Multiple sequence alignment - TraesCS4D01G275200

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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 TraesCS4D01G275200 chr4D 100.000 4722 0 0 1 4722 445712410 445707689 0.000000e+00 8720.0
1 TraesCS4D01G275200 chr4B 94.893 4797 118 43 1 4722 557456801 557452057 0.000000e+00 7384.0
2 TraesCS4D01G275200 chr4A 93.656 4366 157 53 418 4722 21453086 21457392 0.000000e+00 6418.0
3 TraesCS4D01G275200 chr4A 87.619 210 10 8 176 372 21452543 21452749 3.680000e-56 230.0
4 TraesCS4D01G275200 chr6A 80.285 492 82 11 3243 3720 424800176 424800666 1.620000e-94 357.0
5 TraesCS4D01G275200 chr6A 87.805 82 7 2 1310 1388 424798442 424798523 5.030000e-15 93.5
6 TraesCS4D01G275200 chrUn 77.053 414 54 10 3753 4155 369331061 369331444 2.880000e-47 200.0
7 TraesCS4D01G275200 chr2A 83.708 178 26 3 3978 4155 12175011 12175185 1.050000e-36 165.0
8 TraesCS4D01G275200 chr2D 85.271 129 13 4 4550 4674 11560573 11560699 1.380000e-25 128.0


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 TraesCS4D01G275200 chr4D 445707689 445712410 4721 True 8720.00 8720 100.0000 1 4722 1 chr4D.!!$R1 4721
1 TraesCS4D01G275200 chr4B 557452057 557456801 4744 True 7384.00 7384 94.8930 1 4722 1 chr4B.!!$R1 4721
2 TraesCS4D01G275200 chr4A 21452543 21457392 4849 False 3324.00 6418 90.6375 176 4722 2 chr4A.!!$F1 4546
3 TraesCS4D01G275200 chr6A 424798442 424800666 2224 False 225.25 357 84.0450 1310 3720 2 chr6A.!!$F1 2410

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
90 91 0.034477 ATCTGGATTCGGGCCGTTTT 60.034 50.0 27.32 11.87 0.00 2.43 F
302 316 0.251297 ACTGGCATGGCAGCAGTAAA 60.251 50.0 40.26 10.14 35.83 2.01 F
1456 1806 0.336737 TCTTCCTCTCCAGTCTCCCC 59.663 60.0 0.00 0.00 0.00 4.81 F
2213 2580 1.830279 TCTGGTCACACTAGGTACGG 58.170 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2015 0.447801 GCGGCATCGAAATTGTCAGT 59.552 50.000 0.0 0.0 39.00 3.41 R
2213 2580 6.313905 CAGAGTACATGGTATGGAACTTGAAC 59.686 42.308 0.0 0.0 32.82 3.18 R
2428 2807 2.189594 TCAATCCTCTGCCAACACAG 57.810 50.000 0.0 0.0 39.12 3.66 R
3785 4224 0.930726 TCAAACCACCCTCCAAACCT 59.069 50.000 0.0 0.0 0.00 3.50 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
33 34 5.189928 TCTGTTTGTTTCAGCTTTAGGACA 58.810 37.500 0.00 0.00 33.48 4.02
37 38 1.464997 GTTTCAGCTTTAGGACAGCCG 59.535 52.381 0.00 0.00 38.09 5.52
40 41 0.247736 CAGCTTTAGGACAGCCGTCT 59.752 55.000 0.00 0.00 42.21 4.18
42 43 0.741221 GCTTTAGGACAGCCGTCTGG 60.741 60.000 0.00 0.00 44.54 3.86
43 44 0.895530 CTTTAGGACAGCCGTCTGGA 59.104 55.000 0.00 0.00 44.54 3.86
44 45 1.275291 CTTTAGGACAGCCGTCTGGAA 59.725 52.381 0.00 0.00 44.54 3.53
46 47 1.112113 TAGGACAGCCGTCTGGAATC 58.888 55.000 0.00 0.00 44.54 2.52
47 48 0.904865 AGGACAGCCGTCTGGAATCA 60.905 55.000 0.00 0.00 44.54 2.57
48 49 0.460987 GGACAGCCGTCTGGAATCAG 60.461 60.000 0.00 0.00 44.54 2.90
49 50 1.078848 ACAGCCGTCTGGAATCAGC 60.079 57.895 0.00 0.00 44.54 4.26
50 51 1.220206 CAGCCGTCTGGAATCAGCT 59.780 57.895 0.00 0.00 40.69 4.24
51 52 0.392193 CAGCCGTCTGGAATCAGCTT 60.392 55.000 0.00 0.00 40.69 3.74
52 53 0.326264 AGCCGTCTGGAATCAGCTTT 59.674 50.000 0.00 0.00 40.69 3.51
53 54 0.449388 GCCGTCTGGAATCAGCTTTG 59.551 55.000 0.00 0.00 40.69 2.77
54 55 0.449388 CCGTCTGGAATCAGCTTTGC 59.551 55.000 0.00 0.00 40.69 3.68
55 56 1.446907 CGTCTGGAATCAGCTTTGCT 58.553 50.000 0.00 0.00 40.69 3.91
56 57 1.808945 CGTCTGGAATCAGCTTTGCTT 59.191 47.619 0.00 0.00 40.69 3.91
57 58 2.413765 CGTCTGGAATCAGCTTTGCTTG 60.414 50.000 0.00 0.00 40.69 4.01
58 59 2.555757 GTCTGGAATCAGCTTTGCTTGT 59.444 45.455 0.00 0.00 40.69 3.16
86 87 4.049393 GAATCTGGATTCGGGCCG 57.951 61.111 22.51 22.51 37.97 6.13
90 91 0.034477 ATCTGGATTCGGGCCGTTTT 60.034 50.000 27.32 11.87 0.00 2.43
98 99 1.444212 CGGGCCGTTTTCAATGCAG 60.444 57.895 19.97 0.00 0.00 4.41
99 100 1.665442 GGGCCGTTTTCAATGCAGT 59.335 52.632 0.00 0.00 0.00 4.40
101 102 1.139163 GGCCGTTTTCAATGCAGTTG 58.861 50.000 0.00 0.00 39.25 3.16
102 103 1.537990 GGCCGTTTTCAATGCAGTTGT 60.538 47.619 0.00 0.00 38.95 3.32
104 105 2.543653 GCCGTTTTCAATGCAGTTGTCT 60.544 45.455 0.00 0.00 38.95 3.41
105 106 3.044986 CCGTTTTCAATGCAGTTGTCTG 58.955 45.455 0.00 0.00 43.87 3.51
162 163 1.815421 CGGGTGATTCGGAGCCAAG 60.815 63.158 0.00 0.00 0.00 3.61
244 245 4.040217 CCAATATCCCTCTCTGTCTCCAAG 59.960 50.000 0.00 0.00 0.00 3.61
302 316 0.251297 ACTGGCATGGCAGCAGTAAA 60.251 50.000 40.26 10.14 35.83 2.01
331 347 1.213537 CCGAAGGCATTGCTTGGTG 59.786 57.895 8.82 0.00 46.14 4.17
351 367 3.520623 GCATGGTTTGCCCCTCTAT 57.479 52.632 0.00 0.00 46.15 1.98
379 395 1.077429 CCTTGGGTCTTGCTAGGGC 60.077 63.158 0.00 0.00 39.26 5.19
435 743 4.624913 AGAGTGACCATCCTAAGATTCCA 58.375 43.478 0.00 0.00 0.00 3.53
740 1064 6.409704 CAGAGAGAAGAGAAGAGAAGAGAGA 58.590 44.000 0.00 0.00 0.00 3.10
873 1197 0.935194 TCTACCCCCTCCCTCTTCTC 59.065 60.000 0.00 0.00 0.00 2.87
874 1198 0.938192 CTACCCCCTCCCTCTTCTCT 59.062 60.000 0.00 0.00 0.00 3.10
875 1199 1.292546 CTACCCCCTCCCTCTTCTCTT 59.707 57.143 0.00 0.00 0.00 2.85
1015 1353 1.329906 GAACAATGAGAGATGGCTGCG 59.670 52.381 0.00 0.00 0.00 5.18
1054 1392 4.892291 TACCGCCCTCCCATCCCC 62.892 72.222 0.00 0.00 0.00 4.81
1399 1749 2.798148 CTACAGGTTGGTCCACCGCC 62.798 65.000 0.00 0.00 42.33 6.13
1453 1803 3.025322 TCCATCTTCCTCTCCAGTCTC 57.975 52.381 0.00 0.00 0.00 3.36
1454 1804 2.038659 CCATCTTCCTCTCCAGTCTCC 58.961 57.143 0.00 0.00 0.00 3.71
1455 1805 2.038659 CATCTTCCTCTCCAGTCTCCC 58.961 57.143 0.00 0.00 0.00 4.30
1456 1806 0.336737 TCTTCCTCTCCAGTCTCCCC 59.663 60.000 0.00 0.00 0.00 4.81
1486 1839 6.535508 TGTGTGTGGCCTTGTTAATTAAAAAC 59.464 34.615 3.32 0.00 0.00 2.43
2213 2580 1.830279 TCTGGTCACACTAGGTACGG 58.170 55.000 0.00 0.00 0.00 4.02
2283 2650 4.576463 GGAGCCAAAGTACATTATGGTCTG 59.424 45.833 0.00 0.00 35.34 3.51
2321 2688 5.409520 GTGAGTAATCTGTGTTGCAATCTGA 59.590 40.000 0.59 9.25 0.00 3.27
2428 2807 5.707298 TGACATCAGAAATCTCAAGGTTTCC 59.293 40.000 11.26 0.00 35.46 3.13
2502 2888 7.213678 TGTTCGAATGCTATGTGGTTATCATA 58.786 34.615 0.00 0.00 0.00 2.15
2515 2901 8.489990 TGTGGTTATCATAATTTTTGCAATGG 57.510 30.769 0.00 0.00 0.00 3.16
2564 2953 5.804639 TCAAGAGGCATTGTTAGCTTAGAA 58.195 37.500 0.00 0.00 0.00 2.10
3058 3482 1.153509 GTGTACCGTTGGGATCCCG 60.154 63.158 26.03 13.86 39.42 5.14
3331 3755 2.482316 CCCGCCGACATACAAATACTCA 60.482 50.000 0.00 0.00 0.00 3.41
3604 4043 1.338107 TGGAGTCGATCAACCACAGT 58.662 50.000 0.00 0.00 0.00 3.55
3709 4148 0.248907 CGTATGGCTACACCGACCTG 60.249 60.000 0.00 0.00 43.94 4.00
3730 4169 4.918588 TGAATTTCTACTGAAAGGGTCCC 58.081 43.478 0.00 0.00 44.25 4.46
3778 4217 6.093082 TGTTCAATCATGCAACTAGTGATGAG 59.907 38.462 14.48 6.00 33.19 2.90
3785 4224 5.738619 TGCAACTAGTGATGAGAAGGTAA 57.261 39.130 0.00 0.00 0.00 2.85
4029 4468 5.489792 TTGGATACTTTCAGAGAAGCAGT 57.510 39.130 0.00 0.00 37.61 4.40
4057 4496 2.972625 TGGCTAGTTTCACAGGATTCG 58.027 47.619 0.00 0.00 0.00 3.34
4060 4499 4.000988 GGCTAGTTTCACAGGATTCGAAA 58.999 43.478 0.00 0.00 0.00 3.46
4146 4585 7.556996 ACGTCTAATGAACTACTGATCCTAACT 59.443 37.037 0.00 0.00 0.00 2.24
4149 4588 9.069082 TCTAATGAACTACTGATCCTAACTAGC 57.931 37.037 0.00 0.00 0.00 3.42
4151 4590 4.894114 TGAACTACTGATCCTAACTAGCCC 59.106 45.833 0.00 0.00 0.00 5.19
4152 4591 4.817874 ACTACTGATCCTAACTAGCCCT 57.182 45.455 0.00 0.00 0.00 5.19
4393 4833 3.406764 CCCAGCAAAGATAGATACTGCC 58.593 50.000 0.00 0.00 33.41 4.85
4401 4841 6.519382 CAAAGATAGATACTGCCACTGATGA 58.481 40.000 0.00 0.00 0.00 2.92
4513 4969 5.960811 TCTCTCTCTCTCTTTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.719121 AGCTGATTCCAGACGGCT 58.281 55.556 0.00 0.00 43.02 5.52
37 38 2.555757 ACAAGCAAAGCTGATTCCAGAC 59.444 45.455 0.00 0.00 43.02 3.51
40 41 2.555325 CTGACAAGCAAAGCTGATTCCA 59.445 45.455 0.00 0.00 39.62 3.53
42 43 3.251729 TCACTGACAAGCAAAGCTGATTC 59.748 43.478 0.00 0.00 39.62 2.52
43 44 3.216800 TCACTGACAAGCAAAGCTGATT 58.783 40.909 0.00 0.00 39.62 2.57
44 45 2.854963 TCACTGACAAGCAAAGCTGAT 58.145 42.857 0.00 0.00 39.62 2.90
46 47 3.111098 GTTTCACTGACAAGCAAAGCTG 58.889 45.455 0.00 0.00 39.62 4.24
47 48 3.019564 AGTTTCACTGACAAGCAAAGCT 58.980 40.909 0.00 0.00 42.56 3.74
48 49 3.427161 AGTTTCACTGACAAGCAAAGC 57.573 42.857 0.00 0.00 0.00 3.51
98 99 0.110056 CTTGACATGCCGCAGACAAC 60.110 55.000 0.00 0.00 0.00 3.32
99 100 1.236616 CCTTGACATGCCGCAGACAA 61.237 55.000 0.00 4.58 0.00 3.18
101 102 1.672356 ACCTTGACATGCCGCAGAC 60.672 57.895 0.00 0.00 0.00 3.51
102 103 1.672030 CACCTTGACATGCCGCAGA 60.672 57.895 0.00 0.00 0.00 4.26
104 105 0.953471 GTACACCTTGACATGCCGCA 60.953 55.000 0.00 0.00 0.00 5.69
105 106 0.673644 AGTACACCTTGACATGCCGC 60.674 55.000 0.00 0.00 0.00 6.53
106 107 1.732259 GAAGTACACCTTGACATGCCG 59.268 52.381 0.00 0.00 32.03 5.69
107 108 1.732259 CGAAGTACACCTTGACATGCC 59.268 52.381 0.00 0.00 32.03 4.40
108 109 1.732259 CCGAAGTACACCTTGACATGC 59.268 52.381 0.00 0.00 32.03 4.06
109 110 2.736721 CACCGAAGTACACCTTGACATG 59.263 50.000 0.00 0.00 32.03 3.21
110 111 2.289444 CCACCGAAGTACACCTTGACAT 60.289 50.000 0.00 0.00 32.03 3.06
111 112 1.069513 CCACCGAAGTACACCTTGACA 59.930 52.381 0.00 0.00 32.03 3.58
144 145 1.815421 CTTGGCTCCGAATCACCCG 60.815 63.158 0.00 0.00 0.00 5.28
162 163 1.314730 TTCAAACGAAGGCCCTTCAC 58.685 50.000 22.83 0.00 40.17 3.18
226 227 3.307506 CATCTTGGAGACAGAGAGGGAT 58.692 50.000 0.00 0.00 44.54 3.85
244 245 3.360867 TGTGAGAGAGAGGACTTCCATC 58.639 50.000 0.00 0.00 38.89 3.51
435 743 0.811281 GGGAATAAAGCGCTTGCAGT 59.189 50.000 25.80 14.19 42.66 4.40
659 980 2.270257 GGCTGGCAACACTGATGCA 61.270 57.895 12.80 0.00 46.17 3.96
740 1064 7.094032 GGATGAGAACAAAATGTGGATTCTCTT 60.094 37.037 12.16 7.01 43.68 2.85
873 1197 0.323816 GGGGCCAAGGAAGGAAGAAG 60.324 60.000 4.39 0.00 0.00 2.85
874 1198 1.774300 GGGGCCAAGGAAGGAAGAA 59.226 57.895 4.39 0.00 0.00 2.52
875 1199 2.238701 GGGGGCCAAGGAAGGAAGA 61.239 63.158 4.39 0.00 0.00 2.87
979 1317 1.229209 TTCCCTTCCGTCCTCAGCT 60.229 57.895 0.00 0.00 0.00 4.24
988 1326 3.201290 CATCTCTCATTGTTCCCTTCCG 58.799 50.000 0.00 0.00 0.00 4.30
1015 1353 1.876156 CTTGCTCTTCTTGGTGGTGTC 59.124 52.381 0.00 0.00 0.00 3.67
1054 1392 1.650528 ACCAGGAGGAAGAAGACAGG 58.349 55.000 0.00 0.00 38.69 4.00
1226 1564 3.054503 CCCTCCACTCGTCGTCGT 61.055 66.667 1.33 0.00 38.33 4.34
1229 1567 4.988716 TGCCCCTCCACTCGTCGT 62.989 66.667 0.00 0.00 0.00 4.34
1454 1804 4.974721 GGCCACACACACAGGGGG 62.975 72.222 0.00 0.00 0.00 5.40
1455 1805 3.435525 AAGGCCACACACACAGGGG 62.436 63.158 5.01 0.00 0.00 4.79
1456 1806 2.195567 CAAGGCCACACACACAGGG 61.196 63.158 5.01 0.00 0.00 4.45
1486 1839 1.165907 TCCTGCAGGCAGTTTCGTTG 61.166 55.000 28.91 0.00 42.15 4.10
1660 2015 0.447801 GCGGCATCGAAATTGTCAGT 59.552 50.000 0.00 0.00 39.00 3.41
2213 2580 6.313905 CAGAGTACATGGTATGGAACTTGAAC 59.686 42.308 0.00 0.00 32.82 3.18
2283 2650 8.136165 ACAGATTACTCACCACGTCTATTTATC 58.864 37.037 0.00 0.00 0.00 1.75
2321 2688 5.121380 ACCAGGCAATATCTGAAGAACAT 57.879 39.130 0.00 0.00 34.36 2.71
2428 2807 2.189594 TCAATCCTCTGCCAACACAG 57.810 50.000 0.00 0.00 39.12 3.66
2540 2929 5.804639 TCTAAGCTAACAATGCCTCTTGAA 58.195 37.500 0.00 0.00 0.00 2.69
2541 2930 5.420725 TCTAAGCTAACAATGCCTCTTGA 57.579 39.130 0.00 0.00 0.00 3.02
2564 2953 4.850680 TCCTTTGCCGGTTGAATACTATT 58.149 39.130 1.90 0.00 0.00 1.73
2697 3086 3.622163 GGATCTCAAGCACATCTGAGTTG 59.378 47.826 0.00 0.00 0.00 3.16
3058 3482 7.328493 GTGACATAACAATTTTACAGCTTTCCC 59.672 37.037 0.00 0.00 0.00 3.97
3331 3755 3.440173 CGGCATACTTGTCAGAATTGGTT 59.560 43.478 0.00 0.00 0.00 3.67
3448 3884 4.339247 CACAACAGGATCACCAAGTTTCTT 59.661 41.667 0.00 0.00 35.55 2.52
3464 3903 1.499056 GATCGCACCTGCACAACAG 59.501 57.895 0.00 0.00 46.77 3.16
3709 4148 4.944317 CAGGGACCCTTTCAGTAGAAATTC 59.056 45.833 11.56 0.00 42.49 2.17
3730 4169 3.452755 GGGTGTTTTCCCAAAGTTCAG 57.547 47.619 0.00 0.00 46.30 3.02
3759 4198 5.104610 ACCTTCTCATCACTAGTTGCATGAT 60.105 40.000 0.00 0.00 33.28 2.45
3778 4217 2.554564 CCACCCTCCAAACCTTACCTTC 60.555 54.545 0.00 0.00 0.00 3.46
3785 4224 0.930726 TCAAACCACCCTCCAAACCT 59.069 50.000 0.00 0.00 0.00 3.50
3936 4375 7.383102 AGCAAACTAACTGTATTGATCAAGG 57.617 36.000 14.54 6.62 0.00 3.61
4029 4468 4.065088 CTGTGAAACTAGCCAAGCACTTA 58.935 43.478 0.00 0.00 38.04 2.24
4060 4499 8.314751 GCATACCTGTATCCTGTACTGAATTAT 58.685 37.037 0.60 0.00 0.00 1.28
4393 4833 4.571889 CACGATTTTCGATGTCATCAGTG 58.428 43.478 13.22 6.90 43.74 3.66
4401 4841 1.464608 CTGGTGCACGATTTTCGATGT 59.535 47.619 11.45 0.00 43.74 3.06


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

AutoCloner maintained by Alex Coulton.