Multiple sequence alignment - TraesCS4D01G123400

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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 TraesCS4D01G123400 chr4D 100.000 4792 0 0 1 4792 108010960 108015751 0.000000e+00 8850
1 TraesCS4D01G123400 chr4A 95.258 4239 130 24 1 4204 468252403 468248201 0.000000e+00 6649
2 TraesCS4D01G123400 chr4A 91.572 617 32 5 4190 4786 468237483 468236867 0.000000e+00 833
3 TraesCS4D01G123400 chr4A 90.123 243 20 4 4517 4757 148070249 148070009 3.600000e-81 313
4 TraesCS4D01G123400 chr4A 88.571 245 19 5 4515 4758 732340768 732341004 6.070000e-74 289
5 TraesCS4D01G123400 chr4B 95.246 4228 120 30 1 4173 168709053 168704852 0.000000e+00 6619
6 TraesCS4D01G123400 chr4B 93.367 196 9 3 4320 4511 168704660 168704465 2.180000e-73 287
7 TraesCS4D01G123400 chr4B 92.553 94 5 1 4236 4327 168704831 168704738 3.010000e-27 134
8 TraesCS4D01G123400 chr1D 91.286 241 20 1 4517 4757 293950781 293951020 1.290000e-85 327
9 TraesCS4D01G123400 chr5D 91.739 230 18 1 4528 4757 228486294 228486066 7.740000e-83 318
10 TraesCS4D01G123400 chr3A 90.456 241 21 2 4517 4757 483469913 483469675 2.780000e-82 316
11 TraesCS4D01G123400 chr3D 90.041 241 23 1 4517 4757 363119555 363119316 1.300000e-80 311
12 TraesCS4D01G123400 chr3D 87.603 121 11 3 1963 2082 141406650 141406767 2.330000e-28 137
13 TraesCS4D01G123400 chr1A 89.300 243 22 4 4517 4757 592123706 592123946 7.790000e-78 302
14 TraesCS4D01G123400 chr5B 89.686 223 22 1 4517 4739 438163043 438162822 2.820000e-72 283
15 TraesCS4D01G123400 chrUn 90.000 110 9 2 1970 2079 277176621 277176514 1.800000e-29 141
16 TraesCS4D01G123400 chrUn 90.654 107 8 2 1970 2076 300683334 300683438 1.800000e-29 141
17 TraesCS4D01G123400 chr7D 87.603 121 11 3 1963 2082 400205244 400205127 2.330000e-28 137
18 TraesCS4D01G123400 chr2A 87.719 114 11 2 1970 2082 23429830 23429719 3.890000e-26 130
19 TraesCS4D01G123400 chr6B 86.957 115 12 2 1962 2076 430583885 430583774 5.030000e-25 126
20 TraesCS4D01G123400 chr1B 86.842 114 12 2 1970 2082 53255417 53255528 1.810000e-24 124


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 TraesCS4D01G123400 chr4D 108010960 108015751 4791 False 8850.000000 8850 100.000 1 4792 1 chr4D.!!$F1 4791
1 TraesCS4D01G123400 chr4A 468248201 468252403 4202 True 6649.000000 6649 95.258 1 4204 1 chr4A.!!$R3 4203
2 TraesCS4D01G123400 chr4A 468236867 468237483 616 True 833.000000 833 91.572 4190 4786 1 chr4A.!!$R2 596
3 TraesCS4D01G123400 chr4B 168704465 168709053 4588 True 2346.666667 6619 93.722 1 4511 3 chr4B.!!$R1 4510

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
593 603 0.389817 TGCTTTGCTATCGTCTGCGT 60.390 50.000 0.00 0.00 39.49 5.24 F
1066 1092 0.245539 CCCTTGCTGCAAGTTCCATG 59.754 55.000 33.16 20.12 39.58 3.66 F
1143 1169 1.202698 AGGATTCGTGCTATGAAGGGC 60.203 52.381 0.00 0.00 0.00 5.19 F
1954 2002 1.981256 TTGCCACTTTCAGTTCCTCC 58.019 50.000 0.00 0.00 0.00 4.30 F
2059 2107 6.976934 TCTTTTGCTTGAAAGGTCCTATTT 57.023 33.333 0.00 0.00 37.27 1.40 F
3267 3315 1.267732 CCGCTGATTCGATTCTTGCAC 60.268 52.381 18.33 3.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2002 3.182173 GTGATGAAATTGTTTGTGGTGCG 59.818 43.478 0.00 0.0 0.00 5.34 R
2059 2107 8.898761 TGTTAGTTGAAACATAGCTTTCAGAAA 58.101 29.630 0.00 0.0 40.42 2.52 R
3234 3282 0.551396 TCAGCGGGGATGAGAGACTA 59.449 55.000 0.00 0.0 0.00 2.59 R
3246 3294 0.305922 GCAAGAATCGAATCAGCGGG 59.694 55.000 2.82 0.0 0.00 6.13 R
3672 3721 0.528466 ATGTCGACGATGAATGCGCT 60.528 50.000 9.73 0.0 0.00 5.92 R
4729 4904 0.407528 TGAATAGCCCTTTGTGCCCA 59.592 50.000 0.00 0.0 0.00 5.36 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
100 103 4.688413 GGCGATATCTTGTCTCAAGGAATC 59.312 45.833 9.18 10.47 0.00 2.52
103 106 6.294787 GCGATATCTTGTCTCAAGGAATCCTA 60.295 42.308 0.46 0.00 31.13 2.94
111 114 6.595682 TGTCTCAAGGAATCCTATTTCCATC 58.404 40.000 0.46 0.00 46.40 3.51
116 119 8.280258 TCAAGGAATCCTATTTCCATCTGTAT 57.720 34.615 0.46 0.00 46.40 2.29
169 172 4.631813 GCCATTCCAACTATATGATCGGAC 59.368 45.833 0.00 0.00 0.00 4.79
182 185 3.210227 TGATCGGACTTTCTTTGCAACA 58.790 40.909 0.00 0.00 0.00 3.33
185 188 1.065401 CGGACTTTCTTTGCAACAGCA 59.935 47.619 0.00 0.00 36.26 4.41
187 190 2.122564 GACTTTCTTTGCAACAGCAGC 58.877 47.619 0.00 0.00 39.82 5.25
224 227 2.684001 TTAGGATGCAGGTTGGTACG 57.316 50.000 0.00 0.00 0.00 3.67
236 239 2.544267 GGTTGGTACGATATGCTTGCTC 59.456 50.000 0.00 0.00 0.00 4.26
245 248 1.926561 TATGCTTGCTCGTGTGCTAG 58.073 50.000 1.87 1.87 38.48 3.42
376 381 2.192624 CTTCTTGTTTTTGTGCCGTGG 58.807 47.619 0.00 0.00 0.00 4.94
593 603 0.389817 TGCTTTGCTATCGTCTGCGT 60.390 50.000 0.00 0.00 39.49 5.24
596 606 2.196749 CTTTGCTATCGTCTGCGTGAT 58.803 47.619 0.00 0.00 39.49 3.06
617 627 3.816091 TCGCGACACAAATTTTGTATGG 58.184 40.909 14.13 6.34 43.23 2.74
815 825 4.154015 AGTTTGGCTTTGAACAACTTTTGC 59.846 37.500 0.00 0.00 0.00 3.68
898 911 3.634397 TCTGCCTGACTTATTCTTGGG 57.366 47.619 0.00 0.00 0.00 4.12
905 918 4.938226 CCTGACTTATTCTTGGGACACTTC 59.062 45.833 0.00 0.00 39.29 3.01
976 989 4.222145 ACAAGAGCCATTCATTTGATGCTT 59.778 37.500 0.00 0.00 0.00 3.91
1066 1092 0.245539 CCCTTGCTGCAAGTTCCATG 59.754 55.000 33.16 20.12 39.58 3.66
1143 1169 1.202698 AGGATTCGTGCTATGAAGGGC 60.203 52.381 0.00 0.00 0.00 5.19
1513 1541 5.063880 TCCTTCTTCAAAAGTACAAGCCTC 58.936 41.667 0.00 0.00 0.00 4.70
1578 1606 7.043325 GCATATTGAGTCTTTTAGGTACACTCG 60.043 40.741 0.00 0.00 36.98 4.18
1579 1607 5.779529 TTGAGTCTTTTAGGTACACTCGT 57.220 39.130 0.00 0.00 36.98 4.18
1647 1675 6.183359 CCGCAAATAAGTTTGTATTTCTGTGC 60.183 38.462 3.23 0.00 45.14 4.57
1648 1676 6.183359 CGCAAATAAGTTTGTATTTCTGTGCC 60.183 38.462 3.23 0.00 45.14 5.01
1678 1707 8.940397 TCAAATTCAGATAGTTTTCCTCCTTT 57.060 30.769 0.00 0.00 0.00 3.11
1954 2002 1.981256 TTGCCACTTTCAGTTCCTCC 58.019 50.000 0.00 0.00 0.00 4.30
2059 2107 6.976934 TCTTTTGCTTGAAAGGTCCTATTT 57.023 33.333 0.00 0.00 37.27 1.40
3246 3294 4.150980 CGAGTACGTCATAGTCTCTCATCC 59.849 50.000 0.00 0.00 31.75 3.51
3267 3315 1.267732 CCGCTGATTCGATTCTTGCAC 60.268 52.381 18.33 3.00 0.00 4.57
3689 3738 1.270968 CAGCGCATTCATCGTCGAC 59.729 57.895 11.47 5.18 0.00 4.20
3786 3835 1.614241 GCTCCTCCTACCTCGGCAAA 61.614 60.000 0.00 0.00 0.00 3.68
3796 3845 1.146358 CCTCGGCAAACGTAGCTAGC 61.146 60.000 6.62 6.62 44.69 3.42
3815 3864 2.894879 TCGGCCATCGATTTGCGG 60.895 61.111 2.24 14.58 43.74 5.69
3816 3865 3.952675 CGGCCATCGATTTGCGGG 61.953 66.667 2.24 5.57 42.43 6.13
3824 3873 0.609151 TCGATTTGCGGGAGTTGGTA 59.391 50.000 0.00 0.00 41.33 3.25
3870 3925 3.067040 TGCGTACGCCACTGATAATCTAA 59.933 43.478 35.11 10.38 41.09 2.10
3872 3927 4.792057 GCGTACGCCACTGATAATCTAAGT 60.792 45.833 29.51 0.00 34.56 2.24
3873 3928 5.561532 GCGTACGCCACTGATAATCTAAGTA 60.562 44.000 29.51 0.00 34.56 2.24
3874 3929 6.078479 CGTACGCCACTGATAATCTAAGTAG 58.922 44.000 0.52 0.00 0.00 2.57
3875 3930 6.073385 CGTACGCCACTGATAATCTAAGTAGA 60.073 42.308 0.52 0.00 36.65 2.59
3920 3975 2.716398 GTGAACCGCTGTTGTTTCTTC 58.284 47.619 0.00 0.00 33.97 2.87
3954 4011 2.483877 CAGTTCTGACGCCAAATGCTAA 59.516 45.455 0.00 0.00 38.05 3.09
3979 4036 4.379339 AACTAAATCGCTCTCTCTGACC 57.621 45.455 0.00 0.00 0.00 4.02
4025 4087 5.304871 TCAGCTCTAATCTGCATCTCTGAAT 59.695 40.000 0.00 0.00 0.00 2.57
4117 4182 6.070194 TGGGAGACTATTCTCTTAAAACCCAG 60.070 42.308 9.69 0.00 46.80 4.45
4120 4185 7.883833 GGAGACTATTCTCTTAAAACCCAGTTT 59.116 37.037 9.69 0.00 46.80 2.66
4178 4243 1.827969 CAATTGCCCCGGTTTGGAATA 59.172 47.619 0.00 0.00 42.00 1.75
4187 4252 3.439129 CCCGGTTTGGAATAGTTCTGTTC 59.561 47.826 0.00 1.58 42.00 3.18
4221 4287 8.507249 ACTTTTAGAAGATGTGTTGATAACTGC 58.493 33.333 0.00 0.00 36.69 4.40
4228 4294 5.824624 AGATGTGTTGATAACTGCCTTATGG 59.175 40.000 0.00 0.00 0.00 2.74
4660 4835 6.617782 TCATTTTGCAAAATATTCCTGGGA 57.382 33.333 31.33 20.53 36.52 4.37
4716 4891 6.587226 TGACAATTTGCACATAAATGAAGAGC 59.413 34.615 0.00 0.00 31.05 4.09
4723 4898 7.628769 TGCACATAAATGAAGAGCTGATTTA 57.371 32.000 0.00 0.00 0.00 1.40
4727 4902 9.294030 CACATAAATGAAGAGCTGATTTAAACC 57.706 33.333 0.00 0.00 0.00 3.27
4729 4904 6.575162 AAATGAAGAGCTGATTTAAACCGT 57.425 33.333 0.00 0.00 0.00 4.83
4735 4910 1.402325 GCTGATTTAAACCGTGGGCAC 60.402 52.381 0.00 0.00 0.00 5.01
4757 4932 6.327934 CACAAAGGGCTATTCAGAAATCAAG 58.672 40.000 0.00 0.00 0.00 3.02
4765 4940 5.649831 GCTATTCAGAAATCAAGGTGAGGTT 59.350 40.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 103 5.723887 AGGCCTAGATACAGATGGAAATAGG 59.276 44.000 1.29 2.83 33.24 2.57
103 106 6.521527 AAAGGCCTAGATACAGATGGAAAT 57.478 37.500 5.16 0.00 0.00 2.17
111 114 3.567478 AGCCAAAAGGCCTAGATACAG 57.433 47.619 5.16 0.00 35.12 2.74
116 119 3.265737 TGTATGAAGCCAAAAGGCCTAGA 59.734 43.478 5.16 0.00 35.12 2.43
138 141 6.610830 TCATATAGTTGGAATGGCAACCAAAT 59.389 34.615 24.45 24.45 45.75 2.32
224 227 1.293924 AGCACACGAGCAAGCATATC 58.706 50.000 0.00 0.00 36.85 1.63
236 239 3.476295 AATCACATTTGCTAGCACACG 57.524 42.857 19.17 6.07 0.00 4.49
245 248 1.272212 ACCCGTGGAAATCACATTTGC 59.728 47.619 0.00 0.00 46.36 3.68
593 603 3.617540 ACAAAATTTGTGTCGCGATCA 57.382 38.095 14.06 12.63 43.48 2.92
596 606 3.251245 ACCATACAAAATTTGTGTCGCGA 59.749 39.130 20.40 3.71 45.03 5.87
815 825 2.423185 TGTTGTTCTGAAACACAGCCAG 59.577 45.455 0.00 0.00 44.90 4.85
898 911 8.261522 ACCTAATCTAATTCCTGAAGAAGTGTC 58.738 37.037 0.00 0.00 38.07 3.67
905 918 7.610580 AGGAGACCTAATCTAATTCCTGAAG 57.389 40.000 0.00 0.00 38.00 3.02
976 989 1.002888 CTGAGCCCAGCTTCTTCTTCA 59.997 52.381 0.00 0.00 39.88 3.02
1100 1126 2.290577 CCAAAGGGAGACTGAAGAAGGG 60.291 54.545 0.00 0.00 35.59 3.95
1130 1156 2.355010 ATTCCTGCCCTTCATAGCAC 57.645 50.000 0.00 0.00 34.68 4.40
1132 1158 3.220674 AGAATTCCTGCCCTTCATAGC 57.779 47.619 0.65 0.00 0.00 2.97
1143 1169 2.611292 GTGCCTCGATGAAGAATTCCTG 59.389 50.000 0.65 0.00 46.93 3.86
1513 1541 6.453092 AGGAGAACTGAAATTGCTGAATTTG 58.547 36.000 0.00 0.00 41.06 2.32
1647 1675 7.066284 AGGAAAACTATCTGAATTTGATCGTGG 59.934 37.037 0.00 0.00 0.00 4.94
1648 1676 7.978982 AGGAAAACTATCTGAATTTGATCGTG 58.021 34.615 0.00 0.00 0.00 4.35
1954 2002 3.182173 GTGATGAAATTGTTTGTGGTGCG 59.818 43.478 0.00 0.00 0.00 5.34
2059 2107 8.898761 TGTTAGTTGAAACATAGCTTTCAGAAA 58.101 29.630 0.00 0.00 40.42 2.52
3234 3282 0.551396 TCAGCGGGGATGAGAGACTA 59.449 55.000 0.00 0.00 0.00 2.59
3246 3294 0.305922 GCAAGAATCGAATCAGCGGG 59.694 55.000 2.82 0.00 0.00 6.13
3267 3315 2.738846 CGAGATTAATGGCAGAATCCGG 59.261 50.000 16.97 0.00 33.34 5.14
3463 3512 2.956964 GCGCGAAGGAGATGACGG 60.957 66.667 12.10 0.00 0.00 4.79
3672 3721 0.528466 ATGTCGACGATGAATGCGCT 60.528 50.000 9.73 0.00 0.00 5.92
3786 3835 1.464376 ATGGCCGATGCTAGCTACGT 61.464 55.000 23.79 0.00 37.74 3.57
3815 3864 2.038557 TGAGCTTCTTGGTACCAACTCC 59.961 50.000 27.50 16.37 29.66 3.85
3816 3865 3.402628 TGAGCTTCTTGGTACCAACTC 57.597 47.619 25.47 25.47 0.00 3.01
3870 3925 0.594110 GCGCCGAGCTATCTTCTACT 59.406 55.000 0.00 0.00 44.04 2.57
3872 3927 1.164662 ACGCGCCGAGCTATCTTCTA 61.165 55.000 5.73 0.00 45.59 2.10
3873 3928 1.164662 TACGCGCCGAGCTATCTTCT 61.165 55.000 5.73 0.00 45.59 2.85
3874 3929 0.997726 GTACGCGCCGAGCTATCTTC 60.998 60.000 5.73 0.00 45.59 2.87
3875 3930 1.008767 GTACGCGCCGAGCTATCTT 60.009 57.895 5.73 0.00 45.59 2.40
3920 3975 2.731451 TCAGAACTGAATCGAAAGCACG 59.269 45.455 1.79 0.00 36.53 5.34
3954 4011 6.096695 GTCAGAGAGAGCGATTTAGTTTCTT 58.903 40.000 0.00 0.00 0.00 2.52
3979 4036 7.414540 GCTGAGTGATTTAGTCTAACATTTGGG 60.415 40.741 0.00 0.00 0.00 4.12
4025 4087 9.602568 TTCTGTAAACTAGTTACACACATTCAA 57.397 29.630 8.92 2.81 45.76 2.69
4117 4182 7.228308 TGACAAATGGAAAATTGATCCCAAAAC 59.772 33.333 7.81 0.00 36.04 2.43
4120 4185 6.430962 TGACAAATGGAAAATTGATCCCAA 57.569 33.333 7.81 0.00 36.04 4.12
4167 4232 7.172703 AGTTTAGAACAGAACTATTCCAAACCG 59.827 37.037 11.11 0.00 37.22 4.44
4168 4233 8.290325 CAGTTTAGAACAGAACTATTCCAAACC 58.710 37.037 11.11 0.00 37.22 3.27
4187 4252 9.869844 CAACACATCTTCTAAAAGTCAGTTTAG 57.130 33.333 0.00 0.00 40.83 1.85
4221 4287 8.749354 AGTAAATCAAACCTTTTAGCCATAAGG 58.251 33.333 0.04 0.04 45.19 2.69
4228 4294 7.392494 AGGCTAGTAAATCAAACCTTTTAGC 57.608 36.000 0.00 0.00 0.00 3.09
4234 4300 9.700831 ATTCAATAAGGCTAGTAAATCAAACCT 57.299 29.630 0.00 0.00 0.00 3.50
4285 4351 3.980022 TCCAGCATCCACAAAGGGATATA 59.020 43.478 0.00 0.00 45.91 0.86
4618 4793 9.926751 CAAAATGATGTACTTATCATCTCACAC 57.073 33.333 8.65 0.00 44.74 3.82
4620 4795 8.615211 TGCAAAATGATGTACTTATCATCTCAC 58.385 33.333 8.65 2.48 44.74 3.51
4716 4891 1.883275 TGTGCCCACGGTTTAAATCAG 59.117 47.619 0.00 0.00 0.00 2.90
4723 4898 2.131067 CCCTTTGTGCCCACGGTTT 61.131 57.895 0.00 0.00 0.00 3.27
4727 4902 0.965363 AATAGCCCTTTGTGCCCACG 60.965 55.000 0.00 0.00 0.00 4.94
4729 4904 0.407528 TGAATAGCCCTTTGTGCCCA 59.592 50.000 0.00 0.00 0.00 5.36
4735 4910 5.420104 ACCTTGATTTCTGAATAGCCCTTTG 59.580 40.000 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.