Multiple sequence alignment - TraesCS3D01G260500

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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 TraesCS3D01G260500 chr3D 100.000 3106 0 0 1 3106 362854385 362857490 0.000000e+00 5736.0
1 TraesCS3D01G260500 chr3D 90.315 2189 142 35 536 2676 362425205 362423039 0.000000e+00 2804.0
2 TraesCS3D01G260500 chr3D 83.146 356 40 14 181 526 362426018 362425673 1.080000e-79 307.0
3 TraesCS3D01G260500 chr3D 87.027 185 21 1 1 182 362426300 362426116 4.060000e-49 206.0
4 TraesCS3D01G260500 chr3D 95.798 119 4 1 2988 3106 362810587 362810704 1.140000e-44 191.0
5 TraesCS3D01G260500 chr3A 89.907 2358 171 34 584 2878 482929320 482926967 0.000000e+00 2974.0
6 TraesCS3D01G260500 chr3A 88.759 2144 159 32 857 2980 482937243 482935162 0.000000e+00 2549.0
7 TraesCS3D01G260500 chr3A 89.337 347 30 5 518 861 482937616 482937274 2.210000e-116 429.0
8 TraesCS3D01G260500 chr3A 77.493 742 131 21 2250 2977 740573509 740574228 2.230000e-111 412.0
9 TraesCS3D01G260500 chr3A 77.089 742 134 21 2250 2977 740518338 740519057 2.240000e-106 396.0
10 TraesCS3D01G260500 chr3A 87.568 185 19 2 1 182 482961231 482961048 8.730000e-51 211.0
11 TraesCS3D01G260500 chr3A 92.381 105 7 1 2988 3091 483155982 483156086 6.940000e-32 148.0
12 TraesCS3D01G260500 chr3B 94.864 1733 74 6 1355 3074 472586375 472588105 0.000000e+00 2693.0
13 TraesCS3D01G260500 chr3B 90.600 1883 96 29 529 2373 472307494 472305655 0.000000e+00 2422.0
14 TraesCS3D01G260500 chr3B 94.464 849 20 7 525 1355 472584467 472585306 0.000000e+00 1282.0
15 TraesCS3D01G260500 chr3B 92.703 370 13 4 169 528 472584048 472584413 3.550000e-144 521.0
16 TraesCS3D01G260500 chr3B 85.112 356 35 13 179 523 472308319 472307971 6.370000e-92 348.0
17 TraesCS3D01G260500 chr3B 96.491 171 6 0 1 171 472583775 472583945 1.820000e-72 283.0
18 TraesCS3D01G260500 chr3B 94.958 119 5 1 2988 3106 472479075 472479192 5.290000e-43 185.0
19 TraesCS3D01G260500 chr7A 82.877 730 119 5 1338 2064 722767915 722768641 0.000000e+00 651.0
20 TraesCS3D01G260500 chr7A 77.031 357 57 22 2630 2977 19543227 19542887 6.840000e-42 182.0
21 TraesCS3D01G260500 chr7B 82.306 746 124 7 1338 2079 727536981 727536240 9.390000e-180 640.0
22 TraesCS3D01G260500 chr7B 73.008 778 128 58 2239 2977 648699075 648698341 6.790000e-47 198.0
23 TraesCS3D01G260500 chr1D 79.866 894 147 17 1187 2068 342170349 342171221 9.460000e-175 623.0
24 TraesCS3D01G260500 chr1A 79.507 893 152 20 1187 2068 441842088 441842960 9.530000e-170 606.0
25 TraesCS3D01G260500 chr2B 78.456 868 163 17 1176 2034 796277470 796278322 2.110000e-151 545.0
26 TraesCS3D01G260500 chr4B 79.681 753 119 24 2244 2977 65958231 65957494 2.140000e-141 512.0
27 TraesCS3D01G260500 chr2D 74.399 707 141 34 2246 2933 57068109 57068794 1.840000e-67 267.0
28 TraesCS3D01G260500 chr2D 88.889 63 7 0 2924 2986 57070374 57070436 9.230000e-11 78.7
29 TraesCS3D01G260500 chr5A 76.425 386 63 25 2603 2977 18859518 18859886 1.900000e-42 183.0
30 TraesCS3D01G260500 chr6B 76.104 385 65 26 2603 2977 75953873 75953506 3.180000e-40 176.0
31 TraesCS3D01G260500 chr6B 76.042 384 64 25 2603 2975 523059583 523059217 1.140000e-39 174.0
32 TraesCS3D01G260500 chr1B 75.907 386 65 25 2603 2977 635124964 635125332 4.120000e-39 172.0


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 TraesCS3D01G260500 chr3D 362854385 362857490 3105 False 5736.000000 5736 100.000000 1 3106 1 chr3D.!!$F2 3105
1 TraesCS3D01G260500 chr3D 362423039 362426300 3261 True 1105.666667 2804 86.829333 1 2676 3 chr3D.!!$R1 2675
2 TraesCS3D01G260500 chr3A 482926967 482929320 2353 True 2974.000000 2974 89.907000 584 2878 1 chr3A.!!$R1 2294
3 TraesCS3D01G260500 chr3A 482935162 482937616 2454 True 1489.000000 2549 89.048000 518 2980 2 chr3A.!!$R3 2462
4 TraesCS3D01G260500 chr3A 740573509 740574228 719 False 412.000000 412 77.493000 2250 2977 1 chr3A.!!$F3 727
5 TraesCS3D01G260500 chr3A 740518338 740519057 719 False 396.000000 396 77.089000 2250 2977 1 chr3A.!!$F2 727
6 TraesCS3D01G260500 chr3B 472305655 472308319 2664 True 1385.000000 2422 87.856000 179 2373 2 chr3B.!!$R1 2194
7 TraesCS3D01G260500 chr3B 472583775 472588105 4330 False 1194.750000 2693 94.630500 1 3074 4 chr3B.!!$F2 3073
8 TraesCS3D01G260500 chr7A 722767915 722768641 726 False 651.000000 651 82.877000 1338 2064 1 chr7A.!!$F1 726
9 TraesCS3D01G260500 chr7B 727536240 727536981 741 True 640.000000 640 82.306000 1338 2079 1 chr7B.!!$R2 741
10 TraesCS3D01G260500 chr1D 342170349 342171221 872 False 623.000000 623 79.866000 1187 2068 1 chr1D.!!$F1 881
11 TraesCS3D01G260500 chr1A 441842088 441842960 872 False 606.000000 606 79.507000 1187 2068 1 chr1A.!!$F1 881
12 TraesCS3D01G260500 chr2B 796277470 796278322 852 False 545.000000 545 78.456000 1176 2034 1 chr2B.!!$F1 858
13 TraesCS3D01G260500 chr4B 65957494 65958231 737 True 512.000000 512 79.681000 2244 2977 1 chr4B.!!$R1 733

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
46 47 0.178981 ACCACTCACAAGCCTGCATT 60.179 50.0 0.0 0.0 0.00 3.56 F
1043 1821 0.179009 AGCTTCTGGCACACACACAT 60.179 50.0 0.0 0.0 44.79 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 3706 0.834612 TCGAAGGTTTGGGTGACTGT 59.165 50.0 0.00 0.0 0.0 3.55 R
2386 4277 0.466555 TGGCCGGCTTGTGTAGTTTT 60.467 50.0 28.56 0.0 0.0 2.43 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
46 47 0.178981 ACCACTCACAAGCCTGCATT 60.179 50.000 0.00 0.00 0.00 3.56
229 437 7.492994 GGGTTAAAGAGAATGAGTGCTTAGTAG 59.507 40.741 0.00 0.00 0.00 2.57
230 438 8.035984 GGTTAAAGAGAATGAGTGCTTAGTAGT 58.964 37.037 0.00 0.00 0.00 2.73
263 471 0.311165 ACGTCTTGACCGTGAGTCTG 59.689 55.000 0.00 0.00 46.46 3.51
346 566 2.163211 GCTTGAGCCCTTCTTGTCATTC 59.837 50.000 0.00 0.00 34.31 2.67
401 621 7.228314 AGTACGCACATATGTATCTATGGTT 57.772 36.000 8.32 0.00 34.11 3.67
515 741 5.843019 ATCCTGTCTTAACCTGGAAAGAA 57.157 39.130 14.72 3.99 33.70 2.52
527 1229 7.839680 AACCTGGAAAGAAGTGTAATTCAAT 57.160 32.000 0.00 0.00 0.00 2.57
639 1347 1.968050 ATTCCACGTCCGTCCATCCC 61.968 60.000 0.00 0.00 0.00 3.85
1015 1785 3.990092 TGCTGGCTATATAAAGACGTGG 58.010 45.455 0.00 0.00 0.00 4.94
1043 1821 0.179009 AGCTTCTGGCACACACACAT 60.179 50.000 0.00 0.00 44.79 3.21
1596 3478 0.683504 CCTACTCGTGGGGCTACTGT 60.684 60.000 0.00 0.00 0.00 3.55
1824 3706 1.003839 GTGGTTCTGGATGACGCCA 60.004 57.895 0.00 0.00 36.30 5.69
2317 4206 1.593006 CCGGCTAAGATACAAAGTGCG 59.407 52.381 0.00 0.00 0.00 5.34
2445 4336 5.803552 ACATAATGGGAAACAAAACCATGG 58.196 37.500 11.19 11.19 43.88 3.66
2691 4604 1.841302 GCACACATCTCCCCACCTCA 61.841 60.000 0.00 0.00 0.00 3.86
2799 4736 1.301677 GCGCTTTCAAGGAGGACCAG 61.302 60.000 0.00 0.00 38.94 4.00
3000 4949 3.118371 AGGTTTCCGCCTCCTTATACTTG 60.118 47.826 0.00 0.00 32.39 3.16
3024 4973 8.583810 TGTATAGGCGTATTATCAGTGAAAAC 57.416 34.615 3.94 0.00 0.00 2.43
3026 4975 9.903682 GTATAGGCGTATTATCAGTGAAAACTA 57.096 33.333 3.94 0.00 0.00 2.24
3074 5023 4.749099 TGTAAATTGTCAAATGTGCCTTGC 59.251 37.500 0.00 0.00 0.00 4.01
3075 5024 3.472283 AATTGTCAAATGTGCCTTGCA 57.528 38.095 0.00 0.00 35.60 4.08
3076 5025 3.688694 ATTGTCAAATGTGCCTTGCAT 57.311 38.095 0.00 0.00 41.91 3.96
3077 5026 3.472283 TTGTCAAATGTGCCTTGCATT 57.528 38.095 0.00 0.00 41.91 3.56
3078 5027 3.472283 TGTCAAATGTGCCTTGCATTT 57.528 38.095 0.00 0.00 44.46 2.32
3079 5028 3.806380 TGTCAAATGTGCCTTGCATTTT 58.194 36.364 0.00 0.00 42.54 1.82
3080 5029 3.560481 TGTCAAATGTGCCTTGCATTTTG 59.440 39.130 15.49 15.49 42.54 2.44
3081 5030 3.808726 GTCAAATGTGCCTTGCATTTTGA 59.191 39.130 18.21 18.21 43.80 2.69
3082 5031 4.059511 TCAAATGTGCCTTGCATTTTGAG 58.940 39.130 18.21 2.74 42.58 3.02
3083 5032 4.059511 CAAATGTGCCTTGCATTTTGAGA 58.940 39.130 16.14 0.00 42.54 3.27
3084 5033 4.339872 AATGTGCCTTGCATTTTGAGAA 57.660 36.364 0.00 0.00 41.91 2.87
3085 5034 3.815856 TGTGCCTTGCATTTTGAGAAA 57.184 38.095 0.00 0.00 41.91 2.52
3086 5035 3.719924 TGTGCCTTGCATTTTGAGAAAG 58.280 40.909 0.00 0.00 41.91 2.62
3087 5036 3.062042 GTGCCTTGCATTTTGAGAAAGG 58.938 45.455 0.00 0.00 41.91 3.11
3088 5037 2.037511 TGCCTTGCATTTTGAGAAAGGG 59.962 45.455 2.34 0.00 38.27 3.95
3089 5038 2.613725 GCCTTGCATTTTGAGAAAGGGG 60.614 50.000 2.34 0.00 38.27 4.79
3090 5039 2.027837 CCTTGCATTTTGAGAAAGGGGG 60.028 50.000 0.00 0.00 34.90 5.40
3091 5040 2.692709 TGCATTTTGAGAAAGGGGGA 57.307 45.000 0.00 0.00 0.00 4.81
3092 5041 2.528564 TGCATTTTGAGAAAGGGGGAG 58.471 47.619 0.00 0.00 0.00 4.30
3093 5042 2.158325 TGCATTTTGAGAAAGGGGGAGT 60.158 45.455 0.00 0.00 0.00 3.85
3094 5043 3.075283 TGCATTTTGAGAAAGGGGGAGTA 59.925 43.478 0.00 0.00 0.00 2.59
3095 5044 3.696548 GCATTTTGAGAAAGGGGGAGTAG 59.303 47.826 0.00 0.00 0.00 2.57
3096 5045 4.811063 GCATTTTGAGAAAGGGGGAGTAGT 60.811 45.833 0.00 0.00 0.00 2.73
3097 5046 5.572885 GCATTTTGAGAAAGGGGGAGTAGTA 60.573 44.000 0.00 0.00 0.00 1.82
3098 5047 6.663734 CATTTTGAGAAAGGGGGAGTAGTAT 58.336 40.000 0.00 0.00 0.00 2.12
3099 5048 5.693769 TTTGAGAAAGGGGGAGTAGTATG 57.306 43.478 0.00 0.00 0.00 2.39
3100 5049 3.654273 TGAGAAAGGGGGAGTAGTATGG 58.346 50.000 0.00 0.00 0.00 2.74
3101 5050 3.273886 TGAGAAAGGGGGAGTAGTATGGA 59.726 47.826 0.00 0.00 0.00 3.41
3102 5051 3.898741 GAGAAAGGGGGAGTAGTATGGAG 59.101 52.174 0.00 0.00 0.00 3.86
3103 5052 3.275228 AGAAAGGGGGAGTAGTATGGAGT 59.725 47.826 0.00 0.00 0.00 3.85
3104 5053 2.777459 AGGGGGAGTAGTATGGAGTG 57.223 55.000 0.00 0.00 0.00 3.51
3105 5054 1.938069 AGGGGGAGTAGTATGGAGTGT 59.062 52.381 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.206150 GTGGATATGCAACAATCGACCT 58.794 45.455 0.00 0.00 0.00 3.85
46 47 2.621070 ACTAGCCTTTCTCCCAAGACA 58.379 47.619 0.00 0.00 0.00 3.41
229 437 6.089551 GGTCAAGACGTGCATATATCACATAC 59.910 42.308 0.00 6.06 34.27 2.39
230 438 6.156519 GGTCAAGACGTGCATATATCACATA 58.843 40.000 0.00 0.00 34.27 2.29
231 439 4.991056 GGTCAAGACGTGCATATATCACAT 59.009 41.667 0.00 1.60 34.27 3.21
263 471 0.329596 ATCACCCCCTTCACTCTTGC 59.670 55.000 0.00 0.00 0.00 4.01
346 566 3.011760 GAAACGAACGCAGCGGAGG 62.012 63.158 21.15 9.70 0.00 4.30
488 711 3.266772 TCCAGGTTAAGACAGGATTGCAT 59.733 43.478 0.00 0.00 29.72 3.96
515 741 7.834181 ACCAGGCAAACTATATTGAATTACACT 59.166 33.333 0.00 0.00 31.84 3.55
639 1347 3.405170 AACTTTGATCGCCGCATTAAG 57.595 42.857 0.00 0.00 0.00 1.85
1015 1785 3.978272 CCAGAAGCTGGTGCAGTC 58.022 61.111 5.31 0.00 45.82 3.51
1035 1813 3.242518 CTCGTGTAGTGGTATGTGTGTG 58.757 50.000 0.00 0.00 0.00 3.82
1075 1853 3.307242 GCTCAGCTGGTGATTTAGTTACG 59.693 47.826 15.13 0.00 33.51 3.18
1495 3377 2.048222 CACCTCGCGCTTCCTGAA 60.048 61.111 5.56 0.00 0.00 3.02
1596 3478 1.896660 GCCACGCTCCTGGTTGAAA 60.897 57.895 0.00 0.00 33.30 2.69
1824 3706 0.834612 TCGAAGGTTTGGGTGACTGT 59.165 50.000 0.00 0.00 0.00 3.55
2260 4148 7.817418 TTAGTTTGAAGTCTGGTTAAATGCT 57.183 32.000 0.00 0.00 0.00 3.79
2271 4159 8.352942 GTTGATGGTTTCATTAGTTTGAAGTCT 58.647 33.333 0.00 0.00 36.97 3.24
2386 4277 0.466555 TGGCCGGCTTGTGTAGTTTT 60.467 50.000 28.56 0.00 0.00 2.43
2412 4303 4.533919 TTCCCATTATGTTGGCAGTTTG 57.466 40.909 0.00 0.00 35.29 2.93
2445 4336 1.225854 GCATTGTGCTCTTCGACGC 60.226 57.895 0.00 0.00 40.96 5.19
2581 4478 4.703093 GTGCTAGATGTAGGGGAGATAGAC 59.297 50.000 0.00 0.00 0.00 2.59
2582 4479 4.565861 CGTGCTAGATGTAGGGGAGATAGA 60.566 50.000 0.00 0.00 0.00 1.98
2667 4579 1.380302 GGGGAGATGTGTGCCTTGT 59.620 57.895 0.00 0.00 0.00 3.16
2668 4580 0.962356 GTGGGGAGATGTGTGCCTTG 60.962 60.000 0.00 0.00 0.00 3.61
2843 4780 1.009183 CCCTCCTTTAGTCCCCTGGTA 59.991 57.143 0.00 0.00 0.00 3.25
3000 4949 8.813643 AGTTTTCACTGATAATACGCCTATAC 57.186 34.615 0.00 0.00 0.00 1.47
3026 4975 9.429359 CAGTCTTCATTGTCTAAGTTTCACTAT 57.571 33.333 0.00 0.00 0.00 2.12
3074 5023 4.923415 ACTACTCCCCCTTTCTCAAAATG 58.077 43.478 0.00 0.00 0.00 2.32
3075 5024 6.353951 CCATACTACTCCCCCTTTCTCAAAAT 60.354 42.308 0.00 0.00 0.00 1.82
3076 5025 5.045140 CCATACTACTCCCCCTTTCTCAAAA 60.045 44.000 0.00 0.00 0.00 2.44
3077 5026 4.473559 CCATACTACTCCCCCTTTCTCAAA 59.526 45.833 0.00 0.00 0.00 2.69
3078 5027 4.037927 CCATACTACTCCCCCTTTCTCAA 58.962 47.826 0.00 0.00 0.00 3.02
3079 5028 3.273886 TCCATACTACTCCCCCTTTCTCA 59.726 47.826 0.00 0.00 0.00 3.27
3080 5029 3.898741 CTCCATACTACTCCCCCTTTCTC 59.101 52.174 0.00 0.00 0.00 2.87
3081 5030 3.275228 ACTCCATACTACTCCCCCTTTCT 59.725 47.826 0.00 0.00 0.00 2.52
3082 5031 3.388350 CACTCCATACTACTCCCCCTTTC 59.612 52.174 0.00 0.00 0.00 2.62
3083 5032 3.246387 ACACTCCATACTACTCCCCCTTT 60.246 47.826 0.00 0.00 0.00 3.11
3084 5033 2.318207 ACACTCCATACTACTCCCCCTT 59.682 50.000 0.00 0.00 0.00 3.95
3085 5034 1.938069 ACACTCCATACTACTCCCCCT 59.062 52.381 0.00 0.00 0.00 4.79
3086 5035 2.473576 ACACTCCATACTACTCCCCC 57.526 55.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.