Multiple sequence alignment - TraesCS2D01G231600

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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 TraesCS2D01G231600 chr2D 100.000 3318 0 0 1 3318 203453574 203450257 0.000000e+00 6128
1 TraesCS2D01G231600 chr2D 88.506 174 18 2 1259 1431 32763259 32763431 3.350000e-50 209
2 TraesCS2D01G231600 chr2B 94.030 3350 93 42 4 3318 257525463 257522186 0.000000e+00 4979
3 TraesCS2D01G231600 chr2B 87.356 174 20 2 1259 1431 54440327 54440499 7.260000e-47 198
4 TraesCS2D01G231600 chr2A 96.538 2282 53 11 1044 3318 232371213 232368951 0.000000e+00 3753
5 TraesCS2D01G231600 chr2A 91.493 623 11 16 373 966 232372373 232371764 0.000000e+00 819
6 TraesCS2D01G231600 chr2A 89.571 163 15 2 1270 1431 35976015 35976176 4.340000e-49 206
7 TraesCS2D01G231600 chr5B 89.714 175 15 1 1262 1433 112194704 112194530 1.550000e-53 220
8 TraesCS2D01G231600 chr5D 89.143 175 16 1 1262 1433 103175946 103175772 7.210000e-52 215
9 TraesCS2D01G231600 chr5A 89.143 175 16 1 1262 1433 95869236 95869410 7.210000e-52 215
10 TraesCS2D01G231600 chr7D 84.444 180 24 4 1251 1427 174992593 174992771 1.220000e-39 174


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 TraesCS2D01G231600 chr2D 203450257 203453574 3317 True 6128 6128 100.0000 1 3318 1 chr2D.!!$R1 3317
1 TraesCS2D01G231600 chr2B 257522186 257525463 3277 True 4979 4979 94.0300 4 3318 1 chr2B.!!$R1 3314
2 TraesCS2D01G231600 chr2A 232368951 232372373 3422 True 2286 3753 94.0155 373 3318 2 chr2A.!!$R1 2945

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
990 1045 0.027696 TCCTCCCCATCCCATTCCAT 60.028 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2545 3101 0.029834 CACTTGCTTGCGTGCTTCTT 59.97 50.0 2.56 0.0 0.0 2.52 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
57 58 4.468643 GCGAAACCTATGAGAGATAGTCG 58.531 47.826 0.00 0.00 0.00 4.18
89 90 0.322456 TCAACAGATTTGGAGGGCGG 60.322 55.000 0.00 0.00 0.00 6.13
139 140 7.999679 TGAGGCTTCATATTTCTTGTTTATGG 58.000 34.615 0.00 0.00 0.00 2.74
142 143 5.687285 GCTTCATATTTCTTGTTTATGGGCG 59.313 40.000 0.00 0.00 0.00 6.13
154 155 7.774157 TCTTGTTTATGGGCGGTTGTAATATAA 59.226 33.333 0.00 0.00 0.00 0.98
157 158 3.211718 TGGGCGGTTGTAATATAACCC 57.788 47.619 12.37 6.21 43.67 4.11
175 176 1.617947 CCGCCTAGTCTTTGCCCTCT 61.618 60.000 0.00 0.00 0.00 3.69
179 180 1.909302 CCTAGTCTTTGCCCTCTTGGA 59.091 52.381 0.00 0.00 35.39 3.53
184 185 2.959030 GTCTTTGCCCTCTTGGACTTTT 59.041 45.455 0.00 0.00 35.39 2.27
275 276 2.088950 ATGCAAATGCCTGTGCTTTC 57.911 45.000 5.70 0.00 41.48 2.62
294 295 5.163612 GCTTTCAGCCCTATTTCGAAAAGAT 60.164 40.000 15.66 0.77 34.48 2.40
310 311 0.984230 AGATGAAAGAAGTCCGCCCA 59.016 50.000 0.00 0.00 0.00 5.36
316 317 2.067365 AAGAAGTCCGCCCAAAAACT 57.933 45.000 0.00 0.00 0.00 2.66
352 353 5.990408 GCACATATACAAATAGACAGTGCC 58.010 41.667 0.00 0.00 42.74 5.01
374 375 4.142093 CCCCAGTCAATTCAAAGGCAATAG 60.142 45.833 0.00 0.00 0.00 1.73
393 394 6.417044 GCAATAGCATCAATCAGAATGACAAC 59.583 38.462 0.00 0.00 45.50 3.32
502 531 8.665175 CTTTTACAATACAAAGCTCAGATGTG 57.335 34.615 0.00 0.00 0.00 3.21
503 532 7.744087 TTTACAATACAAAGCTCAGATGTGT 57.256 32.000 0.00 0.00 0.00 3.72
504 533 7.744087 TTACAATACAAAGCTCAGATGTGTT 57.256 32.000 0.00 0.00 0.00 3.32
505 534 6.246420 ACAATACAAAGCTCAGATGTGTTC 57.754 37.500 0.00 0.00 0.00 3.18
506 535 5.764686 ACAATACAAAGCTCAGATGTGTTCA 59.235 36.000 0.00 0.00 0.00 3.18
507 536 6.262944 ACAATACAAAGCTCAGATGTGTTCAA 59.737 34.615 0.00 0.00 0.00 2.69
508 537 6.882610 ATACAAAGCTCAGATGTGTTCAAA 57.117 33.333 0.00 0.00 0.00 2.69
509 538 5.581126 ACAAAGCTCAGATGTGTTCAAAA 57.419 34.783 0.00 0.00 0.00 2.44
510 539 5.964758 ACAAAGCTCAGATGTGTTCAAAAA 58.035 33.333 0.00 0.00 0.00 1.94
511 540 6.038356 ACAAAGCTCAGATGTGTTCAAAAAG 58.962 36.000 0.00 0.00 0.00 2.27
512 541 5.841957 AAGCTCAGATGTGTTCAAAAAGT 57.158 34.783 0.00 0.00 0.00 2.66
513 542 6.942532 AAGCTCAGATGTGTTCAAAAAGTA 57.057 33.333 0.00 0.00 0.00 2.24
514 543 6.942532 AGCTCAGATGTGTTCAAAAAGTAA 57.057 33.333 0.00 0.00 0.00 2.24
515 544 7.333528 AGCTCAGATGTGTTCAAAAAGTAAA 57.666 32.000 0.00 0.00 0.00 2.01
516 545 7.771183 AGCTCAGATGTGTTCAAAAAGTAAAA 58.229 30.769 0.00 0.00 0.00 1.52
517 546 8.250332 AGCTCAGATGTGTTCAAAAAGTAAAAA 58.750 29.630 0.00 0.00 0.00 1.94
812 867 3.552294 GCTACTAATCTTGCCTTGTCGTC 59.448 47.826 0.00 0.00 0.00 4.20
838 893 2.665000 CGGAGCTGCAAGGAAGGA 59.335 61.111 5.91 0.00 0.00 3.36
839 894 1.003355 CGGAGCTGCAAGGAAGGAA 60.003 57.895 5.91 0.00 0.00 3.36
840 895 1.023513 CGGAGCTGCAAGGAAGGAAG 61.024 60.000 5.91 0.00 0.00 3.46
841 896 0.679321 GGAGCTGCAAGGAAGGAAGG 60.679 60.000 0.00 0.00 0.00 3.46
989 1044 0.698886 CTCCTCCCCATCCCATTCCA 60.699 60.000 0.00 0.00 0.00 3.53
990 1045 0.027696 TCCTCCCCATCCCATTCCAT 60.028 55.000 0.00 0.00 0.00 3.41
991 1046 0.862554 CCTCCCCATCCCATTCCATT 59.137 55.000 0.00 0.00 0.00 3.16
993 1048 0.859760 TCCCCATCCCATTCCATTCC 59.140 55.000 0.00 0.00 0.00 3.01
995 1050 0.562177 CCCATCCCATTCCATTCCCA 59.438 55.000 0.00 0.00 0.00 4.37
996 1051 1.708341 CCATCCCATTCCATTCCCAC 58.292 55.000 0.00 0.00 0.00 4.61
997 1052 1.708341 CATCCCATTCCATTCCCACC 58.292 55.000 0.00 0.00 0.00 4.61
998 1053 1.218704 CATCCCATTCCATTCCCACCT 59.781 52.381 0.00 0.00 0.00 4.00
1000 1055 0.106015 CCCATTCCATTCCCACCTCC 60.106 60.000 0.00 0.00 0.00 4.30
1001 1056 0.466189 CCATTCCATTCCCACCTCCG 60.466 60.000 0.00 0.00 0.00 4.63
1002 1057 0.255890 CATTCCATTCCCACCTCCGT 59.744 55.000 0.00 0.00 0.00 4.69
1003 1058 0.546598 ATTCCATTCCCACCTCCGTC 59.453 55.000 0.00 0.00 0.00 4.79
1004 1059 1.559065 TTCCATTCCCACCTCCGTCC 61.559 60.000 0.00 0.00 0.00 4.79
1005 1060 2.186903 CATTCCCACCTCCGTCCG 59.813 66.667 0.00 0.00 0.00 4.79
1454 2000 2.285368 AGCAACGGATCAGGGGGA 60.285 61.111 0.00 0.00 0.00 4.81
1886 2432 0.035725 TGGAGGAGCTGCATGTGAAG 60.036 55.000 8.35 0.00 0.00 3.02
1919 2465 4.722700 GGCGAGCACCACCACCAT 62.723 66.667 0.00 0.00 0.00 3.55
2277 2826 5.772672 TCGATTTTTCTCCTCCATTTTTCCA 59.227 36.000 0.00 0.00 0.00 3.53
2374 2925 3.307410 GCTAGAGAGGGAGATGATCTCGA 60.307 52.174 15.64 0.00 44.28 4.04
2422 2973 8.670521 AGATCCAAAAAGAATCATAGGGTTTT 57.329 30.769 0.00 0.00 0.00 2.43
2544 3100 0.528684 GATCAACGCGGAGAAGAGGG 60.529 60.000 12.47 0.00 0.00 4.30
2545 3101 0.970937 ATCAACGCGGAGAAGAGGGA 60.971 55.000 12.47 0.00 0.00 4.20
2546 3102 1.183030 TCAACGCGGAGAAGAGGGAA 61.183 55.000 12.47 0.00 0.00 3.97
2727 3286 3.102972 TGCAAGTAATGAGCCTCTCTCT 58.897 45.455 0.00 0.00 42.38 3.10
2728 3287 3.131933 TGCAAGTAATGAGCCTCTCTCTC 59.868 47.826 0.00 0.00 42.38 3.20
2809 3370 2.010145 TGCCAACTCTCGTTAGATGC 57.990 50.000 0.00 0.00 0.00 3.91
2811 3372 1.661112 GCCAACTCTCGTTAGATGCAC 59.339 52.381 0.00 0.00 0.00 4.57
2953 3516 8.469309 AGAGTGGATTTCTTTCATTTTCTTGA 57.531 30.769 0.00 0.00 0.00 3.02
3071 3634 5.925509 AGTCCCCATATATGTGTGTGTAAC 58.074 41.667 11.73 0.00 37.35 2.50
3139 3702 6.824305 ATAGTTGCTTCACTTTTAGTGCAT 57.176 33.333 1.98 0.00 45.54 3.96
3140 3703 4.863491 AGTTGCTTCACTTTTAGTGCATG 58.137 39.130 1.98 0.00 45.54 4.06
3216 3779 2.435059 GCGCTCCCTCTTGTGGAC 60.435 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.121506 TGGAAGCCCAACCCCTCT 60.122 61.111 0.00 0.00 40.09 3.69
20 21 1.180456 TTCGCCTACAGACCGTGGAA 61.180 55.000 0.00 0.00 0.00 3.53
82 83 2.185387 TCCTATTATTAGGCCGCCCTC 58.815 52.381 5.55 0.00 44.20 4.30
89 90 6.338146 TGCGTCACATATCCTATTATTAGGC 58.662 40.000 5.90 0.00 44.20 3.93
139 140 1.532437 GCGGGTTATATTACAACCGCC 59.468 52.381 18.13 6.02 45.38 6.13
142 143 5.011431 AGACTAGGCGGGTTATATTACAACC 59.989 44.000 0.00 0.00 43.99 3.77
154 155 2.669240 GGCAAAGACTAGGCGGGT 59.331 61.111 0.00 0.00 0.00 5.28
157 158 0.250513 AAGAGGGCAAAGACTAGGCG 59.749 55.000 0.00 0.00 0.00 5.52
275 276 5.818136 TTCATCTTTTCGAAATAGGGCTG 57.182 39.130 12.12 10.17 0.00 4.85
294 295 2.060050 TTTTGGGCGGACTTCTTTCA 57.940 45.000 0.00 0.00 0.00 2.69
310 311 2.430332 TGCTGCACTTTGCCTAGTTTTT 59.570 40.909 0.00 0.00 44.23 1.94
316 317 2.488204 TATGTGCTGCACTTTGCCTA 57.512 45.000 30.43 11.42 44.23 3.93
324 325 6.258727 ACTGTCTATTTGTATATGTGCTGCAC 59.741 38.462 25.15 25.15 34.56 4.57
325 326 6.258507 CACTGTCTATTTGTATATGTGCTGCA 59.741 38.462 0.00 0.00 0.00 4.41
352 353 3.967332 ATTGCCTTTGAATTGACTGGG 57.033 42.857 0.00 0.00 0.00 4.45
374 375 5.463286 TGTTGTTGTCATTCTGATTGATGC 58.537 37.500 5.63 1.46 0.00 3.91
393 394 3.304659 GCTATGTGTGGGAGTTGTTGTTG 60.305 47.826 0.00 0.00 0.00 3.33
514 543 4.406456 TGTGGTGCCATATCTGAGTTTTT 58.594 39.130 0.00 0.00 0.00 1.94
515 544 4.032960 TGTGGTGCCATATCTGAGTTTT 57.967 40.909 0.00 0.00 0.00 2.43
516 545 3.719268 TGTGGTGCCATATCTGAGTTT 57.281 42.857 0.00 0.00 0.00 2.66
517 546 3.548770 CATGTGGTGCCATATCTGAGTT 58.451 45.455 0.00 0.00 0.00 3.01
518 547 3.204306 CATGTGGTGCCATATCTGAGT 57.796 47.619 0.00 0.00 0.00 3.41
593 624 3.951663 AGATGGTTAGGTTTCGAAAGGG 58.048 45.455 11.66 0.00 0.00 3.95
677 728 0.870307 CCCGCGCACATACTACAGTC 60.870 60.000 8.75 0.00 0.00 3.51
834 889 3.005529 TCCTTCCTTCCTTCCTTCCTT 57.994 47.619 0.00 0.00 0.00 3.36
835 890 2.743131 TCCTTCCTTCCTTCCTTCCT 57.257 50.000 0.00 0.00 0.00 3.36
837 892 3.073209 ACACTTCCTTCCTTCCTTCCTTC 59.927 47.826 0.00 0.00 0.00 3.46
838 893 3.056832 ACACTTCCTTCCTTCCTTCCTT 58.943 45.455 0.00 0.00 0.00 3.36
839 894 2.373502 CACACTTCCTTCCTTCCTTCCT 59.626 50.000 0.00 0.00 0.00 3.36
840 895 2.553247 CCACACTTCCTTCCTTCCTTCC 60.553 54.545 0.00 0.00 0.00 3.46
841 896 2.106684 ACCACACTTCCTTCCTTCCTTC 59.893 50.000 0.00 0.00 0.00 3.46
989 1044 2.284405 ACGGACGGAGGTGGGAAT 60.284 61.111 0.00 0.00 0.00 3.01
990 1045 2.993264 GACGGACGGAGGTGGGAA 60.993 66.667 0.00 0.00 0.00 3.97
993 1048 3.122250 GATCGACGGACGGAGGTGG 62.122 68.421 0.00 0.00 42.82 4.61
995 1050 2.937379 ATCGATCGACGGACGGAGGT 62.937 60.000 22.06 0.00 42.82 3.85
996 1051 2.172719 GATCGATCGACGGACGGAGG 62.173 65.000 22.06 0.00 42.82 4.30
997 1052 1.204563 GATCGATCGACGGACGGAG 59.795 63.158 22.06 0.00 42.82 4.63
998 1053 1.496403 CTGATCGATCGACGGACGGA 61.496 60.000 22.06 0.00 42.82 4.69
1000 1055 0.383246 GACTGATCGATCGACGGACG 60.383 60.000 22.06 9.79 42.82 4.79
1001 1056 0.938713 AGACTGATCGATCGACGGAC 59.061 55.000 22.06 17.71 42.82 4.79
1002 1057 1.664873 AAGACTGATCGATCGACGGA 58.335 50.000 22.06 6.16 42.82 4.69
1003 1058 2.376956 GAAAGACTGATCGATCGACGG 58.623 52.381 22.06 19.96 42.82 4.79
1004 1059 2.032302 AGGAAAGACTGATCGATCGACG 59.968 50.000 22.06 14.12 44.09 5.12
1005 1060 3.367607 CAGGAAAGACTGATCGATCGAC 58.632 50.000 22.06 14.65 40.97 4.20
1093 1621 3.299190 GATCTCCTCCTCCGCCCG 61.299 72.222 0.00 0.00 0.00 6.13
1472 2018 2.599281 TTGGAGGAGGCGACGACA 60.599 61.111 2.19 0.00 0.00 4.35
1509 2055 0.248539 GACATGGAGGTAGACGACGC 60.249 60.000 0.00 0.00 0.00 5.19
1919 2465 1.671742 GGTCGCCTTCTTCTGGTGA 59.328 57.895 0.00 0.00 41.23 4.02
1972 2521 0.845591 GACGTTAGACGACGACGACG 60.846 60.000 17.60 17.60 46.05 5.12
1973 2522 2.891247 GACGTTAGACGACGACGAC 58.109 57.895 15.32 8.08 46.05 4.34
2333 2884 3.839778 AGCTACCCAGAGTATTCTCTCC 58.160 50.000 0.00 0.00 46.84 3.71
2374 2925 1.001406 CTGCTTTCTGACCTCCGACTT 59.999 52.381 0.00 0.00 0.00 3.01
2422 2973 1.548719 TCTCCATCGGCGAAAGAGAAA 59.451 47.619 28.92 14.97 30.88 2.52
2544 3100 0.308993 ACTTGCTTGCGTGCTTCTTC 59.691 50.000 2.56 0.00 0.00 2.87
2545 3101 0.029834 CACTTGCTTGCGTGCTTCTT 59.970 50.000 2.56 0.00 0.00 2.52
2546 3102 1.097547 ACACTTGCTTGCGTGCTTCT 61.098 50.000 2.56 0.00 34.58 2.85
2727 3286 6.252599 AGATGAGAGAGAAAGCTAGAGAGA 57.747 41.667 0.00 0.00 0.00 3.10
2728 3287 6.238842 CCAAGATGAGAGAGAAAGCTAGAGAG 60.239 46.154 0.00 0.00 0.00 3.20
2809 3370 7.201893 GGGGAGGAGTACTAGTATTAACTTGTG 60.202 44.444 5.75 0.00 41.04 3.33
2811 3372 7.014422 CAGGGGAGGAGTACTAGTATTAACTTG 59.986 44.444 5.75 0.00 37.15 3.16
2960 3523 6.982852 TGGTACAACAGAGTTTGAACAAAAA 58.017 32.000 1.47 0.00 31.92 1.94
3071 3634 8.466086 TGCGTGCATATAGTATTCATTCTTAG 57.534 34.615 0.00 0.00 0.00 2.18
3139 3702 4.074259 CAAAAGTGAGACATCCATCCACA 58.926 43.478 0.00 0.00 0.00 4.17
3140 3703 3.441572 CCAAAAGTGAGACATCCATCCAC 59.558 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.