Multiple sequence alignment - TraesCS6D01G138200

Loading Multiple Alignment...

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 TraesCS6D01G138200 chr6D 100.000 3296 0 0 1 3296 106891006 106894301 0.000000e+00 6087.0
1 TraesCS6D01G138200 chr6A 93.997 3015 130 18 1 2992 130404774 130407760 0.000000e+00 4518.0
2 TraesCS6D01G138200 chr5A 93.712 2831 136 20 1 2790 491521173 491524002 0.000000e+00 4204.0
3 TraesCS6D01G138200 chr5A 90.293 2421 180 18 310 2702 491368292 491370685 0.000000e+00 3118.0
4 TraesCS6D01G138200 chr5A 90.170 1709 130 15 904 2611 491319265 491317594 0.000000e+00 2191.0
5 TraesCS6D01G138200 chr5A 91.557 379 28 2 2921 3296 491524104 491524481 1.360000e-143 520.0
6 TraesCS6D01G138200 chr5D 92.922 2529 146 19 201 2716 388588317 388590825 0.000000e+00 3648.0
7 TraesCS6D01G138200 chr5D 92.146 2381 157 18 339 2702 388330749 388333116 0.000000e+00 3334.0
8 TraesCS6D01G138200 chr5D 91.765 1360 87 17 904 2262 388423605 388422270 0.000000e+00 1868.0
9 TraesCS6D01G138200 chr5D 87.821 312 28 2 22 323 388330253 388330564 1.120000e-94 357.0
10 TraesCS6D01G138200 chr5D 86.900 229 12 6 1 211 388539129 388539357 1.180000e-59 241.0
11 TraesCS6D01G138200 chr5D 81.469 286 36 7 2316 2598 388422265 388421994 5.540000e-53 219.0
12 TraesCS6D01G138200 chr5D 80.000 170 20 9 231 387 547927478 547927646 2.690000e-21 113.0
13 TraesCS6D01G138200 chr5B 88.902 1649 117 41 1 1588 466972598 466974241 0.000000e+00 1971.0
14 TraesCS6D01G138200 chr5B 89.429 1173 93 11 1482 2638 466974229 466975386 0.000000e+00 1450.0
15 TraesCS6D01G138200 chr3D 79.006 181 25 11 231 400 346982211 346982033 9.670000e-21 111.0
16 TraesCS6D01G138200 chr3D 94.872 39 2 0 369 407 465170406 465170444 9.880000e-06 62.1
17 TraesCS6D01G138200 chr7A 78.453 181 27 10 231 399 80757166 80756986 1.250000e-19 108.0
18 TraesCS6D01G138200 chr3A 79.412 170 21 9 231 387 718940709 718940541 1.250000e-19 108.0
19 TraesCS6D01G138200 chr1B 85.714 91 13 0 231 321 172000511 172000601 2.710000e-16 97.1
20 TraesCS6D01G138200 chr6B 84.848 66 6 2 2431 2494 135139021 135138958 2.750000e-06 63.9
21 TraesCS6D01G138200 chr1D 92.683 41 3 0 711 751 338510213 338510173 3.550000e-05 60.2


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 TraesCS6D01G138200 chr6D 106891006 106894301 3295 False 6087.0 6087 100.0000 1 3296 1 chr6D.!!$F1 3295
1 TraesCS6D01G138200 chr6A 130404774 130407760 2986 False 4518.0 4518 93.9970 1 2992 1 chr6A.!!$F1 2991
2 TraesCS6D01G138200 chr5A 491368292 491370685 2393 False 3118.0 3118 90.2930 310 2702 1 chr5A.!!$F1 2392
3 TraesCS6D01G138200 chr5A 491521173 491524481 3308 False 2362.0 4204 92.6345 1 3296 2 chr5A.!!$F2 3295
4 TraesCS6D01G138200 chr5A 491317594 491319265 1671 True 2191.0 2191 90.1700 904 2611 1 chr5A.!!$R1 1707
5 TraesCS6D01G138200 chr5D 388588317 388590825 2508 False 3648.0 3648 92.9220 201 2716 1 chr5D.!!$F2 2515
6 TraesCS6D01G138200 chr5D 388330253 388333116 2863 False 1845.5 3334 89.9835 22 2702 2 chr5D.!!$F4 2680
7 TraesCS6D01G138200 chr5D 388421994 388423605 1611 True 1043.5 1868 86.6170 904 2598 2 chr5D.!!$R1 1694
8 TraesCS6D01G138200 chr5B 466972598 466975386 2788 False 1710.5 1971 89.1655 1 2638 2 chr5B.!!$F1 2637

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
784 1042 4.432712 ACAATTAATTTGGCGCCAAGATC 58.567 39.130 37.88 7.09 39.80 2.75 F
1062 1324 1.525077 GGACGTTGGACTTGTGGCA 60.525 57.895 0.00 0.00 0.00 4.92 F
1654 2021 1.734655 AGCTTCTGAACCAGGAGGAA 58.265 50.000 4.59 0.00 37.56 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2072 0.559699 GGCAGGGAGGGTAGTAGGTA 59.440 60.000 0.00 0.00 0.00 3.08 R
1998 2371 3.057104 CCTTGAAGATTGCATTGCTGACA 60.057 43.478 10.49 0.00 0.00 3.58 R
2500 2874 4.672283 CGGCCGTGATTAAAACCGTATTTT 60.672 41.667 19.50 0.93 35.99 1.82 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
179 200 7.773864 TTTGTCTTAAACGTATGTGACAAGA 57.226 32.000 19.01 9.30 42.64 3.02
401 593 9.059260 TGCATGATACTAACTTACGATACTACA 57.941 33.333 0.00 0.00 0.00 2.74
411 603 8.455903 AACTTACGATACTACACATTAGGCTA 57.544 34.615 0.00 0.00 0.00 3.93
519 715 5.242171 GGTTTTTCTTCCATCGGGTTTTCTA 59.758 40.000 0.00 0.00 34.93 2.10
784 1042 4.432712 ACAATTAATTTGGCGCCAAGATC 58.567 39.130 37.88 7.09 39.80 2.75
1062 1324 1.525077 GGACGTTGGACTTGTGGCA 60.525 57.895 0.00 0.00 0.00 4.92
1087 1349 4.590487 GCAGGTACGTGCTAAGCA 57.410 55.556 28.50 0.00 40.54 3.91
1501 1763 6.349300 AGGCACTCGATCTACACATTAATTT 58.651 36.000 0.00 0.00 0.00 1.82
1568 1833 6.824553 TGGAGATCATATATAATCTGCAGGC 58.175 40.000 14.40 0.00 42.94 4.85
1654 2021 1.734655 AGCTTCTGAACCAGGAGGAA 58.265 50.000 4.59 0.00 37.56 3.36
1705 2072 4.283722 AGGTTCAAGTCATACTCGAGGTTT 59.716 41.667 18.41 0.00 0.00 3.27
1801 2168 2.293452 ACTCCTCCTCATGGACAAGGAT 60.293 50.000 1.56 0.00 40.83 3.24
1998 2371 6.413052 ACTCTCATTTCTATGCACACAGATT 58.587 36.000 0.00 0.00 0.00 2.40
2381 2754 4.657436 AGGAGTTGATCGATGTACTTCC 57.343 45.455 0.54 9.17 0.00 3.46
2500 2874 6.262944 GGCATATATTGAACTGGTGAACATGA 59.737 38.462 0.00 0.00 0.00 3.07
2524 2898 0.320596 ACGGTTTTAATCACGGCCGA 60.321 50.000 35.90 11.57 41.45 5.54
2534 2908 4.712122 AATCACGGCCGAATACAAAATT 57.288 36.364 35.90 14.88 0.00 1.82
2632 3020 4.949238 TCCCAATCATTACCATCTGTTGTG 59.051 41.667 0.00 0.00 0.00 3.33
2775 3164 0.468226 TTGCCACTCAACCGAGAACT 59.532 50.000 0.00 0.00 42.34 3.01
3209 3624 1.142748 GAGGATCGGCAGTCTGGTG 59.857 63.158 1.14 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 33 9.014297 GTTCGAAAATCCATCTATTTATCCCAT 57.986 33.333 0.00 0.00 0.00 4.00
32 34 8.217799 AGTTCGAAAATCCATCTATTTATCCCA 58.782 33.333 0.00 0.00 0.00 4.37
179 200 4.260825 CGTGATACTCTCATTACGAGCAGT 60.261 45.833 0.00 0.00 39.49 4.40
392 584 6.510879 TGGATAGCCTAATGTGTAGTATCG 57.489 41.667 0.00 0.00 34.31 2.92
401 593 4.287067 CACCCACTATGGATAGCCTAATGT 59.713 45.833 0.00 0.00 40.96 2.71
411 603 1.979809 TTGGACCACCCACTATGGAT 58.020 50.000 0.00 0.00 46.62 3.41
519 715 3.822940 TGGGACGTTGAGGTGTTTTTAT 58.177 40.909 0.00 0.00 0.00 1.40
772 1030 2.342650 GCTTTGGATCTTGGCGCCA 61.343 57.895 29.03 29.03 0.00 5.69
784 1042 0.887933 AACGGCCTATGTTGCTTTGG 59.112 50.000 0.00 0.00 0.00 3.28
1087 1349 3.703127 GGTCGGCCGGTTCTCCTT 61.703 66.667 27.83 0.00 0.00 3.36
1324 1586 2.416244 ACACCGTCGATCACGTTGCT 62.416 55.000 12.57 2.03 44.40 3.91
1568 1833 5.860941 AAGGTGTACTCATGTAGGAGATG 57.139 43.478 0.01 0.00 38.30 2.90
1654 2021 3.087031 CACCATGTTGATGAAGAAGCCT 58.913 45.455 0.00 0.00 0.00 4.58
1705 2072 0.559699 GGCAGGGAGGGTAGTAGGTA 59.440 60.000 0.00 0.00 0.00 3.08
1998 2371 3.057104 CCTTGAAGATTGCATTGCTGACA 60.057 43.478 10.49 0.00 0.00 3.58
2381 2754 9.964354 TTTTATTCCATGGAGGTGATCATATAG 57.036 33.333 15.53 0.00 39.02 1.31
2500 2874 4.672283 CGGCCGTGATTAAAACCGTATTTT 60.672 41.667 19.50 0.93 35.99 1.82
2524 2898 5.163754 GCCTAGTCAGCGTCAATTTTGTATT 60.164 40.000 0.00 0.00 0.00 1.89
2640 3028 8.974060 TTCAAAGGCTATAAAGAATCCGTATT 57.026 30.769 0.00 0.00 0.00 1.89
2960 3375 8.137745 ACTTGTGAAAAATGGACCAATATGAT 57.862 30.769 0.00 0.00 0.00 2.45
2964 3379 8.573035 GTCTAACTTGTGAAAAATGGACCAATA 58.427 33.333 0.00 0.00 0.00 1.90
2965 3380 7.287696 AGTCTAACTTGTGAAAAATGGACCAAT 59.712 33.333 0.00 0.00 0.00 3.16
2966 3381 6.605594 AGTCTAACTTGTGAAAAATGGACCAA 59.394 34.615 0.00 0.00 0.00 3.67
2967 3382 6.126409 AGTCTAACTTGTGAAAAATGGACCA 58.874 36.000 0.00 0.00 0.00 4.02
3177 3592 7.667219 ACTGCCGATCCTCAAATGAATATTATT 59.333 33.333 0.00 0.00 0.00 1.40
3209 3624 9.438228 GATAAATAAATAAGAGCCTAGTGTCCC 57.562 37.037 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.