Multiple sequence alignment - TraesCS4D01G135300

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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 TraesCS4D01G135300 chr4D 100.000 2614 0 0 1 2614 121982136 121979523 0.000000e+00 4828
1 TraesCS4D01G135300 chr4D 87.162 148 15 4 1957 2104 215469202 215469345 5.790000e-37 165
2 TraesCS4D01G135300 chr4A 93.581 888 27 10 532 1391 448747540 448748425 0.000000e+00 1297
3 TraesCS4D01G135300 chr4A 90.306 949 72 14 1580 2515 448751132 448752073 0.000000e+00 1225
4 TraesCS4D01G135300 chr4A 91.620 537 31 5 1 537 448744963 448745485 0.000000e+00 730
5 TraesCS4D01G135300 chr4A 88.034 234 9 4 1371 1585 448748432 448748665 2.580000e-65 259
6 TraesCS4D01G135300 chr4A 79.197 274 44 9 1818 2083 389239247 389239515 7.430000e-41 178
7 TraesCS4D01G135300 chr4B 91.904 877 39 13 532 1391 184890614 184889753 0.000000e+00 1197
8 TraesCS4D01G135300 chr4B 90.773 802 43 10 1373 2148 184889742 184888946 0.000000e+00 1042
9 TraesCS4D01G135300 chr4B 93.515 478 28 3 2139 2614 184887037 184886561 0.000000e+00 708
10 TraesCS4D01G135300 chr5D 79.503 483 76 11 1610 2079 540173092 540173564 3.250000e-84 322
11 TraesCS4D01G135300 chr5D 80.516 426 66 12 1680 2096 220708314 220707897 7.020000e-81 311
12 TraesCS4D01G135300 chr5D 78.673 211 39 5 1741 1947 421495614 421495406 4.540000e-28 135
13 TraesCS4D01G135300 chr7A 74.920 622 130 19 1675 2283 435728286 435728894 7.180000e-66 261
14 TraesCS4D01G135300 chr7A 75.506 445 84 19 1665 2093 21722609 21723044 7.380000e-46 195
15 TraesCS4D01G135300 chr6D 78.066 424 67 16 1685 2092 284503699 284503286 7.230000e-61 244
16 TraesCS4D01G135300 chr3D 75.949 395 75 14 1665 2044 471580638 471580249 4.440000e-43 185
17 TraesCS4D01G135300 chr5B 76.901 342 62 14 1669 2002 655579010 655579342 7.430000e-41 178
18 TraesCS4D01G135300 chr7D 74.444 450 85 20 1665 2096 21118522 21118085 1.610000e-37 167
19 TraesCS4D01G135300 chr3A 76.860 242 46 9 1970 2204 512267532 512267770 7.590000e-26 128
20 TraesCS4D01G135300 chr1B 77.056 231 41 11 1874 2097 660464119 660464344 3.530000e-24 122
21 TraesCS4D01G135300 chr2A 81.633 147 25 2 1951 2097 655218077 655217933 1.270000e-23 121


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 TraesCS4D01G135300 chr4D 121979523 121982136 2613 True 4828.000000 4828 100.00000 1 2614 1 chr4D.!!$R1 2613
1 TraesCS4D01G135300 chr4A 448744963 448752073 7110 False 877.750000 1297 90.88525 1 2515 4 chr4A.!!$F2 2514
2 TraesCS4D01G135300 chr4B 184886561 184890614 4053 True 982.333333 1197 92.06400 532 2614 3 chr4B.!!$R1 2082
3 TraesCS4D01G135300 chr7A 435728286 435728894 608 False 261.000000 261 74.92000 1675 2283 1 chr7A.!!$F2 608

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
230 231 0.037232 CTGTGGAAAGGACGAGGGTC 60.037 60.0 0.0 0.0 42.66 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 6443 0.03601 CTCGGCAGAACCTCCAATGT 60.036 55.0 0.0 0.0 35.61 2.71 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
27 28 5.140454 GGTGGTAAAGGCATAATTGGAGAT 58.860 41.667 0.00 0.00 0.00 2.75
78 79 1.065564 GGAGCTTGGATCTTGAGCACT 60.066 52.381 14.69 0.00 38.85 4.40
112 113 2.677573 AAGGGCGTCGCTTTTGTTGC 62.678 55.000 18.11 0.00 32.78 4.17
116 117 1.355210 CGTCGCTTTTGTTGCTGGT 59.645 52.632 0.00 0.00 0.00 4.00
134 135 3.138798 GGAGGACGCGAGGCACTA 61.139 66.667 15.93 0.00 45.40 2.74
143 144 1.604755 CGCGAGGCACTAGATCTTAGT 59.395 52.381 0.00 0.00 41.55 2.24
145 146 2.350007 GCGAGGCACTAGATCTTAGTCG 60.350 54.545 0.00 3.09 41.55 4.18
146 147 2.873472 CGAGGCACTAGATCTTAGTCGT 59.127 50.000 0.00 0.11 41.55 4.34
149 150 2.031857 GGCACTAGATCTTAGTCGTCGG 60.032 54.545 0.00 0.00 0.00 4.79
172 173 2.202610 TCGTTCGCTCGAGCCATG 60.203 61.111 30.66 21.78 37.91 3.66
182 183 0.984230 TCGAGCCATGGTTTTCCTCT 59.016 50.000 14.67 0.00 41.38 3.69
184 185 1.756430 GAGCCATGGTTTTCCTCTCC 58.244 55.000 14.67 0.00 41.38 3.71
223 224 1.064825 TTCCTCCCTGTGGAAAGGAC 58.935 55.000 7.05 0.00 41.17 3.85
225 226 1.192146 CCTCCCTGTGGAAAGGACGA 61.192 60.000 0.00 0.00 41.17 4.20
230 231 0.037232 CTGTGGAAAGGACGAGGGTC 60.037 60.000 0.00 0.00 42.66 4.46
265 266 1.131826 CGAATGACGCGGTCCAAAC 59.868 57.895 12.47 3.52 34.51 2.93
271 272 4.072088 CGCGGTCCAAACTGACGC 62.072 66.667 0.00 0.00 36.07 5.19
273 274 2.355363 CGGTCCAAACTGACGCGA 60.355 61.111 15.93 0.00 36.07 5.87
283 284 1.081774 CTGACGCGATCGATCTCCC 60.082 63.158 21.57 9.22 39.41 4.30
284 285 1.511318 CTGACGCGATCGATCTCCCT 61.511 60.000 21.57 2.04 39.41 4.20
294 295 1.048724 CGATCTCCCTGGGCCAACTA 61.049 60.000 8.04 0.00 0.00 2.24
374 375 3.124560 GGTGTAGCTAGATTTTCTCCGC 58.875 50.000 0.00 0.00 0.00 5.54
381 382 3.670991 GCTAGATTTTCTCCGCGTATCAG 59.329 47.826 4.92 0.00 0.00 2.90
418 419 4.161377 AGCTAGAACACTTTGGAGATCCTC 59.839 45.833 0.00 0.00 36.82 3.71
451 452 5.066968 AGCTAGAGAGTAGAACACTTTGC 57.933 43.478 0.00 0.00 37.72 3.68
495 496 9.819267 AGCTAGAATACAATACTTGGTTCTAAC 57.181 33.333 0.00 10.74 39.37 2.34
611 2672 5.826208 GGAGCATATGCATATGATGATTGGA 59.174 40.000 38.83 5.39 42.05 3.53
890 2983 2.890945 GAGAAGAGATGCTCTCCCTACC 59.109 54.545 8.89 0.00 44.42 3.18
891 2984 2.517980 AGAAGAGATGCTCTCCCTACCT 59.482 50.000 8.89 0.00 44.42 3.08
892 2985 2.380064 AGAGATGCTCTCCCTACCTG 57.620 55.000 8.89 0.00 44.42 4.00
893 2986 1.573376 AGAGATGCTCTCCCTACCTGT 59.427 52.381 8.89 0.00 44.42 4.00
894 2987 2.786445 AGAGATGCTCTCCCTACCTGTA 59.214 50.000 8.89 0.00 44.42 2.74
895 2988 3.153919 GAGATGCTCTCCCTACCTGTAG 58.846 54.545 0.00 0.00 37.55 2.74
896 2989 2.516277 AGATGCTCTCCCTACCTGTAGT 59.484 50.000 3.80 0.00 0.00 2.73
897 2990 2.438800 TGCTCTCCCTACCTGTAGTC 57.561 55.000 3.80 0.00 0.00 2.59
898 2991 1.063867 TGCTCTCCCTACCTGTAGTCC 60.064 57.143 3.80 0.00 0.00 3.85
899 2992 1.754910 GCTCTCCCTACCTGTAGTCCC 60.755 61.905 3.80 0.00 0.00 4.46
905 2998 2.963782 CCCTACCTGTAGTCCCATACAC 59.036 54.545 3.80 0.00 32.36 2.90
963 3068 3.617263 CGAGTACTTGGTCATTAGTTGGC 59.383 47.826 1.70 0.00 0.00 4.52
1399 3541 5.073144 TCTGGACTTTCCTTTTCCACTACAT 59.927 40.000 0.00 0.00 37.46 2.29
1497 3647 1.603739 GGGCTGCCTCGTTCCTTTT 60.604 57.895 19.68 0.00 0.00 2.27
1540 3700 5.880332 TGTATAGAAGCGCAAAGAGGAAATT 59.120 36.000 11.47 0.00 0.00 1.82
1542 3702 3.149196 AGAAGCGCAAAGAGGAAATTCA 58.851 40.909 11.47 0.00 0.00 2.57
1599 6231 3.964221 TAGCGAGCTCGTGCGTTGG 62.964 63.158 34.46 7.30 45.42 3.77
1699 6331 1.004277 TGTTGCCGCTTATCCTCCTTT 59.996 47.619 0.00 0.00 0.00 3.11
1913 6546 6.645306 TGATTTCAAATACGGATCTACACCA 58.355 36.000 0.00 0.00 0.00 4.17
1951 6584 4.143115 CGGATCGTGCGCTATTGATTAAAT 60.143 41.667 9.73 0.00 0.00 1.40
1964 6603 9.959775 GCTATTGATTAAATCGTAAGTAGCATC 57.040 33.333 0.00 0.00 39.48 3.91
2157 8718 9.372369 GTGGGTTGATTACTAATATATCAGAGC 57.628 37.037 0.00 0.00 30.64 4.09
2213 8775 2.265589 AAAACAGGACCACGGGTTAG 57.734 50.000 0.00 0.00 35.25 2.34
2286 8848 5.427481 AGTCTCATTTAAAATAGGACCCCGA 59.573 40.000 0.00 0.00 0.00 5.14
2339 8901 1.872952 CAAACATCGCAACAGACAGGA 59.127 47.619 0.00 0.00 0.00 3.86
2369 8931 6.037281 GCACTTCTTCCTTTATTAGTGGCTAC 59.963 42.308 0.00 0.00 34.92 3.58
2400 8962 0.613260 CCCATTCACTTGGACTCCGA 59.387 55.000 0.00 0.00 39.25 4.55
2405 8967 0.966920 TCACTTGGACTCCGACCTTC 59.033 55.000 0.00 0.00 0.00 3.46
2435 8997 5.224135 ACGACTTCTCTAGAACTTTTGCTC 58.776 41.667 0.00 0.00 0.00 4.26
2488 9050 4.947388 TGTGGTAAAAGCAAACTCTCAACT 59.053 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.787567 GCTCCGCCCCTCTAGTGAC 61.788 68.421 0.00 0.00 0.00 3.67
78 79 1.619363 CCTTGACCCCCTCCATCCA 60.619 63.158 0.00 0.00 0.00 3.41
112 113 4.135153 CCTCGCGTCCTCCACCAG 62.135 72.222 5.77 0.00 0.00 4.00
116 117 3.931190 TAGTGCCTCGCGTCCTCCA 62.931 63.158 5.77 0.00 0.00 3.86
134 135 3.076104 TCGCCGACGACTAAGATCT 57.924 52.632 0.00 0.00 45.12 2.75
172 173 1.066787 CAGAGGTCGGAGAGGAAAACC 60.067 57.143 0.00 0.00 36.95 3.27
198 199 0.476771 TCCACAGGGAGGAAAACCAC 59.523 55.000 0.00 0.00 38.64 4.16
225 226 3.007323 GTAACCCTGCCCGACCCT 61.007 66.667 0.00 0.00 0.00 4.34
265 266 1.081774 GGGAGATCGATCGCGTCAG 60.082 63.158 20.70 0.00 38.98 3.51
271 272 2.653702 GCCCAGGGAGATCGATCG 59.346 66.667 19.33 9.36 0.00 3.69
273 274 1.384502 TTGGCCCAGGGAGATCGAT 60.385 57.895 10.89 0.00 0.00 3.59
294 295 1.371558 GTCGGAGAACCACAAGCCT 59.628 57.895 0.00 0.00 39.69 4.58
324 325 4.990535 TCATTTGGATGCAAGGGATCCCT 61.991 47.826 28.96 28.96 39.01 4.20
374 375 4.395542 GCTACCTAGGGATACACTGATACG 59.604 50.000 14.81 0.00 39.74 3.06
381 382 5.241285 GTGTTCTAGCTACCTAGGGATACAC 59.759 48.000 14.81 11.08 41.18 2.90
425 426 7.041712 GCAAAGTGTTCTACTCTCTAGCTTTTT 60.042 37.037 0.00 0.00 39.18 1.94
426 427 6.425417 GCAAAGTGTTCTACTCTCTAGCTTTT 59.575 38.462 0.00 0.00 39.18 2.27
427 428 5.929415 GCAAAGTGTTCTACTCTCTAGCTTT 59.071 40.000 0.00 0.00 39.18 3.51
428 429 5.474825 GCAAAGTGTTCTACTCTCTAGCTT 58.525 41.667 0.00 0.00 39.18 3.74
429 430 4.081917 GGCAAAGTGTTCTACTCTCTAGCT 60.082 45.833 0.00 0.00 39.18 3.32
430 431 4.081917 AGGCAAAGTGTTCTACTCTCTAGC 60.082 45.833 0.00 0.00 39.18 3.42
431 432 5.184096 TGAGGCAAAGTGTTCTACTCTCTAG 59.816 44.000 0.00 0.00 39.18 2.43
432 433 5.077564 TGAGGCAAAGTGTTCTACTCTCTA 58.922 41.667 0.00 0.00 39.18 2.43
433 434 3.898123 TGAGGCAAAGTGTTCTACTCTCT 59.102 43.478 0.00 0.00 39.18 3.10
434 435 4.258702 TGAGGCAAAGTGTTCTACTCTC 57.741 45.455 0.00 0.00 39.18 3.20
435 436 4.689612 TTGAGGCAAAGTGTTCTACTCT 57.310 40.909 0.00 0.00 39.18 3.24
436 437 5.751243 TTTTGAGGCAAAGTGTTCTACTC 57.249 39.130 0.00 0.00 39.18 2.59
437 438 5.885912 TCTTTTTGAGGCAAAGTGTTCTACT 59.114 36.000 0.00 0.00 42.89 2.57
438 439 6.131544 TCTTTTTGAGGCAAAGTGTTCTAC 57.868 37.500 0.00 0.00 34.72 2.59
890 2983 2.890808 ATGCGTGTATGGGACTACAG 57.109 50.000 0.00 0.00 32.45 2.74
891 2984 3.293337 AGTATGCGTGTATGGGACTACA 58.707 45.455 0.00 0.00 0.00 2.74
892 2985 5.443185 TTAGTATGCGTGTATGGGACTAC 57.557 43.478 0.00 0.00 0.00 2.73
893 2986 6.468333 TTTTAGTATGCGTGTATGGGACTA 57.532 37.500 0.00 0.00 0.00 2.59
894 2987 5.347620 TTTTAGTATGCGTGTATGGGACT 57.652 39.130 0.00 0.00 0.00 3.85
895 2988 6.613755 AATTTTAGTATGCGTGTATGGGAC 57.386 37.500 0.00 0.00 0.00 4.46
896 2989 7.769507 TGTAAATTTTAGTATGCGTGTATGGGA 59.230 33.333 0.00 0.00 0.00 4.37
897 2990 7.853929 GTGTAAATTTTAGTATGCGTGTATGGG 59.146 37.037 0.00 0.00 0.00 4.00
898 2991 8.391859 TGTGTAAATTTTAGTATGCGTGTATGG 58.608 33.333 0.00 0.00 0.00 2.74
899 2992 9.762062 TTGTGTAAATTTTAGTATGCGTGTATG 57.238 29.630 0.00 0.00 0.00 2.39
963 3068 7.972527 ACTAGTACCGATGCTATTTATAGTCG 58.027 38.462 0.00 1.89 32.15 4.18
1150 3261 1.304217 TCCTTTCTCCGGCGTCTCT 60.304 57.895 6.01 0.00 0.00 3.10
1399 3541 1.367346 TTGAAGTCACCAGGGCCATA 58.633 50.000 6.18 0.00 0.00 2.74
1540 3700 1.801771 CCAGCGGTCGTTTTACATTGA 59.198 47.619 0.00 0.00 0.00 2.57
1542 3702 0.519961 GCCAGCGGTCGTTTTACATT 59.480 50.000 0.00 0.00 0.00 2.71
1672 6304 3.071602 AGGATAAGCGGCAACATAGATGT 59.928 43.478 1.45 0.00 44.20 3.06
1759 6391 6.471233 TGTGGAGATAGACACCTTAGAATG 57.529 41.667 0.00 0.00 36.80 2.67
1810 6443 0.036010 CTCGGCAGAACCTCCAATGT 60.036 55.000 0.00 0.00 35.61 2.71
1913 6546 3.240069 CGATCCGTCTTTGTTTCGTACT 58.760 45.455 0.00 0.00 0.00 2.73
2213 8775 3.725490 ACTCACTGACCTTTCGGTTAAC 58.275 45.455 0.00 0.00 45.73 2.01
2249 8811 8.776680 TTTAAATGAGACTAAAAAGTGTTCGC 57.223 30.769 0.00 0.00 0.00 4.70
2286 8848 4.260784 GCTTGTTGTTTTCAGACATCGACT 60.261 41.667 0.00 0.00 0.00 4.18
2293 8855 2.844122 ACCGCTTGTTGTTTTCAGAC 57.156 45.000 0.00 0.00 0.00 3.51
2369 8931 7.334171 GTCCAAGTGAATGGGGAAATAAATTTG 59.666 37.037 0.00 0.00 41.05 2.32
2405 8967 6.168164 AGTTCTAGAGAAGTCGTTTCTACG 57.832 41.667 5.21 0.00 46.12 3.51
2435 8997 6.575201 GTGTGAGAAAGCTACGAATCTTTTTG 59.425 38.462 0.00 0.00 33.14 2.44


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

AutoCloner maintained by Alex Coulton.