Multiple sequence alignment - TraesCS4A01G152700

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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 TraesCS4A01G152700 chr4A 100.000 2697 0 0 1 2697 309450027 309447331 0.000000e+00 4981
1 TraesCS4A01G152700 chr4A 97.368 114 3 0 1 114 532595571 532595458 7.620000e-46 195
2 TraesCS4A01G152700 chr3A 96.031 2721 81 7 1 2697 105560601 105557884 0.000000e+00 4401
3 TraesCS4A01G152700 chr1A 95.817 2725 83 8 1 2697 554478613 554481334 0.000000e+00 4372
4 TraesCS4A01G152700 chr1B 95.583 2717 92 11 1 2697 633713341 633716049 0.000000e+00 4327
5 TraesCS4A01G152700 chr1B 91.598 2309 154 16 1 2304 427665009 427662736 0.000000e+00 3153
6 TraesCS4A01G152700 chr1D 94.586 2715 118 10 1 2697 51835587 51832884 0.000000e+00 4172
7 TraesCS4A01G152700 chr1D 96.820 1698 53 1 1000 2697 254456798 254458494 0.000000e+00 2835
8 TraesCS4A01G152700 chr5D 96.884 1797 54 2 902 2697 6256002 6254207 0.000000e+00 3007
9 TraesCS4A01G152700 chr5D 96.096 1716 48 2 1000 2697 503336802 503338516 0.000000e+00 2780
10 TraesCS4A01G152700 chr5D 95.489 1441 45 2 1276 2697 481595400 481596839 0.000000e+00 2283
11 TraesCS4A01G152700 chr7B 96.219 1719 58 6 1 1715 137682776 137684491 0.000000e+00 2808
12 TraesCS4A01G152700 chr7B 94.892 1116 41 1 1597 2696 662757072 662755957 0.000000e+00 1731
13 TraesCS4A01G152700 chr7B 95.112 1023 47 3 1526 2546 592597075 592598096 0.000000e+00 1609
14 TraesCS4A01G152700 chr6B 95.525 1743 68 6 1 1736 18741911 18740172 0.000000e+00 2778
15 TraesCS4A01G152700 chrUn 96.618 1567 46 6 82 1644 388893553 388895116 0.000000e+00 2593
16 TraesCS4A01G152700 chrUn 94.737 323 17 0 1581 1903 300486573 300486251 1.110000e-138 503
17 TraesCS4A01G152700 chr4D 93.653 1733 98 9 1 1731 206973246 206971524 0.000000e+00 2580
18 TraesCS4A01G152700 chr3B 95.246 1199 39 1 1517 2697 101922754 101923952 0.000000e+00 1882


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 TraesCS4A01G152700 chr4A 309447331 309450027 2696 True 4981 4981 100.000 1 2697 1 chr4A.!!$R1 2696
1 TraesCS4A01G152700 chr3A 105557884 105560601 2717 True 4401 4401 96.031 1 2697 1 chr3A.!!$R1 2696
2 TraesCS4A01G152700 chr1A 554478613 554481334 2721 False 4372 4372 95.817 1 2697 1 chr1A.!!$F1 2696
3 TraesCS4A01G152700 chr1B 633713341 633716049 2708 False 4327 4327 95.583 1 2697 1 chr1B.!!$F1 2696
4 TraesCS4A01G152700 chr1B 427662736 427665009 2273 True 3153 3153 91.598 1 2304 1 chr1B.!!$R1 2303
5 TraesCS4A01G152700 chr1D 51832884 51835587 2703 True 4172 4172 94.586 1 2697 1 chr1D.!!$R1 2696
6 TraesCS4A01G152700 chr1D 254456798 254458494 1696 False 2835 2835 96.820 1000 2697 1 chr1D.!!$F1 1697
7 TraesCS4A01G152700 chr5D 6254207 6256002 1795 True 3007 3007 96.884 902 2697 1 chr5D.!!$R1 1795
8 TraesCS4A01G152700 chr5D 503336802 503338516 1714 False 2780 2780 96.096 1000 2697 1 chr5D.!!$F2 1697
9 TraesCS4A01G152700 chr5D 481595400 481596839 1439 False 2283 2283 95.489 1276 2697 1 chr5D.!!$F1 1421
10 TraesCS4A01G152700 chr7B 137682776 137684491 1715 False 2808 2808 96.219 1 1715 1 chr7B.!!$F1 1714
11 TraesCS4A01G152700 chr7B 662755957 662757072 1115 True 1731 1731 94.892 1597 2696 1 chr7B.!!$R1 1099
12 TraesCS4A01G152700 chr7B 592597075 592598096 1021 False 1609 1609 95.112 1526 2546 1 chr7B.!!$F2 1020
13 TraesCS4A01G152700 chr6B 18740172 18741911 1739 True 2778 2778 95.525 1 1736 1 chr6B.!!$R1 1735
14 TraesCS4A01G152700 chrUn 388893553 388895116 1563 False 2593 2593 96.618 82 1644 1 chrUn.!!$F1 1562
15 TraesCS4A01G152700 chr4D 206971524 206973246 1722 True 2580 2580 93.653 1 1731 1 chr4D.!!$R1 1730
16 TraesCS4A01G152700 chr3B 101922754 101923952 1198 False 1882 1882 95.246 1517 2697 1 chr3B.!!$F1 1180

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
454 455 0.400594 AAAAGCTGCCCTACGAGGTT 59.599 50.0 0.0 0.0 31.93 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1746 0.314935 ACGCAGTTGCCCAAGAATTG 59.685 50.0 0.0 0.0 43.33 2.32 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
36 37 7.725397 TCAATTGATTCATTATCCCCGAATCTT 59.275 33.333 3.38 0.00 43.48 2.40
258 259 2.940410 GCGGGTTTTCGAAGATGGAATA 59.060 45.455 0.00 0.00 35.04 1.75
345 346 8.725148 GCTTTGGATGAATCGATCTATTATTGT 58.275 33.333 0.00 0.00 0.00 2.71
370 371 8.129211 GTGTAATCTTATTGTGAATAACAGGGC 58.871 37.037 0.00 0.00 40.74 5.19
422 423 7.257722 TCTAAAGCAAGTTTTCAAGAAACTGG 58.742 34.615 5.06 3.68 40.10 4.00
454 455 0.400594 AAAAGCTGCCCTACGAGGTT 59.599 50.000 0.00 0.00 31.93 3.50
464 465 3.804036 CCCTACGAGGTTGCATTGATTA 58.196 45.455 0.00 0.00 31.93 1.75
535 540 8.581578 GTTGGTAGAGGATTCCAAAAATTTGTA 58.418 33.333 5.29 0.00 41.86 2.41
553 558 2.028476 TGTACATCGTTCCCCACAAGAG 60.028 50.000 0.00 0.00 0.00 2.85
602 613 4.371855 TCTATTCGCGTCAGAAATGAGT 57.628 40.909 5.77 0.00 33.43 3.41
671 683 8.791355 ACGTAACAAACAATTTTTATGAGACC 57.209 30.769 0.00 0.00 0.00 3.85
769 782 9.614792 AGACTTTTGAACTTAGAACACTAACAT 57.385 29.630 0.00 0.00 0.00 2.71
891 907 8.296211 ACTCTTATCTTAGTACAAGGTTCTCC 57.704 38.462 0.00 0.00 0.00 3.71
1274 1293 0.620030 TCAGCTGCAATAAGGGCTCA 59.380 50.000 9.47 0.00 32.30 4.26
1369 1388 8.764524 TTCTCAATTTAGAGACTTAAGAGCAC 57.235 34.615 10.09 0.00 43.91 4.40
1490 1509 5.991933 ATATATGACGAGATTGCCAGACT 57.008 39.130 0.00 0.00 0.00 3.24
1501 1520 1.511850 TGCCAGACTTTGTGATCGTG 58.488 50.000 0.00 0.00 0.00 4.35
1549 1568 4.644685 GCTCTTAGGGAATGTGCCATTTTA 59.355 41.667 2.53 0.00 0.00 1.52
1635 1654 4.103627 TCCAGCCAATGATGACACTATGAT 59.896 41.667 0.00 0.00 0.00 2.45
1696 1715 2.680841 CTGTGAGGGTCGTTCTCTCTAG 59.319 54.545 10.43 6.37 43.66 2.43
1707 1726 7.013464 GGGTCGTTCTCTCTAGATAAGAAATCA 59.987 40.741 15.59 4.51 32.46 2.57
1747 1766 0.314935 AATTCTTGGGCAACTGCGTG 59.685 50.000 0.00 0.00 43.26 5.34
2000 2074 7.360113 ACCTTGTTCCATTAAAACACTCAAT 57.640 32.000 0.00 0.00 36.41 2.57
2058 2132 6.322201 CCAACACTTCTATTGGCAAATAGGAT 59.678 38.462 18.86 4.27 43.75 3.24
2158 2233 1.633432 TCGGAATCCACAAACCATCCT 59.367 47.619 0.00 0.00 0.00 3.24
2162 2237 3.562176 GGAATCCACAAACCATCCTGACT 60.562 47.826 0.00 0.00 0.00 3.41
2166 2241 2.487086 CCACAAACCATCCTGACTGACA 60.487 50.000 0.00 0.00 0.00 3.58
2241 2316 6.590068 ACTCAGATTGGAGAAGAATATGGTG 58.410 40.000 0.00 0.00 38.30 4.17
2408 2485 0.099968 TACTCACGTCAGCGGCATAC 59.900 55.000 1.45 0.00 43.45 2.39
2416 2493 2.607635 CGTCAGCGGCATACTTTTATGT 59.392 45.455 1.45 0.00 37.92 2.29
2512 2589 8.697507 AACATCCTAGAAGATTTCACAAAACT 57.302 30.769 0.00 0.00 0.00 2.66
2546 2623 4.332819 AGCTTTCGACTTTTCGGGAATATG 59.667 41.667 0.00 0.00 45.90 1.78
2573 2650 4.724036 GCGGATGAATTAGTCGTTGTTGTC 60.724 45.833 0.00 0.00 0.00 3.18
2644 2721 8.826710 TCTTGGATTATTTACAAGCAGTATTCG 58.173 33.333 0.00 0.00 40.93 3.34
2673 2750 2.515926 TTTTGCAACATTAGCCGCAA 57.484 40.000 0.00 0.00 42.29 4.85
2676 2753 1.175347 TGCAACATTAGCCGCAACCA 61.175 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.519183 TCCAATCCTCAATTCTCCTTTCA 57.481 39.130 0.00 0.00 0.00 2.69
217 218 3.549827 CGCACTTTTGATGTTACTTGGCA 60.550 43.478 0.00 0.00 0.00 4.92
345 346 7.284489 GGCCCTGTTATTCACAATAAGATTACA 59.716 37.037 0.00 0.00 34.23 2.41
370 371 6.014012 TGAAACTTTGGGTATTTAGGGAAGG 58.986 40.000 0.00 0.00 0.00 3.46
400 401 5.793817 ACCAGTTTCTTGAAAACTTGCTTT 58.206 33.333 0.58 0.00 38.32 3.51
454 455 4.766373 TCAAGCCTTTCACTAATCAATGCA 59.234 37.500 0.00 0.00 0.00 3.96
464 465 5.659440 TGTTTTCTTTCAAGCCTTTCACT 57.341 34.783 0.00 0.00 0.00 3.41
516 521 7.312899 ACGATGTACAAATTTTTGGAATCCTC 58.687 34.615 0.00 0.00 42.34 3.71
517 522 7.227049 ACGATGTACAAATTTTTGGAATCCT 57.773 32.000 0.00 0.00 42.34 3.24
535 540 1.348064 TCTCTTGTGGGGAACGATGT 58.652 50.000 0.00 0.00 0.00 3.06
578 583 5.233050 ACTCATTTCTGACGCGAATAGATTG 59.767 40.000 15.93 13.03 0.00 2.67
671 683 8.255206 GGTTAAATGTTAAATGGGGGTTCTTAG 58.745 37.037 0.00 0.00 0.00 2.18
1379 1398 6.131904 TGGGAGATGGTGGAATTTTCCCAT 62.132 45.833 5.28 4.19 45.79 4.00
1549 1568 7.783596 TCGACTAAAGAAATAGTAGGAATCCCT 59.216 37.037 0.00 0.00 46.62 4.20
1583 1602 3.518998 CGCGAGATCCGGGTCACT 61.519 66.667 19.03 0.00 44.85 3.41
1621 1640 8.667076 ATCGAATTGAAATCATAGTGTCATCA 57.333 30.769 0.00 0.00 0.00 3.07
1656 1675 9.793252 CCTCACAGATTGAAAATACTAATTTGG 57.207 33.333 0.00 0.00 35.46 3.28
1727 1746 0.314935 ACGCAGTTGCCCAAGAATTG 59.685 50.000 0.00 0.00 43.33 2.32
2000 2074 8.330993 TCTACACCTGATATATCGTATAACCCA 58.669 37.037 8.19 0.00 0.00 4.51
2058 2132 3.390639 ACTTGGGCATGAATTTGGAAACA 59.609 39.130 0.00 0.00 39.83 2.83
2162 2237 8.859090 ACATATTCCAAAAATTTCTGACTGTCA 58.141 29.630 10.50 10.50 0.00 3.58
2180 2255 7.494625 TCTCGAATAAACACAAGGACATATTCC 59.505 37.037 0.00 0.00 46.33 3.01
2194 2269 6.260050 AGTTTTGCTCAAGTCTCGAATAAACA 59.740 34.615 0.00 0.00 0.00 2.83
2288 2364 1.995376 AAAGAGCACCCGACCAAATT 58.005 45.000 0.00 0.00 0.00 1.82
2290 2366 2.223745 GTAAAAGAGCACCCGACCAAA 58.776 47.619 0.00 0.00 0.00 3.28
2512 2589 7.766219 AAAAGTCGAAAGCTAAGCGATAATA 57.234 32.000 8.42 0.00 36.37 0.98
2546 2623 2.277084 ACGACTAATTCATCCGCCAAC 58.723 47.619 0.00 0.00 0.00 3.77
2573 2650 5.877491 ACTAAGGGGACTAAAGAAACAAGG 58.123 41.667 0.00 0.00 42.68 3.61
2644 2721 6.254373 GGCTAATGTTGCAAAAATAAGAGCTC 59.746 38.462 5.27 5.27 29.43 4.09
2673 2750 6.131972 CTCCATGGATTCACCTATATTGGT 57.868 41.667 16.63 2.68 41.77 3.67


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

AutoCloner maintained by Alex Coulton.