Multiple sequence alignment - TraesCS2B01G265400

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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 TraesCS2B01G265400 chr2B 100.000 1640 0 0 1 1640 357691897 357690258 0.000000e+00 3029
1 TraesCS2B01G265400 chr2B 95.879 1650 57 4 1 1640 357466347 357467995 0.000000e+00 2660
2 TraesCS2B01G265400 chr2B 96.159 1510 48 3 140 1640 500759802 500758294 0.000000e+00 2459
3 TraesCS2B01G265400 chr2B 100.000 495 0 0 1976 2470 357689922 357689428 0.000000e+00 915
4 TraesCS2B01G265400 chr2B 96.970 495 10 4 1976 2470 357468031 357468520 0.000000e+00 826
5 TraesCS2B01G265400 chr2B 98.333 60 1 0 2410 2469 357340221 357340280 3.360000e-19 106
6 TraesCS2B01G265400 chr1A 97.348 1546 31 3 105 1640 238107543 238105998 0.000000e+00 2619
7 TraesCS2B01G265400 chr1A 97.283 1546 32 3 105 1640 238152928 238151383 0.000000e+00 2614
8 TraesCS2B01G265400 chr1A 97.987 298 3 2 1976 2273 94694592 94694298 4.710000e-142 514
9 TraesCS2B01G265400 chr5A 97.219 1546 32 4 105 1640 16575718 16574174 0.000000e+00 2606
10 TraesCS2B01G265400 chr7A 97.025 1546 34 5 105 1640 60326808 60325265 0.000000e+00 2590
11 TraesCS2B01G265400 chr6B 96.839 1550 34 4 105 1640 596655108 596653560 0.000000e+00 2577
12 TraesCS2B01G265400 chr6B 95.340 515 15 2 105 611 638949508 638948995 0.000000e+00 809
13 TraesCS2B01G265400 chr6B 100.000 138 0 0 2273 2410 307003820 307003957 3.150000e-64 255
14 TraesCS2B01G265400 chr6B 99.275 138 1 0 2273 2410 394406790 394406653 1.470000e-62 250
15 TraesCS2B01G265400 chr6B 98.361 61 1 0 2410 2470 388301336 388301276 9.340000e-20 108
16 TraesCS2B01G265400 chr3A 96.833 1547 37 5 105 1640 247672979 247674524 0.000000e+00 2575
17 TraesCS2B01G265400 chr3A 96.456 1411 39 3 105 1506 122209439 122208031 0.000000e+00 2318
18 TraesCS2B01G265400 chr4B 96.184 1546 46 5 105 1640 209049057 209050599 0.000000e+00 2516
19 TraesCS2B01G265400 chr4B 96.296 108 4 0 1 108 159080288 159080395 7.020000e-41 178
20 TraesCS2B01G265400 chr3D 92.978 769 45 2 105 865 308600493 308599726 0.000000e+00 1112
21 TraesCS2B01G265400 chr3D 91.667 108 9 0 1 108 602845966 602846073 1.530000e-32 150
22 TraesCS2B01G265400 chr3D 90.741 108 10 0 1 108 3636371 3636478 7.120000e-31 145
23 TraesCS2B01G265400 chrUn 95.927 491 12 1 105 587 182412827 182412337 0.000000e+00 789
24 TraesCS2B01G265400 chrUn 97.651 298 4 2 1976 2273 186171011 186170717 2.190000e-140 508
25 TraesCS2B01G265400 chrUn 97.651 298 4 2 1976 2273 399326676 399326382 2.190000e-140 508
26 TraesCS2B01G265400 chrUn 99.275 138 1 0 2273 2410 171054408 171054271 1.470000e-62 250
27 TraesCS2B01G265400 chrUn 99.275 138 1 0 2273 2410 264053842 264053979 1.470000e-62 250
28 TraesCS2B01G265400 chrUn 99.275 138 1 0 2273 2410 266523746 266523883 1.470000e-62 250
29 TraesCS2B01G265400 chr4D 98.322 298 4 1 1976 2273 123601750 123602046 2.810000e-144 521
30 TraesCS2B01G265400 chr4D 97.651 298 4 2 1976 2273 6632074 6632368 2.190000e-140 508
31 TraesCS2B01G265400 chr4D 97.651 298 3 3 1976 2273 123528641 123528934 2.190000e-140 508
32 TraesCS2B01G265400 chr5D 97.987 298 3 2 1976 2273 562939706 562939412 4.710000e-142 514
33 TraesCS2B01G265400 chr7B 97.651 298 6 1 1976 2273 54033233 54033529 6.090000e-141 510
34 TraesCS2B01G265400 chr7B 99.275 138 1 0 2273 2410 644459603 644459466 1.470000e-62 250
35 TraesCS2B01G265400 chr1B 99.275 138 1 0 2273 2410 668813003 668813140 1.470000e-62 250
36 TraesCS2B01G265400 chr1B 99.275 138 1 0 2273 2410 672471577 672471440 1.470000e-62 250
37 TraesCS2B01G265400 chr1B 97.647 85 2 0 24 108 135135203 135135119 1.980000e-31 147
38 TraesCS2B01G265400 chr1B 92.233 103 8 0 6 108 135157981 135158083 1.980000e-31 147
39 TraesCS2B01G265400 chr1B 100.000 61 0 0 2410 2470 487322507 487322567 2.010000e-21 113
40 TraesCS2B01G265400 chr4A 95.370 108 5 0 1 108 721669902 721670009 3.270000e-39 172
41 TraesCS2B01G265400 chr4A 89.815 108 11 0 1 108 520028653 520028760 3.310000e-29 139
42 TraesCS2B01G265400 chr6A 90.090 111 8 1 1 108 559141901 559141791 9.210000e-30 141
43 TraesCS2B01G265400 chr7D 98.361 61 1 0 2410 2470 322738878 322738938 9.340000e-20 108
44 TraesCS2B01G265400 chr5B 98.361 61 1 0 2410 2470 455583781 455583721 9.340000e-20 108
45 TraesCS2B01G265400 chr3B 98.361 61 1 0 2410 2470 669852702 669852642 9.340000e-20 108
46 TraesCS2B01G265400 chr2D 98.361 61 1 0 2410 2470 39702785 39702845 9.340000e-20 108
47 TraesCS2B01G265400 chr6D 96.721 61 2 0 2410 2470 102370586 102370526 4.350000e-18 102


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 TraesCS2B01G265400 chr2B 357689428 357691897 2469 True 1972 3029 100.0000 1 2470 2 chr2B.!!$R2 2469
1 TraesCS2B01G265400 chr2B 500758294 500759802 1508 True 2459 2459 96.1590 140 1640 1 chr2B.!!$R1 1500
2 TraesCS2B01G265400 chr2B 357466347 357468520 2173 False 1743 2660 96.4245 1 2470 2 chr2B.!!$F2 2469
3 TraesCS2B01G265400 chr1A 238105998 238107543 1545 True 2619 2619 97.3480 105 1640 1 chr1A.!!$R2 1535
4 TraesCS2B01G265400 chr1A 238151383 238152928 1545 True 2614 2614 97.2830 105 1640 1 chr1A.!!$R3 1535
5 TraesCS2B01G265400 chr5A 16574174 16575718 1544 True 2606 2606 97.2190 105 1640 1 chr5A.!!$R1 1535
6 TraesCS2B01G265400 chr7A 60325265 60326808 1543 True 2590 2590 97.0250 105 1640 1 chr7A.!!$R1 1535
7 TraesCS2B01G265400 chr6B 596653560 596655108 1548 True 2577 2577 96.8390 105 1640 1 chr6B.!!$R3 1535
8 TraesCS2B01G265400 chr6B 638948995 638949508 513 True 809 809 95.3400 105 611 1 chr6B.!!$R4 506
9 TraesCS2B01G265400 chr3A 247672979 247674524 1545 False 2575 2575 96.8330 105 1640 1 chr3A.!!$F1 1535
10 TraesCS2B01G265400 chr3A 122208031 122209439 1408 True 2318 2318 96.4560 105 1506 1 chr3A.!!$R1 1401
11 TraesCS2B01G265400 chr4B 209049057 209050599 1542 False 2516 2516 96.1840 105 1640 1 chr4B.!!$F2 1535
12 TraesCS2B01G265400 chr3D 308599726 308600493 767 True 1112 1112 92.9780 105 865 1 chr3D.!!$R1 760

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
38 39 0.040514 CGAGCTAGTCATGCCTCTCG 60.041 60.0 1.19 1.19 37.65 4.04 F
457 466 0.242825 TTCACGAAGTAGGCACTCCG 59.757 55.0 0.00 0.00 41.61 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 1461 4.451891 TGATATTATGCTTCCTTGCCCA 57.548 40.909 0.0 0.0 0.0 5.36 R
2260 2277 1.537202 GCCTTTTAGCACACCAGTCTG 59.463 52.381 0.0 0.0 0.0 3.51 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
30 31 2.884012 CTCACTCCATCGAGCTAGTCAT 59.116 50.000 0.00 0.00 40.03 3.06
38 39 0.040514 CGAGCTAGTCATGCCTCTCG 60.041 60.000 1.19 1.19 37.65 4.04
64 65 1.028905 CTCCTCGAGGCTAGGAACAG 58.971 60.000 27.39 12.24 42.56 3.16
67 68 0.741915 CTCGAGGCTAGGAACAGTCC 59.258 60.000 3.91 0.00 45.35 3.85
234 235 9.456147 ACAGTACTAATAATGGCATTTGTTGTA 57.544 29.630 19.21 13.80 30.44 2.41
457 466 0.242825 TTCACGAAGTAGGCACTCCG 59.757 55.000 0.00 0.00 41.61 4.63
497 506 0.867753 ATCTGCGCGATCGTTCACTC 60.868 55.000 17.81 0.00 38.14 3.51
542 551 4.712337 GTGAGGGAGGAGATACTCTTCAAA 59.288 45.833 11.70 0.00 38.17 2.69
614 623 4.722193 CCACCAATCTGGCGAAGT 57.278 55.556 0.00 0.00 42.67 3.01
734 743 0.611618 AGCAAATGATGGGGCGAACA 60.612 50.000 0.00 0.00 0.00 3.18
756 765 3.311110 AGGCCCGTCTTCTTCGCA 61.311 61.111 0.00 0.00 0.00 5.10
842 853 3.453868 TCTCCAGATCCAGTGGAAATCA 58.546 45.455 17.71 0.00 43.68 2.57
848 859 5.887598 CCAGATCCAGTGGAAATCATTTACA 59.112 40.000 17.71 0.00 37.23 2.41
849 860 6.039047 CCAGATCCAGTGGAAATCATTTACAG 59.961 42.308 17.71 0.00 37.23 2.74
1343 1359 2.567615 AGAAATAAGTGGCTCACGAGGT 59.432 45.455 0.00 0.00 39.64 3.85
1432 1448 7.385752 CACTTGTTGGAAAAACATAATGCTCAT 59.614 33.333 0.00 0.00 0.00 2.90
1445 1461 6.774170 ACATAATGCTCATACATGTTCCACAT 59.226 34.615 2.30 0.00 39.91 3.21
1632 1649 0.765903 TGGAGATCATGAGGCCCCTC 60.766 60.000 7.39 7.39 43.01 4.30
2128 2145 7.152645 TGAACTTCATAGACAGACTTACCAAC 58.847 38.462 0.00 0.00 0.00 3.77
2164 2181 3.849527 AGCAAATTTCTTCTTCCTGGGT 58.150 40.909 0.00 0.00 0.00 4.51
2178 2195 2.446036 GGGTGGGGCGGACTCTAT 60.446 66.667 0.00 0.00 0.00 1.98
2250 2267 8.880991 AGTAGTCTCCTTTTCAAGTAGATACA 57.119 34.615 0.00 0.00 0.00 2.29
2319 2336 1.991070 CATCCCCTGGATAAGCCTCAT 59.009 52.381 0.00 0.00 40.98 2.90
2441 2458 4.704540 AGACAATTGGTTTCAACTGTGTCA 59.295 37.500 10.83 0.00 42.45 3.58
2443 2460 6.545666 AGACAATTGGTTTCAACTGTGTCATA 59.454 34.615 10.83 0.00 42.45 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.515901 GTGGGAGACATGGACTTTAGTCT 59.484 47.826 9.56 0.00 44.20 3.24
234 235 5.998363 GGCTATTCCTTGAACTCCGAATAAT 59.002 40.000 0.00 0.00 29.33 1.28
394 403 4.631813 GTCAACTCCGCAATTATGTCTTCT 59.368 41.667 0.00 0.00 0.00 2.85
497 506 9.726232 CTCACTATTCCACAATACATGATTTTG 57.274 33.333 0.00 2.62 0.00 2.44
542 551 7.442666 GGCTTCCGTATAATCAGAGAAGATTTT 59.557 37.037 0.00 0.00 38.97 1.82
553 562 0.682852 CCCCGGCTTCCGTATAATCA 59.317 55.000 0.00 0.00 46.80 2.57
580 589 2.618241 GGTGGCTATTGCGATGAATTCA 59.382 45.455 11.26 11.26 40.82 2.57
652 661 4.028490 AAAGGCGCATCGGGGTCA 62.028 61.111 10.83 0.00 33.32 4.02
734 743 2.470938 GAAGAAGACGGGCCTGCCTT 62.471 60.000 13.69 13.69 36.10 4.35
756 765 4.591321 TCATCCCACCTTTTATGCTTCT 57.409 40.909 0.00 0.00 0.00 2.85
762 771 5.072741 CCGAATCATCATCCCACCTTTTAT 58.927 41.667 0.00 0.00 0.00 1.40
842 853 3.624777 CTTGTGCATCCCCTCTGTAAAT 58.375 45.455 0.00 0.00 0.00 1.40
848 859 0.253160 TACCCTTGTGCATCCCCTCT 60.253 55.000 0.00 0.00 0.00 3.69
849 860 0.107165 GTACCCTTGTGCATCCCCTC 60.107 60.000 0.00 0.00 0.00 4.30
903 914 4.100373 AGAACTCAGATAGAAAGGCAGGT 58.900 43.478 0.00 0.00 0.00 4.00
1169 1185 4.717280 TCTTCCAGATTCTTAGGGTCCTTC 59.283 45.833 0.00 0.00 0.00 3.46
1445 1461 4.451891 TGATATTATGCTTCCTTGCCCA 57.548 40.909 0.00 0.00 0.00 5.36
2001 2018 5.259832 AGATAGCCGTGTTAAACTAGTCC 57.740 43.478 0.00 0.00 0.00 3.85
2043 2060 7.913674 CTTTTTCAAGCTCTACAAGTCCTAT 57.086 36.000 0.00 0.00 0.00 2.57
2086 2103 3.117888 AGTTCAGTGCCCAGAAAAAGAGA 60.118 43.478 0.00 0.00 0.00 3.10
2087 2104 3.217626 AGTTCAGTGCCCAGAAAAAGAG 58.782 45.455 0.00 0.00 0.00 2.85
2088 2105 3.297134 AGTTCAGTGCCCAGAAAAAGA 57.703 42.857 0.00 0.00 0.00 2.52
2089 2106 3.381272 TGAAGTTCAGTGCCCAGAAAAAG 59.619 43.478 0.08 0.00 0.00 2.27
2090 2107 3.360867 TGAAGTTCAGTGCCCAGAAAAA 58.639 40.909 0.08 0.00 0.00 1.94
2128 2145 4.978083 ATTTGCTACTTTGGCTCATCAG 57.022 40.909 0.00 0.00 0.00 2.90
2164 2181 1.622607 CCAACATAGAGTCCGCCCCA 61.623 60.000 0.00 0.00 0.00 4.96
2178 2195 8.463930 AGAAATGAAAGTTTGATCTACCAACA 57.536 30.769 0.00 0.00 0.00 3.33
2260 2277 1.537202 GCCTTTTAGCACACCAGTCTG 59.463 52.381 0.00 0.00 0.00 3.51
2319 2336 1.766496 CCTTCTATTAAGTCCCGGCCA 59.234 52.381 2.24 0.00 0.00 5.36
2410 2427 6.038714 AGTTGAAACCAATTGTCTCTCACTTC 59.961 38.462 4.43 0.00 0.00 3.01
2441 2458 5.071923 GCAGGTCTAAGAATACAACCCCTAT 59.928 44.000 0.00 0.00 0.00 2.57
2443 2460 3.200165 GCAGGTCTAAGAATACAACCCCT 59.800 47.826 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.