Multiple sequence alignment - TraesCS7B01G187700

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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 TraesCS7B01G187700 chr7B 100.000 2549 0 0 1 2549 316361187 316358639 0 4708
1 TraesCS7B01G187700 chr7B 92.682 1749 118 5 1 1743 36428065 36426321 0 2512
2 TraesCS7B01G187700 chr3D 93.561 1755 100 8 1 1743 558679304 558681057 0 2603
3 TraesCS7B01G187700 chr3D 93.651 819 43 7 1738 2549 237753885 237753069 0 1216
4 TraesCS7B01G187700 chr6B 93.333 1755 103 6 1 1743 567118186 567116434 0 2580
5 TraesCS7B01G187700 chr6B 93.109 1756 107 6 1 1743 147950686 147948932 0 2560
6 TraesCS7B01G187700 chr6B 92.707 1755 114 6 1 1743 223247733 223249485 0 2519
7 TraesCS7B01G187700 chr4D 92.947 1744 114 8 3 1743 473971217 473969480 0 2531
8 TraesCS7B01G187700 chr4D 92.173 856 54 11 1704 2549 203932683 203931831 0 1197
9 TraesCS7B01G187700 chr5B 93.060 1729 104 6 1 1717 659536141 659537865 0 2514
10 TraesCS7B01G187700 chr2B 92.198 1756 120 9 1 1743 664330483 664328732 0 2468
11 TraesCS7B01G187700 chr5D 92.146 1757 116 10 1 1743 387241780 387243528 0 2460
12 TraesCS7B01G187700 chr5D 93.966 812 44 4 1741 2549 187981460 187980651 0 1223
13 TraesCS7B01G187700 chr5D 93.958 811 44 4 1741 2549 241362892 241362085 0 1221
14 TraesCS7B01G187700 chr5D 93.850 813 45 4 1741 2549 185639980 185640791 0 1219
15 TraesCS7B01G187700 chr3B 94.458 812 40 4 1740 2549 349368053 349367245 0 1245
16 TraesCS7B01G187700 chr3B 93.835 811 48 1 1741 2549 335216441 335217251 0 1219
17 TraesCS7B01G187700 chr6D 93.966 812 43 5 1741 2549 212374950 212374142 0 1223
18 TraesCS7B01G187700 chr6D 87.161 958 120 2 712 1669 345634637 345635591 0 1085
19 TraesCS7B01G187700 chr2D 93.842 812 46 3 1741 2549 272420614 272421424 0 1219


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 TraesCS7B01G187700 chr7B 316358639 316361187 2548 True 4708 4708 100.000 1 2549 1 chr7B.!!$R2 2548
1 TraesCS7B01G187700 chr7B 36426321 36428065 1744 True 2512 2512 92.682 1 1743 1 chr7B.!!$R1 1742
2 TraesCS7B01G187700 chr3D 558679304 558681057 1753 False 2603 2603 93.561 1 1743 1 chr3D.!!$F1 1742
3 TraesCS7B01G187700 chr3D 237753069 237753885 816 True 1216 1216 93.651 1738 2549 1 chr3D.!!$R1 811
4 TraesCS7B01G187700 chr6B 567116434 567118186 1752 True 2580 2580 93.333 1 1743 1 chr6B.!!$R2 1742
5 TraesCS7B01G187700 chr6B 147948932 147950686 1754 True 2560 2560 93.109 1 1743 1 chr6B.!!$R1 1742
6 TraesCS7B01G187700 chr6B 223247733 223249485 1752 False 2519 2519 92.707 1 1743 1 chr6B.!!$F1 1742
7 TraesCS7B01G187700 chr4D 473969480 473971217 1737 True 2531 2531 92.947 3 1743 1 chr4D.!!$R2 1740
8 TraesCS7B01G187700 chr4D 203931831 203932683 852 True 1197 1197 92.173 1704 2549 1 chr4D.!!$R1 845
9 TraesCS7B01G187700 chr5B 659536141 659537865 1724 False 2514 2514 93.060 1 1717 1 chr5B.!!$F1 1716
10 TraesCS7B01G187700 chr2B 664328732 664330483 1751 True 2468 2468 92.198 1 1743 1 chr2B.!!$R1 1742
11 TraesCS7B01G187700 chr5D 387241780 387243528 1748 False 2460 2460 92.146 1 1743 1 chr5D.!!$F2 1742
12 TraesCS7B01G187700 chr5D 187980651 187981460 809 True 1223 1223 93.966 1741 2549 1 chr5D.!!$R1 808
13 TraesCS7B01G187700 chr5D 241362085 241362892 807 True 1221 1221 93.958 1741 2549 1 chr5D.!!$R2 808
14 TraesCS7B01G187700 chr5D 185639980 185640791 811 False 1219 1219 93.850 1741 2549 1 chr5D.!!$F1 808
15 TraesCS7B01G187700 chr3B 349367245 349368053 808 True 1245 1245 94.458 1740 2549 1 chr3B.!!$R1 809
16 TraesCS7B01G187700 chr3B 335216441 335217251 810 False 1219 1219 93.835 1741 2549 1 chr3B.!!$F1 808
17 TraesCS7B01G187700 chr6D 212374142 212374950 808 True 1223 1223 93.966 1741 2549 1 chr6D.!!$R1 808
18 TraesCS7B01G187700 chr6D 345634637 345635591 954 False 1085 1085 87.161 712 1669 1 chr6D.!!$F1 957
19 TraesCS7B01G187700 chr2D 272420614 272421424 810 False 1219 1219 93.842 1741 2549 1 chr2D.!!$F1 808

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
204 205 0.108774 TGGATTACGGTGGTGTTGCA 59.891 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1909 0.396435 TGGTCAGGTTGATCGTGCTT 59.604 50.0 0.0 0.0 27.66 3.91 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
25 26 3.756082 TCTTAGGCATTCCCAAACCAT 57.244 42.857 0.00 0.00 35.39 3.55
33 34 1.182385 TTCCCAAACCATCGCCAACC 61.182 55.000 0.00 0.00 0.00 3.77
102 103 0.875059 GGTTTCAAGCAGGGAAGTCG 59.125 55.000 0.00 0.00 0.00 4.18
204 205 0.108774 TGGATTACGGTGGTGTTGCA 59.891 50.000 0.00 0.00 0.00 4.08
267 268 1.141053 CCTCATAAGTACCACTGGCCC 59.859 57.143 0.00 0.00 0.00 5.80
324 325 3.245016 ACTTGCATGTTTCTGATGGGAGA 60.245 43.478 0.00 0.00 0.00 3.71
366 367 1.349688 ACATTGGAAGCCACGAGGTTA 59.650 47.619 0.00 0.00 35.97 2.85
411 412 1.149174 CCTTGACCAGCCACAGTGT 59.851 57.895 0.00 0.00 0.00 3.55
551 553 3.255725 TGAAATAGTTTGGTAGCGGTCG 58.744 45.455 0.00 0.00 0.00 4.79
566 568 1.463674 GGTCGTTTCATGGAGCCATT 58.536 50.000 0.00 0.00 33.90 3.16
581 583 4.009675 GAGCCATTGGACATCAACAACTA 58.990 43.478 6.95 0.00 38.31 2.24
594 596 6.489700 ACATCAACAACTATGGACAATGTGAA 59.510 34.615 0.00 0.00 0.00 3.18
736 738 1.801332 CGTGGAGGACGGACTAGTG 59.199 63.158 0.00 0.00 44.85 2.74
766 768 0.904649 TGCATGAGGTGGGACTACTG 59.095 55.000 0.00 0.00 0.00 2.74
802 804 2.122167 CGGGCGAGTCTTAGAGGCT 61.122 63.158 0.00 0.00 29.26 4.58
879 882 2.084546 AGGCCTATTGACGTTTTGCTC 58.915 47.619 1.29 0.00 0.00 4.26
983 988 6.038161 TGTTGACATCTTTCACTAACAACCAG 59.962 38.462 0.00 0.00 36.56 4.00
1027 1032 0.976073 ATCCGGTTCCATGACGAGGT 60.976 55.000 0.00 0.00 0.00 3.85
1068 1073 2.040813 AGACATGCTGAACAAGTGGGAT 59.959 45.455 0.00 0.00 28.28 3.85
1080 1085 1.200519 AGTGGGATAACGCCAAGCTA 58.799 50.000 0.00 0.00 0.00 3.32
1228 1233 3.055719 CACATGACCGGGCGCTTT 61.056 61.111 7.64 0.00 0.00 3.51
1254 1259 1.491668 ACGCCTATGATGTACCACCA 58.508 50.000 0.00 0.00 0.00 4.17
1353 1359 0.962356 CACCGCCTCCTCTTTGCAAT 60.962 55.000 0.00 0.00 0.00 3.56
1359 1365 3.938963 CGCCTCCTCTTTGCAATTACTTA 59.061 43.478 0.00 0.00 0.00 2.24
1546 1552 3.648507 AAGAGAAGGCTGCTCATGAAT 57.351 42.857 24.37 0.00 34.85 2.57
1684 1691 9.778741 TTGAAGTTGTATGTCTGAGACTATTTT 57.221 29.630 14.42 0.00 33.15 1.82
1685 1692 9.778741 TGAAGTTGTATGTCTGAGACTATTTTT 57.221 29.630 14.42 0.29 33.15 1.94
1771 1793 1.843368 AGGTGTCCCGTCTTTCGATA 58.157 50.000 0.00 0.00 42.86 2.92
1791 1813 9.777297 TTCGATAAGATGGTGATTATCATTTCA 57.223 29.630 0.00 0.00 37.98 2.69
1821 1844 2.334838 ACTTTGACGATCCAACTACGC 58.665 47.619 0.00 0.00 0.00 4.42
1886 1909 0.108520 GAGGTTATTGTCCACGCCGA 60.109 55.000 0.00 0.00 0.00 5.54
1906 1929 0.615331 AGCACGATCAACCTGACCAT 59.385 50.000 0.00 0.00 0.00 3.55
1932 1955 2.742053 GTCTATTTCCTGCGAGCAAACA 59.258 45.455 0.00 0.00 0.00 2.83
2051 2074 4.502558 GTCGTTGAACACAAACGAAGTAG 58.497 43.478 12.38 0.00 45.00 2.57
2071 2094 1.647545 GCGAAGTTGCAGCTATGGCA 61.648 55.000 2.53 0.00 41.70 4.92
2133 2156 5.529289 CCCTAAGGGCTGTATATATGGAGA 58.471 45.833 0.00 0.00 35.35 3.71
2188 2217 3.774616 GGTCCGAACAACCCTATCC 57.225 57.895 0.00 0.00 0.00 2.59
2199 2228 2.311841 CAACCCTATCCCTTGTTTCCCT 59.688 50.000 0.00 0.00 0.00 4.20
2207 2236 5.994416 ATCCCTTGTTTCCCTACACATAT 57.006 39.130 0.00 0.00 0.00 1.78
2351 2380 1.251251 GTCCAAGGCTTCATGCACTT 58.749 50.000 0.00 0.00 45.15 3.16
2431 2460 2.583143 CACATGCCATCATCTCCATGT 58.417 47.619 0.00 0.00 46.50 3.21
2480 2509 2.027385 CCAAGCTAGGCCCTTCATTTC 58.973 52.381 0.00 0.00 0.00 2.17
2518 2547 4.866508 ATCCAATTTAGGCAGCATCATG 57.133 40.909 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.672854 CTCACCTATCCGGTTGGCGA 61.673 60.000 0.00 1.05 46.37 5.54
61 62 5.009631 CCTCAACCAATCATCAACCTTGTA 58.990 41.667 0.00 0.00 0.00 2.41
102 103 7.188834 TGAATCTAATGATTTGTTGATGCGAC 58.811 34.615 0.00 0.00 42.43 5.19
188 189 4.819630 CCTTATATGCAACACCACCGTAAT 59.180 41.667 0.00 0.00 0.00 1.89
339 340 2.508526 GTGGCTTCCAATGTGAACTCT 58.491 47.619 0.00 0.00 34.18 3.24
366 367 0.532115 GAAATCAAGGCGCCCATGTT 59.468 50.000 26.15 15.04 0.00 2.71
411 412 1.131638 GTGGGCCATCATACTCAGGA 58.868 55.000 10.70 0.00 0.00 3.86
524 526 5.354234 CCGCTACCAAACTATTTCATTCTGT 59.646 40.000 0.00 0.00 0.00 3.41
551 553 2.170166 TGTCCAATGGCTCCATGAAAC 58.830 47.619 1.59 2.23 36.68 2.78
566 568 4.632327 TGTCCATAGTTGTTGATGTCCA 57.368 40.909 0.00 0.00 0.00 4.02
581 583 2.421952 CCCGGATCTTCACATTGTCCAT 60.422 50.000 0.73 0.00 0.00 3.41
594 596 2.170607 CCTAACATTGTGTCCCGGATCT 59.829 50.000 0.73 0.00 0.00 2.75
633 635 2.100631 CGTGTTGGCATCGGTCCTC 61.101 63.158 0.00 0.00 0.00 3.71
736 738 3.430929 CCACCTCATGCACTACCTCTAAC 60.431 52.174 0.00 0.00 0.00 2.34
766 768 3.998672 TCCTCCACGCCCACGAAC 61.999 66.667 0.00 0.00 43.93 3.95
802 804 4.608774 ACGACCACCTCCACCGGA 62.609 66.667 9.46 0.00 0.00 5.14
879 882 8.109705 TCATATTATTTCAACCATCCGGATTG 57.890 34.615 16.19 14.84 35.59 2.67
964 969 6.867662 AAGACTGGTTGTTAGTGAAAGATG 57.132 37.500 0.00 0.00 0.00 2.90
983 988 7.035004 TGAAGCCATGCATACAAAAATAAGAC 58.965 34.615 0.00 0.00 0.00 3.01
997 1002 1.001020 AACCGGATGAAGCCATGCA 60.001 52.632 9.46 0.00 40.64 3.96
1068 1073 0.454600 CCTCGTCTAGCTTGGCGTTA 59.545 55.000 20.91 2.79 0.00 3.18
1080 1085 4.625607 ATCTTTTTCCTTCACCTCGTCT 57.374 40.909 0.00 0.00 0.00 4.18
1228 1233 3.936453 GGTACATCATAGGCGTTTGTTGA 59.064 43.478 12.76 0.73 0.00 3.18
1329 1335 1.831652 AAAGAGGAGGCGGTGACTGG 61.832 60.000 0.00 0.00 0.00 4.00
1359 1365 9.152327 TCTAGAACATCTTGATCTATCCATGTT 57.848 33.333 9.86 9.86 32.49 2.71
1415 1421 2.180276 ACAGTCGTTGCCTCCTAAGAT 58.820 47.619 0.00 0.00 0.00 2.40
1448 1454 2.765135 TCTTCATCCAAGCCTCTCTGAG 59.235 50.000 0.00 0.00 31.26 3.35
1546 1552 3.679389 CAAGCTTTCTTGCCCTCTCTTA 58.321 45.455 0.00 0.00 42.66 2.10
1629 1636 6.111382 TGCATCTCAAGATCACTAAGGAAAG 58.889 40.000 0.00 0.00 31.21 2.62
1684 1691 7.230309 TCACAATATCATCAAATATCCGGCAAA 59.770 33.333 0.00 0.00 0.00 3.68
1685 1692 6.714356 TCACAATATCATCAAATATCCGGCAA 59.286 34.615 0.00 0.00 0.00 4.52
1771 1793 7.809238 TCCTCTGAAATGATAATCACCATCTT 58.191 34.615 0.00 0.00 0.00 2.40
1791 1813 3.949113 GGATCGTCAAAGTCTACTCCTCT 59.051 47.826 0.00 0.00 0.00 3.69
1877 1900 3.982372 GATCGTGCTTCGGCGTGGA 62.982 63.158 6.85 0.00 45.37 4.02
1886 1909 0.396435 TGGTCAGGTTGATCGTGCTT 59.604 50.000 0.00 0.00 27.66 3.91
1906 1929 1.757118 CTCGCAGGAAATAGACCCTCA 59.243 52.381 0.00 0.00 0.00 3.86
1932 1955 6.705863 ATCTCAGTTTCTTGCTTGTTCTTT 57.294 33.333 0.00 0.00 0.00 2.52
2051 2074 1.723870 CCATAGCTGCAACTTCGCC 59.276 57.895 1.02 0.00 0.00 5.54
2096 2119 3.492829 CCCTTAGGGCATCGTTTAGACTC 60.493 52.174 3.52 0.00 35.35 3.36
2188 2217 7.070074 AGAGTCTATATGTGTAGGGAAACAAGG 59.930 40.741 0.00 0.00 0.00 3.61
2199 2228 8.978472 AGGCTGTTTTTAGAGTCTATATGTGTA 58.022 33.333 0.00 0.00 0.00 2.90
2207 2236 8.818622 TGAGTATAGGCTGTTTTTAGAGTCTA 57.181 34.615 0.00 0.00 0.00 2.59
2351 2380 3.199071 AGGACGTTGAAGCCACCATAATA 59.801 43.478 0.00 0.00 0.00 0.98
2431 2460 4.998671 TGAACATTGGAGCAAGAACAAA 57.001 36.364 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.