Multiple sequence alignment - TraesCS4A01G220800

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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 TraesCS4A01G220800 chr4A 100.000 3032 0 0 1 3032 525042352 525045383 0 5600
1 TraesCS4A01G220800 chr4B 93.654 3057 168 7 1 3032 243462774 243465829 0 4547
2 TraesCS4A01G220800 chr1A 93.495 3059 170 9 1 3032 224505639 224508695 0 4519
3 TraesCS4A01G220800 chr1A 86.817 1282 139 19 1771 3032 20747726 20746455 0 1404
4 TraesCS4A01G220800 chr7B 93.357 3056 176 10 1 3032 314049080 314052132 0 4494
5 TraesCS4A01G220800 chr7B 86.509 3091 326 45 1 3032 291042541 291045599 0 3314
6 TraesCS4A01G220800 chr6B 92.607 3057 189 9 1 3032 356664548 356661504 0 4359
7 TraesCS4A01G220800 chr3D 89.609 3070 262 25 2 3032 146108958 146105907 0 3849
8 TraesCS4A01G220800 chr3D 86.750 3102 334 46 1 3032 218446128 218449222 0 3380
9 TraesCS4A01G220800 chr4D 89.314 3060 273 22 2 3022 402743384 402746428 0 3790
10 TraesCS4A01G220800 chr5A 91.427 2368 180 13 1 2354 236984540 236982182 0 3227
11 TraesCS4A01G220800 chr5A 87.063 2458 244 45 639 3032 454838896 454841343 0 2710
12 TraesCS4A01G220800 chr7A 86.588 2453 262 38 639 3032 611096923 611094479 0 2645
13 TraesCS4A01G220800 chr6A 86.419 2452 271 36 639 3032 246843940 246841493 0 2627
14 TraesCS4A01G220800 chr6D 95.015 1364 59 7 1674 3032 183626035 183624676 0 2134
15 TraesCS4A01G220800 chr6D 94.270 1239 69 2 1 1237 183633445 183632207 0 1893
16 TraesCS4A01G220800 chr6D 87.574 1175 111 17 1886 3032 81901857 81900690 0 1328
17 TraesCS4A01G220800 chr2A 90.402 1094 88 6 1 1082 659575398 659574310 0 1423
18 TraesCS4A01G220800 chrUn 90.455 901 72 4 1 890 115365699 115366596 0 1175
19 TraesCS4A01G220800 chrUn 92.579 822 54 4 2215 3032 115393206 115394024 0 1173


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 TraesCS4A01G220800 chr4A 525042352 525045383 3031 False 5600 5600 100.000 1 3032 1 chr4A.!!$F1 3031
1 TraesCS4A01G220800 chr4B 243462774 243465829 3055 False 4547 4547 93.654 1 3032 1 chr4B.!!$F1 3031
2 TraesCS4A01G220800 chr1A 224505639 224508695 3056 False 4519 4519 93.495 1 3032 1 chr1A.!!$F1 3031
3 TraesCS4A01G220800 chr1A 20746455 20747726 1271 True 1404 1404 86.817 1771 3032 1 chr1A.!!$R1 1261
4 TraesCS4A01G220800 chr7B 314049080 314052132 3052 False 4494 4494 93.357 1 3032 1 chr7B.!!$F2 3031
5 TraesCS4A01G220800 chr7B 291042541 291045599 3058 False 3314 3314 86.509 1 3032 1 chr7B.!!$F1 3031
6 TraesCS4A01G220800 chr6B 356661504 356664548 3044 True 4359 4359 92.607 1 3032 1 chr6B.!!$R1 3031
7 TraesCS4A01G220800 chr3D 146105907 146108958 3051 True 3849 3849 89.609 2 3032 1 chr3D.!!$R1 3030
8 TraesCS4A01G220800 chr3D 218446128 218449222 3094 False 3380 3380 86.750 1 3032 1 chr3D.!!$F1 3031
9 TraesCS4A01G220800 chr4D 402743384 402746428 3044 False 3790 3790 89.314 2 3022 1 chr4D.!!$F1 3020
10 TraesCS4A01G220800 chr5A 236982182 236984540 2358 True 3227 3227 91.427 1 2354 1 chr5A.!!$R1 2353
11 TraesCS4A01G220800 chr5A 454838896 454841343 2447 False 2710 2710 87.063 639 3032 1 chr5A.!!$F1 2393
12 TraesCS4A01G220800 chr7A 611094479 611096923 2444 True 2645 2645 86.588 639 3032 1 chr7A.!!$R1 2393
13 TraesCS4A01G220800 chr6A 246841493 246843940 2447 True 2627 2627 86.419 639 3032 1 chr6A.!!$R1 2393
14 TraesCS4A01G220800 chr6D 183624676 183626035 1359 True 2134 2134 95.015 1674 3032 1 chr6D.!!$R2 1358
15 TraesCS4A01G220800 chr6D 183632207 183633445 1238 True 1893 1893 94.270 1 1237 1 chr6D.!!$R3 1236
16 TraesCS4A01G220800 chr6D 81900690 81901857 1167 True 1328 1328 87.574 1886 3032 1 chr6D.!!$R1 1146
17 TraesCS4A01G220800 chr2A 659574310 659575398 1088 True 1423 1423 90.402 1 1082 1 chr2A.!!$R1 1081
18 TraesCS4A01G220800 chrUn 115365699 115366596 897 False 1175 1175 90.455 1 890 1 chrUn.!!$F1 889
19 TraesCS4A01G220800 chrUn 115393206 115394024 818 False 1173 1173 92.579 2215 3032 1 chrUn.!!$F2 817

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
117 118 0.539986 CCAGTATGTACACGGGCCTT 59.460 55.0 0.84 0.0 0.00 4.35 F
1488 1526 0.108520 GCCGTCGGTGACAAAGGATA 60.109 55.0 13.94 0.0 32.09 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1942 1.135859 GTGCTGCCAGAAATGACTTCG 60.136 52.381 0.00 0.00 39.22 3.79 R
2837 2959 2.180017 GCCACTTCAAGCATGCCG 59.820 61.111 15.66 6.18 0.00 5.69 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
109 110 3.515502 AGAAGAAGCTGCCAGTATGTACA 59.484 43.478 0.00 0.00 0.00 2.90
117 118 0.539986 CCAGTATGTACACGGGCCTT 59.460 55.000 0.84 0.00 0.00 4.35
144 145 1.000060 GCTTGTGGTGCACATGATGTT 60.000 47.619 20.43 0.00 44.16 2.71
157 158 3.004210 ACATGATGTTGTGCTTAAACGCA 59.996 39.130 0.00 0.00 37.62 5.24
160 161 3.004210 TGATGTTGTGCTTAAACGCATGT 59.996 39.130 0.00 0.00 42.62 3.21
164 165 1.001924 TGTGCTTAAACGCATGTGTGG 60.002 47.619 13.66 5.25 42.62 4.17
176 177 2.032071 GTGTGGGGCGCTACTTGT 59.968 61.111 17.92 0.00 0.00 3.16
186 187 1.878953 CGCTACTTGTTGGTCCTGTT 58.121 50.000 0.00 0.00 0.00 3.16
271 272 2.985847 GACGCTTGGGCTTGGCTT 60.986 61.111 0.00 0.00 36.09 4.35
434 436 1.899814 TCTCGTGGAGTAAATGGCAGT 59.100 47.619 0.00 0.00 0.00 4.40
571 573 4.394920 CGGCAACAACAATGGTTAGTCTAT 59.605 41.667 0.00 0.00 34.87 1.98
645 677 7.766278 TCTGTGGCACTTAATTTCTAGAGAATC 59.234 37.037 19.83 0.00 33.54 2.52
703 735 8.420374 TTGTTCTAAATATTCTGAAGTAGGCG 57.580 34.615 0.00 0.00 0.00 5.52
754 788 4.715534 TGGTACCCAGACAATCAAAAGA 57.284 40.909 10.07 0.00 0.00 2.52
827 862 2.154074 GGGTGGTTGAGGAGGTGGT 61.154 63.158 0.00 0.00 0.00 4.16
958 993 5.220662 CGCAAGAAGATACCATTTGATTCGT 60.221 40.000 0.00 0.00 43.02 3.85
1002 1040 6.366315 TGAGCAAAAGAACTACGCTTAAAA 57.634 33.333 0.00 0.00 31.86 1.52
1028 1066 3.089573 GCTAATGAGCTTCAAATGGCC 57.910 47.619 0.00 0.00 45.98 5.36
1124 1162 2.299013 TGATGACAACAAGCTAGGTCGT 59.701 45.455 0.00 0.00 33.04 4.34
1255 1293 9.664332 CACTAAAGGTACTCAGAACTACTACTA 57.336 37.037 0.00 0.00 38.49 1.82
1263 1301 4.525024 TCAGAACTACTACTAGGCACCTC 58.475 47.826 0.00 0.00 0.00 3.85
1364 1402 5.059161 CCTCGTTATGATGATCATGGTGTT 58.941 41.667 17.74 0.00 37.70 3.32
1416 1454 3.309954 GCCGTTCACATATCAGGACTTTC 59.690 47.826 0.00 0.00 0.00 2.62
1467 1505 2.290768 GGGGAAGAGGTAACCAAGGTTC 60.291 54.545 7.93 0.75 39.31 3.62
1488 1526 0.108520 GCCGTCGGTGACAAAGGATA 60.109 55.000 13.94 0.00 32.09 2.59
1554 1592 1.613437 CTTTGTGGCCAACTTCGGAAT 59.387 47.619 7.24 0.00 0.00 3.01
1605 1643 8.523915 AGATAATGCAAAGACACATATTTCCA 57.476 30.769 0.00 0.00 0.00 3.53
1610 1648 6.389091 TGCAAAGACACATATTTCCATGAAC 58.611 36.000 0.00 0.00 0.00 3.18
1631 1669 0.173255 ACAGTGTGTTTTGTGCAGCC 59.827 50.000 0.00 0.00 0.00 4.85
1763 1802 5.402630 AGATGTCCCCTGGTAAAATTGTTT 58.597 37.500 0.00 0.00 0.00 2.83
1764 1803 5.843969 AGATGTCCCCTGGTAAAATTGTTTT 59.156 36.000 0.00 0.00 36.67 2.43
1769 1808 9.155785 TGTCCCCTGGTAAAATTGTTTTTATTA 57.844 29.630 0.00 0.00 39.00 0.98
1861 1901 0.597377 CATGCATGCGCGAGGTACTA 60.597 55.000 14.93 0.00 42.97 1.82
1902 1942 2.812011 GGTACAAGGTTCCACACATGAC 59.188 50.000 0.00 0.00 0.00 3.06
1926 1966 0.035317 TCATTTCTGGCAGCACTCGT 59.965 50.000 10.34 0.00 0.00 4.18
2002 2042 1.030457 CCCTTCCAGATGCTTGATGC 58.970 55.000 0.00 0.00 43.25 3.91
2017 2057 0.642800 GATGCACTTCTCGTCGCTTC 59.357 55.000 0.00 0.00 0.00 3.86
2230 2311 2.404215 TGAGAGTAGAACGTTGCAAGC 58.596 47.619 5.00 0.00 0.00 4.01
2298 2379 8.310406 TGTATGATGTCACTAAACAAACTCAG 57.690 34.615 0.00 0.00 31.81 3.35
2320 2402 6.041409 TCAGGCAATACAAAAATGACTTTGGA 59.959 34.615 1.57 0.00 40.03 3.53
2365 2447 5.825679 TCACACCAAATGTTTAGTGCTAAGT 59.174 36.000 4.36 0.00 40.64 2.24
2419 2504 7.227512 GGTCGTTTCTTCATCATCTTTGGATAT 59.772 37.037 0.00 0.00 0.00 1.63
2420 2505 9.261180 GTCGTTTCTTCATCATCTTTGGATATA 57.739 33.333 0.00 0.00 0.00 0.86
2697 2803 6.619801 AGTTGTGGCACTAAAAGTTAGAAG 57.380 37.500 19.83 0.00 0.00 2.85
2749 2871 9.154632 TGATGGATAAGAGCAAAGGTATAAGTA 57.845 33.333 0.00 0.00 0.00 2.24
2939 3064 2.559698 TGGAAGAATTTGCAGACCGA 57.440 45.000 0.00 0.00 30.57 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 2.203337 GCACCACAAGCCTGTCCA 60.203 61.111 0.00 0.00 31.64 4.02
157 158 1.377202 CAAGTAGCGCCCCACACAT 60.377 57.895 2.29 0.00 0.00 3.21
160 161 1.599518 CAACAAGTAGCGCCCCACA 60.600 57.895 2.29 0.00 0.00 4.17
164 165 2.038837 GGACCAACAAGTAGCGCCC 61.039 63.158 2.29 0.00 0.00 6.13
176 177 2.112297 GCCCGACAACAGGACCAA 59.888 61.111 0.00 0.00 0.00 3.67
315 316 1.956043 TGGAACAACTTCGCCATGC 59.044 52.632 0.00 0.00 31.92 4.06
461 463 2.281517 CGGATGCATGGGTTAACGTTA 58.718 47.619 2.46 3.29 0.00 3.18
1028 1066 6.430925 TCAACCTTCTCCATAATGTTGTCTTG 59.569 38.462 0.00 0.00 36.75 3.02
1124 1162 7.176865 TCCAACATGGATAAACAAAACCGAATA 59.823 33.333 0.00 0.00 42.67 1.75
1255 1293 2.290577 GGTTCTTCTTCATGAGGTGCCT 60.291 50.000 4.57 0.00 0.00 4.75
1263 1301 4.319333 GCTGCGATATGGTTCTTCTTCATG 60.319 45.833 0.00 0.00 0.00 3.07
1364 1402 5.892686 TCCAATCTTGCCATCAAATGTCATA 59.107 36.000 0.00 0.00 0.00 2.15
1467 1505 2.317609 CCTTTGTCACCGACGGCAG 61.318 63.158 15.39 7.25 34.95 4.85
1544 1582 2.388232 GCGTCCGCATTCCGAAGTT 61.388 57.895 6.82 0.00 41.49 2.66
1545 1583 2.813908 GCGTCCGCATTCCGAAGT 60.814 61.111 6.82 0.00 41.49 3.01
1595 1633 5.122239 CACACTGTCGTTCATGGAAATATGT 59.878 40.000 0.00 0.00 0.00 2.29
1605 1643 3.730662 GCACAAAACACACTGTCGTTCAT 60.731 43.478 0.00 0.00 0.00 2.57
1610 1648 1.813896 CTGCACAAAACACACTGTCG 58.186 50.000 0.00 0.00 0.00 4.35
1637 1675 2.774234 CCTAATATCCCATCCATCCGCT 59.226 50.000 0.00 0.00 0.00 5.52
1861 1901 2.552373 CCGGTTACCTCCTTTCTGCTTT 60.552 50.000 0.00 0.00 0.00 3.51
1902 1942 1.135859 GTGCTGCCAGAAATGACTTCG 60.136 52.381 0.00 0.00 39.22 3.79
1926 1966 2.358898 GGTACTACGTCCGGAAGCATTA 59.641 50.000 17.91 0.12 0.00 1.90
2002 2042 3.759418 TGATAAGAAGCGACGAGAAGTG 58.241 45.455 0.00 0.00 0.00 3.16
2230 2311 8.877779 TGAAGTTCATTTTGTTGGTTACATTTG 58.122 29.630 0.08 0.00 36.44 2.32
2298 2379 5.988561 TGTCCAAAGTCATTTTTGTATTGCC 59.011 36.000 0.00 0.00 36.54 4.52
2320 2402 8.239314 GTGTGATCTCATAAATTGTCATTGTGT 58.761 33.333 0.02 0.00 0.00 3.72
2365 2447 6.782082 AATCAGTGATGCAAGTACTCTCTA 57.218 37.500 6.34 0.00 0.00 2.43
2419 2504 3.861276 ACGTCCTTGATGACATCGTTA 57.139 42.857 10.79 0.00 34.88 3.18
2420 2505 2.743636 ACGTCCTTGATGACATCGTT 57.256 45.000 10.79 0.00 34.88 3.85
2749 2871 5.300792 ACATCACCGATTTTTGGTTAGTTGT 59.699 36.000 0.00 0.00 37.72 3.32
2837 2959 2.180017 GCCACTTCAAGCATGCCG 59.820 61.111 15.66 6.18 0.00 5.69


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

AutoCloner maintained by Alex Coulton.