Multiple sequence alignment - TraesCS3A01G197300

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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 TraesCS3A01G197300 chr3A 100.000 5456 0 0 1 5456 307918454 307912999 0.000000e+00 10076
1 TraesCS3A01G197300 chr3B 96.273 3756 91 14 1733 5456 348490224 348486486 0.000000e+00 6115
2 TraesCS3A01G197300 chr3B 94.658 1142 22 10 615 1735 348491470 348490347 0.000000e+00 1735
3 TraesCS3A01G197300 chr3D 96.762 3582 93 11 1 3572 248813799 248810231 0.000000e+00 5951
4 TraesCS3A01G197300 chr3D 96.144 1919 45 6 3567 5456 248807970 248806052 0.000000e+00 3107
5 TraesCS3A01G197300 chr7B 88.841 690 39 9 4794 5456 357528900 357528222 0.000000e+00 813
6 TraesCS3A01G197300 chr7A 84.527 433 46 13 4933 5353 82508041 82508464 5.090000e-110 409
7 TraesCS3A01G197300 chr4A 82.648 438 45 20 4911 5332 700562456 700562878 5.200000e-95 359
8 TraesCS3A01G197300 chr4A 81.114 413 58 13 4941 5340 700731579 700731984 4.100000e-81 313
9 TraesCS3A01G197300 chr1B 81.988 322 33 16 791 1111 672332985 672333282 3.260000e-62 250
10 TraesCS3A01G197300 chr1B 81.677 322 34 16 791 1111 672685667 672685370 1.520000e-60 244
11 TraesCS3A01G197300 chr2A 87.619 105 13 0 5346 5450 477116208 477116312 7.420000e-24 122
12 TraesCS3A01G197300 chr7D 90.909 88 8 0 4937 5024 29048037 29047950 9.600000e-23 119


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 TraesCS3A01G197300 chr3A 307912999 307918454 5455 True 10076 10076 100.0000 1 5456 1 chr3A.!!$R1 5455
1 TraesCS3A01G197300 chr3B 348486486 348491470 4984 True 3925 6115 95.4655 615 5456 2 chr3B.!!$R1 4841
2 TraesCS3A01G197300 chr3D 248806052 248813799 7747 True 4529 5951 96.4530 1 5456 2 chr3D.!!$R1 5455
3 TraesCS3A01G197300 chr7B 357528222 357528900 678 True 813 813 88.8410 4794 5456 1 chr7B.!!$R1 662

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
441 448 0.107703 TCATGGACAACCTCATCGCC 60.108 55.0 0.00 0.0 37.04 5.54 F
882 891 0.250295 CCAGGCTGTCCTCGTTTCAA 60.250 55.0 14.43 0.0 41.93 2.69 F
2079 2234 0.830648 TACTCAATTCAGGGGAGCCG 59.169 55.0 0.00 0.0 31.88 5.52 F
2730 2885 0.249073 CTACCTCGATGGGCAAGACG 60.249 60.0 5.98 0.0 41.11 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1969 4.078571 TCCCTCTGTCCCACATATAAGAGT 60.079 45.833 0.00 0.0 31.28 3.24 R
2167 2322 5.557576 ACATATGCATCATCTGTACCAGT 57.442 39.130 0.19 0.0 31.13 4.00 R
4013 6441 0.179059 TGTCGAGCAGCACAAGGAAA 60.179 50.000 0.00 0.0 0.00 3.13 R
4603 7031 2.287915 CGGCTAATCATCAAACTTCCCG 59.712 50.000 0.00 0.0 0.00 5.14 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
25 26 4.907269 TCCTCATCACCCTTATGAGCAATA 59.093 41.667 7.42 0.00 45.94 1.90
30 31 6.328934 TCATCACCCTTATGAGCAATACCTTA 59.671 38.462 0.00 0.00 30.46 2.69
81 84 3.127548 GTCATAGTTGGTTGCTGACATGG 59.872 47.826 0.00 0.00 36.94 3.66
84 87 0.604578 GTTGGTTGCTGACATGGCAT 59.395 50.000 0.00 0.00 39.54 4.40
102 105 3.327626 GCATCCTGATCATGTCTAGCAG 58.672 50.000 0.00 0.00 0.00 4.24
118 121 0.889306 GCAGGAGGTCTAGTTGACGT 59.111 55.000 0.00 0.00 46.24 4.34
131 134 2.128035 GTTGACGTGTCAGACCTTCTG 58.872 52.381 0.00 0.00 45.59 3.02
213 220 4.214119 AGACATCGTCACAAAAATCACTGG 59.786 41.667 0.00 0.00 34.60 4.00
221 228 4.344679 TCACAAAAATCACTGGCAATCCTT 59.655 37.500 0.00 0.00 0.00 3.36
227 234 4.696479 ATCACTGGCAATCCTTAGGTAG 57.304 45.455 0.00 0.00 0.00 3.18
239 246 3.433513 CTTAGGTAGGACAAGTACGGC 57.566 52.381 0.00 0.00 0.00 5.68
248 255 1.227263 CAAGTACGGCGGGATCCAG 60.227 63.158 15.23 11.38 0.00 3.86
338 345 1.134367 CGAGGACGAGAGGTATTGCAA 59.866 52.381 0.00 0.00 42.66 4.08
380 387 3.161450 TAGCTCCATCGCCACCCC 61.161 66.667 0.00 0.00 0.00 4.95
439 446 2.967599 TCTCATGGACAACCTCATCG 57.032 50.000 0.00 0.00 37.04 3.84
441 448 0.107703 TCATGGACAACCTCATCGCC 60.108 55.000 0.00 0.00 37.04 5.54
443 450 0.327924 ATGGACAACCTCATCGCCAA 59.672 50.000 0.00 0.00 37.04 4.52
462 469 1.742308 ACTTTCCTAGGAGCCACCAA 58.258 50.000 12.26 1.17 42.04 3.67
463 470 1.351350 ACTTTCCTAGGAGCCACCAAC 59.649 52.381 12.26 0.00 42.04 3.77
464 471 1.630878 CTTTCCTAGGAGCCACCAACT 59.369 52.381 12.26 0.00 42.04 3.16
512 519 1.153349 GACCAGATTCTCCCACCGC 60.153 63.158 0.00 0.00 0.00 5.68
552 560 1.092348 GGGTTTTGATACACCGGCTC 58.908 55.000 0.00 0.00 33.34 4.70
557 565 2.672961 TTGATACACCGGCTCTTCTG 57.327 50.000 0.00 0.00 0.00 3.02
573 581 2.046988 TGCCACGCACTCATCCTG 60.047 61.111 0.00 0.00 31.71 3.86
584 592 1.478510 ACTCATCCTGTTGAGGTAGCG 59.521 52.381 9.39 0.00 46.04 4.26
588 596 3.512329 TCATCCTGTTGAGGTAGCGTTAA 59.488 43.478 0.00 0.00 40.76 2.01
595 603 6.401796 CCTGTTGAGGTAGCGTTAACATTTAC 60.402 42.308 6.39 4.77 34.16 2.01
598 606 6.276832 TGAGGTAGCGTTAACATTTACTCT 57.723 37.500 6.39 4.71 0.00 3.24
729 738 6.215845 ACAGCCAAATTTCAGAATAACACAC 58.784 36.000 0.00 0.00 0.00 3.82
809 818 1.275421 CCCTTCCCTTCAGGTCTCCC 61.275 65.000 0.00 0.00 36.75 4.30
882 891 0.250295 CCAGGCTGTCCTCGTTTCAA 60.250 55.000 14.43 0.00 41.93 2.69
922 931 3.997064 CTCGCTTCAGGTCGCCCAG 62.997 68.421 0.00 0.00 0.00 4.45
1225 1254 4.201940 TGGCTTATCATTTCTGCACAATCG 60.202 41.667 0.00 0.00 0.00 3.34
1282 1311 9.030301 CGGAAACAAAGATGATTTTTGTAGTTT 57.970 29.630 13.50 5.78 45.28 2.66
1832 1987 5.943416 CCAAAACACTCTTATATGTGGGACA 59.057 40.000 0.00 0.00 38.39 4.02
1855 2010 7.838884 ACAGAGGGAGTAGTTGTTAATAGTTC 58.161 38.462 0.00 0.00 0.00 3.01
2079 2234 0.830648 TACTCAATTCAGGGGAGCCG 59.169 55.000 0.00 0.00 31.88 5.52
2093 2248 2.665185 GCCGCGTGAAAGTGGACT 60.665 61.111 4.92 0.00 44.18 3.85
2112 2267 4.171754 GACTTTCTACTGATAACCGCGTT 58.828 43.478 4.92 1.95 0.00 4.84
2167 2322 1.536418 AGCACCACTGCCTCTACCA 60.536 57.895 0.00 0.00 45.53 3.25
2431 2586 2.044793 AGGATTGAGTCTTCCACCCA 57.955 50.000 13.19 0.00 34.27 4.51
2540 2695 0.729116 TGCTTATGCTCTTTGCTCGC 59.271 50.000 1.96 0.00 43.37 5.03
2730 2885 0.249073 CTACCTCGATGGGCAAGACG 60.249 60.000 5.98 0.00 41.11 4.18
2937 3092 4.142600 GCCTCTTGTCACACAAATGATACC 60.143 45.833 0.00 0.00 37.69 2.73
3147 3302 3.233231 TGTGCTTTGCCTTGGCCC 61.233 61.111 9.35 0.00 0.00 5.80
3301 3458 4.141274 TCCTTGTCTCCAATGTCCTTTTCA 60.141 41.667 0.00 0.00 0.00 2.69
3380 3537 1.495584 TTGCGCTTCGTGACCTTGTC 61.496 55.000 9.73 0.00 0.00 3.18
3461 3618 7.648142 TGAGTTTGTGACCTTTATCAATTGAC 58.352 34.615 11.07 0.00 0.00 3.18
3611 6035 9.807649 ATTTGCTCGCTATTTCTTCATTATTTT 57.192 25.926 0.00 0.00 0.00 1.82
4013 6441 0.253894 TGTGTGCTATGATGCTGGCT 59.746 50.000 0.00 0.00 0.00 4.75
4129 6557 3.814283 GCAGCCTCATCTTCATTCCTAAG 59.186 47.826 0.00 0.00 0.00 2.18
4388 6816 5.171476 TCTTTCGAAAGCAAGGTCAGATAG 58.829 41.667 29.10 5.30 35.01 2.08
4430 6858 4.158949 CAGCAATCCTGTGATTTTGATGGA 59.841 41.667 0.00 0.00 39.20 3.41
4439 6867 6.288941 TGTGATTTTGATGGATTCATTGCT 57.711 33.333 0.00 0.00 33.34 3.91
4879 7309 5.930569 AGGGAAACACACTTTATTACTCGAC 59.069 40.000 0.00 0.00 0.00 4.20
5148 7596 8.482943 TCCATCGAAGGAAGAATGAATTAACTA 58.517 33.333 6.98 0.00 33.93 2.24
5188 7636 3.963622 GCACTTGCGATGACTTCAG 57.036 52.632 0.00 0.00 0.00 3.02
5208 7656 6.276832 TCAGTAAAACAGTACGCTTCCTAT 57.723 37.500 0.00 0.00 0.00 2.57
5290 7745 8.573035 CCTAGTTTTTAGAAAATTGTAGTGCCA 58.427 33.333 0.00 0.00 0.00 4.92
5299 7754 1.191535 TTGTAGTGCCAGGCGTATCT 58.808 50.000 7.03 5.29 0.00 1.98
5305 7760 1.007618 GCCAGGCGTATCTCCGTAC 60.008 63.158 0.00 0.00 0.00 3.67
5307 7762 1.658673 CAGGCGTATCTCCGTACCC 59.341 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 47 6.072286 CCAACTATGACATGACTTTGCTCTTT 60.072 38.462 0.00 0.00 0.00 2.52
64 67 0.467844 TGCCATGTCAGCAACCAACT 60.468 50.000 0.00 0.00 37.28 3.16
81 84 3.327626 CTGCTAGACATGATCAGGATGC 58.672 50.000 15.42 11.99 34.76 3.91
102 105 1.884579 TGACACGTCAACTAGACCTCC 59.115 52.381 0.00 0.00 44.66 4.30
131 134 9.921637 CCCTATACTTATGTCTTCTCTTGATTC 57.078 37.037 0.00 0.00 0.00 2.52
144 147 3.567164 CACGACGGTCCCTATACTTATGT 59.433 47.826 1.91 0.00 0.00 2.29
155 158 0.386731 CAAATTTGCACGACGGTCCC 60.387 55.000 5.01 0.00 0.00 4.46
221 228 1.382522 CGCCGTACTTGTCCTACCTA 58.617 55.000 0.00 0.00 0.00 3.08
227 234 1.227176 GATCCCGCCGTACTTGTCC 60.227 63.158 0.00 0.00 0.00 4.02
253 260 4.593864 GGATCGCCGGGCTGTCTC 62.594 72.222 18.34 7.83 0.00 3.36
263 270 4.778143 AGTTGCCGGTGGATCGCC 62.778 66.667 1.90 0.00 0.00 5.54
264 271 3.195698 GAGTTGCCGGTGGATCGC 61.196 66.667 1.90 0.00 0.00 4.58
318 325 0.738975 TGCAATACCTCTCGTCCTCG 59.261 55.000 0.00 0.00 38.55 4.63
355 362 2.196925 CGATGGAGCTAGGCGTCCT 61.197 63.158 3.87 3.87 37.71 3.85
439 446 0.328258 TGGCTCCTAGGAAAGTTGGC 59.672 55.000 13.77 13.31 0.00 4.52
441 448 1.351017 TGGTGGCTCCTAGGAAAGTTG 59.649 52.381 13.77 1.41 37.07 3.16
443 450 1.351350 GTTGGTGGCTCCTAGGAAAGT 59.649 52.381 13.77 0.00 37.07 2.66
486 493 1.078759 GAGAATCTGGTCGTGGTGCG 61.079 60.000 0.00 0.00 43.01 5.34
552 560 1.364626 GGATGAGTGCGTGGCAGAAG 61.365 60.000 0.00 0.00 40.08 2.85
557 565 1.672356 AACAGGATGAGTGCGTGGC 60.672 57.895 0.00 0.00 39.69 5.01
573 581 6.589139 AGAGTAAATGTTAACGCTACCTCAAC 59.411 38.462 13.46 0.00 0.00 3.18
584 592 5.811100 CGGAAGGGAGAGAGTAAATGTTAAC 59.189 44.000 0.00 0.00 0.00 2.01
588 596 3.442076 ACGGAAGGGAGAGAGTAAATGT 58.558 45.455 0.00 0.00 0.00 2.71
595 603 6.128227 CGACTTATAATACGGAAGGGAGAGAG 60.128 46.154 0.00 0.00 0.00 3.20
598 606 5.380043 ACGACTTATAATACGGAAGGGAGA 58.620 41.667 13.26 0.00 0.00 3.71
729 738 1.829349 GATCTGCTGGATCGCTTGCG 61.829 60.000 8.87 8.87 40.99 4.85
1011 1040 2.178890 CCGTAGTCGTCCTCTCGGG 61.179 68.421 0.00 0.00 37.24 5.14
1025 1054 0.608856 TGGTACCTGAAGACGCCGTA 60.609 55.000 14.36 0.00 0.00 4.02
1225 1254 2.902343 GCCCTATCCCGCAAGTGC 60.902 66.667 0.00 0.00 37.78 4.40
1815 1969 4.078571 TCCCTCTGTCCCACATATAAGAGT 60.079 45.833 0.00 0.00 31.28 3.24
1832 1987 7.190501 AGGAACTATTAACAACTACTCCCTCT 58.809 38.462 0.00 0.00 36.02 3.69
1855 2010 9.927668 ACAAAATTTGACCATATTTGTAGAAGG 57.072 29.630 13.19 0.00 0.00 3.46
2093 2248 8.757789 CATTATTAACGCGGTTATCAGTAGAAA 58.242 33.333 12.47 0.00 0.00 2.52
2112 2267 6.772360 TGCTGATTTTGGTGAGCATTATTA 57.228 33.333 0.00 0.00 36.54 0.98
2167 2322 5.557576 ACATATGCATCATCTGTACCAGT 57.442 39.130 0.19 0.00 31.13 4.00
2431 2586 7.337942 GGACTCTTTCTCAACATTTATCCATGT 59.662 37.037 0.00 0.00 39.17 3.21
2540 2695 5.828328 GGTGTTCCAAAGGGATAATTAGAGG 59.172 44.000 0.00 0.00 44.48 3.69
2937 3092 4.093952 CTTGCTGGCAGAACCGCG 62.094 66.667 20.86 0.00 43.94 6.46
3196 3353 1.986882 AAGGAAAGGGTTGACAGCAG 58.013 50.000 0.00 0.00 0.00 4.24
3301 3458 9.320295 CTCCTAATCCTCTAAATATGGAGTTCT 57.680 37.037 0.00 0.00 35.25 3.01
3380 3537 1.028905 AAGCTCCCTTCGAGAGATCG 58.971 55.000 4.46 0.00 41.63 3.69
3461 3618 6.706055 ACATGTACATCTTTTACACTGTCG 57.294 37.500 5.07 0.00 32.30 4.35
3611 6035 6.405731 GGCTGCAATTTCTGTTTGATATACCA 60.406 38.462 0.50 0.00 0.00 3.25
3849 6275 5.994250 TCAACTTCTATCTAATGGCTTGCT 58.006 37.500 0.00 0.00 0.00 3.91
3865 6291 7.095187 ACACCTTGAGATTACGATTTCAACTTC 60.095 37.037 0.00 0.00 33.04 3.01
3868 6294 6.481954 ACACCTTGAGATTACGATTTCAAC 57.518 37.500 0.00 0.00 33.04 3.18
4013 6441 0.179059 TGTCGAGCAGCACAAGGAAA 60.179 50.000 0.00 0.00 0.00 3.13
4388 6816 3.003480 CTGTCTCTCGGTTTCCAAATCC 58.997 50.000 0.00 0.00 0.00 3.01
4430 6858 5.698089 CACATAGACGTATCCAGCAATGAAT 59.302 40.000 0.00 0.00 0.00 2.57
4439 6867 4.202020 GCTGAACTCACATAGACGTATCCA 60.202 45.833 0.00 0.00 0.00 3.41
4603 7031 2.287915 CGGCTAATCATCAAACTTCCCG 59.712 50.000 0.00 0.00 0.00 5.14
4731 7159 1.891919 GGTGTCTTGCCGAGCACAA 60.892 57.895 8.23 0.00 38.71 3.33
4879 7309 4.184079 TCACCTCATGATCTGCATATCG 57.816 45.455 7.49 0.00 34.82 2.92
4946 7394 3.941483 AGAGTTCACAACCAGTTCACAAG 59.059 43.478 0.00 0.00 0.00 3.16
5120 7568 4.551702 TTCATTCTTCCTTCGATGGACA 57.448 40.909 18.99 6.79 35.58 4.02
5151 7599 7.307337 GCAAGTGCTTAACAAATACTGCATTTT 60.307 33.333 0.00 0.00 34.82 1.82
5156 7604 3.603770 CGCAAGTGCTTAACAAATACTGC 59.396 43.478 1.21 0.00 39.32 4.40
5188 7636 6.956299 TTGATAGGAAGCGTACTGTTTTAC 57.044 37.500 0.00 0.00 0.00 2.01
5257 7712 9.729281 ACAATTTTCTAAAAACTAGGATACGGA 57.271 29.630 0.00 0.00 46.39 4.69
5284 7739 2.786495 CGGAGATACGCCTGGCACT 61.786 63.158 20.29 11.54 0.00 4.40
5290 7745 4.170947 GGGTACGGAGATACGCCT 57.829 61.111 0.00 0.00 37.37 5.52
5381 7836 5.970317 TGCATGTTTGATCTTCATGTCTT 57.030 34.783 18.65 0.00 40.40 3.01


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

AutoCloner maintained by Alex Coulton.