Multiple sequence alignment - TraesCS3D01G197600

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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 TraesCS3D01G197600 chr3D 100.000 2447 0 0 1 2447 207947089 207944643 0 4519
1 TraesCS3D01G197600 chr3D 90.696 2472 185 29 1 2447 213696721 213694270 0 3249
2 TraesCS3D01G197600 chr2A 89.128 2465 236 20 1 2447 267980587 267983037 0 3038
3 TraesCS3D01G197600 chr7B 88.771 2449 250 16 1 2434 456122103 456124541 0 2976
4 TraesCS3D01G197600 chr7B 88.245 2450 256 20 1 2434 638611654 638609221 0 2900
5 TraesCS3D01G197600 chr3B 88.082 2450 265 18 1 2434 331024948 331027386 0 2881
6 TraesCS3D01G197600 chr3B 87.774 2462 274 18 1 2447 81050297 81052746 0 2854
7 TraesCS3D01G197600 chr3B 87.868 2448 267 26 1 2434 533671481 533669050 0 2848
8 TraesCS3D01G197600 chr1B 87.013 2464 279 23 1 2447 287516458 287518897 0 2739
9 TraesCS3D01G197600 chr1B 86.762 2455 293 24 1 2434 200995206 200997649 0 2704
10 TraesCS3D01G197600 chr4A 88.416 1692 160 19 768 2447 500279486 500277819 0 2006


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 TraesCS3D01G197600 chr3D 207944643 207947089 2446 True 4519 4519 100.000 1 2447 1 chr3D.!!$R1 2446
1 TraesCS3D01G197600 chr3D 213694270 213696721 2451 True 3249 3249 90.696 1 2447 1 chr3D.!!$R2 2446
2 TraesCS3D01G197600 chr2A 267980587 267983037 2450 False 3038 3038 89.128 1 2447 1 chr2A.!!$F1 2446
3 TraesCS3D01G197600 chr7B 456122103 456124541 2438 False 2976 2976 88.771 1 2434 1 chr7B.!!$F1 2433
4 TraesCS3D01G197600 chr7B 638609221 638611654 2433 True 2900 2900 88.245 1 2434 1 chr7B.!!$R1 2433
5 TraesCS3D01G197600 chr3B 331024948 331027386 2438 False 2881 2881 88.082 1 2434 1 chr3B.!!$F2 2433
6 TraesCS3D01G197600 chr3B 81050297 81052746 2449 False 2854 2854 87.774 1 2447 1 chr3B.!!$F1 2446
7 TraesCS3D01G197600 chr3B 533669050 533671481 2431 True 2848 2848 87.868 1 2434 1 chr3B.!!$R1 2433
8 TraesCS3D01G197600 chr1B 287516458 287518897 2439 False 2739 2739 87.013 1 2447 1 chr1B.!!$F2 2446
9 TraesCS3D01G197600 chr1B 200995206 200997649 2443 False 2704 2704 86.762 1 2434 1 chr1B.!!$F1 2433
10 TraesCS3D01G197600 chr4A 500277819 500279486 1667 True 2006 2006 88.416 768 2447 1 chr4A.!!$R1 1679

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
195 196 0.396435 TTCACCCGCTGAATGTCAGT 59.604 50.0 7.08 0.0 45.94 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1462 0.68792 TTCTTCGTGTGTGCCCCATA 59.312 50.0 0.0 0.0 0.0 2.74 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
168 169 6.610830 TCCTACATGCCATATTTGTGGATTTT 59.389 34.615 0.00 0.00 42.02 1.82
195 196 0.396435 TTCACCCGCTGAATGTCAGT 59.604 50.000 7.08 0.00 45.94 3.41
209 210 4.527509 ATGTCAGTGTGGTTACTCTCAG 57.472 45.455 0.00 0.00 0.00 3.35
243 244 2.517875 GCATGAGCTTCGCCCCAT 60.518 61.111 0.00 0.00 37.91 4.00
343 344 5.851720 TGAGATCTCATCATTTGCCTCTAC 58.148 41.667 21.67 0.00 34.14 2.59
453 454 1.355381 ACCAGGAGATGTTGCCAATGA 59.645 47.619 0.00 0.00 0.00 2.57
454 455 2.022195 CCAGGAGATGTTGCCAATGAG 58.978 52.381 0.00 0.00 0.00 2.90
456 457 1.637553 AGGAGATGTTGCCAATGAGGT 59.362 47.619 0.00 0.00 40.61 3.85
485 486 6.545448 TGGTCCTCCATTTGGTCAACCAAT 62.545 45.833 15.05 3.71 45.84 3.16
521 522 2.964464 TGCCCACACAAGATGATTTTGT 59.036 40.909 0.00 0.00 39.23 2.83
631 635 6.425210 TGAAGATCAAGAGTGGAAAAGAGA 57.575 37.500 0.00 0.00 0.00 3.10
672 676 3.686726 AGATTGAGAAGAACATCAACGCC 59.313 43.478 0.00 0.00 38.19 5.68
733 737 4.302930 TGGGATATCCATTGAGGTGTGTA 58.697 43.478 23.27 0.00 41.46 2.90
771 775 2.104451 ACATCCAGCTGAGCAAGATAGG 59.896 50.000 17.39 0.81 0.00 2.57
880 884 7.432350 AGAAATCAAGTTGAAGACTCATCAC 57.568 36.000 10.14 0.00 37.72 3.06
947 951 6.409524 TGAAGAACCAGAAATTCATTTGCT 57.590 33.333 0.00 0.00 0.00 3.91
948 952 6.218019 TGAAGAACCAGAAATTCATTTGCTG 58.782 36.000 0.00 0.00 0.00 4.41
981 985 1.394917 GAGCGTGATGTAGCAGGTTTG 59.605 52.381 0.00 0.00 35.48 2.93
995 999 3.127721 GCAGGTTTGTCTAATCCTCTTGC 59.872 47.826 0.00 0.00 34.49 4.01
1063 1067 7.148340 GCATGATACCATCAATTAAGCTAGACC 60.148 40.741 0.00 0.00 43.50 3.85
1073 1077 8.099364 TCAATTAAGCTAGACCTGAAAAACTG 57.901 34.615 0.00 0.00 0.00 3.16
1106 1110 7.237471 TGGACATGATCATACATACCCTGTTAT 59.763 37.037 8.15 0.00 39.39 1.89
1114 1118 7.066142 TCATACATACCCTGTTATTGGCATTT 58.934 34.615 0.00 0.00 39.39 2.32
1195 1202 3.776969 TCATTCCCATGCTAGTCTTGAGT 59.223 43.478 0.00 0.00 0.00 3.41
1261 1268 7.402054 TGATTTCTACCATCCTAAACATGTGT 58.598 34.615 0.00 0.00 0.00 3.72
1455 1462 0.106335 CATGGCGATGAGGAGAAGCT 59.894 55.000 1.91 0.00 0.00 3.74
1479 1487 1.140816 GGCACACACGAAGAAGAGTC 58.859 55.000 0.00 0.00 0.00 3.36
1485 1493 3.126831 CACACGAAGAAGAGTCAAGCTT 58.873 45.455 0.00 0.00 0.00 3.74
1495 1503 1.736681 GAGTCAAGCTTGAGCATCCAC 59.263 52.381 29.13 15.82 45.16 4.02
1530 1545 0.761187 AAGAGCTGCAGTTGGTGAGA 59.239 50.000 16.64 0.00 0.00 3.27
1575 1592 2.032681 GCCCGGTGAGCTGTTTCT 59.967 61.111 0.00 0.00 0.00 2.52
1587 1604 4.041567 TGAGCTGTTTCTTGACCCATTCTA 59.958 41.667 0.00 0.00 0.00 2.10
1635 1653 7.334171 GCTAAAATCAATTGCTATTTGGGTTGT 59.666 33.333 0.00 0.00 0.00 3.32
1773 1794 5.772825 TGCTTTGCTGAAAGTAGTGAAAT 57.227 34.783 0.00 0.00 40.77 2.17
1917 1938 3.674997 TGAGAGCAATCACTTTACCACC 58.325 45.455 0.00 0.00 0.00 4.61
1938 1959 6.291377 CACCATGGACTAGTATGCTATGTTT 58.709 40.000 21.47 0.00 0.00 2.83
2118 2140 9.042008 CGTGTTAGCTTGGACAGTAATTAATAT 57.958 33.333 0.00 0.00 0.00 1.28
2184 2206 1.979308 TCGGTGGTATGTTCCTTTGGA 59.021 47.619 0.00 0.00 0.00 3.53
2249 2278 0.179000 ATGTTCTCAGGATCGGTGGC 59.821 55.000 0.00 0.00 0.00 5.01
2380 2422 4.934356 TCTCTTTAGGAACCATTTGGCAT 58.066 39.130 0.00 0.00 39.32 4.40
2381 2423 4.706476 TCTCTTTAGGAACCATTTGGCATG 59.294 41.667 0.00 0.00 39.32 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 5.608860 AGCTAGGCCTATCCTCAAAAACTAT 59.391 40.000 14.30 0.00 43.20 2.12
168 169 2.690881 AGCGGGTGAATGGCCCTA 60.691 61.111 0.00 0.00 43.92 3.53
195 196 1.267121 GGAGGCTGAGAGTAACCACA 58.733 55.000 0.00 0.00 0.00 4.17
209 210 0.465460 TGCCATAACAATCGGGAGGC 60.465 55.000 0.00 0.00 40.93 4.70
243 244 9.241317 GTAATTGTTTTAGTATGAGCTACGCTA 57.759 33.333 0.00 0.00 39.88 4.26
258 259 6.322712 GGCCACCCATATGAGTAATTGTTTTA 59.677 38.462 3.65 0.00 0.00 1.52
343 344 5.388654 ACCTAATTCCCTGCAATGGATAAG 58.611 41.667 5.52 4.31 27.99 1.73
485 486 1.213182 TGGGCACTTGTGTTGAAGGTA 59.787 47.619 2.61 0.00 0.00 3.08
521 522 6.351711 AGCAATGTGAGCTTGTCTATATCAA 58.648 36.000 0.00 0.00 39.87 2.57
631 635 8.380742 TCAATCTTCCTTACTTCTTCCACTAT 57.619 34.615 0.00 0.00 0.00 2.12
672 676 2.076100 TGTGAAGAAATAGTGCTGCCG 58.924 47.619 0.00 0.00 0.00 5.69
771 775 6.838382 AGGTATCTCTTCCTCTAGACTCTTC 58.162 44.000 0.00 0.00 0.00 2.87
798 802 8.455903 TGTCTTTGAGTTCATCTTCTTCAATT 57.544 30.769 0.00 0.00 0.00 2.32
858 862 6.302269 AGGTGATGAGTCTTCAACTTGATTT 58.698 36.000 18.40 0.00 37.92 2.17
947 951 6.515832 ACATCACGCTCTTATATGACAATCA 58.484 36.000 0.00 0.00 0.00 2.57
948 952 7.201393 GCTACATCACGCTCTTATATGACAATC 60.201 40.741 0.00 0.00 0.00 2.67
981 985 3.559242 GCATGTCAGCAAGAGGATTAGAC 59.441 47.826 0.00 0.00 0.00 2.59
1063 1067 4.493547 TGTCCAAGCAAACAGTTTTTCAG 58.506 39.130 0.00 0.00 0.00 3.02
1073 1077 5.565592 TGTATGATCATGTCCAAGCAAAC 57.434 39.130 18.72 4.83 0.00 2.93
1106 1110 7.339976 TGTCATCATAAATGAGAGAAATGCCAA 59.660 33.333 0.00 0.00 40.64 4.52
1139 1146 5.736951 AAGCATAGGACTAGCATAAGGAG 57.263 43.478 0.00 0.00 0.00 3.69
1293 1300 8.606830 GGGATAATACCCTCTAAGTCATCAATT 58.393 37.037 0.00 0.00 45.90 2.32
1455 1462 0.687920 TTCTTCGTGTGTGCCCCATA 59.312 50.000 0.00 0.00 0.00 2.74
1479 1487 0.725686 CTCGTGGATGCTCAAGCTTG 59.274 55.000 20.81 20.81 42.66 4.01
1495 1503 2.615869 CTCTTCTCCTTTGCTTCCTCG 58.384 52.381 0.00 0.00 0.00 4.63
1550 1565 2.409870 GCTCACCGGGCTTTGATGG 61.410 63.158 6.32 0.00 0.00 3.51
1827 1848 7.817418 TCTAAGTGTTTCAAGGTAAAAGCAT 57.183 32.000 0.00 0.00 0.00 3.79
1917 1938 6.648310 CAGGAAACATAGCATACTAGTCCATG 59.352 42.308 0.00 0.00 0.00 3.66
1938 1959 2.195727 TCACATGCTACCAATCCAGGA 58.804 47.619 0.00 0.00 0.00 3.86
2032 2053 8.630917 TGCTACTGTAGGTATTCAGACTTATTC 58.369 37.037 16.09 0.00 35.84 1.75
2066 2088 0.816825 CATGCCACCGATCAAGGGAG 60.817 60.000 0.00 0.00 35.02 4.30
2238 2267 1.224592 GGAACATGCCACCGATCCT 59.775 57.895 0.00 0.00 0.00 3.24
2380 2422 8.408043 AGATCAACAAGTTTAAATGATGACCA 57.592 30.769 6.07 0.00 32.25 4.02
2381 2423 9.346725 GAAGATCAACAAGTTTAAATGATGACC 57.653 33.333 6.07 0.00 32.25 4.02


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

AutoCloner maintained by Alex Coulton.