Multiple sequence alignment - TraesCS5B01G086300

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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 TraesCS5B01G086300 chr5B 100.000 4732 0 0 1 4732 109774005 109769274 0.000000e+00 8739.0
1 TraesCS5B01G086300 chr5B 83.168 101 12 4 4518 4615 549777327 549777425 2.350000e-13 87.9
2 TraesCS5B01G086300 chr5B 97.222 36 1 0 1567 1602 109772369 109772334 1.420000e-05 62.1
3 TraesCS5B01G086300 chr5B 97.222 36 1 0 1637 1672 109772439 109772404 1.420000e-05 62.1
4 TraesCS5B01G086300 chr5D 96.209 3825 117 15 345 4163 101453481 101449679 0.000000e+00 6235.0
5 TraesCS5B01G086300 chr5D 91.785 353 16 8 1 345 101453857 101453510 3.310000e-131 479.0
6 TraesCS5B01G086300 chr5A 95.791 2970 112 6 345 3304 99019019 99021985 0.000000e+00 4780.0
7 TraesCS5B01G086300 chr5A 91.715 869 34 13 3301 4163 99023370 99024206 0.000000e+00 1171.0
8 TraesCS5B01G086300 chr5A 91.746 315 16 4 36 345 99018681 99018990 3.380000e-116 429.0
9 TraesCS5B01G086300 chr5A 97.222 36 1 0 1637 1672 99020242 99020277 1.420000e-05 62.1
10 TraesCS5B01G086300 chr5A 97.222 36 1 0 1567 1602 99020312 99020347 1.420000e-05 62.1
11 TraesCS5B01G086300 chr4B 97.544 570 14 0 4163 4732 117023135 117022566 0.000000e+00 976.0


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 TraesCS5B01G086300 chr5B 109769274 109774005 4731 True 2954.40 8739 98.1480 1 4732 3 chr5B.!!$R1 4731
1 TraesCS5B01G086300 chr5D 101449679 101453857 4178 True 3357.00 6235 93.9970 1 4163 2 chr5D.!!$R1 4162
2 TraesCS5B01G086300 chr5A 99018681 99024206 5525 False 1300.84 4780 94.7392 36 4163 5 chr5A.!!$F1 4127
3 TraesCS5B01G086300 chr4B 117022566 117023135 569 True 976.00 976 97.5440 4163 4732 1 chr4B.!!$R1 569

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
429 468 0.250467 TTGTTGCTCTGTCTCCTGGC 60.250 55.0 0.00 0.0 0.00 4.85 F
618 657 0.331616 ACCATCTGTAAAGGTGGGGC 59.668 55.0 16.99 0.0 36.05 5.80 F
1006 1050 0.679002 ACTTGCAGGCTACATGGCAG 60.679 55.0 0.00 0.0 44.55 4.85 F
2310 2355 1.463553 TTGAGGTGCGTGAGAGCTGA 61.464 55.0 0.00 0.0 38.13 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1430 0.245266 TTTGCTGCCACATGCTCATG 59.755 50.000 8.21 8.21 44.15 3.07 R
1533 1577 1.270550 CATTTTGGAACGAGCAGGCTT 59.729 47.619 0.00 0.00 0.00 4.35 R
2567 2612 1.459209 TGCTGCAAGTTACAACGATCG 59.541 47.619 14.88 14.88 35.30 3.69 R
4191 5636 2.048222 CGACCGGCTCAAGCTTCA 60.048 61.111 0.00 0.00 41.70 3.02 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
22 23 2.758979 CGCAGTTCTAGAGGAGGGTAAA 59.241 50.000 0.00 0.00 0.00 2.01
31 32 7.196637 TCTAGAGGAGGGTAAAGATTTTTCC 57.803 40.000 0.00 0.00 0.00 3.13
53 57 2.170607 CCCCTCCATGTGTATTCTCGTT 59.829 50.000 0.00 0.00 0.00 3.85
77 81 1.668751 TCCGTGTTCTTGTTTGTGCTC 59.331 47.619 0.00 0.00 0.00 4.26
93 97 4.710167 TCGAGCCTCCGTGGACGA 62.710 66.667 0.00 0.00 43.02 4.20
117 121 1.444933 TTGTGGATTCCTGACAGGGT 58.555 50.000 21.56 10.64 35.59 4.34
127 131 1.059913 CTGACAGGGTTGAAGGGAGT 58.940 55.000 0.00 0.00 0.00 3.85
171 175 1.497991 TTGCTCTCGGTTCGTCAAAG 58.502 50.000 0.00 0.00 0.00 2.77
212 216 5.755849 TGTTCTTCTTTCTTTCTTGGAGGT 58.244 37.500 0.00 0.00 0.00 3.85
214 218 4.718961 TCTTCTTTCTTTCTTGGAGGTGG 58.281 43.478 0.00 0.00 0.00 4.61
226 235 1.301293 GAGGTGGGGAAAGGAGCAG 59.699 63.158 0.00 0.00 0.00 4.24
238 247 0.768221 AGGAGCAGAGTGTTTCCCCA 60.768 55.000 0.00 0.00 0.00 4.96
242 251 3.561313 GGAGCAGAGTGTTTCCCCATTAA 60.561 47.826 0.00 0.00 0.00 1.40
253 262 1.920351 TCCCCATTAACCAGTCCTTCC 59.080 52.381 0.00 0.00 0.00 3.46
254 263 1.063942 CCCCATTAACCAGTCCTTCCC 60.064 57.143 0.00 0.00 0.00 3.97
422 461 3.316308 AGGAAATGTGTTGTTGCTCTGTC 59.684 43.478 0.00 0.00 0.00 3.51
429 468 0.250467 TTGTTGCTCTGTCTCCTGGC 60.250 55.000 0.00 0.00 0.00 4.85
455 494 0.697079 CCTGGATCATCCCCATCCTG 59.303 60.000 0.00 0.23 40.66 3.86
595 634 1.001641 GTGGAGGCAGCATCTTGGT 60.002 57.895 7.07 0.00 0.00 3.67
615 654 3.506067 GGTTGAACCATCTGTAAAGGTGG 59.494 47.826 11.01 11.01 38.42 4.61
618 657 0.331616 ACCATCTGTAAAGGTGGGGC 59.668 55.000 16.99 0.00 36.05 5.80
754 793 0.706433 ATGAGGAACATGCCAAGGGT 59.294 50.000 0.00 0.00 37.87 4.34
771 810 4.497291 AGGGTGGCGATTTATGAACTTA 57.503 40.909 0.00 0.00 0.00 2.24
778 817 7.415206 GGTGGCGATTTATGAACTTAAATGAGT 60.415 37.037 9.35 0.00 33.11 3.41
789 828 5.836024 ACTTAAATGAGTGGGGTGTCTTA 57.164 39.130 0.00 0.00 0.00 2.10
805 844 7.505923 GGGGTGTCTTATGCTTATTTTCCTATT 59.494 37.037 0.00 0.00 0.00 1.73
882 921 6.830324 TGAGCTATTTTGGTTCATAGAAGCAT 59.170 34.615 11.78 1.52 0.00 3.79
931 972 1.527034 CACCACAGCAACACTAGCAT 58.473 50.000 0.00 0.00 0.00 3.79
1006 1050 0.679002 ACTTGCAGGCTACATGGCAG 60.679 55.000 0.00 0.00 44.55 4.85
1021 1065 1.978473 GCAGACAGCAGAGGAAGGA 59.022 57.895 0.00 0.00 44.79 3.36
1026 1070 2.027377 AGACAGCAGAGGAAGGAATGTG 60.027 50.000 0.00 0.00 0.00 3.21
1084 1128 6.105122 AGATATACTACCATAGGGATGCCA 57.895 41.667 5.86 0.00 38.05 4.92
1129 1173 9.431887 TCAAGACTATGGTTGATAAAGTTGTAC 57.568 33.333 0.00 0.00 0.00 2.90
1186 1230 9.929180 CCGAATTCCTGAATACTATTGATAAGA 57.071 33.333 0.00 0.00 0.00 2.10
1224 1268 5.068723 GGAAAAACTCCAGCATGATCATGAT 59.931 40.000 34.65 28.14 44.67 2.45
1386 1430 6.869315 AGAAGGAGCTTGAAGAAGTAAAAC 57.131 37.500 0.00 0.00 0.00 2.43
1533 1577 4.584325 AGCAACAAATTGGAAGTGCTTCTA 59.416 37.500 11.18 3.11 39.45 2.10
1603 1647 7.606456 ACAACTATTTAGAATTTGGAGCTTCGA 59.394 33.333 0.00 0.00 0.00 3.71
1606 1650 7.770897 ACTATTTAGAATTTGGAGCTTCGATGT 59.229 33.333 0.00 0.00 0.00 3.06
1815 1859 6.425504 CCGATGAAATATCTCTCTTGTTTGC 58.574 40.000 0.00 0.00 0.00 3.68
1853 1897 3.449377 TGCAATGAACAATCATGGAGCAT 59.551 39.130 8.71 0.00 45.60 3.79
1951 1995 6.327365 TCCTTGATAGAATAGCCTCATGTTCA 59.673 38.462 0.00 0.00 0.00 3.18
2079 2123 3.243873 ACAATGACACAGACAGACATCGT 60.244 43.478 0.00 0.00 0.00 3.73
2154 2198 2.806019 GCATTCAGGCAGAGATGACGAT 60.806 50.000 0.00 0.00 0.00 3.73
2163 2207 2.692557 CAGAGATGACGATCAGGAGGTT 59.307 50.000 0.00 0.00 0.00 3.50
2219 2264 7.042797 ACAAACTTGAACTGAATACTGCATT 57.957 32.000 0.00 0.00 0.00 3.56
2310 2355 1.463553 TTGAGGTGCGTGAGAGCTGA 61.464 55.000 0.00 0.00 38.13 4.26
2511 2556 5.452077 GCAGGAACTACTCGATAGTCCAAAT 60.452 44.000 16.23 3.27 43.79 2.32
2532 2577 3.662759 TGGAAACCCTTCAAGTCTGTT 57.337 42.857 0.00 0.00 32.75 3.16
2623 2673 9.691362 TCAATTCTTAAGGTTAACAGATTTTGC 57.309 29.630 8.10 0.00 0.00 3.68
2627 2677 3.282831 AGGTTAACAGATTTTGCGTGC 57.717 42.857 8.10 0.00 0.00 5.34
2719 2769 1.819632 GGCCCCTACAATGCTGTCG 60.820 63.158 0.00 0.00 36.96 4.35
3397 4836 4.274950 CGGTTTTAACTCAGAAAGGAAGCA 59.725 41.667 0.00 0.00 0.00 3.91
3473 4912 7.956420 AAACTCAAAACATGACACGTCTATA 57.044 32.000 0.00 0.00 33.47 1.31
3510 4949 8.956426 TGGTGGATTTCTCTTACATTATCAAAC 58.044 33.333 0.00 0.00 0.00 2.93
3686 5125 2.016318 TCGGCAGCAAGTAATGAATGG 58.984 47.619 0.00 0.00 0.00 3.16
3757 5196 1.391144 GCAGGCTTTTATTTTGCGCAG 59.609 47.619 11.31 0.00 0.00 5.18
3833 5272 5.220989 GGTGTTACCTTGGTTTCAACTTCTC 60.221 44.000 0.00 0.00 34.73 2.87
4002 5443 2.930950 TGCTAGTGCACTCTTGGTTTT 58.069 42.857 25.56 0.00 45.31 2.43
4117 5558 2.031560 TGAATTTCGTCTGTGTGTGTGC 59.968 45.455 0.00 0.00 0.00 4.57
4308 5753 3.446570 CCTTACGTCCGCCCGAGT 61.447 66.667 0.00 0.00 0.00 4.18
4418 5863 5.896678 CCTTCTTCTCTCCCTTATCTCTTCA 59.103 44.000 0.00 0.00 0.00 3.02
4536 5981 2.801631 CGTGAGGAGGGGAGGCATC 61.802 68.421 0.00 0.00 0.00 3.91
4616 6061 1.485838 CTGAGCAGCACTAATCGGCG 61.486 60.000 0.00 0.00 34.54 6.46
4643 6088 2.003548 GGGTGGGAGGAGCTGGAAT 61.004 63.158 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.070758 CGAGAATACACATGGAGGGGG 59.929 57.143 0.00 0.00 0.00 5.40
53 57 1.021202 CAAACAAGAACACGGAGGCA 58.979 50.000 0.00 0.00 0.00 4.75
77 81 2.938539 GAATCGTCCACGGAGGCTCG 62.939 65.000 8.69 6.62 40.29 5.03
93 97 4.338879 CCTGTCAGGAATCCACAAAGAAT 58.661 43.478 14.26 0.00 37.67 2.40
117 121 4.199310 CACAGACAAGAAACTCCCTTCAA 58.801 43.478 0.00 0.00 0.00 2.69
212 216 0.768221 ACACTCTGCTCCTTTCCCCA 60.768 55.000 0.00 0.00 0.00 4.96
214 218 2.155279 GAAACACTCTGCTCCTTTCCC 58.845 52.381 0.00 0.00 0.00 3.97
226 235 3.756963 GACTGGTTAATGGGGAAACACTC 59.243 47.826 0.00 0.00 31.84 3.51
253 262 4.128388 GACCAAATTGCGCGGGGG 62.128 66.667 8.83 2.04 0.00 5.40
254 263 3.051392 GAGACCAAATTGCGCGGGG 62.051 63.158 8.83 1.63 0.00 5.73
318 327 6.704289 TCCGATTCCGAAATAAGAGAGTTA 57.296 37.500 0.00 0.00 38.22 2.24
422 461 0.987294 TCCAGGAAGAAAGCCAGGAG 59.013 55.000 0.00 0.00 36.31 3.69
429 468 2.511218 TGGGGATGATCCAGGAAGAAAG 59.489 50.000 14.36 0.00 38.64 2.62
572 611 0.403271 AGATGCTGCCTCCACAACTT 59.597 50.000 0.00 0.00 0.00 2.66
573 612 0.403271 AAGATGCTGCCTCCACAACT 59.597 50.000 0.00 0.00 0.00 3.16
576 615 1.001764 CCAAGATGCTGCCTCCACA 60.002 57.895 0.00 0.00 0.00 4.17
595 634 3.499563 CCCCACCTTTACAGATGGTTCAA 60.500 47.826 0.00 0.00 33.74 2.69
604 643 2.299013 GGAAAAAGCCCCACCTTTACAG 59.701 50.000 0.00 0.00 34.12 2.74
615 654 3.131755 CCAAGATGATGAGGAAAAAGCCC 59.868 47.826 0.00 0.00 0.00 5.19
618 657 6.040878 GCAATCCAAGATGATGAGGAAAAAG 58.959 40.000 0.00 0.00 33.17 2.27
754 793 7.415095 CCACTCATTTAAGTTCATAAATCGCCA 60.415 37.037 0.00 0.00 34.15 5.69
771 810 3.010584 AGCATAAGACACCCCACTCATTT 59.989 43.478 0.00 0.00 0.00 2.32
778 817 4.953579 GGAAAATAAGCATAAGACACCCCA 59.046 41.667 0.00 0.00 0.00 4.96
789 828 8.782137 AACACCCATAATAGGAAAATAAGCAT 57.218 30.769 0.00 0.00 0.00 3.79
805 844 6.969043 ACAGAATGGATAAGAAACACCCATA 58.031 36.000 0.00 0.00 43.62 2.74
848 887 9.851686 ATGAACCAAAATAGCTCATTGATAGTA 57.148 29.630 0.00 0.00 0.00 1.82
849 888 8.757982 ATGAACCAAAATAGCTCATTGATAGT 57.242 30.769 0.00 0.00 0.00 2.12
931 972 7.180587 TCACCTTACACCACATTATACTACCAA 59.819 37.037 0.00 0.00 0.00 3.67
1006 1050 2.289945 ACACATTCCTTCCTCTGCTGTC 60.290 50.000 0.00 0.00 0.00 3.51
1021 1065 7.175467 TGAAGTCAAAGCATCAATAGACACATT 59.825 33.333 0.00 0.00 0.00 2.71
1084 1128 4.166246 TGATATCCAGGTACTCGACAGT 57.834 45.455 0.00 0.00 34.60 3.55
1186 1230 5.009710 GGAGTTTTTCCTTTTCTTCCACGAT 59.990 40.000 0.00 0.00 43.16 3.73
1224 1268 4.269183 ACAACATGAAAGTTCACAGACCA 58.731 39.130 0.00 0.00 40.49 4.02
1386 1430 0.245266 TTTGCTGCCACATGCTCATG 59.755 50.000 8.21 8.21 44.15 3.07
1533 1577 1.270550 CATTTTGGAACGAGCAGGCTT 59.729 47.619 0.00 0.00 0.00 4.35
1603 1647 9.807649 GTTGCAAGATTAAAATTATGAGGACAT 57.192 29.630 0.00 0.00 40.16 3.06
1925 1969 6.949117 ACATGAGGCTATTCTATCAAGGAT 57.051 37.500 0.00 0.00 0.00 3.24
2154 2198 3.808728 CTTTTGTCTGACAACCTCCTGA 58.191 45.455 21.95 3.84 37.90 3.86
2163 2207 3.817084 CCTTGATCAGCTTTTGTCTGACA 59.183 43.478 6.36 6.36 42.63 3.58
2277 2322 7.921214 TCACGCACCTCAAATTTACAAATTTAA 59.079 29.630 11.29 0.00 44.38 1.52
2511 2556 3.662759 ACAGACTTGAAGGGTTTCCAA 57.337 42.857 0.00 0.00 34.83 3.53
2561 2606 4.510711 TGCAAGTTACAACGATCGGTAAAA 59.489 37.500 20.98 7.67 31.83 1.52
2567 2612 1.459209 TGCTGCAAGTTACAACGATCG 59.541 47.619 14.88 14.88 35.30 3.69
2600 2650 7.807907 CACGCAAAATCTGTTAACCTTAAGAAT 59.192 33.333 3.36 0.00 0.00 2.40
2627 2677 2.299521 CCTCCTCCTAGTCACGTAAGG 58.700 57.143 0.00 0.00 46.39 2.69
2719 2769 3.674997 TCCTCTCAACCAATGCACTAAC 58.325 45.455 0.00 0.00 0.00 2.34
2991 3042 2.564947 AGCCCACAACTGAAACACAAAA 59.435 40.909 0.00 0.00 0.00 2.44
3114 3165 7.227314 TGGATGTCTAAACAGAATATGCATGAC 59.773 37.037 10.16 4.53 39.20 3.06
3397 4836 2.787473 TCCTTTCGATTCCACATGCT 57.213 45.000 0.00 0.00 0.00 3.79
3473 4912 5.895534 AGAGAAATCCACCATGCATATTTGT 59.104 36.000 8.70 5.41 0.00 2.83
3583 5022 2.223572 CGCAAGAAGCCAGAAACAAACT 60.224 45.455 0.00 0.00 41.38 2.66
3591 5030 2.359107 CCTGCGCAAGAAGCCAGA 60.359 61.111 13.05 0.00 43.86 3.86
3686 5125 4.199432 AGTGTTGGACATCTGATGACTC 57.801 45.455 23.59 11.54 0.00 3.36
3757 5196 2.857592 AATCAGACGCATGAAATGGC 57.142 45.000 0.00 0.00 46.86 4.40
3833 5272 5.562506 ATTCATGCATCAGAGTTCTTGTG 57.437 39.130 0.00 0.00 0.00 3.33
4002 5443 2.522836 TGTTACCGCCGTAGTCAAAA 57.477 45.000 0.00 0.00 0.00 2.44
4117 5558 8.142994 AGGCTTCTATATTAATTTCACACACG 57.857 34.615 0.00 0.00 0.00 4.49
4190 5635 2.097038 CGACCGGCTCAAGCTTCAG 61.097 63.158 0.00 0.00 41.70 3.02
4191 5636 2.048222 CGACCGGCTCAAGCTTCA 60.048 61.111 0.00 0.00 41.70 3.02
4384 5829 3.056328 GAAGAAGGTGGGCGGTGC 61.056 66.667 0.00 0.00 0.00 5.01
4418 5863 1.303317 GCGGATGGGGTTTGACTGT 60.303 57.895 0.00 0.00 0.00 3.55
4536 5981 1.835483 GATAGCTTGCATCACGGGCG 61.835 60.000 0.00 0.00 0.00 6.13
4549 5994 1.139734 CAGCACCGACGTGATAGCT 59.860 57.895 0.00 0.00 43.14 3.32
4616 6061 4.394712 CTCCCACCCCGTCAGTGC 62.395 72.222 0.00 0.00 33.75 4.40
4643 6088 2.687200 CTCCCCGGGTCACCATCA 60.687 66.667 21.85 0.00 36.13 3.07


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

AutoCloner maintained by Alex Coulton.