Multiple sequence alignment - TraesCS2D01G251200

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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 TraesCS2D01G251200 chr2D 100.000 4056 0 0 1 4056 299893082 299897137 0.000000e+00 7491.0
1 TraesCS2D01G251200 chr2D 95.349 43 2 0 3649 3691 360992170 360992128 7.270000e-08 69.4
2 TraesCS2D01G251200 chr2A 94.368 1900 61 12 2166 4056 376107458 376109320 0.000000e+00 2874.0
3 TraesCS2D01G251200 chr2A 95.062 972 34 6 865 1833 376100283 376101243 0.000000e+00 1517.0
4 TraesCS2D01G251200 chr2A 96.404 862 19 6 1 852 376085885 376086744 0.000000e+00 1410.0
5 TraesCS2D01G251200 chr2A 97.347 377 10 0 1794 2170 376101244 376101620 3.420000e-180 641.0
6 TraesCS2D01G251200 chr2A 84.305 223 20 9 3284 3502 279056371 279056160 1.910000e-48 204.0
7 TraesCS2D01G251200 chr2A 79.545 176 20 11 3277 3448 510852781 510852944 1.190000e-20 111.0
8 TraesCS2D01G251200 chr2A 95.238 42 2 0 3650 3691 315809755 315809796 2.620000e-07 67.6
9 TraesCS2D01G251200 chr2B 94.937 1659 39 11 2404 4056 371159706 371158087 0.000000e+00 2556.0
10 TraesCS2D01G251200 chr2B 94.099 949 25 5 1 926 371162319 371161379 0.000000e+00 1413.0
11 TraesCS2D01G251200 chr2B 96.395 860 14 7 914 1767 371161351 371160503 0.000000e+00 1400.0
12 TraesCS2D01G251200 chr2B 88.235 221 19 7 1787 2004 371160515 371160299 1.450000e-64 257.0
13 TraesCS2D01G251200 chr1B 88.424 311 27 3 1500 1809 27303090 27302788 2.300000e-97 366.0
14 TraesCS2D01G251200 chr1B 97.674 43 1 0 3649 3691 547029458 547029500 1.560000e-09 75.0
15 TraesCS2D01G251200 chr7A 84.581 227 21 10 3284 3506 204737001 204736785 3.180000e-51 213.0
16 TraesCS2D01G251200 chr7A 82.143 224 32 7 3284 3503 19184064 19184283 6.920000e-43 185.0
17 TraesCS2D01G251200 chr7A 82.143 224 26 10 3284 3503 221262320 221262533 3.220000e-41 180.0
18 TraesCS2D01G251200 chr5A 84.821 224 20 7 3284 3503 210535438 210535651 3.180000e-51 213.0
19 TraesCS2D01G251200 chr5A 85.388 219 17 9 3287 3501 444536674 444536881 3.180000e-51 213.0
20 TraesCS2D01G251200 chr5A 93.333 45 3 0 3647 3691 78965458 78965502 2.620000e-07 67.6
21 TraesCS2D01G251200 chr5D 84.375 224 21 7 3284 3503 201312019 201312232 1.480000e-49 207.0
22 TraesCS2D01G251200 chr6A 83.482 224 20 10 3284 3502 475431182 475430971 4.140000e-45 193.0
23 TraesCS2D01G251200 chr6A 83.036 224 24 10 3284 3503 504475793 504476006 1.490000e-44 191.0
24 TraesCS2D01G251200 chr3B 80.269 223 32 8 3277 3497 95465450 95465238 1.510000e-34 158.0
25 TraesCS2D01G251200 chr1A 87.050 139 14 2 1487 1625 20700149 20700283 1.950000e-33 154.0
26 TraesCS2D01G251200 chr1A 100.000 32 0 0 3250 3281 117215119 117215150 4.380000e-05 60.2
27 TraesCS2D01G251200 chr6D 79.911 224 30 11 3284 3503 461683525 461683313 2.530000e-32 150.0
28 TraesCS2D01G251200 chr6D 100.000 32 0 0 3250 3281 388956975 388957006 4.380000e-05 60.2
29 TraesCS2D01G251200 chr5B 95.349 43 2 0 3649 3691 81370553 81370511 7.270000e-08 69.4
30 TraesCS2D01G251200 chr4B 95.349 43 2 0 3649 3691 483511809 483511767 7.270000e-08 69.4
31 TraesCS2D01G251200 chr1D 93.023 43 3 0 3649 3691 274943927 274943969 3.380000e-06 63.9
32 TraesCS2D01G251200 chr3D 97.143 35 1 0 3250 3284 522131294 522131260 4.380000e-05 60.2
33 TraesCS2D01G251200 chr3D 94.444 36 2 0 3246 3281 286670406 286670441 5.660000e-04 56.5
34 TraesCS2D01G251200 chr3A 94.737 38 2 0 3246 3283 374672458 374672495 4.380000e-05 60.2
35 TraesCS2D01G251200 chr6B 97.059 34 1 0 3247 3280 691795853 691795886 1.570000e-04 58.4
36 TraesCS2D01G251200 chr4D 100.000 31 0 0 3250 3280 111553975 111554005 1.570000e-04 58.4


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 TraesCS2D01G251200 chr2D 299893082 299897137 4055 False 7491.0 7491 100.0000 1 4056 1 chr2D.!!$F1 4055
1 TraesCS2D01G251200 chr2A 376107458 376109320 1862 False 2874.0 2874 94.3680 2166 4056 1 chr2A.!!$F3 1890
2 TraesCS2D01G251200 chr2A 376085885 376086744 859 False 1410.0 1410 96.4040 1 852 1 chr2A.!!$F2 851
3 TraesCS2D01G251200 chr2A 376100283 376101620 1337 False 1079.0 1517 96.2045 865 2170 2 chr2A.!!$F5 1305
4 TraesCS2D01G251200 chr2B 371158087 371162319 4232 True 1406.5 2556 93.4165 1 4056 4 chr2B.!!$R1 4055

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
858 885 0.182775 GATTGGGCCGTTATGGGTCT 59.817 55.0 0.00 0.00 38.63 3.85 F
1570 1643 0.249911 AGCTCACCAACAGGTTCGTC 60.250 55.0 0.00 0.00 31.84 4.20 F
2397 2855 0.403271 AGATGGTTGCAGCCTGTCTT 59.597 50.0 21.11 6.46 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2343 0.604073 CAAACATCATGGTGCAGGCA 59.396 50.0 5.69 0.0 0.00 4.75 R
2400 2858 0.814457 AACAAGGCACAACGCTGAAA 59.186 45.0 0.00 0.0 41.91 2.69 R
4016 4486 0.179081 GGGTGAAGGGATGCTACGTC 60.179 60.0 0.00 0.0 0.00 4.34 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
216 217 1.150567 CGATCTCAAGCGCTTCCCTG 61.151 60.000 22.21 10.48 0.00 4.45
538 540 1.512201 TACGGGTGGAGGGAGAAGGA 61.512 60.000 0.00 0.00 0.00 3.36
623 625 1.346068 AGAGGGTGAGCAGTCAGTTTC 59.654 52.381 0.00 0.00 31.53 2.78
683 688 1.822506 GGGAGAGCAGGTGGTTTTAC 58.177 55.000 0.00 0.00 0.00 2.01
687 692 3.067833 GAGAGCAGGTGGTTTTACTGTC 58.932 50.000 0.00 0.00 34.79 3.51
699 707 6.544931 GTGGTTTTACTGTCTTCTTTTAGGGT 59.455 38.462 0.00 0.00 0.00 4.34
858 885 0.182775 GATTGGGCCGTTATGGGTCT 59.817 55.000 0.00 0.00 38.63 3.85
859 886 0.629058 ATTGGGCCGTTATGGGTCTT 59.371 50.000 0.00 0.00 38.63 3.01
860 887 0.322997 TTGGGCCGTTATGGGTCTTG 60.323 55.000 0.00 0.00 38.63 3.02
861 888 1.301954 GGGCCGTTATGGGTCTTGT 59.698 57.895 0.00 0.00 38.63 3.16
862 889 0.542805 GGGCCGTTATGGGTCTTGTA 59.457 55.000 0.00 0.00 38.63 2.41
863 890 1.660167 GGCCGTTATGGGTCTTGTAC 58.340 55.000 0.00 0.00 38.63 2.90
935 1004 1.407618 CGACGACCCATCATAAGTCCA 59.592 52.381 0.00 0.00 0.00 4.02
942 1011 3.117512 ACCCATCATAAGTCCAATGGTCC 60.118 47.826 0.00 0.00 37.54 4.46
1318 1391 1.949631 GAGGTATTTCGGCTCCGCG 60.950 63.158 0.00 0.00 39.59 6.46
1319 1392 2.105528 GGTATTTCGGCTCCGCGA 59.894 61.111 8.23 0.00 39.59 5.87
1320 1393 2.235699 GGTATTTCGGCTCCGCGAC 61.236 63.158 8.23 0.00 39.59 5.19
1321 1394 1.226888 GTATTTCGGCTCCGCGACT 60.227 57.895 8.23 0.00 39.59 4.18
1322 1395 1.065273 TATTTCGGCTCCGCGACTC 59.935 57.895 8.23 0.00 39.59 3.36
1323 1396 2.345880 TATTTCGGCTCCGCGACTCC 62.346 60.000 8.23 3.78 39.59 3.85
1570 1643 0.249911 AGCTCACCAACAGGTTCGTC 60.250 55.000 0.00 0.00 31.84 4.20
2094 2209 5.160641 GGCAGAAATTTAAAAGCGATGACA 58.839 37.500 0.00 0.00 0.00 3.58
2251 2366 3.305950 GCCTGCACCATGATGTTTGTAAA 60.306 43.478 0.00 0.00 0.00 2.01
2309 2425 3.027974 ACCTACTTTTCTGTCTCGTGC 57.972 47.619 0.00 0.00 0.00 5.34
2396 2854 1.065854 GTAGATGGTTGCAGCCTGTCT 60.066 52.381 23.61 23.61 0.00 3.41
2397 2855 0.403271 AGATGGTTGCAGCCTGTCTT 59.597 50.000 21.11 6.46 0.00 3.01
2398 2856 0.807496 GATGGTTGCAGCCTGTCTTC 59.193 55.000 21.11 6.28 0.00 2.87
2399 2857 0.111061 ATGGTTGCAGCCTGTCTTCA 59.889 50.000 21.11 0.00 0.00 3.02
2400 2858 0.111061 TGGTTGCAGCCTGTCTTCAT 59.889 50.000 21.11 0.00 0.00 2.57
2422 2880 2.103934 GCGTTGTGCCTTGTTGCA 59.896 55.556 0.00 0.00 39.37 4.08
2458 2916 6.096282 TGAATGTTGAGTAGATCGATACCACA 59.904 38.462 0.00 0.00 0.00 4.17
2465 2923 7.327975 TGAGTAGATCGATACCACAAAAATGT 58.672 34.615 0.00 0.00 0.00 2.71
2500 2958 4.414337 ACCTGATCTGAATAGGCTGTTC 57.586 45.455 16.16 16.16 34.93 3.18
2546 3004 4.608170 TGGCAATCTTATTTCCTTCCCT 57.392 40.909 0.00 0.00 0.00 4.20
2732 3190 2.664916 CTCCTGAATTTTGCAACCACG 58.335 47.619 0.00 0.00 0.00 4.94
3215 3673 6.073385 TCGTACGACACAGATATCTGATAACC 60.073 42.308 34.16 18.01 46.59 2.85
3220 3678 4.284490 ACACAGATATCTGATAACCGCCAT 59.716 41.667 34.16 9.23 46.59 4.40
3221 3679 5.221722 ACACAGATATCTGATAACCGCCATT 60.222 40.000 34.16 8.73 46.59 3.16
3346 3804 9.667989 TTCGATTGTTTGATTGCATTATATGAG 57.332 29.630 0.00 0.00 0.00 2.90
3347 3805 9.054922 TCGATTGTTTGATTGCATTATATGAGA 57.945 29.630 0.00 0.00 0.00 3.27
3348 3806 9.836076 CGATTGTTTGATTGCATTATATGAGAT 57.164 29.630 0.00 0.00 0.00 2.75
3540 3998 5.652452 GGAGCCCTTAGTGTTTGATGTAAAT 59.348 40.000 0.00 0.00 0.00 1.40
3731 4195 5.510520 GGATCTATCCATCTCCACAACACTC 60.511 48.000 4.04 0.00 46.38 3.51
3798 4268 0.391263 CCCTCGGACAGGTTACAAGC 60.391 60.000 0.00 0.00 41.51 4.01
3846 4316 5.625251 CAAGTTTGGAACATCAGATCGAAG 58.375 41.667 0.00 0.00 39.30 3.79
3992 4462 2.549778 GGTAGCAGGAGCATTGAGGATC 60.550 54.545 0.00 0.00 45.49 3.36
3993 4463 1.509373 AGCAGGAGCATTGAGGATCT 58.491 50.000 0.00 0.00 45.49 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 217 1.480789 GAGGGTCTCTGAAGGAGTCC 58.519 60.000 0.00 0.00 45.34 3.85
282 283 5.070001 TCCGGTTGATTTGTCTGAATTTCT 58.930 37.500 0.00 0.00 0.00 2.52
623 625 0.026803 GCGATTTGCTGCTCTTACCG 59.973 55.000 0.00 0.00 41.73 4.02
683 688 6.996282 TCACCTTTAACCCTAAAAGAAGACAG 59.004 38.462 0.00 0.00 36.27 3.51
687 692 6.655425 CCTCTCACCTTTAACCCTAAAAGAAG 59.345 42.308 0.00 0.00 36.27 2.85
699 707 2.234908 GCTCTGCTCCTCTCACCTTTAA 59.765 50.000 0.00 0.00 0.00 1.52
858 885 6.058833 TGTTTGGAAGTTATGCTGAGTACAA 58.941 36.000 0.00 0.00 0.00 2.41
859 886 5.616270 TGTTTGGAAGTTATGCTGAGTACA 58.384 37.500 0.00 0.00 0.00 2.90
860 887 5.701290 ACTGTTTGGAAGTTATGCTGAGTAC 59.299 40.000 0.00 0.00 0.00 2.73
861 888 5.865085 ACTGTTTGGAAGTTATGCTGAGTA 58.135 37.500 0.00 0.00 0.00 2.59
862 889 4.718961 ACTGTTTGGAAGTTATGCTGAGT 58.281 39.130 0.00 0.00 0.00 3.41
863 890 5.455392 CAACTGTTTGGAAGTTATGCTGAG 58.545 41.667 0.00 0.00 35.70 3.35
935 1004 1.302993 CGGTTTGGGTCGGACCATT 60.303 57.895 27.32 0.00 41.02 3.16
942 1011 1.076533 CGATGTCTCGGTTTGGGTCG 61.077 60.000 0.00 0.00 41.27 4.79
1238 1311 1.075600 CACTCCTCCTCCTCCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
2052 2167 2.752903 GCCAAAGGACACCAAATACGAT 59.247 45.455 0.00 0.00 0.00 3.73
2228 2343 0.604073 CAAACATCATGGTGCAGGCA 59.396 50.000 5.69 0.00 0.00 4.75
2251 2366 9.280174 TCCGAAAAATAACTTGAAATGTCTAGT 57.720 29.630 0.00 0.00 40.93 2.57
2287 2403 4.381718 GGCACGAGACAGAAAAGTAGGTAT 60.382 45.833 0.00 0.00 0.00 2.73
2396 2854 1.317613 AGGCACAACGCTGAAATGAA 58.682 45.000 0.00 0.00 41.91 2.57
2397 2855 1.001487 CAAGGCACAACGCTGAAATGA 60.001 47.619 0.00 0.00 41.91 2.57
2398 2856 1.269206 ACAAGGCACAACGCTGAAATG 60.269 47.619 0.00 0.00 41.91 2.32
2399 2857 1.032014 ACAAGGCACAACGCTGAAAT 58.968 45.000 0.00 0.00 41.91 2.17
2400 2858 0.814457 AACAAGGCACAACGCTGAAA 59.186 45.000 0.00 0.00 41.91 2.69
2449 2907 7.359595 TGAAGAGAAACATTTTTGTGGTATCG 58.640 34.615 0.00 0.00 0.00 2.92
2458 2916 9.354673 TCAGGTTAGATGAAGAGAAACATTTTT 57.645 29.630 0.00 0.00 0.00 1.94
2465 2923 7.724490 TCAGATCAGGTTAGATGAAGAGAAA 57.276 36.000 0.00 0.00 0.00 2.52
2546 3004 6.878923 CCATACCTGTAGAAATTTCTCACACA 59.121 38.462 23.70 19.94 38.70 3.72
3321 3779 9.054922 TCTCATATAATGCAATCAAACAATCGA 57.945 29.630 0.00 0.00 0.00 3.59
3322 3780 9.836076 ATCTCATATAATGCAATCAAACAATCG 57.164 29.630 0.00 0.00 0.00 3.34
3353 3811 6.317642 TCTTCGAAACAATCCTCTGTTTTTCA 59.682 34.615 0.00 0.00 46.84 2.69
3362 3820 5.924475 TCAAACTCTTCGAAACAATCCTC 57.076 39.130 0.00 0.00 0.00 3.71
3508 3966 4.178956 ACACTAAGGGCTCCTTCAAAAA 57.821 40.909 9.46 0.00 43.57 1.94
3511 3969 3.137544 TCAAACACTAAGGGCTCCTTCAA 59.862 43.478 9.46 0.00 43.57 2.69
3540 3998 9.322773 GATCATGAGAAGAATGATACTGTGAAA 57.677 33.333 0.09 0.00 43.25 2.69
3731 4195 2.292267 ACCTTCAACACTTGCTGTCTG 58.708 47.619 0.00 0.00 30.29 3.51
3798 4268 5.738370 CAACCGAATAAAAAGCTATCCTCG 58.262 41.667 0.00 0.00 0.00 4.63
3846 4316 2.880719 TAATGGCATGCGCGGTTTGC 62.881 55.000 12.44 13.85 39.92 3.68
4016 4486 0.179081 GGGTGAAGGGATGCTACGTC 60.179 60.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.