Multiple sequence alignment - TraesCS1B01G290000

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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 TraesCS1B01G290000 chr1B 100.000 3027 0 0 1 3027 505657890 505654864 0.000000e+00 5590
1 TraesCS1B01G290000 chr1D 93.223 2346 93 23 723 3025 378106754 378104432 0.000000e+00 3391
2 TraesCS1B01G290000 chr1D 88.336 583 57 6 7 584 378107740 378107164 0.000000e+00 689
3 TraesCS1B01G290000 chr1A 90.405 1803 93 30 559 2296 478629301 478627514 0.000000e+00 2298
4 TraesCS1B01G290000 chr1A 94.565 736 29 7 2297 3025 478627440 478626709 0.000000e+00 1127
5 TraesCS1B01G290000 chr1A 90.126 476 39 3 1 473 478629901 478629431 1.990000e-171 612


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 TraesCS1B01G290000 chr1B 505654864 505657890 3026 True 5590.000000 5590 100.000000 1 3027 1 chr1B.!!$R1 3026
1 TraesCS1B01G290000 chr1D 378104432 378107740 3308 True 2040.000000 3391 90.779500 7 3025 2 chr1D.!!$R1 3018
2 TraesCS1B01G290000 chr1A 478626709 478629901 3192 True 1345.666667 2298 91.698667 1 3025 3 chr1A.!!$R1 3024

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
102 103 1.124780 TTGTCCCGACTCTTGTGGAA 58.875 50.0 0.00 0.00 0.0 3.53 F
1177 1562 0.868406 GGGATGTGATTCGGCGATTC 59.132 55.0 21.28 21.28 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1568 1.107538 TCGGGCAGGAGATAACGAGG 61.108 60.000 0.0 0.0 0.0 4.63 R
2863 3373 3.077359 GCCAGCTCTCAACAAACAGTAT 58.923 45.455 0.0 0.0 0.0 2.12 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
42 43 3.921021 GGCACTAATTAGATGTCGGATCG 59.079 47.826 19.38 0.00 0.00 3.69
60 61 4.333649 GGATCGCATTTCTCAGATGTTTGA 59.666 41.667 0.00 0.00 0.00 2.69
65 66 6.017933 CGCATTTCTCAGATGTTTGAACTAC 58.982 40.000 0.00 0.00 0.00 2.73
67 68 7.533426 GCATTTCTCAGATGTTTGAACTACAT 58.467 34.615 0.00 0.00 38.86 2.29
83 84 4.493618 ACTACATGGGCATCTATGGTAGT 58.506 43.478 0.00 0.00 36.35 2.73
84 85 4.907875 ACTACATGGGCATCTATGGTAGTT 59.092 41.667 0.00 0.00 36.35 2.24
92 93 3.799232 GCATCTATGGTAGTTGTCCCGAC 60.799 52.174 0.00 0.00 0.00 4.79
95 96 2.233305 ATGGTAGTTGTCCCGACTCT 57.767 50.000 0.00 0.00 29.93 3.24
102 103 1.124780 TTGTCCCGACTCTTGTGGAA 58.875 50.000 0.00 0.00 0.00 3.53
121 122 1.369625 ATCACGGCGGAATTCAGAAC 58.630 50.000 13.24 0.59 0.00 3.01
143 144 8.708378 AGAACTATCCAGACATACATTTGATGA 58.292 33.333 0.00 0.00 0.00 2.92
208 209 8.293699 AGTTTAGCATAACCCAAAGAAATAGG 57.706 34.615 0.00 0.00 0.00 2.57
235 236 7.649533 TCTCATAGAAAACGGTGGTAATAGA 57.350 36.000 0.00 0.00 0.00 1.98
236 237 8.246430 TCTCATAGAAAACGGTGGTAATAGAT 57.754 34.615 0.00 0.00 0.00 1.98
237 238 8.701895 TCTCATAGAAAACGGTGGTAATAGATT 58.298 33.333 0.00 0.00 0.00 2.40
238 239 9.976511 CTCATAGAAAACGGTGGTAATAGATTA 57.023 33.333 0.00 0.00 0.00 1.75
239 240 9.754382 TCATAGAAAACGGTGGTAATAGATTAC 57.246 33.333 4.15 4.15 41.38 1.89
256 257 5.946486 AGATTACCAAGGGAATGGATCTTC 58.054 41.667 0.16 0.00 43.54 2.87
607 686 6.914757 CACTCCTCAAATTCTCTTTGTCAAAC 59.085 38.462 0.00 0.00 0.00 2.93
760 1135 2.094675 GCTGCCTAGGAAAGCAAATGA 58.905 47.619 24.65 0.00 38.82 2.57
809 1184 1.162800 CCCGAAATAGCAGAGCAGGC 61.163 60.000 0.00 0.00 0.00 4.85
812 1187 1.307097 GAAATAGCAGAGCAGGCCTG 58.693 55.000 29.34 29.34 34.88 4.85
1092 1475 2.676822 AGCTCCGTCTTCTCCGCA 60.677 61.111 0.00 0.00 0.00 5.69
1177 1562 0.868406 GGGATGTGATTCGGCGATTC 59.132 55.000 21.28 21.28 0.00 2.52
1183 1568 3.381045 TGTGATTCGGCGATTCTGATAC 58.619 45.455 26.12 18.27 0.00 2.24
1224 1611 5.164041 CGATTCTTTTCCTCTTGAGTTCGTC 60.164 44.000 0.00 0.00 0.00 4.20
1284 1671 4.904154 GCGAGTTCTGTATGTTTGTTGTTC 59.096 41.667 0.00 0.00 0.00 3.18
1286 1673 6.073980 GCGAGTTCTGTATGTTTGTTGTTCTA 60.074 38.462 0.00 0.00 0.00 2.10
1435 1823 2.195683 CGGGGGCATTGCAGGTAT 59.804 61.111 11.39 0.00 0.00 2.73
1436 1824 1.898574 CGGGGGCATTGCAGGTATC 60.899 63.158 11.39 0.00 0.00 2.24
1437 1825 1.531602 GGGGGCATTGCAGGTATCC 60.532 63.158 11.39 0.79 0.00 2.59
1438 1826 1.538666 GGGGCATTGCAGGTATCCT 59.461 57.895 11.39 0.00 0.00 3.24
1439 1827 0.538287 GGGGCATTGCAGGTATCCTC 60.538 60.000 11.39 0.00 0.00 3.71
1440 1828 0.475906 GGGCATTGCAGGTATCCTCT 59.524 55.000 11.39 0.00 0.00 3.69
1441 1829 1.699634 GGGCATTGCAGGTATCCTCTA 59.300 52.381 11.39 0.00 0.00 2.43
1442 1830 2.307098 GGGCATTGCAGGTATCCTCTAT 59.693 50.000 11.39 0.00 0.00 1.98
1443 1831 3.245052 GGGCATTGCAGGTATCCTCTATT 60.245 47.826 11.39 0.00 0.00 1.73
1446 1848 4.505566 GCATTGCAGGTATCCTCTATTCCA 60.506 45.833 3.15 0.00 0.00 3.53
1487 1889 6.721442 GTGTTAAATTTGTGAACACCGTAC 57.279 37.500 18.54 1.13 44.60 3.67
1488 1890 6.256686 GTGTTAAATTTGTGAACACCGTACA 58.743 36.000 18.54 0.00 44.60 2.90
1592 2018 9.366216 GATATGTGATACAACAGTGAACTAACA 57.634 33.333 0.00 0.00 32.52 2.41
1593 2019 6.838198 TGTGATACAACAGTGAACTAACAC 57.162 37.500 0.00 1.54 40.60 3.32
1644 2071 2.047769 TCCCAAGGCAACCCTACTAA 57.952 50.000 0.00 0.00 41.90 2.24
1645 2072 2.568979 TCCCAAGGCAACCCTACTAAT 58.431 47.619 0.00 0.00 41.90 1.73
1657 2084 2.354303 CCCTACTAATGGTCGTGTTGCA 60.354 50.000 0.00 0.00 0.00 4.08
1660 2087 5.297547 CCTACTAATGGTCGTGTTGCATAT 58.702 41.667 0.00 0.00 0.00 1.78
1795 2222 7.040617 GCTGATGAATCATCCAGAAATGTACAT 60.041 37.037 19.38 1.41 39.87 2.29
1895 2322 7.397221 CAATCCAGTATAAGGAGGATAATGCA 58.603 38.462 0.00 0.00 39.86 3.96
2071 2498 3.753294 ACTGTGAACAAGGTACTCCTG 57.247 47.619 0.00 0.00 44.35 3.86
2139 2567 3.243201 GCCCTTATGTTGCTTGTGCTATC 60.243 47.826 0.00 0.00 40.48 2.08
2144 2572 3.407424 TGTTGCTTGTGCTATCTCTGT 57.593 42.857 0.00 0.00 40.48 3.41
2193 2621 5.873164 GTGGTAGGTTAACAACAGTATCTGG 59.127 44.000 8.10 0.00 35.51 3.86
2205 2633 8.135382 ACAACAGTATCTGGAAGTGTAGTTAT 57.865 34.615 1.90 0.00 35.51 1.89
2313 2814 4.744795 AATAGGTGTAACAGAGAGCTGG 57.255 45.455 0.00 0.00 46.60 4.85
2340 2847 7.049133 TGCTTAGTCTTTTGTACAAGGTACAA 58.951 34.615 15.74 15.74 35.84 2.41
2341 2848 7.553402 TGCTTAGTCTTTTGTACAAGGTACAAA 59.447 33.333 23.44 23.44 43.24 2.83
2391 2898 3.374988 TGCAATCAACTAAGGCTCATTCG 59.625 43.478 0.00 0.00 0.00 3.34
2425 2934 2.602676 GGTGGACTGCCCTTAGCCA 61.603 63.158 0.00 0.00 42.71 4.75
2437 2946 2.509964 CCCTTAGCCATAACCTCCAACT 59.490 50.000 0.00 0.00 0.00 3.16
2486 2995 9.129209 CCTAGTACACACACATAATATGATTCG 57.871 37.037 7.33 0.00 0.00 3.34
2549 3058 9.667107 TTTTGGTGTCTATAATTAAGTCCTGAG 57.333 33.333 0.00 0.00 0.00 3.35
2660 3170 5.909621 AATGATTGACTGTCCTGAATTGG 57.090 39.130 5.17 0.00 0.00 3.16
2832 3342 7.875327 ATTAATATTGCTCCTACGTTTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
2850 3360 7.807433 CGTTTTGGTCATTTATCTCATGTTCAA 59.193 33.333 0.00 0.00 0.00 2.69
2932 3442 2.158385 AGTTCCCTTAACATGGCAACCA 60.158 45.455 0.00 0.00 40.83 3.67
2952 3462 9.757227 GCAACCAGTTGGCATTATATTATTTAA 57.243 29.630 12.20 0.00 40.74 1.52
2979 3489 2.544685 CCTGAGTCTTTCACATAGGCG 58.455 52.381 0.00 0.00 0.00 5.52
2980 3490 1.929836 CTGAGTCTTTCACATAGGCGC 59.070 52.381 0.00 0.00 0.00 6.53
3025 3535 5.416271 TGTTTTCTACATAGGTCTCACCC 57.584 43.478 0.00 0.00 39.75 4.61
3026 3536 4.841813 TGTTTTCTACATAGGTCTCACCCA 59.158 41.667 0.00 0.00 39.75 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.902341 TGTAGTTCAAACATCTGAGAAATGC 58.098 36.000 0.00 0.00 0.00 3.56
60 61 4.907875 ACTACCATAGATGCCCATGTAGTT 59.092 41.667 0.00 0.00 0.00 2.24
65 66 4.067896 GACAACTACCATAGATGCCCATG 58.932 47.826 0.00 0.00 32.44 3.66
67 68 2.438021 GGACAACTACCATAGATGCCCA 59.562 50.000 0.00 0.00 32.60 5.36
83 84 1.124780 TTCCACAAGAGTCGGGACAA 58.875 50.000 1.17 0.00 0.00 3.18
84 85 1.275291 GATTCCACAAGAGTCGGGACA 59.725 52.381 1.17 0.00 0.00 4.02
92 93 1.361668 CCGCCGTGATTCCACAAGAG 61.362 60.000 0.00 0.00 43.34 2.85
95 96 0.322098 ATTCCGCCGTGATTCCACAA 60.322 50.000 0.00 0.00 43.34 3.33
102 103 1.066143 AGTTCTGAATTCCGCCGTGAT 60.066 47.619 2.27 0.00 0.00 3.06
121 122 9.933723 TGTATCATCAAATGTATGTCTGGATAG 57.066 33.333 0.00 0.00 0.00 2.08
208 209 6.790285 TTACCACCGTTTTCTATGAGAAAC 57.210 37.500 1.16 0.00 43.25 2.78
213 214 9.754382 GTAATCTATTACCACCGTTTTCTATGA 57.246 33.333 2.04 0.00 37.30 2.15
235 236 4.166144 ACGAAGATCCATTCCCTTGGTAAT 59.834 41.667 0.00 0.00 38.01 1.89
236 237 3.521937 ACGAAGATCCATTCCCTTGGTAA 59.478 43.478 0.00 0.00 38.01 2.85
237 238 3.112263 ACGAAGATCCATTCCCTTGGTA 58.888 45.455 0.00 0.00 38.01 3.25
238 239 1.916181 ACGAAGATCCATTCCCTTGGT 59.084 47.619 0.00 0.00 38.01 3.67
239 240 2.684881 CAACGAAGATCCATTCCCTTGG 59.315 50.000 0.00 0.00 38.18 3.61
256 257 2.811431 TGGGTCATAAAGCTCAACAACG 59.189 45.455 0.00 0.00 0.00 4.10
556 563 9.543783 GGTTACAAACCCACAATTTTGTATTAA 57.456 29.630 7.53 0.00 43.97 1.40
607 686 3.372206 TGTTTTTCGCAACAACCATTTGG 59.628 39.130 0.00 0.00 37.00 3.28
760 1135 3.692406 GCCGGACGGGAAGAGTGT 61.692 66.667 5.05 0.00 38.47 3.55
783 1158 3.827625 CTCTGCTATTTCGGGAGATACG 58.172 50.000 0.00 0.00 39.57 3.06
790 1165 1.162800 GCCTGCTCTGCTATTTCGGG 61.163 60.000 0.00 0.00 0.00 5.14
791 1166 1.162800 GGCCTGCTCTGCTATTTCGG 61.163 60.000 0.00 0.00 0.00 4.30
809 1184 0.546598 ATAAAGGCTCCGGGAACAGG 59.453 55.000 0.00 0.00 0.00 4.00
812 1187 3.494573 CCTCTTATAAAGGCTCCGGGAAC 60.495 52.174 0.00 0.00 0.00 3.62
878 1255 1.594310 GGAGGAGCTCGCACTTCTT 59.406 57.895 7.83 0.00 0.00 2.52
974 1354 1.074872 GGCGGTTTAGGAGACGAACG 61.075 60.000 0.00 0.00 33.73 3.95
1177 1562 3.057174 GGCAGGAGATAACGAGGTATCAG 60.057 52.174 10.39 0.00 33.60 2.90
1183 1568 1.107538 TCGGGCAGGAGATAACGAGG 61.108 60.000 0.00 0.00 0.00 4.63
1224 1611 3.066203 GCCCCGAAATTAGTAACCACATG 59.934 47.826 0.00 0.00 0.00 3.21
1284 1671 8.980481 AGGTATTCCCAAACAGATGTTTATAG 57.020 34.615 10.43 3.57 45.54 1.31
1286 1673 7.557719 CAGAGGTATTCCCAAACAGATGTTTAT 59.442 37.037 10.43 4.12 45.54 1.40
1331 1719 2.892852 TGGATTTGCCTTTCAGGTCAAG 59.107 45.455 0.00 0.00 37.80 3.02
1411 1799 4.738998 CAATGCCCCCGCCACTCA 62.739 66.667 0.00 0.00 0.00 3.41
1446 1848 2.158564 ACACTATATGCCCAGCAATGCT 60.159 45.455 0.00 0.00 43.62 3.79
1504 1906 8.976353 ACTATCAACATCAGTAGAAGAACTCAT 58.024 33.333 0.00 0.00 0.00 2.90
1548 1970 8.047911 TCACATATCAATCAATTGCCCAAATTT 58.952 29.630 0.00 0.00 36.28 1.82
1635 2062 2.354403 GCAACACGACCATTAGTAGGGT 60.354 50.000 0.00 0.00 39.74 4.34
1644 2071 5.239306 CCATCTTTATATGCAACACGACCAT 59.761 40.000 0.00 0.00 0.00 3.55
1645 2072 4.574421 CCATCTTTATATGCAACACGACCA 59.426 41.667 0.00 0.00 0.00 4.02
1841 2268 9.590451 CATATAGGAAACATTCAAAACATTGCT 57.410 29.630 0.00 0.00 0.00 3.91
1842 2269 9.369904 ACATATAGGAAACATTCAAAACATTGC 57.630 29.630 0.00 0.00 0.00 3.56
1845 2272 9.253832 TGGACATATAGGAAACATTCAAAACAT 57.746 29.630 0.00 0.00 0.00 2.71
1846 2273 8.642935 TGGACATATAGGAAACATTCAAAACA 57.357 30.769 0.00 0.00 0.00 2.83
1895 2322 1.768077 GGTAGCCAGGGAGCCATCT 60.768 63.158 0.00 0.00 0.00 2.90
1989 2416 8.999431 GTGAACCTGACAGAAAATTATAGTCAA 58.001 33.333 3.32 0.00 38.58 3.18
2139 2567 6.566197 AACTGGAAAAGAAATGCTACAGAG 57.434 37.500 0.00 0.00 0.00 3.35
2144 2572 7.106439 TGTTCAAACTGGAAAAGAAATGCTA 57.894 32.000 0.00 0.00 0.00 3.49
2193 2621 7.758528 ACATGGACGACTAAATAACTACACTTC 59.241 37.037 0.00 0.00 0.00 3.01
2205 2633 5.361427 TCTGTCAAAACATGGACGACTAAA 58.639 37.500 0.00 0.00 36.83 1.85
2313 2814 6.373186 ACCTTGTACAAAAGACTAAGCAAC 57.627 37.500 10.03 0.00 0.00 4.17
2391 2898 5.357032 CAGTCCACCCATAGATTACAAAACC 59.643 44.000 0.00 0.00 0.00 3.27
2425 2934 5.723887 AGATCAAGAGTGAGTTGGAGGTTAT 59.276 40.000 0.00 0.00 37.14 1.89
2437 2946 3.358111 ACGAGAGGAGATCAAGAGTGA 57.642 47.619 0.00 0.00 38.41 3.41
2740 3250 9.423061 CAAATATATGATAACACTCATGACGGA 57.577 33.333 0.00 0.00 36.55 4.69
2850 3360 9.230122 TCAACAAACAGTATATTCATGTCATGT 57.770 29.630 12.54 0.00 31.91 3.21
2863 3373 3.077359 GCCAGCTCTCAACAAACAGTAT 58.923 45.455 0.00 0.00 0.00 2.12
2952 3462 7.512992 CCTATGTGAAAGACTCAGGGATTAAT 58.487 38.462 0.00 0.00 33.60 1.40
2979 3489 7.553044 ACAACCAAATACTAGACTAATTGAGGC 59.447 37.037 0.00 0.00 0.00 4.70
2980 3490 9.449719 AACAACCAAATACTAGACTAATTGAGG 57.550 33.333 0.00 0.61 0.00 3.86


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

AutoCloner maintained by Alex Coulton.