Multiple sequence alignment - TraesCS3B01G271100

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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 TraesCS3B01G271100 chr3B 100.000 3657 0 0 1 3657 436729446 436725790 0.000000e+00 6754.0
1 TraesCS3B01G271100 chr3B 89.883 1028 97 6 1399 2421 436574738 436575763 0.000000e+00 1315.0
2 TraesCS3B01G271100 chr3D 94.342 2775 106 26 258 3007 338350962 338348214 0.000000e+00 4207.0
3 TraesCS3B01G271100 chr3D 88.900 1027 104 5 1403 2421 338321170 338322194 0.000000e+00 1256.0
4 TraesCS3B01G271100 chr3D 94.825 657 28 4 3005 3657 338348166 338347512 0.000000e+00 1020.0
5 TraesCS3B01G271100 chr3D 96.935 261 8 0 1 261 338351250 338350990 4.340000e-119 438.0
6 TraesCS3B01G271100 chr3A 92.197 1948 91 30 1108 3008 456700944 456699011 0.000000e+00 2699.0
7 TraesCS3B01G271100 chr3A 89.731 1042 96 7 1389 2421 456452183 456453222 0.000000e+00 1321.0
8 TraesCS3B01G271100 chr3A 93.303 657 31 5 3005 3657 456698982 456698335 0.000000e+00 957.0
9 TraesCS3B01G271100 chr3A 87.544 843 64 20 258 1072 456701772 456700943 0.000000e+00 937.0
10 TraesCS3B01G271100 chr3A 91.418 268 11 5 1 260 456703470 456703207 1.250000e-94 357.0
11 TraesCS3B01G271100 chr2D 93.333 135 8 1 1517 1650 536380669 536380803 8.010000e-47 198.0
12 TraesCS3B01G271100 chr2B 92.537 134 10 0 1517 1650 637775928 637776061 3.730000e-45 193.0
13 TraesCS3B01G271100 chr6B 92.308 65 5 0 1846 1910 347591962 347591898 3.890000e-15 93.5
14 TraesCS3B01G271100 chr6B 93.750 48 3 0 2582 2629 40678305 40678258 5.070000e-09 73.1
15 TraesCS3B01G271100 chr1D 91.667 48 4 0 2582 2629 327220586 327220539 2.360000e-07 67.6
16 TraesCS3B01G271100 chr7D 85.484 62 9 0 2572 2633 103820622 103820561 8.480000e-07 65.8
17 TraesCS3B01G271100 chr5A 85.938 64 6 3 2572 2633 427829165 427829103 8.480000e-07 65.8
18 TraesCS3B01G271100 chr2A 82.051 78 12 1 2573 2648 713152778 713152855 8.480000e-07 65.8
19 TraesCS3B01G271100 chr4B 88.462 52 6 0 2582 2633 536409015 536408964 3.050000e-06 63.9
20 TraesCS3B01G271100 chr1A 89.583 48 5 0 2582 2629 251695777 251695730 1.100000e-05 62.1


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 TraesCS3B01G271100 chr3B 436725790 436729446 3656 True 6754.000000 6754 100.000000 1 3657 1 chr3B.!!$R1 3656
1 TraesCS3B01G271100 chr3B 436574738 436575763 1025 False 1315.000000 1315 89.883000 1399 2421 1 chr3B.!!$F1 1022
2 TraesCS3B01G271100 chr3D 338347512 338351250 3738 True 1888.333333 4207 95.367333 1 3657 3 chr3D.!!$R1 3656
3 TraesCS3B01G271100 chr3D 338321170 338322194 1024 False 1256.000000 1256 88.900000 1403 2421 1 chr3D.!!$F1 1018
4 TraesCS3B01G271100 chr3A 456452183 456453222 1039 False 1321.000000 1321 89.731000 1389 2421 1 chr3A.!!$F1 1032
5 TraesCS3B01G271100 chr3A 456698335 456703470 5135 True 1237.500000 2699 91.115500 1 3657 4 chr3A.!!$R1 3656

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
120 129 0.524862 CCAGCTAACCGTAGTCGTGT 59.475 55.0 0.0 0.0 35.01 4.49 F
1343 2848 0.246360 TACACCTGGACGAGTGCATG 59.754 55.0 0.0 0.0 37.51 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 2892 0.106335 TCGCAACAACTCCCGGTAAA 59.894 50.0 0.0 0.0 0.0 2.01 R
2720 4265 0.603065 GTGGATTTGGTCTTGCCCAC 59.397 55.0 0.0 0.0 37.5 4.61 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
120 129 0.524862 CCAGCTAACCGTAGTCGTGT 59.475 55.000 0.00 0.00 35.01 4.49
224 233 5.977635 TGAGTGGGAATGACAGTATTACAG 58.022 41.667 0.00 0.00 0.00 2.74
233 242 9.517609 GGAATGACAGTATTACAGTGTTACTAG 57.482 37.037 0.00 2.68 41.06 2.57
270 1716 3.881688 CTGATGCTTTGTAGATCCCTTGG 59.118 47.826 0.00 0.00 0.00 3.61
284 1730 4.150897 TCCCTTGGTTGCATACTATCAC 57.849 45.455 0.00 0.00 0.00 3.06
294 1740 5.728637 TGCATACTATCACTACCAGATGG 57.271 43.478 0.00 0.00 42.17 3.51
311 1757 5.345702 CAGATGGTACCAATGAATTTGCAG 58.654 41.667 20.76 0.00 33.73 4.41
588 2034 5.062308 GCTAGTCGAGGTTTTGTATGTCTTG 59.938 44.000 0.00 0.00 0.00 3.02
589 2035 3.746492 AGTCGAGGTTTTGTATGTCTTGC 59.254 43.478 0.00 0.00 0.00 4.01
624 2072 2.293122 TGGCAGTTGTTGTAGTTCATGC 59.707 45.455 0.00 0.00 0.00 4.06
713 2161 8.981647 CGAAATCAAATTCAGAAAATGGTCTTT 58.018 29.630 0.00 0.00 0.00 2.52
768 2243 3.851976 ATCTTACACTGACGAGGTGTC 57.148 47.619 13.68 0.00 45.23 3.67
931 2407 5.297029 GGCTGTAATCCACCAGTTCTAATTC 59.703 44.000 0.00 0.00 0.00 2.17
960 2438 4.161377 GGTACAGAGAGGAGAAAGAAGCAT 59.839 45.833 0.00 0.00 0.00 3.79
1001 2479 5.567037 TGGATGATGGAATAAAGACCGAT 57.433 39.130 0.00 0.00 0.00 4.18
1081 2559 2.289565 CGGAAGCTTAACCATTCCCTC 58.710 52.381 0.00 0.00 39.50 4.30
1083 2561 2.656002 GAAGCTTAACCATTCCCTCCC 58.344 52.381 0.00 0.00 0.00 4.30
1085 2563 2.288525 AGCTTAACCATTCCCTCCCTT 58.711 47.619 0.00 0.00 0.00 3.95
1086 2564 3.470868 AGCTTAACCATTCCCTCCCTTA 58.529 45.455 0.00 0.00 0.00 2.69
1087 2565 3.202373 AGCTTAACCATTCCCTCCCTTAC 59.798 47.826 0.00 0.00 0.00 2.34
1088 2566 3.053917 GCTTAACCATTCCCTCCCTTACA 60.054 47.826 0.00 0.00 0.00 2.41
1089 2567 4.386424 GCTTAACCATTCCCTCCCTTACAT 60.386 45.833 0.00 0.00 0.00 2.29
1091 2569 3.151542 ACCATTCCCTCCCTTACATCT 57.848 47.619 0.00 0.00 0.00 2.90
1093 2571 3.048600 CCATTCCCTCCCTTACATCTGA 58.951 50.000 0.00 0.00 0.00 3.27
1094 2572 3.072184 CCATTCCCTCCCTTACATCTGAG 59.928 52.174 0.00 0.00 0.00 3.35
1095 2573 1.794714 TCCCTCCCTTACATCTGAGC 58.205 55.000 0.00 0.00 0.00 4.26
1099 2577 2.364970 CCTCCCTTACATCTGAGCAGAG 59.635 54.545 6.34 1.73 41.33 3.35
1101 2579 1.483827 CCCTTACATCTGAGCAGAGCA 59.516 52.381 6.34 0.00 41.33 4.26
1103 2581 2.483363 CCTTACATCTGAGCAGAGCAGG 60.483 54.545 6.34 4.90 41.33 4.85
1104 2582 0.463204 TACATCTGAGCAGAGCAGGC 59.537 55.000 6.34 0.00 41.33 4.85
1105 2583 1.883544 CATCTGAGCAGAGCAGGCG 60.884 63.158 6.34 0.00 41.33 5.52
1304 2782 0.673022 CTCAAGCTGGTCAGTGCTCC 60.673 60.000 0.00 0.00 38.75 4.70
1305 2783 2.031516 CAAGCTGGTCAGTGCTCCG 61.032 63.158 0.00 0.00 38.75 4.63
1308 2786 1.185618 AGCTGGTCAGTGCTCCGTAA 61.186 55.000 0.00 0.00 33.90 3.18
1317 2795 1.137513 GTGCTCCGTAATCCGTATGC 58.862 55.000 0.00 0.00 33.66 3.14
1324 2802 2.349275 CCGTAATCCGTATGCGTTTGTT 59.651 45.455 1.69 0.00 36.15 2.83
1325 2803 3.551082 CCGTAATCCGTATGCGTTTGTTA 59.449 43.478 1.69 0.00 36.15 2.41
1329 2834 2.067766 TCCGTATGCGTTTGTTACACC 58.932 47.619 1.69 0.00 36.15 4.16
1336 2841 1.855513 CGTTTGTTACACCTGGACGA 58.144 50.000 0.00 0.00 0.00 4.20
1343 2848 0.246360 TACACCTGGACGAGTGCATG 59.754 55.000 0.00 0.00 37.51 4.06
1428 2935 1.272147 GGTTGATGCAGGAAGAACCCT 60.272 52.381 0.00 0.00 40.05 4.34
1653 3160 2.345880 CGGACTACATCCCGTTCCGG 62.346 65.000 0.00 0.00 46.04 5.14
2136 3652 1.450312 GCTGCCGCACCTCTACATT 60.450 57.895 0.00 0.00 35.78 2.71
2537 4067 2.771372 GGGGTTAATGATGTGCCCAATT 59.229 45.455 0.00 0.00 41.02 2.32
2538 4068 3.181466 GGGGTTAATGATGTGCCCAATTC 60.181 47.826 0.00 0.00 41.02 2.17
2576 4108 8.700973 ACCCAATTTGACATATTGGTTTATACC 58.299 33.333 26.37 0.00 46.91 2.73
2583 4115 4.042435 ACATATTGGTTTATACCCTCCCCG 59.958 45.833 0.00 0.00 44.35 5.73
2609 4141 9.683069 GTCCCATAATATAAGATGTTTTTGCAG 57.317 33.333 0.00 0.00 0.00 4.41
2683 4227 5.411977 AGATCTTGTCGAAGTCGTCTCTAAA 59.588 40.000 0.00 0.00 40.80 1.85
2690 4234 5.062308 GTCGAAGTCGTCTCTAAATTGCATT 59.938 40.000 0.00 0.00 40.80 3.56
2702 4247 2.818130 ATTGCATTGTGTTCCACCAC 57.182 45.000 0.00 0.00 32.73 4.16
2707 4252 2.575532 CATTGTGTTCCACCACTGACT 58.424 47.619 0.00 0.00 36.30 3.41
2708 4253 2.036958 TTGTGTTCCACCACTGACTG 57.963 50.000 0.00 0.00 36.30 3.51
2711 4256 2.102420 TGTGTTCCACCACTGACTGTAG 59.898 50.000 0.00 0.00 36.30 2.74
2790 4344 9.479549 AGATTGTAAATAAGTGGGATCACATTT 57.520 29.630 10.82 10.82 45.91 2.32
2817 4371 5.778862 TGATCGCGGATGAATAGTTATTGA 58.221 37.500 6.13 0.00 0.00 2.57
2851 4405 7.775053 ACAAAGGCTTATGGTTTGAATCTAA 57.225 32.000 0.00 0.00 35.55 2.10
2873 4427 2.113139 CAGGTGCACCCCGAGTTT 59.887 61.111 32.29 9.20 36.42 2.66
2890 4444 2.635427 AGTTTCTTGAGAGGGTGGAGAC 59.365 50.000 0.00 0.00 0.00 3.36
2907 4463 3.466836 GAGACACAACATGGAACTCACA 58.533 45.455 0.00 0.00 31.74 3.58
3001 4557 4.729868 AGTGCTAACATCAAAAGGACCTT 58.270 39.130 0.00 0.00 32.55 3.50
3062 4668 5.409520 GGAAATGTTTCATCAAAAGGGCTTC 59.590 40.000 7.69 0.00 38.92 3.86
3133 4739 1.963515 GAAAGGTGATTGTTGCAGGGT 59.036 47.619 0.00 0.00 0.00 4.34
3136 4742 1.039856 GGTGATTGTTGCAGGGTTGT 58.960 50.000 0.00 0.00 0.00 3.32
3141 4747 1.846007 TTGTTGCAGGGTTGTCAACT 58.154 45.000 15.17 0.00 39.69 3.16
3323 4930 8.851106 AGGCCATATGAATCTAGAGAATGATA 57.149 34.615 5.01 0.00 0.00 2.15
3468 5075 7.542477 AGTTCTTATCAGTACTCAAACATGACG 59.458 37.037 0.00 0.00 0.00 4.35
3469 5076 6.920817 TCTTATCAGTACTCAAACATGACGT 58.079 36.000 0.00 0.00 0.00 4.34
3572 5182 7.437267 CCTAAAATTGATGATGCTGAAACCATC 59.563 37.037 0.00 0.00 39.56 3.51
3573 5183 6.540438 AAATTGATGATGCTGAAACCATCT 57.460 33.333 0.00 0.00 39.76 2.90
3598 5208 2.832129 TGCCGAGAAGAAGTGGTTCTAT 59.168 45.455 0.00 0.00 42.59 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.140623 TCCCCAAGCGTTACAGTTTAAC 58.859 45.455 0.00 0.00 0.00 2.01
120 129 2.550277 TGAGGTGCCTCTCCTTATCA 57.450 50.000 17.96 0.00 43.12 2.15
270 1716 5.928839 CCATCTGGTAGTGATAGTATGCAAC 59.071 44.000 0.00 0.00 0.00 4.17
284 1730 6.460123 GCAAATTCATTGGTACCATCTGGTAG 60.460 42.308 17.17 4.28 43.84 3.18
294 1740 3.193267 TCAGGCTGCAAATTCATTGGTAC 59.807 43.478 10.34 0.00 39.54 3.34
300 1746 2.161855 TCGTTCAGGCTGCAAATTCAT 58.838 42.857 10.34 0.00 0.00 2.57
311 1757 1.468914 GGGAGACAAAATCGTTCAGGC 59.531 52.381 0.00 0.00 0.00 4.85
624 2072 1.078709 AGTTGCATGAACCGTGATCG 58.921 50.000 0.00 0.00 34.80 3.69
768 2243 3.309138 CAGCAAATCAGTCGAGGATCAAG 59.691 47.826 0.00 0.00 33.17 3.02
931 2407 2.382882 TCTCCTCTCTGTACCATGCTG 58.617 52.381 0.00 0.00 0.00 4.41
973 2451 6.122277 GTCTTTATTCCATCATCCAACCAGA 58.878 40.000 0.00 0.00 0.00 3.86
1001 2479 1.726571 GCGCGGCGAAACTTTTTATCA 60.727 47.619 28.54 0.00 0.00 2.15
1081 2559 1.483827 TGCTCTGCTCAGATGTAAGGG 59.516 52.381 0.00 0.00 36.76 3.95
1083 2561 2.823984 CCTGCTCTGCTCAGATGTAAG 58.176 52.381 0.00 0.00 36.76 2.34
1085 2563 0.463204 GCCTGCTCTGCTCAGATGTA 59.537 55.000 0.00 0.00 36.76 2.29
1086 2564 1.221293 GCCTGCTCTGCTCAGATGT 59.779 57.895 0.00 0.00 36.76 3.06
1087 2565 1.883544 CGCCTGCTCTGCTCAGATG 60.884 63.158 0.00 0.00 36.76 2.90
1088 2566 1.611474 TTCGCCTGCTCTGCTCAGAT 61.611 55.000 0.00 0.00 36.76 2.90
1089 2567 1.820010 TTTCGCCTGCTCTGCTCAGA 61.820 55.000 0.00 0.00 33.54 3.27
1091 2569 0.952497 CTTTTCGCCTGCTCTGCTCA 60.952 55.000 0.00 0.00 0.00 4.26
1093 2571 1.673665 CCTTTTCGCCTGCTCTGCT 60.674 57.895 0.00 0.00 0.00 4.24
1094 2572 2.873288 CCTTTTCGCCTGCTCTGC 59.127 61.111 0.00 0.00 0.00 4.26
1095 2573 1.919956 CTGCCTTTTCGCCTGCTCTG 61.920 60.000 0.00 0.00 0.00 3.35
1099 2577 3.673484 TGCTGCCTTTTCGCCTGC 61.673 61.111 0.00 0.00 0.00 4.85
1101 2579 2.113986 AGTGCTGCCTTTTCGCCT 59.886 55.556 0.00 0.00 0.00 5.52
1304 2782 5.995133 GTGTAACAAACGCATACGGATTACG 60.995 44.000 0.00 0.00 42.69 3.18
1305 2783 5.250332 GTGTAACAAACGCATACGGATTAC 58.750 41.667 0.00 0.00 39.79 1.89
1308 2786 2.674357 GGTGTAACAAACGCATACGGAT 59.326 45.455 0.00 0.00 41.46 4.18
1317 2795 1.790623 CTCGTCCAGGTGTAACAAACG 59.209 52.381 0.00 0.00 39.98 3.60
1324 2802 0.246360 CATGCACTCGTCCAGGTGTA 59.754 55.000 0.00 0.00 36.03 2.90
1325 2803 1.004560 CATGCACTCGTCCAGGTGT 60.005 57.895 0.00 0.00 36.03 4.16
1329 2834 2.819422 CAAATCATGCACTCGTCCAG 57.181 50.000 0.00 0.00 0.00 3.86
1343 2848 1.006805 CGCGAATGTGCAATGCAAATC 60.007 47.619 11.79 8.52 41.47 2.17
1380 2885 3.293337 ACAACTCCCGGTAAAGCTTTTT 58.707 40.909 18.47 0.00 0.00 1.94
1381 2886 2.940158 ACAACTCCCGGTAAAGCTTTT 58.060 42.857 18.47 1.58 0.00 2.27
1382 2887 2.621526 CAACAACTCCCGGTAAAGCTTT 59.378 45.455 17.30 17.30 0.00 3.51
1383 2888 2.227194 CAACAACTCCCGGTAAAGCTT 58.773 47.619 0.00 0.00 0.00 3.74
1384 2889 1.892209 CAACAACTCCCGGTAAAGCT 58.108 50.000 0.00 0.00 0.00 3.74
1385 2890 0.240145 GCAACAACTCCCGGTAAAGC 59.760 55.000 0.00 0.00 0.00 3.51
1386 2891 0.515564 CGCAACAACTCCCGGTAAAG 59.484 55.000 0.00 0.00 0.00 1.85
1387 2892 0.106335 TCGCAACAACTCCCGGTAAA 59.894 50.000 0.00 0.00 0.00 2.01
1388 2893 0.322322 ATCGCAACAACTCCCGGTAA 59.678 50.000 0.00 0.00 0.00 2.85
1428 2935 2.363276 ACCATCCGCCGGTAGTCA 60.363 61.111 1.63 0.00 34.02 3.41
1429 2936 1.745320 ATCACCATCCGCCGGTAGTC 61.745 60.000 1.63 0.00 34.02 2.59
2062 3578 2.126149 CTCGCTCTCGCTGTTGCT 60.126 61.111 0.00 0.00 36.97 3.91
2136 3652 3.257375 AGCAGATGTAGTCGTTGGTGTTA 59.743 43.478 0.00 0.00 0.00 2.41
2576 4108 4.359105 TCTTATATTATGGGACGGGGAGG 58.641 47.826 0.00 0.00 0.00 4.30
2583 4115 9.683069 CTGCAAAAACATCTTATATTATGGGAC 57.317 33.333 0.00 0.00 0.00 4.46
2609 4141 7.978975 TCCACAATTTTGCAAGTTAATATAGCC 59.021 33.333 0.00 0.00 0.00 3.93
2720 4265 0.603065 GTGGATTTGGTCTTGCCCAC 59.397 55.000 0.00 0.00 37.50 4.61
2790 4344 4.322080 ACTATTCATCCGCGATCAAAGA 57.678 40.909 8.23 0.00 0.00 2.52
2817 4371 9.845740 AAACCATAAGCCTTTGTTTTTAATCTT 57.154 25.926 0.00 0.00 0.00 2.40
2851 4405 2.257409 CTCGGGGTGCACCTGCTAAT 62.257 60.000 33.91 0.00 45.92 1.73
2873 4427 1.133167 TGTGTCTCCACCCTCTCAAGA 60.133 52.381 0.00 0.00 41.09 3.02
2927 4483 7.173907 TCCTAACTTCAGCAAAAATCTTCTCAG 59.826 37.037 0.00 0.00 0.00 3.35
3022 4628 3.737559 TTTCCTGCCATATTGGTCACT 57.262 42.857 0.00 0.00 40.46 3.41
3062 4668 7.220741 TCTTCCTCGTCATAGATATGAAAGG 57.779 40.000 18.24 18.24 43.65 3.11
3182 4788 7.765360 TGTTTAAAAGTGTACATACTATCCCCG 59.235 37.037 0.00 0.00 0.00 5.73
3190 4796 8.995220 TCAGACCATGTTTAAAAGTGTACATAC 58.005 33.333 0.00 0.00 30.53 2.39
3214 4821 1.629861 TCAGTGCCCATCAGAACATCA 59.370 47.619 0.00 0.00 0.00 3.07
3323 4930 6.962182 TCTGATAAACATTCTTCAGGTCCAT 58.038 36.000 0.00 0.00 36.95 3.41
3388 4995 7.498900 CCATGCTATCAATAGTAAACTTGGTCA 59.501 37.037 0.00 0.00 32.96 4.02
3468 5075 5.460419 CGTAGAAATCATAAGGAGTCAGCAC 59.540 44.000 0.00 0.00 0.00 4.40
3469 5076 5.127194 ACGTAGAAATCATAAGGAGTCAGCA 59.873 40.000 0.00 0.00 0.00 4.41
3572 5182 2.028930 ACCACTTCTTCTCGGCAACTAG 60.029 50.000 0.00 0.00 0.00 2.57
3573 5183 1.968493 ACCACTTCTTCTCGGCAACTA 59.032 47.619 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.