Multiple sequence alignment - TraesCS7A01G165200

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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 TraesCS7A01G165200 chr7A 100.000 4104 0 0 1 4104 120925841 120921738 0 7579
1 TraesCS7A01G165200 chr7A 98.368 4106 63 4 1 4104 671960568 671956465 0 7208
2 TraesCS7A01G165200 chr7A 98.124 4105 71 5 1 4104 120828848 120824749 0 7149
3 TraesCS7A01G165200 chr7A 100.000 3344 0 0 4256 7599 120921586 120918243 0 6176
4 TraesCS7A01G165200 chr7A 98.110 3334 51 4 4267 7599 671956410 671953088 0 5797
5 TraesCS7A01G165200 chr7B 98.539 4106 56 4 1 4104 743066305 743070408 0 7247
6 TraesCS7A01G165200 chr5A 98.466 4108 59 3 1 4104 16623275 16619168 0 7234
7 TraesCS7A01G165200 chr5A 98.320 4106 66 3 1 4104 300048565 300052669 0 7197
8 TraesCS7A01G165200 chr5A 98.029 3348 51 5 4256 7599 300053109 300056445 0 5803
9 TraesCS7A01G165200 chr2A 98.173 4106 72 3 1 4104 735172799 735176903 0 7164
10 TraesCS7A01G165200 chr2D 98.174 4107 68 5 1 4104 635037260 635041362 0 7162
11 TraesCS7A01G165200 chr2D 97.847 3344 53 5 4256 7599 635041398 635044722 0 5758
12 TraesCS7A01G165200 chr2D 97.490 3346 64 7 4256 7599 17963080 17959753 0 5696
13 TraesCS7A01G165200 chr3B 98.149 4105 71 4 1 4104 201635803 201631703 0 7155
14 TraesCS7A01G165200 chr3D 98.052 4107 74 5 1 4104 202611946 202616049 0 7136
15 TraesCS7A01G165200 chr7D 98.356 3346 38 6 4256 7599 382010025 382006695 0 5858
16 TraesCS7A01G165200 chr4D 97.967 3345 52 6 4256 7599 123582720 123586049 0 5786
17 TraesCS7A01G165200 chr6B 98.447 3285 48 3 4317 7599 525682386 525685669 0 5781
18 TraesCS7A01G165200 chr4B 97.818 3345 62 4 4256 7599 209145465 209142131 0 5762
19 TraesCS7A01G165200 chr4A 97.579 3346 67 5 4256 7599 67550769 67547436 0 5718


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 TraesCS7A01G165200 chr7A 120918243 120925841 7598 True 6877.5 7579 100.0000 1 7599 2 chr7A.!!$R2 7598
1 TraesCS7A01G165200 chr7A 120824749 120828848 4099 True 7149.0 7149 98.1240 1 4104 1 chr7A.!!$R1 4103
2 TraesCS7A01G165200 chr7A 671953088 671960568 7480 True 6502.5 7208 98.2390 1 7599 2 chr7A.!!$R3 7598
3 TraesCS7A01G165200 chr7B 743066305 743070408 4103 False 7247.0 7247 98.5390 1 4104 1 chr7B.!!$F1 4103
4 TraesCS7A01G165200 chr5A 16619168 16623275 4107 True 7234.0 7234 98.4660 1 4104 1 chr5A.!!$R1 4103
5 TraesCS7A01G165200 chr5A 300048565 300056445 7880 False 6500.0 7197 98.1745 1 7599 2 chr5A.!!$F1 7598
6 TraesCS7A01G165200 chr2A 735172799 735176903 4104 False 7164.0 7164 98.1730 1 4104 1 chr2A.!!$F1 4103
7 TraesCS7A01G165200 chr2D 635037260 635044722 7462 False 6460.0 7162 98.0105 1 7599 2 chr2D.!!$F1 7598
8 TraesCS7A01G165200 chr2D 17959753 17963080 3327 True 5696.0 5696 97.4900 4256 7599 1 chr2D.!!$R1 3343
9 TraesCS7A01G165200 chr3B 201631703 201635803 4100 True 7155.0 7155 98.1490 1 4104 1 chr3B.!!$R1 4103
10 TraesCS7A01G165200 chr3D 202611946 202616049 4103 False 7136.0 7136 98.0520 1 4104 1 chr3D.!!$F1 4103
11 TraesCS7A01G165200 chr7D 382006695 382010025 3330 True 5858.0 5858 98.3560 4256 7599 1 chr7D.!!$R1 3343
12 TraesCS7A01G165200 chr4D 123582720 123586049 3329 False 5786.0 5786 97.9670 4256 7599 1 chr4D.!!$F1 3343
13 TraesCS7A01G165200 chr6B 525682386 525685669 3283 False 5781.0 5781 98.4470 4317 7599 1 chr6B.!!$F1 3282
14 TraesCS7A01G165200 chr4B 209142131 209145465 3334 True 5762.0 5762 97.8180 4256 7599 1 chr4B.!!$R1 3343
15 TraesCS7A01G165200 chr4A 67547436 67550769 3333 True 5718.0 5718 97.5790 4256 7599 1 chr4A.!!$R1 3343

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
181 184 0.179029 CCCCGGTCAGTTCACTTTGT 60.179 55.000 0.0 0.0 0.00 2.83 F
636 639 0.623324 ACCAATGCCCCACCTAGCTA 60.623 55.000 0.0 0.0 0.00 3.32 F
1167 1174 0.754217 CGTATCCCCCTGTTCCTCGA 60.754 60.000 0.0 0.0 0.00 4.04 F
1893 1900 1.553248 CCAGGGATGGACGTAAACTCA 59.447 52.381 0.0 0.0 0.00 3.41 F
3624 3637 0.906775 TGCACTGGCTCATCTCATGA 59.093 50.000 0.0 0.0 41.91 3.07 F
3964 3977 0.768622 TTGGGGACAGGTGAACGAAT 59.231 50.000 0.0 0.0 44.54 3.34 F
4003 4016 1.112113 CATCCGCCGCCTATACCTAT 58.888 55.000 0.0 0.0 0.00 2.57 F
5526 5968 1.305201 TGGTTGGTCTTTCTCAACGC 58.695 50.000 0.0 0.0 42.81 4.84 F
6326 6776 0.623617 GAGTTGGGGTGGGGGTCTAT 60.624 60.000 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 1990 0.678048 GCCAAGAACTCTCCGGCAAT 60.678 55.000 12.88 0.00 41.51 3.56 R
2030 2042 2.282446 GGTCGATCCTCCCCTCCA 59.718 66.667 0.00 0.00 0.00 3.86 R
3043 3056 1.202510 GCACACATGTTTTGGCCTTGA 60.203 47.619 3.32 0.00 0.00 3.02 R
3773 3786 1.499049 GAAAGTGACTTCGGTTCGCT 58.501 50.000 0.00 0.00 0.00 4.93 R
4641 5071 0.179032 TGGGAAAAGCAGCGAACTCA 60.179 50.000 0.00 0.00 0.00 3.41 R
5111 5541 0.679321 GTTCTACGGTCCCTCGGAGT 60.679 60.000 4.02 0.00 41.53 3.85 R
5800 6242 1.654743 GAAGAGTACGCGCGCTAGG 60.655 63.158 32.58 16.59 0.00 3.02 R
6350 6800 0.326264 AGTTGCGCATCTTTCTCCCT 59.674 50.000 12.75 0.00 0.00 4.20 R
7368 7824 8.488668 TCTCATCATCATATTGAAGGAAACTCA 58.511 33.333 0.00 0.00 42.68 3.41 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
181 184 0.179029 CCCCGGTCAGTTCACTTTGT 60.179 55.000 0.00 0.00 0.00 2.83
460 463 2.367241 TCCGTTGGTGACTTTCTGATCA 59.633 45.455 0.00 0.00 0.00 2.92
636 639 0.623324 ACCAATGCCCCACCTAGCTA 60.623 55.000 0.00 0.00 0.00 3.32
727 730 7.537596 TTTGCCAGATGGATTCTTTAGAAAA 57.462 32.000 2.18 0.00 37.39 2.29
854 861 1.133181 TCATGACTTCCCACTGGGCA 61.133 55.000 9.60 1.77 43.94 5.36
1032 1039 6.546395 ACATTTCTGTGAATGCTATTTCGAC 58.454 36.000 0.00 0.00 39.97 4.20
1146 1153 7.010023 GTCTGTGCGTTTCTCTTATTACTTTG 58.990 38.462 0.00 0.00 0.00 2.77
1148 1155 6.884187 TGTGCGTTTCTCTTATTACTTTGTC 58.116 36.000 0.00 0.00 0.00 3.18
1167 1174 0.754217 CGTATCCCCCTGTTCCTCGA 60.754 60.000 0.00 0.00 0.00 4.04
1487 1494 3.243704 GGAGCTGAGCATCTTCTATTCGT 60.244 47.826 7.39 0.00 34.92 3.85
1775 1782 2.122167 GGGGGTGTGTTTGTTCGCA 61.122 57.895 0.00 0.00 0.00 5.10
1893 1900 1.553248 CCAGGGATGGACGTAAACTCA 59.447 52.381 0.00 0.00 0.00 3.41
1934 1946 6.785963 AGGGATAATCGTCCAGGTCTTATTAA 59.214 38.462 0.00 0.00 40.17 1.40
1978 1990 1.623811 GGCAGGTTAGTTCCTCTGTCA 59.376 52.381 0.00 0.00 35.37 3.58
2030 2042 9.309224 ACCTTAGGATAAGTTGCTAAAACAAAT 57.691 29.630 4.77 0.00 37.74 2.32
2519 2532 3.502123 TGGGGTTCGAGACAAAGAAAT 57.498 42.857 0.00 0.00 0.00 2.17
3043 3056 7.669722 ACCTATTTTGAGTTATGGACACACAAT 59.330 33.333 0.00 0.00 34.84 2.71
3065 3078 1.047596 AGGCCAAAACATGTGTGCCA 61.048 50.000 22.52 0.00 41.33 4.92
3186 3199 4.805744 TCCTAAAACAAAACCCCTTAGCA 58.194 39.130 0.00 0.00 0.00 3.49
3235 3248 3.054503 CAGACAGCAGCAGCACCC 61.055 66.667 3.17 0.00 45.49 4.61
3624 3637 0.906775 TGCACTGGCTCATCTCATGA 59.093 50.000 0.00 0.00 41.91 3.07
3660 3673 8.339714 GCAAATGTAGTTAGTTGTCTTGTTGTA 58.660 33.333 0.00 0.00 0.00 2.41
3678 3691 4.719369 GTTCGCCGCCTCGACACT 62.719 66.667 0.00 0.00 38.30 3.55
3683 3696 2.342279 CCGCCTCGACACTTTCCA 59.658 61.111 0.00 0.00 0.00 3.53
3773 3786 1.819288 CGAGGAGTTGAGCCTGAACTA 59.181 52.381 0.00 0.00 35.44 2.24
3871 3884 1.202256 CGAACGTGAGCTGCTATACCA 60.202 52.381 0.15 0.00 0.00 3.25
3958 3971 3.199442 TCTTCTATTGGGGACAGGTGA 57.801 47.619 0.00 0.00 44.54 4.02
3964 3977 0.768622 TTGGGGACAGGTGAACGAAT 59.231 50.000 0.00 0.00 44.54 3.34
4003 4016 1.112113 CATCCGCCGCCTATACCTAT 58.888 55.000 0.00 0.00 0.00 2.57
4991 5421 1.523938 GGAGCACGTAGGAATGCCC 60.524 63.158 0.00 0.00 43.12 5.36
5111 5541 2.337359 ACTACCTGCCTAACCCTTCA 57.663 50.000 0.00 0.00 0.00 3.02
5526 5968 1.305201 TGGTTGGTCTTTCTCAACGC 58.695 50.000 0.00 0.00 42.81 4.84
5565 6007 8.721133 AAAAACCATTCTTTACAAGATAGGGT 57.279 30.769 8.68 4.83 37.38 4.34
5720 6162 4.692475 GGGGTGTTGCCGTAGCGT 62.692 66.667 0.00 0.00 44.31 5.07
5800 6242 3.059884 GTTTTTAAGCTGGCTGCCTTTC 58.940 45.455 21.03 8.65 44.23 2.62
6144 6594 3.798511 GCCTCTCGGGAAAGGGGG 61.799 72.222 0.00 0.00 37.39 5.40
6188 6638 1.264045 GGGAGCAGCTGAGAGGTTCT 61.264 60.000 20.43 2.06 0.00 3.01
6227 6677 2.407090 CAGAACTTCAGTGCGTGATCA 58.593 47.619 0.00 0.00 34.17 2.92
6254 6704 2.033755 CACCTCGTCTCGTCCTCGT 61.034 63.158 0.00 0.00 38.33 4.18
6285 6735 6.238786 CGAAGAGTACCTATGCACTATGTTCT 60.239 42.308 0.00 0.00 0.00 3.01
6326 6776 0.623617 GAGTTGGGGTGGGGGTCTAT 60.624 60.000 0.00 0.00 0.00 1.98
6350 6800 6.260663 TGATGTGATACTATAGTATGCCCCA 58.739 40.000 26.51 16.33 40.99 4.96
6637 7087 5.473504 TCTTCAGCCCTTTTTCTATGTGTTC 59.526 40.000 0.00 0.00 0.00 3.18
6774 7224 1.668419 CCGGCACTAGCAGCTTTATT 58.332 50.000 0.00 0.00 44.61 1.40
6855 7305 2.024414 GCGCTTGGGATGATTTTAGGT 58.976 47.619 0.00 0.00 0.00 3.08
7175 7626 2.299297 GGACCGAGAGAAAGAAAGGACA 59.701 50.000 0.00 0.00 0.00 4.02
7176 7627 3.580731 GACCGAGAGAAAGAAAGGACAG 58.419 50.000 0.00 0.00 0.00 3.51
7177 7628 2.300437 ACCGAGAGAAAGAAAGGACAGG 59.700 50.000 0.00 0.00 0.00 4.00
7368 7824 2.169352 AGTTCTTATGGCAGAGCACGAT 59.831 45.455 0.00 0.00 0.00 3.73
7416 7872 1.689813 TGGAAACCAGAAGCACGACTA 59.310 47.619 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 184 6.656632 ATCTAAGAATCCGATGAACTGCTA 57.343 37.500 0.00 0.00 0.00 3.49
636 639 4.634443 CAGGTAGCTTTGTTACGCCTATTT 59.366 41.667 0.00 0.00 0.00 1.40
727 730 6.555463 TCTACTGAACTTTATCCGGGAATT 57.445 37.500 0.00 0.00 0.00 2.17
826 830 1.488393 GGGAAGTCATGAGGCTAGCTT 59.512 52.381 15.72 6.94 0.00 3.74
827 831 1.127343 GGGAAGTCATGAGGCTAGCT 58.873 55.000 15.72 0.00 0.00 3.32
1032 1039 4.342665 GGACAGAGAATAGGACCACTTAGG 59.657 50.000 0.00 0.00 45.67 2.69
1146 1153 0.751452 GAGGAACAGGGGGATACGAC 59.249 60.000 0.00 0.00 37.60 4.34
1148 1155 0.754217 TCGAGGAACAGGGGGATACG 60.754 60.000 0.00 0.00 37.60 3.06
1167 1174 4.989168 GCCGTAGAAGGATCGAATTGTATT 59.011 41.667 0.00 0.00 0.00 1.89
1487 1494 3.424703 CAGAGGAAAAGCTTGATCCCAA 58.575 45.455 21.92 0.00 33.55 4.12
1775 1782 6.602406 CCTGACTTGATGAGGAATTCATTCTT 59.398 38.462 7.93 2.87 46.51 2.52
1978 1990 0.678048 GCCAAGAACTCTCCGGCAAT 60.678 55.000 12.88 0.00 41.51 3.56
2030 2042 2.282446 GGTCGATCCTCCCCTCCA 59.718 66.667 0.00 0.00 0.00 3.86
2372 2385 2.362397 ACGTGAGACTTCCGCATCATAT 59.638 45.455 0.00 0.00 0.00 1.78
2519 2532 6.039717 GGAAAAACTGATATGCTGCCTTGATA 59.960 38.462 0.00 0.00 0.00 2.15
3043 3056 1.202510 GCACACATGTTTTGGCCTTGA 60.203 47.619 3.32 0.00 0.00 3.02
3065 3078 4.015406 TTGATGGGTCGCACGCCT 62.015 61.111 0.00 0.00 0.00 5.52
3235 3248 1.846782 CGATTCGGACTTTGTAGAGCG 59.153 52.381 0.00 0.00 0.00 5.03
3624 3637 7.597288 ACTAACTACATTTGCTTTTTCCCTT 57.403 32.000 0.00 0.00 0.00 3.95
3660 3673 4.719369 GTGTCGAGGCGGCGAACT 62.719 66.667 12.98 7.86 42.55 3.01
3773 3786 1.499049 GAAAGTGACTTCGGTTCGCT 58.501 50.000 0.00 0.00 0.00 4.93
3871 3884 3.738745 GATGGCCAGCGGGGGATTT 62.739 63.158 13.05 0.00 37.04 2.17
3958 3971 2.940410 ACGTTTGGAGTTGTCATTCGTT 59.060 40.909 0.00 0.00 0.00 3.85
3964 3977 2.093921 TGTCTGACGTTTGGAGTTGTCA 60.094 45.455 2.98 0.00 38.91 3.58
4003 4016 1.302192 GCTGGTGCCACCTAAACGA 60.302 57.895 16.23 0.00 39.58 3.85
4641 5071 0.179032 TGGGAAAAGCAGCGAACTCA 60.179 50.000 0.00 0.00 0.00 3.41
4991 5421 1.290203 CAGCGGCTTATGTAGTGGTG 58.710 55.000 0.00 0.00 0.00 4.17
5111 5541 0.679321 GTTCTACGGTCCCTCGGAGT 60.679 60.000 4.02 0.00 41.53 3.85
5443 5885 3.262915 GGAGGTGCTCCTTATGATGCTAT 59.737 47.826 9.08 0.00 46.41 2.97
5526 5968 3.255725 TGGTTTTTCGTGCTATAGACCG 58.744 45.455 3.21 4.56 0.00 4.79
5565 6007 6.852858 TTGTATTGTCTTTCATGTGAACGA 57.147 33.333 0.00 0.00 33.13 3.85
5720 6162 3.356639 CTACGCTTGCTCTCCGGCA 62.357 63.158 0.00 0.00 40.74 5.69
5800 6242 1.654743 GAAGAGTACGCGCGCTAGG 60.655 63.158 32.58 16.59 0.00 3.02
6146 6596 1.846584 GATAGGTAGGCCCACCCCC 60.847 68.421 17.64 2.56 39.62 5.40
6147 6597 1.846584 GGATAGGTAGGCCCACCCC 60.847 68.421 17.64 7.58 39.62 4.95
6188 6638 1.972198 CCCTTCGGCTCGGCATATA 59.028 57.895 0.00 0.00 0.00 0.86
6227 6677 3.806380 ACGAGACGAGGTGACATACTAT 58.194 45.455 0.00 0.00 0.00 2.12
6254 6704 4.023107 GTGCATAGGTACTCTTCGATGCTA 60.023 45.833 13.18 0.00 41.75 3.49
6285 6735 6.897966 ACTCTATCTTCCTTATCAGTGAACCA 59.102 38.462 0.00 0.00 0.00 3.67
6326 6776 6.260663 TGGGGCATACTATAGTATCACATCA 58.739 40.000 20.38 14.49 39.06 3.07
6350 6800 0.326264 AGTTGCGCATCTTTCTCCCT 59.674 50.000 12.75 0.00 0.00 4.20
6457 6907 7.444487 GGCTTTCTAACTCCACTTCTTTTTCTA 59.556 37.037 0.00 0.00 0.00 2.10
6637 7087 6.577800 GTCTTATGTCGGTCATATAGAACACG 59.422 42.308 0.00 0.00 38.59 4.49
6774 7224 7.202102 GCTCCTACTAAGATTAGAAATTCCCCA 60.202 40.741 6.61 0.00 34.84 4.96
6815 7265 3.490933 CGCAGCTAATGTGGCTACTAAGA 60.491 47.826 0.64 0.00 38.03 2.10
6855 7305 2.125310 CACAGGGAATACGCCGCA 60.125 61.111 0.00 0.00 0.00 5.69
7368 7824 8.488668 TCTCATCATCATATTGAAGGAAACTCA 58.511 33.333 0.00 0.00 42.68 3.41


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

AutoCloner maintained by Alex Coulton.