Multiple sequence alignment - TraesCS4D01G117400

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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 TraesCS4D01G117400 chr4D 100.000 1624 0 0 692 2315 97970931 97969308 0.000000e+00 3000.0
1 TraesCS4D01G117400 chr4D 88.991 981 96 6 1342 2315 97962503 97961528 0.000000e+00 1203.0
2 TraesCS4D01G117400 chr4D 100.000 483 0 0 1 483 97971622 97971140 0.000000e+00 893.0
3 TraesCS4D01G117400 chr4D 82.556 493 84 2 1823 2314 435198755 435198264 1.270000e-117 433.0
4 TraesCS4D01G117400 chr4B 98.152 974 18 0 1342 2315 139572242 139571269 0.000000e+00 1700.0
5 TraesCS4D01G117400 chr4B 88.342 995 89 12 1342 2315 139549281 139548293 0.000000e+00 1170.0
6 TraesCS4D01G117400 chr4B 94.556 349 14 4 1 345 139572576 139572229 3.390000e-148 534.0
7 TraesCS4D01G117400 chr4A 87.090 976 99 15 1359 2312 478209508 478210478 0.000000e+00 1079.0
8 TraesCS4D01G117400 chr4A 79.762 336 41 17 30 345 478209184 478209512 3.870000e-53 219.0
9 TraesCS4D01G117400 chr1B 86.158 997 109 14 1343 2315 487405524 487406515 0.000000e+00 1050.0
10 TraesCS4D01G117400 chr6D 95.552 652 26 2 692 1340 94685436 94684785 0.000000e+00 1040.0
11 TraesCS4D01G117400 chr6D 82.597 724 83 20 1342 2054 61002837 61003528 1.180000e-167 599.0
12 TraesCS4D01G117400 chr6D 98.571 70 1 0 414 483 94687187 94687118 8.680000e-25 124.0
13 TraesCS4D01G117400 chr1D 87.191 929 95 11 1411 2315 363861164 363862092 0.000000e+00 1035.0
14 TraesCS4D01G117400 chr1A 84.855 997 121 13 1343 2315 463218534 463219524 0.000000e+00 977.0
15 TraesCS4D01G117400 chr1A 89.706 136 12 2 346 480 321869442 321869576 3.060000e-39 172.0
16 TraesCS4D01G117400 chr2B 89.433 653 66 2 692 1341 105813819 105813167 0.000000e+00 821.0
17 TraesCS4D01G117400 chr2B 89.264 652 65 4 692 1340 547007324 547006675 0.000000e+00 811.0
18 TraesCS4D01G117400 chr2B 89.706 136 13 1 348 483 105827439 105827305 3.060000e-39 172.0
19 TraesCS4D01G117400 chr2B 89.051 137 14 1 348 483 547007504 547007368 3.960000e-38 169.0
20 TraesCS4D01G117400 chr6B 81.192 973 145 24 1347 2314 134838207 134839146 0.000000e+00 749.0
21 TraesCS4D01G117400 chr7D 85.758 653 87 4 692 1341 615562663 615562014 0.000000e+00 686.0
22 TraesCS4D01G117400 chr3D 85.518 656 89 5 692 1343 32310285 32310938 0.000000e+00 680.0
23 TraesCS4D01G117400 chr3D 83.806 494 76 4 1823 2314 533959905 533959414 1.250000e-127 466.0
24 TraesCS4D01G117400 chr3A 85.561 651 89 4 692 1339 523541382 523540734 0.000000e+00 676.0
25 TraesCS4D01G117400 chr5D 85.321 654 93 2 692 1342 491568209 491568862 0.000000e+00 673.0
26 TraesCS4D01G117400 chr5D 85.168 654 93 2 692 1341 365346218 365346871 0.000000e+00 667.0
27 TraesCS4D01G117400 chr5D 76.554 563 121 7 1629 2187 58947101 58947656 4.840000e-77 298.0
28 TraesCS4D01G117400 chr5D 81.651 109 16 4 37 143 100037965 100037859 1.140000e-13 87.9
29 TraesCS4D01G117400 chr2D 84.940 664 94 5 692 1351 586955873 586956534 0.000000e+00 667.0
30 TraesCS4D01G117400 chr2D 97.122 139 3 1 346 483 71925128 71924990 1.380000e-57 233.0
31 TraesCS4D01G117400 chr3B 84.178 493 76 2 1823 2314 706028707 706028216 5.790000e-131 477.0
32 TraesCS4D01G117400 chr3B 82.692 520 82 8 1799 2314 706754860 706755375 2.710000e-124 455.0
33 TraesCS4D01G117400 chr3B 82.031 512 88 4 1805 2314 706183064 706183573 1.270000e-117 433.0
34 TraesCS4D01G117400 chr2A 78.069 611 104 24 1596 2186 32497323 32497923 2.190000e-95 359.0
35 TraesCS4D01G117400 chr5B 76.773 564 113 16 1632 2187 72631208 72630655 1.340000e-77 300.0


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 TraesCS4D01G117400 chr4D 97969308 97971622 2314 True 1946.5 3000 100.0000 1 2315 2 chr4D.!!$R3 2314
1 TraesCS4D01G117400 chr4D 97961528 97962503 975 True 1203.0 1203 88.9910 1342 2315 1 chr4D.!!$R1 973
2 TraesCS4D01G117400 chr4B 139548293 139549281 988 True 1170.0 1170 88.3420 1342 2315 1 chr4B.!!$R1 973
3 TraesCS4D01G117400 chr4B 139571269 139572576 1307 True 1117.0 1700 96.3540 1 2315 2 chr4B.!!$R2 2314
4 TraesCS4D01G117400 chr4A 478209184 478210478 1294 False 649.0 1079 83.4260 30 2312 2 chr4A.!!$F1 2282
5 TraesCS4D01G117400 chr1B 487405524 487406515 991 False 1050.0 1050 86.1580 1343 2315 1 chr1B.!!$F1 972
6 TraesCS4D01G117400 chr6D 61002837 61003528 691 False 599.0 599 82.5970 1342 2054 1 chr6D.!!$F1 712
7 TraesCS4D01G117400 chr6D 94684785 94687187 2402 True 582.0 1040 97.0615 414 1340 2 chr6D.!!$R1 926
8 TraesCS4D01G117400 chr1D 363861164 363862092 928 False 1035.0 1035 87.1910 1411 2315 1 chr1D.!!$F1 904
9 TraesCS4D01G117400 chr1A 463218534 463219524 990 False 977.0 977 84.8550 1343 2315 1 chr1A.!!$F2 972
10 TraesCS4D01G117400 chr2B 105813167 105813819 652 True 821.0 821 89.4330 692 1341 1 chr2B.!!$R1 649
11 TraesCS4D01G117400 chr2B 547006675 547007504 829 True 490.0 811 89.1575 348 1340 2 chr2B.!!$R3 992
12 TraesCS4D01G117400 chr6B 134838207 134839146 939 False 749.0 749 81.1920 1347 2314 1 chr6B.!!$F1 967
13 TraesCS4D01G117400 chr7D 615562014 615562663 649 True 686.0 686 85.7580 692 1341 1 chr7D.!!$R1 649
14 TraesCS4D01G117400 chr3D 32310285 32310938 653 False 680.0 680 85.5180 692 1343 1 chr3D.!!$F1 651
15 TraesCS4D01G117400 chr3A 523540734 523541382 648 True 676.0 676 85.5610 692 1339 1 chr3A.!!$R1 647
16 TraesCS4D01G117400 chr5D 491568209 491568862 653 False 673.0 673 85.3210 692 1342 1 chr5D.!!$F3 650
17 TraesCS4D01G117400 chr5D 365346218 365346871 653 False 667.0 667 85.1680 692 1341 1 chr5D.!!$F2 649
18 TraesCS4D01G117400 chr5D 58947101 58947656 555 False 298.0 298 76.5540 1629 2187 1 chr5D.!!$F1 558
19 TraesCS4D01G117400 chr2D 586955873 586956534 661 False 667.0 667 84.9400 692 1351 1 chr2D.!!$F1 659
20 TraesCS4D01G117400 chr3B 706754860 706755375 515 False 455.0 455 82.6920 1799 2314 1 chr3B.!!$F2 515
21 TraesCS4D01G117400 chr3B 706183064 706183573 509 False 433.0 433 82.0310 1805 2314 1 chr3B.!!$F1 509
22 TraesCS4D01G117400 chr2A 32497323 32497923 600 False 359.0 359 78.0690 1596 2186 1 chr2A.!!$F1 590
23 TraesCS4D01G117400 chr5B 72630655 72631208 553 True 300.0 300 76.7730 1632 2187 1 chr5B.!!$R1 555

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
426 449 0.179111 TCAGTTTATGCTCGGAGGCG 60.179 55.0 7.2 0.0 34.52 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 2877 0.188587 TCTGTGGACTGGAGTGGAGT 59.811 55.0 0.0 0.0 0.0 3.85 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
56 58 1.777101 TTTTTGCGCCATTTTCCTCG 58.223 45.000 4.18 0.00 0.00 4.63
63 65 2.009774 CGCCATTTTCCTCGAATGTCT 58.990 47.619 0.00 0.00 33.65 3.41
94 96 8.836268 AGATGAAATTTTGCAAGCTATCAAAA 57.164 26.923 20.97 20.97 43.55 2.44
180 193 5.815740 GCTCGGGATTAGAATAACACTTTCA 59.184 40.000 0.00 0.00 0.00 2.69
343 365 3.020274 GGAGCAATTTCCCTTCTCTTCC 58.980 50.000 0.00 0.00 0.00 3.46
344 366 2.680339 GAGCAATTTCCCTTCTCTTCCG 59.320 50.000 0.00 0.00 0.00 4.30
345 367 1.745653 GCAATTTCCCTTCTCTTCCGG 59.254 52.381 0.00 0.00 0.00 5.14
346 368 2.618045 GCAATTTCCCTTCTCTTCCGGA 60.618 50.000 0.00 0.00 0.00 5.14
366 388 2.507944 GCCTCTGCCGGATGATGT 59.492 61.111 5.05 0.00 0.00 3.06
369 391 1.953138 CTCTGCCGGATGATGTCGC 60.953 63.158 5.05 0.00 0.00 5.19
370 392 2.969238 CTGCCGGATGATGTCGCC 60.969 66.667 5.05 0.00 0.00 5.54
374 396 1.889105 CCGGATGATGTCGCCCTTG 60.889 63.158 0.00 0.00 0.00 3.61
426 449 0.179111 TCAGTTTATGCTCGGAGGCG 60.179 55.000 7.20 0.00 34.52 5.52
993 2493 3.190874 CTCTCTTGAGGCGGAATTACAC 58.809 50.000 0.00 0.00 36.70 2.90
1023 2523 0.035458 AAGGTATGGCGCTGGCTATC 59.965 55.000 7.64 0.00 39.85 2.08
1114 2614 2.419574 GCCCTCCAACGTTCAGCTTATA 60.420 50.000 0.00 0.00 0.00 0.98
1116 2616 3.118738 CCCTCCAACGTTCAGCTTATAGT 60.119 47.826 0.00 0.00 0.00 2.12
1131 2631 6.150976 CAGCTTATAGTCAATTGGTGTTGGAA 59.849 38.462 5.42 0.00 0.00 3.53
1159 2659 8.508601 TCAAGTACTTATCTGGTATTAGGGAGA 58.491 37.037 8.04 0.00 0.00 3.71
1160 2660 9.144298 CAAGTACTTATCTGGTATTAGGGAGAA 57.856 37.037 8.04 0.00 0.00 2.87
1178 2681 6.498651 AGGGAGAATTCTCAGAAACTTAGTCA 59.501 38.462 31.29 0.00 44.60 3.41
1195 2698 9.778741 AACTTAGTCATGTTCAAAATAGAGTGA 57.221 29.630 0.00 0.00 0.00 3.41
1262 2765 1.488393 GTGGCTAGGCTCAATTCCTCT 59.512 52.381 18.18 0.00 35.21 3.69
1364 2873 2.781595 TTCTCTTCCGCCGTTCCTGC 62.782 60.000 0.00 0.00 0.00 4.85
1365 2874 3.302347 CTCTTCCGCCGTTCCTGCT 62.302 63.158 0.00 0.00 0.00 4.24
1366 2875 2.815647 CTTCCGCCGTTCCTGCTC 60.816 66.667 0.00 0.00 0.00 4.26
1367 2876 4.735132 TTCCGCCGTTCCTGCTCG 62.735 66.667 0.00 0.00 0.00 5.03
1379 2900 1.510383 CTGCTCGACTCCACTCCAG 59.490 63.158 0.00 0.00 0.00 3.86
1563 3090 1.306141 TGCTCTCCCGGATCCACTT 60.306 57.895 13.41 0.00 0.00 3.16
1627 3158 3.141488 CTCCTCCCCCACGACTCG 61.141 72.222 0.00 0.00 0.00 4.18
2290 3882 5.180304 GTCCTTCTTTGAAGAAATCGCTCTT 59.820 40.000 8.69 0.00 43.84 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 6.012658 TGAAAAGACATTCGAGGAAAATGG 57.987 37.500 0.00 0.00 38.23 3.16
135 138 5.193679 AGCTAGGGCGAACAGAAAAATAAT 58.806 37.500 0.00 0.00 44.37 1.28
143 146 2.415608 CCGAGCTAGGGCGAACAGA 61.416 63.158 4.68 0.00 44.37 3.41
331 353 1.338136 GCCATCCGGAAGAGAAGGGA 61.338 60.000 9.01 0.00 0.00 4.20
332 354 1.147153 GCCATCCGGAAGAGAAGGG 59.853 63.158 9.01 0.00 0.00 3.95
333 355 1.147153 GGCCATCCGGAAGAGAAGG 59.853 63.158 9.01 5.12 0.00 3.46
334 356 0.105778 GAGGCCATCCGGAAGAGAAG 59.894 60.000 9.01 0.00 37.47 2.85
335 357 0.325671 AGAGGCCATCCGGAAGAGAA 60.326 55.000 9.01 0.00 37.47 2.87
336 358 1.045350 CAGAGGCCATCCGGAAGAGA 61.045 60.000 9.01 0.00 37.47 3.10
337 359 1.445095 CAGAGGCCATCCGGAAGAG 59.555 63.158 9.01 0.37 37.47 2.85
338 360 2.735772 GCAGAGGCCATCCGGAAGA 61.736 63.158 9.01 0.00 37.47 2.87
339 361 2.203126 GCAGAGGCCATCCGGAAG 60.203 66.667 9.01 3.04 37.47 3.46
358 380 1.154205 CGACAAGGGCGACATCATCC 61.154 60.000 0.00 0.00 0.00 3.51
370 392 3.906720 TTCCTTCCCTTATCGACAAGG 57.093 47.619 15.86 15.86 44.11 3.61
374 396 2.104963 AGCCATTCCTTCCCTTATCGAC 59.895 50.000 0.00 0.00 0.00 4.20
426 449 6.318648 TCAACAAGATTACCATATCTGCAACC 59.681 38.462 0.00 0.00 35.12 3.77
858 2357 1.596934 GTGGAAGGAGCCATCGACA 59.403 57.895 2.65 0.00 40.68 4.35
929 2428 2.019249 TGTATGCTGCAAAGAGGATGC 58.981 47.619 6.36 0.00 44.08 3.91
993 2493 0.514255 CCATACCTTGCATCATCGCG 59.486 55.000 0.00 0.00 33.35 5.87
1034 2534 0.391130 TTGAAGAATCACCGGAGCCG 60.391 55.000 9.46 1.06 34.61 5.52
1035 2535 1.943340 GATTGAAGAATCACCGGAGCC 59.057 52.381 9.46 0.00 38.33 4.70
1114 2614 5.363580 ACTTGATTTCCAACACCAATTGACT 59.636 36.000 7.12 0.00 0.00 3.41
1116 2616 5.867903 ACTTGATTTCCAACACCAATTGA 57.132 34.783 7.12 0.00 0.00 2.57
1131 2631 9.670442 TCCCTAATACCAGATAAGTACTTGATT 57.330 33.333 18.56 2.90 0.00 2.57
1159 2659 8.908786 TGAACATGACTAAGTTTCTGAGAATT 57.091 30.769 0.00 0.00 0.00 2.17
1160 2660 8.908786 TTGAACATGACTAAGTTTCTGAGAAT 57.091 30.769 0.00 0.00 0.00 2.40
1178 2681 5.520288 CGATCGGTCACTCTATTTTGAACAT 59.480 40.000 7.38 0.00 29.19 2.71
1195 2698 2.172851 TAGTTTGCCAAACGATCGGT 57.827 45.000 20.98 10.86 45.88 4.69
1262 2765 5.376625 GAGGCCATACATCCTCAATACAAA 58.623 41.667 5.01 0.00 46.24 2.83
1364 2873 0.609406 TGGACTGGAGTGGAGTCGAG 60.609 60.000 0.00 0.00 40.77 4.04
1365 2874 0.894184 GTGGACTGGAGTGGAGTCGA 60.894 60.000 0.00 0.00 40.77 4.20
1366 2875 1.179174 TGTGGACTGGAGTGGAGTCG 61.179 60.000 0.00 0.00 40.77 4.18
1367 2876 0.605589 CTGTGGACTGGAGTGGAGTC 59.394 60.000 0.00 0.00 39.38 3.36
1368 2877 0.188587 TCTGTGGACTGGAGTGGAGT 59.811 55.000 0.00 0.00 0.00 3.85
1379 2900 2.807045 CGCGTGCTCTCTGTGGAC 60.807 66.667 0.00 0.00 0.00 4.02
2187 3779 1.194781 ATTCCCGTGGACACAGAGCT 61.195 55.000 3.12 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.