Multiple sequence alignment - TraesCS7B01G188800

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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 TraesCS7B01G188800 chr7B 100.000 4627 0 0 1 4627 321340147 321344773 0 8545
1 TraesCS7B01G188800 chr7A 95.420 4651 137 26 1 4625 403195075 403190475 0 7339
2 TraesCS7B01G188800 chr7D 96.906 2327 61 7 2304 4627 365316516 365314198 0 3888
3 TraesCS7B01G188800 chr7D 96.117 1339 39 10 1 1334 365318994 365317664 0 2172
4 TraesCS7B01G188800 chr7D 94.890 998 22 11 1320 2306 365317636 365316657 0 1533


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 TraesCS7B01G188800 chr7B 321340147 321344773 4626 False 8545 8545 100.000 1 4627 1 chr7B.!!$F1 4626
1 TraesCS7B01G188800 chr7A 403190475 403195075 4600 True 7339 7339 95.420 1 4625 1 chr7A.!!$R1 4624
2 TraesCS7B01G188800 chr7D 365314198 365318994 4796 True 2531 3888 95.971 1 4627 3 chr7D.!!$R1 4626

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
964 976 0.682209 CCCATCCCAAAGGCAGACAG 60.682 60.000 0.00 0.00 0.00 3.51 F
1408 1465 3.328343 TCAGGGTTTCTTTCGGTGGATAA 59.672 43.478 0.00 0.00 0.00 1.75 F
2180 2248 4.821260 GTGAAAAATTGGCCACCATTCTTT 59.179 37.500 3.88 7.38 31.53 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2185 2.602211 TGCACAAACAGATGCGTTTTTG 59.398 40.909 6.93 6.93 45.13 2.44 R
2734 2951 3.448686 CATACGGAACTCAGCTAAGTGG 58.551 50.000 0.00 0.00 0.00 4.00 R
3719 3938 0.106708 TTCGGCAGAAGCAGTTCACT 59.893 50.000 0.00 0.00 44.61 3.41 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
43 44 5.579511 TGCGAATGCTGATATACTCATGATG 59.420 40.000 0.00 0.00 43.34 3.07
309 310 3.430895 GCTTGATGGCAAAATGTTGTCTG 59.569 43.478 1.16 0.00 40.21 3.51
332 333 6.822442 TGTGACTGTCATCCTACTTTTTGTA 58.178 36.000 14.37 0.00 0.00 2.41
336 337 7.225931 TGACTGTCATCCTACTTTTTGTAACAC 59.774 37.037 6.36 0.00 0.00 3.32
413 414 5.465532 TTGCTGAATTAATGCACTTTCCA 57.534 34.783 0.00 0.00 36.37 3.53
570 572 5.454471 CCATCGAGATCATTTCCCTTTCTCT 60.454 44.000 0.00 0.00 32.50 3.10
640 643 3.469008 TGTTGGTTGCGGATATAGGAG 57.531 47.619 0.00 0.00 0.00 3.69
685 689 0.945743 GCTGTCTGTGACGTGCATGA 60.946 55.000 14.17 0.00 35.74 3.07
724 728 2.698274 GACAAAACCAACCACCCATCTT 59.302 45.455 0.00 0.00 0.00 2.40
729 733 3.258722 ACCAACCACCCATCTTGAATT 57.741 42.857 0.00 0.00 0.00 2.17
758 762 4.024472 GGAGGATTTTCTAGAATTCTGCGC 60.024 45.833 18.47 0.00 0.00 6.09
920 932 4.637483 ATAACCTTTGATTGGTCATGCG 57.363 40.909 0.00 0.00 36.69 4.73
930 942 1.725641 TGGTCATGCGCAACTTAGAG 58.274 50.000 17.11 0.00 0.00 2.43
940 952 4.082190 TGCGCAACTTAGAGTAGATTCTGT 60.082 41.667 8.16 0.00 0.00 3.41
941 953 4.501198 GCGCAACTTAGAGTAGATTCTGTC 59.499 45.833 0.30 0.00 0.00 3.51
942 954 5.677598 GCGCAACTTAGAGTAGATTCTGTCT 60.678 44.000 0.30 1.38 41.11 3.41
943 955 5.741510 CGCAACTTAGAGTAGATTCTGTCTG 59.258 44.000 9.54 0.00 37.83 3.51
964 976 0.682209 CCCATCCCAAAGGCAGACAG 60.682 60.000 0.00 0.00 0.00 3.51
1119 1132 6.289834 TGAGACATTTCCATTGCAAACATTT 58.710 32.000 1.71 0.00 0.00 2.32
1159 1172 6.550854 AGATCAACTTTGGTTCAGAAAATCCA 59.449 34.615 0.00 0.00 32.73 3.41
1201 1214 6.839124 TGTATTTTGGCTCTCACAATTGAT 57.161 33.333 13.59 0.00 29.56 2.57
1258 1271 6.041865 CAGTTCATCCTACATCATTCTCTCCT 59.958 42.308 0.00 0.00 0.00 3.69
1353 1410 9.163894 AGGAAGATTTATCCTGTGATCTATGAA 57.836 33.333 0.00 0.00 45.60 2.57
1354 1411 9.956640 GGAAGATTTATCCTGTGATCTATGAAT 57.043 33.333 0.00 0.00 33.98 2.57
1363 1420 8.426569 TCCTGTGATCTATGAATATGATGACA 57.573 34.615 0.00 0.00 34.32 3.58
1364 1421 8.873144 TCCTGTGATCTATGAATATGATGACAA 58.127 33.333 0.00 0.00 34.88 3.18
1365 1422 9.152595 CCTGTGATCTATGAATATGATGACAAG 57.847 37.037 0.00 0.00 34.88 3.16
1366 1423 9.708092 CTGTGATCTATGAATATGATGACAAGT 57.292 33.333 0.00 0.00 34.88 3.16
1408 1465 3.328343 TCAGGGTTTCTTTCGGTGGATAA 59.672 43.478 0.00 0.00 0.00 1.75
1574 1631 6.223852 AGCAGGGTGTTATTTCAGTATATCG 58.776 40.000 0.00 0.00 0.00 2.92
1937 1995 7.094205 ACAAATCCTATGGTGTTCATTTCTGTC 60.094 37.037 0.00 0.00 37.30 3.51
2001 2059 6.860023 CCAATTTGCTCAAAAGTGACTCTTAG 59.140 38.462 0.00 0.00 44.69 2.18
2004 2062 7.807977 TTTGCTCAAAAGTGACTCTTAGAAT 57.192 32.000 0.00 0.00 35.02 2.40
2068 2136 5.011635 TGCAATGAACAGAGGTAGTTCTACA 59.988 40.000 11.34 0.00 44.30 2.74
2110 2178 6.268617 TCCATCATGGTTTAATGTTTTGACCA 59.731 34.615 2.79 0.00 43.82 4.02
2117 2185 8.202745 TGGTTTAATGTTTTGACCACATTTTC 57.797 30.769 3.75 0.00 41.19 2.29
2180 2248 4.821260 GTGAAAAATTGGCCACCATTCTTT 59.179 37.500 3.88 7.38 31.53 2.52
2434 2651 6.183360 GGAAGGTGCTAAATATTTTGCCTCAT 60.183 38.462 25.12 15.93 37.97 2.90
2440 2657 7.707893 GTGCTAAATATTTTGCCTCATGAACAT 59.292 33.333 25.12 0.00 37.97 2.71
2734 2951 7.009568 TCGTCTTCTACTCGGTAGTTTTATC 57.990 40.000 9.84 0.63 37.41 1.75
2745 2962 5.419788 TCGGTAGTTTTATCCACTTAGCTGA 59.580 40.000 0.00 0.00 0.00 4.26
2746 2963 5.749109 CGGTAGTTTTATCCACTTAGCTGAG 59.251 44.000 3.53 3.53 0.00 3.35
2747 2964 6.627508 CGGTAGTTTTATCCACTTAGCTGAGT 60.628 42.308 5.11 5.11 0.00 3.41
2794 3011 8.963725 ACATCTGATTCTATTGCATTTTTCTCA 58.036 29.630 0.00 0.00 0.00 3.27
2838 3055 4.202295 ACATGAGATGAGCATAATGACGGT 60.202 41.667 0.00 0.00 0.00 4.83
2953 3170 1.134946 ACCACAGTGCTGTTTTCTTGC 59.865 47.619 1.57 0.00 42.83 4.01
2968 3185 6.151985 TGTTTTCTTGCTAAGTTTCCAACTGA 59.848 34.615 0.00 0.00 41.91 3.41
3143 3362 5.010617 GGGCCTTAATTCTTGTCTGTTTTGA 59.989 40.000 0.84 0.00 0.00 2.69
3239 3458 4.768448 TGAGGTTGATGCACATTTCATCTT 59.232 37.500 0.00 0.00 40.59 2.40
3401 3620 6.374894 TGCATTCATTCATGTTAGTGACATCA 59.625 34.615 0.00 0.00 45.88 3.07
3572 3791 5.625197 GCATGGCTTGTTGACATCCTTAAAT 60.625 40.000 2.12 0.00 41.43 1.40
3719 3938 4.636648 ACACAAAGTTGACGGTGAATGTTA 59.363 37.500 0.00 0.00 35.33 2.41
3917 4136 1.862201 CAACGGTGAAGCGTGTTAGAA 59.138 47.619 8.46 0.00 0.00 2.10
3970 4189 7.284034 TCAAAGATGAAAGCATTTAGGATCTCC 59.716 37.037 0.00 0.00 39.27 3.71
4074 4293 9.956640 ATCTCTGAAGAAACAGATTACTCAATT 57.043 29.630 0.00 0.00 44.32 2.32
4303 4522 7.526142 AAGAAAAAGGGGAAGATTACAACTC 57.474 36.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 310 7.225931 TGTTACAAAAAGTAGGATGACAGTCAC 59.774 37.037 5.05 0.00 33.43 3.67
332 333 8.079203 TCGAAGTTAATGCAACATTATTGTGTT 58.921 29.630 0.00 0.00 42.75 3.32
336 337 9.890085 CAATTCGAAGTTAATGCAACATTATTG 57.110 29.630 3.35 0.00 39.81 1.90
393 394 7.428020 TGATATGGAAAGTGCATTAATTCAGC 58.572 34.615 0.00 0.00 29.08 4.26
413 414 3.118112 CCAGAGTGCAGGGAGTTTGATAT 60.118 47.826 0.00 0.00 0.00 1.63
570 572 5.240623 GGACAACACAAAGGAACATCATACA 59.759 40.000 0.00 0.00 0.00 2.29
640 643 6.707290 AGGGGTTATAAAATGCTTTTGTTCC 58.293 36.000 0.00 2.49 34.19 3.62
685 689 7.255486 GGTTTTGTCCTTCTAAGCAGTTTATGT 60.255 37.037 0.00 0.00 0.00 2.29
724 728 7.642186 TCTAGAAAATCCTCCATTCCAATTCA 58.358 34.615 0.00 0.00 0.00 2.57
729 733 7.776969 CAGAATTCTAGAAAATCCTCCATTCCA 59.223 37.037 9.71 0.00 0.00 3.53
758 762 9.591404 GCATGAATTTCAGAAGATACTAATTCG 57.409 33.333 5.21 0.00 35.71 3.34
920 932 6.039616 CCAGACAGAATCTACTCTAAGTTGC 58.960 44.000 0.00 0.00 35.15 4.17
930 942 2.224402 GGATGGGCCAGACAGAATCTAC 60.224 54.545 13.78 0.00 35.15 2.59
940 952 3.099171 CCTTTGGGATGGGCCAGA 58.901 61.111 13.78 0.00 38.95 3.86
941 953 2.761213 GCCTTTGGGATGGGCCAG 60.761 66.667 13.78 0.00 39.96 4.85
942 954 3.598887 TGCCTTTGGGATGGGCCA 61.599 61.111 9.61 9.61 44.71 5.36
943 955 2.761213 CTGCCTTTGGGATGGGCC 60.761 66.667 0.00 0.00 44.71 5.80
964 976 1.336240 GGCATGAATAAATCCCTGCGC 60.336 52.381 0.00 0.00 36.86 6.09
1119 1132 5.624159 AGTTGATCTGGACATGAAAACTCA 58.376 37.500 0.00 0.00 0.00 3.41
1258 1271 7.389232 TGATCTAGAGCAAGTTCTTGATTTGA 58.611 34.615 8.55 9.32 38.95 2.69
1353 1410 7.776969 ACCATAAGCAGAAACTTGTCATCATAT 59.223 33.333 0.00 0.00 0.00 1.78
1354 1411 7.112122 ACCATAAGCAGAAACTTGTCATCATA 58.888 34.615 0.00 0.00 0.00 2.15
1356 1413 5.316167 ACCATAAGCAGAAACTTGTCATCA 58.684 37.500 0.00 0.00 0.00 3.07
1357 1414 5.645497 AGACCATAAGCAGAAACTTGTCATC 59.355 40.000 0.00 0.00 0.00 2.92
1359 1416 4.756642 CAGACCATAAGCAGAAACTTGTCA 59.243 41.667 0.00 0.00 0.00 3.58
1360 1417 4.154918 CCAGACCATAAGCAGAAACTTGTC 59.845 45.833 0.00 0.00 0.00 3.18
1361 1418 4.074970 CCAGACCATAAGCAGAAACTTGT 58.925 43.478 0.00 0.00 0.00 3.16
1362 1419 3.119708 GCCAGACCATAAGCAGAAACTTG 60.120 47.826 0.00 0.00 0.00 3.16
1363 1420 3.084786 GCCAGACCATAAGCAGAAACTT 58.915 45.455 0.00 0.00 0.00 2.66
1364 1421 2.307098 AGCCAGACCATAAGCAGAAACT 59.693 45.455 0.00 0.00 0.00 2.66
1365 1422 2.716217 AGCCAGACCATAAGCAGAAAC 58.284 47.619 0.00 0.00 0.00 2.78
1366 1423 3.244875 TGAAGCCAGACCATAAGCAGAAA 60.245 43.478 0.00 0.00 0.00 2.52
1408 1465 7.199766 TGAATGTTGCGACTAAAATTTCAACT 58.800 30.769 15.20 1.65 35.96 3.16
1509 1566 7.444629 ACTGAACTAATGTACACTACTTCGA 57.555 36.000 0.00 0.00 0.00 3.71
1792 1850 6.367374 TTGGACTTATCATCAACTGTACCA 57.633 37.500 0.00 0.00 0.00 3.25
1922 1980 5.551760 ATTCATCGACAGAAATGAACACC 57.448 39.130 6.26 0.00 42.82 4.16
2009 2067 7.738847 TGTATGATATCCTGCAAAGAATGAGA 58.261 34.615 0.00 0.00 0.00 3.27
2010 2068 7.876582 TCTGTATGATATCCTGCAAAGAATGAG 59.123 37.037 0.00 0.00 0.00 2.90
2011 2069 7.738847 TCTGTATGATATCCTGCAAAGAATGA 58.261 34.615 0.00 0.00 0.00 2.57
2068 2136 6.505048 TGATGGAGATGTAATGGTGATCTT 57.495 37.500 0.00 0.00 0.00 2.40
2110 2178 6.091986 ACAAACAGATGCGTTTTTGAAAATGT 59.908 30.769 12.86 0.00 36.98 2.71
2117 2185 2.602211 TGCACAAACAGATGCGTTTTTG 59.398 40.909 6.93 6.93 45.13 2.44
2593 2810 6.663944 ACAATTATTTACTTCGAGCTGGTC 57.336 37.500 0.00 0.00 0.00 4.02
2734 2951 3.448686 CATACGGAACTCAGCTAAGTGG 58.551 50.000 0.00 0.00 0.00 4.00
2745 2962 9.998106 ATGTTTAGATTATTAGCATACGGAACT 57.002 29.630 0.00 0.00 0.00 3.01
2800 3017 7.275183 TCATCTCATGTTACGGATGAAAGATT 58.725 34.615 0.00 0.00 40.69 2.40
2817 3034 4.613925 ACCGTCATTATGCTCATCTCAT 57.386 40.909 0.00 0.00 0.00 2.90
2819 3036 4.811024 TCAAACCGTCATTATGCTCATCTC 59.189 41.667 0.00 0.00 0.00 2.75
3143 3362 8.408601 CAATTAGATAAAGTACCTGCATTGCTT 58.591 33.333 10.49 0.00 0.00 3.91
3239 3458 7.630242 AACAGAAGTGTTGAAAGAAATGAGA 57.370 32.000 0.00 0.00 45.58 3.27
3286 3505 8.561212 AGTTCATAAGAGCGATAGTAGTAACAG 58.439 37.037 0.00 0.00 39.35 3.16
3348 3567 5.863935 GGACAAAGAATAAGTCATGCAAACC 59.136 40.000 0.00 0.00 34.04 3.27
3605 3824 2.238646 TCACCTGTGCCCTCGAAAATAT 59.761 45.455 0.00 0.00 0.00 1.28
3657 3876 0.108585 TGTTGAGGAGACAGTTGCCC 59.891 55.000 0.00 0.00 0.00 5.36
3692 3911 3.827625 TCACCGTCAACTTTGTGTTTTG 58.172 40.909 0.00 0.00 36.63 2.44
3719 3938 0.106708 TTCGGCAGAAGCAGTTCACT 59.893 50.000 0.00 0.00 44.61 3.41
3917 4136 2.887151 ACCTGCATAAGCCTGAACTT 57.113 45.000 0.00 0.00 41.13 2.66
4074 4293 6.478512 AAGAACTTAATTTCAAACCTGCCA 57.521 33.333 8.13 0.00 0.00 4.92
4205 4424 3.557577 TGCGAAGACACCATTCATTTG 57.442 42.857 0.00 0.00 0.00 2.32
4303 4522 2.482336 TGTGCTATTGCTAACAACCACG 59.518 45.455 0.00 0.00 38.99 4.94


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

AutoCloner maintained by Alex Coulton.