Multiple sequence alignment - TraesCS7A01G320800

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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 TraesCS7A01G320800 chr7A 100.000 2877 0 0 969 3845 462984511 462987387 0.000000e+00 5313
1 TraesCS7A01G320800 chr7A 100.000 581 0 0 1 581 462983543 462984123 0.000000e+00 1074
2 TraesCS7A01G320800 chr7B 94.829 2901 95 34 988 3842 413579168 413582059 0.000000e+00 4475
3 TraesCS7A01G320800 chr7B 84.095 591 44 18 1 579 413578435 413578987 3.400000e-145 525
4 TraesCS7A01G320800 chr7D 94.762 2883 85 20 988 3842 404062504 404065348 0.000000e+00 4427
5 TraesCS7A01G320800 chr7D 87.306 386 18 10 194 579 404061955 404062309 2.760000e-111 412
6 TraesCS7A01G320800 chr7D 90.385 156 10 4 2 152 404061791 404061946 2.340000e-47 200
7 TraesCS7A01G320800 chr3D 78.988 257 45 7 1330 1580 496406624 496406371 2.380000e-37 167
8 TraesCS7A01G320800 chr3B 76.562 256 53 5 1330 1580 655422580 655422327 2.410000e-27 134
9 TraesCS7A01G320800 chr1A 94.366 71 4 0 3547 3617 432732279 432732349 4.060000e-20 110


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 TraesCS7A01G320800 chr7A 462983543 462987387 3844 False 3193.500000 5313 100.000000 1 3845 2 chr7A.!!$F1 3844
1 TraesCS7A01G320800 chr7B 413578435 413582059 3624 False 2500.000000 4475 89.462000 1 3842 2 chr7B.!!$F1 3841
2 TraesCS7A01G320800 chr7D 404061791 404065348 3557 False 1679.666667 4427 90.817667 2 3842 3 chr7D.!!$F1 3840

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
66 67 0.031178 GTCCGACACACCAAGTACGT 59.969 55.000 0.00 0.0 0.0 3.57 F
376 396 0.099791 CTCGAGTCGCTTCTTCCTCC 59.900 60.000 7.92 0.0 0.0 4.30 F
497 517 0.969409 AAGGAAGATTGCCAGCCAGC 60.969 55.000 0.00 0.0 0.0 4.85 F
1512 1551 1.285667 TCCGTCTACCTCCACACCATA 59.714 52.381 0.00 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1551 0.038526 CGTTGAGCTTGTAGTCCGGT 60.039 55.000 0.00 0.0 0.00 5.28 R
1685 1761 1.000385 TCAGCCACAAATTTTCCGCAG 60.000 47.619 0.00 0.0 0.00 5.18 R
2052 2135 1.202891 AGGTTGACACTTTAGCCCCAC 60.203 52.381 0.00 0.0 0.00 4.61 R
3313 3418 1.001020 CCACCAATGGCAGGCTGTA 60.001 57.895 17.16 6.2 39.82 2.74 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
65 66 1.000233 CGTCCGACACACCAAGTACG 61.000 60.000 0.00 0.00 0.00 3.67
66 67 0.031178 GTCCGACACACCAAGTACGT 59.969 55.000 0.00 0.00 0.00 3.57
67 68 0.746063 TCCGACACACCAAGTACGTT 59.254 50.000 0.00 0.00 0.00 3.99
149 154 6.980577 TCTTCCCACCCAAATCAATTACTAT 58.019 36.000 0.00 0.00 0.00 2.12
150 155 7.418378 TCTTCCCACCCAAATCAATTACTATT 58.582 34.615 0.00 0.00 0.00 1.73
151 156 8.561769 TCTTCCCACCCAAATCAATTACTATTA 58.438 33.333 0.00 0.00 0.00 0.98
152 157 9.196139 CTTCCCACCCAAATCAATTACTATTAA 57.804 33.333 0.00 0.00 0.00 1.40
153 158 8.760980 TCCCACCCAAATCAATTACTATTAAG 57.239 34.615 0.00 0.00 0.00 1.85
154 159 8.340757 TCCCACCCAAATCAATTACTATTAAGT 58.659 33.333 0.00 0.00 39.91 2.24
191 205 7.968405 CGGTTTCAGTCATTTATTTTTAGGAGG 59.032 37.037 0.00 0.00 0.00 4.30
192 206 8.251026 GGTTTCAGTCATTTATTTTTAGGAGGG 58.749 37.037 0.00 0.00 0.00 4.30
193 207 9.020731 GTTTCAGTCATTTATTTTTAGGAGGGA 57.979 33.333 0.00 0.00 0.00 4.20
194 208 8.807948 TTCAGTCATTTATTTTTAGGAGGGAG 57.192 34.615 0.00 0.00 0.00 4.30
293 307 1.135632 CGACCACTCGGAGAAGAAGAC 60.136 57.143 12.86 0.00 36.16 3.01
301 315 0.179158 GGAGAAGAAGACGACGAGGC 60.179 60.000 0.00 0.00 0.00 4.70
333 347 2.225117 GCCAGCTCCCATAAATACCCAT 60.225 50.000 0.00 0.00 0.00 4.00
357 377 3.507009 CTCCGTCCCCGACTCGAC 61.507 72.222 0.00 0.00 35.63 4.20
374 394 0.806241 GACTCGAGTCGCTTCTTCCT 59.194 55.000 28.46 0.00 35.12 3.36
375 395 0.806241 ACTCGAGTCGCTTCTTCCTC 59.194 55.000 13.58 0.00 0.00 3.71
376 396 0.099791 CTCGAGTCGCTTCTTCCTCC 59.900 60.000 7.92 0.00 0.00 4.30
377 397 1.139947 CGAGTCGCTTCTTCCTCCC 59.860 63.158 0.00 0.00 0.00 4.30
454 474 1.939082 TTCCTCCTCCTCCTCCTCCG 61.939 65.000 0.00 0.00 0.00 4.63
455 475 2.520741 CTCCTCCTCCTCCTCCGC 60.521 72.222 0.00 0.00 0.00 5.54
456 476 4.144727 TCCTCCTCCTCCTCCGCC 62.145 72.222 0.00 0.00 0.00 6.13
474 494 3.404899 CGCCTTACCCACTAAGAAACAA 58.595 45.455 0.00 0.00 34.69 2.83
481 501 7.255486 CCTTACCCACTAAGAAACAAAGAAAGG 60.255 40.741 0.00 0.00 34.69 3.11
493 513 3.006217 ACAAAGAAAGGAAGATTGCCAGC 59.994 43.478 0.00 0.00 0.00 4.85
494 514 1.844687 AGAAAGGAAGATTGCCAGCC 58.155 50.000 0.00 0.00 0.00 4.85
495 515 1.076024 AGAAAGGAAGATTGCCAGCCA 59.924 47.619 0.00 0.00 0.00 4.75
496 516 1.475682 GAAAGGAAGATTGCCAGCCAG 59.524 52.381 0.00 0.00 0.00 4.85
497 517 0.969409 AAGGAAGATTGCCAGCCAGC 60.969 55.000 0.00 0.00 0.00 4.85
498 518 2.421399 GGAAGATTGCCAGCCAGCC 61.421 63.158 0.00 0.00 0.00 4.85
499 519 2.363406 AAGATTGCCAGCCAGCCC 60.363 61.111 0.00 0.00 0.00 5.19
500 520 3.970746 AAGATTGCCAGCCAGCCCC 62.971 63.158 0.00 0.00 0.00 5.80
526 546 1.376037 CCTCCTCCTTGCCGTGTTC 60.376 63.158 0.00 0.00 0.00 3.18
1512 1551 1.285667 TCCGTCTACCTCCACACCATA 59.714 52.381 0.00 0.00 0.00 2.74
1593 1632 6.071896 CCAGCGAGGTACTATAATCAATCTCA 60.072 42.308 0.00 0.00 41.55 3.27
1610 1653 7.158021 TCAATCTCAAGTCTCTTCTTTTCCTC 58.842 38.462 0.00 0.00 0.00 3.71
1640 1716 3.469739 ACCTTAATGAAACGAACCGTGT 58.530 40.909 0.00 0.00 39.99 4.49
1654 1730 5.086058 CGAACCGTGTAAAAATCAGATTGG 58.914 41.667 0.00 0.00 0.00 3.16
1668 1744 8.918202 AAATCAGATTGGTAGTTAGTTGAACA 57.082 30.769 0.00 0.00 40.86 3.18
1734 1817 1.841302 TAGCTGGTGCCTTGGTGGAG 61.841 60.000 0.00 0.00 40.80 3.86
1845 1928 2.290577 CCTCTAGGGGAATATGCTTGCC 60.291 54.545 0.73 0.00 0.00 4.52
1959 2042 9.823098 GATGCTTAATCTACAATATTCTGCTTG 57.177 33.333 0.00 0.00 32.01 4.01
1993 2076 9.613428 CCACTAAATAATTAGTCAAGGATGTCA 57.387 33.333 0.00 0.00 46.97 3.58
2045 2128 9.600646 GTACTCTGCTTTTCTTCTTTTATGTTC 57.399 33.333 0.00 0.00 0.00 3.18
2091 2174 3.742882 ACCTCAAATATCGATGCGATGTG 59.257 43.478 8.54 0.00 46.43 3.21
2220 2303 0.905357 AGGAAGTGTCTTGGGGATCG 59.095 55.000 0.00 0.00 0.00 3.69
2232 2315 0.396811 GGGGATCGATAACCCTGGTG 59.603 60.000 23.84 0.00 44.97 4.17
2293 2376 1.928503 TCTCGAACGAGCGTTTTGTTT 59.071 42.857 17.71 0.00 41.71 2.83
2373 2456 0.179045 ACTCGGAGCACAGCTTTGTT 60.179 50.000 4.58 0.00 39.88 2.83
2568 2651 0.759346 GACCATCTTGCTACCCGGAT 59.241 55.000 0.73 0.00 0.00 4.18
2598 2681 7.834881 TTACATACCGACCTATCTTCATCTT 57.165 36.000 0.00 0.00 0.00 2.40
2661 2744 0.846427 ATTGGTCAAGAGGAGGCCCA 60.846 55.000 0.00 0.00 33.88 5.36
2724 2807 1.909700 TCAAGGCCATCAGGAACAAC 58.090 50.000 5.01 0.00 36.89 3.32
2757 2840 2.329379 CTCTACAACTCGAAGCACACC 58.671 52.381 0.00 0.00 0.00 4.16
2778 2861 1.416030 TCTGTGTGCTACCTCTTTGCA 59.584 47.619 0.00 0.00 0.00 4.08
2832 2915 1.608055 TGAACCTCACTTCGACGGTA 58.392 50.000 0.00 0.00 0.00 4.02
2952 3039 0.826715 TGCTAGCTCAGGGACATGTC 59.173 55.000 17.91 17.91 0.00 3.06
2995 3087 4.379243 CGAGGACGCTTGGCTGGT 62.379 66.667 0.00 0.00 0.00 4.00
3081 3173 1.134818 ACGAATGGCGCTACAAGATCA 60.135 47.619 7.64 0.00 46.04 2.92
3288 3386 1.010797 GCCGCGCACTTGATACATG 60.011 57.895 8.75 0.00 0.00 3.21
3319 3424 2.884639 TCAAAACCTTGAAGCTACAGCC 59.115 45.455 0.00 0.00 38.65 4.85
3454 3559 3.181450 ACTGTCTCCACAAGAAAGGAAGG 60.181 47.826 0.00 0.00 42.92 3.46
3519 3624 4.846779 TGTTGCTACAAATTCTTGGACC 57.153 40.909 0.00 0.00 36.82 4.46
3554 3659 3.466836 TGTACTTGTTTGGCTGTGAGAG 58.533 45.455 0.00 0.00 0.00 3.20
3602 3707 1.398958 AATTGGCCTGTGCGTTTGGT 61.399 50.000 3.32 0.00 38.85 3.67
3691 3796 1.020437 GCTCTTGTCATGCCCTTAGC 58.980 55.000 0.00 0.00 44.14 3.09
3712 3817 6.006275 AGCCAGTGATTACAATAATCCACT 57.994 37.500 6.20 0.00 0.00 4.00
3842 3951 3.132925 GCCTACGTGGTGTTTGTTTAGA 58.867 45.455 0.00 0.00 38.35 2.10
3843 3952 3.560896 GCCTACGTGGTGTTTGTTTAGAA 59.439 43.478 0.00 0.00 38.35 2.10
3844 3953 4.214758 GCCTACGTGGTGTTTGTTTAGAAT 59.785 41.667 0.00 0.00 38.35 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.360956 CGTAAAACGTACTTGGTGTGTCG 60.361 47.826 0.00 0.00 36.74 4.35
59 60 3.552890 GGGGTGACTCGTAAAACGTACTT 60.553 47.826 0.00 0.00 43.14 2.24
149 154 5.553123 TGAAACCGAGCCTGATTAACTTAA 58.447 37.500 0.00 0.00 0.00 1.85
150 155 5.155278 TGAAACCGAGCCTGATTAACTTA 57.845 39.130 0.00 0.00 0.00 2.24
151 156 4.003648 CTGAAACCGAGCCTGATTAACTT 58.996 43.478 0.00 0.00 0.00 2.66
152 157 3.008049 ACTGAAACCGAGCCTGATTAACT 59.992 43.478 0.00 0.00 0.00 2.24
153 158 3.335579 ACTGAAACCGAGCCTGATTAAC 58.664 45.455 0.00 0.00 0.00 2.01
154 159 3.007506 TGACTGAAACCGAGCCTGATTAA 59.992 43.478 0.00 0.00 0.00 1.40
156 161 1.347707 TGACTGAAACCGAGCCTGATT 59.652 47.619 0.00 0.00 0.00 2.57
157 162 0.976641 TGACTGAAACCGAGCCTGAT 59.023 50.000 0.00 0.00 0.00 2.90
159 164 1.813513 AATGACTGAAACCGAGCCTG 58.186 50.000 0.00 0.00 0.00 4.85
161 166 4.965119 AATAAATGACTGAAACCGAGCC 57.035 40.909 0.00 0.00 0.00 4.70
162 167 7.484959 CCTAAAAATAAATGACTGAAACCGAGC 59.515 37.037 0.00 0.00 0.00 5.03
163 168 8.726988 TCCTAAAAATAAATGACTGAAACCGAG 58.273 33.333 0.00 0.00 0.00 4.63
164 169 8.624367 TCCTAAAAATAAATGACTGAAACCGA 57.376 30.769 0.00 0.00 0.00 4.69
165 170 7.968405 CCTCCTAAAAATAAATGACTGAAACCG 59.032 37.037 0.00 0.00 0.00 4.44
166 171 8.251026 CCCTCCTAAAAATAAATGACTGAAACC 58.749 37.037 0.00 0.00 0.00 3.27
193 207 9.442047 GGGTAATTGATCGATCATCTTATTTCT 57.558 33.333 27.75 7.22 36.56 2.52
194 208 8.669243 GGGGTAATTGATCGATCATCTTATTTC 58.331 37.037 27.75 19.59 36.56 2.17
247 261 4.856607 GGCGAGACGAAGAGGCCG 62.857 72.222 0.00 0.00 33.58 6.13
248 262 4.856607 CGGCGAGACGAAGAGGCC 62.857 72.222 0.00 0.00 40.36 5.19
249 263 4.117661 ACGGCGAGACGAAGAGGC 62.118 66.667 16.62 0.00 37.61 4.70
250 264 2.100603 GACGGCGAGACGAAGAGG 59.899 66.667 16.62 0.00 37.61 3.69
251 265 2.100603 GGACGGCGAGACGAAGAG 59.899 66.667 16.62 0.00 37.61 2.85
252 266 3.796443 CGGACGGCGAGACGAAGA 61.796 66.667 16.62 0.00 37.61 2.87
310 324 2.508526 GGTATTTATGGGAGCTGGCTG 58.491 52.381 0.00 0.00 0.00 4.85
357 377 0.099791 GGAGGAAGAAGCGACTCGAG 59.900 60.000 11.84 11.84 0.00 4.04
454 474 5.067954 TCTTTGTTTCTTAGTGGGTAAGGC 58.932 41.667 0.00 0.00 39.03 4.35
455 475 7.255486 CCTTTCTTTGTTTCTTAGTGGGTAAGG 60.255 40.741 0.00 0.00 39.03 2.69
456 476 7.501225 TCCTTTCTTTGTTTCTTAGTGGGTAAG 59.499 37.037 0.00 0.00 39.80 2.34
474 494 2.174360 GGCTGGCAATCTTCCTTTCTT 58.826 47.619 0.00 0.00 0.00 2.52
481 501 2.421399 GGGCTGGCTGGCAATCTTC 61.421 63.158 19.11 0.00 43.83 2.87
499 519 4.806339 AGGAGGAGGGAAGGCGGG 62.806 72.222 0.00 0.00 0.00 6.13
500 520 2.689034 AAGGAGGAGGGAAGGCGG 60.689 66.667 0.00 0.00 0.00 6.13
501 521 2.586792 CAAGGAGGAGGGAAGGCG 59.413 66.667 0.00 0.00 0.00 5.52
502 522 2.273776 GCAAGGAGGAGGGAAGGC 59.726 66.667 0.00 0.00 0.00 4.35
503 523 3.002371 GGCAAGGAGGAGGGAAGG 58.998 66.667 0.00 0.00 0.00 3.46
504 524 2.294078 ACGGCAAGGAGGAGGGAAG 61.294 63.158 0.00 0.00 0.00 3.46
505 525 2.203938 ACGGCAAGGAGGAGGGAA 60.204 61.111 0.00 0.00 0.00 3.97
506 526 3.003173 CACGGCAAGGAGGAGGGA 61.003 66.667 0.00 0.00 0.00 4.20
507 527 2.804828 GAACACGGCAAGGAGGAGGG 62.805 65.000 0.00 0.00 0.00 4.30
1512 1551 0.038526 CGTTGAGCTTGTAGTCCGGT 60.039 55.000 0.00 0.00 0.00 5.28
1610 1653 9.511144 GGTTCGTTTCATTAAGGTAAATTATGG 57.489 33.333 0.00 0.00 0.00 2.74
1668 1744 2.287547 CGCAGGCAACACAACATAGTTT 60.288 45.455 0.00 0.00 41.41 2.66
1685 1761 1.000385 TCAGCCACAAATTTTCCGCAG 60.000 47.619 0.00 0.00 0.00 5.18
1993 2076 9.447157 CACAAATAAACAAATTCCCAACCATAT 57.553 29.630 0.00 0.00 0.00 1.78
2045 2128 5.620206 TGACACTTTAGCCCCACATATATG 58.380 41.667 11.29 11.29 0.00 1.78
2052 2135 1.202891 AGGTTGACACTTTAGCCCCAC 60.203 52.381 0.00 0.00 0.00 4.61
2091 2174 8.076178 ACACTGTTAAATACTGAAAGAATGCAC 58.924 33.333 0.00 0.00 37.43 4.57
2220 2303 1.490490 TCAGCATCCACCAGGGTTATC 59.510 52.381 0.00 0.00 38.11 1.75
2373 2456 2.230508 GGTGTCGATGTTGTAGGACTCA 59.769 50.000 0.00 0.00 0.00 3.41
2505 2588 5.559799 CGAGTAATACTTGTAGTCCGCTACC 60.560 48.000 0.00 0.00 45.24 3.18
2523 2606 2.097036 TGCTTCCGGAAGATCGAGTAA 58.903 47.619 41.64 16.29 40.79 2.24
2568 2651 5.077564 AGATAGGTCGGTATGTAATGCTCA 58.922 41.667 0.00 0.00 0.00 4.26
2598 2681 1.595929 GTTGAGCGACCCGTGGAAA 60.596 57.895 0.00 0.00 0.00 3.13
2661 2744 2.579873 GCACCATATCTTGCTGGATGT 58.420 47.619 0.00 0.00 36.35 3.06
2724 2807 1.226603 GTAGAGGCACTGCGTACCG 60.227 63.158 0.00 0.00 41.55 4.02
2757 2840 2.072298 GCAAAGAGGTAGCACACAGAG 58.928 52.381 0.00 0.00 0.00 3.35
2778 2861 1.986882 CACTGGGAGCAAACTTCCTT 58.013 50.000 0.00 0.00 42.96 3.36
2832 2915 1.168714 GCCGAGCTCAAAAGTCCAAT 58.831 50.000 15.40 0.00 0.00 3.16
2952 3039 6.712095 ACAGCAGTCTCTCATCTATCTAAGAG 59.288 42.308 0.00 0.00 37.74 2.85
2995 3087 2.213513 TCCCACACAGCGTCATCCA 61.214 57.895 0.00 0.00 0.00 3.41
3070 3162 4.727507 TGTCCTCTCTTGATCTTGTAGC 57.272 45.455 0.00 0.00 0.00 3.58
3081 3173 3.009584 GGGAGGTGAAAATGTCCTCTCTT 59.990 47.826 9.74 0.00 43.34 2.85
3163 3255 8.267620 TGACCAAGTCATTACAATAAGTGATG 57.732 34.615 0.00 0.00 43.52 3.07
3225 3318 1.301165 CCAAGCCAAGCCAAGCAAC 60.301 57.895 0.00 0.00 0.00 4.17
3272 3370 1.010797 GCCATGTATCAAGTGCGCG 60.011 57.895 0.00 0.00 0.00 6.86
3313 3418 1.001020 CCACCAATGGCAGGCTGTA 60.001 57.895 17.16 6.20 39.82 2.74
3454 3559 4.271049 GCCTTTCAAAAAGAACCAGCTTTC 59.729 41.667 1.06 0.00 37.12 2.62
3519 3624 6.545504 AACAAGTACAATCTGTAACAGCAG 57.454 37.500 0.00 0.00 34.21 4.24
3554 3659 3.435671 GTCCCCGCAATACTATTATGCAC 59.564 47.826 0.00 0.00 0.00 4.57
3602 3707 4.009675 CCAATCCTAGTTTTGTGCAGCTA 58.990 43.478 0.00 0.00 0.00 3.32
3666 3771 1.154338 GCATGACAAGAGCGTGTGC 60.154 57.895 0.00 0.00 43.24 4.57
3691 3796 5.009010 GCCAGTGGATTATTGTAATCACTGG 59.991 44.000 29.00 29.00 45.65 4.00
3712 3817 6.000246 TGAAATATTCATAGACCTGTGCCA 58.000 37.500 0.00 0.00 34.08 4.92
3737 3842 9.844257 AATCCATAGACTTTCTTCTATTTCAGG 57.156 33.333 0.00 0.00 36.79 3.86
3757 3862 7.541783 CACACATCACACGAAAAATTAATCCAT 59.458 33.333 0.00 0.00 0.00 3.41
3771 3876 1.139989 GGTCAGACACACATCACACG 58.860 55.000 2.17 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.