Multiple sequence alignment - TraesCS2D01G536300

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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 TraesCS2D01G536300 chr2D 100.000 2312 0 0 1 2312 618869481 618867170 0.000000e+00 4270.0
1 TraesCS2D01G536300 chr2D 93.651 189 12 0 1791 1979 247847771 247847583 1.350000e-72 283.0
2 TraesCS2D01G536300 chr2D 91.626 203 16 1 1788 1989 318260886 318261088 1.750000e-71 279.0
3 TraesCS2D01G536300 chr2B 89.791 1577 102 17 3 1575 756158024 756156503 0.000000e+00 1965.0
4 TraesCS2D01G536300 chr2B 92.308 533 26 5 1791 2312 756154031 756153503 0.000000e+00 743.0
5 TraesCS2D01G536300 chr2B 93.243 444 25 3 1306 1745 756154952 756154510 0.000000e+00 649.0
6 TraesCS2D01G536300 chr2B 93.651 189 11 1 1791 1979 323100741 323100554 4.860000e-72 281.0
7 TraesCS2D01G536300 chr2B 87.983 233 18 2 1071 1303 756155217 756154995 1.360000e-67 267.0
8 TraesCS2D01G536300 chr2A 90.644 1336 86 13 411 1735 749855892 749854585 0.000000e+00 1738.0
9 TraesCS2D01G536300 chr2A 92.565 538 22 7 1791 2312 749853067 749852532 0.000000e+00 756.0
10 TraesCS2D01G536300 chr2A 91.566 415 23 6 1 414 749859967 749859564 1.550000e-156 562.0
11 TraesCS2D01G536300 chr2A 94.536 183 8 1 1797 1979 285635088 285634908 4.860000e-72 281.0
12 TraesCS2D01G536300 chr2A 77.223 461 75 20 894 1350 749626639 749626205 2.300000e-60 243.0
13 TraesCS2D01G536300 chr1B 91.827 208 16 1 1791 1997 198656475 198656268 2.910000e-74 289.0
14 TraesCS2D01G536300 chr3B 93.122 189 12 1 1792 1980 126568338 126568525 2.260000e-70 276.0
15 TraesCS2D01G536300 chr1D 92.670 191 13 1 1791 1980 256080175 256079985 8.140000e-70 274.0
16 TraesCS2D01G536300 chr1D 100.000 30 0 0 1981 2010 463327100 463327129 3.210000e-04 56.5
17 TraesCS2D01G536300 chr7B 100.000 29 0 0 21 49 615023076 615023104 1.000000e-03 54.7


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 TraesCS2D01G536300 chr2D 618867170 618869481 2311 True 4270.000000 4270 100.000000 1 2312 1 chr2D.!!$R2 2311
1 TraesCS2D01G536300 chr2B 756153503 756158024 4521 True 906.000000 1965 90.831250 3 2312 4 chr2B.!!$R2 2309
2 TraesCS2D01G536300 chr2A 749852532 749859967 7435 True 1018.666667 1738 91.591667 1 2312 3 chr2A.!!$R3 2311

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
552 4231 0.728129 TCTGTCGTCGTGCGTTGATC 60.728 55.0 0.0 0.0 42.13 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 7125 0.40675 AGGGACCTTAAAAACCCCGG 59.593 55.0 0.0 0.0 42.97 5.73 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
49 50 5.811613 TCAAGATTTTTCTTTGGCAGTTGTG 59.188 36.000 0.00 0.00 0.00 3.33
50 51 5.343307 AGATTTTTCTTTGGCAGTTGTGT 57.657 34.783 0.00 0.00 0.00 3.72
51 52 5.351458 AGATTTTTCTTTGGCAGTTGTGTC 58.649 37.500 0.00 0.00 0.00 3.67
52 53 4.799564 TTTTTCTTTGGCAGTTGTGTCT 57.200 36.364 0.00 0.00 0.00 3.41
53 54 3.781079 TTTCTTTGGCAGTTGTGTCTG 57.219 42.857 0.00 0.00 38.35 3.51
54 55 2.418368 TCTTTGGCAGTTGTGTCTGT 57.582 45.000 0.00 0.00 37.70 3.41
55 56 2.016318 TCTTTGGCAGTTGTGTCTGTG 58.984 47.619 0.00 0.00 37.70 3.66
82 83 1.419374 CGCAATAGACTACCATCGGC 58.581 55.000 0.00 0.00 0.00 5.54
106 107 3.495001 GTGGAAGTGTAGAAGCTGAACAC 59.505 47.826 15.22 15.22 43.02 3.32
193 194 3.691118 TGATTCTTGGCTCATTTCCTTCG 59.309 43.478 0.00 0.00 0.00 3.79
278 279 1.997311 CAGTGGGAGGCTCATGGGA 60.997 63.158 17.69 0.00 0.00 4.37
283 284 1.487850 GGGAGGCTCATGGGATCTCC 61.488 65.000 20.84 20.84 40.13 3.71
299 300 2.016318 TCTCCCACGCAAATTAGCATG 58.984 47.619 0.00 0.00 0.00 4.06
321 322 4.140536 GGCTTATCTTTTCTATGCTGCCT 58.859 43.478 0.00 0.00 34.42 4.75
353 354 9.305925 CCTATGGCAAATTAGAAACAAAATCTC 57.694 33.333 0.00 0.00 0.00 2.75
445 4122 5.355910 GTGAAAACCTCTAAACAAGACCACA 59.644 40.000 0.00 0.00 0.00 4.17
518 4195 3.615811 TCAGGGAGGAGGGCCACT 61.616 66.667 6.18 2.65 36.29 4.00
544 4221 2.159379 TGGAGATTGATCTGTCGTCGTG 60.159 50.000 0.00 0.00 37.25 4.35
545 4222 1.849219 GAGATTGATCTGTCGTCGTGC 59.151 52.381 0.00 0.00 37.25 5.34
552 4231 0.728129 TCTGTCGTCGTGCGTTGATC 60.728 55.000 0.00 0.00 42.13 2.92
582 4261 2.014018 TCATGTCGTGTGTCGTGCG 61.014 57.895 0.00 0.00 40.80 5.34
687 4367 6.207025 TGTTATAAACGCTTTAAGGCCTTCAA 59.793 34.615 24.49 17.16 0.00 2.69
689 4369 4.600692 AAACGCTTTAAGGCCTTCAATT 57.399 36.364 24.49 6.08 0.00 2.32
691 4371 3.153919 ACGCTTTAAGGCCTTCAATTCA 58.846 40.909 24.49 0.00 0.00 2.57
710 4390 1.260561 CACTAAAGTCGTGCAAGCGTT 59.739 47.619 0.00 0.00 0.00 4.84
715 4395 1.204312 GTCGTGCAAGCGTTTCCTC 59.796 57.895 0.00 0.00 0.00 3.71
721 4401 2.413453 GTGCAAGCGTTTCCTCTCTAAG 59.587 50.000 0.00 0.00 0.00 2.18
851 4531 7.563724 AGTTAGGTTTAGAAGATTGGGTACA 57.436 36.000 0.00 0.00 0.00 2.90
892 4573 4.771590 TGGTCTAGAAACGTTACATCGT 57.228 40.909 0.00 0.00 46.19 3.73
902 4583 1.141019 TTACATCGTCTGCCTCGCC 59.859 57.895 0.00 0.00 0.00 5.54
903 4584 1.320344 TTACATCGTCTGCCTCGCCT 61.320 55.000 0.00 0.00 0.00 5.52
1016 4697 2.513026 ATCATGGCTAGATCGGCGGC 62.513 60.000 7.21 0.00 0.00 6.53
1017 4698 3.233980 ATGGCTAGATCGGCGGCA 61.234 61.111 10.53 9.76 37.63 5.69
1018 4699 3.231889 ATGGCTAGATCGGCGGCAG 62.232 63.158 10.53 0.00 36.64 4.85
1022 4703 2.758327 TAGATCGGCGGCAGTGGT 60.758 61.111 10.53 0.00 0.00 4.16
1054 4735 1.515521 GCTTGTAGTGGTGGTGGCAC 61.516 60.000 9.70 9.70 0.00 5.01
1076 4757 3.283684 TGCGGTGGCGGAAAAGTG 61.284 61.111 0.00 0.00 44.10 3.16
1085 4766 0.589708 GCGGAAAAGTGGGTGTGTAC 59.410 55.000 0.00 0.00 0.00 2.90
1096 4777 2.224426 TGGGTGTGTACTGCTAAGTTGG 60.224 50.000 0.00 0.00 37.88 3.77
1105 4786 6.316390 GTGTACTGCTAAGTTGGATATGCTTT 59.684 38.462 0.00 0.00 37.88 3.51
1106 4787 6.884295 TGTACTGCTAAGTTGGATATGCTTTT 59.116 34.615 0.00 0.00 37.88 2.27
1110 4791 4.098501 GCTAAGTTGGATATGCTTTTGCCT 59.901 41.667 0.00 0.00 46.87 4.75
1114 4795 2.177734 TGGATATGCTTTTGCCTTGCA 58.822 42.857 0.00 0.00 46.87 4.08
1133 4814 3.702548 TGCAATCCATCCATCAAAGAAGG 59.297 43.478 0.00 0.00 0.00 3.46
1149 4830 2.358737 GGACCTTGGAGTGCACCG 60.359 66.667 14.63 0.00 0.00 4.94
1226 4907 0.981183 TACTTGCAGGATCCGGTGTT 59.019 50.000 13.75 0.00 0.00 3.32
1254 4935 1.463674 ACATCAATCGCCCCAACTTC 58.536 50.000 0.00 0.00 0.00 3.01
1342 5023 5.873179 ACGGGTTATTGTACATCTGTTTG 57.127 39.130 0.00 0.00 0.00 2.93
1371 5056 1.956629 AACGGCATCTTCGACGGGAT 61.957 55.000 0.00 0.00 0.00 3.85
1382 5067 1.019278 CGACGGGATGGAAGTTGGTG 61.019 60.000 0.00 0.00 0.00 4.17
1383 5068 0.036306 GACGGGATGGAAGTTGGTGT 59.964 55.000 0.00 0.00 0.00 4.16
1426 6929 1.204312 GCAACCGCGTTCTCACTTC 59.796 57.895 4.92 0.00 0.00 3.01
1461 6964 0.960364 TTGGCCGTTCTCTGAATGCC 60.960 55.000 0.00 13.34 39.33 4.40
1463 6966 0.678048 GGCCGTTCTCTGAATGCCTT 60.678 55.000 13.10 0.00 35.99 4.35
1535 7038 2.705658 TGTATTCTGCTCCGGATTCCAT 59.294 45.455 3.57 0.00 0.00 3.41
1586 7089 7.896274 CGTAATCAATAACGTGTCGAATTTCTT 59.104 33.333 0.00 0.00 34.48 2.52
1619 7125 8.252624 ACAATATAGGAAGTAGTTTCTCCCTC 57.747 38.462 0.00 0.00 36.03 4.30
1646 7152 6.295462 GGGGTTTTTAAGGTCCCTTGTATTTC 60.295 42.308 8.86 0.00 39.80 2.17
1650 7156 2.693267 AGGTCCCTTGTATTTCGAGC 57.307 50.000 0.00 0.00 0.00 5.03
1918 8887 7.043258 GCAATATTCATGCAAATGAATCGAACA 60.043 33.333 16.79 2.64 45.24 3.18
2056 9025 5.278858 GGTCGGTACAATAGTAATAGCTGCT 60.279 44.000 7.57 7.57 30.67 4.24
2216 9201 5.901552 ACAAATGAAACAAAATCGAGGTGT 58.098 33.333 0.00 0.00 0.00 4.16
2254 9239 8.394040 TCTAGGAGAACATAGGTATCATCATGA 58.606 37.037 0.00 0.00 32.20 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.462125 TATTGCGCACAGGCCACAGA 62.462 55.000 11.12 0.00 36.38 3.41
51 52 1.985447 CTATTGCGCACAGGCCACAG 61.985 60.000 11.12 0.00 36.38 3.66
52 53 2.033294 TATTGCGCACAGGCCACA 59.967 55.556 11.12 0.00 36.38 4.17
53 54 1.745115 TCTATTGCGCACAGGCCAC 60.745 57.895 11.12 0.00 36.38 5.01
54 55 1.745115 GTCTATTGCGCACAGGCCA 60.745 57.895 11.12 0.00 36.38 5.36
55 56 0.179084 TAGTCTATTGCGCACAGGCC 60.179 55.000 11.12 0.00 36.38 5.19
82 83 3.667497 TCAGCTTCTACACTTCCACAG 57.333 47.619 0.00 0.00 0.00 3.66
106 107 1.375908 CACATGTCGTCCCCCACTG 60.376 63.158 0.00 0.00 0.00 3.66
193 194 1.281867 TGACATCTTGGACACATCCCC 59.718 52.381 0.00 0.00 45.59 4.81
278 279 2.418368 TGCTAATTTGCGTGGGAGAT 57.582 45.000 7.37 0.00 35.36 2.75
299 300 4.140536 AGGCAGCATAGAAAAGATAAGCC 58.859 43.478 0.00 0.00 38.65 4.35
445 4122 2.560542 CGCCTCAATAGTAGATGCCTCT 59.439 50.000 0.00 0.00 35.39 3.69
518 4195 5.592054 GACGACAGATCAATCTCCATGTTA 58.408 41.667 0.00 0.00 34.22 2.41
544 4221 1.337260 ACCAGACTGACAGATCAACGC 60.337 52.381 10.08 0.00 33.30 4.84
545 4222 2.029918 TGACCAGACTGACAGATCAACG 60.030 50.000 10.08 0.00 33.30 4.10
552 4231 1.270826 ACGACATGACCAGACTGACAG 59.729 52.381 3.32 0.00 0.00 3.51
582 4261 4.363138 CCAAAGGCTCAAGAGACAAAAAC 58.637 43.478 5.61 0.00 39.50 2.43
613 4293 7.535489 ACAAATAACTAAGTTCGATACAGGC 57.465 36.000 0.00 0.00 0.00 4.85
646 4326 7.326789 CGTTTATAACAAGGTTCTACGACAAGA 59.673 37.037 0.00 0.00 0.00 3.02
655 4335 7.574404 GCCTTAAAGCGTTTATAACAAGGTTCT 60.574 37.037 9.95 0.00 34.06 3.01
687 4367 2.157668 CGCTTGCACGACTTTAGTGAAT 59.842 45.455 0.00 0.00 41.83 2.57
689 4369 1.136690 CGCTTGCACGACTTTAGTGA 58.863 50.000 0.00 0.00 41.83 3.41
691 4371 1.578583 AACGCTTGCACGACTTTAGT 58.421 45.000 3.48 0.00 36.70 2.24
880 4561 1.731424 CGAGGCAGACGATGTAACGTT 60.731 52.381 5.88 5.88 46.52 3.99
902 4583 4.867047 CCACTCATATTTATAGGCGCAGAG 59.133 45.833 10.83 2.73 0.00 3.35
903 4584 4.283467 ACCACTCATATTTATAGGCGCAGA 59.717 41.667 10.83 0.00 0.00 4.26
919 4600 0.472044 TAAGCCAAGCACACCACTCA 59.528 50.000 0.00 0.00 0.00 3.41
1016 4697 1.597854 ACCACGCACATCACCACTG 60.598 57.895 0.00 0.00 0.00 3.66
1017 4698 1.597854 CACCACGCACATCACCACT 60.598 57.895 0.00 0.00 0.00 4.00
1018 4699 2.945984 CACCACGCACATCACCAC 59.054 61.111 0.00 0.00 0.00 4.16
1022 4703 0.250081 TACAAGCACCACGCACATCA 60.250 50.000 0.00 0.00 46.13 3.07
1063 4744 1.826487 ACACCCACTTTTCCGCCAC 60.826 57.895 0.00 0.00 0.00 5.01
1066 4747 0.589708 GTACACACCCACTTTTCCGC 59.410 55.000 0.00 0.00 0.00 5.54
1068 4749 1.607148 GCAGTACACACCCACTTTTCC 59.393 52.381 0.00 0.00 0.00 3.13
1069 4750 2.572290 AGCAGTACACACCCACTTTTC 58.428 47.619 0.00 0.00 0.00 2.29
1076 4757 2.038033 TCCAACTTAGCAGTACACACCC 59.962 50.000 0.00 0.00 30.68 4.61
1085 4766 5.039333 GCAAAAGCATATCCAACTTAGCAG 58.961 41.667 0.00 0.00 0.00 4.24
1106 4787 1.342175 TGATGGATGGATTGCAAGGCA 60.342 47.619 4.94 0.00 36.47 4.75
1110 4791 4.160814 CCTTCTTTGATGGATGGATTGCAA 59.839 41.667 0.00 0.00 31.99 4.08
1114 4795 4.231426 AGGTCCTTCTTTGATGGATGGATT 59.769 41.667 5.66 0.00 38.00 3.01
1120 4801 2.986019 TCCAAGGTCCTTCTTTGATGGA 59.014 45.455 0.00 1.27 35.53 3.41
1121 4802 3.245052 ACTCCAAGGTCCTTCTTTGATGG 60.245 47.826 0.00 0.00 35.53 3.51
1133 4814 1.668151 GACGGTGCACTCCAAGGTC 60.668 63.158 17.98 10.62 0.00 3.85
1149 4830 3.474034 GAGCAGCACAGCGTCGAC 61.474 66.667 5.18 5.18 40.15 4.20
1226 4907 1.000607 GGCGATTGATGTAGCCGTAGA 60.001 52.381 0.00 0.00 40.17 2.59
1254 4935 2.301296 ACATGAGGTGAGTGTCTTGAGG 59.699 50.000 0.00 0.00 0.00 3.86
1342 5023 6.127403 GTCGAAGATGCCGTTTATTATTGTC 58.873 40.000 0.00 0.00 40.67 3.18
1371 5056 1.142060 CTACCACCACACCAACTTCCA 59.858 52.381 0.00 0.00 0.00 3.53
1382 5067 6.015010 AGTCTCTTGATATATGCTACCACCAC 60.015 42.308 0.00 0.00 0.00 4.16
1383 5068 6.015095 CAGTCTCTTGATATATGCTACCACCA 60.015 42.308 0.00 0.00 0.00 4.17
1461 6964 6.453943 AGATAGTGCTATCATGTGTGCTAAG 58.546 40.000 18.15 0.00 43.27 2.18
1463 6966 6.266330 AGAAGATAGTGCTATCATGTGTGCTA 59.734 38.462 18.15 0.00 43.27 3.49
1505 7008 4.109766 CGGAGCAGAATACACAATACGAA 58.890 43.478 0.00 0.00 0.00 3.85
1507 7010 2.794910 CCGGAGCAGAATACACAATACG 59.205 50.000 0.00 0.00 0.00 3.06
1511 7014 3.531538 GAATCCGGAGCAGAATACACAA 58.468 45.455 11.34 0.00 0.00 3.33
1535 7038 7.437713 AACATCAATATACAGAGTTCCCAGA 57.562 36.000 0.00 0.00 0.00 3.86
1619 7125 0.406750 AGGGACCTTAAAAACCCCGG 59.593 55.000 0.00 0.00 42.97 5.73
1646 7152 2.154462 AGATGGTCAAACTTTGGCTCG 58.846 47.619 6.09 0.00 35.12 5.03
1768 8295 8.175069 ACACAAAAAGTATATGCTACAATCACG 58.825 33.333 0.00 0.00 0.00 4.35
1770 8297 8.673711 GGACACAAAAAGTATATGCTACAATCA 58.326 33.333 0.00 0.00 0.00 2.57
1771 8298 7.850982 CGGACACAAAAAGTATATGCTACAATC 59.149 37.037 0.00 0.00 0.00 2.67
1772 8299 7.335924 ACGGACACAAAAAGTATATGCTACAAT 59.664 33.333 0.00 0.00 0.00 2.71
1773 8300 6.651643 ACGGACACAAAAAGTATATGCTACAA 59.348 34.615 0.00 0.00 0.00 2.41
1777 8320 5.163893 CGAACGGACACAAAAAGTATATGCT 60.164 40.000 0.00 0.00 0.00 3.79
1783 8326 3.485378 CGTACGAACGGACACAAAAAGTA 59.515 43.478 10.44 0.00 45.50 2.24
1784 8327 2.282290 CGTACGAACGGACACAAAAAGT 59.718 45.455 10.44 0.00 45.50 2.66
1785 8328 2.882876 CGTACGAACGGACACAAAAAG 58.117 47.619 10.44 0.00 45.50 2.27
1786 8329 2.994716 CGTACGAACGGACACAAAAA 57.005 45.000 10.44 0.00 45.50 1.94
2028 8997 6.015603 AGCTATTACTATTGTACCGACCTTCC 60.016 42.308 0.00 0.00 0.00 3.46
2216 9201 4.528206 TGTTCTCCTAGAATGAGTGCAAGA 59.472 41.667 0.00 0.00 36.50 3.02
2271 9256 9.197306 GATTTGGTCAAAACTATAGGGGTATTT 57.803 33.333 4.43 0.00 33.56 1.40
2272 9257 8.566109 AGATTTGGTCAAAACTATAGGGGTATT 58.434 33.333 4.43 0.00 32.67 1.89
2273 9258 8.114301 AGATTTGGTCAAAACTATAGGGGTAT 57.886 34.615 4.43 0.00 32.67 2.73


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

AutoCloner maintained by Alex Coulton.