Multiple sequence alignment - TraesCS4B01G295100

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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 TraesCS4B01G295100 chr4B 100.000 2798 0 0 1 2798 580792449 580789652 0.000000e+00 5168
1 TraesCS4B01G295100 chr4D 93.001 2229 109 19 2 2208 464395680 464393477 0.000000e+00 3208
2 TraesCS4B01G295100 chr4D 89.016 610 43 12 2208 2794 362451078 362451686 0.000000e+00 734
3 TraesCS4B01G295100 chr4A 93.795 1660 73 12 562 2208 5706288 5707930 0.000000e+00 2468
4 TraesCS4B01G295100 chr4A 84.441 572 65 12 2 569 5705534 5706085 2.450000e-150 542
5 TraesCS4B01G295100 chr4A 91.011 89 7 1 2121 2208 5708191 5708279 4.900000e-23 119
6 TraesCS4B01G295100 chr3A 87.398 611 52 7 2208 2794 27874515 27875124 0.000000e+00 678
7 TraesCS4B01G295100 chr5A 84.833 600 68 10 2218 2794 460992449 460991850 1.440000e-162 582


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 TraesCS4B01G295100 chr4B 580789652 580792449 2797 True 5168 5168 100.000 1 2798 1 chr4B.!!$R1 2797
1 TraesCS4B01G295100 chr4D 464393477 464395680 2203 True 3208 3208 93.001 2 2208 1 chr4D.!!$R1 2206
2 TraesCS4B01G295100 chr4D 362451078 362451686 608 False 734 734 89.016 2208 2794 1 chr4D.!!$F1 586
3 TraesCS4B01G295100 chr4A 5705534 5708279 2745 False 1043 2468 89.749 2 2208 3 chr4A.!!$F1 2206
4 TraesCS4B01G295100 chr3A 27874515 27875124 609 False 678 678 87.398 2208 2794 1 chr3A.!!$F1 586
5 TraesCS4B01G295100 chr5A 460991850 460992449 599 True 582 582 84.833 2218 2794 1 chr5A.!!$R1 576

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
136 137 0.03563 GATCAGGGCACTGCAAGAGT 60.036 55.0 12.37 0.0 44.54 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2293 0.178953 AGCAAACCCAGCCAACTCAT 60.179 50.0 0.0 0.0 0.0 2.9 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
38 39 2.671596 GTTGGCGCTAGAAATGCAAAA 58.328 42.857 7.64 0.00 0.00 2.44
44 45 3.980775 GCGCTAGAAATGCAAAACTTTCA 59.019 39.130 11.89 0.05 34.52 2.69
48 49 7.023575 CGCTAGAAATGCAAAACTTTCACTAT 58.976 34.615 11.89 0.00 34.52 2.12
56 57 5.157067 GCAAAACTTTCACTATGAAGCTCC 58.843 41.667 0.00 0.00 37.70 4.70
62 63 2.307768 TCACTATGAAGCTCCCCTACG 58.692 52.381 0.00 0.00 0.00 3.51
63 64 1.341531 CACTATGAAGCTCCCCTACGG 59.658 57.143 0.00 0.00 0.00 4.02
79 80 0.251653 ACGGCACCAAGAGGAGTCTA 60.252 55.000 0.00 0.00 38.69 2.59
88 89 3.370104 CAAGAGGAGTCTAGGTCACCAT 58.630 50.000 0.00 0.00 30.45 3.55
95 96 4.222145 GGAGTCTAGGTCACCATTACAACA 59.778 45.833 0.00 0.00 0.00 3.33
99 100 2.514803 AGGTCACCATTACAACAAGGC 58.485 47.619 0.00 0.00 0.00 4.35
110 111 1.973281 AACAAGGCCCAGCACATCG 60.973 57.895 0.00 0.00 0.00 3.84
136 137 0.035630 GATCAGGGCACTGCAAGAGT 60.036 55.000 12.37 0.00 44.54 3.24
142 143 1.276421 GGGCACTGCAAGAGTAGAGAA 59.724 52.381 2.82 0.00 37.43 2.87
145 146 3.393800 GCACTGCAAGAGTAGAGAACAA 58.606 45.455 0.00 0.00 37.43 2.83
198 202 1.272490 GTCCACACGACCAAGAGATGA 59.728 52.381 0.00 0.00 35.23 2.92
200 204 2.069273 CCACACGACCAAGAGATGAAC 58.931 52.381 0.00 0.00 0.00 3.18
233 238 1.617804 CCAATGTGAAGCCACCATCCT 60.618 52.381 0.00 0.00 42.53 3.24
245 250 3.790437 CATCCTGGACCGCTGCCT 61.790 66.667 0.00 0.00 0.00 4.75
246 251 3.790437 ATCCTGGACCGCTGCCTG 61.790 66.667 0.00 0.00 0.00 4.85
430 437 2.031157 CCTTTTGCTTGACGACGGAAAT 60.031 45.455 0.00 0.00 0.00 2.17
434 441 1.798223 TGCTTGACGACGGAAATGAAG 59.202 47.619 0.00 0.00 0.00 3.02
456 463 4.954202 AGTAATATCTGAACACTCACCGGA 59.046 41.667 9.46 0.00 0.00 5.14
484 491 7.772332 TGATAAAGCTCGGTTATCTTTCTTC 57.228 36.000 14.67 0.00 38.33 2.87
551 558 1.697432 TCTTTTCTCGGAAAGGAGGCA 59.303 47.619 6.97 0.00 37.27 4.75
658 875 0.526662 AGCTGGACGTAAACTCCTCG 59.473 55.000 0.00 0.00 0.00 4.63
708 925 0.904394 ATTTGGTGGCCGGAAGCAAT 60.904 50.000 19.03 9.54 46.50 3.56
710 927 4.133796 GGTGGCCGGAAGCAATGC 62.134 66.667 5.05 0.00 46.50 3.56
727 944 6.698380 AGCAATGCAATTCAAAGATTCTTCT 58.302 32.000 8.35 0.00 31.22 2.85
729 946 6.672357 GCAATGCAATTCAAAGATTCTTCTGC 60.672 38.462 0.00 5.23 31.22 4.26
741 958 3.565764 TTCTTCTGCCGATCAATCCAT 57.434 42.857 0.00 0.00 0.00 3.41
742 959 3.117491 TCTTCTGCCGATCAATCCATC 57.883 47.619 0.00 0.00 0.00 3.51
743 960 2.702478 TCTTCTGCCGATCAATCCATCT 59.298 45.455 0.00 0.00 0.00 2.90
744 961 2.827800 TCTGCCGATCAATCCATCTC 57.172 50.000 0.00 0.00 0.00 2.75
745 962 2.041701 TCTGCCGATCAATCCATCTCA 58.958 47.619 0.00 0.00 0.00 3.27
746 963 2.636403 TCTGCCGATCAATCCATCTCAT 59.364 45.455 0.00 0.00 0.00 2.90
747 964 3.834231 TCTGCCGATCAATCCATCTCATA 59.166 43.478 0.00 0.00 0.00 2.15
748 965 4.468868 TCTGCCGATCAATCCATCTCATAT 59.531 41.667 0.00 0.00 0.00 1.78
818 1039 3.255379 CGGCCGCTAAGCTTCGTC 61.255 66.667 14.67 0.00 0.00 4.20
1167 1393 3.204827 GACGGCTGCGGCATCATT 61.205 61.111 21.31 0.00 40.87 2.57
1298 1524 3.181451 TGCCATCTCTGAGTGTTTCAACT 60.181 43.478 4.32 0.00 34.81 3.16
1301 1527 4.450419 CCATCTCTGAGTGTTTCAACTGAC 59.550 45.833 4.32 0.00 34.81 3.51
1413 1639 3.126001 CTGGTGTTCAGCTTACAGGAA 57.874 47.619 0.00 0.00 36.60 3.36
1420 1646 2.244695 TCAGCTTACAGGAACCGAAGA 58.755 47.619 0.00 0.00 0.00 2.87
1578 1804 4.273148 AGCACAGGTAAAGTTCTACCAG 57.727 45.455 13.38 9.51 43.42 4.00
1579 1805 2.742589 GCACAGGTAAAGTTCTACCAGC 59.257 50.000 13.38 10.89 43.42 4.85
1689 1926 0.842635 GAGTGAAGGGGATGATGGCT 59.157 55.000 0.00 0.00 0.00 4.75
1914 2157 1.298859 GGGCCGCTATATTTGCTCCG 61.299 60.000 0.00 0.00 0.00 4.63
1940 2183 4.020218 TCAATGGTAGTCTGGAGGTGAAAG 60.020 45.833 0.00 0.00 0.00 2.62
2050 2293 3.201930 TCATGTTTGCCTATGCCCTAGAA 59.798 43.478 0.00 0.00 36.33 2.10
2074 2318 3.994853 GGCTGGGTTTGCTGCCAC 61.995 66.667 0.00 0.00 44.34 5.01
2076 2320 3.673484 CTGGGTTTGCTGCCACGG 61.673 66.667 0.00 0.00 0.00 4.94
2080 2324 3.670377 GTTTGCTGCCACGGTCCC 61.670 66.667 0.00 0.00 0.00 4.46
2118 2362 4.841813 TGGAGGTGACTTTAATACTGTCCA 59.158 41.667 0.00 0.00 44.43 4.02
2119 2363 5.487488 TGGAGGTGACTTTAATACTGTCCAT 59.513 40.000 0.00 0.00 44.43 3.41
2125 2369 7.047891 GTGACTTTAATACTGTCCATCATGGA 58.952 38.462 0.66 0.66 45.98 3.41
2248 2842 1.272816 TGGACCTGACGGACATCCTTA 60.273 52.381 0.00 0.00 31.13 2.69
2259 2853 3.118038 CGGACATCCTTAATTCCTTCCCA 60.118 47.826 0.00 0.00 0.00 4.37
2260 2854 4.207955 GGACATCCTTAATTCCTTCCCAC 58.792 47.826 0.00 0.00 0.00 4.61
2330 2924 2.853731 AGGCGTCTCAAGAGAATACG 57.146 50.000 0.57 3.62 39.48 3.06
2367 2961 0.407139 ACAAGATTGGGGCTCAGCTT 59.593 50.000 0.00 0.00 0.00 3.74
2380 2994 1.347707 CTCAGCTTACACCTTGGACCA 59.652 52.381 0.00 0.00 0.00 4.02
2435 3049 4.261155 CGGCAATCACCATTTACTACATGG 60.261 45.833 0.00 0.30 46.07 3.66
2507 3121 1.536073 GGCCTTTCTTTGGGCTGGAC 61.536 60.000 0.00 0.00 46.80 4.02
2508 3122 0.827507 GCCTTTCTTTGGGCTGGACA 60.828 55.000 0.00 0.00 44.48 4.02
2618 3233 3.637432 CAAAATTTGCCTCTGCGTTACA 58.363 40.909 0.00 0.00 41.78 2.41
2625 3240 1.734477 CTCTGCGTTACAGCTGCGT 60.734 57.895 15.27 0.00 46.76 5.24
2626 3241 0.456142 CTCTGCGTTACAGCTGCGTA 60.456 55.000 15.27 8.25 46.76 4.42
2638 3253 0.882927 GCTGCGTAGGTTGTGGTTCA 60.883 55.000 1.76 0.00 0.00 3.18
2650 3265 5.010282 GGTTGTGGTTCAAATGGATAGACT 58.990 41.667 0.00 0.00 37.81 3.24
2702 3318 1.001048 TGTGACTCGAACGACCGAAAT 60.001 47.619 0.00 0.00 38.17 2.17
2769 3386 0.326238 ATCCTTCTGGGGTCGGCTTA 60.326 55.000 0.00 0.00 35.33 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.167908 TTGCATTTCTAGCGCCAACG 59.832 50.000 2.29 0.00 44.07 4.10
20 21 1.885887 AGTTTTGCATTTCTAGCGCCA 59.114 42.857 2.29 0.00 33.85 5.69
26 27 9.897744 CTTCATAGTGAAAGTTTTGCATTTCTA 57.102 29.630 10.86 0.00 35.73 2.10
38 39 3.185455 AGGGGAGCTTCATAGTGAAAGT 58.815 45.455 0.00 0.00 35.73 2.66
56 57 1.961180 CTCCTCTTGGTGCCGTAGGG 61.961 65.000 0.00 0.00 41.13 3.53
62 63 0.827368 CCTAGACTCCTCTTGGTGCC 59.173 60.000 0.00 0.00 35.35 5.01
79 80 2.514803 GCCTTGTTGTAATGGTGACCT 58.485 47.619 2.11 0.00 0.00 3.85
88 89 0.106469 TGTGCTGGGCCTTGTTGTAA 60.106 50.000 4.53 0.00 0.00 2.41
95 96 2.045926 GTCGATGTGCTGGGCCTT 60.046 61.111 4.53 0.00 0.00 4.35
99 100 1.742880 CTGGTGTCGATGTGCTGGG 60.743 63.158 0.00 0.00 0.00 4.45
110 111 0.392193 CAGTGCCCTGATCTGGTGTC 60.392 60.000 16.63 6.81 41.50 3.67
136 137 4.404073 GGAGGCTCTGATCTTTGTTCTCTA 59.596 45.833 15.23 0.00 0.00 2.43
142 143 1.661463 TGGGAGGCTCTGATCTTTGT 58.339 50.000 15.23 0.00 0.00 2.83
145 146 1.767681 GTGATGGGAGGCTCTGATCTT 59.232 52.381 15.23 0.78 0.00 2.40
195 199 1.678970 GCTTTCCGGCAGGGTTCAT 60.679 57.895 2.05 0.00 38.33 2.57
198 202 3.897122 TGGCTTTCCGGCAGGGTT 61.897 61.111 2.05 0.00 44.12 4.11
246 251 2.768022 CCTAGGGGGTTGGATGCCC 61.768 68.421 0.00 0.00 45.35 5.36
254 259 2.375345 CGGTGATGCCTAGGGGGTT 61.375 63.158 11.72 0.00 37.43 4.11
256 261 2.445845 TCGGTGATGCCTAGGGGG 60.446 66.667 11.72 0.00 38.36 5.40
430 437 6.330278 CGGTGAGTGTTCAGATATTACTTCA 58.670 40.000 0.00 0.00 32.98 3.02
434 441 5.041940 GTCCGGTGAGTGTTCAGATATTAC 58.958 45.833 0.00 0.00 32.98 1.89
456 463 7.770897 AGAAAGATAACCGAGCTTTATCATTGT 59.229 33.333 15.64 8.25 43.79 2.71
484 491 1.229984 AACAGGGAGGGGAGGAAGG 60.230 63.158 0.00 0.00 0.00 3.46
516 523 2.380084 AAAGAATGCCTGCATGCAAG 57.620 45.000 22.88 17.42 45.84 4.01
517 524 2.300723 AGAAAAGAATGCCTGCATGCAA 59.699 40.909 22.88 7.52 45.84 4.08
526 533 3.081804 TCCTTTCCGAGAAAAGAATGCC 58.918 45.455 6.50 0.00 38.30 4.40
579 796 4.037021 GCGCCTAAACGTGTTAAACTTTT 58.963 39.130 0.00 0.00 34.80 2.27
613 830 4.955450 ACATAAGGATTGTGCCTAATTGCA 59.045 37.500 0.00 0.00 41.28 4.08
625 842 4.876107 ACGTCCAGCTAAACATAAGGATTG 59.124 41.667 0.00 0.00 0.00 2.67
658 875 4.376146 TGTGTTTATGCCTTTGCCTTTTC 58.624 39.130 0.00 0.00 36.33 2.29
708 925 4.616604 CGGCAGAAGAATCTTTGAATTGCA 60.617 41.667 0.00 0.00 32.03 4.08
710 927 5.300969 TCGGCAGAAGAATCTTTGAATTG 57.699 39.130 0.00 0.00 32.03 2.32
727 944 4.831674 ATATGAGATGGATTGATCGGCA 57.168 40.909 0.00 0.00 0.00 5.69
729 946 6.047870 GGAGAATATGAGATGGATTGATCGG 58.952 44.000 0.00 0.00 0.00 4.18
741 958 3.963374 CAGGACCACAGGAGAATATGAGA 59.037 47.826 0.00 0.00 0.00 3.27
742 959 3.494048 GCAGGACCACAGGAGAATATGAG 60.494 52.174 0.00 0.00 0.00 2.90
743 960 2.435805 GCAGGACCACAGGAGAATATGA 59.564 50.000 0.00 0.00 0.00 2.15
744 961 2.804572 CGCAGGACCACAGGAGAATATG 60.805 54.545 0.00 0.00 0.00 1.78
745 962 1.414181 CGCAGGACCACAGGAGAATAT 59.586 52.381 0.00 0.00 0.00 1.28
746 963 0.824109 CGCAGGACCACAGGAGAATA 59.176 55.000 0.00 0.00 0.00 1.75
747 964 1.194781 ACGCAGGACCACAGGAGAAT 61.195 55.000 0.00 0.00 0.00 2.40
748 965 0.541063 TACGCAGGACCACAGGAGAA 60.541 55.000 0.00 0.00 0.00 2.87
1023 1249 0.976641 AGATCTTGCTGACAACCGGA 59.023 50.000 9.46 0.00 0.00 5.14
1209 1435 0.548031 TGTGGATGAAGAGGATGGCC 59.452 55.000 0.00 0.00 0.00 5.36
1298 1524 2.110213 GTGACACCGGCCAAGTCA 59.890 61.111 15.57 15.57 39.74 3.41
1301 1527 2.669569 CCTGTGACACCGGCCAAG 60.670 66.667 0.00 0.00 0.00 3.61
1394 1620 2.486548 GGTTCCTGTAAGCTGAACACCA 60.487 50.000 13.88 0.00 32.65 4.17
1578 1804 5.241662 ACTCAACTCCTTTGACTTATCAGC 58.758 41.667 0.00 0.00 39.45 4.26
1579 1805 6.459066 TGACTCAACTCCTTTGACTTATCAG 58.541 40.000 0.00 0.00 39.45 2.90
1646 1877 8.697846 TCCAATCTAGTTCACACGTTATTAAG 57.302 34.615 0.00 0.00 0.00 1.85
1647 1878 8.308931 ACTCCAATCTAGTTCACACGTTATTAA 58.691 33.333 0.00 0.00 0.00 1.40
1689 1926 4.989458 TGGTAGAAGTCCCTGCCA 57.011 55.556 0.00 0.00 44.80 4.92
1889 2126 2.035832 GCAAATATAGCGGCCCAACAAT 59.964 45.455 0.00 0.00 0.00 2.71
1914 2157 3.100671 ACCTCCAGACTACCATTGAGAC 58.899 50.000 0.00 0.00 0.00 3.36
2022 2265 2.646930 CATAGGCAAACATGAGGAGCA 58.353 47.619 0.00 0.00 0.00 4.26
2050 2293 0.178953 AGCAAACCCAGCCAACTCAT 60.179 50.000 0.00 0.00 0.00 2.90
2074 2318 4.733542 AACATTGGGGCGGGACCG 62.734 66.667 6.35 6.35 40.62 4.79
2076 2320 0.970427 AATGAACATTGGGGCGGGAC 60.970 55.000 0.00 0.00 0.00 4.46
2118 2362 3.517901 TCACCGGTACTTTTCTCCATGAT 59.482 43.478 6.87 0.00 0.00 2.45
2119 2363 2.901192 TCACCGGTACTTTTCTCCATGA 59.099 45.455 6.87 0.00 0.00 3.07
2125 2369 3.495629 GGAAAGGTCACCGGTACTTTTCT 60.496 47.826 28.93 14.82 40.69 2.52
2248 2842 1.678970 GCTGCGGTGGGAAGGAATT 60.679 57.895 0.00 0.00 0.00 2.17
2259 2853 4.250305 AAGGTGGAACGCTGCGGT 62.250 61.111 26.95 21.79 38.12 5.68
2260 2854 3.423154 GAAGGTGGAACGCTGCGG 61.423 66.667 26.95 8.45 38.12 5.69
2312 2906 1.201343 GCGTATTCTCTTGAGACGCC 58.799 55.000 18.34 6.57 45.40 5.68
2330 2924 0.609406 GTCCTCAAGGGGTTGGAAGC 60.609 60.000 0.00 0.00 35.41 3.86
2367 2961 1.488705 CCTGCCTGGTCCAAGGTGTA 61.489 60.000 0.34 0.00 39.75 2.90
2435 3049 2.202892 CGGGAGGTTTAGAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
2463 3077 3.181503 CCGGAGTGCATCAATCTTCTTTG 60.182 47.826 0.00 0.00 0.00 2.77
2491 3105 2.229784 GTCATGTCCAGCCCAAAGAAAG 59.770 50.000 0.00 0.00 0.00 2.62
2614 3229 1.606994 CCACAACCTACGCAGCTGTAA 60.607 52.381 16.64 0.00 0.00 2.41
2616 3231 1.301716 CCACAACCTACGCAGCTGT 60.302 57.895 16.64 0.00 0.00 4.40
2618 3233 0.602905 GAACCACAACCTACGCAGCT 60.603 55.000 0.00 0.00 0.00 4.24
2625 3240 6.012858 AGTCTATCCATTTGAACCACAACCTA 60.013 38.462 0.00 0.00 38.29 3.08
2626 3241 5.010282 GTCTATCCATTTGAACCACAACCT 58.990 41.667 0.00 0.00 38.29 3.50
2638 3253 2.746472 GCTTGGCCGAGTCTATCCATTT 60.746 50.000 21.55 0.00 0.00 2.32
2688 3304 5.045215 AGCAAATATATTTCGGTCGTTCGA 58.955 37.500 7.76 0.00 37.38 3.71


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

AutoCloner maintained by Alex Coulton.