Multiple sequence alignment - TraesCS6D01G208900

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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 TraesCS6D01G208900 chr6D 100.000 2390 0 0 1 2390 295142932 295145321 0.000000e+00 4414.0
1 TraesCS6D01G208900 chr6D 81.654 387 53 10 1083 1464 295068549 295068922 2.980000e-79 305.0
2 TraesCS6D01G208900 chr6D 79.156 379 55 11 1091 1464 295110331 295110690 8.540000e-60 241.0
3 TraesCS6D01G208900 chr6D 80.556 144 25 3 376 518 39061765 39061906 9.030000e-20 108.0
4 TraesCS6D01G208900 chr6B 94.370 1705 65 15 211 1907 459382599 459384280 0.000000e+00 2588.0
5 TraesCS6D01G208900 chr6B 79.737 380 51 13 1091 1464 459229004 459229363 3.940000e-63 252.0
6 TraesCS6D01G208900 chr6B 80.625 320 42 9 1152 1464 459265402 459265708 1.850000e-56 230.0
7 TraesCS6D01G208900 chr6B 91.824 159 5 4 2236 2390 459387164 459387318 5.170000e-52 215.0
8 TraesCS6D01G208900 chr6B 90.667 150 13 1 1 150 459381452 459381600 5.210000e-47 198.0
9 TraesCS6D01G208900 chr6B 88.166 169 13 2 2000 2168 459384693 459384854 6.740000e-46 195.0
10 TraesCS6D01G208900 chr6A 92.266 1862 59 27 579 2390 425862436 425860610 0.000000e+00 2562.0
11 TraesCS6D01G208900 chr6A 90.566 530 47 1 6 532 425863495 425862966 0.000000e+00 699.0
12 TraesCS6D01G208900 chr6A 89.697 165 15 2 88 251 153366875 153367038 2.410000e-50 209.0
13 TraesCS6D01G208900 chr6A 94.521 73 1 3 524 594 425862849 425862778 2.510000e-20 110.0
14 TraesCS6D01G208900 chr6A 84.375 96 14 1 358 453 27148807 27148901 2.530000e-15 93.5
15 TraesCS6D01G208900 chr3D 91.358 162 12 2 88 248 87926160 87926000 1.110000e-53 220.0
16 TraesCS6D01G208900 chr3D 88.824 170 16 3 83 251 537154699 537154866 3.110000e-49 206.0
17 TraesCS6D01G208900 chr5A 89.474 171 14 4 88 256 320214404 320214236 1.860000e-51 213.0
18 TraesCS6D01G208900 chr2D 90.123 162 14 2 88 248 299891555 299891715 2.410000e-50 209.0
19 TraesCS6D01G208900 chr2D 88.439 173 16 4 78 248 296364039 296364209 3.110000e-49 206.0
20 TraesCS6D01G208900 chr2B 88.439 173 16 4 78 248 366017689 366017519 3.110000e-49 206.0
21 TraesCS6D01G208900 chr2B 77.070 157 31 4 363 518 147493833 147493681 4.230000e-13 86.1
22 TraesCS6D01G208900 chr4D 87.293 181 16 6 88 266 34661528 34661703 1.450000e-47 200.0
23 TraesCS6D01G208900 chr5D 82.292 96 16 1 262 357 524494707 524494613 5.480000e-12 82.4
24 TraesCS6D01G208900 chr5D 94.000 50 3 0 376 425 541427888 541427839 2.550000e-10 76.8
25 TraesCS6D01G208900 chr1B 83.721 86 12 2 363 448 416169097 416169014 1.970000e-11 80.5
26 TraesCS6D01G208900 chr1B 80.808 99 16 3 254 352 599342609 599342704 9.160000e-10 75.0
27 TraesCS6D01G208900 chr1D 83.951 81 12 1 371 451 291079488 291079567 2.550000e-10 76.8
28 TraesCS6D01G208900 chr7D 80.412 97 15 3 373 468 434913484 434913391 1.190000e-08 71.3
29 TraesCS6D01G208900 chr7A 89.583 48 5 0 253 300 110405620 110405667 7.130000e-06 62.1


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 TraesCS6D01G208900 chr6D 295142932 295145321 2389 False 4414.000000 4414 100.00000 1 2390 1 chr6D.!!$F4 2389
1 TraesCS6D01G208900 chr6B 459381452 459387318 5866 False 799.000000 2588 91.25675 1 2390 4 chr6B.!!$F3 2389
2 TraesCS6D01G208900 chr6A 425860610 425863495 2885 True 1123.666667 2562 92.45100 6 2390 3 chr6A.!!$R1 2384

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
359 1301 1.20258 ACCGCTATGAGCATCTTCACC 60.203 52.381 0.0 0.0 42.58 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 3409 0.107214 TGTCATCCGGGGAGCAATTC 60.107 55.0 0.0 0.0 0.0 2.17 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
200 758 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
202 760 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
208 766 3.251729 GCTCCGTATGTAGTCCGTATTGA 59.748 47.826 0.00 0.00 0.00 2.57
307 1249 5.924254 ACGCTTATACATACGCACATACAAT 59.076 36.000 0.00 0.00 0.00 2.71
359 1301 1.202580 ACCGCTATGAGCATCTTCACC 60.203 52.381 0.00 0.00 42.58 4.02
361 1303 2.484417 CCGCTATGAGCATCTTCACCTT 60.484 50.000 0.00 0.00 42.58 3.50
367 1309 3.476552 TGAGCATCTTCACCTTTTCGTT 58.523 40.909 0.00 0.00 34.92 3.85
707 2136 1.605712 CCAGATTAATCCGCGGGAGTC 60.606 57.143 27.83 16.58 34.05 3.36
732 2162 2.202479 CGCGCGTGATCAGAGTGA 60.202 61.111 24.19 0.00 0.00 3.41
872 2302 2.806608 TAAATCCATCGTCCGCTACC 57.193 50.000 0.00 0.00 0.00 3.18
879 2310 1.546589 ATCGTCCGCTACCCCACAAA 61.547 55.000 0.00 0.00 0.00 2.83
920 2351 1.967066 AGGAGACCTGCTATCGATTGG 59.033 52.381 1.71 4.10 29.57 3.16
1141 2576 4.824515 CGGAGGAGGAGGGCGAGT 62.825 72.222 0.00 0.00 0.00 4.18
1239 2674 3.507924 TACGGGTACGCGCACGAT 61.508 61.111 29.56 14.05 46.04 3.73
1570 3022 3.437741 AGTAAAATTTTGTAGCCCCGACG 59.562 43.478 13.76 0.00 0.00 5.12
1671 3125 3.951680 TCCGCTTTTCTTCTTTTCTTGGT 59.048 39.130 0.00 0.00 0.00 3.67
1672 3126 4.401202 TCCGCTTTTCTTCTTTTCTTGGTT 59.599 37.500 0.00 0.00 0.00 3.67
1673 3127 5.105513 TCCGCTTTTCTTCTTTTCTTGGTTT 60.106 36.000 0.00 0.00 0.00 3.27
1674 3128 6.095720 TCCGCTTTTCTTCTTTTCTTGGTTTA 59.904 34.615 0.00 0.00 0.00 2.01
1720 3174 1.140452 CAGACACCCATGATCCAGAGG 59.860 57.143 0.00 0.00 0.00 3.69
1734 3188 2.025605 TCCAGAGGAAGCTTAGGACGTA 60.026 50.000 0.00 0.00 0.00 3.57
1870 3325 8.679288 AAATTGAGAATTGTGATTGTTCGATC 57.321 30.769 0.00 0.00 0.00 3.69
1902 3357 2.635915 TCACCTTGGAATACTCGTGGTT 59.364 45.455 0.00 0.00 0.00 3.67
1938 3393 3.433957 CGACGTCCTCGATCATTCTATCT 59.566 47.826 10.58 0.00 46.14 1.98
1954 3409 6.540438 TTCTATCTATTGCCCCCTAATACG 57.460 41.667 0.00 0.00 0.00 3.06
1983 3499 2.358898 CCCCGGATGACAATCACATTTC 59.641 50.000 0.73 0.00 34.17 2.17
2030 3835 8.257306 GCTCAAATTTTGGGTTATATCCTTCAA 58.743 33.333 10.58 0.00 32.32 2.69
2149 3954 0.953471 TGATTTTGTCCGCCGAGTGG 60.953 55.000 0.00 0.00 38.77 4.00
2192 3997 2.427506 CTTTGTCAGGCTTGTAGACCC 58.572 52.381 0.00 0.00 0.00 4.46
2194 3999 0.685097 TGTCAGGCTTGTAGACCCAC 59.315 55.000 0.00 0.00 0.00 4.61
2195 4000 0.977395 GTCAGGCTTGTAGACCCACT 59.023 55.000 0.00 0.00 0.00 4.00
2197 4002 1.623811 TCAGGCTTGTAGACCCACTTC 59.376 52.381 0.00 0.00 0.00 3.01
2260 6319 6.040278 TCAATAAAGTTTGCATGAGGTTCACA 59.960 34.615 0.00 0.00 0.00 3.58
2261 6320 4.734398 AAAGTTTGCATGAGGTTCACAA 57.266 36.364 0.00 0.00 0.00 3.33
2335 6394 6.595772 ATTGTCATCGTTCAATTCTAGCTC 57.404 37.500 0.00 0.00 31.35 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.725312 GGAGAGGCGACATGAGGCA 61.725 63.158 17.91 0.0 36.55 4.75
189 747 5.632347 GGATTTCAATACGGACTACATACGG 59.368 44.000 0.00 0.0 0.00 4.02
200 758 7.625828 AGTCTTTTTAGGGATTTCAATACGG 57.374 36.000 0.00 0.0 0.00 4.02
307 1249 3.938963 GTGCCTCCGTTCATAAGAATGAA 59.061 43.478 1.48 0.0 46.06 2.57
323 1265 2.033194 GGTAGGTTGTGCGTGCCTC 61.033 63.158 0.00 0.0 35.33 4.70
325 1267 3.419759 CGGTAGGTTGTGCGTGCC 61.420 66.667 0.00 0.0 34.94 5.01
435 1377 1.608590 ACTTTGGCATTGGTTCTCGTG 59.391 47.619 0.00 0.0 0.00 4.35
441 1383 6.719370 TCAAGTAATAGACTTTGGCATTGGTT 59.281 34.615 0.00 0.0 46.79 3.67
537 1605 6.852420 ACACAAGTAACTCCTAGCAAGATA 57.148 37.500 0.00 0.0 0.00 1.98
539 1607 5.546621 AACACAAGTAACTCCTAGCAAGA 57.453 39.130 0.00 0.0 0.00 3.02
677 2105 3.802685 CGGATTAATCTGGACCGTTCTTC 59.197 47.826 15.47 0.0 38.97 2.87
726 2156 1.584380 GGTGCGTCGGTACTCACTCT 61.584 60.000 0.00 0.0 40.45 3.24
732 2162 4.093952 CGTCGGTGCGTCGGTACT 62.094 66.667 0.00 0.0 35.18 2.73
872 2302 1.336755 CTTCCGGTTTGAGTTTGTGGG 59.663 52.381 0.00 0.0 0.00 4.61
879 2310 3.231818 TCTCTTCTCTTCCGGTTTGAGT 58.768 45.455 0.00 0.0 0.00 3.41
920 2351 2.024871 CTCGACTGCGGGATCGAC 59.975 66.667 4.26 0.0 41.67 4.20
1673 3127 9.389755 TCAATTCGATCACCAGAACAATAAATA 57.610 29.630 0.00 0.0 0.00 1.40
1674 3128 8.184192 GTCAATTCGATCACCAGAACAATAAAT 58.816 33.333 0.00 0.0 0.00 1.40
1720 3174 4.635324 AGACACTAGTACGTCCTAAGCTTC 59.365 45.833 0.00 0.0 32.33 3.86
1734 3188 6.239176 GGCAATTAGATCAGCTAGACACTAGT 60.239 42.308 0.00 0.0 0.00 2.57
1896 3351 2.271800 GAGTCAGCCAATAGAACCACG 58.728 52.381 0.00 0.0 0.00 4.94
1902 3357 1.460504 ACGTCGAGTCAGCCAATAGA 58.539 50.000 0.00 0.0 0.00 1.98
1938 3393 4.076394 GCAATTCGTATTAGGGGGCAATA 58.924 43.478 0.00 0.0 0.00 1.90
1954 3409 0.107214 TGTCATCCGGGGAGCAATTC 60.107 55.000 0.00 0.0 0.00 2.17
2014 3819 6.012337 TGATGCTTTGAAGGATATAACCCA 57.988 37.500 0.00 0.0 37.20 4.51
2030 3835 0.607489 AGCGCCAACTTCTGATGCTT 60.607 50.000 2.29 0.0 33.18 3.91
2031 3836 0.607489 AAGCGCCAACTTCTGATGCT 60.607 50.000 2.29 0.0 37.03 3.79
2123 3928 0.521735 GCGGACAAAATCAGGACACC 59.478 55.000 0.00 0.0 0.00 4.16
2192 3997 6.367149 CGGATATGGAATGTGTATCTGAAGTG 59.633 42.308 0.00 0.0 34.58 3.16
2194 3999 6.691508 TCGGATATGGAATGTGTATCTGAAG 58.308 40.000 0.00 0.0 37.32 3.02
2195 4000 6.664428 TCGGATATGGAATGTGTATCTGAA 57.336 37.500 0.00 0.0 37.32 3.02
2197 4002 6.931281 ACTTTCGGATATGGAATGTGTATCTG 59.069 38.462 4.68 0.0 32.54 2.90


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

AutoCloner maintained by Alex Coulton.