Multiple sequence alignment - TraesCS3B01G441900

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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 TraesCS3B01G441900 chr3B 100.000 2627 0 0 1 2627 681202520 681199894 0 4852
1 TraesCS3B01G441900 chr3B 98.433 2616 40 1 1 2616 731127443 731130057 0 4602
2 TraesCS3B01G441900 chr7B 98.641 2208 30 0 1 2208 554160874 554163081 0 3912
3 TraesCS3B01G441900 chr7B 97.970 591 12 0 2026 2616 554163425 554164015 0 1026
4 TraesCS3B01G441900 chr5A 98.551 2208 32 0 1 2208 346306687 346308894 0 3901
5 TraesCS3B01G441900 chr5A 94.322 634 31 5 1985 2616 346308720 346309350 0 966
6 TraesCS3B01G441900 chr4B 98.505 2208 33 0 1 2208 139743014 139745221 0 3895
7 TraesCS3B01G441900 chr4B 98.116 2176 41 0 1 2176 2599090 2601265 0 3792
8 TraesCS3B01G441900 chr4B 94.006 634 33 5 1985 2616 139745047 139745677 0 955
9 TraesCS3B01G441900 chr3A 98.505 2208 33 0 1 2208 199412448 199414655 0 3895
10 TraesCS3B01G441900 chr3A 93.849 634 34 5 1985 2616 199414481 199415111 0 950
11 TraesCS3B01G441900 chr1A 98.485 2178 33 0 1 2178 63763310 63761133 0 3840
12 TraesCS3B01G441900 chr1A 94.872 585 26 4 2034 2616 320477390 320476808 0 911
13 TraesCS3B01G441900 chr1B 98.614 2165 30 0 1 2165 167929736 167927572 0 3832
14 TraesCS3B01G441900 chr1B 94.881 586 25 5 2034 2616 167927752 167927169 0 911
15 TraesCS3B01G441900 chr5B 98.308 2068 35 0 1 2068 383536694 383534627 0 3626
16 TraesCS3B01G441900 chr5B 95.214 585 24 4 2034 2616 56908667 56909249 0 922
17 TraesCS3B01G441900 chr4A 95.214 585 24 4 2034 2616 683249668 683249086 0 922


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 TraesCS3B01G441900 chr3B 681199894 681202520 2626 True 4852.0 4852 100.0000 1 2627 1 chr3B.!!$R1 2626
1 TraesCS3B01G441900 chr3B 731127443 731130057 2614 False 4602.0 4602 98.4330 1 2616 1 chr3B.!!$F1 2615
2 TraesCS3B01G441900 chr7B 554160874 554164015 3141 False 2469.0 3912 98.3055 1 2616 2 chr7B.!!$F1 2615
3 TraesCS3B01G441900 chr5A 346306687 346309350 2663 False 2433.5 3901 96.4365 1 2616 2 chr5A.!!$F1 2615
4 TraesCS3B01G441900 chr4B 2599090 2601265 2175 False 3792.0 3792 98.1160 1 2176 1 chr4B.!!$F1 2175
5 TraesCS3B01G441900 chr4B 139743014 139745677 2663 False 2425.0 3895 96.2555 1 2616 2 chr4B.!!$F2 2615
6 TraesCS3B01G441900 chr3A 199412448 199415111 2663 False 2422.5 3895 96.1770 1 2616 2 chr3A.!!$F1 2615
7 TraesCS3B01G441900 chr1A 63761133 63763310 2177 True 3840.0 3840 98.4850 1 2178 1 chr1A.!!$R1 2177
8 TraesCS3B01G441900 chr1A 320476808 320477390 582 True 911.0 911 94.8720 2034 2616 1 chr1A.!!$R2 582
9 TraesCS3B01G441900 chr1B 167927169 167929736 2567 True 2371.5 3832 96.7475 1 2616 2 chr1B.!!$R1 2615
10 TraesCS3B01G441900 chr5B 383534627 383536694 2067 True 3626.0 3626 98.3080 1 2068 1 chr5B.!!$R1 2067
11 TraesCS3B01G441900 chr5B 56908667 56909249 582 False 922.0 922 95.2140 2034 2616 1 chr5B.!!$F1 582
12 TraesCS3B01G441900 chr4A 683249086 683249668 582 True 922.0 922 95.2140 2034 2616 1 chr4A.!!$R1 582

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
21 22 0.390472 GAGAACTCAAGCCTCCCGTG 60.390 60.000 0.0 0.0 0.0 4.94 F
298 299 1.409241 GCATGGGAAGCCATCAGAGAA 60.409 52.381 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1228 2.029739 CACCAATTCAGCTGTGCATTGA 60.030 45.455 25.0 2.29 0.0 2.57 R
2054 2055 1.573108 TTTTGGGTTTTGGTGGCTCA 58.427 45.000 0.0 0.00 0.0 4.26 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
21 22 0.390472 GAGAACTCAAGCCTCCCGTG 60.390 60.000 0.00 0.00 0.00 4.94
70 71 3.055819 GGCTCAATCAGGTCAGTTACTCA 60.056 47.826 0.00 0.00 0.00 3.41
129 130 3.913799 TGGGGATTTTTCTGTCTAGGTGA 59.086 43.478 0.00 0.00 0.00 4.02
298 299 1.409241 GCATGGGAAGCCATCAGAGAA 60.409 52.381 0.00 0.00 0.00 2.87
553 554 7.446001 GCTAAATATAGGCTCAAGCATTCTT 57.554 36.000 4.13 0.00 44.36 2.52
886 887 6.595682 ACATTAGCTACTGGCATGAACTAAT 58.404 36.000 14.83 0.00 44.79 1.73
982 983 3.117474 TGGGTTTGTTCAGTGGGTTGATA 60.117 43.478 0.00 0.00 0.00 2.15
1615 1616 2.087461 AAGGGGATCCAGGCCATCC 61.087 63.158 15.23 9.01 39.45 3.51
1677 1678 2.041620 CAGACCTTTTGGGAAGGATGGA 59.958 50.000 11.52 0.00 46.08 3.41
1708 1709 9.778741 CAATGGCCTAGTAACTTAGAATTATGA 57.221 33.333 3.32 0.00 0.00 2.15
2054 2055 2.430704 TAGGTGGTTCCGTCGACCCT 62.431 60.000 10.58 11.01 41.99 4.34
2103 2104 3.618750 GTGGTTCCGTCGACCCCA 61.619 66.667 10.58 8.31 36.30 4.96
2408 2459 8.795513 CATCCACATCAACAAAAGCCATATATA 58.204 33.333 0.00 0.00 0.00 0.86
2409 2460 8.759481 TCCACATCAACAAAAGCCATATATAA 57.241 30.769 0.00 0.00 0.00 0.98
2616 3145 0.252467 CACCTCTCCCTCTCCCAACT 60.252 60.000 0.00 0.00 0.00 3.16
2617 3146 0.252467 ACCTCTCCCTCTCCCAACTG 60.252 60.000 0.00 0.00 0.00 3.16
2618 3147 0.252467 CCTCTCCCTCTCCCAACTGT 60.252 60.000 0.00 0.00 0.00 3.55
2619 3148 0.901124 CTCTCCCTCTCCCAACTGTG 59.099 60.000 0.00 0.00 0.00 3.66
2620 3149 0.487325 TCTCCCTCTCCCAACTGTGA 59.513 55.000 0.00 0.00 0.00 3.58
2621 3150 0.610687 CTCCCTCTCCCAACTGTGAC 59.389 60.000 0.00 0.00 0.00 3.67
2622 3151 0.191064 TCCCTCTCCCAACTGTGACT 59.809 55.000 0.00 0.00 0.00 3.41
2623 3152 1.059913 CCCTCTCCCAACTGTGACTT 58.940 55.000 0.00 0.00 0.00 3.01
2624 3153 1.421646 CCCTCTCCCAACTGTGACTTT 59.578 52.381 0.00 0.00 0.00 2.66
2625 3154 2.551071 CCCTCTCCCAACTGTGACTTTC 60.551 54.545 0.00 0.00 0.00 2.62
2626 3155 2.370189 CCTCTCCCAACTGTGACTTTCT 59.630 50.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.648467 GGAGGTTTCGGAGTGCATGC 61.648 60.000 11.82 11.82 0.00 4.06
70 71 1.495148 GCCCTAACCCTAGCTCCAATT 59.505 52.381 0.00 0.00 0.00 2.32
129 130 3.679389 ACGAAATCCTCACAGCAAAGAT 58.321 40.909 0.00 0.00 0.00 2.40
298 299 3.132646 TGTTCCTTCAAATGCAACAAGCT 59.867 39.130 0.00 0.00 45.94 3.74
550 551 4.361420 CATTCATGTGCACACAACAAAGA 58.639 39.130 24.37 8.68 45.41 2.52
553 554 2.471818 GCATTCATGTGCACACAACAA 58.528 42.857 24.37 12.54 45.41 2.83
747 748 9.988815 TTTGCATAATAACCAACTTACAATTGT 57.011 25.926 16.68 16.68 0.00 2.71
982 983 2.677968 ATTGTTGGGGGCCACTGCTT 62.678 55.000 7.61 0.00 37.74 3.91
1227 1228 2.029739 CACCAATTCAGCTGTGCATTGA 60.030 45.455 25.00 2.29 0.00 2.57
1615 1616 9.784680 CTTAATTCATCTTGTTCATTTCTCCAG 57.215 33.333 0.00 0.00 0.00 3.86
1677 1678 3.652057 AGTTACTAGGCCATTGCACAT 57.348 42.857 5.01 0.00 40.13 3.21
2054 2055 1.573108 TTTTGGGTTTTGGTGGCTCA 58.427 45.000 0.00 0.00 0.00 4.26
2103 2104 3.077088 TCAACTAGGGTCTAGGGTGTCTT 59.923 47.826 6.86 0.00 0.00 3.01
2408 2459 7.504238 TGGTGGTGTACTTTAAGAATCAATGTT 59.496 33.333 0.00 0.00 0.00 2.71
2409 2460 7.001674 TGGTGGTGTACTTTAAGAATCAATGT 58.998 34.615 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.