Multiple sequence alignment - TraesCS3D01G174200

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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 TraesCS3D01G174200 chr3D 100.000 3234 0 0 1 3234 155675215 155678448 0.000000e+00 5973
1 TraesCS3D01G174200 chr3D 97.926 2604 52 2 632 3234 374010879 374008277 0.000000e+00 4508
2 TraesCS3D01G174200 chr3D 96.731 2233 72 1 632 2863 609771287 609769055 0.000000e+00 3718
3 TraesCS3D01G174200 chr3D 96.336 1883 50 3 1371 3234 580651490 580649608 0.000000e+00 3077
4 TraesCS3D01G174200 chr3D 79.062 597 104 16 56 635 182334494 182335086 1.090000e-104 390
5 TraesCS3D01G174200 chr3D 77.759 607 111 16 36 630 182320453 182321047 5.130000e-93 351
6 TraesCS3D01G174200 chr3D 75.189 528 120 10 107 630 148699899 148699379 4.170000e-59 239
7 TraesCS3D01G174200 chr3D 74.435 575 124 18 57 624 148336474 148335916 3.250000e-55 226
8 TraesCS3D01G174200 chr3D 74.286 560 113 27 57 605 55084616 55084077 1.180000e-49 207
9 TraesCS3D01G174200 chr3D 75.378 463 91 19 54 509 55742548 55742994 5.470000e-48 202
10 TraesCS3D01G174200 chr3D 74.271 377 82 14 139 509 55577814 55578181 9.350000e-31 145
11 TraesCS3D01G174200 chr1D 97.812 2605 54 3 633 3234 422850795 422848191 0.000000e+00 4492
12 TraesCS3D01G174200 chr2D 97.580 2603 61 2 633 3234 535662318 535664919 0.000000e+00 4457
13 TraesCS3D01G174200 chr2D 96.503 2631 62 3 632 3234 207006263 207003635 0.000000e+00 4322
14 TraesCS3D01G174200 chr2D 96.305 2625 60 14 633 3232 77209587 77212199 0.000000e+00 4276
15 TraesCS3D01G174200 chr2D 95.313 2603 89 5 633 3234 633747075 633749645 0.000000e+00 4100
16 TraesCS3D01G174200 chr6D 97.157 2603 71 3 633 3234 445278100 445275500 0.000000e+00 4394
17 TraesCS3D01G174200 chr6D 95.790 2613 65 5 624 3234 387624686 387622117 0.000000e+00 4174
18 TraesCS3D01G174200 chr5D 97.083 2605 73 2 631 3234 504761412 504764014 0.000000e+00 4386
19 TraesCS3D01G174200 chr3B 95.440 636 28 1 1 635 226004551 226003916 0.000000e+00 1013
20 TraesCS3D01G174200 chr3B 79.089 593 105 14 56 635 260842537 260843123 1.090000e-104 390
21 TraesCS3D01G174200 chr3B 74.355 581 132 13 54 630 207733959 207734526 6.980000e-57 231
22 TraesCS3D01G174200 chr3B 74.182 550 129 12 86 630 205775733 205776274 1.950000e-52 217
23 TraesCS3D01G174200 chr3A 95.440 636 19 2 1 635 174542672 174543298 0.000000e+00 1005
24 TraesCS3D01G174200 chr3A 74.483 580 133 11 54 630 164611254 164611821 1.500000e-58 237
25 TraesCS3D01G174200 chr3A 73.702 578 123 21 57 624 65480421 65479863 7.080000e-47 198


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 TraesCS3D01G174200 chr3D 155675215 155678448 3233 False 5973 5973 100.000 1 3234 1 chr3D.!!$F3 3233
1 TraesCS3D01G174200 chr3D 374008277 374010879 2602 True 4508 4508 97.926 632 3234 1 chr3D.!!$R4 2602
2 TraesCS3D01G174200 chr3D 609769055 609771287 2232 True 3718 3718 96.731 632 2863 1 chr3D.!!$R6 2231
3 TraesCS3D01G174200 chr3D 580649608 580651490 1882 True 3077 3077 96.336 1371 3234 1 chr3D.!!$R5 1863
4 TraesCS3D01G174200 chr3D 182334494 182335086 592 False 390 390 79.062 56 635 1 chr3D.!!$F5 579
5 TraesCS3D01G174200 chr3D 182320453 182321047 594 False 351 351 77.759 36 630 1 chr3D.!!$F4 594
6 TraesCS3D01G174200 chr3D 148699379 148699899 520 True 239 239 75.189 107 630 1 chr3D.!!$R3 523
7 TraesCS3D01G174200 chr3D 148335916 148336474 558 True 226 226 74.435 57 624 1 chr3D.!!$R2 567
8 TraesCS3D01G174200 chr3D 55084077 55084616 539 True 207 207 74.286 57 605 1 chr3D.!!$R1 548
9 TraesCS3D01G174200 chr1D 422848191 422850795 2604 True 4492 4492 97.812 633 3234 1 chr1D.!!$R1 2601
10 TraesCS3D01G174200 chr2D 535662318 535664919 2601 False 4457 4457 97.580 633 3234 1 chr2D.!!$F2 2601
11 TraesCS3D01G174200 chr2D 207003635 207006263 2628 True 4322 4322 96.503 632 3234 1 chr2D.!!$R1 2602
12 TraesCS3D01G174200 chr2D 77209587 77212199 2612 False 4276 4276 96.305 633 3232 1 chr2D.!!$F1 2599
13 TraesCS3D01G174200 chr2D 633747075 633749645 2570 False 4100 4100 95.313 633 3234 1 chr2D.!!$F3 2601
14 TraesCS3D01G174200 chr6D 445275500 445278100 2600 True 4394 4394 97.157 633 3234 1 chr6D.!!$R2 2601
15 TraesCS3D01G174200 chr6D 387622117 387624686 2569 True 4174 4174 95.790 624 3234 1 chr6D.!!$R1 2610
16 TraesCS3D01G174200 chr5D 504761412 504764014 2602 False 4386 4386 97.083 631 3234 1 chr5D.!!$F1 2603
17 TraesCS3D01G174200 chr3B 226003916 226004551 635 True 1013 1013 95.440 1 635 1 chr3B.!!$R1 634
18 TraesCS3D01G174200 chr3B 260842537 260843123 586 False 390 390 79.089 56 635 1 chr3B.!!$F3 579
19 TraesCS3D01G174200 chr3B 207733959 207734526 567 False 231 231 74.355 54 630 1 chr3B.!!$F2 576
20 TraesCS3D01G174200 chr3B 205775733 205776274 541 False 217 217 74.182 86 630 1 chr3B.!!$F1 544
21 TraesCS3D01G174200 chr3A 174542672 174543298 626 False 1005 1005 95.440 1 635 1 chr3A.!!$F2 634
22 TraesCS3D01G174200 chr3A 164611254 164611821 567 False 237 237 74.483 54 630 1 chr3A.!!$F1 576

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
264 274 0.613853 TCGGGAAGTGGGTCGAGAAT 60.614 55.0 0.0 0.0 0.0 2.40 F
924 955 0.676184 TTCTGCTCTCACGCTCACTT 59.324 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1274 5.045213 TCAAATGCAACATACTTCCTCCCTA 60.045 40.0 0.0 0.0 0.0 3.53 R
2699 2822 0.107703 CCCAACGCCTGAAGATGCTA 60.108 55.0 0.0 0.0 0.0 3.49 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
64 65 2.126228 CCGAACCGCGCTACTTCA 60.126 61.111 5.56 0.00 39.11 3.02
70 71 1.320344 ACCGCGCTACTTCATCCTCA 61.320 55.000 5.56 0.00 0.00 3.86
264 274 0.613853 TCGGGAAGTGGGTCGAGAAT 60.614 55.000 0.00 0.00 0.00 2.40
344 354 3.775654 GAGGCTCTGGTGGGTCGG 61.776 72.222 7.40 0.00 0.00 4.79
466 476 1.685491 GGGGAGAGTCCGACATGTACT 60.685 57.143 0.00 0.00 37.43 2.73
523 542 3.015327 GTCGACACCTACTACATGGACT 58.985 50.000 11.55 0.00 0.00 3.85
540 568 4.306967 TGTGTCATCGGCGGCACA 62.307 61.111 10.53 17.86 39.21 4.57
549 577 4.054825 GGCGGCACACCCAACATG 62.055 66.667 3.07 0.00 0.00 3.21
718 749 2.658268 GCAAAAGCCACCGCACAC 60.658 61.111 0.00 0.00 37.52 3.82
778 809 2.668550 GCGGTTGAGGGCGTTTCT 60.669 61.111 0.00 0.00 0.00 2.52
921 952 0.961753 TCTTTCTGCTCTCACGCTCA 59.038 50.000 0.00 0.00 0.00 4.26
924 955 0.676184 TTCTGCTCTCACGCTCACTT 59.324 50.000 0.00 0.00 0.00 3.16
1116 1147 5.385198 TGCTCATTTCTGTTCTAGGGTTTT 58.615 37.500 0.00 0.00 0.00 2.43
1243 1274 3.698040 GTGATTTGTGAGCATGGGAATCT 59.302 43.478 0.00 0.00 0.00 2.40
1435 1493 7.928706 GGTTCATAGTTACTGCTCATGTTCTAT 59.071 37.037 0.00 0.00 0.00 1.98
1845 1908 5.787494 TCTTGGATTATAAGGATAGCCAGCT 59.213 40.000 0.00 0.00 36.29 4.24
2069 2153 3.432749 GGAGATTTGCTATGCTGACCTGA 60.433 47.826 0.00 0.00 0.00 3.86
2070 2154 4.194640 GAGATTTGCTATGCTGACCTGAA 58.805 43.478 0.00 0.00 0.00 3.02
2071 2155 4.197750 AGATTTGCTATGCTGACCTGAAG 58.802 43.478 0.00 0.00 0.00 3.02
2072 2156 3.701205 TTTGCTATGCTGACCTGAAGA 57.299 42.857 0.00 0.00 0.00 2.87
2073 2157 3.701205 TTGCTATGCTGACCTGAAGAA 57.299 42.857 0.00 0.00 0.00 2.52
2074 2158 3.701205 TGCTATGCTGACCTGAAGAAA 57.299 42.857 0.00 0.00 0.00 2.52
2075 2159 3.603532 TGCTATGCTGACCTGAAGAAAG 58.396 45.455 0.00 0.00 0.00 2.62
2076 2160 3.261643 TGCTATGCTGACCTGAAGAAAGA 59.738 43.478 0.00 0.00 0.00 2.52
2077 2161 3.870419 GCTATGCTGACCTGAAGAAAGAG 59.130 47.826 0.00 0.00 0.00 2.85
2078 2162 4.382470 GCTATGCTGACCTGAAGAAAGAGA 60.382 45.833 0.00 0.00 0.00 3.10
2079 2163 4.630644 ATGCTGACCTGAAGAAAGAGAA 57.369 40.909 0.00 0.00 0.00 2.87
2080 2164 4.000331 TGCTGACCTGAAGAAAGAGAAG 58.000 45.455 0.00 0.00 0.00 2.85
2081 2165 3.244353 TGCTGACCTGAAGAAAGAGAAGG 60.244 47.826 0.00 0.00 0.00 3.46
2082 2166 3.007398 GCTGACCTGAAGAAAGAGAAGGA 59.993 47.826 0.00 0.00 0.00 3.36
2083 2167 4.323409 GCTGACCTGAAGAAAGAGAAGGAT 60.323 45.833 0.00 0.00 0.00 3.24
2084 2168 5.157940 TGACCTGAAGAAAGAGAAGGATG 57.842 43.478 0.00 0.00 0.00 3.51
2085 2169 4.840680 TGACCTGAAGAAAGAGAAGGATGA 59.159 41.667 0.00 0.00 0.00 2.92
2086 2170 5.159273 ACCTGAAGAAAGAGAAGGATGAC 57.841 43.478 0.00 0.00 0.00 3.06
2087 2171 4.019771 ACCTGAAGAAAGAGAAGGATGACC 60.020 45.833 0.00 0.00 0.00 4.02
2231 2315 2.158696 AGCAACAAGAGGAAGCTTCACT 60.159 45.455 27.02 21.02 29.98 3.41
2282 2366 3.627577 AGTTGTGTTGTTGTCTGACCATC 59.372 43.478 5.17 0.00 0.00 3.51
2392 2476 6.186957 AGCAATGAACCTTGGATTGTATGTA 58.813 36.000 0.00 0.00 31.03 2.29
2699 2822 4.141390 ACAACATGTCACTCCTCCTTCTTT 60.141 41.667 0.00 0.00 0.00 2.52
2745 2869 1.064803 GCACGTCATTGTTGTTCACCA 59.935 47.619 0.00 0.00 0.00 4.17
2930 3054 1.078637 GAGCTGCACATCAGGCTCA 60.079 57.895 16.09 0.00 43.06 4.26
3006 3130 4.523173 AGGAGTAGTCGTCAGTTTCATCAA 59.477 41.667 0.00 0.00 0.00 2.57
3182 3306 1.003112 GTACATCCACCAACGGGCA 60.003 57.895 0.00 0.00 37.90 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.842462 TCGTGCCAGTGGACACCT 60.842 61.111 22.84 0.00 33.09 4.00
30 31 2.734591 GAGTCGTGCCAGTGGACA 59.265 61.111 15.20 7.85 33.18 4.02
64 65 2.746277 GGCGTTGGCGTTGAGGAT 60.746 61.111 0.00 0.00 41.24 3.24
94 101 3.646715 CTTGGGTTCGGGGAGGCA 61.647 66.667 0.00 0.00 0.00 4.75
289 299 1.299850 CGATGGGCGCGAAGATGTA 60.300 57.895 12.10 0.00 0.00 2.29
290 300 2.586079 CGATGGGCGCGAAGATGT 60.586 61.111 12.10 0.00 0.00 3.06
344 354 3.704231 ATGACGCCCCATGTGAGGC 62.704 63.158 8.27 8.27 46.17 4.70
413 423 4.947147 GCAACACCCTGTCCGGCA 62.947 66.667 0.00 0.00 0.00 5.69
427 437 2.829384 AAGCTTCCCTGGACCGCAA 61.829 57.895 0.00 0.00 0.00 4.85
523 542 4.306967 TGTGCCGCCGATGACACA 62.307 61.111 0.00 0.00 40.53 3.72
540 568 1.600636 CCACACGCTCATGTTGGGT 60.601 57.895 0.00 0.00 0.00 4.51
718 749 5.862811 GCACTCTGCAAAACTATTACTGAG 58.137 41.667 0.00 0.00 44.26 3.35
921 952 1.004440 GCGTGGGAGCAGAGAAAGT 60.004 57.895 0.00 0.00 37.05 2.66
924 955 2.973899 GAGCGTGGGAGCAGAGAA 59.026 61.111 0.00 0.00 40.15 2.87
1116 1147 6.418057 AATCAAGCAAATGTTCAACCCTAA 57.582 33.333 0.00 0.00 0.00 2.69
1243 1274 5.045213 TCAAATGCAACATACTTCCTCCCTA 60.045 40.000 0.00 0.00 0.00 3.53
1595 1657 6.994421 ATTTCCAACACCCTACAAAAGAAT 57.006 33.333 0.00 0.00 0.00 2.40
1845 1908 5.415701 GCATCATTCTTCTGGTTTACCTCAA 59.584 40.000 0.00 0.00 36.82 3.02
2069 2153 7.560796 TCTTTAGGTCATCCTTCTCTTTCTT 57.439 36.000 0.00 0.00 42.12 2.52
2070 2154 7.560796 TTCTTTAGGTCATCCTTCTCTTTCT 57.439 36.000 0.00 0.00 42.12 2.52
2071 2155 8.097662 TCTTTCTTTAGGTCATCCTTCTCTTTC 58.902 37.037 0.00 0.00 42.12 2.62
2072 2156 7.978925 TCTTTCTTTAGGTCATCCTTCTCTTT 58.021 34.615 0.00 0.00 42.12 2.52
2073 2157 7.456269 TCTCTTTCTTTAGGTCATCCTTCTCTT 59.544 37.037 0.00 0.00 42.12 2.85
2074 2158 6.957020 TCTCTTTCTTTAGGTCATCCTTCTCT 59.043 38.462 0.00 0.00 42.12 3.10
2075 2159 7.176589 TCTCTTTCTTTAGGTCATCCTTCTC 57.823 40.000 0.00 0.00 42.12 2.87
2076 2160 7.310983 CCTTCTCTTTCTTTAGGTCATCCTTCT 60.311 40.741 0.00 0.00 42.12 2.85
2077 2161 6.821160 CCTTCTCTTTCTTTAGGTCATCCTTC 59.179 42.308 0.00 0.00 42.12 3.46
2078 2162 6.502158 TCCTTCTCTTTCTTTAGGTCATCCTT 59.498 38.462 0.00 0.00 42.12 3.36
2080 2164 6.301169 TCCTTCTCTTTCTTTAGGTCATCC 57.699 41.667 0.00 0.00 0.00 3.51
2081 2165 9.541143 CTTATCCTTCTCTTTCTTTAGGTCATC 57.459 37.037 0.00 0.00 0.00 2.92
2082 2166 7.990314 GCTTATCCTTCTCTTTCTTTAGGTCAT 59.010 37.037 0.00 0.00 0.00 3.06
2083 2167 7.181125 AGCTTATCCTTCTCTTTCTTTAGGTCA 59.819 37.037 0.00 0.00 0.00 4.02
2084 2168 7.494298 CAGCTTATCCTTCTCTTTCTTTAGGTC 59.506 40.741 0.00 0.00 0.00 3.85
2085 2169 7.334858 CAGCTTATCCTTCTCTTTCTTTAGGT 58.665 38.462 0.00 0.00 0.00 3.08
2086 2170 6.765512 CCAGCTTATCCTTCTCTTTCTTTAGG 59.234 42.308 0.00 0.00 0.00 2.69
2087 2171 7.560368 TCCAGCTTATCCTTCTCTTTCTTTAG 58.440 38.462 0.00 0.00 0.00 1.85
2088 2172 7.496346 TCCAGCTTATCCTTCTCTTTCTTTA 57.504 36.000 0.00 0.00 0.00 1.85
2089 2173 6.380079 TCCAGCTTATCCTTCTCTTTCTTT 57.620 37.500 0.00 0.00 0.00 2.52
2231 2315 8.150945 GTCCTCATCACAAATAGCCTTAATCTA 58.849 37.037 0.00 0.00 0.00 1.98
2282 2366 7.194607 ACTACAAAAGACATCATTGACACAG 57.805 36.000 0.00 0.00 0.00 3.66
2392 2476 5.812642 CACAAACAGAGTACTCTCACAAACT 59.187 40.000 22.76 0.00 42.66 2.66
2699 2822 0.107703 CCCAACGCCTGAAGATGCTA 60.108 55.000 0.00 0.00 0.00 3.49
2745 2869 1.679898 CCAAGAAGAAGAGGGCGGT 59.320 57.895 0.00 0.00 0.00 5.68
2930 3054 0.538516 CCTCCGACTCCTCCGATGAT 60.539 60.000 0.00 0.00 0.00 2.45
3006 3130 3.488363 AGTCCTCTGACGACTACAACTT 58.512 45.455 7.42 0.00 46.51 2.66


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

AutoCloner maintained by Alex Coulton.