Multiple sequence alignment - TraesCS4A01G479600

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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 TraesCS4A01G479600 chr4A 100.000 4391 0 0 1 4391 736306397 736310787 0.000000e+00 8109
1 TraesCS4A01G479600 chr4A 92.275 2356 114 22 1595 3922 737068808 737066493 0.000000e+00 3280
2 TraesCS4A01G479600 chr4A 92.173 1597 90 8 1 1593 737070480 737068915 0.000000e+00 2224
3 TraesCS4A01G479600 chr4A 85.197 1628 150 29 2809 4391 737085976 737084395 0.000000e+00 1587
4 TraesCS4A01G479600 chr4A 82.031 1664 171 46 1146 2769 737087558 737085983 0.000000e+00 1299
5 TraesCS4A01G479600 chr4A 83.452 1124 101 40 1 1088 737089765 737088691 0.000000e+00 966
6 TraesCS4A01G479600 chr4A 93.381 423 27 1 3954 4375 737066494 737066072 3.730000e-175 625
7 TraesCS4A01G479600 chr4A 79.771 875 133 26 665 1523 737064037 737063191 2.920000e-166 595
8 TraesCS4A01G479600 chr4A 79.260 622 96 13 3772 4391 737060977 737060387 1.900000e-108 403
9 TraesCS4A01G479600 chr4A 75.802 748 130 30 2713 3439 737062177 737061460 9.100000e-87 331
10 TraesCS4A01G479600 chr7D 95.934 4402 155 15 1 4391 5413811 5418199 0.000000e+00 7116
11 TraesCS4A01G479600 chr7D 86.788 1930 179 30 1146 3056 5388289 5390161 0.000000e+00 2082
12 TraesCS4A01G479600 chr7D 91.416 1165 84 7 3239 4388 5390314 5391477 0.000000e+00 1583
13 TraesCS4A01G479600 chr7D 86.484 1095 91 29 1 1088 5386155 5387199 0.000000e+00 1149
14 TraesCS4A01G479600 chr7D 92.941 85 4 2 3210 3292 5390245 5390329 5.960000e-24 122
15 TraesCS4A01G479600 chr7A 85.882 1792 171 32 2649 4391 6865553 6867311 0.000000e+00 1832
16 TraesCS4A01G479600 chr7A 88.830 761 77 5 1090 1843 6864176 6864935 0.000000e+00 928
17 TraesCS4A01G479600 chr7A 88.788 553 41 4 545 1092 6863473 6864009 0.000000e+00 658
18 TraesCS4A01G479600 chr7A 91.328 369 30 2 177 543 6863133 6863501 1.820000e-138 503
19 TraesCS4A01G479600 chr7A 87.634 186 21 2 2324 2508 6865329 6865513 9.560000e-52 215
20 TraesCS4A01G479600 chr7A 79.511 327 39 13 1905 2228 6864934 6865235 1.600000e-49 207


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 TraesCS4A01G479600 chr4A 736306397 736310787 4390 False 8109.000000 8109 100.000000 1 4391 1 chr4A.!!$F1 4390
1 TraesCS4A01G479600 chr4A 737084395 737089765 5370 True 1284.000000 1587 83.560000 1 4391 3 chr4A.!!$R2 4390
2 TraesCS4A01G479600 chr4A 737060387 737070480 10093 True 1243.000000 3280 85.443667 1 4391 6 chr4A.!!$R1 4390
3 TraesCS4A01G479600 chr7D 5413811 5418199 4388 False 7116.000000 7116 95.934000 1 4391 1 chr7D.!!$F1 4390
4 TraesCS4A01G479600 chr7D 5386155 5391477 5322 False 1234.000000 2082 89.407250 1 4388 4 chr7D.!!$F2 4387
5 TraesCS4A01G479600 chr7A 6863133 6867311 4178 False 723.833333 1832 86.995500 177 4391 6 chr7A.!!$F1 4214

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
958 1009 0.180406 TTTCCCCTCATCGCTTAGCC 59.820 55.000 0.0 0.0 0.0 3.93 F
1287 2454 1.068250 GCGAGGAGGGTGAGCATAC 59.932 63.158 0.0 0.0 0.0 2.39 F
1475 2642 1.143684 AGAAACAGTGCATGGTGAGGT 59.856 47.619 0.0 0.0 0.0 3.85 F
2233 3546 1.210478 TCCAGATCCACCTTGCTAAGC 59.790 52.381 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2878 4250 3.584733 AACCCAACTTTGCTCTTCTCT 57.415 42.857 0.00 0.00 0.0 3.10 R
3098 4473 8.367911 CAGTGGAGTTAGCCAAATATGTCTATA 58.632 37.037 0.00 0.00 40.2 1.31 R
3369 4825 4.077108 CCTATGGTATGAACATGCTGCAT 58.923 43.478 9.81 9.81 0.0 3.96 R
4042 5545 0.659957 CTCCTGCTTTATTGCTCCGC 59.340 55.000 0.00 0.00 0.0 5.54 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
112 113 3.384816 CCATCGATGGCTAGTTGCA 57.615 52.632 30.53 0.00 45.15 4.08
113 114 1.667236 CCATCGATGGCTAGTTGCAA 58.333 50.000 30.53 0.00 45.15 4.08
114 115 1.331756 CCATCGATGGCTAGTTGCAAC 59.668 52.381 30.53 22.17 45.15 4.17
292 304 6.666678 CATTGCCACCATTATCCCTATATCT 58.333 40.000 0.00 0.00 0.00 1.98
309 321 7.761704 CCCTATATCTTCGTAATCCACATTGAG 59.238 40.741 0.00 0.00 0.00 3.02
413 425 6.483307 CCAACGAAAATAGCAATGGATCTAGA 59.517 38.462 0.00 0.00 0.00 2.43
587 602 9.822185 AATTTAATATTCAACATCCTGGAAAGC 57.178 29.630 0.00 0.00 0.00 3.51
612 627 4.706962 AGAGGCAAATGAAAGGTATCCAAC 59.293 41.667 0.00 0.00 0.00 3.77
852 870 0.746204 GCAGCCCTCTGTTTCTAGCC 60.746 60.000 0.00 0.00 42.29 3.93
864 882 2.760092 GTTTCTAGCCATGGCCAATGAA 59.240 45.455 33.14 25.33 43.17 2.57
944 995 2.102578 CCACATCACCCTCATTTTCCC 58.897 52.381 0.00 0.00 0.00 3.97
958 1009 0.180406 TTTCCCCTCATCGCTTAGCC 59.820 55.000 0.00 0.00 0.00 3.93
1026 1080 1.841663 CGGCGGAGTCAAACCAACTG 61.842 60.000 0.00 0.00 0.00 3.16
1030 1084 1.541233 CGGAGTCAAACCAACTGAGCT 60.541 52.381 0.00 0.00 0.00 4.09
1054 1108 1.774110 TGTGGCCAACATGTTCACTT 58.226 45.000 22.26 0.00 32.36 3.16
1095 1318 2.687425 CCGATGCCATTTGTGTGGATTA 59.313 45.455 0.00 0.00 42.02 1.75
1186 2353 4.703379 TTCTTTCGTGGGTTAGGGTTTA 57.297 40.909 0.00 0.00 0.00 2.01
1204 2371 2.118313 TACTGGACGATCAGTTCCGA 57.882 50.000 17.27 1.31 44.74 4.55
1287 2454 1.068250 GCGAGGAGGGTGAGCATAC 59.932 63.158 0.00 0.00 0.00 2.39
1455 2622 4.074259 CACATTTGTGGATCAACTCTGGA 58.926 43.478 1.02 0.00 42.10 3.86
1475 2642 1.143684 AGAAACAGTGCATGGTGAGGT 59.856 47.619 0.00 0.00 0.00 3.85
1517 2684 4.304110 TGTCCTCTTCGTATGTGTTTGTC 58.696 43.478 0.00 0.00 0.00 3.18
1526 2693 5.702865 TCGTATGTGTTTGTCCAGTAGTAC 58.297 41.667 0.00 0.00 0.00 2.73
1531 2698 5.463286 TGTGTTTGTCCAGTAGTACGTATG 58.537 41.667 0.00 0.00 0.00 2.39
1533 2700 6.071784 TGTGTTTGTCCAGTAGTACGTATGAT 60.072 38.462 0.00 0.00 0.00 2.45
1695 2967 2.046314 CCTGAATTGACCGGGCGT 60.046 61.111 6.32 0.00 0.00 5.68
2202 3485 7.542477 CCACTTAGTATAAATCACATAGCTCCG 59.458 40.741 0.00 0.00 0.00 4.63
2233 3546 1.210478 TCCAGATCCACCTTGCTAAGC 59.790 52.381 0.00 0.00 0.00 3.09
2304 3642 7.546358 TGTGGTGCTTAATGATTTAAATCCAG 58.454 34.615 22.42 14.56 34.50 3.86
2350 3692 2.224305 ACGGCTCAAAGAGTAGCACTTT 60.224 45.455 0.00 0.00 40.61 2.66
2683 4055 4.459337 GCTTACACTGGGCTTTCATAGTTT 59.541 41.667 0.00 0.00 0.00 2.66
2731 4103 5.467063 GTGGTACATCTATTTGCTTAGGAGC 59.533 44.000 0.00 0.00 45.99 4.70
2733 4105 9.735432 GTGGTACATCTATTTGCTTAGGAGCCA 62.735 44.444 0.00 0.00 45.45 4.75
2770 4142 9.561270 GAAAGAACTACCATGCTAATTTTCTTC 57.439 33.333 0.00 0.00 32.29 2.87
2779 4151 8.815912 ACCATGCTAATTTTCTTCCATTAAAGT 58.184 29.630 0.00 0.00 0.00 2.66
2878 4250 3.615155 TCAGTTCCATGTGTGTTGTCAA 58.385 40.909 0.00 0.00 0.00 3.18
3222 4630 6.655930 TCCTACCAGTGTAGAGTTTTGTTTT 58.344 36.000 1.40 0.00 46.18 2.43
3353 4809 6.537355 TGAAGACACTGGATTCTTTGAGAAT 58.463 36.000 2.99 2.99 46.84 2.40
3438 4924 9.678260 ATCTTGTCTTGAAATCTAAGTAGCATT 57.322 29.630 0.00 0.00 0.00 3.56
3439 4925 9.507329 TCTTGTCTTGAAATCTAAGTAGCATTT 57.493 29.630 0.00 0.00 0.00 2.32
3609 5095 7.278646 TGCATTACAACAGAAGATAGACATGTC 59.721 37.037 18.47 18.47 0.00 3.06
3679 5166 5.578727 TGTGCTAATTGTGGAAAACAAACAC 59.421 36.000 0.00 3.43 44.97 3.32
3681 5168 4.801516 GCTAATTGTGGAAAACAAACACGT 59.198 37.500 0.00 0.00 44.97 4.49
3734 5223 3.952967 CCTAGAGGTACTACTTGGTGTCC 59.047 52.174 0.00 0.00 41.55 4.02
3834 5330 4.979335 TCATGTACCTCAAAATGGTCACA 58.021 39.130 0.00 0.00 38.88 3.58
3864 5364 6.349611 GCCTCAAAACTTATCACATGTCACAT 60.350 38.462 0.00 0.00 0.00 3.21
4042 5545 3.304559 GCAGCATGTCGTAAACTGTAGAG 59.695 47.826 0.00 0.00 39.31 2.43
4161 5664 4.162509 GCTTCTGTGGGGTCTATAGTTCTT 59.837 45.833 0.00 0.00 0.00 2.52
4201 5704 3.467374 TCTGGTTTTGATTTTGGTGGC 57.533 42.857 0.00 0.00 0.00 5.01
4212 5715 0.180642 TTTGGTGGCACTGTCCGTAA 59.819 50.000 18.45 0.00 0.00 3.18
4219 5722 2.746904 TGGCACTGTCCGTAATTTCATG 59.253 45.455 0.00 0.00 0.00 3.07
4316 5819 4.099824 GTTCTAGTCAGTTTCTAGCTCGC 58.900 47.826 0.00 0.00 36.00 5.03
4343 5847 2.379005 TCAGTGGCAGTGTATCTCGAT 58.621 47.619 21.06 0.00 0.00 3.59
4362 5866 4.270084 TCGATAAAATCATGTGTCTTCGGC 59.730 41.667 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 2.490115 TGTTTTCCGAACTGTTGCAACT 59.510 40.909 28.61 10.38 0.00 3.16
107 108 2.869897 TGTTTTCCGAACTGTTGCAAC 58.130 42.857 22.83 22.83 0.00 4.17
108 109 3.791973 ATGTTTTCCGAACTGTTGCAA 57.208 38.095 0.00 0.00 0.00 4.08
109 110 3.791973 AATGTTTTCCGAACTGTTGCA 57.208 38.095 0.00 0.00 0.00 4.08
110 111 4.023536 TCCTAATGTTTTCCGAACTGTTGC 60.024 41.667 0.00 0.00 0.00 4.17
111 112 5.468746 TCTCCTAATGTTTTCCGAACTGTTG 59.531 40.000 0.00 0.00 0.00 3.33
112 113 5.469084 GTCTCCTAATGTTTTCCGAACTGTT 59.531 40.000 0.00 0.00 0.00 3.16
113 114 4.995487 GTCTCCTAATGTTTTCCGAACTGT 59.005 41.667 0.00 0.00 0.00 3.55
114 115 4.994852 TGTCTCCTAATGTTTTCCGAACTG 59.005 41.667 0.00 0.00 0.00 3.16
149 159 4.267214 CGAAGTGACAACTGCATCTATCTG 59.733 45.833 0.00 0.00 36.51 2.90
561 575 9.822185 GCTTTCCAGGATGTTGAATATTAAATT 57.178 29.630 0.00 0.00 0.00 1.82
563 577 7.338196 TCGCTTTCCAGGATGTTGAATATTAAA 59.662 33.333 0.00 0.00 0.00 1.52
587 602 3.561725 GGATACCTTTCATTTGCCTCTCG 59.438 47.826 0.00 0.00 0.00 4.04
612 627 4.058817 GGTTAGATCCAGGCATAGTTTCG 58.941 47.826 0.00 0.00 0.00 3.46
827 845 0.112995 AAACAGAGGGCTGCCATTCA 59.887 50.000 22.05 0.00 46.26 2.57
944 995 2.478831 GAGAAAGGCTAAGCGATGAGG 58.521 52.381 0.00 0.00 0.00 3.86
958 1009 2.834549 TCAGTTAGCAGGGAGGAGAAAG 59.165 50.000 0.00 0.00 0.00 2.62
1012 1066 2.147150 GGAGCTCAGTTGGTTTGACTC 58.853 52.381 17.19 0.00 0.00 3.36
1026 1080 1.973812 GTTGGCCACAAGGGAGCTC 60.974 63.158 3.88 4.71 40.01 4.09
1030 1084 0.105760 AACATGTTGGCCACAAGGGA 60.106 50.000 11.07 0.00 39.50 4.20
1054 1108 3.490249 CGGAATTGTACATAGCTCACCGA 60.490 47.826 0.00 0.00 39.11 4.69
1095 1318 3.852578 ACATCCACCTTGGGAGAAACTAT 59.147 43.478 0.00 0.00 41.08 2.12
1154 2321 5.785243 ACCCACGAAAGAAAAAGAAAACAA 58.215 33.333 0.00 0.00 0.00 2.83
1155 2322 5.394224 ACCCACGAAAGAAAAAGAAAACA 57.606 34.783 0.00 0.00 0.00 2.83
1156 2323 6.474427 CCTAACCCACGAAAGAAAAAGAAAAC 59.526 38.462 0.00 0.00 0.00 2.43
1161 2328 3.887110 ACCCTAACCCACGAAAGAAAAAG 59.113 43.478 0.00 0.00 0.00 2.27
1171 2338 1.624813 TCCAGTAAACCCTAACCCACG 59.375 52.381 0.00 0.00 0.00 4.94
1204 2371 1.627329 TCTTGGAGCATCTCAAGCTGT 59.373 47.619 0.00 0.00 43.58 4.40
1315 2482 8.978843 TGATCAGATCACATGACATGGCAACA 62.979 42.308 19.39 0.00 43.21 3.33
1455 2622 1.143684 ACCTCACCATGCACTGTTTCT 59.856 47.619 0.00 0.00 0.00 2.52
1475 2642 4.389374 ACATGGAAGAAGAAGAAAAGCGA 58.611 39.130 0.00 0.00 0.00 4.93
1517 2684 8.774890 ACTATAGTCATCATACGTACTACTGG 57.225 38.462 0.00 0.00 0.00 4.00
1695 2967 0.601057 TCAATCCGCACTCGTTGAGA 59.399 50.000 0.00 0.00 33.32 3.27
1706 2978 4.843728 TCCCCATATTTATCTCAATCCGC 58.156 43.478 0.00 0.00 0.00 5.54
1707 2979 5.431765 CCTCCCCATATTTATCTCAATCCG 58.568 45.833 0.00 0.00 0.00 4.18
2021 3302 9.553064 GGTTTGTCAGATCTTAATCATACATCT 57.447 33.333 0.00 0.00 32.29 2.90
2182 3465 6.265649 ACTCACGGAGCTATGTGATTTATACT 59.734 38.462 17.92 0.00 43.59 2.12
2202 3485 3.633065 GGTGGATCTGGAGTACTACTCAC 59.367 52.174 16.49 7.02 46.79 3.51
2233 3546 5.234757 TCCGAATAATTAATTGGACGAACCG 59.765 40.000 11.05 3.58 42.61 4.44
2350 3692 6.786122 AGCCCACTTTAAGAAGGTAAATGTA 58.214 36.000 0.00 0.00 37.19 2.29
2705 4077 5.665812 TCCTAAGCAAATAGATGTACCACCT 59.334 40.000 0.00 0.00 0.00 4.00
2731 4103 4.092116 AGTTCTTTCCCTTCACTTCTGG 57.908 45.455 0.00 0.00 0.00 3.86
2733 4105 4.658901 TGGTAGTTCTTTCCCTTCACTTCT 59.341 41.667 0.00 0.00 0.00 2.85
2770 4142 9.586435 GAAAGACCCATAAAATCACTTTAATGG 57.414 33.333 0.00 0.00 33.20 3.16
2779 4151 6.953520 ACAATGAGGAAAGACCCATAAAATCA 59.046 34.615 0.00 0.00 40.05 2.57
2878 4250 3.584733 AACCCAACTTTGCTCTTCTCT 57.415 42.857 0.00 0.00 0.00 3.10
3098 4473 8.367911 CAGTGGAGTTAGCCAAATATGTCTATA 58.632 37.037 0.00 0.00 40.20 1.31
3193 4599 9.263446 ACAAAACTCTACACTGGTAGGATTATA 57.737 33.333 2.37 0.00 45.76 0.98
3225 4633 8.470657 TGCTAATGGCCATTACAATTTACATA 57.529 30.769 30.39 11.00 40.92 2.29
3353 4809 7.664318 ACATGCTGCATAGATCATAGAAATCAA 59.336 33.333 15.78 0.00 0.00 2.57
3369 4825 4.077108 CCTATGGTATGAACATGCTGCAT 58.923 43.478 9.81 9.81 0.00 3.96
3537 5023 9.594936 AGCCTCATATCTACTGTTTAGTTCTAT 57.405 33.333 0.00 0.00 38.36 1.98
3609 5095 6.237384 GCAAACTAGTCGCATTCATTTCATTG 60.237 38.462 11.36 1.98 0.00 2.82
3734 5223 4.464244 TCAACTGAGATTCTGGTAGTCCTG 59.536 45.833 0.00 0.00 34.23 3.86
3834 5330 4.323417 TGTGATAAGTTTTGAGGCGACAT 58.677 39.130 0.00 0.00 0.00 3.06
3935 5437 3.819337 GAGGACCCAAAGAGTTAAACACC 59.181 47.826 0.00 0.00 0.00 4.16
4030 5533 2.649331 TGCTCCGCTCTACAGTTTAC 57.351 50.000 0.00 0.00 0.00 2.01
4042 5545 0.659957 CTCCTGCTTTATTGCTCCGC 59.340 55.000 0.00 0.00 0.00 5.54
4071 5574 5.358090 ACATCAAACACAATGTGCAATCAA 58.642 33.333 14.01 0.00 36.98 2.57
4180 5683 3.198635 TGCCACCAAAATCAAAACCAGAA 59.801 39.130 0.00 0.00 0.00 3.02
4201 5704 2.223021 CCGCATGAAATTACGGACAGTG 60.223 50.000 0.00 0.00 44.13 3.66
4212 5715 4.405358 ACCACCAATAATTCCGCATGAAAT 59.595 37.500 0.00 0.00 36.33 2.17
4219 5722 3.859411 TTTGACCACCAATAATTCCGC 57.141 42.857 0.00 0.00 34.23 5.54
4316 5819 4.940046 AGATACACTGCCACTGAATTTCTG 59.060 41.667 2.09 2.09 0.00 3.02
4343 5847 2.675844 CGGCCGAAGACACATGATTTTA 59.324 45.455 24.07 0.00 0.00 1.52
4362 5866 0.319555 CACCATAGTCCATACGCCGG 60.320 60.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.