Multiple sequence alignment - TraesCS3B01G238000

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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 TraesCS3B01G238000 chr3B 100.000 2999 0 0 1 2999 373196184 373193186 0.000000e+00 5539
1 TraesCS3B01G238000 chr3B 98.237 2042 36 0 1 2042 373191733 373193774 0.000000e+00 3572
2 TraesCS3B01G238000 chr2B 97.796 2042 45 0 1 2042 705902890 705900849 0.000000e+00 3522
3 TraesCS3B01G238000 chr2B 98.642 957 13 0 2043 2999 705900481 705901437 0.000000e+00 1696
4 TraesCS3B01G238000 chr3D 96.718 1310 41 2 735 2042 429608339 429609648 0.000000e+00 2180
5 TraesCS3B01G238000 chr3D 96.177 1308 50 0 735 2042 489594414 489595721 0.000000e+00 2139
6 TraesCS3B01G238000 chr3D 96.872 959 28 2 2043 2999 429610018 429609060 0.000000e+00 1604
7 TraesCS3B01G238000 chr3D 96.767 959 29 2 2043 2999 489596091 489595133 0.000000e+00 1598
8 TraesCS3B01G238000 chr3D 92.110 507 18 5 1 507 429607421 429607905 0.000000e+00 695
9 TraesCS3B01G238000 chr7D 96.409 1309 45 2 735 2042 1787233 1788540 0.000000e+00 2156
10 TraesCS3B01G238000 chr7D 96.254 1308 49 0 735 2042 285354559 285353252 0.000000e+00 2145
11 TraesCS3B01G238000 chr7D 92.899 507 18 1 1 507 1786313 1786801 0.000000e+00 721
12 TraesCS3B01G238000 chr7D 91.716 507 32 7 1 507 285355487 285354991 0.000000e+00 695
13 TraesCS3B01G238000 chr6D 96.257 1309 48 1 735 2042 148847366 148846058 0.000000e+00 2145
14 TraesCS3B01G238000 chr6D 95.963 966 36 3 2036 2999 148845682 148846646 0.000000e+00 1565
15 TraesCS3B01G238000 chr6D 96.142 959 35 2 2043 2999 385339010 385338052 0.000000e+00 1565
16 TraesCS3B01G238000 chr6D 95.933 959 37 2 2043 2999 329381515 329380557 0.000000e+00 1554
17 TraesCS3B01G238000 chr6D 91.599 738 43 2 1 738 329378956 329379674 0.000000e+00 1002
18 TraesCS3B01G238000 chr6D 92.505 507 20 1 1 507 148848286 148847798 0.000000e+00 710
19 TraesCS3B01G238000 chr6D 92.216 501 21 1 7 507 385336419 385336901 0.000000e+00 693
20 TraesCS3B01G238000 chr6D 91.736 242 12 1 505 738 385336929 385337170 2.230000e-86 329
21 TraesCS3B01G238000 chr2D 96.260 1310 46 3 735 2042 607746168 607744860 0.000000e+00 2145
22 TraesCS3B01G238000 chr2D 95.933 959 37 2 2043 2999 607744490 607745448 0.000000e+00 1554
23 TraesCS3B01G238000 chr2D 92.308 507 21 1 1 507 607747086 607746598 0.000000e+00 704
24 TraesCS3B01G238000 chr5D 96.254 1308 47 2 735 2042 468506037 468507342 0.000000e+00 2143
25 TraesCS3B01G238000 chr5D 95.954 964 35 4 2038 2999 468507716 468506755 0.000000e+00 1561
26 TraesCS3B01G238000 chr5D 91.519 507 25 4 1 507 468505117 468505605 0.000000e+00 682
27 TraesCS3B01G238000 chr6A 96.062 965 31 5 2040 2999 35313267 35314229 0.000000e+00 1565
28 TraesCS3B01G238000 chr6A 94.444 234 13 0 505 738 35315346 35315113 7.900000e-96 361
29 TraesCS3B01G238000 chr6A 93.162 234 16 0 505 738 395601350 395601583 7.960000e-91 344
30 TraesCS3B01G238000 chr3A 90.786 738 48 2 1 738 736999147 736998430 0.000000e+00 968
31 TraesCS3B01G238000 chr2A 94.444 234 13 0 505 738 351179018 351179251 7.900000e-96 361
32 TraesCS3B01G238000 chr2A 94.017 234 14 0 505 738 315571568 315571801 3.680000e-94 355


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 TraesCS3B01G238000 chr3B 373193186 373196184 2998 True 5539.0 5539 100.0000 1 2999 1 chr3B.!!$R1 2998
1 TraesCS3B01G238000 chr3B 373191733 373193774 2041 False 3572.0 3572 98.2370 1 2042 1 chr3B.!!$F1 2041
2 TraesCS3B01G238000 chr2B 705900849 705902890 2041 True 3522.0 3522 97.7960 1 2042 1 chr2B.!!$R1 2041
3 TraesCS3B01G238000 chr2B 705900481 705901437 956 False 1696.0 1696 98.6420 2043 2999 1 chr2B.!!$F1 956
4 TraesCS3B01G238000 chr3D 489594414 489595721 1307 False 2139.0 2139 96.1770 735 2042 1 chr3D.!!$F1 1307
5 TraesCS3B01G238000 chr3D 429609060 429610018 958 True 1604.0 1604 96.8720 2043 2999 1 chr3D.!!$R1 956
6 TraesCS3B01G238000 chr3D 489595133 489596091 958 True 1598.0 1598 96.7670 2043 2999 1 chr3D.!!$R2 956
7 TraesCS3B01G238000 chr3D 429607421 429609648 2227 False 1437.5 2180 94.4140 1 2042 2 chr3D.!!$F2 2041
8 TraesCS3B01G238000 chr7D 1786313 1788540 2227 False 1438.5 2156 94.6540 1 2042 2 chr7D.!!$F1 2041
9 TraesCS3B01G238000 chr7D 285353252 285355487 2235 True 1420.0 2145 93.9850 1 2042 2 chr7D.!!$R1 2041
10 TraesCS3B01G238000 chr6D 148845682 148846646 964 False 1565.0 1565 95.9630 2036 2999 1 chr6D.!!$F1 963
11 TraesCS3B01G238000 chr6D 385338052 385339010 958 True 1565.0 1565 96.1420 2043 2999 1 chr6D.!!$R2 956
12 TraesCS3B01G238000 chr6D 329380557 329381515 958 True 1554.0 1554 95.9330 2043 2999 1 chr6D.!!$R1 956
13 TraesCS3B01G238000 chr6D 148846058 148848286 2228 True 1427.5 2145 94.3810 1 2042 2 chr6D.!!$R3 2041
14 TraesCS3B01G238000 chr6D 329378956 329379674 718 False 1002.0 1002 91.5990 1 738 1 chr6D.!!$F2 737
15 TraesCS3B01G238000 chr6D 385336419 385337170 751 False 511.0 693 91.9760 7 738 2 chr6D.!!$F3 731
16 TraesCS3B01G238000 chr2D 607744490 607745448 958 False 1554.0 1554 95.9330 2043 2999 1 chr2D.!!$F1 956
17 TraesCS3B01G238000 chr2D 607744860 607747086 2226 True 1424.5 2145 94.2840 1 2042 2 chr2D.!!$R1 2041
18 TraesCS3B01G238000 chr5D 468506755 468507716 961 True 1561.0 1561 95.9540 2038 2999 1 chr5D.!!$R1 961
19 TraesCS3B01G238000 chr5D 468505117 468507342 2225 False 1412.5 2143 93.8865 1 2042 2 chr5D.!!$F1 2041
20 TraesCS3B01G238000 chr6A 35313267 35314229 962 False 1565.0 1565 96.0620 2040 2999 1 chr6A.!!$F1 959
21 TraesCS3B01G238000 chr3A 736998430 736999147 717 True 968.0 968 90.7860 1 738 1 chr3A.!!$R1 737

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
206 233 2.365617 AGTGGGATACAGGAACTATGCG 59.634 50.0 0.0 0.0 36.02 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2583 9.355215 GAGTAGATCATTTTTAGTTCTTCACGA 57.645 33.333 0.0 0.0 0.0 4.35 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
78 87 4.580167 TCTGCAACTGATTTATACATGCCC 59.420 41.667 0.00 0.00 0.00 5.36
101 128 5.508489 CCTGATGCTGTTGTGTCTGAATTTT 60.508 40.000 0.00 0.00 0.00 1.82
102 129 5.904941 TGATGCTGTTGTGTCTGAATTTTT 58.095 33.333 0.00 0.00 0.00 1.94
123 150 4.944962 TTATTGTGTCTGAATTGGCTCG 57.055 40.909 0.00 0.00 0.00 5.03
192 219 6.212840 TGGGCATAAACAATATAGTGGGAT 57.787 37.500 5.03 0.00 0.00 3.85
206 233 2.365617 AGTGGGATACAGGAACTATGCG 59.634 50.000 0.00 0.00 36.02 4.73
576 667 6.817765 TCATGTTAATGAAGTTCCTTCCAC 57.182 37.500 0.00 0.00 39.92 4.02
611 702 9.634163 CAGTTCGTAAGTTATATACATGGCATA 57.366 33.333 0.00 0.00 39.48 3.14
747 1017 6.929606 ACACTAGTCTAAAAGTTTCGAATGCT 59.070 34.615 0.00 0.00 0.00 3.79
810 1082 6.265876 GGTTTCCTCCATGGTAGTTTTTGTAA 59.734 38.462 12.58 0.00 37.07 2.41
938 1210 9.712305 AGTGTAAAAGTAGGATCATATGTATGC 57.288 33.333 1.90 1.06 33.76 3.14
1971 2246 4.273148 ACTATCCCTGTTGTGACTTGAC 57.727 45.455 0.00 0.00 0.00 3.18
2059 2334 4.082949 GCTATACAAGGTTGGAAAAAGCGT 60.083 41.667 0.00 0.00 0.00 5.07
2257 2533 6.282576 TCCCTCCATCCCATGATATAAGATT 58.717 40.000 0.00 0.00 0.00 2.40
2304 2583 3.181329 TGGAGGGAGTACATCACAACAT 58.819 45.455 0.00 0.00 31.63 2.71
2648 2927 1.153667 CACGCCTTCTCTGAGCTCC 60.154 63.158 12.15 0.00 0.00 4.70
2670 2949 1.542547 GCTCACGGGAAGTCTTTTCCA 60.543 52.381 8.10 0.00 40.32 3.53
2834 3113 7.382759 TGGTTACAAAACAAACACTTCACTTTC 59.617 33.333 0.00 0.00 37.34 2.62
2899 3178 6.463049 CCCACATCATCCGACTTTATCTTACT 60.463 42.308 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 87 4.761235 AATTCAGACACAACAGCATCAG 57.239 40.909 0.00 0.0 0.00 2.90
101 128 4.759693 ACGAGCCAATTCAGACACAATAAA 59.240 37.500 0.00 0.0 0.00 1.40
102 129 4.154015 CACGAGCCAATTCAGACACAATAA 59.846 41.667 0.00 0.0 0.00 1.40
103 130 3.684305 CACGAGCCAATTCAGACACAATA 59.316 43.478 0.00 0.0 0.00 1.90
104 131 2.485426 CACGAGCCAATTCAGACACAAT 59.515 45.455 0.00 0.0 0.00 2.71
105 132 1.872952 CACGAGCCAATTCAGACACAA 59.127 47.619 0.00 0.0 0.00 3.33
106 133 1.511850 CACGAGCCAATTCAGACACA 58.488 50.000 0.00 0.0 0.00 3.72
107 134 0.166814 GCACGAGCCAATTCAGACAC 59.833 55.000 0.00 0.0 33.58 3.67
108 135 0.250252 TGCACGAGCCAATTCAGACA 60.250 50.000 1.39 0.0 41.13 3.41
109 136 1.089920 ATGCACGAGCCAATTCAGAC 58.910 50.000 1.39 0.0 41.13 3.51
110 137 1.825090 AATGCACGAGCCAATTCAGA 58.175 45.000 1.39 0.0 41.13 3.27
111 138 2.642139 AAATGCACGAGCCAATTCAG 57.358 45.000 1.39 0.0 41.13 3.02
112 139 2.816672 TGTAAATGCACGAGCCAATTCA 59.183 40.909 1.39 0.0 41.13 2.57
113 140 3.485947 TGTAAATGCACGAGCCAATTC 57.514 42.857 1.39 0.0 41.13 2.17
114 141 3.505680 TCTTGTAAATGCACGAGCCAATT 59.494 39.130 1.39 0.0 41.13 2.32
115 142 3.081061 TCTTGTAAATGCACGAGCCAAT 58.919 40.909 1.39 0.0 41.13 3.16
116 143 2.499197 TCTTGTAAATGCACGAGCCAA 58.501 42.857 1.39 0.0 41.13 4.52
117 144 2.177394 TCTTGTAAATGCACGAGCCA 57.823 45.000 1.39 0.0 41.13 4.75
118 145 2.420022 ACATCTTGTAAATGCACGAGCC 59.580 45.455 1.39 0.0 41.13 4.70
123 150 9.619316 TGTATTTGTTACATCTTGTAAATGCAC 57.381 29.630 1.89 0.0 43.57 4.57
192 219 0.179084 GCCTGCGCATAGTTCCTGTA 60.179 55.000 12.24 0.0 34.03 2.74
206 233 1.200948 CAGCTTTTACCTTGAGCCTGC 59.799 52.381 0.00 0.0 37.11 4.85
527 618 6.594788 AGTGCACAAAATGATTACCTTCAT 57.405 33.333 21.04 0.0 37.96 2.57
576 667 8.783999 ATATAACTTACGAACTGAGACAATCG 57.216 34.615 0.00 0.0 40.90 3.34
611 702 4.202441 GTCCAGTATCACATCTTGGCATT 58.798 43.478 0.00 0.0 0.00 3.56
810 1082 9.436957 ACTTTCTGTTGTGAAGTAAATCGATAT 57.563 29.630 0.00 0.0 0.00 1.63
938 1210 5.236478 CCATAGTAAAGATTACCAGCAACCG 59.764 44.000 0.00 0.0 0.00 4.44
2304 2583 9.355215 GAGTAGATCATTTTTAGTTCTTCACGA 57.645 33.333 0.00 0.0 0.00 4.35
2648 2927 1.801178 GAAAAGACTTCCCGTGAGCTG 59.199 52.381 0.00 0.0 0.00 4.24
2670 2949 4.159557 GAGGAGGCATCTAAGAAGAGGAT 58.840 47.826 0.00 0.0 35.51 3.24
2899 3178 0.884704 GTTGCTGGAAGAGAACGCCA 60.885 55.000 0.00 0.0 34.07 5.69


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

AutoCloner maintained by Alex Coulton.