Multiple sequence alignment - TraesCS2A01G364800

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 TraesCS2A01G364800 chr2A 100.000 2654 0 0 1 2654 608773862 608776515 0 4902
1 TraesCS2A01G364800 chr2A 90.851 940 84 1 1 940 670072882 670071945 0 1258
2 TraesCS2A01G364800 chr2A 96.078 510 16 2 2148 2654 667242941 667242433 0 828
3 TraesCS2A01G364800 chr2A 95.481 509 21 1 2148 2654 460301573 460301065 0 811
4 TraesCS2A01G364800 chr2D 93.755 1217 34 13 954 2147 468808972 468810169 0 1788
5 TraesCS2A01G364800 chr3D 94.006 951 55 1 1 951 457651023 457651971 0 1439
6 TraesCS2A01G364800 chr3D 90.576 955 60 13 1 955 594932604 594931680 0 1238
7 TraesCS2A01G364800 chr7D 93.711 954 58 1 1 954 400211309 400210358 0 1428
8 TraesCS2A01G364800 chr6D 93.936 940 55 1 1 940 36258309 36257372 0 1419
9 TraesCS2A01G364800 chr6D 93.501 954 60 1 1 954 263938405 263939356 0 1417
10 TraesCS2A01G364800 chr3A 92.727 935 58 7 1 934 566078185 566077260 0 1341
11 TraesCS2A01G364800 chr2B 92.857 910 20 15 954 1831 547040566 547041462 0 1279
12 TraesCS2A01G364800 chr7A 91.118 957 61 8 1 955 217772625 217771691 0 1275
13 TraesCS2A01G364800 chr7A 96.109 514 17 2 2144 2654 108707796 108707283 0 835
14 TraesCS2A01G364800 chr7A 95.858 507 20 1 2148 2654 150179109 150178604 0 819
15 TraesCS2A01G364800 chr7A 95.155 516 22 1 2142 2654 191100291 191099776 0 811
16 TraesCS2A01G364800 chr6B 90.963 675 58 2 261 934 474509368 474510040 0 905
17 TraesCS2A01G364800 chr4A 96.282 511 16 1 2147 2654 637284635 637284125 0 835
18 TraesCS2A01G364800 chr6A 96.260 508 17 2 2148 2654 1735937 1735431 0 832
19 TraesCS2A01G364800 chr6A 95.669 508 20 1 2149 2654 419638532 419638025 0 815
20 TraesCS2A01G364800 chr5A 96.252 507 18 1 2148 2654 626960030 626960535 0 830


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 TraesCS2A01G364800 chr2A 608773862 608776515 2653 False 4902 4902 100.000 1 2654 1 chr2A.!!$F1 2653
1 TraesCS2A01G364800 chr2A 670071945 670072882 937 True 1258 1258 90.851 1 940 1 chr2A.!!$R3 939
2 TraesCS2A01G364800 chr2A 667242433 667242941 508 True 828 828 96.078 2148 2654 1 chr2A.!!$R2 506
3 TraesCS2A01G364800 chr2A 460301065 460301573 508 True 811 811 95.481 2148 2654 1 chr2A.!!$R1 506
4 TraesCS2A01G364800 chr2D 468808972 468810169 1197 False 1788 1788 93.755 954 2147 1 chr2D.!!$F1 1193
5 TraesCS2A01G364800 chr3D 457651023 457651971 948 False 1439 1439 94.006 1 951 1 chr3D.!!$F1 950
6 TraesCS2A01G364800 chr3D 594931680 594932604 924 True 1238 1238 90.576 1 955 1 chr3D.!!$R1 954
7 TraesCS2A01G364800 chr7D 400210358 400211309 951 True 1428 1428 93.711 1 954 1 chr7D.!!$R1 953
8 TraesCS2A01G364800 chr6D 36257372 36258309 937 True 1419 1419 93.936 1 940 1 chr6D.!!$R1 939
9 TraesCS2A01G364800 chr6D 263938405 263939356 951 False 1417 1417 93.501 1 954 1 chr6D.!!$F1 953
10 TraesCS2A01G364800 chr3A 566077260 566078185 925 True 1341 1341 92.727 1 934 1 chr3A.!!$R1 933
11 TraesCS2A01G364800 chr2B 547040566 547041462 896 False 1279 1279 92.857 954 1831 1 chr2B.!!$F1 877
12 TraesCS2A01G364800 chr7A 217771691 217772625 934 True 1275 1275 91.118 1 955 1 chr7A.!!$R4 954
13 TraesCS2A01G364800 chr7A 108707283 108707796 513 True 835 835 96.109 2144 2654 1 chr7A.!!$R1 510
14 TraesCS2A01G364800 chr7A 150178604 150179109 505 True 819 819 95.858 2148 2654 1 chr7A.!!$R2 506
15 TraesCS2A01G364800 chr7A 191099776 191100291 515 True 811 811 95.155 2142 2654 1 chr7A.!!$R3 512
16 TraesCS2A01G364800 chr6B 474509368 474510040 672 False 905 905 90.963 261 934 1 chr6B.!!$F1 673
17 TraesCS2A01G364800 chr4A 637284125 637284635 510 True 835 835 96.282 2147 2654 1 chr4A.!!$R1 507
18 TraesCS2A01G364800 chr6A 1735431 1735937 506 True 832 832 96.260 2148 2654 1 chr6A.!!$R1 506
19 TraesCS2A01G364800 chr6A 419638025 419638532 507 True 815 815 95.669 2149 2654 1 chr6A.!!$R2 505
20 TraesCS2A01G364800 chr5A 626960030 626960535 505 False 830 830 96.252 2148 2654 1 chr5A.!!$F1 506

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
583 585 0.177141 CGCCCATTTCGTTCCCTCTA 59.823 55.0 0.0 0.0 0.0 2.43 F
1287 1302 0.669077 ATCGACAGCTACATCCGGTC 59.331 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1579 0.170116 TACGGTTACGGTGCTAACGG 59.83 55.0 5.81 0.0 46.48 4.44 R
2449 2485 0.320160 GCACGAACCGGGACTAAAGT 60.32 55.0 6.32 0.0 28.17 2.66 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
95 96 3.000819 TCCTCGCCGGTCCATGTT 61.001 61.111 1.90 0.00 0.00 2.71
168 169 1.604378 CGGGAGGCCTTGTTCTGAT 59.396 57.895 6.77 0.00 0.00 2.90
231 232 2.047274 ACCAACACGCGATGGAGG 60.047 61.111 27.86 20.98 37.24 4.30
371 372 0.537371 TCAGGCGGAGATAGATGCGA 60.537 55.000 0.00 0.00 35.89 5.10
385 386 2.503356 AGATGCGACCTTCAAGGAGATT 59.497 45.455 11.59 0.00 37.67 2.40
433 434 2.815298 GAGCGAGGACGAGGACGAG 61.815 68.421 0.00 0.00 42.66 4.18
434 435 2.818714 GCGAGGACGAGGACGAGA 60.819 66.667 0.00 0.00 42.66 4.04
448 449 1.275291 GACGAGACATTCCCAACTCCA 59.725 52.381 0.00 0.00 0.00 3.86
519 520 2.512515 GCCGGCAGCGAAGAAGAT 60.513 61.111 24.80 0.00 0.00 2.40
522 523 1.651987 CCGGCAGCGAAGAAGATTAA 58.348 50.000 0.00 0.00 0.00 1.40
575 577 2.359478 GACCACCGCCCATTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
583 585 0.177141 CGCCCATTTCGTTCCCTCTA 59.823 55.000 0.00 0.00 0.00 2.43
612 614 1.201414 CTTGGCGGGCTTAAAATCGTT 59.799 47.619 2.38 0.00 0.00 3.85
652 654 2.826488 AGTTGTGGAGGCAGAGACTAT 58.174 47.619 0.00 0.00 0.00 2.12
696 698 1.152694 TAATGCTCATGGCCAGCCC 60.153 57.895 13.05 0.00 40.92 5.19
712 714 3.254657 CCAGCCCAAAATGAAAGAACGTA 59.745 43.478 0.00 0.00 0.00 3.57
849 851 6.183360 GCAAGTATGAACGAATACTTTTCGGA 60.183 38.462 15.40 0.00 46.44 4.55
942 945 2.462468 CGTTACAACGCACGGACG 59.538 61.111 1.04 0.00 46.06 4.79
1091 1105 8.512966 TCAGTCTTCCTGATATATATCTTCGG 57.487 38.462 20.74 17.38 45.34 4.30
1287 1302 0.669077 ATCGACAGCTACATCCGGTC 59.331 55.000 0.00 0.00 0.00 4.79
1564 1579 2.032071 CAACCCCCGTGTGGAGAC 59.968 66.667 0.00 0.00 37.49 3.36
1565 1580 3.246880 AACCCCCGTGTGGAGACC 61.247 66.667 0.00 0.00 37.49 3.85
1568 1583 3.622826 CCCCGTGTGGAGACCGTT 61.623 66.667 0.00 0.00 37.49 4.44
1683 1719 7.225341 TCAGTCTGATAAACGATGGATTCAATG 59.775 37.037 0.00 0.00 0.00 2.82
1796 1832 9.424319 TGATCTAGAGTAGTTGATTTGTTTGAC 57.576 33.333 0.00 0.00 0.00 3.18
1835 1871 4.155099 TGGTTGTGCTATGTATTCCGTTTG 59.845 41.667 0.00 0.00 0.00 2.93
1842 1878 4.270325 GCTATGTATTCCGTTTGGTCTGAC 59.730 45.833 0.00 0.00 36.30 3.51
1996 2032 0.179124 GAGGAGCTCGTGTCATGGAC 60.179 60.000 14.78 0.00 0.00 4.02
2062 2098 4.883083 AGAAGACGTCAATACTGCAAAGA 58.117 39.130 19.50 0.00 0.00 2.52
2083 2119 1.595382 GGGTGATCCGAATCCAGCG 60.595 63.158 0.00 0.00 33.83 5.18
2139 2175 4.624125 GCTCTAACTTGTGGGAGCTAATGT 60.624 45.833 15.61 0.00 45.15 2.71
2283 2319 2.600173 CCACGTGGGCCATTGGTT 60.600 61.111 27.57 0.03 0.00 3.67
2296 2332 2.617788 CCATTGGTTCCGGTTCATCTGA 60.618 50.000 0.00 0.00 0.00 3.27
2358 2394 3.329889 TCGCTCCTGGCCCACAAT 61.330 61.111 0.00 0.00 37.74 2.71
2377 2413 1.302192 CATTGGTCCCGGTTCGTGT 60.302 57.895 0.00 0.00 0.00 4.49
2405 2441 3.705072 ACCGGGACTAAAGATTAGACCTG 59.295 47.826 6.32 15.89 36.14 4.00
2449 2485 1.557832 CGGGACTAATGGGGTTGAGAA 59.442 52.381 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 232 2.280797 TGTGCCAGCGGTGAGTTC 60.281 61.111 17.83 4.28 0.00 3.01
340 341 2.786495 CGCCTGACGCTGGAGGTAT 61.786 63.158 6.89 0.00 34.21 2.73
345 346 2.904178 TATCTCCGCCTGACGCTGGA 62.904 60.000 6.89 0.00 41.76 3.86
371 372 2.234908 CCTCGTGAATCTCCTTGAAGGT 59.765 50.000 11.60 0.00 36.53 3.50
385 386 2.154798 CTTCGTTGGCCTCCTCGTGA 62.155 60.000 3.32 0.00 0.00 4.35
433 434 1.534729 GTGGTGGAGTTGGGAATGTC 58.465 55.000 0.00 0.00 0.00 3.06
434 435 0.250727 CGTGGTGGAGTTGGGAATGT 60.251 55.000 0.00 0.00 0.00 2.71
459 460 1.152483 ATGGTTGTGGCAGCAAGGT 60.152 52.632 0.00 0.00 0.00 3.50
519 520 0.748005 GGCGAGCTCCCATGCTTTAA 60.748 55.000 8.47 0.00 44.17 1.52
522 523 4.845580 CGGCGAGCTCCCATGCTT 62.846 66.667 17.97 0.00 44.17 3.91
677 679 1.458639 GGGCTGGCCATGAGCATTAC 61.459 60.000 16.34 0.05 46.50 1.89
678 680 1.152694 GGGCTGGCCATGAGCATTA 60.153 57.895 16.34 0.00 46.50 1.90
696 698 5.164196 CGCCAACATACGTTCTTTCATTTTG 60.164 40.000 0.00 0.00 31.13 2.44
703 705 1.802365 GACCGCCAACATACGTTCTTT 59.198 47.619 0.00 0.00 31.13 2.52
712 714 0.887933 GTCCAAATGACCGCCAACAT 59.112 50.000 0.00 0.00 38.09 2.71
824 826 5.957796 CCGAAAAGTATTCGTTCATACTTGC 59.042 40.000 14.15 10.39 45.41 4.01
929 932 0.240678 TACATACGTCCGTGCGTTGT 59.759 50.000 6.81 12.01 43.04 3.32
1041 1047 0.754957 CCGAGAGCCTCACCTCAGAT 60.755 60.000 0.00 0.00 34.26 2.90
1416 1431 1.526917 CCTCCCGGATCATGTTGGC 60.527 63.158 0.73 0.00 0.00 4.52
1564 1579 0.170116 TACGGTTACGGTGCTAACGG 59.830 55.000 5.81 0.00 46.48 4.44
1565 1580 1.913403 CTTACGGTTACGGTGCTAACG 59.087 52.381 5.81 0.00 46.48 3.18
1567 1582 2.166829 TCCTTACGGTTACGGTGCTAA 58.833 47.619 5.81 0.00 46.48 3.09
1568 1583 1.832883 TCCTTACGGTTACGGTGCTA 58.167 50.000 5.81 0.00 46.48 3.49
1665 1701 7.094634 GCTCATACCATTGAATCCATCGTTTAT 60.095 37.037 0.00 0.00 0.00 1.40
1683 1719 2.570442 GCTATAGGAGCGCTCATACC 57.430 55.000 36.27 21.49 42.62 2.73
1748 1784 9.811995 GATCAATGATTCAAAAAGGATGATGAA 57.188 29.630 0.00 0.00 36.35 2.57
1754 1790 9.917887 ACTCTAGATCAATGATTCAAAAAGGAT 57.082 29.630 0.00 0.00 0.00 3.24
1796 1832 5.801947 GCACAACCATTTAATACAAGCTGAG 59.198 40.000 0.00 0.00 0.00 3.35
1835 1871 1.546476 AGATCAAGTGACCGTCAGACC 59.454 52.381 0.08 0.00 0.00 3.85
1996 2032 1.133025 GCTCCACCATGAAATCAACCG 59.867 52.381 0.00 0.00 0.00 4.44
2062 2098 1.477558 GCTGGATTCGGATCACCCATT 60.478 52.381 5.94 0.00 33.77 3.16
2139 2175 6.940298 CCCTGTTTTCTACTAGTGATTGGAAA 59.060 38.462 5.39 5.82 0.00 3.13
2296 2332 1.133294 ACCAATCGGGACCAAAAGGTT 60.133 47.619 0.00 0.00 41.15 3.50
2358 2394 1.004320 CACGAACCGGGACCAATGA 60.004 57.895 6.32 0.00 28.17 2.57
2377 2413 4.903045 AATCTTTAGTCCCGGTTTGAGA 57.097 40.909 0.00 0.00 0.00 3.27
2405 2441 0.672711 GTGCCTCAAACCGGGACTAC 60.673 60.000 6.32 0.00 39.49 2.73
2449 2485 0.320160 GCACGAACCGGGACTAAAGT 60.320 55.000 6.32 0.00 28.17 2.66
2513 2553 2.989422 AAAACTGAAAAGGCGATCCG 57.011 45.000 0.00 0.00 37.47 4.18


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

AutoCloner maintained by Alex Coulton.