Multiple sequence alignment - TraesCS3B01G166300

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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 TraesCS3B01G166300 chr3B 100.000 3284 0 0 1 3284 166543438 166546721 0 6065
1 TraesCS3B01G166300 chr3B 91.223 3304 222 41 1 3284 1089965 1093220 0 4433
2 TraesCS3B01G166300 chr3B 93.657 2680 155 10 2 2672 444087698 444085025 0 3993
3 TraesCS3B01G166300 chr3B 86.277 2689 325 40 629 3284 361602578 361605255 0 2881
4 TraesCS3B01G166300 chr3B 92.888 914 58 7 1 912 17151025 17151933 0 1321
5 TraesCS3B01G166300 chr2B 92.135 3293 204 22 1 3284 608936808 608933562 0 4595
6 TraesCS3B01G166300 chr2B 90.855 2373 194 17 925 3284 141327212 141329574 0 3158
7 TraesCS3B01G166300 chr2B 86.840 2690 309 37 629 3284 107102844 107105522 0 2964
8 TraesCS3B01G166300 chr1B 93.768 3065 166 16 1 3057 439485580 439488627 0 4578
9 TraesCS3B01G166300 chr1B 90.965 2125 154 21 3 2097 417454054 417456170 0 2826
10 TraesCS3B01G166300 chr1B 91.783 1144 64 8 1 1142 599544842 599545957 0 1565
11 TraesCS3B01G166300 chr6B 90.143 3297 286 26 1 3284 670218815 670222085 0 4252
12 TraesCS3B01G166300 chr6B 86.150 2686 331 38 629 3284 459222750 459220076 0 2861
13 TraesCS3B01G166300 chr4B 90.694 2493 195 24 811 3284 1279609 1277135 0 3284
14 TraesCS3B01G166300 chr5B 88.927 2321 174 29 1 2295 10384576 10386839 0 2785
15 TraesCS3B01G166300 chr2D 91.173 963 78 7 1 963 395576912 395577867 0 1301


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 TraesCS3B01G166300 chr3B 166543438 166546721 3283 False 6065 6065 100.000 1 3284 1 chr3B.!!$F3 3283
1 TraesCS3B01G166300 chr3B 1089965 1093220 3255 False 4433 4433 91.223 1 3284 1 chr3B.!!$F1 3283
2 TraesCS3B01G166300 chr3B 444085025 444087698 2673 True 3993 3993 93.657 2 2672 1 chr3B.!!$R1 2670
3 TraesCS3B01G166300 chr3B 361602578 361605255 2677 False 2881 2881 86.277 629 3284 1 chr3B.!!$F4 2655
4 TraesCS3B01G166300 chr3B 17151025 17151933 908 False 1321 1321 92.888 1 912 1 chr3B.!!$F2 911
5 TraesCS3B01G166300 chr2B 608933562 608936808 3246 True 4595 4595 92.135 1 3284 1 chr2B.!!$R1 3283
6 TraesCS3B01G166300 chr2B 141327212 141329574 2362 False 3158 3158 90.855 925 3284 1 chr2B.!!$F2 2359
7 TraesCS3B01G166300 chr2B 107102844 107105522 2678 False 2964 2964 86.840 629 3284 1 chr2B.!!$F1 2655
8 TraesCS3B01G166300 chr1B 439485580 439488627 3047 False 4578 4578 93.768 1 3057 1 chr1B.!!$F2 3056
9 TraesCS3B01G166300 chr1B 417454054 417456170 2116 False 2826 2826 90.965 3 2097 1 chr1B.!!$F1 2094
10 TraesCS3B01G166300 chr1B 599544842 599545957 1115 False 1565 1565 91.783 1 1142 1 chr1B.!!$F3 1141
11 TraesCS3B01G166300 chr6B 670218815 670222085 3270 False 4252 4252 90.143 1 3284 1 chr6B.!!$F1 3283
12 TraesCS3B01G166300 chr6B 459220076 459222750 2674 True 2861 2861 86.150 629 3284 1 chr6B.!!$R1 2655
13 TraesCS3B01G166300 chr4B 1277135 1279609 2474 True 3284 3284 90.694 811 3284 1 chr4B.!!$R1 2473
14 TraesCS3B01G166300 chr5B 10384576 10386839 2263 False 2785 2785 88.927 1 2295 1 chr5B.!!$F1 2294
15 TraesCS3B01G166300 chr2D 395576912 395577867 955 False 1301 1301 91.173 1 963 1 chr2D.!!$F1 962

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
280 282 1.162698 TTCTACAGACTACGCAGCGT 58.837 50.0 26.25 26.25 44.35 5.07 F
1639 2007 0.175302 CAGCAAGCACACAAACCCAA 59.825 50.0 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 2111 0.250945 TGTTGCTTACGGATTGCCCA 60.251 50.0 0.00 0.0 34.14 5.36 R
3234 3743 0.172803 GGTCACCACTACGCGATCTT 59.827 55.0 15.93 0.0 0.00 2.40 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
72 73 2.567615 AGACGCTAGGACCATTCTTTGT 59.432 45.455 0.00 0.00 0.00 2.83
77 78 4.327680 GCTAGGACCATTCTTTGTTGACT 58.672 43.478 0.00 0.00 0.00 3.41
280 282 1.162698 TTCTACAGACTACGCAGCGT 58.837 50.000 26.25 26.25 44.35 5.07
564 566 3.025262 TGCCATCTAGAATGCAATGCAA 58.975 40.909 13.45 0.00 43.62 4.08
644 646 6.055588 AGTAACCATGATATGTAGTTGCCAC 58.944 40.000 0.00 0.00 0.00 5.01
708 734 2.554032 GCCATGTTTACTCAACTGCAGT 59.446 45.455 15.25 15.25 36.21 4.40
761 811 5.549347 TGTTTAATGAAATGCAGTTGCCAT 58.451 33.333 3.09 0.00 41.18 4.40
859 980 5.549347 TGCCATGTTTAATGAAATGCAGTT 58.451 33.333 0.00 0.00 0.00 3.16
860 981 5.408909 TGCCATGTTTAATGAAATGCAGTTG 59.591 36.000 3.09 0.00 0.00 3.16
861 982 5.671825 GCCATGTTTAATGAAATGCAGTTGC 60.672 40.000 3.09 0.00 42.50 4.17
862 983 5.163834 CCATGTTTAATGAAATGCAGTTGCC 60.164 40.000 3.09 0.00 41.18 4.52
873 994 3.316071 TGCAGTTGCCATGTTTAATGG 57.684 42.857 1.06 0.00 41.18 3.16
934 1296 9.236691 CATGTTTAATGTACTGTATTTGCCATC 57.763 33.333 0.00 0.00 0.00 3.51
1053 1418 3.756434 CCAGGAAGAAATAAAGCGTCCAA 59.244 43.478 0.00 0.00 35.49 3.53
1160 1526 4.502604 CGGACAAAGGAAGGAACTACTTCA 60.503 45.833 4.11 0.00 46.73 3.02
1227 1594 1.573829 TTCGAACAGGACGGCATTGC 61.574 55.000 0.00 0.00 0.00 3.56
1251 1618 6.522761 CGTGCTGTCACATACTAAAAGTAAC 58.477 40.000 0.00 0.00 43.28 2.50
1330 1697 3.422303 GCTGACGACGCATTGGCA 61.422 61.111 0.00 0.00 41.24 4.92
1358 1725 4.887071 AGACATCAAACACAGTTTTGGCTA 59.113 37.500 1.83 0.00 37.13 3.93
1399 1766 3.545124 AACCATGGAAGCCGTGCGA 62.545 57.895 21.47 0.00 39.07 5.10
1456 1823 1.127582 GATGAAGCGTGCAAGAGTGAC 59.872 52.381 2.99 0.00 0.00 3.67
1464 1831 1.032794 TGCAAGAGTGACGAGACAGT 58.967 50.000 0.00 0.00 0.00 3.55
1508 1876 2.269940 AGGCCCTGAAAAGAGAGCTTA 58.730 47.619 0.00 0.00 32.98 3.09
1591 1959 3.399105 TTCGTCCATGGGGCCATCG 62.399 63.158 13.02 7.80 33.90 3.84
1639 2007 0.175302 CAGCAAGCACACAAACCCAA 59.825 50.000 0.00 0.00 0.00 4.12
1644 2012 1.102978 AGCACACAAACCCAAGTCAC 58.897 50.000 0.00 0.00 0.00 3.67
1743 2111 4.530553 ACACAAGAAAACAAAGAAAGGGGT 59.469 37.500 0.00 0.00 0.00 4.95
1850 2227 8.704849 TTAAAAATGGGAGAATGACTCTTGAA 57.295 30.769 0.00 0.00 44.37 2.69
1858 2235 2.725221 ATGACTCTTGAAGGGCATCC 57.275 50.000 0.00 0.00 0.00 3.51
1965 2342 7.967890 TCTGCCATGTTATGTATACTGAATG 57.032 36.000 4.17 1.89 0.00 2.67
1989 2414 8.972458 TGTGCCATGCTAATTTATACTAAAGA 57.028 30.769 0.00 0.00 0.00 2.52
2076 2549 5.830799 TGGATCTGCCATGTTGAGTATAT 57.169 39.130 0.00 0.00 43.33 0.86
2145 2618 6.893583 ACTGAATCTGCCATGTTAGTTCTAT 58.106 36.000 0.00 0.00 0.00 1.98
2207 2682 4.073293 AGATTTCCGTGTTCAGTCAACT 57.927 40.909 0.00 0.00 35.79 3.16
2220 2695 6.019075 TGTTCAGTCAACTCATTTTAGTCACG 60.019 38.462 0.00 0.00 35.79 4.35
2273 2751 2.413310 AGTTGAAAAGGGTCACGTGT 57.587 45.000 16.51 0.00 0.00 4.49
2401 2880 6.455646 CGATAACTTTCACTAACCATGTCTGC 60.456 42.308 0.00 0.00 0.00 4.26
2571 3054 6.250819 ACAGAAAATATTCAAATGTCGCTCG 58.749 36.000 0.00 0.00 38.06 5.03
2611 3103 0.623723 ACGGGGGTTGCAGTCATAAT 59.376 50.000 0.00 0.00 0.00 1.28
2699 3194 2.621070 AGGTAGGCATTCGGTATGGAT 58.379 47.619 0.00 0.00 34.66 3.41
2791 3286 5.507315 GGACCACGTGTTGAAATCTTCATTT 60.507 40.000 15.65 0.00 39.84 2.32
2840 3335 1.820519 GGAGCTCAATGACCATTGCAA 59.179 47.619 17.19 0.00 45.77 4.08
3041 3550 8.910944 CACATGAAGAAAGAGATGGGAAATTAT 58.089 33.333 0.00 0.00 0.00 1.28
3092 3601 7.174946 ACGTACTCAATTGGAAAATGTCTGATT 59.825 33.333 5.42 0.00 0.00 2.57
3226 3735 3.951680 ACCTCAAAACGTTGGTTCTTCAT 59.048 39.130 0.00 0.00 34.62 2.57
3234 3743 3.138304 CGTTGGTTCTTCATGTCAAGGA 58.862 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.135890 TGCAGCTCTGGACAGTCAA 58.864 52.632 2.17 0.00 0.00 3.18
98 99 2.022129 GGTCCACGCACAACTCGAG 61.022 63.158 11.84 11.84 0.00 4.04
280 282 1.075374 ACAGCATTGAACCCCTTGCTA 59.925 47.619 0.00 0.00 43.25 3.49
375 377 6.810911 TCTTGCTTTAGCTTAGATCCTAGTG 58.189 40.000 0.00 0.00 42.66 2.74
386 388 4.335594 AGTGTTCGTTTCTTGCTTTAGCTT 59.664 37.500 0.00 0.00 42.66 3.74
392 394 1.268032 CGCAGTGTTCGTTTCTTGCTT 60.268 47.619 0.00 0.00 0.00 3.91
644 646 3.035942 GCAAACTGCAGTTGAGTAAACG 58.964 45.455 31.73 13.69 44.26 3.60
708 734 5.996513 ACTGCATTTCATTAAACATGGCAAA 59.003 32.000 0.00 0.00 0.00 3.68
761 811 2.612285 TCCATACCAACATGCCCAAA 57.388 45.000 0.00 0.00 0.00 3.28
859 980 2.492881 CTGCAGTCCATTAAACATGGCA 59.507 45.455 5.25 0.00 39.01 4.92
860 981 2.493278 ACTGCAGTCCATTAAACATGGC 59.507 45.455 15.25 0.00 39.01 4.40
861 982 4.487948 CAACTGCAGTCCATTAAACATGG 58.512 43.478 21.95 0.00 40.48 3.66
862 983 3.922240 GCAACTGCAGTCCATTAAACATG 59.078 43.478 21.95 11.54 41.59 3.21
873 994 3.641437 TTAAACATGGCAACTGCAGTC 57.359 42.857 21.95 8.57 44.36 3.51
934 1296 7.481798 GCCAATAGAAGTACATTTCGTTTGAAG 59.518 37.037 0.00 0.00 35.06 3.02
1006 1369 6.799926 ATCTGCAAGTTTTTGTGTGTTTTT 57.200 29.167 0.00 0.00 36.65 1.94
1053 1418 2.158813 ACCTGGAAAGTCGTGAACATGT 60.159 45.455 0.00 0.00 0.00 3.21
1251 1618 2.431771 TCACCGCGTTCATGTCCG 60.432 61.111 4.92 0.00 0.00 4.79
1330 1697 1.229428 CTGTGTTTGATGTCTGCGGT 58.771 50.000 0.00 0.00 0.00 5.68
1358 1725 1.408340 CTCTGGTCTCTCGTCATGCAT 59.592 52.381 0.00 0.00 0.00 3.96
1456 1823 2.179517 GCGACCCTCACTGTCTCG 59.820 66.667 0.00 0.00 0.00 4.04
1464 1831 1.305201 GTGTTTTTCTGCGACCCTCA 58.695 50.000 0.00 0.00 0.00 3.86
1508 1876 5.881443 CAGCTTTCCTCTTCTTGATCTCATT 59.119 40.000 0.00 0.00 0.00 2.57
1591 1959 2.824341 TCCTACCTCCGAGTTTTCAGAC 59.176 50.000 0.00 0.00 0.00 3.51
1639 2007 4.003788 CAGGGCGGGTTCGTGACT 62.004 66.667 0.00 0.00 38.89 3.41
1644 2012 4.323477 TGGAACAGGGCGGGTTCG 62.323 66.667 11.98 0.00 44.29 3.95
1743 2111 0.250945 TGTTGCTTACGGATTGCCCA 60.251 50.000 0.00 0.00 34.14 5.36
1850 2227 1.284785 TCCTTCAAATTCGGATGCCCT 59.715 47.619 0.00 0.00 0.00 5.19
1858 2235 5.170021 TCATGGCATTTTCCTTCAAATTCG 58.830 37.500 0.00 0.00 0.00 3.34
1965 2342 9.831737 CATCTTTAGTATAAATTAGCATGGCAC 57.168 33.333 0.00 0.00 0.00 5.01
2015 2440 5.181009 CAGATCCAGTACACACAACATGAT 58.819 41.667 0.00 0.00 0.00 2.45
2097 2570 8.922676 AGTATAAACAACACGACAGATTTAGTG 58.077 33.333 0.00 0.00 40.17 2.74
2220 2695 9.702726 CATAGTTTTGCACACAATACACTATAC 57.297 33.333 0.00 0.00 39.40 1.47
2362 2841 8.739461 GTGAAAGTTATCGTCGTTTTTCATTTT 58.261 29.630 11.94 0.00 37.04 1.82
2401 2880 8.586570 TTTAAAACATGGCAAATGTAGTTCAG 57.413 30.769 4.84 0.00 0.00 3.02
2438 2917 3.708563 CCAGTTTGGTGTTTCGAATGT 57.291 42.857 0.00 0.00 31.35 2.71
2571 3054 4.608951 GTGTAGCCTAGTATGTAGTGTGC 58.391 47.826 0.00 0.00 0.00 4.57
2611 3103 5.968254 TCAAAACTATGTCCGTGTGCTATA 58.032 37.500 0.00 0.00 0.00 1.31
2699 3194 2.626266 AGTACAAGTGATCACGTGGTGA 59.374 45.455 34.69 21.78 46.90 4.02
2791 3286 2.727123 ACACATGGAACTGGTTGACA 57.273 45.000 0.00 0.00 0.00 3.58
2896 3391 1.374758 CAGGACGGACTGTGGCTTC 60.375 63.158 0.00 0.00 33.81 3.86
3041 3550 1.414919 ACTACGAAGCAAGGGAACACA 59.585 47.619 0.00 0.00 0.00 3.72
3092 3601 2.702592 ACGAACACTCAAAGGTCCAA 57.297 45.000 0.00 0.00 0.00 3.53
3126 3635 6.302269 ACTTCATCAACAACCTCAAAGAGAT 58.698 36.000 0.00 0.00 0.00 2.75
3189 3698 2.516906 TGAGGTGCTTGATTCAATGCA 58.483 42.857 15.15 15.15 0.00 3.96
3226 3735 1.816835 ACTACGCGATCTTCCTTGACA 59.183 47.619 15.93 0.00 0.00 3.58
3234 3743 0.172803 GGTCACCACTACGCGATCTT 59.827 55.000 15.93 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.