Multiple sequence alignment - TraesCS5A01G393600

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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 TraesCS5A01G393600 chr5A 100.000 3125 0 0 1 3125 589286376 589283252 0.000000e+00 5771.0
1 TraesCS5A01G393600 chr5A 95.724 1450 47 3 449 1885 474030107 474031554 0.000000e+00 2320.0
2 TraesCS5A01G393600 chr5A 95.594 1430 48 3 469 1885 474163264 474164691 0.000000e+00 2278.0
3 TraesCS5A01G393600 chr5A 93.798 129 8 0 1 129 474029401 474029529 8.840000e-46 195.0
4 TraesCS5A01G393600 chr5A 91.473 129 11 0 1 129 474295043 474295171 8.910000e-41 178.0
5 TraesCS5A01G393600 chr7A 94.948 2771 104 11 371 3125 111947068 111949818 0.000000e+00 4309.0
6 TraesCS5A01G393600 chr7A 93.724 2645 138 15 500 3125 714969500 714972135 0.000000e+00 3940.0
7 TraesCS5A01G393600 chr7A 91.880 234 11 1 1 226 111946250 111946483 1.400000e-83 320.0
8 TraesCS5A01G393600 chr4A 93.622 2744 146 10 406 3125 177774306 177771568 0.000000e+00 4071.0
9 TraesCS5A01G393600 chr3A 95.939 2487 85 8 648 3120 26628172 26625688 0.000000e+00 4019.0
10 TraesCS5A01G393600 chr3A 94.757 2556 109 18 587 3125 609945191 609942644 0.000000e+00 3954.0
11 TraesCS5A01G393600 chr3A 93.505 2556 140 11 591 3125 734661759 734659209 0.000000e+00 3777.0
12 TraesCS5A01G393600 chr3A 94.008 2370 121 7 770 3125 144301117 144298755 0.000000e+00 3570.0
13 TraesCS5A01G393600 chr2D 93.667 2700 140 17 452 3125 635127661 635124967 0.000000e+00 4010.0
14 TraesCS5A01G393600 chr5D 93.993 2497 133 7 641 3122 208495123 208497617 0.000000e+00 3764.0
15 TraesCS5A01G393600 chr5D 91.228 1197 82 9 479 1659 57020108 57021297 0.000000e+00 1607.0
16 TraesCS5A01G393600 chrUn 92.183 2661 179 14 479 3125 96943793 96946438 0.000000e+00 3735.0
17 TraesCS5A01G393600 chr1D 91.748 2666 191 14 474 3125 363527209 363524559 0.000000e+00 3677.0
18 TraesCS5A01G393600 chr1D 92.878 2443 166 6 684 3125 232137328 232134893 0.000000e+00 3541.0
19 TraesCS5A01G393600 chr6D 91.779 1192 78 7 479 1655 90429551 90430737 0.000000e+00 1640.0
20 TraesCS5A01G393600 chr3D 90.894 1230 88 9 461 1673 475904898 475903676 0.000000e+00 1629.0
21 TraesCS5A01G393600 chr7D 86.682 428 51 6 422 846 13364849 13365273 1.310000e-128 470.0
22 TraesCS5A01G393600 chr3B 91.892 37 3 0 1 37 16176522 16176558 6.000000e-03 52.8


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 TraesCS5A01G393600 chr5A 589283252 589286376 3124 True 5771.0 5771 100.000 1 3125 1 chr5A.!!$R1 3124
1 TraesCS5A01G393600 chr5A 474163264 474164691 1427 False 2278.0 2278 95.594 469 1885 1 chr5A.!!$F1 1416
2 TraesCS5A01G393600 chr5A 474029401 474031554 2153 False 1257.5 2320 94.761 1 1885 2 chr5A.!!$F3 1884
3 TraesCS5A01G393600 chr7A 714969500 714972135 2635 False 3940.0 3940 93.724 500 3125 1 chr7A.!!$F1 2625
4 TraesCS5A01G393600 chr7A 111946250 111949818 3568 False 2314.5 4309 93.414 1 3125 2 chr7A.!!$F2 3124
5 TraesCS5A01G393600 chr4A 177771568 177774306 2738 True 4071.0 4071 93.622 406 3125 1 chr4A.!!$R1 2719
6 TraesCS5A01G393600 chr3A 26625688 26628172 2484 True 4019.0 4019 95.939 648 3120 1 chr3A.!!$R1 2472
7 TraesCS5A01G393600 chr3A 609942644 609945191 2547 True 3954.0 3954 94.757 587 3125 1 chr3A.!!$R3 2538
8 TraesCS5A01G393600 chr3A 734659209 734661759 2550 True 3777.0 3777 93.505 591 3125 1 chr3A.!!$R4 2534
9 TraesCS5A01G393600 chr3A 144298755 144301117 2362 True 3570.0 3570 94.008 770 3125 1 chr3A.!!$R2 2355
10 TraesCS5A01G393600 chr2D 635124967 635127661 2694 True 4010.0 4010 93.667 452 3125 1 chr2D.!!$R1 2673
11 TraesCS5A01G393600 chr5D 208495123 208497617 2494 False 3764.0 3764 93.993 641 3122 1 chr5D.!!$F2 2481
12 TraesCS5A01G393600 chr5D 57020108 57021297 1189 False 1607.0 1607 91.228 479 1659 1 chr5D.!!$F1 1180
13 TraesCS5A01G393600 chrUn 96943793 96946438 2645 False 3735.0 3735 92.183 479 3125 1 chrUn.!!$F1 2646
14 TraesCS5A01G393600 chr1D 363524559 363527209 2650 True 3677.0 3677 91.748 474 3125 1 chr1D.!!$R2 2651
15 TraesCS5A01G393600 chr1D 232134893 232137328 2435 True 3541.0 3541 92.878 684 3125 1 chr1D.!!$R1 2441
16 TraesCS5A01G393600 chr6D 90429551 90430737 1186 False 1640.0 1640 91.779 479 1655 1 chr6D.!!$F1 1176
17 TraesCS5A01G393600 chr3D 475903676 475904898 1222 True 1629.0 1629 90.894 461 1673 1 chr3D.!!$R1 1212

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
644 1148 0.802494 CTGTAGCGCGGGATTTTTGT 59.198 50.0 8.83 0.0 0.00 2.83 F
1643 2168 0.307760 AAAGTTCGCAAGCCTCAACG 59.692 50.0 0.00 0.0 37.18 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2417 0.669077 GGCGTAGAGATCATCACGGT 59.331 55.0 12.82 0.0 34.83 4.83 R
2987 3528 0.321298 CGTTCCAAGAACACGGGGAT 60.321 55.0 8.11 0.0 0.00 3.85 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
26 27 1.735198 GTTCCGGATGAACGCGACA 60.735 57.895 15.93 13.50 43.65 4.35
52 53 1.664321 GCATCCCGAGACGTACTGGT 61.664 60.000 0.00 0.00 0.00 4.00
644 1148 0.802494 CTGTAGCGCGGGATTTTTGT 59.198 50.000 8.83 0.00 0.00 2.83
1012 1537 2.363306 ATTGCAGATGGCCGGAATTA 57.637 45.000 5.05 0.00 43.89 1.40
1336 1861 1.550976 AGTGGATCCGTCTGAGGTTTC 59.449 52.381 7.39 0.00 0.00 2.78
1398 1923 3.194968 ACCGGATTTGTACGACTCTTCAT 59.805 43.478 9.46 0.00 0.00 2.57
1426 1951 3.442625 TGGTACTCAGATTACCGACACTG 59.557 47.826 11.40 0.00 41.87 3.66
1643 2168 0.307760 AAAGTTCGCAAGCCTCAACG 59.692 50.000 0.00 0.00 37.18 4.10
1685 2211 0.844221 AAGAAGAAGGGCCCTCAGCT 60.844 55.000 28.84 20.15 43.05 4.24
1743 2275 0.902516 GGCAGAGACCTCAGGACTGT 60.903 60.000 0.00 0.00 0.00 3.55
1972 2504 2.289072 GCTTTGGCTGTCTCTAGTGACA 60.289 50.000 22.61 22.61 43.72 3.58
2231 2766 8.802267 AGCATAAACTTATTCTTTACTTTGGCA 58.198 29.630 0.00 0.00 0.00 4.92
2331 2872 6.851222 ATTAATGTAGCGTCTTCCTCATTG 57.149 37.500 0.00 0.00 0.00 2.82
2537 3078 6.377429 CGAGCCACTATTATACTTCCTATGGA 59.623 42.308 0.00 0.00 0.00 3.41
2630 3171 0.109365 CGCGCCAATGGTTTTCATGA 60.109 50.000 0.00 0.00 35.99 3.07
2651 3192 2.365582 TGAGACCGATGATGAGAACGA 58.634 47.619 0.00 0.00 0.00 3.85
2749 3290 9.155785 ACACAGGGCTATACTACACTAAAATAT 57.844 33.333 0.00 0.00 0.00 1.28
2805 3346 6.645415 CCGTTTTTAGAAGCTCTGAACTCTTA 59.355 38.462 0.00 0.00 0.00 2.10
3107 3649 4.220382 CCTCTAAATGGTCCAATGTTTGCA 59.780 41.667 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.249073 CGTCTCGGGATGCGATCTTT 60.249 55.000 0.00 0.00 0.00 2.52
644 1148 5.489637 TCTGGAAACTACAGGGGCTAAATTA 59.510 40.000 0.00 0.00 36.62 1.40
1012 1537 2.107204 ACTCAGCAAACTCCTTGTGGAT 59.893 45.455 0.00 0.00 42.29 3.41
1188 1713 1.816835 GTAGGTGACAGGTGATGACGA 59.183 52.381 0.00 0.00 0.00 4.20
1336 1861 0.949105 CCAACCGTCTTGAAGTCCGG 60.949 60.000 19.14 19.14 45.72 5.14
1398 1923 5.066893 GTCGGTAATCTGAGTACCACACATA 59.933 44.000 27.74 8.20 41.04 2.29
1426 1951 6.540551 GTGGATAGGGTTTTCTCAATCTTCTC 59.459 42.308 0.00 0.00 0.00 2.87
1495 2020 3.762288 TCTGAATACCTCGTGTAGTTGCT 59.238 43.478 0.00 0.00 31.61 3.91
1643 2168 3.268103 TTGCGGCCCCTCTTCTTCC 62.268 63.158 0.00 0.00 0.00 3.46
1743 2275 1.890041 CACCGAGCCACACCGAAAA 60.890 57.895 0.00 0.00 0.00 2.29
1838 2370 2.747855 CCTGAACCAAGGCGAGGC 60.748 66.667 0.00 0.00 0.00 4.70
1885 2417 0.669077 GGCGTAGAGATCATCACGGT 59.331 55.000 12.82 0.00 34.83 4.83
1949 2481 1.002430 CACTAGAGACAGCCAAAGCCA 59.998 52.381 0.00 0.00 41.25 4.75
1972 2504 1.603455 CCTCCATGGCAACGTTGGT 60.603 57.895 28.33 0.00 41.81 3.67
2062 2597 6.740960 GCAATCTCCATACTAGTGAGCTGATT 60.741 42.308 5.39 7.41 0.00 2.57
2182 2717 7.856145 CTCTCATAGAGCTTACAACCAAATT 57.144 36.000 0.00 0.00 35.30 1.82
2537 3078 7.814107 ACGCATCATTAATGATCAAAGTTGTTT 59.186 29.630 24.94 1.36 45.23 2.83
2630 3171 2.952310 TCGTTCTCATCATCGGTCTCAT 59.048 45.455 0.00 0.00 0.00 2.90
2651 3192 3.838317 TGTGATAAGTAGGCACTCCTTGT 59.162 43.478 0.00 0.00 40.66 3.16
2756 3297 1.263356 GAGGGTAGTGTACACAGGCA 58.737 55.000 27.06 7.11 33.51 4.75
2818 3359 1.114722 CCGGGGTGGCGTAACCTATA 61.115 60.000 8.31 0.00 40.35 1.31
2827 3368 4.157120 CCTAAGTCCGGGGTGGCG 62.157 72.222 0.00 0.00 37.80 5.69
2987 3528 0.321298 CGTTCCAAGAACACGGGGAT 60.321 55.000 8.11 0.00 0.00 3.85
3016 3558 3.535561 CTGAATTGGACCGCTTATGTCT 58.464 45.455 0.00 0.00 33.22 3.41
3023 3565 2.044946 GGGCTGAATTGGACCGCT 60.045 61.111 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.