524 4.440000e-104 388.0
24 TraesCS2D01G141700 chr2A 93.436 259 12 2 3398 3656 83987003 83987256 2.670000e-101 379.0
25 TraesCS2D01G141700 chr2A 90.226 266 24 2 99 363 83984445 83984709 2.710000e-91 346.0
26 TraesCS2D01G141700 chr2A 91.176 102 8 1 2 103 83959099 83959199 1.780000e-28 137.0
27 TraesCS2D01G141700 chr2A 82.911 158 15 5 1083 1237 84012618 84012766 8.260000e-27 132.0
28 TraesCS2D01G141700 chr2A 96.875 32 1 0 326 357 755745421 755745452 2.000000e-03 54.7
29 TraesCS2D01G141700 chrUn 99.826 1728 2 1 1 1727 362505107 362506834 0.000000e+00 3173.0
30 TraesCS2D01G141700 chrUn 100.000 996 0 0 1 996 333571028 333572023 0.000000e+00 1840.0
31 TraesCS2D01G141700 chrUn 91.600 881 47 12 2801 3668 25418011 25417145 0.000000e+00 1192.0
32 TraesCS2D01G141700 chrUn 89.650 657 53 8 362 1011 91182125 91181477 0.000000e+00 822.0
33 TraesCS2D01G141700 chr5A 90.235 2130 124 41 1076 3191 326438158 326436099 0.000000e+00 2704.0
34 TraesCS2D01G141700 chr7D 89.650 657 53 8 362 1011 63272122 63272770 0.000000e+00 822.0
35 TraesCS2D01G141700 chr4A 87.596 653 71 6 363 1008 66601857 66602506 0.000000e+00 749.0
36 TraesCS2D01G141700 chr1A 87.031 640 76 3 374 1008 25557690 25558327 0.000000e+00 715.0
37 TraesCS2D01G141700 chr1A 85.276 652 87 7 363 1008 169472330 169472978 0.000000e+00 664.0
38 TraesCS2D01G141700 chr3B 83.739 658 93 10 358 1008 786840960 786841610 8.710000e-171 610.0
39 TraesCS2D01G141700 chr3B 82.774 656 104 8 358 1008 455499207 455498556 8.830000e-161 577.0
40 TraesCS2D01G141700 chr3B 96.875 32 1 0 326 357 10210344 10210313 2.000000e-03 54.7
41 TraesCS2D01G141700 chr3D 83.587 658 96 9 358 1008 90167461 90168113 1.130000e-169 606.0
42 TraesCS2D01G141700 chr6D 85.283 530 72 3 359 884 472146398 472146925 3.220000e-150 542.0
43 TraesCS2D01G141700 chr6A 96.875 32 1 0 326 357 68141640 68141671 2.000000e-03 54.7
44 TraesCS2D01G141700 chr5B 90.476 42 3 1 317 357 269985330 269985289 2.000000e-03 54.7
45 TraesCS2D01G141700 chr1B 100.000 28 0 0 330 357 89507787 89507814 7.000000e-03 52.8


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 TraesCS2D01G141700 chr2D 83223892 83227559 3667 False 6774.0 6774 100.0000 1 3668 1 chr2D.!!$F1 3667
1 TraesCS2D01G141700 chr2D 83529823 83531757 1934 False 2693.0 2693 91.8780 1235 3176 1 chr2D.!!$F2 1941
2 TraesCS2D01G141700 chr2D 127819489 127821683 2194 True 2562.0 2562 87.8020 1005 3251 1 chr2D.!!$R1 2246
3 TraesCS2D01G141700 chr2D 83187726 83190750 3024 False 2435.5 4320 95.0590 2 3668 2 chr2D.!!$F3 3666
4 TraesCS2D01G141700 chr2B 135197899 135200247 2348 False 3740.0 3740 95.5220 1180 3517 1 chr2B.!!$F2 2337
5 TraesCS2D01G141700 chr2B 182150993 182153466 2473 True 3557.0 3557 92.7120 1180 3656 1 chr2B.!!$R3 2476
6 TraesCS2D01G141700 chr2B 135126478 135128621 2143 False 2976.0 2976 91.6370 1083 3270 1 chr2B.!!$F1 2187
7 TraesCS2D01G141700 chr2B 137812805 137814521 1716 True 2169.0 2169 89.4860 1300 3034 1 chr2B.!!$R2 1734
8 TraesCS2D01G141700 chr2B 137347644 137349321 1677 True 2167.0 2167 90.0000 1340 3034 1 chr2B.!!$R1 1694
9 TraesCS2D01G141700 chr2B 135357799 135360340 2541 False 1858.5 3546 95.1185 1161 3668 2 chr2B.!!$F5 2507
10 TraesCS2D01G141700 chr2B 135463199 135465613 2414 False 1772.5 3369 93.5565 2 3268 2 chr2B.!!$F6 3266
11 TraesCS2D01G141700 chr2B 135515489 135516018 529 False 263.0 385 94.4710 3325 3668 2 chr2B.!!$F7 343
12 TraesCS2D01G141700 chr2A 134865512 134867797 2285 True 2590.0 2590 87.2400 1005 3328 1 chr2A.!!$R1 2323
13 TraesCS2D01G141700 chr2A 84143486 84145526 2040 False 2303.0 2303 87.1500 1166 3268 1 chr2A.!!$F3 2102
14 TraesCS2D01G141700 chr2A 83984445 83992524 8079 False 1360.2 3241 91.4202 99 3656 5 chr2A.!!$F6 3557
15 TraesCS2D01G141700 chr2A 451547151 451547799 648 False 909.0 909 92.0120 362 1008 1 chr2A.!!$F4 646
16 TraesCS2D01G141700 chrUn 362505107 362506834 1727 False 3173.0 3173 99.8260 1 1727 1 chrUn.!!$F2 1726
17 TraesCS2D01G141700 chrUn 333571028 333572023 995 False 1840.0 1840 100.0000 1 996 1 chrUn.!!$F1 995
18 TraesCS2D01G141700 chrUn 25417145 25418011 866 True 1192.0 1192 91.6000 2801 3668 1 chrUn.!!$R1 867
19 TraesCS2D01G141700 chrUn 91181477 91182125 648 True 822.0 822 89.6500 362 1011 1 chrUn.!!$R2 649
20 TraesCS2D01G141700 chr5A 326436099 326438158 2059 True 2704.0 2704 90.2350 1076 3191 1 chr5A.!!$R1 2115
21 TraesCS2D01G141700 chr7D 63272122 63272770 648 False 822.0 822 89.6500 362 1011 1 chr7D.!!$F1 649
22 TraesCS2D01G141700 chr4A 66601857 66602506 649 False 749.0 749 87.5960 363 1008 1 chr4A.!!$F1 645
23 TraesCS2D01G141700 chr1A 25557690 25558327 637 False 715.0 715 87.0310 374 1008 1 chr1A.!!$F1 634
24 TraesCS2D01G141700 chr1A 169472330 169472978 648 False 664.0 664 85.2760 363 1008 1 chr1A.!!$F2 645
25 TraesCS2D01G141700 chr3B 786840960 786841610 650 False 610.0 610 83.7390 358 1008 1 chr3B.!!$F1 650
26 TraesCS2D01G141700 chr3B 455498556 455499207 651 True 577.0 577 82.7740 358 1008 1 chr3B.!!$R2 650
27 TraesCS2D01G141700 chr3D 90167461 90168113 652 False 606.0 606 83.5870 358 1008 1 chr3D.!!$F1 650
28 TraesCS2D01G141700 chr6D 472146398 472146925 527 False 542.0 542 85.2830 359 884 1 chr6D.!!$F1 525

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
2397 2710 1.521681 GGCTGCGTCCAGTGGTATC 60.522 63.158 9.54 0.53 41.26 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3637 9552 5.059833 GGTCCAGAATATGAATCACCTGAC 58.94 45.833 0.0 0.0 0.0 3.51 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
2397 2710 1.521681 GGCTGCGTCCAGTGGTATC 60.522 63.158 9.54 0.53 41.26 2.24
2538 2852 9.590451 CCCGTTCAGTCATTAGTAATTTTACTA 57.410 33.333 6.17 6.17 43.36 1.82
2698 3018 7.709149 AAGTAAAGCAGATGAGCCTAAAAAT 57.291 32.000 0.00 0.00 34.23 1.82
2699 3019 7.709149 AGTAAAGCAGATGAGCCTAAAAATT 57.291 32.000 0.00 0.00 34.23 1.82
2754 3074 3.416382 TAAAACGCACTCGCCGCC 61.416 61.111 0.00 0.00 39.84 6.13
3219 8682 2.316792 GTACGATCCGATGGATTCACG 58.683 52.381 0.00 2.19 43.27 4.35
3270 8735 1.806758 GCGCATGGACATGTTTGGC 60.807 57.895 13.29 1.13 40.80 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1753 1806 3.621805 TGGCGGCGGAGTTCTTGA 61.622 61.111 9.78 0.00 0.00 3.02
2397 2710 2.474410 AAAAGACTAGGGAAGGCGTG 57.526 50.000 0.00 0.00 38.81 5.34
2538 2852 1.202989 TGGAGACTCTGCTGACACTCT 60.203 52.381 16.11 6.41 0.00 3.24
2539 2853 1.252175 TGGAGACTCTGCTGACACTC 58.748 55.000 1.74 11.30 0.00 3.51
2675 2991 7.709149 AATTTTTAGGCTCATCTGCTTTACT 57.291 32.000 0.00 0.00 0.00 2.24
2698 3018 5.123186 CCGGAATTGCAGTACATGAGTTTAA 59.877 40.000 0.00 0.00 0.00 1.52
2699 3019 4.634004 CCGGAATTGCAGTACATGAGTTTA 59.366 41.667 0.00 0.00 0.00 2.01
2754 3074 2.095819 GCAAACGGGCATTTTGGATTTG 60.096 45.455 10.86 0.00 34.97 2.32
3270 8735 5.462398 GCTGTATCTGTAACCATAAACTCCG 59.538 44.000 0.00 0.00 0.00 4.63
3637 9552 5.059833 GGTCCAGAATATGAATCACCTGAC 58.940 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.