Multiple sequence alignment - TraesCS2D01G190900

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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 TraesCS2D01G190900 chr2D 100.000 3537 0 0 1 3537 134929303 134932839 0.000000e+00 6532
1 TraesCS2D01G190900 chr2B 93.216 2624 94 22 563 3149 191877410 191879986 0.000000e+00 3783
2 TraesCS2D01G190900 chr2B 91.512 377 28 3 3164 3537 191881195 191881570 1.880000e-142 516
3 TraesCS2D01G190900 chr2A 93.649 2299 85 16 892 3143 143027263 143029547 0.000000e+00 3380
4 TraesCS2D01G190900 chr2A 93.635 597 26 5 1 594 143024757 143025344 0.000000e+00 881
5 TraesCS2D01G190900 chr2A 87.467 375 22 14 3164 3537 143029858 143030208 3.290000e-110 409
6 TraesCS2D01G190900 chr2A 85.172 290 18 10 609 894 143026967 143027235 1.250000e-69 274


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 TraesCS2D01G190900 chr2D 134929303 134932839 3536 False 6532.0 6532 100.00000 1 3537 1 chr2D.!!$F1 3536
1 TraesCS2D01G190900 chr2B 191877410 191881570 4160 False 2149.5 3783 92.36400 563 3537 2 chr2B.!!$F1 2974
2 TraesCS2D01G190900 chr2A 143024757 143030208 5451 False 1236.0 3380 89.98075 1 3537 4 chr2A.!!$F1 3536

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
58 60 0.625316 TCCTGGCTGCATGTGGTAAT 59.375 50.000 0.5 0.0 0.0 1.89 F
59 61 1.005805 TCCTGGCTGCATGTGGTAATT 59.994 47.619 0.5 0.0 0.0 1.40 F
142 146 1.271217 GGGTGTGTCTACTTGGGGTTC 60.271 57.143 0.0 0.0 0.0 3.62 F
1359 3045 1.076632 CCTCCCACTACCGCTCTCT 60.077 63.158 0.0 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 3023 1.076192 AGCGGTAGTGGGAGGTAGG 60.076 63.158 0.0 0.0 0.00 3.18 R
1349 3035 2.547211 GCGATTGTACTAGAGAGCGGTA 59.453 50.000 0.0 0.0 0.00 4.02 R
2075 3783 1.215673 TGGTAAACCCTGCCTTTCACA 59.784 47.619 0.0 0.0 34.29 3.58 R
2861 4571 0.668401 GGCATCAAACCAAGCAGCAC 60.668 55.000 0.0 0.0 0.00 4.40 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
40 41 2.291741 GGCCTATAACTGCAGCATGTTC 59.708 50.000 15.27 0.00 39.31 3.18
58 60 0.625316 TCCTGGCTGCATGTGGTAAT 59.375 50.000 0.50 0.00 0.00 1.89
59 61 1.005805 TCCTGGCTGCATGTGGTAATT 59.994 47.619 0.50 0.00 0.00 1.40
60 62 1.826720 CCTGGCTGCATGTGGTAATTT 59.173 47.619 0.50 0.00 0.00 1.82
61 63 2.234414 CCTGGCTGCATGTGGTAATTTT 59.766 45.455 0.50 0.00 0.00 1.82
62 64 3.306919 CCTGGCTGCATGTGGTAATTTTT 60.307 43.478 0.50 0.00 0.00 1.94
123 127 5.590259 CCAATAGTGAGAACTAAATGGGTGG 59.410 44.000 10.83 0.00 33.36 4.61
124 128 3.721087 AGTGAGAACTAAATGGGTGGG 57.279 47.619 0.00 0.00 0.00 4.61
130 134 2.579410 ACTAAATGGGTGGGTGTGTC 57.421 50.000 0.00 0.00 0.00 3.67
142 146 1.271217 GGGTGTGTCTACTTGGGGTTC 60.271 57.143 0.00 0.00 0.00 3.62
205 209 5.757320 ACTCTCATGTGTGTTCAAGAAGAAG 59.243 40.000 0.00 0.00 36.78 2.85
206 210 5.917462 TCTCATGTGTGTTCAAGAAGAAGA 58.083 37.500 0.00 0.00 36.78 2.87
207 211 6.348498 TCTCATGTGTGTTCAAGAAGAAGAA 58.652 36.000 0.00 0.00 36.78 2.52
208 212 6.481313 TCTCATGTGTGTTCAAGAAGAAGAAG 59.519 38.462 0.00 0.00 36.78 2.85
209 213 6.348498 TCATGTGTGTTCAAGAAGAAGAAGA 58.652 36.000 0.00 0.00 36.78 2.87
210 214 6.823182 TCATGTGTGTTCAAGAAGAAGAAGAA 59.177 34.615 0.00 0.00 36.78 2.52
264 268 6.348458 CGTCAATCTTCTTTATGCTTGGTTGA 60.348 38.462 0.00 0.00 0.00 3.18
312 316 8.713271 GTTTACTTGATCACTAGCCTATTATGC 58.287 37.037 0.00 0.00 0.00 3.14
318 322 5.201713 TCACTAGCCTATTATGCTGTCAC 57.798 43.478 3.97 0.00 39.91 3.67
326 330 5.240891 CCTATTATGCTGTCACACCCTATG 58.759 45.833 0.00 0.00 0.00 2.23
377 381 7.614124 AAGCAAGTTTGTTGTTTGAATGAAT 57.386 28.000 0.00 0.00 0.00 2.57
379 383 7.465989 AGCAAGTTTGTTGTTTGAATGAATTG 58.534 30.769 0.00 0.00 0.00 2.32
406 410 8.496707 AACATGAAGGAAATTTGCAATAATCC 57.503 30.769 12.54 14.02 0.00 3.01
453 457 4.181309 TGGCGAAACAAATAACCCATTC 57.819 40.909 0.00 0.00 0.00 2.67
476 480 7.733773 TCTTGAGGATGACAAAGTAGGATAA 57.266 36.000 0.00 0.00 0.00 1.75
535 539 7.616313 TGTTTCTAAAACTTCAAACCATTGGT 58.384 30.769 1.37 1.37 37.15 3.67
1337 3023 4.688413 GGAGCTCGTAATCCTCATTCATTC 59.312 45.833 7.83 0.00 32.51 2.67
1349 3035 3.713764 CTCATTCATTCCTACCTCCCACT 59.286 47.826 0.00 0.00 0.00 4.00
1359 3045 1.076632 CCTCCCACTACCGCTCTCT 60.077 63.158 0.00 0.00 0.00 3.10
1479 3165 4.722535 AGCGAGGAGGCCCTGGAA 62.723 66.667 0.00 0.00 44.53 3.53
1671 3357 2.295349 CAGCTCTCCACAATTGTGCTTT 59.705 45.455 29.42 10.75 44.34 3.51
1676 3362 5.735922 GCTCTCCACAATTGTGCTTTGTTTA 60.736 40.000 29.42 9.79 44.34 2.01
1733 3424 1.816224 GCTCCCTGCCGAAATTTACAA 59.184 47.619 0.00 0.00 35.15 2.41
1781 3472 5.294306 CAGTAAACTGAATGCCACGTATCAT 59.706 40.000 3.99 0.00 46.59 2.45
1807 3498 6.609237 TGAATGAATTCTCAAGGAATAGCG 57.391 37.500 7.05 0.00 43.17 4.26
1808 3499 5.008019 TGAATGAATTCTCAAGGAATAGCGC 59.992 40.000 7.05 0.00 43.17 5.92
1809 3500 2.866156 TGAATTCTCAAGGAATAGCGCG 59.134 45.455 0.00 0.00 43.17 6.86
1972 3679 7.467557 TGAAAGCAAAAATCAAGACACATTC 57.532 32.000 0.00 0.00 0.00 2.67
2030 3738 4.746466 TGTGGGTTTTGATTCCTGGTTAT 58.254 39.130 0.00 0.00 0.00 1.89
2075 3783 5.420104 CAGGAAAGGGCTAATTTCTCACAAT 59.580 40.000 9.19 0.00 36.96 2.71
2082 3790 6.071728 AGGGCTAATTTCTCACAATGTGAAAG 60.072 38.462 17.41 6.90 42.26 2.62
2134 3842 1.585668 CGCACGTTGTCTGATCTGATC 59.414 52.381 10.72 10.72 0.00 2.92
2135 3843 2.733542 CGCACGTTGTCTGATCTGATCT 60.734 50.000 17.82 0.00 0.00 2.75
2136 3844 2.602211 GCACGTTGTCTGATCTGATCTG 59.398 50.000 17.82 16.82 0.00 2.90
2137 3845 3.674410 GCACGTTGTCTGATCTGATCTGA 60.674 47.826 19.44 19.44 35.29 3.27
2138 3846 4.680702 CACGTTGTCTGATCTGATCTGAT 58.319 43.478 24.08 14.33 39.06 2.90
2222 3930 9.023962 ACAACTTCATCCATTTTCTGCTTATTA 57.976 29.630 0.00 0.00 0.00 0.98
2246 3955 7.798596 ATTCTCTGTATTGCTTGTTATCCTG 57.201 36.000 0.00 0.00 0.00 3.86
2247 3956 6.299805 TCTCTGTATTGCTTGTTATCCTGT 57.700 37.500 0.00 0.00 0.00 4.00
2341 4051 4.098654 ACATTTGTGTTTGGAATCAACGGA 59.901 37.500 0.00 0.00 31.78 4.69
2477 4187 1.047801 TAGCTCCACAAGTGACAGCA 58.952 50.000 19.58 8.46 38.19 4.41
2506 4216 3.511540 ACAGTAGTGACTTGCAGCAGATA 59.488 43.478 4.09 0.00 31.73 1.98
2517 4227 2.168313 TGCAGCAGATATCGGACAAGAA 59.832 45.455 7.08 0.00 0.00 2.52
2533 4243 6.128391 CGGACAAGAATAAAAACTCATCGGAA 60.128 38.462 0.00 0.00 0.00 4.30
2542 4252 4.744795 AAACTCATCGGAATAGCTGAGT 57.255 40.909 0.00 5.58 45.91 3.41
2544 4254 2.292016 ACTCATCGGAATAGCTGAGTCG 59.708 50.000 0.00 0.00 41.94 4.18
2575 4285 4.919754 GCAGTTGCCAAAATTCAAGAGTAG 59.080 41.667 0.00 0.00 34.31 2.57
2639 4349 4.806330 TCTTAGGCTCTACTGTCGTTTTG 58.194 43.478 0.00 0.00 0.00 2.44
2650 4360 3.880490 ACTGTCGTTTTGGAGTGCAAATA 59.120 39.130 10.84 0.00 0.00 1.40
2732 4442 7.938563 TGAACTGCAAAAATACATTTGGTAC 57.061 32.000 2.39 0.00 39.99 3.34
2733 4443 6.926272 TGAACTGCAAAAATACATTTGGTACC 59.074 34.615 4.43 4.43 39.99 3.34
2792 4502 7.797123 CAGAAACTATTGTTCTACGGTTTGAAC 59.203 37.037 15.23 15.23 41.87 3.18
2855 4565 2.571653 ACTGTTGCTGCCCTGTAATAGA 59.428 45.455 0.00 0.00 0.00 1.98
2861 4571 4.960938 TGCTGCCCTGTAATAGATACAAG 58.039 43.478 0.00 0.00 43.75 3.16
2895 4605 3.124560 TGATGCCAATATTTTGCATGCG 58.875 40.909 21.17 0.00 33.02 4.73
3040 4751 2.501723 ACCGATAACCTCAGCAATGTCT 59.498 45.455 0.00 0.00 0.00 3.41
3110 4821 2.159324 GCTATCCCAAAGAAACTGCAGC 60.159 50.000 15.27 0.00 0.00 5.25
3125 4836 3.198068 CTGCAGCGGAAATAAGCTCTAA 58.802 45.455 0.00 0.00 42.52 2.10
3290 6458 2.489722 TCGATATCGGAGATCAAGCAGG 59.510 50.000 24.12 0.00 45.12 4.85
3291 6459 2.615869 GATATCGGAGATCAAGCAGGC 58.384 52.381 7.71 0.00 45.12 4.85
3310 6478 1.299648 CCCCTTCTGTGATTCGGCA 59.700 57.895 0.00 0.00 0.00 5.69
3340 6508 2.322658 ACCACTCCAAGAAACTACGGA 58.677 47.619 0.00 0.00 0.00 4.69
3341 6509 2.904434 ACCACTCCAAGAAACTACGGAT 59.096 45.455 0.00 0.00 0.00 4.18
3347 6515 6.090898 CACTCCAAGAAACTACGGATTAACTG 59.909 42.308 0.00 0.00 0.00 3.16
3371 6539 3.402110 CACAAGGACACAAGCAGATACA 58.598 45.455 0.00 0.00 0.00 2.29
3373 6541 4.005650 ACAAGGACACAAGCAGATACATG 58.994 43.478 0.00 0.00 0.00 3.21
3418 6594 2.795329 ACCCCACTTCTGCTTTATGTG 58.205 47.619 0.00 0.00 0.00 3.21
3421 6597 3.057315 CCCCACTTCTGCTTTATGTGTTG 60.057 47.826 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.477553 AATTACCACATGCAGCCAGG 58.522 50.000 0.00 0.00 0.00 4.45
61 63 4.141287 ACATGGCTACACTAGTGCAAAAA 58.859 39.130 22.90 6.70 0.00 1.94
62 64 3.750371 ACATGGCTACACTAGTGCAAAA 58.250 40.909 22.90 5.61 0.00 2.44
123 127 1.697982 AGAACCCCAAGTAGACACACC 59.302 52.381 0.00 0.00 0.00 4.16
124 128 2.104281 ACAGAACCCCAAGTAGACACAC 59.896 50.000 0.00 0.00 0.00 3.82
236 240 5.584649 CCAAGCATAAAGAAGATTGACGGTA 59.415 40.000 0.00 0.00 0.00 4.02
240 244 6.913170 TCAACCAAGCATAAAGAAGATTGAC 58.087 36.000 0.00 0.00 0.00 3.18
312 316 4.836825 ACTCATTTCATAGGGTGTGACAG 58.163 43.478 0.00 0.00 0.00 3.51
318 322 9.123902 TGATAATCAAACTCATTTCATAGGGTG 57.876 33.333 0.00 0.00 0.00 4.61
377 381 7.804843 ATTGCAAATTTCCTTCATGTTTCAA 57.195 28.000 1.71 0.00 0.00 2.69
379 383 9.977762 GATTATTGCAAATTTCCTTCATGTTTC 57.022 29.630 1.71 0.00 0.00 2.78
453 457 8.970859 ATTTATCCTACTTTGTCATCCTCAAG 57.029 34.615 0.00 0.00 0.00 3.02
485 489 9.657419 CAAAGTTATAATCTCTTTTGGCCAAAT 57.343 29.630 30.78 17.40 30.41 2.32
486 490 8.646900 ACAAAGTTATAATCTCTTTTGGCCAAA 58.353 29.630 27.13 27.13 30.41 3.28
1257 2943 1.153349 GAAGACGGAGATGGCACCC 60.153 63.158 0.00 0.00 0.00 4.61
1337 3023 1.076192 AGCGGTAGTGGGAGGTAGG 60.076 63.158 0.00 0.00 0.00 3.18
1349 3035 2.547211 GCGATTGTACTAGAGAGCGGTA 59.453 50.000 0.00 0.00 0.00 4.02
1359 3045 4.202182 GGAATGTAGGGTGCGATTGTACTA 60.202 45.833 0.88 0.00 0.00 1.82
1479 3165 2.898738 CTCACCATCCTCAGCGCT 59.101 61.111 2.64 2.64 0.00 5.92
1733 3424 6.040391 TGCTATTGTAAAACAACTGCCTTTCT 59.960 34.615 12.90 0.00 41.40 2.52
1781 3472 8.777413 CGCTATTCCTTGAGAATTCATTCATAA 58.223 33.333 8.44 0.35 42.86 1.90
1804 3495 8.988934 TCAGAATTAATCTTTATTAATCGCGCT 58.011 29.630 5.56 0.00 44.09 5.92
1805 3496 9.594038 TTCAGAATTAATCTTTATTAATCGCGC 57.406 29.630 0.00 0.00 44.09 6.86
2030 3738 6.945435 TCCTGTAATTCATTTTCCAGCACTAA 59.055 34.615 0.00 0.00 0.00 2.24
2075 3783 1.215673 TGGTAAACCCTGCCTTTCACA 59.784 47.619 0.00 0.00 34.29 3.58
2082 3790 8.520351 GTTATAATTCATATGGTAAACCCTGCC 58.480 37.037 2.13 0.00 34.29 4.85
2134 3842 8.566008 AGAAAAACAAAAACAGATTCGATCAG 57.434 30.769 0.00 0.00 0.00 2.90
2135 3843 8.925161 AAGAAAAACAAAAACAGATTCGATCA 57.075 26.923 0.00 0.00 0.00 2.92
2136 3844 9.019764 TGAAGAAAAACAAAAACAGATTCGATC 57.980 29.630 0.00 0.00 0.00 3.69
2137 3845 8.925161 TGAAGAAAAACAAAAACAGATTCGAT 57.075 26.923 0.00 0.00 0.00 3.59
2138 3846 7.487829 CCTGAAGAAAAACAAAAACAGATTCGA 59.512 33.333 0.00 0.00 0.00 3.71
2222 3930 7.341805 ACAGGATAACAAGCAATACAGAGAAT 58.658 34.615 0.00 0.00 0.00 2.40
2247 3956 9.769093 GCAATTTTCTTTTAATTAGACTCGCTA 57.231 29.630 0.00 0.00 0.00 4.26
2398 4108 2.222886 TCTACGGATGAGCTGCTAGTC 58.777 52.381 0.15 3.54 0.00 2.59
2399 4109 2.158740 TCTCTACGGATGAGCTGCTAGT 60.159 50.000 0.15 0.90 0.00 2.57
2477 4187 3.699538 TGCAAGTCACTACTGTCCGATAT 59.300 43.478 0.00 0.00 35.62 1.63
2506 4216 6.037172 CCGATGAGTTTTTATTCTTGTCCGAT 59.963 38.462 0.00 0.00 0.00 4.18
2517 4227 7.721286 CTCAGCTATTCCGATGAGTTTTTAT 57.279 36.000 0.00 0.00 41.27 1.40
2533 4243 2.141517 GCATTGCATCGACTCAGCTAT 58.858 47.619 3.15 0.00 0.00 2.97
2596 4306 3.459232 TGAGAATAATGGCTCCTCACG 57.541 47.619 0.00 0.00 0.00 4.35
2639 4349 7.496529 TTCATTAGCATAGTATTTGCACTCC 57.503 36.000 0.00 0.00 42.62 3.85
2650 4360 9.971922 GCCTAATTGAAATTTCATTAGCATAGT 57.028 29.630 25.69 14.00 37.00 2.12
2732 4442 1.267806 GCCGATGGCTATTCATTGTGG 59.732 52.381 0.00 0.00 46.69 4.17
2733 4443 2.693797 GCCGATGGCTATTCATTGTG 57.306 50.000 0.00 0.00 46.69 3.33
2792 4502 4.088648 GTGAGGAAATGCGATTAACGTTG 58.911 43.478 11.99 0.00 44.60 4.10
2861 4571 0.668401 GGCATCAAACCAAGCAGCAC 60.668 55.000 0.00 0.00 0.00 4.40
2895 4605 7.384660 TGTCAAATGTTGTCTTGCCAATTATTC 59.615 33.333 0.00 0.00 0.00 1.75
3040 4751 2.769095 ACCAAAAAGCACTTGCCCTTTA 59.231 40.909 0.00 0.00 43.38 1.85
3110 4821 9.405587 CTAGAGATTCTTTAGAGCTTATTTCCG 57.594 37.037 5.50 0.00 0.00 4.30
3290 6458 1.452108 CCGAATCACAGAAGGGGGC 60.452 63.158 0.00 0.00 0.00 5.80
3291 6459 1.452108 GCCGAATCACAGAAGGGGG 60.452 63.158 0.00 0.00 0.00 5.40
3310 6478 1.075536 CTTGGAGTGGTTTAGCCCCTT 59.924 52.381 0.00 0.00 36.04 3.95
3340 6508 2.158534 TGTGTCCTTGTGCCCAGTTAAT 60.159 45.455 0.00 0.00 0.00 1.40
3341 6509 1.213182 TGTGTCCTTGTGCCCAGTTAA 59.787 47.619 0.00 0.00 0.00 2.01
3347 6515 1.799258 CTGCTTGTGTCCTTGTGCCC 61.799 60.000 0.00 0.00 0.00 5.36
3371 6539 2.034066 CCGGTGCCCTGAACACAT 59.966 61.111 0.00 0.00 39.87 3.21
3373 6541 2.358737 CTCCGGTGCCCTGAACAC 60.359 66.667 0.00 0.00 37.31 3.32
3400 6576 3.820467 TCAACACATAAAGCAGAAGTGGG 59.180 43.478 0.00 0.00 34.65 4.61
3402 6578 4.756642 TCCTCAACACATAAAGCAGAAGTG 59.243 41.667 0.00 0.00 36.34 3.16
3406 6582 4.019411 TCCATCCTCAACACATAAAGCAGA 60.019 41.667 0.00 0.00 0.00 4.26
3407 6583 4.264253 TCCATCCTCAACACATAAAGCAG 58.736 43.478 0.00 0.00 0.00 4.24
3418 6594 5.300752 ACGATGTTATCATCCATCCTCAAC 58.699 41.667 7.97 0.00 45.32 3.18
3421 6597 6.634805 ACATACGATGTTATCATCCATCCTC 58.365 40.000 7.97 0.00 45.32 3.71
3442 6618 5.078411 AGCTCATCTCGAGTTTGTAACAT 57.922 39.130 13.13 0.00 44.33 2.71


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

AutoCloner maintained by Alex Coulton.