Multiple sequence alignment - TraesCS2A01G277800

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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 TraesCS2A01G277800 chr2A 100.000 2367 0 0 1 2367 460473683 460471317 0.000000e+00 4372
1 TraesCS2A01G277800 chr2A 96.073 2368 89 4 1 2367 299510925 299508561 0.000000e+00 3855
2 TraesCS2A01G277800 chr5D 96.447 2111 71 3 258 2367 489744915 489742808 0.000000e+00 3480
3 TraesCS2A01G277800 chr5D 95.865 266 11 0 1 266 489746013 489745748 4.670000e-117 431
4 TraesCS2A01G277800 chr2D 95.358 2111 82 2 258 2367 232180210 232178115 0.000000e+00 3341
5 TraesCS2A01G277800 chr4D 95.263 2111 95 5 258 2367 200715519 200713413 0.000000e+00 3339
6 TraesCS2A01G277800 chr4D 95.113 266 13 0 1 266 200716613 200716348 1.010000e-113 420
7 TraesCS2A01G277800 chr3D 94.794 2113 88 6 260 2367 497288667 497290762 0.000000e+00 3273
8 TraesCS2A01G277800 chr3D 95.708 1398 60 0 970 2367 172531322 172529925 0.000000e+00 2250
9 TraesCS2A01G277800 chr3D 94.558 441 20 4 423 860 71520939 71520500 0.000000e+00 678
10 TraesCS2A01G277800 chr3D 95.113 266 13 0 1 266 497287569 497287834 1.010000e-113 420
11 TraesCS2A01G277800 chr7B 94.600 2111 107 2 258 2367 193200829 193202933 0.000000e+00 3260
12 TraesCS2A01G277800 chr7B 95.489 266 12 0 1 266 193199734 193199999 2.170000e-115 425
13 TraesCS2A01G277800 chr6D 92.937 1968 117 8 421 2367 219292803 219290837 0.000000e+00 2844
14 TraesCS2A01G277800 chr7D 91.981 1509 120 1 860 2367 72785637 72787145 0.000000e+00 2115
15 TraesCS2A01G277800 chr7A 90.486 1398 84 23 421 1795 540916366 540917737 0.000000e+00 1799
16 TraesCS2A01G277800 chr4B 96.241 266 10 0 1 266 614205672 614205407 1.000000e-118 436
17 TraesCS2A01G277800 chr4B 91.270 126 11 0 298 423 213964789 213964914 3.130000e-39 172
18 TraesCS2A01G277800 chr1B 96.169 261 10 0 6 266 34738269 34738009 6.050000e-116 427
19 TraesCS2A01G277800 chrUn 95.489 266 12 0 1 266 168654174 168654439 2.170000e-115 425
20 TraesCS2A01G277800 chr4A 95.489 266 12 0 1 266 706767229 706767494 2.170000e-115 425


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 TraesCS2A01G277800 chr2A 460471317 460473683 2366 True 4372.0 4372 100.0000 1 2367 1 chr2A.!!$R2 2366
1 TraesCS2A01G277800 chr2A 299508561 299510925 2364 True 3855.0 3855 96.0730 1 2367 1 chr2A.!!$R1 2366
2 TraesCS2A01G277800 chr5D 489742808 489746013 3205 True 1955.5 3480 96.1560 1 2367 2 chr5D.!!$R1 2366
3 TraesCS2A01G277800 chr2D 232178115 232180210 2095 True 3341.0 3341 95.3580 258 2367 1 chr2D.!!$R1 2109
4 TraesCS2A01G277800 chr4D 200713413 200716613 3200 True 1879.5 3339 95.1880 1 2367 2 chr4D.!!$R1 2366
5 TraesCS2A01G277800 chr3D 172529925 172531322 1397 True 2250.0 2250 95.7080 970 2367 1 chr3D.!!$R2 1397
6 TraesCS2A01G277800 chr3D 497287569 497290762 3193 False 1846.5 3273 94.9535 1 2367 2 chr3D.!!$F1 2366
7 TraesCS2A01G277800 chr7B 193199734 193202933 3199 False 1842.5 3260 95.0445 1 2367 2 chr7B.!!$F1 2366
8 TraesCS2A01G277800 chr6D 219290837 219292803 1966 True 2844.0 2844 92.9370 421 2367 1 chr6D.!!$R1 1946
9 TraesCS2A01G277800 chr7D 72785637 72787145 1508 False 2115.0 2115 91.9810 860 2367 1 chr7D.!!$F1 1507
10 TraesCS2A01G277800 chr7A 540916366 540917737 1371 False 1799.0 1799 90.4860 421 1795 1 chr7A.!!$F1 1374

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
544 1389 0.537188 CTGTCCTATGCCGTGTCCTT 59.463 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2978 1.003003 TGCCATTGAACATCAGTCCGA 59.997 47.619 0.0 0.0 0.0 4.55 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
38 39 1.896220 ACGTGAAATCTGTGCCACAT 58.104 45.000 0.00 0.00 0.00 3.21
55 56 2.916716 CACATAGTTTGCGTTTGGATGC 59.083 45.455 0.00 0.00 38.31 3.91
256 257 0.952984 GTTCCACTCACAGCCTCAGC 60.953 60.000 0.00 0.00 40.32 4.26
504 1349 3.857157 AGCTCTAACAACCCAGTTCAA 57.143 42.857 0.00 0.00 33.07 2.69
544 1389 0.537188 CTGTCCTATGCCGTGTCCTT 59.463 55.000 0.00 0.00 0.00 3.36
795 1641 6.246420 GTGTTAGTCACAATGATCAGCTTT 57.754 37.500 0.09 0.00 45.51 3.51
959 1850 3.369175 TCTCTCTATCTTTCTGCAGGCA 58.631 45.455 15.13 0.00 0.00 4.75
1011 1902 1.208776 CACTGGAGCATGGATCAGACA 59.791 52.381 0.00 0.00 0.00 3.41
1179 2070 2.483714 GCGTTCTGGCCTGATTGATCTA 60.484 50.000 13.72 0.00 0.00 1.98
1184 2075 6.517362 CGTTCTGGCCTGATTGATCTATTCTA 60.517 42.308 13.72 0.00 0.00 2.10
1245 2136 0.179129 CGATGCTCATTTTGGGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
1297 2188 5.241949 GGAGTACGACATGATCCAGAACTAT 59.758 44.000 0.00 0.00 0.00 2.12
1380 2271 0.750850 GCTTAGGTATCTGCCCGTGA 59.249 55.000 0.00 0.00 0.00 4.35
1488 2379 5.253330 GTGTGTGGGGATTCAATCTAGAAA 58.747 41.667 0.00 0.00 0.00 2.52
1556 2447 9.076596 GTGATTTGATAACTGACTAAATTTGCC 57.923 33.333 0.00 0.00 0.00 4.52
1598 2489 4.800993 GCTCATTGCTGTGTACAGTACTAG 59.199 45.833 12.07 10.77 45.45 2.57
1637 2528 7.106439 TGTCTTGTTTCCACACAACATTAAT 57.894 32.000 0.00 0.00 34.13 1.40
2096 2988 5.430886 TCATCAACAATGATTCGGACTGAT 58.569 37.500 0.00 0.00 43.89 2.90
2103 2997 5.649395 ACAATGATTCGGACTGATGTTCAAT 59.351 36.000 0.00 0.00 0.00 2.57
2104 2998 5.746307 ATGATTCGGACTGATGTTCAATG 57.254 39.130 0.00 0.00 0.00 2.82
2120 3014 4.833811 TGGCAGAACCATCGATCG 57.166 55.556 9.36 9.36 46.36 3.69
2137 3031 5.224135 TCGATCGTATCAACACAAAGTCAA 58.776 37.500 15.94 0.00 0.00 3.18
2183 3077 2.154567 AAGGGCATGATGCTTGATGT 57.845 45.000 17.84 0.00 44.28 3.06
2310 3204 5.302568 TCAAATGGAACTTTGATCTGCTGTT 59.697 36.000 0.00 0.00 39.55 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.499197 TCAGCATCCAAACGCAAACTA 58.501 42.857 0.00 0.00 0.00 2.24
55 56 8.037382 TCAGCTACTTTCAGAAATCAAATCAG 57.963 34.615 0.00 0.00 0.00 2.90
504 1349 4.821805 CAGGCCACTCCGTAATTGAAATAT 59.178 41.667 5.01 0.00 40.77 1.28
1011 1902 2.373707 GGAGCTCCACCTCCTGCAT 61.374 63.158 28.43 0.00 46.39 3.96
1202 2093 0.750911 GCAGCCATCTAAGCCAAGCT 60.751 55.000 0.00 0.00 42.56 3.74
1245 2136 2.919229 GCATCGAAATTCACCTGCAAAG 59.081 45.455 0.00 0.00 0.00 2.77
1380 2271 7.172868 TGCAAGACACAATCATGGATAAATT 57.827 32.000 0.00 0.00 0.00 1.82
1488 2379 4.261322 GCTGACATCAATCACACACAACTT 60.261 41.667 0.00 0.00 0.00 2.66
1556 2447 6.367686 TGAGCATAACTTCAATACTGCATG 57.632 37.500 0.00 0.00 32.18 4.06
1637 2528 7.667043 ACATTCAAAAAGCACGACTCTAATA 57.333 32.000 0.00 0.00 0.00 0.98
1770 2661 3.438087 CGATTGAAACCAATCAGAGCAGT 59.562 43.478 15.64 0.00 46.31 4.40
1800 2691 4.403752 TGATACTCAGAGTGTTGGATGAGG 59.596 45.833 13.84 0.00 42.76 3.86
2014 2905 4.510711 CCATGCAAAATGTTACACAAGCAA 59.489 37.500 7.45 0.00 32.55 3.91
2087 2978 1.003003 TGCCATTGAACATCAGTCCGA 59.997 47.619 0.00 0.00 0.00 4.55
2104 2998 2.288213 TGATACGATCGATGGTTCTGCC 60.288 50.000 24.34 4.77 37.90 4.85
2120 3014 8.774586 AGAACATACTTGACTTTGTGTTGATAC 58.225 33.333 0.00 0.00 30.70 2.24
2137 3031 7.047891 TCTGTTCAACAAGACAAGAACATACT 58.952 34.615 7.22 0.00 46.26 2.12


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

AutoCloner maintained by Alex Coulton.