Multiple sequence alignment - TraesCS1A01G187200

Loading Multiple Alignment...

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 TraesCS1A01G187200 chr1A 100.000 2469 0 0 1 2469 338132079 338129611 0 4560
1 TraesCS1A01G187200 chr7D 92.922 1865 87 20 1 1834 461787289 461789139 0 2671
2 TraesCS1A01G187200 chr7D 92.123 1879 99 14 1 1834 473126761 473124887 0 2604
3 TraesCS1A01G187200 chr7D 92.180 1867 88 26 1 1834 117569314 117571155 0 2586
4 TraesCS1A01G187200 chr6D 92.094 1872 106 16 1 1834 48970127 48971994 0 2599
5 TraesCS1A01G187200 chr6D 93.231 1625 78 13 239 1834 143363484 143365105 0 2362
6 TraesCS1A01G187200 chr6D 90.634 1751 100 17 112 1834 344613384 344611670 0 2266
7 TraesCS1A01G187200 chr6D 92.249 1174 62 11 688 1834 11450637 11449466 0 1637
8 TraesCS1A01G187200 chr4B 91.998 1862 118 14 1 1834 158231278 158233136 0 2584
9 TraesCS1A01G187200 chr4B 91.363 1864 117 24 1 1834 192628318 192630167 0 2510
10 TraesCS1A01G187200 chr1D 91.778 1873 106 28 1 1834 380264535 380262672 0 2562
11 TraesCS1A01G187200 chr1D 91.743 1865 88 24 1 1834 385736479 385734650 0 2531
12 TraesCS1A01G187200 chr1B 91.725 1873 108 21 1 1834 592832889 592831025 0 2556
13 TraesCS1A01G187200 chr2D 91.720 1872 108 13 4 1834 40405224 40403359 0 2555
14 TraesCS1A01G187200 chr2D 92.189 1754 95 15 1 1727 511279369 511281107 0 2442
15 TraesCS1A01G187200 chr2D 94.984 638 28 4 1834 2469 282101866 282101231 0 998
16 TraesCS1A01G187200 chr4A 91.288 1871 117 17 1 1834 431592233 431594094 0 2510
17 TraesCS1A01G187200 chr4A 91.441 923 51 12 938 1834 641351022 641351942 0 1242
18 TraesCS1A01G187200 chr2A 91.328 1868 117 23 1 1834 95695755 95693899 0 2510
19 TraesCS1A01G187200 chr2A 95.141 638 27 4 1834 2469 63300094 63300729 0 1003
20 TraesCS1A01G187200 chr3D 91.298 1287 71 14 586 1832 299047188 299048473 0 1718
21 TraesCS1A01G187200 chr7A 95.455 638 25 4 1834 2469 517410527 517411162 0 1014
22 TraesCS1A01G187200 chr3A 95.298 638 26 4 1834 2469 744574341 744573706 0 1009
23 TraesCS1A01G187200 chr3A 95.118 635 30 1 1836 2469 369377168 369376534 0 1000
24 TraesCS1A01G187200 chr3A 94.343 654 33 4 1820 2469 369395658 369395005 0 1000
25 TraesCS1A01G187200 chr3A 94.860 642 28 5 1830 2469 53926424 53927062 0 998
26 TraesCS1A01G187200 chr5D 95.298 638 25 5 1834 2469 537628122 537627488 0 1007
27 TraesCS1A01G187200 chr5A 94.860 642 29 4 1830 2469 111672280 111672919 0 1000


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 TraesCS1A01G187200 chr1A 338129611 338132079 2468 True 4560 4560 100.000 1 2469 1 chr1A.!!$R1 2468
1 TraesCS1A01G187200 chr7D 461787289 461789139 1850 False 2671 2671 92.922 1 1834 1 chr7D.!!$F2 1833
2 TraesCS1A01G187200 chr7D 473124887 473126761 1874 True 2604 2604 92.123 1 1834 1 chr7D.!!$R1 1833
3 TraesCS1A01G187200 chr7D 117569314 117571155 1841 False 2586 2586 92.180 1 1834 1 chr7D.!!$F1 1833
4 TraesCS1A01G187200 chr6D 48970127 48971994 1867 False 2599 2599 92.094 1 1834 1 chr6D.!!$F1 1833
5 TraesCS1A01G187200 chr6D 143363484 143365105 1621 False 2362 2362 93.231 239 1834 1 chr6D.!!$F2 1595
6 TraesCS1A01G187200 chr6D 344611670 344613384 1714 True 2266 2266 90.634 112 1834 1 chr6D.!!$R2 1722
7 TraesCS1A01G187200 chr6D 11449466 11450637 1171 True 1637 1637 92.249 688 1834 1 chr6D.!!$R1 1146
8 TraesCS1A01G187200 chr4B 158231278 158233136 1858 False 2584 2584 91.998 1 1834 1 chr4B.!!$F1 1833
9 TraesCS1A01G187200 chr4B 192628318 192630167 1849 False 2510 2510 91.363 1 1834 1 chr4B.!!$F2 1833
10 TraesCS1A01G187200 chr1D 380262672 380264535 1863 True 2562 2562 91.778 1 1834 1 chr1D.!!$R1 1833
11 TraesCS1A01G187200 chr1D 385734650 385736479 1829 True 2531 2531 91.743 1 1834 1 chr1D.!!$R2 1833
12 TraesCS1A01G187200 chr1B 592831025 592832889 1864 True 2556 2556 91.725 1 1834 1 chr1B.!!$R1 1833
13 TraesCS1A01G187200 chr2D 40403359 40405224 1865 True 2555 2555 91.720 4 1834 1 chr2D.!!$R1 1830
14 TraesCS1A01G187200 chr2D 511279369 511281107 1738 False 2442 2442 92.189 1 1727 1 chr2D.!!$F1 1726
15 TraesCS1A01G187200 chr2D 282101231 282101866 635 True 998 998 94.984 1834 2469 1 chr2D.!!$R2 635
16 TraesCS1A01G187200 chr4A 431592233 431594094 1861 False 2510 2510 91.288 1 1834 1 chr4A.!!$F1 1833
17 TraesCS1A01G187200 chr4A 641351022 641351942 920 False 1242 1242 91.441 938 1834 1 chr4A.!!$F2 896
18 TraesCS1A01G187200 chr2A 95693899 95695755 1856 True 2510 2510 91.328 1 1834 1 chr2A.!!$R1 1833
19 TraesCS1A01G187200 chr2A 63300094 63300729 635 False 1003 1003 95.141 1834 2469 1 chr2A.!!$F1 635
20 TraesCS1A01G187200 chr3D 299047188 299048473 1285 False 1718 1718 91.298 586 1832 1 chr3D.!!$F1 1246
21 TraesCS1A01G187200 chr7A 517410527 517411162 635 False 1014 1014 95.455 1834 2469 1 chr7A.!!$F1 635
22 TraesCS1A01G187200 chr3A 744573706 744574341 635 True 1009 1009 95.298 1834 2469 1 chr3A.!!$R3 635
23 TraesCS1A01G187200 chr3A 369376534 369377168 634 True 1000 1000 95.118 1836 2469 1 chr3A.!!$R1 633
24 TraesCS1A01G187200 chr3A 369395005 369395658 653 True 1000 1000 94.343 1820 2469 1 chr3A.!!$R2 649
25 TraesCS1A01G187200 chr3A 53926424 53927062 638 False 998 998 94.860 1830 2469 1 chr3A.!!$F1 639
26 TraesCS1A01G187200 chr5D 537627488 537628122 634 True 1007 1007 95.298 1834 2469 1 chr5D.!!$R1 635
27 TraesCS1A01G187200 chr5A 111672280 111672919 639 False 1000 1000 94.860 1830 2469 1 chr5A.!!$F1 639

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
921 967 0.392327 GCCACTCCTCTGCTTCTTCC 60.392 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2544 0.468214 CGAGAGGGCCCAGAGATACA 60.468 60.0 27.56 0.0 0.0 2.29 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
160 167 9.674068 AAACTAAGTTCAGATCCTTCTTATTCC 57.326 33.333 0.00 0.0 0.00 3.01
162 169 5.638530 AGTTCAGATCCTTCTTATTCCCC 57.361 43.478 0.00 0.0 0.00 4.81
191 199 6.973229 ATCAAGCTTTGGTGATATTTTTGC 57.027 33.333 0.00 0.0 32.68 3.68
519 548 4.729595 ACGGCGAAGGTTTCATATTTTTC 58.270 39.130 16.62 0.0 0.00 2.29
569 599 1.112916 AGCCTTTGAAACCCCGTTGG 61.113 55.000 0.00 0.0 41.37 3.77
576 606 2.757980 GAAACCCCGTTGGCCAGCTA 62.758 60.000 18.19 0.0 37.83 3.32
582 612 0.958822 CCGTTGGCCAGCTAAAAACT 59.041 50.000 18.19 0.0 0.00 2.66
624 654 1.049402 GCCTAACCCTAGCTCCGAAT 58.951 55.000 0.00 0.0 0.00 3.34
627 657 2.434702 CCTAACCCTAGCTCCGAATGTT 59.565 50.000 0.00 0.0 0.00 2.71
921 967 0.392327 GCCACTCCTCTGCTTCTTCC 60.392 60.000 0.00 0.0 0.00 3.46
1047 1093 1.580132 CGCGCCGCTAATGTTGTTC 60.580 57.895 7.78 0.0 0.00 3.18
1082 1128 2.101783 CAAGAATGGCAACTATGGGCA 58.898 47.619 0.00 0.0 45.36 5.36
1142 1188 7.255070 GCAGGTTAGATCTCATGATTTTTCTCC 60.255 40.741 0.00 0.0 32.19 3.71
1454 1522 7.206687 TCCCTTTTATTTTTGTGTAGTTGCTG 58.793 34.615 0.00 0.0 0.00 4.41
1468 1536 6.148811 GTGTAGTTGCTGTAGGATTTGCTTAA 59.851 38.462 0.00 0.0 0.00 1.85
1599 1704 2.299867 TGTGCTCTATGCTCTGTGTTGA 59.700 45.455 0.00 0.0 43.37 3.18
1600 1705 3.244181 TGTGCTCTATGCTCTGTGTTGAA 60.244 43.478 0.00 0.0 43.37 2.69
1619 1779 8.028354 GTGTTGAATAATTTGTGGATCATGTGA 58.972 33.333 0.00 0.0 0.00 3.58
1697 1884 8.573035 TCAGTTTTGTACACTTTCAGTTTCTTT 58.427 29.630 0.00 0.0 0.00 2.52
1761 1966 4.126520 AGGGCCCAAATTGAAACTAAGA 57.873 40.909 27.56 0.0 0.00 2.10
1999 2206 5.205056 AGTATGCCTCTACTTGACTAGCTT 58.795 41.667 0.00 0.0 0.00 3.74
2115 2322 4.653801 TGACCCATCTGTTAGCTTAGCATA 59.346 41.667 7.07 0.0 0.00 3.14
2140 2347 7.792374 ATGATCGTTACAGTTTCATTGCTAT 57.208 32.000 0.00 0.0 0.00 2.97
2305 2512 5.181811 TGTTTGTTGAGTTGGCATAGATCAG 59.818 40.000 0.00 0.0 0.00 2.90
2357 2565 0.178987 GTATCTCTGGGCCCTCTCGA 60.179 60.000 25.70 14.4 0.00 4.04
2363 2571 1.051812 CTGGGCCCTCTCGATAATGT 58.948 55.000 25.70 0.0 0.00 2.71
2382 2590 9.155975 GATAATGTACATCACTATAAGCCTTGG 57.844 37.037 9.23 0.0 0.00 3.61
2394 2602 3.439857 AAGCCTTGGAAGCAATGTAGA 57.560 42.857 0.00 0.0 0.00 2.59
2418 2626 9.310449 AGATAATGAGTTAGTTACGGGATGTAT 57.690 33.333 0.00 0.0 31.81 2.29
2448 2656 4.544651 GAACGAGTAAAGAGACTTTCCGT 58.455 43.478 0.00 0.0 31.12 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 114 8.563123 TCCATTTTCATATGGTAAACGTGTTA 57.437 30.769 2.13 0.00 44.48 2.41
233 247 6.176183 CAATGTTTCATAGAGACCAAGGAGT 58.824 40.000 0.00 0.00 0.00 3.85
389 408 5.941058 TCGAGGTAAAATGAGCACCATTAAA 59.059 36.000 5.03 0.00 44.28 1.52
569 599 4.156190 GGTTTAGAGGAGTTTTTAGCTGGC 59.844 45.833 0.00 0.00 0.00 4.85
576 606 2.511659 GCGGGGTTTAGAGGAGTTTTT 58.488 47.619 0.00 0.00 0.00 1.94
582 612 3.078836 CCCGCGGGGTTTAGAGGA 61.079 66.667 37.42 0.00 38.25 3.71
624 654 1.338973 GGTATGATCGGACGGCTAACA 59.661 52.381 0.00 0.00 0.00 2.41
627 657 0.111832 AGGGTATGATCGGACGGCTA 59.888 55.000 0.00 0.00 0.00 3.93
661 691 7.363031 ACTTCTAGAATACCACATCTAAGGGA 58.637 38.462 5.44 0.00 0.00 4.20
676 706 4.654262 TGCCCTCGGAATTACTTCTAGAAT 59.346 41.667 5.44 0.00 0.00 2.40
782 812 1.013596 CACAACCAACAAGTCTCGCA 58.986 50.000 0.00 0.00 0.00 5.10
921 967 2.125512 CCCAAAGTCGCCGGAGAG 60.126 66.667 8.65 0.00 0.00 3.20
1035 1081 4.451096 TCCTTCGAAGTGAACAACATTAGC 59.549 41.667 23.03 0.00 31.87 3.09
1041 1087 2.801111 GACCTCCTTCGAAGTGAACAAC 59.199 50.000 23.03 5.54 31.87 3.32
1043 1089 2.036387 TGACCTCCTTCGAAGTGAACA 58.964 47.619 23.03 13.19 31.87 3.18
1047 1093 3.386768 TTCTTGACCTCCTTCGAAGTG 57.613 47.619 23.03 14.56 0.00 3.16
1288 1334 0.108472 CTGACGGCAGATTGAGCTCA 60.108 55.000 14.96 13.74 45.17 4.26
1375 1443 7.031372 GCTTGTTCAATTGAATCATCTGCTTA 58.969 34.615 23.05 6.54 36.33 3.09
1454 1522 5.125417 TGACCAGCAATTAAGCAAATCCTAC 59.875 40.000 0.00 0.00 36.85 3.18
1468 1536 2.479566 AACGAGTGATGACCAGCAAT 57.520 45.000 0.00 0.00 0.00 3.56
1619 1779 8.906867 ACAAATTAAGCAACACATAGCATAGAT 58.093 29.630 0.00 0.00 0.00 1.98
1628 1788 6.343716 TGATCCACAAATTAAGCAACACAT 57.656 33.333 0.00 0.00 0.00 3.21
1697 1884 2.358582 TCGGTGTTGTCTGACGAAACTA 59.641 45.455 16.12 4.58 0.00 2.24
1761 1966 1.274703 ATGAGACGGCCCAACCAGAT 61.275 55.000 0.00 0.00 39.03 2.90
1999 2206 9.362151 AGGAAACTTAACCATCTTTGATTAACA 57.638 29.630 0.00 0.00 37.44 2.41
2115 2322 6.500684 AGCAATGAAACTGTAACGATCATT 57.499 33.333 0.00 0.00 40.37 2.57
2140 2347 8.565896 ACATGTATAAGTCATGAAGAAAGCAA 57.434 30.769 11.92 0.00 43.47 3.91
2205 2412 2.412870 TGATAGCACACAAGGTGTTCG 58.587 47.619 0.00 0.00 45.08 3.95
2305 2512 4.141914 ACTCGGAGTGACAAATCCTAATCC 60.142 45.833 10.41 0.00 33.12 3.01
2337 2544 0.468214 CGAGAGGGCCCAGAGATACA 60.468 60.000 27.56 0.00 0.00 2.29
2357 2565 8.880244 TCCAAGGCTTATAGTGATGTACATTAT 58.120 33.333 10.30 6.78 35.92 1.28
2363 2571 5.130311 TGCTTCCAAGGCTTATAGTGATGTA 59.870 40.000 0.00 0.00 0.00 2.29
2394 2602 9.085645 TGATACATCCCGTAACTAACTCATTAT 57.914 33.333 0.00 0.00 32.59 1.28
2418 2626 5.413833 AGTCTCTTTACTCGTTCCGTAATGA 59.586 40.000 0.00 0.00 33.08 2.57


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

AutoCloner maintained by Alex Coulton.