Multiple sequence alignment - TraesCS1A01G230900

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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 TraesCS1A01G230900 chr1A 100.000 2664 0 0 1 2664 403631277 403633940 0.000000e+00 4920.0
1 TraesCS1A01G230900 chr1B 88.533 2468 141 65 297 2664 432380110 432377685 0.000000e+00 2859.0
2 TraesCS1A01G230900 chr1B 94.030 134 7 1 130 262 432380251 432380118 4.500000e-48 202.0
3 TraesCS1A01G230900 chr1B 77.733 247 32 14 272 508 432379877 432380110 2.150000e-26 130.0
4 TraesCS1A01G230900 chr1B 91.954 87 7 0 54 140 432380611 432380525 3.600000e-24 122.0
5 TraesCS1A01G230900 chr1D 90.180 1110 55 18 860 1928 319618133 319617037 0.000000e+00 1397.0
6 TraesCS1A01G230900 chr1D 88.175 778 63 19 10 767 319618900 319618132 0.000000e+00 900.0
7 TraesCS1A01G230900 chr1D 93.415 410 19 6 2256 2664 319616051 319615649 3.790000e-168 601.0
8 TraesCS1A01G230900 chr1D 87.826 345 20 8 1931 2257 319616976 319616636 4.160000e-103 385.0
9 TraesCS1A01G230900 chr2B 80.526 1217 102 61 614 1719 7684514 7683322 0.000000e+00 809.0
10 TraesCS1A01G230900 chr2A 79.648 1194 122 61 642 1719 2709303 2708115 0.000000e+00 747.0
11 TraesCS1A01G230900 chr2D 78.901 1237 116 68 615 1719 3004302 3005525 0.000000e+00 704.0
12 TraesCS1A01G230900 chr7D 84.868 304 18 9 2381 2664 470227796 470227501 5.610000e-72 281.0
13 TraesCS1A01G230900 chr7D 89.177 231 14 5 2076 2296 470228025 470227796 7.260000e-71 278.0
14 TraesCS1A01G230900 chr7D 75.380 329 48 24 255 570 48362462 48362770 7.740000e-26 128.0
15 TraesCS1A01G230900 chr7D 97.222 36 1 0 2016 2051 470228059 470228024 7.960000e-06 62.1
16 TraesCS1A01G230900 chr3D 82.877 292 36 5 283 572 20693103 20692824 1.580000e-62 250.0
17 TraesCS1A01G230900 chr5D 78.361 305 48 14 271 571 517281373 517281663 5.860000e-42 182.0
18 TraesCS1A01G230900 chr5D 78.571 196 30 5 376 571 40181280 40181463 4.660000e-23 119.0
19 TraesCS1A01G230900 chr5D 82.258 124 15 4 409 532 72874682 72874566 1.690000e-17 100.0
20 TraesCS1A01G230900 chr5D 83.133 83 12 2 448 528 40919823 40919905 1.020000e-09 75.0
21 TraesCS1A01G230900 chr5A 79.851 268 35 16 271 533 644359551 644359804 7.580000e-41 178.0
22 TraesCS1A01G230900 chr3B 77.124 306 50 15 276 571 801157346 801157641 2.740000e-35 159.0
23 TraesCS1A01G230900 chr4D 77.288 295 40 22 272 550 357262663 357262946 5.940000e-32 148.0
24 TraesCS1A01G230900 chr4B 78.148 270 34 17 273 532 440583997 440584251 5.940000e-32 148.0
25 TraesCS1A01G230900 chr4A 73.288 292 41 24 271 550 625068603 625068337 3.680000e-09 73.1


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 TraesCS1A01G230900 chr1A 403631277 403633940 2663 False 4920.000000 4920 100.000000 1 2664 1 chr1A.!!$F1 2663
1 TraesCS1A01G230900 chr1B 432377685 432380611 2926 True 1061.000000 2859 91.505667 54 2664 3 chr1B.!!$R1 2610
2 TraesCS1A01G230900 chr1D 319615649 319618900 3251 True 820.750000 1397 89.899000 10 2664 4 chr1D.!!$R1 2654
3 TraesCS1A01G230900 chr2B 7683322 7684514 1192 True 809.000000 809 80.526000 614 1719 1 chr2B.!!$R1 1105
4 TraesCS1A01G230900 chr2A 2708115 2709303 1188 True 747.000000 747 79.648000 642 1719 1 chr2A.!!$R1 1077
5 TraesCS1A01G230900 chr2D 3004302 3005525 1223 False 704.000000 704 78.901000 615 1719 1 chr2D.!!$F1 1104
6 TraesCS1A01G230900 chr7D 470227501 470228059 558 True 207.033333 281 90.422333 2016 2664 3 chr7D.!!$R1 648


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
248 540 0.752054 TACCGGACGTGGTGTTTCTT 59.248 50.0 9.46 0.0 43.68 2.52 F
1039 1493 0.901124 CCACCTCCTGTCTCCAAGAG 59.099 60.0 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1765 1.180456 TGTCGCCGTTGAAGTAGGGA 61.180 55.0 0.00 0.0 0.00 4.2 R
1970 2550 1.263356 GGTTTTAGAAACCAGGGGGC 58.737 55.0 15.71 0.0 40.03 5.8 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
35 36 2.037136 CAAGGAGCAGGTGGAAGCG 61.037 63.158 0.00 0.00 40.95 4.68
127 418 1.435105 GGCCGTCCGGAGTAGTAAC 59.565 63.158 3.06 0.00 37.50 2.50
128 419 1.315257 GGCCGTCCGGAGTAGTAACA 61.315 60.000 3.06 0.00 37.50 2.41
136 427 5.406175 CGTCCGGAGTAGTAACAATTTTCAA 59.594 40.000 3.06 0.00 0.00 2.69
140 431 8.852135 TCCGGAGTAGTAACAATTTTCAATTTT 58.148 29.630 0.00 0.00 0.00 1.82
208 500 2.595124 ATCGTATTGATGGTGACGCA 57.405 45.000 0.00 0.00 35.45 5.24
248 540 0.752054 TACCGGACGTGGTGTTTCTT 59.248 50.000 9.46 0.00 43.68 2.52
262 554 4.583073 GGTGTTTCTTGGGTGAACAGTAAT 59.417 41.667 0.00 0.00 0.00 1.89
264 556 6.263617 GGTGTTTCTTGGGTGAACAGTAATAA 59.736 38.462 0.00 0.00 0.00 1.40
265 557 7.201839 GGTGTTTCTTGGGTGAACAGTAATAAA 60.202 37.037 0.00 0.00 0.00 1.40
266 558 8.192110 GTGTTTCTTGGGTGAACAGTAATAAAA 58.808 33.333 0.00 0.00 0.00 1.52
267 559 8.919145 TGTTTCTTGGGTGAACAGTAATAAAAT 58.081 29.630 0.00 0.00 0.00 1.82
268 560 9.406828 GTTTCTTGGGTGAACAGTAATAAAATC 57.593 33.333 0.00 0.00 0.00 2.17
269 561 7.696992 TCTTGGGTGAACAGTAATAAAATCC 57.303 36.000 0.00 0.00 0.00 3.01
325 618 2.808543 GACAAAAGTTCTCGGTGCTCAT 59.191 45.455 0.00 0.00 0.00 2.90
358 651 6.984740 TCACGAAATAACATTTGTGAAAGC 57.015 33.333 7.47 0.00 45.97 3.51
359 652 6.734137 TCACGAAATAACATTTGTGAAAGCT 58.266 32.000 7.47 0.00 45.97 3.74
364 657 8.015087 CGAAATAACATTTGTGAAAGCTGTAGA 58.985 33.333 0.00 0.00 0.00 2.59
396 689 6.311935 CCATAATTGATGCTCCAAAAGTGTTG 59.688 38.462 0.00 0.00 33.79 3.33
401 694 5.108517 TGATGCTCCAAAAGTGTTGTTTTC 58.891 37.500 0.00 0.00 0.00 2.29
407 700 6.183360 GCTCCAAAAGTGTTGTTTTCGAAAAT 60.183 34.615 24.93 6.48 0.00 1.82
484 777 2.979151 TCGTGATGAAATTTTGCAAGCG 59.021 40.909 0.00 0.00 0.00 4.68
486 779 2.733026 GTGATGAAATTTTGCAAGCGCT 59.267 40.909 2.64 2.64 39.64 5.92
497 790 1.405105 TGCAAGCGCTGAGAACTTTTT 59.595 42.857 12.58 0.00 39.64 1.94
609 939 4.410228 ACATACAGTATGCCTCAAGATGGT 59.590 41.667 18.99 0.00 42.53 3.55
724 1057 3.120649 GCTCGAAATACGCTTTTCTGTGT 60.121 43.478 8.49 0.00 42.26 3.72
772 1143 4.128643 TGCCTTTGCTCCAAATTTTCAAG 58.871 39.130 0.00 0.00 38.71 3.02
781 1152 3.134804 TCCAAATTTTCAAGGGCGGAAAA 59.865 39.130 11.11 11.11 45.25 2.29
819 1209 3.536917 CCGGGCTCGCATCCACTA 61.537 66.667 0.00 0.00 34.56 2.74
822 1212 0.946221 CGGGCTCGCATCCACTATTC 60.946 60.000 0.00 0.00 0.00 1.75
865 1263 3.633986 CCCTTCCCTCTGTATTTTGCATC 59.366 47.826 0.00 0.00 0.00 3.91
869 1267 2.032550 CCCTCTGTATTTTGCATCAGCG 59.967 50.000 0.00 0.00 46.23 5.18
938 1356 1.557443 CGTTTGGACACCACTCGCTC 61.557 60.000 0.00 0.00 30.78 5.03
961 1379 2.430694 GCTTCTTCTCTTCTCCTCTCCC 59.569 54.545 0.00 0.00 0.00 4.30
1004 1452 2.023673 TGATTGGTCGGAATCAATGGC 58.976 47.619 11.08 1.80 39.00 4.40
1005 1453 1.338020 GATTGGTCGGAATCAATGGCC 59.662 52.381 11.08 0.00 34.18 5.36
1039 1493 0.901124 CCACCTCCTGTCTCCAAGAG 59.099 60.000 0.00 0.00 0.00 2.85
1205 1680 2.187946 CGGCCTGGTGATCCTCAC 59.812 66.667 0.00 0.00 46.23 3.51
1216 1691 1.033574 GATCCTCACCGTCTACCTGG 58.966 60.000 0.00 0.00 0.00 4.45
1235 1710 4.070552 GGTGAAGCCGAGGACGCT 62.071 66.667 0.00 0.00 38.29 5.07
1254 1729 1.445582 GTCCTTCGACGTCGCCAAT 60.446 57.895 32.19 0.00 39.60 3.16
1275 1750 1.750930 CGCCCTCCACAGCATCTAT 59.249 57.895 0.00 0.00 0.00 1.98
1287 1762 1.662608 CATCTATGTCGGCTCGCCT 59.337 57.895 6.35 0.00 0.00 5.52
1290 1765 2.123854 TATGTCGGCTCGCCTCCT 60.124 61.111 6.35 0.00 0.00 3.69
1447 1930 3.014036 CGCAGCGTGTTCACAGTT 58.986 55.556 6.65 0.00 0.00 3.16
1558 2059 1.732117 TCAAGGTCCGGGAAAGGTTA 58.268 50.000 0.00 0.00 0.00 2.85
1811 2328 8.124823 CACAGCAATCTAAAATTATCACACGAT 58.875 33.333 0.00 0.00 35.50 3.73
1886 2408 9.592196 CTACTGGTACCATATTTAGGTAGGTTA 57.408 37.037 16.75 0.00 42.01 2.85
1969 2549 2.430465 ACAATCTGTGAAAGCGATGCT 58.570 42.857 0.00 0.00 42.56 3.79
1970 2550 2.161012 ACAATCTGTGAAAGCGATGCTG 59.839 45.455 0.00 0.00 39.62 4.41
1971 2551 0.731417 ATCTGTGAAAGCGATGCTGC 59.269 50.000 0.00 0.00 39.62 5.25
1984 2564 1.214305 ATGCTGCCCCCTGGTTTCTA 61.214 55.000 0.00 0.00 0.00 2.10
2006 2586 8.698973 TCTAAAACCAATTTCCATCACAACTA 57.301 30.769 0.00 0.00 32.27 2.24
2073 2653 3.982701 TGCAAAACTCAAGATTGAATGCG 59.017 39.130 13.13 0.00 36.36 4.73
2083 2663 4.222124 AGATTGAATGCGTTCCCTTAGT 57.778 40.909 15.96 0.00 33.26 2.24
2134 2717 2.293598 AAGGACCCCTCCAAGATCAT 57.706 50.000 0.00 0.00 39.39 2.45
2342 3530 4.473477 AGGATAGAAGAAACACCTTCGG 57.527 45.455 0.00 0.00 45.32 4.30
2429 3617 9.965902 ATCTTTCTGTTAGAACTTTGGTATCAT 57.034 29.630 0.00 0.00 33.26 2.45
2567 3775 3.857010 GCTGGTTTGTTCCAAGTATGTGC 60.857 47.826 0.00 0.00 37.01 4.57
2580 3788 3.600388 AGTATGTGCTGGCTGTACTTTC 58.400 45.455 13.17 5.78 32.31 2.62
2622 3830 2.423446 GTGGATGGGGAGCTAGCG 59.577 66.667 9.55 0.00 0.00 4.26
2643 3851 3.120199 CGCTTCTTTTGTGGGTGTATCAG 60.120 47.826 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.679153 GCTCCTTGTTTCCAAAACGGA 59.321 47.619 0.00 0.09 44.40 4.69
5 6 1.407258 TGCTCCTTGTTTCCAAAACGG 59.593 47.619 0.00 0.00 0.00 4.44
6 7 2.543653 CCTGCTCCTTGTTTCCAAAACG 60.544 50.000 0.00 0.00 0.00 3.60
7 8 2.430694 ACCTGCTCCTTGTTTCCAAAAC 59.569 45.455 0.00 0.00 0.00 2.43
8 9 2.430332 CACCTGCTCCTTGTTTCCAAAA 59.570 45.455 0.00 0.00 0.00 2.44
22 23 3.482232 AAGCACGCTTCCACCTGCT 62.482 57.895 0.00 0.00 41.83 4.24
114 121 7.989416 AATTGAAAATTGTTACTACTCCGGA 57.011 32.000 2.93 2.93 0.00 5.14
136 427 9.691362 AGCTTAATTTTCGTGTATGTGAAAAAT 57.309 25.926 4.48 0.00 44.50 1.82
140 431 7.866729 TCAAGCTTAATTTTCGTGTATGTGAA 58.133 30.769 0.00 0.00 0.00 3.18
248 540 7.841282 TTTGGATTTTATTACTGTTCACCCA 57.159 32.000 0.00 0.00 0.00 4.51
277 570 9.941325 AATGTTTGCACCAAATAAAATCAGATA 57.059 25.926 0.00 0.00 35.74 1.98
278 571 8.723311 CAATGTTTGCACCAAATAAAATCAGAT 58.277 29.630 0.00 0.00 35.74 2.90
284 577 7.615582 TTGTCAATGTTTGCACCAAATAAAA 57.384 28.000 0.00 0.00 35.74 1.52
288 581 5.647225 ACTTTTGTCAATGTTTGCACCAAAT 59.353 32.000 0.00 0.00 35.74 2.32
292 585 4.869861 AGAACTTTTGTCAATGTTTGCACC 59.130 37.500 0.00 0.00 31.96 5.01
374 667 6.403866 ACAACACTTTTGGAGCATCAATTA 57.596 33.333 0.00 0.00 36.25 1.40
396 689 7.381139 TCAGCACTCCAAAATATTTTCGAAAAC 59.619 33.333 24.68 8.01 0.00 2.43
401 694 7.816945 AAATCAGCACTCCAAAATATTTTCG 57.183 32.000 10.53 4.86 0.00 3.46
407 700 8.729805 AAAAACAAAATCAGCACTCCAAAATA 57.270 26.923 0.00 0.00 0.00 1.40
435 728 5.613329 ACATTCGTAGAAGTGGTGGTAAAA 58.387 37.500 0.00 0.00 45.90 1.52
436 729 5.217978 ACATTCGTAGAAGTGGTGGTAAA 57.782 39.130 0.00 0.00 45.90 2.01
437 730 4.281435 TGACATTCGTAGAAGTGGTGGTAA 59.719 41.667 0.00 0.00 45.90 2.85
438 731 3.827876 TGACATTCGTAGAAGTGGTGGTA 59.172 43.478 0.00 0.00 45.90 3.25
465 758 2.733026 AGCGCTTGCAAAATTTCATCAC 59.267 40.909 2.64 0.00 42.66 3.06
554 853 9.638239 GAGGCAAAATGATGAACAGTAAAATTA 57.362 29.630 0.00 0.00 0.00 1.40
571 870 5.570320 ACTGTATGTGGTAAGAGGCAAAAT 58.430 37.500 0.00 0.00 0.00 1.82
724 1057 5.076873 GTGATTGGGGCCTGCTTTATATAA 58.923 41.667 0.84 0.00 0.00 0.98
772 1143 2.282887 TTGGCTCCTTTTCCGCCC 60.283 61.111 0.00 0.00 43.12 6.13
788 1172 2.361610 CCGGCCTGCCATTGTCTT 60.362 61.111 9.17 0.00 35.37 3.01
808 1198 3.904800 TTTGGAGAATAGTGGATGCGA 57.095 42.857 0.00 0.00 0.00 5.10
819 1209 7.212976 GGAAAAAGAAGAAGCTTTTGGAGAAT 58.787 34.615 0.00 0.00 44.79 2.40
822 1212 5.069648 AGGGAAAAAGAAGAAGCTTTTGGAG 59.930 40.000 0.00 0.00 44.79 3.86
865 1263 3.445857 GAGGTAAAAGTAGGCTACGCTG 58.554 50.000 18.41 0.00 0.00 5.18
869 1267 9.486497 GTAATAATGGAGGTAAAAGTAGGCTAC 57.514 37.037 16.93 16.93 0.00 3.58
938 1356 2.099098 GAGAGGAGAAGAGAAGAAGCCG 59.901 54.545 0.00 0.00 0.00 5.52
1004 1452 2.040178 GGTGGTATGGAGTAGGAGTGG 58.960 57.143 0.00 0.00 0.00 4.00
1005 1453 2.959707 GAGGTGGTATGGAGTAGGAGTG 59.040 54.545 0.00 0.00 0.00 3.51
1039 1493 1.869767 GATGATCTTGGTGACGATGGC 59.130 52.381 0.00 0.00 0.00 4.40
1235 1710 2.149803 ATTGGCGACGTCGAAGGACA 62.150 55.000 39.74 24.56 43.61 4.02
1264 1739 1.495878 GAGCCGACATAGATGCTGTG 58.504 55.000 0.00 0.00 33.41 3.66
1270 1745 1.528292 GGAGGCGAGCCGACATAGAT 61.528 60.000 8.63 0.00 37.34 1.98
1287 1762 1.601419 CGCCGTTGAAGTAGGGAGGA 61.601 60.000 0.00 0.00 0.00 3.71
1290 1765 1.180456 TGTCGCCGTTGAAGTAGGGA 61.180 55.000 0.00 0.00 0.00 4.20
1437 1912 2.093921 TGGACGTTGAGAACTGTGAACA 60.094 45.455 0.00 0.00 0.00 3.18
1447 1930 3.215642 CAGCATGTGGACGTTGAGA 57.784 52.632 0.00 0.00 0.00 3.27
1481 1982 2.573009 TCATCTGGTTCAGCATCTCCAA 59.427 45.455 0.00 0.00 0.00 3.53
1487 1988 2.026542 TGCTCTTCATCTGGTTCAGCAT 60.027 45.455 0.00 0.00 30.57 3.79
1558 2059 1.362224 AGGTGTAGTGCCAAGACCAT 58.638 50.000 0.00 0.00 32.78 3.55
1702 2217 9.716531 CTGCTATACATCCTCTGAAATTTGATA 57.283 33.333 0.00 0.00 0.00 2.15
1712 2227 5.239744 AGTTCGTACTGCTATACATCCTCTG 59.760 44.000 0.00 0.00 31.99 3.35
1780 2296 8.749499 GTGATAATTTTAGATTGCTGTGAATGC 58.251 33.333 0.00 0.00 0.00 3.56
1811 2328 6.831353 TGGTTTTCAGACATAAACAGAGGAAA 59.169 34.615 0.00 0.00 36.27 3.13
1887 2409 9.685276 TCCAATGATTTTCTTCTTCAGCTATTA 57.315 29.630 0.00 0.00 0.00 0.98
1892 2414 5.860716 GTGTCCAATGATTTTCTTCTTCAGC 59.139 40.000 0.00 0.00 0.00 4.26
1943 2523 4.992688 TCGCTTTCACAGATTGTTTTTGT 58.007 34.783 0.00 0.00 0.00 2.83
1953 2533 1.300971 GGCAGCATCGCTTTCACAGA 61.301 55.000 0.00 0.00 36.40 3.41
1969 2549 1.481615 GGTTTTAGAAACCAGGGGGCA 60.482 52.381 15.71 0.00 40.03 5.36
1970 2550 1.263356 GGTTTTAGAAACCAGGGGGC 58.737 55.000 15.71 0.00 40.03 5.80
1971 2551 2.687003 TGGTTTTAGAAACCAGGGGG 57.313 50.000 18.55 0.00 44.74 5.40
1984 2564 7.360113 AGTAGTTGTGATGGAAATTGGTTTT 57.640 32.000 0.00 0.00 0.00 2.43
2073 2653 8.044908 TCTGGTACAATGAATTACTAAGGGAAC 58.955 37.037 0.00 0.00 38.70 3.62
2224 2826 7.566760 TTAAGCTTGAGATTGTTTGTTGAGA 57.433 32.000 9.86 0.00 0.00 3.27
2442 3630 2.573462 TGCTGATACCAAAGAGCTTCCT 59.427 45.455 0.00 0.00 32.41 3.36
2443 3631 2.991250 TGCTGATACCAAAGAGCTTCC 58.009 47.619 0.00 0.00 32.41 3.46
2444 3632 3.944015 ACATGCTGATACCAAAGAGCTTC 59.056 43.478 0.00 0.00 32.41 3.86
2447 3635 4.082571 ACAAACATGCTGATACCAAAGAGC 60.083 41.667 2.54 0.00 0.00 4.09
2567 3775 3.005554 CAGACCATGAAAGTACAGCCAG 58.994 50.000 0.00 0.00 0.00 4.85
2580 3788 6.347160 CGATGCATACAGAATTACAGACCATG 60.347 42.308 0.00 0.00 0.00 3.66
2622 3830 3.191371 CCTGATACACCCACAAAAGAAGC 59.809 47.826 0.00 0.00 0.00 3.86
2643 3851 3.788333 TCTTTGCAAGCATATCAAGCC 57.212 42.857 0.00 0.00 0.00 4.35



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

AutoCloner maintained by Alex Coulton.