Multiple sequence alignment - TraesCS4B01G378400

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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 TraesCS4B01G378400 chr4B 100.000 2972 0 0 1 2972 660447575 660444604 0.000000e+00 5489
1 TraesCS4B01G378400 chr4B 97.503 2203 44 5 1 2193 660418267 660416066 0.000000e+00 3753
2 TraesCS4B01G378400 chr4B 92.413 1687 104 11 1121 2795 660401776 660400102 0.000000e+00 2385
3 TraesCS4B01G378400 chr4B 85.616 146 18 2 620 765 660436794 660436652 1.850000e-32 150
4 TraesCS4B01G378400 chrUn 89.869 2892 178 48 1 2860 110328143 110325335 0.000000e+00 3611
5 TraesCS4B01G378400 chrUn 85.188 2282 243 52 614 2860 110271506 110269285 0.000000e+00 2254
6 TraesCS4B01G378400 chrUn 85.013 2282 247 52 614 2860 110209102 110206881 0.000000e+00 2231
7 TraesCS4B01G378400 chrUn 85.839 2069 214 40 819 2860 278955089 278953073 0.000000e+00 2124
8 TraesCS4B01G378400 chrUn 86.835 1899 183 39 984 2860 184220180 184222033 0.000000e+00 2060
9 TraesCS4B01G378400 chrUn 90.723 1563 107 17 1309 2860 110320435 110318900 0.000000e+00 2049
10 TraesCS4B01G378400 chrUn 90.723 1563 107 16 1309 2860 187710510 187708975 0.000000e+00 2049
11 TraesCS4B01G378400 chrUn 90.653 1562 110 15 1309 2860 110306215 110304680 0.000000e+00 2043
12 TraesCS4B01G378400 chrUn 90.659 1563 109 17 1309 2860 187698832 187697296 0.000000e+00 2043
13 TraesCS4B01G378400 chrUn 90.595 1563 109 17 1309 2860 110243569 110242034 0.000000e+00 2037
14 TraesCS4B01G378400 chrUn 90.403 1563 113 15 1309 2860 110255260 110253724 0.000000e+00 2021
15 TraesCS4B01G378400 chrUn 90.236 1567 115 16 1309 2864 110300519 110298980 0.000000e+00 2012
16 TraesCS4B01G378400 chrUn 90.108 1567 115 18 1309 2864 187693137 187691600 0.000000e+00 1999
17 TraesCS4B01G378400 chrUn 88.030 1320 117 21 1554 2860 184210561 184211852 0.000000e+00 1524
18 TraesCS4B01G378400 chrUn 87.682 1031 91 16 1845 2864 437093163 437092158 0.000000e+00 1168
19 TraesCS4B01G378400 chrUn 92.000 125 10 0 2740 2864 110235532 110235408 3.040000e-40 176
20 TraesCS4B01G378400 chrUn 93.519 108 4 1 2868 2972 110235376 110235269 1.100000e-34 158
21 TraesCS4B01G378400 chrUn 93.519 108 4 1 2868 2972 187691568 187691461 1.100000e-34 158
22 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110253688 110253581 5.130000e-33 152
23 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110293309 110293202 5.130000e-33 152
24 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110298948 110298841 5.130000e-33 152
25 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110304644 110304537 5.130000e-33 152
26 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110318864 110318757 5.130000e-33 152
27 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 110325299 110325192 5.130000e-33 152
28 TraesCS4B01G378400 chrUn 92.593 108 5 1 2868 2972 187708939 187708832 5.130000e-33 152
29 TraesCS4B01G378400 chrUn 84.868 152 20 2 614 765 278955324 278955176 1.850000e-32 150
30 TraesCS4B01G378400 chrUn 85.616 146 18 2 620 765 322030374 322030232 1.850000e-32 150
31 TraesCS4B01G378400 chrUn 84.868 152 20 2 614 765 441917374 441917226 1.850000e-32 150
32 TraesCS4B01G378400 chr5A 89.497 2885 213 39 1 2860 700371187 700374006 0.000000e+00 3567
33 TraesCS4B01G378400 chr5A 85.970 2067 213 39 819 2860 699708138 699710152 0.000000e+00 2139
34 TraesCS4B01G378400 chr5A 85.935 2069 212 40 819 2860 699561903 699563919 0.000000e+00 2135
35 TraesCS4B01G378400 chr5A 85.659 2071 215 42 819 2860 699629490 699631507 0.000000e+00 2104
36 TraesCS4B01G378400 chr5A 86.888 1899 183 39 984 2860 699703134 699704988 0.000000e+00 2067
37 TraesCS4B01G378400 chr5A 82.428 1252 159 32 984 2196 699521119 699519890 0.000000e+00 1037
38 TraesCS4B01G378400 chr5A 84.868 152 20 2 614 765 699561668 699561816 1.850000e-32 150
39 TraesCS4B01G378400 chr5A 84.868 152 20 2 614 765 699629255 699629403 1.850000e-32 150


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 TraesCS4B01G378400 chr4B 660444604 660447575 2971 True 5489.0 5489 100.0000 1 2972 1 chr4B.!!$R4 2971
1 TraesCS4B01G378400 chr4B 660416066 660418267 2201 True 3753.0 3753 97.5030 1 2193 1 chr4B.!!$R2 2192
2 TraesCS4B01G378400 chr4B 660400102 660401776 1674 True 2385.0 2385 92.4130 1121 2795 1 chr4B.!!$R1 1674
3 TraesCS4B01G378400 chrUn 110269285 110271506 2221 True 2254.0 2254 85.1880 614 2860 1 chrUn.!!$R3 2246
4 TraesCS4B01G378400 chrUn 110206881 110209102 2221 True 2231.0 2231 85.0130 614 2860 1 chrUn.!!$R1 2246
5 TraesCS4B01G378400 chrUn 184220180 184222033 1853 False 2060.0 2060 86.8350 984 2860 1 chrUn.!!$F2 1876
6 TraesCS4B01G378400 chrUn 187697296 187698832 1536 True 2043.0 2043 90.6590 1309 2860 1 chrUn.!!$R5 1551
7 TraesCS4B01G378400 chrUn 110242034 110243569 1535 True 2037.0 2037 90.5950 1309 2860 1 chrUn.!!$R2 1551
8 TraesCS4B01G378400 chrUn 110325192 110328143 2951 True 1881.5 3611 91.2310 1 2972 2 chrUn.!!$R14 2971
9 TraesCS4B01G378400 chrUn 184210561 184211852 1291 False 1524.0 1524 88.0300 1554 2860 1 chrUn.!!$F1 1306
10 TraesCS4B01G378400 chrUn 437092158 437093163 1005 True 1168.0 1168 87.6820 1845 2864 1 chrUn.!!$R7 1019
11 TraesCS4B01G378400 chrUn 278953073 278955324 2251 True 1137.0 2124 85.3535 614 2860 2 chrUn.!!$R17 2246
12 TraesCS4B01G378400 chrUn 110318757 110320435 1678 True 1100.5 2049 91.6580 1309 2972 2 chrUn.!!$R13 1663
13 TraesCS4B01G378400 chrUn 187708832 187710510 1678 True 1100.5 2049 91.6580 1309 2972 2 chrUn.!!$R16 1663
14 TraesCS4B01G378400 chrUn 110304537 110306215 1678 True 1097.5 2043 91.6230 1309 2972 2 chrUn.!!$R12 1663
15 TraesCS4B01G378400 chrUn 110253581 110255260 1679 True 1086.5 2021 91.4980 1309 2972 2 chrUn.!!$R10 1663
16 TraesCS4B01G378400 chrUn 110298841 110300519 1678 True 1082.0 2012 91.4145 1309 2972 2 chrUn.!!$R11 1663
17 TraesCS4B01G378400 chrUn 187691461 187693137 1676 True 1078.5 1999 91.8135 1309 2972 2 chrUn.!!$R15 1663
18 TraesCS4B01G378400 chr5A 700371187 700374006 2819 False 3567.0 3567 89.4970 1 2860 1 chr5A.!!$F1 2859
19 TraesCS4B01G378400 chr5A 699703134 699710152 7018 False 2103.0 2139 86.4290 819 2860 2 chr5A.!!$F4 2041
20 TraesCS4B01G378400 chr5A 699561668 699563919 2251 False 1142.5 2135 85.4015 614 2860 2 chr5A.!!$F2 2246
21 TraesCS4B01G378400 chr5A 699629255 699631507 2252 False 1127.0 2104 85.2635 614 2860 2 chr5A.!!$F3 2246
22 TraesCS4B01G378400 chr5A 699519890 699521119 1229 True 1037.0 1037 82.4280 984 2196 1 chr5A.!!$R1 1212

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
1570 6863 2.432628 GACTCAACACCCTCGGCG 60.433 66.667 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2884 8291 0.039527 GTTAGCGTGTTTGGCTTGGG 60.04 55.0 0.0 0.0 41.8 4.12 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
1570 6863 2.432628 GACTCAACACCCTCGGCG 60.433 66.667 0.00 0.0 0.00 6.46
1761 7054 1.535462 GGTGATGTGTTTGTCTTCCCG 59.465 52.381 0.00 0.0 0.00 5.14
1814 7107 3.972276 CCACAAACCCGCCGTTGG 61.972 66.667 0.00 0.0 33.93 3.77
1878 7171 1.081509 CAATGCGGTGTTTGGGTCG 60.082 57.895 0.00 0.0 0.00 4.79
2262 7586 6.018669 CCGAAGCAAGAGATGATTAGGTTAAC 60.019 42.308 0.00 0.0 42.95 2.01
2265 7589 7.856145 AGCAAGAGATGATTAGGTTAACAAG 57.144 36.000 8.10 0.0 0.00 3.16
2304 7631 9.399797 TGATTATCTGGCAATCCATTATATGTC 57.600 33.333 0.00 0.0 42.51 3.06
2392 7739 5.530915 CCCGATTGTGCTCAGGATTTAAATA 59.469 40.000 0.00 0.0 0.00 1.40
2474 7821 5.979993 TGGTGCATGCAATAAGAAATTGAT 58.020 33.333 24.58 0.0 0.00 2.57
2490 7837 4.989279 ATTGATGGTTCCTGCATGTAAC 57.011 40.909 0.00 0.0 0.00 2.50
2498 7846 5.772672 TGGTTCCTGCATGTAACATTTTAGT 59.227 36.000 0.00 0.0 0.00 2.24
2507 7855 9.606631 TGCATGTAACATTTTAGTTTCCTTTTT 57.393 25.926 0.00 0.0 33.07 1.94
2565 7913 7.039152 TGCTTTAATGGAAATTTGATGAGGTGA 60.039 33.333 0.00 0.0 0.00 4.02
2574 7923 7.495606 GGAAATTTGATGAGGTGACTTGTTTTT 59.504 33.333 0.00 0.0 44.43 1.94
2580 7929 7.648142 TGATGAGGTGACTTGTTTTTATCAAC 58.352 34.615 0.00 0.0 44.43 3.18
2663 8015 3.626930 TGTTTTAGAAACTGGGCACACT 58.373 40.909 5.30 0.0 0.00 3.55
2699 8051 9.705290 ATTCCAAAAATTAACTCCAACATACAC 57.295 29.630 0.00 0.0 0.00 2.90
2717 8069 8.035165 ACATACACATAGAAAACGTGCATAAA 57.965 30.769 0.00 0.0 33.89 1.40
2718 8070 7.960738 ACATACACATAGAAAACGTGCATAAAC 59.039 33.333 0.00 0.0 33.89 2.01
2719 8071 6.554334 ACACATAGAAAACGTGCATAAACT 57.446 33.333 0.00 0.0 33.89 2.66
2720 8072 6.966021 ACACATAGAAAACGTGCATAAACTT 58.034 32.000 0.00 0.0 33.89 2.66
2721 8073 8.090250 ACACATAGAAAACGTGCATAAACTTA 57.910 30.769 0.00 0.0 33.89 2.24
2722 8074 8.013378 ACACATAGAAAACGTGCATAAACTTAC 58.987 33.333 0.00 0.0 33.89 2.34
2723 8075 8.012809 CACATAGAAAACGTGCATAAACTTACA 58.987 33.333 0.00 0.0 0.00 2.41
2724 8076 8.561212 ACATAGAAAACGTGCATAAACTTACAA 58.439 29.630 0.00 0.0 0.00 2.41
2725 8077 9.388346 CATAGAAAACGTGCATAAACTTACAAA 57.612 29.630 0.00 0.0 0.00 2.83
2726 8078 9.953697 ATAGAAAACGTGCATAAACTTACAAAA 57.046 25.926 0.00 0.0 0.00 2.44
2727 8079 8.335256 AGAAAACGTGCATAAACTTACAAAAG 57.665 30.769 0.00 0.0 38.77 2.27
2728 8080 8.185505 AGAAAACGTGCATAAACTTACAAAAGA 58.814 29.630 0.00 0.0 36.50 2.52
2729 8081 8.690680 AAAACGTGCATAAACTTACAAAAGAA 57.309 26.923 0.00 0.0 36.50 2.52
2730 8082 8.690680 AAACGTGCATAAACTTACAAAAGAAA 57.309 26.923 0.00 0.0 36.50 2.52
2731 8083 8.690680 AACGTGCATAAACTTACAAAAGAAAA 57.309 26.923 0.00 0.0 36.50 2.29
2732 8084 8.335256 ACGTGCATAAACTTACAAAAGAAAAG 57.665 30.769 0.00 0.0 36.50 2.27
2733 8085 8.185505 ACGTGCATAAACTTACAAAAGAAAAGA 58.814 29.630 0.00 0.0 36.50 2.52
2734 8086 9.180678 CGTGCATAAACTTACAAAAGAAAAGAT 57.819 29.630 0.00 0.0 36.50 2.40
2812 8191 8.106247 TGAGTTGTTTCTTTGTAACAAGACTT 57.894 30.769 0.00 0.0 43.78 3.01
2866 8273 1.503542 CGCTTGGCTGAATGGTGAC 59.496 57.895 0.00 0.0 0.00 3.67
2884 8291 2.162208 TGACGATCAAAGAAAGCATGGC 59.838 45.455 0.00 0.0 0.00 4.40
2906 8316 2.116366 CAAGCCAAACACGCTAACAAC 58.884 47.619 0.00 0.0 34.84 3.32
2942 8352 2.593468 TTAGACGCCTCCAGCATGCC 62.593 60.000 15.66 0.0 44.04 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1570 6863 1.649348 CGATGCGCGCAATTGAGAC 60.649 57.895 39.68 20.06 0.00 3.36
1761 7054 0.681243 GGAAGTGAATGAGCCCCACC 60.681 60.000 0.00 0.00 0.00 4.61
1878 7171 3.485463 TCATCGGATATTTGTGGGTCC 57.515 47.619 0.00 0.00 0.00 4.46
2204 7526 7.303261 GGAAAAGAACCGAAAATAACGATTCT 58.697 34.615 0.00 0.00 44.10 2.40
2205 7527 6.525628 GGGAAAAGAACCGAAAATAACGATTC 59.474 38.462 0.00 0.00 33.99 2.52
2262 7586 7.031372 CAGATAATCATGTGTTGTTTCCCTTG 58.969 38.462 0.00 0.00 0.00 3.61
2265 7589 5.679638 GCCAGATAATCATGTGTTGTTTCCC 60.680 44.000 0.00 0.00 0.00 3.97
2304 7631 4.148128 AGGTGCTCAATCCTAACATCAG 57.852 45.455 0.00 0.00 31.66 2.90
2320 7647 5.997746 TGTATTGCAAGATAATCCTAGGTGC 59.002 40.000 9.08 9.94 0.00 5.01
2392 7739 5.280654 ACTTTTGCACATTCAACTTCCAT 57.719 34.783 0.00 0.00 0.00 3.41
2474 7821 5.772672 ACTAAAATGTTACATGCAGGAACCA 59.227 36.000 4.84 0.00 0.00 3.67
2498 7846 7.928706 TGACAAGAGTTTTGAACAAAAAGGAAA 59.071 29.630 13.13 0.00 41.37 3.13
2507 7855 6.567687 TTGAACTGACAAGAGTTTTGAACA 57.432 33.333 0.00 0.12 36.27 3.18
2642 7994 3.380004 CAGTGTGCCCAGTTTCTAAAACA 59.620 43.478 5.46 0.00 0.00 2.83
2663 8015 7.010160 AGTTAATTTTTGGAATCTGGTCTCCA 58.990 34.615 0.00 0.00 40.03 3.86
2686 8038 6.147164 CACGTTTTCTATGTGTATGTTGGAGT 59.853 38.462 0.00 0.00 38.67 3.85
2699 8051 8.942669 TTGTAAGTTTATGCACGTTTTCTATG 57.057 30.769 0.00 0.00 0.00 2.23
2812 8191 9.558648 CGTTTTGTGATCAAATGATTCTATGAA 57.441 29.630 0.00 0.00 42.14 2.57
2821 8200 5.559991 CGAAGTCCGTTTTGTGATCAAATGA 60.560 40.000 0.00 0.00 42.14 2.57
2827 8206 1.136057 GCCGAAGTCCGTTTTGTGATC 60.136 52.381 0.00 0.00 36.31 2.92
2860 8239 2.844946 TGCTTTCTTTGATCGTCACCA 58.155 42.857 0.00 0.00 0.00 4.17
2866 8273 1.202336 GGGCCATGCTTTCTTTGATCG 60.202 52.381 4.39 0.00 0.00 3.69
2884 8291 0.039527 GTTAGCGTGTTTGGCTTGGG 60.040 55.000 0.00 0.00 41.80 4.12
2906 8316 0.322997 TAATTGGGCACTTCCGGTGG 60.323 55.000 0.00 0.00 45.44 4.61
2942 8352 2.169789 CATGTGCTTCCTCTCGGCG 61.170 63.158 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.