Multiple sequence alignment - TraesCS5D01G163300

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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 TraesCS5D01G163300 chr5D 100.000 3598 0 0 676 4273 254832877 254829280 0.000000e+00 6645
1 TraesCS5D01G163300 chr5D 100.000 297 0 0 1 297 254833552 254833256 2.250000e-152 549
2 TraesCS5D01G163300 chr5B 95.271 3616 127 17 676 4273 287794429 287798018 0.000000e+00 5690
3 TraesCS5D01G163300 chr5B 90.228 307 14 5 1 297 287794031 287794331 1.860000e-103 387
4 TraesCS5D01G163300 chr5A 94.251 2922 116 20 697 3602 338232407 338229522 0.000000e+00 4418
5 TraesCS5D01G163300 chr5A 93.129 684 32 2 3605 4273 338229491 338228808 0.000000e+00 989
6 TraesCS5D01G163300 chr5A 88.421 285 18 5 22 297 338232812 338232534 3.190000e-86 329


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 TraesCS5D01G163300 chr5D 254829280 254833552 4272 True 3597.0 6645 100.000000 1 4273 2 chr5D.!!$R1 4272
1 TraesCS5D01G163300 chr5B 287794031 287798018 3987 False 3038.5 5690 92.749500 1 4273 2 chr5B.!!$F1 4272
2 TraesCS5D01G163300 chr5A 338228808 338232812 4004 True 1912.0 4418 91.933667 22 4273 3 chr5A.!!$R1 4251

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
946 978 0.034863 ACGACTCCACTCTCCTCTCC 60.035 60.0 0.0 0.0 0.0 3.71 F
1698 1732 0.035598 TGTCCAACCATACCACCGTG 59.964 55.0 0.0 0.0 0.0 4.94 F
2672 2716 0.257328 TGTTGGTCCTTGTTGCCTCA 59.743 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 2481 0.109458 CGACGAAGACGGTCCAATGA 60.109 55.0 4.14 0.0 42.66 2.57 R
3254 3302 0.744414 TTTAGCTGGTCTGCATCGCC 60.744 55.0 0.00 0.0 34.99 5.54 R
3781 3861 0.178944 TGGTCAAGTCCTTCCTCGGA 60.179 55.0 0.00 0.0 0.00 4.55 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
78 79 2.154462 CAATCAAAGAGGTCGGTTGCT 58.846 47.619 0.00 0.00 0.00 3.91
143 150 5.848833 ATTGGTACTGTAGCAGGTAGTAC 57.151 43.478 17.89 0.00 43.66 2.73
168 175 0.459063 GTTTCGGTTCGGCGAGGTAT 60.459 55.000 10.46 0.00 0.00 2.73
734 759 3.149196 AGATTGTTGTCAATGGCGAAGT 58.851 40.909 0.00 0.00 43.33 3.01
735 760 3.189287 AGATTGTTGTCAATGGCGAAGTC 59.811 43.478 0.00 0.00 43.33 3.01
844 873 0.940833 GCCGACGGGTAGTAGTAGAC 59.059 60.000 17.22 0.00 34.97 2.59
881 910 1.002544 AGACCGGGCTTCTTCTTCTTG 59.997 52.381 2.12 0.00 0.00 3.02
937 969 2.283966 CCTCCCCACGACTCCACT 60.284 66.667 0.00 0.00 0.00 4.00
944 976 0.322997 CCACGACTCCACTCTCCTCT 60.323 60.000 0.00 0.00 0.00 3.69
945 977 1.091537 CACGACTCCACTCTCCTCTC 58.908 60.000 0.00 0.00 0.00 3.20
946 978 0.034863 ACGACTCCACTCTCCTCTCC 60.035 60.000 0.00 0.00 0.00 3.71
951 983 0.553862 TCCACTCTCCTCTCCCTCCT 60.554 60.000 0.00 0.00 0.00 3.69
1053 1085 3.648067 ACCTCATCTCCAAGAACAAGTCA 59.352 43.478 0.00 0.00 0.00 3.41
1202 1234 3.499563 CCCTACCACCAATTCAACTTCCA 60.500 47.826 0.00 0.00 0.00 3.53
1257 1289 2.760092 AGAGATCTGGAGCTCACTCAAC 59.240 50.000 17.19 2.14 45.64 3.18
1277 1309 5.067283 TCAACCTAAACTTGCCTTCTGTTTC 59.933 40.000 0.00 0.00 35.77 2.78
1429 1463 3.769844 ACATCTCCAACCTCGACTACAAT 59.230 43.478 0.00 0.00 0.00 2.71
1460 1494 3.429547 CGAGGACATCAAGGTAAGACCAG 60.430 52.174 0.00 0.00 41.95 4.00
1472 1506 3.203934 GGTAAGACCAGTAGACCCTCCTA 59.796 52.174 0.00 0.00 38.42 2.94
1499 1533 4.273300 AGAACCCTAGGAATAGCAGTCT 57.727 45.455 11.48 0.00 0.00 3.24
1520 1554 2.061773 CTGTTCTCCTGTGCGTGTTAG 58.938 52.381 0.00 0.00 0.00 2.34
1532 1566 1.002366 CGTGTTAGCCATCTCAGCAC 58.998 55.000 0.00 0.00 0.00 4.40
1537 1571 0.538584 TAGCCATCTCAGCACACCTG 59.461 55.000 0.00 0.00 43.17 4.00
1565 1599 5.471556 TGGTTTCGACAGTAGGATAACAA 57.528 39.130 0.00 0.00 0.00 2.83
1567 1601 5.011329 TGGTTTCGACAGTAGGATAACAACT 59.989 40.000 0.00 0.00 0.00 3.16
1698 1732 0.035598 TGTCCAACCATACCACCGTG 59.964 55.000 0.00 0.00 0.00 4.94
1699 1733 1.003112 TCCAACCATACCACCGTGC 60.003 57.895 0.00 0.00 0.00 5.34
1700 1734 2.043980 CCAACCATACCACCGTGCC 61.044 63.158 0.00 0.00 0.00 5.01
1787 1821 6.976088 TCTCTTTATTCATCGTCTCATCCTC 58.024 40.000 0.00 0.00 0.00 3.71
1793 1827 9.884636 TTTATTCATCGTCTCATCCTCTTAAAA 57.115 29.630 0.00 0.00 0.00 1.52
1947 1988 3.996150 CAGTGTCTGCCTTTTGAACAT 57.004 42.857 0.00 0.00 0.00 2.71
2000 2041 6.212589 TCACCTCATTACTGTAACTCCATTCA 59.787 38.462 1.73 0.00 0.00 2.57
2323 2367 2.163613 CCCTTTGGGTTGATTAGCGTTC 59.836 50.000 0.00 0.00 38.25 3.95
2343 2387 0.529378 GCACAATTAGGCAGCAGCTT 59.471 50.000 0.00 0.00 41.70 3.74
2430 2474 5.470098 ACTTAGCATGTTGTTAGTTGGACAG 59.530 40.000 0.00 0.00 0.00 3.51
2437 2481 4.762765 TGTTGTTAGTTGGACAGTTTGTGT 59.237 37.500 0.00 0.00 44.49 3.72
2453 2497 1.068474 GTGTCATTGGACCGTCTTCG 58.932 55.000 0.00 0.00 43.65 3.79
2495 2539 2.094078 GCATGAATTACCTTTGCCTGCA 60.094 45.455 0.00 0.00 0.00 4.41
2553 2597 6.149129 TCTAATGCATTACTGTGTCTCGAT 57.851 37.500 15.21 0.00 0.00 3.59
2664 2708 2.819608 CAAGGGTATGTGTTGGTCCTTG 59.180 50.000 0.00 0.00 43.17 3.61
2671 2715 0.668535 GTGTTGGTCCTTGTTGCCTC 59.331 55.000 0.00 0.00 0.00 4.70
2672 2716 0.257328 TGTTGGTCCTTGTTGCCTCA 59.743 50.000 0.00 0.00 0.00 3.86
2753 2797 1.140312 TGACCAAAGGGAGAGCAAGT 58.860 50.000 0.00 0.00 38.05 3.16
2758 2802 2.355209 CCAAAGGGAGAGCAAGTAGACC 60.355 54.545 0.00 0.00 35.59 3.85
2772 2816 3.636325 AAGTAGACCTTGCCCATAGGGAT 60.636 47.826 6.20 0.00 46.48 3.85
2773 2817 4.389841 AAGTAGACCTTGCCCATAGGGATA 60.390 45.833 6.20 0.00 46.48 2.59
2848 2895 0.681243 CCTAAGCTCCCAACCTTGCC 60.681 60.000 0.00 0.00 0.00 4.52
3254 3302 1.254026 TGGACAAGTACCACTCGGAG 58.746 55.000 2.83 2.83 35.59 4.63
3302 3350 4.790962 CTGCCGCACCTGCATCCT 62.791 66.667 0.00 0.00 42.21 3.24
3469 3521 1.228657 GCAGTTGAGACGGTTGGACC 61.229 60.000 0.00 0.00 34.05 4.46
3532 3584 7.545965 ACATTTGCTGTCTGTTGATAGTAGTAC 59.454 37.037 0.00 0.00 34.46 2.73
3781 3861 3.005539 AGTGCCTCCCTCGCATGT 61.006 61.111 0.00 0.00 38.76 3.21
3835 3915 0.329596 AGAAGATTCCTTTGCCGGCT 59.670 50.000 29.70 4.49 31.62 5.52
3847 3927 2.342279 CCGGCTTCAAGGTCGACA 59.658 61.111 18.91 0.00 36.31 4.35
3856 3936 1.186200 CAAGGTCGACATCCTCCTCA 58.814 55.000 18.91 0.00 33.76 3.86
3864 3947 1.277557 GACATCCTCCTCAAGCAGTGT 59.722 52.381 0.00 0.00 0.00 3.55
3916 3999 1.141881 CTTCATGTCCGCGCCTAGT 59.858 57.895 0.00 0.00 0.00 2.57
3947 4030 4.873129 CGGCGGTGTCGATGAGGG 62.873 72.222 0.00 0.00 39.00 4.30
4027 4110 0.320771 CCTTGTCGTAGCAGCTGGTT 60.321 55.000 25.47 0.42 0.00 3.67
4054 4137 1.283793 CGCCAGCCACAGAAAGTTG 59.716 57.895 0.00 0.00 0.00 3.16
4165 4260 2.194597 GGTGCCAGTCCAACCACA 59.805 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.619801 ACTGTACTTTGTTGCCTCTTTTAG 57.380 37.500 0.00 0.00 0.00 1.85
18 19 4.947388 TGAACTGTACTTTGTTGCCTCTTT 59.053 37.500 0.00 0.00 0.00 2.52
20 21 4.150897 TGAACTGTACTTTGTTGCCTCT 57.849 40.909 0.00 0.00 0.00 3.69
61 62 3.260884 AGATTAGCAACCGACCTCTTTGA 59.739 43.478 0.00 0.00 0.00 2.69
62 63 3.600388 AGATTAGCAACCGACCTCTTTG 58.400 45.455 0.00 0.00 0.00 2.77
63 64 3.983044 AGATTAGCAACCGACCTCTTT 57.017 42.857 0.00 0.00 0.00 2.52
64 65 4.024670 ACTAGATTAGCAACCGACCTCTT 58.975 43.478 0.00 0.00 0.00 2.85
78 79 1.203262 AGGCCCGGGCATACTAGATTA 60.203 52.381 44.46 0.00 44.11 1.75
110 111 6.842280 TGCTACAGTACCAATTAGGATTAGGA 59.158 38.462 0.00 0.00 41.22 2.94
111 112 7.062749 TGCTACAGTACCAATTAGGATTAGG 57.937 40.000 0.00 0.00 41.22 2.69
115 116 4.969359 ACCTGCTACAGTACCAATTAGGAT 59.031 41.667 0.00 0.00 41.22 3.24
124 125 4.885907 TGATGTACTACCTGCTACAGTACC 59.114 45.833 8.25 0.00 42.52 3.34
143 150 0.179225 CGCCGAACCGAAACTTGATG 60.179 55.000 0.00 0.00 0.00 3.07
168 175 3.315596 TCCCCGTATGTCTCTCTCTCTA 58.684 50.000 0.00 0.00 0.00 2.43
734 759 1.835531 GGGAAGGGATAACTTGACCGA 59.164 52.381 0.00 0.00 0.00 4.69
735 760 1.838077 AGGGAAGGGATAACTTGACCG 59.162 52.381 0.00 0.00 32.36 4.79
773 798 5.625721 CGTATGTATCGTGTCATCTTCTTCC 59.374 44.000 0.00 0.00 0.00 3.46
881 910 2.533266 TTGGCACACAAGAGAGAGAC 57.467 50.000 0.00 0.00 39.29 3.36
937 969 3.063197 GCGGAGGAGGGAGAGGAGA 62.063 68.421 0.00 0.00 0.00 3.71
1202 1234 2.285818 TTCACCATACCGGGGGCT 60.286 61.111 6.32 0.00 39.52 5.19
1257 1289 3.255888 GGGAAACAGAAGGCAAGTTTAGG 59.744 47.826 0.00 0.00 35.77 2.69
1460 1494 4.446167 GGTTCTAGGAGTAGGAGGGTCTAC 60.446 54.167 0.00 0.00 39.76 2.59
1499 1533 0.464036 AACACGCACAGGAGAACAGA 59.536 50.000 0.00 0.00 0.00 3.41
1520 1554 0.250234 TACAGGTGTGCTGAGATGGC 59.750 55.000 0.00 0.00 0.00 4.40
1532 1566 2.140717 GTCGAAACCAGGTTACAGGTG 58.859 52.381 4.87 0.00 36.50 4.00
1537 1571 3.256631 TCCTACTGTCGAAACCAGGTTAC 59.743 47.826 4.87 0.53 34.16 2.50
1565 1599 4.225942 TCAGGATGAAGCTGTGGATTAAGT 59.774 41.667 0.00 0.00 45.97 2.24
1567 1601 4.842531 TCAGGATGAAGCTGTGGATTAA 57.157 40.909 0.00 0.00 45.97 1.40
1594 1628 7.539034 AAATAATTGGTAGCCTTGTCAACTT 57.461 32.000 0.00 0.00 0.00 2.66
1598 1632 6.423182 AGCTAAATAATTGGTAGCCTTGTCA 58.577 36.000 11.22 0.00 40.96 3.58
1698 1732 1.852895 CTTGTCTACTCGTAATGCGGC 59.147 52.381 0.00 0.00 41.72 6.53
1699 1733 2.460918 CCTTGTCTACTCGTAATGCGG 58.539 52.381 0.00 0.00 41.72 5.69
1700 1734 1.852895 GCCTTGTCTACTCGTAATGCG 59.147 52.381 0.00 0.00 43.01 4.73
1931 1972 4.978580 GTGAAAGATGTTCAAAAGGCAGAC 59.021 41.667 0.00 0.00 0.00 3.51
1947 1988 4.037565 TGAGCACTCGAACTAAGTGAAAGA 59.962 41.667 7.42 0.00 45.64 2.52
2000 2041 1.062488 AACCTCTGCAGTTCCCTGGT 61.062 55.000 14.67 10.39 39.22 4.00
2323 2367 1.226491 GCTGCTGCCTAATTGTGCG 60.226 57.895 3.85 0.00 0.00 5.34
2343 2387 4.365514 TGAATCTTTAACAGCCAGTGGA 57.634 40.909 15.20 0.00 0.00 4.02
2413 2457 5.417580 ACACAAACTGTCCAACTAACAACAT 59.582 36.000 0.00 0.00 0.00 2.71
2430 2474 2.218603 AGACGGTCCAATGACACAAAC 58.781 47.619 4.14 0.00 43.65 2.93
2437 2481 0.109458 CGACGAAGACGGTCCAATGA 60.109 55.000 4.14 0.00 42.66 2.57
2438 2482 2.359792 CGACGAAGACGGTCCAATG 58.640 57.895 4.14 0.00 42.66 2.82
2453 2497 0.380378 TTGCTTGCACTTTGGACGAC 59.620 50.000 0.00 0.00 0.00 4.34
2553 2597 7.185453 GCAAATAAACAAAACAATGCTGAACA 58.815 30.769 0.00 0.00 0.00 3.18
2664 2708 3.758554 TCATTTTAAGCTCCTGAGGCAAC 59.241 43.478 0.00 0.00 0.00 4.17
2671 2715 2.744202 ACGCACTCATTTTAAGCTCCTG 59.256 45.455 0.00 0.00 0.00 3.86
2672 2716 2.744202 CACGCACTCATTTTAAGCTCCT 59.256 45.455 0.00 0.00 0.00 3.69
2709 2753 1.616628 GGTCCTGGTCCTGGTCCAT 60.617 63.158 21.28 0.00 32.81 3.41
2753 2797 2.815357 ATCCCTATGGGCAAGGTCTA 57.185 50.000 0.00 0.00 43.94 2.59
2758 2802 1.067295 TGGCTATCCCTATGGGCAAG 58.933 55.000 0.00 0.00 44.53 4.01
2839 2886 2.769893 CCCAAGAAATTGGCAAGGTTG 58.230 47.619 5.96 6.39 40.74 3.77
2848 2895 2.809696 CCTTTGCAAGCCCAAGAAATTG 59.190 45.455 0.00 0.00 0.00 2.32
2862 2909 4.040217 ACAAGCATATTTGGTTCCTTTGCA 59.960 37.500 0.00 0.00 41.48 4.08
3206 3254 3.557595 CGTCTAGATCATTGGCAGAAACC 59.442 47.826 0.00 0.00 0.00 3.27
3254 3302 0.744414 TTTAGCTGGTCTGCATCGCC 60.744 55.000 0.00 0.00 34.99 5.54
3532 3584 7.117523 TGTTCAAAGGAAAAACAAACACTCATG 59.882 33.333 0.00 0.00 34.13 3.07
3627 3707 2.370189 CTGAACCTCAGTCTCCAACCTT 59.630 50.000 0.00 0.00 39.58 3.50
3781 3861 0.178944 TGGTCAAGTCCTTCCTCGGA 60.179 55.000 0.00 0.00 0.00 4.55
3835 3915 1.825474 GAGGAGGATGTCGACCTTGAA 59.175 52.381 14.12 0.00 37.93 2.69
3847 3927 1.830477 GAGACACTGCTTGAGGAGGAT 59.170 52.381 4.53 0.00 37.85 3.24
3856 3936 1.821061 CGTCCCTGGAGACACTGCTT 61.821 60.000 13.40 0.00 36.52 3.91
3888 3971 0.955428 GGACATGAAGCGCTTCCACA 60.955 55.000 39.25 26.34 38.77 4.17
4073 4156 0.388649 CTGCTGAAGAAGTACGCGGT 60.389 55.000 12.47 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.