Multiple sequence alignment - TraesCS4B01G382500

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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 TraesCS4B01G382500 chr4B 100.000 3110 0 0 1 3110 661684366 661681257 0.000000e+00 5744
1 TraesCS4B01G382500 chr4B 93.860 2671 159 3 4 2670 661492491 661495160 0.000000e+00 4019
2 TraesCS4B01G382500 chr4B 98.218 449 8 0 2657 3105 661495189 661495637 0.000000e+00 785
3 TraesCS4B01G382500 chr4D 90.475 3118 267 17 1 3109 505993112 505990016 0.000000e+00 4085
4 TraesCS4B01G382500 chr5A 88.597 3122 293 23 1 3110 702142032 702138962 0.000000e+00 3735
5 TraesCS4B01G382500 chr7B 78.458 1193 211 25 1942 3105 746601411 746600236 0.000000e+00 737
6 TraesCS4B01G382500 chr7B 78.290 1193 213 25 1942 3105 746573103 746571928 0.000000e+00 726
7 TraesCS4B01G382500 chr7B 84.766 256 36 3 2851 3103 744679438 744679183 1.430000e-63 254
8 TraesCS4B01G382500 chrUn 78.623 1118 188 34 2011 3105 88950109 88951198 0.000000e+00 693
9 TraesCS4B01G382500 chrUn 78.642 1119 186 36 2011 3105 269543288 269542199 0.000000e+00 693
10 TraesCS4B01G382500 chrUn 78.335 1117 191 35 2011 3104 88958458 88959546 0.000000e+00 675


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 TraesCS4B01G382500 chr4B 661681257 661684366 3109 True 5744 5744 100.000 1 3110 1 chr4B.!!$R1 3109
1 TraesCS4B01G382500 chr4B 661492491 661495637 3146 False 2402 4019 96.039 4 3105 2 chr4B.!!$F1 3101
2 TraesCS4B01G382500 chr4D 505990016 505993112 3096 True 4085 4085 90.475 1 3109 1 chr4D.!!$R1 3108
3 TraesCS4B01G382500 chr5A 702138962 702142032 3070 True 3735 3735 88.597 1 3110 1 chr5A.!!$R1 3109
4 TraesCS4B01G382500 chr7B 746600236 746601411 1175 True 737 737 78.458 1942 3105 1 chr7B.!!$R3 1163
5 TraesCS4B01G382500 chr7B 746571928 746573103 1175 True 726 726 78.290 1942 3105 1 chr7B.!!$R2 1163
6 TraesCS4B01G382500 chrUn 88950109 88951198 1089 False 693 693 78.623 2011 3105 1 chrUn.!!$F1 1094
7 TraesCS4B01G382500 chrUn 269542199 269543288 1089 True 693 693 78.642 2011 3105 1 chrUn.!!$R1 1094
8 TraesCS4B01G382500 chrUn 88958458 88959546 1088 False 675 675 78.335 2011 3104 1 chrUn.!!$F2 1093

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
519 523 0.461163 CACGTGTGACCTGTCAACCA 60.461 55.0 7.58 0.0 41.85 3.67 F
1402 1410 0.253044 TATCTCCAACCAGCTGCCAC 59.747 55.0 8.66 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1721 0.036010 CTGAGACCGCCACTTGGAAT 60.036 55.0 0.0 0.0 37.39 3.01 R
2479 2514 0.461548 TCACTCTGCCGTGGATGATC 59.538 55.0 0.0 0.0 35.63 2.92 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
34 35 3.040147 GAGACATCCTCAAAACCGACA 57.960 47.619 0.00 0.00 41.58 4.35
35 36 3.399330 GAGACATCCTCAAAACCGACAA 58.601 45.455 0.00 0.00 41.58 3.18
45 46 5.163622 CCTCAAAACCGACAAGCATGATAAT 60.164 40.000 0.00 0.00 0.00 1.28
110 111 2.365635 ACGGGTGGCCTCTATGCT 60.366 61.111 3.32 0.00 0.00 3.79
226 229 1.202348 GTGTCTACAAATGCAAGGGGC 59.798 52.381 0.00 0.00 45.13 5.80
349 353 6.942576 AGAACATTACTACTCCAAACAGCATT 59.057 34.615 0.00 0.00 0.00 3.56
375 379 2.415759 GCGGTGCATGTCATTCATTGAA 60.416 45.455 0.75 0.75 35.70 2.69
382 386 3.133141 TGTCATTCATTGAACCCGTCA 57.867 42.857 0.15 0.00 35.70 4.35
469 473 5.195185 TCTGTAATGACGGTATACCACTCA 58.805 41.667 21.76 19.42 35.14 3.41
519 523 0.461163 CACGTGTGACCTGTCAACCA 60.461 55.000 7.58 0.00 41.85 3.67
521 525 0.867746 CGTGTGACCTGTCAACCATG 59.132 55.000 0.75 0.00 41.85 3.66
541 545 4.536364 TGAAATTATGTCGCTAGCAAGC 57.464 40.909 16.45 4.38 45.86 4.01
592 596 3.763360 CCTCAGAACAAATACATTGCCCA 59.237 43.478 0.00 0.00 43.13 5.36
699 703 6.007936 AGTGCGCTCTGAGTTCTATATAAG 57.992 41.667 11.84 0.00 0.00 1.73
801 805 3.084786 GGAAGCAATTCTAGCAACACCT 58.915 45.455 0.00 0.00 0.00 4.00
807 811 2.859165 TTCTAGCAACACCTCCTTGG 57.141 50.000 0.00 0.00 42.93 3.61
826 830 9.597681 CTCCTTGGAGTAAGTTATAGGGTAATA 57.402 37.037 8.45 0.00 34.45 0.98
841 845 3.312697 GGGTAATAGAAGCAAGAAAGCCG 59.687 47.826 0.00 0.00 34.23 5.52
913 920 9.667107 CTCCAACTATAGTCAAATCCAAAACTA 57.333 33.333 5.70 0.00 0.00 2.24
914 921 9.444600 TCCAACTATAGTCAAATCCAAAACTAC 57.555 33.333 5.70 0.00 0.00 2.73
920 927 6.787085 AGTCAAATCCAAAACTACTCTTCG 57.213 37.500 0.00 0.00 0.00 3.79
947 954 7.037873 ACCCTTTCTTTCCCAAAAGTTTAACTT 60.038 33.333 4.30 4.30 42.17 2.66
952 959 7.878036 TCTTTCCCAAAAGTTTAACTTATCCG 58.122 34.615 10.97 0.41 42.17 4.18
1055 1063 3.387091 TGACACCTATGCGCCGGT 61.387 61.111 4.18 6.06 0.00 5.28
1072 1080 0.541863 GGTTGTCTCATCGGACCCAT 59.458 55.000 0.00 0.00 35.54 4.00
1080 1088 1.383525 ATCGGACCCATTACCCGGT 60.384 57.895 0.00 0.00 43.16 5.28
1093 1101 2.679342 CCCGGTGACATCCATGGGT 61.679 63.158 13.02 0.00 38.08 4.51
1165 1173 3.247173 GGCTAATGTGCTCTCATCGAAAG 59.753 47.826 0.00 0.00 0.00 2.62
1209 1217 3.818787 GCCATCAGCGCCAACCAG 61.819 66.667 2.29 0.00 0.00 4.00
1237 1245 1.935873 CATCATCAATGCCGTCGTTCT 59.064 47.619 0.00 0.00 0.00 3.01
1293 1301 2.288763 TGTGTGCATCGTTAAGAGCTCA 60.289 45.455 17.77 0.00 0.00 4.26
1332 1340 3.957586 CTCCAGGCCACACCAGCA 61.958 66.667 5.01 0.00 43.14 4.41
1402 1410 0.253044 TATCTCCAACCAGCTGCCAC 59.747 55.000 8.66 0.00 0.00 5.01
1405 1413 4.954970 CCAACCAGCTGCCACGGT 62.955 66.667 8.66 0.00 33.32 4.83
1406 1414 3.357079 CAACCAGCTGCCACGGTC 61.357 66.667 8.66 0.00 30.91 4.79
1447 1455 2.516227 AGACCACTCCTTCTCATCGA 57.484 50.000 0.00 0.00 0.00 3.59
1452 1460 1.064803 CACTCCTTCTCATCGACCTCG 59.935 57.143 0.00 0.00 41.45 4.63
1461 1469 2.422479 CTCATCGACCTCGTCCTTTGTA 59.578 50.000 0.00 0.00 40.80 2.41
1468 1476 4.320788 CGACCTCGTCCTTTGTAAGTAACT 60.321 45.833 0.00 0.00 34.11 2.24
1492 1500 4.285517 AGGACAGTGTTTCTCATCTCATGT 59.714 41.667 0.00 0.00 0.00 3.21
1497 1505 6.017605 ACAGTGTTTCTCATCTCATGTTTGAC 60.018 38.462 0.00 0.00 0.00 3.18
1593 1601 0.899717 ATTTCAGGGTGCCACGCAAT 60.900 50.000 14.73 2.61 41.47 3.56
1610 1618 3.244215 CGCAATAGCCTCCTATCAAAGGA 60.244 47.826 0.00 0.00 45.04 3.36
1691 1699 0.940126 GATAATGTGCAGTGGGCTCG 59.060 55.000 0.00 0.00 45.15 5.03
1778 1786 3.454375 GGATTTATGACGGCTTCTTCGA 58.546 45.455 0.00 0.00 0.00 3.71
1806 1814 0.242825 CGACCGACTACCTCTTTGCA 59.757 55.000 0.00 0.00 0.00 4.08
1854 1862 1.118965 TCAAGGGTGTGCTCTCGGAA 61.119 55.000 0.00 0.00 0.00 4.30
1860 1868 1.197721 GGTGTGCTCTCGGAAAACATG 59.802 52.381 0.00 0.00 0.00 3.21
1861 1869 2.143122 GTGTGCTCTCGGAAAACATGA 58.857 47.619 0.00 0.00 0.00 3.07
1879 1887 0.445436 GAAGTGCAATGAGCCGACAG 59.555 55.000 0.00 0.00 44.83 3.51
1920 1928 1.213678 TCCCTGAATGGAGGCAATCAG 59.786 52.381 0.00 0.00 39.16 2.90
1963 1971 2.939261 GCGAAGAGGGGTCGGACAA 61.939 63.158 10.76 0.00 38.93 3.18
2001 2009 1.217057 ATTCTGCCATGTCTGGGGGT 61.217 55.000 0.00 0.00 43.36 4.95
2078 2086 2.807676 GGAGGAGGCATTTTTCAAGGA 58.192 47.619 0.00 0.00 0.00 3.36
2164 2172 3.665675 ATGAAGGGCGAGGACGTGC 62.666 63.158 0.00 0.00 41.98 5.34
2176 2184 3.457234 GAGGACGTGCATGTGATGAATA 58.543 45.455 18.17 0.00 0.00 1.75
2241 2249 5.465390 CGATCTTAATAACATCCTCGGCAAA 59.535 40.000 0.00 0.00 0.00 3.68
2305 2337 1.121407 TGGCCTACAGTCTGTGCAGT 61.121 55.000 16.03 0.00 0.00 4.40
2310 2342 3.668447 CCTACAGTCTGTGCAGTTCAAT 58.332 45.455 16.03 0.00 0.00 2.57
2430 2462 1.272092 TGTGCTTCTTGGAATCTGGGG 60.272 52.381 0.00 0.00 0.00 4.96
2454 2486 5.011227 GGATACAGGAGGTAAAGAGGATCAC 59.989 48.000 0.00 0.00 34.15 3.06
2455 2487 3.791320 ACAGGAGGTAAAGAGGATCACA 58.209 45.455 0.00 0.00 37.82 3.58
2457 2489 3.772025 CAGGAGGTAAAGAGGATCACAGT 59.228 47.826 0.00 0.00 37.82 3.55
2466 2501 7.064728 GGTAAAGAGGATCACAGTTGAACATAC 59.935 40.741 0.00 0.00 37.82 2.39
2479 2514 5.007039 AGTTGAACATACTGATAGCAATGCG 59.993 40.000 0.00 0.00 0.00 4.73
2568 2605 3.531262 GGTACACACCAATCAAACGAC 57.469 47.619 0.00 0.00 45.04 4.34
2594 2631 5.129320 TCTCTTTTCTACTCCAGCATGCATA 59.871 40.000 21.98 3.30 31.97 3.14
2874 2954 4.917385 ACAATAGTGTTGTTCCTGCCATA 58.083 39.130 0.00 0.00 32.58 2.74
3044 3125 5.863965 TCCTGAAATGTCAATCTACACACA 58.136 37.500 0.00 0.00 31.88 3.72
3096 3177 0.031178 GCAGCCAAAGTGGAACAGTG 59.969 55.000 0.00 0.00 43.84 3.66
3105 3186 4.957759 AAGTGGAACAGTGTGTTGTTAC 57.042 40.909 0.00 0.00 43.84 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.250234 GTAGACCACAGAGGCATGCA 59.750 55.000 21.36 0.00 43.14 3.96
134 137 3.870419 GAGTTGCCTGCAAACAAATGAAA 59.130 39.130 6.07 0.00 37.70 2.69
195 198 0.882927 TGTAGACACCAAGTTGCGCC 60.883 55.000 4.18 0.00 0.00 6.53
344 348 0.452987 CATGCACCGCTTACAATGCT 59.547 50.000 0.00 0.00 38.90 3.79
349 353 1.737236 GAATGACATGCACCGCTTACA 59.263 47.619 0.00 0.00 0.00 2.41
382 386 3.068873 TCAAATTTGGTTTAGCCGCTTGT 59.931 39.130 17.90 0.00 41.21 3.16
469 473 1.414181 CAGGCAACGTGGATAGAGGAT 59.586 52.381 0.00 0.00 46.39 3.24
519 523 5.100751 GCTTGCTAGCGACATAATTTCAT 57.899 39.130 10.77 0.00 37.71 2.57
541 545 3.120991 CGTTCAGTTTCAACGCTAAGGAG 60.121 47.826 0.00 0.00 40.14 3.69
592 596 8.616076 GGTTTGATTTCTTGAAGATACGATGAT 58.384 33.333 0.00 0.00 0.00 2.45
699 703 0.813821 GAAATGGCCTCACTTCCTGC 59.186 55.000 3.32 0.00 0.00 4.85
801 805 9.597681 CTATTACCCTATAACTTACTCCAAGGA 57.402 37.037 0.00 0.00 38.70 3.36
826 830 0.610232 ATGGCGGCTTTCTTGCTTCT 60.610 50.000 11.43 0.00 0.00 2.85
841 845 3.904339 TCCCTCCTTAGAGTGAATATGGC 59.096 47.826 0.00 0.00 38.58 4.40
874 878 1.098712 GTTGGAGTTGGGCGACACAA 61.099 55.000 0.00 0.00 0.00 3.33
913 920 2.038689 GGGAAAGAAAGGGTCGAAGAGT 59.961 50.000 0.00 0.00 36.95 3.24
914 921 2.038557 TGGGAAAGAAAGGGTCGAAGAG 59.961 50.000 0.00 0.00 36.95 2.85
920 927 5.353394 AAACTTTTGGGAAAGAAAGGGTC 57.647 39.130 5.95 0.00 44.03 4.46
947 954 0.830444 CGGAATGGAGGGGACGGATA 60.830 60.000 0.00 0.00 0.00 2.59
952 959 4.547367 CGGCGGAATGGAGGGGAC 62.547 72.222 0.00 0.00 0.00 4.46
1023 1031 0.037326 TGTCACCGGAGAAGCATGTC 60.037 55.000 9.46 0.00 0.00 3.06
1055 1063 2.169769 GGTAATGGGTCCGATGAGACAA 59.830 50.000 0.00 0.00 38.59 3.18
1072 1080 0.544223 CCATGGATGTCACCGGGTAA 59.456 55.000 5.56 0.00 0.00 2.85
1080 1088 2.568546 AGGAGTACCCATGGATGTCA 57.431 50.000 15.22 0.00 37.41 3.58
1093 1101 4.901197 TTGGCACATACTTGAAGGAGTA 57.099 40.909 0.00 0.00 39.30 2.59
1165 1173 3.198872 CGGATAAAGAGAAGAAGGGTGC 58.801 50.000 0.00 0.00 0.00 5.01
1209 1217 1.068748 GGCATTGATGATGATGTCGCC 60.069 52.381 0.00 0.00 38.03 5.54
1237 1245 3.018856 CCATCAACTCATTAAGCAGGCA 58.981 45.455 0.00 0.00 0.00 4.75
1293 1301 3.446570 GCAGCGGCAAAGGAGCAT 61.447 61.111 3.18 0.00 40.72 3.79
1375 1383 3.900601 AGCTGGTTGGAGATAGTGGATAG 59.099 47.826 0.00 0.00 0.00 2.08
1402 1410 2.511600 GGACATGAAGGCCGACCG 60.512 66.667 0.00 0.00 42.76 4.79
1447 1455 5.184671 CCTAGTTACTTACAAAGGACGAGGT 59.815 44.000 12.30 0.00 37.09 3.85
1461 1469 6.726490 TGAGAAACACTGTCCTAGTTACTT 57.274 37.500 0.00 0.00 37.60 2.24
1468 1476 5.481824 ACATGAGATGAGAAACACTGTCCTA 59.518 40.000 0.00 0.00 0.00 2.94
1492 1500 4.858680 TGTGGCGCCGTGGTCAAA 62.859 61.111 23.90 0.00 0.00 2.69
1562 1570 0.539051 CCTGAAATCGAGCCTGGAGT 59.461 55.000 0.00 0.00 0.00 3.85
1662 1670 1.498865 GCACATTATCGCTCGGTGGG 61.499 60.000 0.00 0.00 0.00 4.61
1713 1721 0.036010 CTGAGACCGCCACTTGGAAT 60.036 55.000 0.00 0.00 37.39 3.01
1719 1727 1.680651 CTCCTCTGAGACCGCCACT 60.681 63.158 6.17 0.00 41.42 4.00
1778 1786 0.669077 GTAGTCGGTCGCATCTGGAT 59.331 55.000 0.00 0.00 0.00 3.41
1854 1862 2.352030 CGGCTCATTGCACTTCATGTTT 60.352 45.455 0.00 0.00 45.15 2.83
1860 1868 0.445436 CTGTCGGCTCATTGCACTTC 59.555 55.000 0.00 0.00 45.15 3.01
1861 1869 1.580845 GCTGTCGGCTCATTGCACTT 61.581 55.000 0.00 0.00 45.15 3.16
1879 1887 5.298026 GGGAAAAGAGATGATTAGAAGTGGC 59.702 44.000 0.00 0.00 0.00 5.01
1920 1928 3.743886 CTTACGTTCAAATTTCGGGCTC 58.256 45.455 0.00 0.00 0.00 4.70
1927 1935 1.400500 CGCCGGCTTACGTTCAAATTT 60.400 47.619 26.68 0.00 42.24 1.82
1963 1971 3.721087 ATTGTCCTTCTCCGGATGTTT 57.279 42.857 3.57 0.00 35.11 2.83
2001 2009 0.616395 TCTGGTGTATCTTCGGGCCA 60.616 55.000 4.39 0.00 0.00 5.36
2009 2017 2.761208 CCGAGGACTTTCTGGTGTATCT 59.239 50.000 0.00 0.00 0.00 1.98
2078 2086 2.604686 TCGCACCCTCCTCTGCTT 60.605 61.111 0.00 0.00 0.00 3.91
2164 2172 3.999001 CTGTCCCCGATATTCATCACATG 59.001 47.826 0.00 0.00 0.00 3.21
2176 2184 2.697761 CGACACGACTGTCCCCGAT 61.698 63.158 1.55 0.00 43.64 4.18
2241 2249 0.674895 GCAGATCCTTCGGTGTTGCT 60.675 55.000 0.00 0.00 0.00 3.91
2305 2337 6.942005 ACAGAGGTATTGTGTTCATCATTGAA 59.058 34.615 0.00 0.00 39.54 2.69
2310 2342 5.863965 TCAACAGAGGTATTGTGTTCATCA 58.136 37.500 0.00 0.00 40.96 3.07
2430 2462 5.011227 GTGATCCTCTTTACCTCCTGTATCC 59.989 48.000 0.00 0.00 0.00 2.59
2454 2486 6.197276 GCATTGCTATCAGTATGTTCAACTG 58.803 40.000 0.16 0.00 44.66 3.16
2455 2487 5.007039 CGCATTGCTATCAGTATGTTCAACT 59.993 40.000 7.12 0.00 37.40 3.16
2457 2489 5.115480 TCGCATTGCTATCAGTATGTTCAA 58.885 37.500 7.12 0.00 37.40 2.69
2466 2501 3.124806 GTGGATGATCGCATTGCTATCAG 59.875 47.826 24.48 3.52 42.37 2.90
2479 2514 0.461548 TCACTCTGCCGTGGATGATC 59.538 55.000 0.00 0.00 35.63 2.92
2566 2603 3.057456 TGCTGGAGTAGAAAAGAGACGTC 60.057 47.826 7.70 7.70 0.00 4.34
2568 2605 3.577649 TGCTGGAGTAGAAAAGAGACG 57.422 47.619 0.00 0.00 0.00 4.18
2594 2631 1.278985 TGGTCGGAGATGTGCTTGAAT 59.721 47.619 0.00 0.00 40.67 2.57
2874 2954 8.137437 CAGTTTTTAGGTTCTTCATCAACATGT 58.863 33.333 0.00 0.00 0.00 3.21
2938 3018 6.647334 TCACAGTTTCAATGGCTTTCATAA 57.353 33.333 0.00 0.00 34.44 1.90
3044 3125 7.850935 AAATGAGCATCCCTTGAATTATCAT 57.149 32.000 0.00 0.00 34.96 2.45


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

AutoCloner maintained by Alex Coulton.