Multiple sequence alignment - TraesCS3D01G170400

Loading Multiple Alignment...

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 TraesCS3D01G170400 chr3D 100.000 3383 0 0 1 3383 149543111 149546493 0.000000e+00 6248.0
1 TraesCS3D01G170400 chr3D 97.661 2309 33 9 1 2307 149203957 149206246 0.000000e+00 3945.0
2 TraesCS3D01G170400 chr3D 98.439 1409 15 5 633 2039 147336520 147335117 0.000000e+00 2473.0
3 TraesCS3D01G170400 chr3D 96.136 647 24 1 3 649 147337188 147336543 0.000000e+00 1055.0
4 TraesCS3D01G170400 chr3D 95.652 414 12 4 2973 3383 149767523 149767113 0.000000e+00 660.0
5 TraesCS3D01G170400 chr3D 97.071 239 6 1 2073 2310 147334799 147334561 5.260000e-108 401.0
6 TraesCS3D01G170400 chr3D 86.544 379 30 13 2973 3348 149207004 149207364 6.800000e-107 398.0
7 TraesCS3D01G170400 chr3D 78.964 637 66 34 1 613 149517976 149518568 4.120000e-99 372.0
8 TraesCS3D01G170400 chr3D 77.672 421 60 22 4 397 147425500 147425087 3.400000e-55 226.0
9 TraesCS3D01G170400 chr3D 93.421 76 5 0 2732 2807 141412094 141412169 2.760000e-21 113.0
10 TraesCS3D01G170400 chr3A 92.526 1512 59 7 926 2429 166923254 166924719 0.000000e+00 2117.0
11 TraesCS3D01G170400 chr3A 93.951 1025 47 6 2370 3383 166924691 166925711 0.000000e+00 1535.0
12 TraesCS3D01G170400 chr3A 88.037 1187 100 19 1035 2206 159831904 159833063 0.000000e+00 1367.0
13 TraesCS3D01G170400 chr3A 93.961 414 18 4 2973 3383 181107338 181107747 1.330000e-173 619.0
14 TraesCS3D01G170400 chr3A 82.143 168 10 11 850 998 177859704 177859870 3.540000e-25 126.0
15 TraesCS3D01G170400 chr3A 86.316 95 13 0 2713 2807 159834370 159834464 1.660000e-18 104.0
16 TraesCS3D01G170400 chr3A 84.211 95 14 1 2713 2807 159441284 159441377 1.290000e-14 91.6
17 TraesCS3D01G170400 chr3B 92.231 1197 57 12 1555 2742 221749621 221750790 0.000000e+00 1663.0
18 TraesCS3D01G170400 chr3B 92.364 1087 63 9 1000 2084 221912358 221913426 0.000000e+00 1530.0
19 TraesCS3D01G170400 chr3B 91.536 1087 62 13 1000 2084 221979838 221980896 0.000000e+00 1471.0
20 TraesCS3D01G170400 chr3B 92.593 1026 64 8 1000 2025 215385072 215386085 0.000000e+00 1463.0
21 TraesCS3D01G170400 chr3B 91.651 1066 67 8 1000 2065 215104678 215105721 0.000000e+00 1456.0
22 TraesCS3D01G170400 chr3B 90.424 1086 60 14 1004 2084 215572008 215573054 0.000000e+00 1389.0
23 TraesCS3D01G170400 chr3B 90.962 1029 65 9 1000 2025 215310446 215311449 0.000000e+00 1360.0
24 TraesCS3D01G170400 chr3B 88.596 1026 65 12 1000 2025 221457757 221458730 0.000000e+00 1199.0
25 TraesCS3D01G170400 chr3B 90.209 909 46 22 2514 3383 221981527 221982431 0.000000e+00 1146.0
26 TraesCS3D01G170400 chr3B 89.758 908 51 20 2514 3383 221914043 221914946 0.000000e+00 1123.0
27 TraesCS3D01G170400 chr3B 87.872 907 66 22 2513 3383 215386788 215387686 0.000000e+00 1026.0
28 TraesCS3D01G170400 chr3B 90.945 751 56 8 2063 2807 215114802 215115546 0.000000e+00 1000.0
29 TraesCS3D01G170400 chr3B 93.841 552 27 2 2832 3383 215115615 215116159 0.000000e+00 824.0
30 TraesCS3D01G170400 chr3B 93.682 554 29 4 2832 3383 221753057 221753606 0.000000e+00 824.0
31 TraesCS3D01G170400 chr3B 83.843 817 84 30 1 790 215383801 215384596 0.000000e+00 734.0
32 TraesCS3D01G170400 chr3B 83.681 815 86 28 1 790 215308328 215309120 0.000000e+00 725.0
33 TraesCS3D01G170400 chr3B 83.088 816 90 17 1 790 221978747 221979540 0.000000e+00 699.0
34 TraesCS3D01G170400 chr3B 82.927 820 89 32 1 790 221456500 221457298 0.000000e+00 691.0
35 TraesCS3D01G170400 chr3B 95.046 323 16 0 3061 3383 221467865 221468187 3.010000e-140 508.0
36 TraesCS3D01G170400 chr3B 84.201 557 42 18 2513 3033 221467325 221467871 1.810000e-137 499.0
37 TraesCS3D01G170400 chr3B 91.089 303 18 5 489 790 221748577 221748871 5.260000e-108 401.0
38 TraesCS3D01G170400 chr3B 90.873 252 15 4 540 790 215571443 215571687 7.000000e-87 331.0
39 TraesCS3D01G170400 chr3B 90.795 239 14 4 554 790 221911829 221912061 2.530000e-81 313.0
40 TraesCS3D01G170400 chr3B 92.683 164 10 1 2151 2314 221466813 221466974 5.640000e-58 235.0
41 TraesCS3D01G170400 chr3B 92.683 164 10 1 2151 2314 221980920 221981081 5.640000e-58 235.0
42 TraesCS3D01G170400 chr3B 92.073 164 11 1 2151 2314 221913450 221913611 2.630000e-56 230.0
43 TraesCS3D01G170400 chr3B 93.548 155 7 2 2151 2304 215573078 215573230 9.440000e-56 228.0
44 TraesCS3D01G170400 chr3B 97.849 93 2 0 784 876 221912177 221912269 9.710000e-36 161.0
45 TraesCS3D01G170400 chr3B 96.774 93 3 0 784 876 221979657 221979749 4.520000e-34 156.0
46 TraesCS3D01G170400 chr3B 95.699 93 4 0 784 876 215309240 215309332 2.100000e-32 150.0
47 TraesCS3D01G170400 chr3B 95.699 93 4 0 784 876 215571813 215571905 2.100000e-32 150.0
48 TraesCS3D01G170400 chr3B 94.737 76 4 0 784 859 221748991 221749066 5.930000e-23 119.0
49 TraesCS3D01G170400 chr3B 87.629 97 11 1 482 578 90168107 90168202 9.920000e-21 111.0
50 TraesCS3D01G170400 chr4B 84.211 114 15 3 482 594 2688924 2689035 1.280000e-19 108.0


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 TraesCS3D01G170400 chr3D 149543111 149546493 3382 False 6248.000000 6248 100.000000 1 3383 1 chr3D.!!$F3 3382
1 TraesCS3D01G170400 chr3D 149203957 149207364 3407 False 2171.500000 3945 92.102500 1 3348 2 chr3D.!!$F4 3347
2 TraesCS3D01G170400 chr3D 147334561 147337188 2627 True 1309.666667 2473 97.215333 3 2310 3 chr3D.!!$R3 2307
3 TraesCS3D01G170400 chr3D 149517976 149518568 592 False 372.000000 372 78.964000 1 613 1 chr3D.!!$F2 612
4 TraesCS3D01G170400 chr3A 166923254 166925711 2457 False 1826.000000 2117 93.238500 926 3383 2 chr3A.!!$F5 2457
5 TraesCS3D01G170400 chr3A 159831904 159834464 2560 False 735.500000 1367 87.176500 1035 2807 2 chr3A.!!$F4 1772
6 TraesCS3D01G170400 chr3B 215104678 215105721 1043 False 1456.000000 1456 91.651000 1000 2065 1 chr3B.!!$F2 1065
7 TraesCS3D01G170400 chr3B 215383801 215387686 3885 False 1074.333333 1463 88.102667 1 3383 3 chr3B.!!$F5 3382
8 TraesCS3D01G170400 chr3B 221456500 221458730 2230 False 945.000000 1199 85.761500 1 2025 2 chr3B.!!$F7 2024
9 TraesCS3D01G170400 chr3B 215114802 215116159 1357 False 912.000000 1000 92.393000 2063 3383 2 chr3B.!!$F3 1320
10 TraesCS3D01G170400 chr3B 221748577 221753606 5029 False 751.750000 1663 92.934750 489 3383 4 chr3B.!!$F9 2894
11 TraesCS3D01G170400 chr3B 215308328 215311449 3121 False 745.000000 1360 90.114000 1 2025 3 chr3B.!!$F4 2024
12 TraesCS3D01G170400 chr3B 221978747 221982431 3684 False 741.400000 1471 90.858000 1 3383 5 chr3B.!!$F11 3382
13 TraesCS3D01G170400 chr3B 221911829 221914946 3117 False 671.400000 1530 92.567800 554 3383 5 chr3B.!!$F10 2829
14 TraesCS3D01G170400 chr3B 215571443 215573230 1787 False 524.500000 1389 92.636000 540 2304 4 chr3B.!!$F6 1764
15 TraesCS3D01G170400 chr3B 221466813 221468187 1374 False 414.000000 508 90.643333 2151 3383 3 chr3B.!!$F8 1232

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
343 373 1.056700 ATCCTGCGAGGCAATAGGGT 61.057 55.0 0.00 0.0 38.41 4.34 F
393 423 2.914756 TAGCGTAGACCCGGGCATGA 62.915 60.0 24.08 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 3774 2.736995 TAGCACAAGCACGTCGCC 60.737 61.111 6.39 0.0 45.49 5.54 R
2529 5601 3.505680 TGTCGATTGCAATTGTAGCCTTT 59.494 39.130 23.14 0.0 0.00 3.11 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
196 223 9.794685 AAATCAACAGAGAAAGAAAGAAAGAAC 57.205 29.630 0.00 0.0 0.00 3.01
197 224 7.005062 TCAACAGAGAAAGAAAGAAAGAACG 57.995 36.000 0.00 0.0 0.00 3.95
293 323 1.583495 GGAGGCCCAAAAGTACGCAC 61.583 60.000 0.00 0.0 0.00 5.34
343 373 1.056700 ATCCTGCGAGGCAATAGGGT 61.057 55.000 0.00 0.0 38.41 4.34
393 423 2.914756 TAGCGTAGACCCGGGCATGA 62.915 60.000 24.08 0.0 0.00 3.07
2529 5601 9.316730 GGCTGCAAAATTGATAAATTTCTGATA 57.683 29.630 1.03 0.0 31.66 2.15
2606 5680 3.249189 TCGTCCAAGGGGCTGCTT 61.249 61.111 0.00 0.0 0.00 3.91
2730 5834 4.443457 GCCGCATATCACCATCATATAGGT 60.443 45.833 0.00 0.0 39.10 3.08
2905 8647 2.353376 CAACCGTTGTTGCTGGCG 60.353 61.111 2.87 0.0 44.86 5.69
3035 8802 3.887621 AGCAAAATCTACTGCCTACGA 57.112 42.857 0.00 0.0 39.47 3.43
3036 8803 3.522553 AGCAAAATCTACTGCCTACGAC 58.477 45.455 0.00 0.0 39.47 4.34
3037 8804 2.281762 GCAAAATCTACTGCCTACGACG 59.718 50.000 0.00 0.0 32.18 5.12
3262 9031 4.020218 TCAAGGTCTCCATAACCTGTGAAG 60.020 45.833 0.00 0.0 46.54 3.02
3306 9075 7.040062 ACCCGACAGAAACATCAAAATCATAAA 60.040 33.333 0.00 0.0 0.00 1.40
3329 9099 4.846779 TGTAAGGGTGCAAGAAAATCAC 57.153 40.909 0.00 0.0 0.00 3.06
3375 9145 5.531122 TTCCTACCACACTAGCATGATAC 57.469 43.478 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
393 423 2.032071 CTTTCGGGTCGGGCTGTT 59.968 61.111 0.00 0.00 0.00 3.16
961 2689 2.160822 ATCTGATTCTTGGATCCGCG 57.839 50.000 7.39 0.00 0.00 6.46
1984 3774 2.736995 TAGCACAAGCACGTCGCC 60.737 61.111 6.39 0.00 45.49 5.54
2529 5601 3.505680 TGTCGATTGCAATTGTAGCCTTT 59.494 39.130 23.14 0.00 0.00 3.11
2542 5614 2.664916 ACAGTTTGCATTGTCGATTGC 58.335 42.857 10.07 10.07 39.33 3.56
2744 7913 7.342318 CAGTTGGCTGTTTTATTCTTCAATG 57.658 36.000 0.00 0.00 37.92 2.82
2905 8647 1.556911 TGCAGAGGGGAGACTTGATTC 59.443 52.381 0.00 0.00 0.00 2.52
3035 8802 0.544595 AGTAGCTTGTTCCCCTCCGT 60.545 55.000 0.00 0.00 0.00 4.69
3036 8803 0.175989 GAGTAGCTTGTTCCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
3037 8804 1.208293 CAGAGTAGCTTGTTCCCCTCC 59.792 57.143 0.00 0.00 0.00 4.30
3262 9031 4.117685 CGGGTACTTATTGTAGTCTTGCC 58.882 47.826 0.00 0.00 0.00 4.52
3306 9075 5.564651 CGTGATTTTCTTGCACCCTTACAAT 60.565 40.000 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.