Multiple sequence alignment - TraesCS4A01G302700

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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 TraesCS4A01G302700 chr4A 100.000 4453 0 0 1 4453 599085563 599081111 0.000000e+00 8224
1 TraesCS4A01G302700 chr4A 96.262 2301 81 5 1 2298 599180666 599178368 0.000000e+00 3768
2 TraesCS4A01G302700 chr4A 96.261 2300 82 4 1 2298 599224093 599221796 0.000000e+00 3768
3 TraesCS4A01G302700 chr4A 96.174 2300 84 4 1 2298 599103287 599100990 0.000000e+00 3757
4 TraesCS4A01G302700 chr4A 95.832 2279 86 7 1 2276 599147503 599145231 0.000000e+00 3674
5 TraesCS4A01G302700 chr4A 96.253 2162 77 4 2293 4453 599178309 599176151 0.000000e+00 3541
6 TraesCS4A01G302700 chr4A 96.161 2162 79 4 2293 4453 599221737 599219579 0.000000e+00 3530
7 TraesCS4A01G302700 chr4A 95.952 2174 72 8 2293 4453 599100931 599098761 0.000000e+00 3513
8 TraesCS4A01G302700 chr4A 94.313 2163 118 4 2293 4453 599157453 599155294 0.000000e+00 3308
9 TraesCS4A01G302700 chr4A 94.172 2162 123 2 2293 4453 599246532 599244373 0.000000e+00 3291
10 TraesCS4A01G302700 chr4A 94.123 2161 125 1 2293 4453 599124494 599122336 0.000000e+00 3286
11 TraesCS4A01G302700 chr4A 96.132 1965 74 2 2293 4257 599144449 599142487 0.000000e+00 3206
12 TraesCS4A01G302700 chr4A 93.402 2046 111 17 1 2029 599126779 599124741 0.000000e+00 3009
13 TraesCS4A01G302700 chr4A 93.307 2047 113 16 1 2029 599159740 599157700 0.000000e+00 3000
14 TraesCS4A01G302700 chr4A 93.060 2046 120 15 1 2029 599248819 599246779 0.000000e+00 2972
15 TraesCS4A01G302700 chrUn 94.403 2162 118 2 2293 4453 216674651 216672492 0.000000e+00 3319
16 TraesCS4A01G302700 chrUn 95.716 1984 76 7 296 2276 360633605 360631628 0.000000e+00 3184
17 TraesCS4A01G302700 chrUn 97.324 1196 31 1 1 1195 216652974 216651779 0.000000e+00 2030
18 TraesCS4A01G302700 chrUn 92.350 366 26 2 4089 4453 360632885 360632521 1.840000e-143 520
19 TraesCS4A01G302700 chr4B 90.776 1843 118 10 2290 4085 7354975 7356812 0.000000e+00 2414
20 TraesCS4A01G302700 chr4B 89.962 1584 119 15 730 2295 7353355 7354916 0.000000e+00 2008
21 TraesCS4A01G302700 chr4D 90.474 1816 112 28 508 2295 4416666 4418448 0.000000e+00 2338
22 TraesCS4A01G302700 chr6A 92.617 1639 83 15 665 2298 593027288 593025683 0.000000e+00 2322
23 TraesCS4A01G302700 chr6A 93.795 1386 80 2 3073 4453 593024889 593023505 0.000000e+00 2078
24 TraesCS4A01G302700 chr1B 78.920 574 99 16 1725 2294 46651283 46650728 1.960000e-98 370


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 TraesCS4A01G302700 chr4A 599081111 599085563 4452 True 8224.0 8224 100.0000 1 4453 1 chr4A.!!$R1 4452
1 TraesCS4A01G302700 chr4A 599176151 599180666 4515 True 3654.5 3768 96.2575 1 4453 2 chr4A.!!$R6 4452
2 TraesCS4A01G302700 chr4A 599219579 599224093 4514 True 3649.0 3768 96.2110 1 4453 2 chr4A.!!$R7 4452
3 TraesCS4A01G302700 chr4A 599098761 599103287 4526 True 3635.0 3757 96.0630 1 4453 2 chr4A.!!$R2 4452
4 TraesCS4A01G302700 chr4A 599142487 599147503 5016 True 3440.0 3674 95.9820 1 4257 2 chr4A.!!$R4 4256
5 TraesCS4A01G302700 chr4A 599155294 599159740 4446 True 3154.0 3308 93.8100 1 4453 2 chr4A.!!$R5 4452
6 TraesCS4A01G302700 chr4A 599122336 599126779 4443 True 3147.5 3286 93.7625 1 4453 2 chr4A.!!$R3 4452
7 TraesCS4A01G302700 chr4A 599244373 599248819 4446 True 3131.5 3291 93.6160 1 4453 2 chr4A.!!$R8 4452
8 TraesCS4A01G302700 chrUn 216672492 216674651 2159 True 3319.0 3319 94.4030 2293 4453 1 chrUn.!!$R2 2160
9 TraesCS4A01G302700 chrUn 216651779 216652974 1195 True 2030.0 2030 97.3240 1 1195 1 chrUn.!!$R1 1194
10 TraesCS4A01G302700 chrUn 360631628 360633605 1977 True 1852.0 3184 94.0330 296 4453 2 chrUn.!!$R3 4157
11 TraesCS4A01G302700 chr4B 7353355 7356812 3457 False 2211.0 2414 90.3690 730 4085 2 chr4B.!!$F1 3355
12 TraesCS4A01G302700 chr4D 4416666 4418448 1782 False 2338.0 2338 90.4740 508 2295 1 chr4D.!!$F1 1787
13 TraesCS4A01G302700 chr6A 593023505 593027288 3783 True 2200.0 2322 93.2060 665 4453 2 chr6A.!!$R1 3788
14 TraesCS4A01G302700 chr1B 46650728 46651283 555 True 370.0 370 78.9200 1725 2294 1 chr1B.!!$R1 569

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
520 525 0.108329 ATGACTGGACGTAAAGGGCG 60.108 55.0 0.0 0.0 0.00 6.13 F
1250 1294 0.103026 CGACGCCTCCAAGATCATCA 59.897 55.0 0.0 0.0 0.00 3.07 F
2271 2423 0.666913 AGTTGTGTCTCGTGTAGCGT 59.333 50.0 0.0 0.0 42.13 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1850 0.321210 ACAACATCGATGCCGTGGAA 60.321 50.0 25.11 0.0 37.05 3.53 R
2461 3382 0.386476 CACTTGCTGTGCACCAACAT 59.614 50.0 15.69 0.0 38.71 2.71 R
3574 4586 0.534203 GAGCCCAAAGTTCCGACACA 60.534 55.0 0.00 0.0 0.00 3.72 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
122 125 0.165944 CAAAGTGACGAACGGATGCC 59.834 55.000 0.00 0.00 0.00 4.40
156 159 3.517296 TCTGTTGAATAGTTTGGGCCA 57.483 42.857 0.00 0.00 0.00 5.36
226 229 6.752285 TTAGTTAGTTGGTCAGGTAAAGGT 57.248 37.500 0.00 0.00 0.00 3.50
277 280 7.094377 GGTCTTTTTGAATGATTAGCCACACTA 60.094 37.037 0.00 0.00 0.00 2.74
394 398 4.373156 AGGTCAATGCTCCTTGTAAAGT 57.627 40.909 0.00 0.00 44.25 2.66
438 442 2.494073 CGGCAGAACTAGAGGAAGAAGT 59.506 50.000 0.00 0.00 0.00 3.01
520 525 0.108329 ATGACTGGACGTAAAGGGCG 60.108 55.000 0.00 0.00 0.00 6.13
712 721 2.866762 GTTGAAACAGACGCTCACTTCT 59.133 45.455 0.00 0.00 0.00 2.85
861 874 3.047280 CGCTGCCAAACGCCTACA 61.047 61.111 0.00 0.00 36.24 2.74
945 958 2.329339 GCATCCGCAGCCGAATTC 59.671 61.111 0.00 0.00 38.36 2.17
970 985 2.681778 CTCCACCGCTCAGTCCCT 60.682 66.667 0.00 0.00 0.00 4.20
1058 1078 2.238847 ATCGCCGGCATGTACACTGT 62.239 55.000 28.98 0.00 0.00 3.55
1187 1231 1.286260 GACACGTTCGAGGAGCTGT 59.714 57.895 0.00 0.00 0.00 4.40
1250 1294 0.103026 CGACGCCTCCAAGATCATCA 59.897 55.000 0.00 0.00 0.00 3.07
1353 1399 7.500992 TCTTAATTATCTGCTCTGGAAATCGT 58.499 34.615 0.00 0.00 0.00 3.73
1422 1468 2.267006 CTCATGCGGTGCACCTCT 59.733 61.111 32.28 14.55 43.04 3.69
1455 1501 5.104318 ACCATCATAAACCCTTTCTCTCTCC 60.104 44.000 0.00 0.00 0.00 3.71
1498 1552 2.661537 GTTTGTTTGCCCGCTGCC 60.662 61.111 0.00 0.00 40.16 4.85
1510 1564 2.029288 CGCTGCCTCAATGTCGTGT 61.029 57.895 0.00 0.00 0.00 4.49
1517 1571 2.483877 GCCTCAATGTCGTGTGATTCAA 59.516 45.455 0.00 0.00 0.00 2.69
1522 1576 6.313658 CCTCAATGTCGTGTGATTCAAATCTA 59.686 38.462 4.50 0.00 36.39 1.98
1574 1628 1.302949 GGTTGCACTGCCCCATAGA 59.697 57.895 0.00 0.00 0.00 1.98
1603 1657 8.547967 AATTAGAAGAATCGAGTTTAGTTGCA 57.452 30.769 0.00 0.00 0.00 4.08
1665 1729 8.578448 TCAATGATGAGGATAAATTGTTGTCA 57.422 30.769 0.00 0.00 31.63 3.58
1671 1735 9.859427 GATGAGGATAAATTGTTGTCATTTTCA 57.141 29.630 0.00 0.00 32.09 2.69
1824 1893 2.779755 TATTTGGATGTGTCGGCACT 57.220 45.000 22.43 6.77 45.44 4.40
1865 1934 1.501741 CCGCACAATTGAGGTTCGG 59.498 57.895 13.59 9.09 37.89 4.30
1880 1949 1.000938 GTTCGGTGTCGTTCTACAGGT 60.001 52.381 0.00 0.00 37.69 4.00
1996 2065 1.253100 GGCGAGGGGAATTTTTGTCA 58.747 50.000 0.00 0.00 0.00 3.58
2022 2171 6.606234 TTGCAAACGTTTGTTCTACTATCA 57.394 33.333 34.39 20.92 40.24 2.15
2158 2309 6.537453 TTTTTCTGTTTCTCCATTGGAACA 57.463 33.333 6.88 7.61 0.00 3.18
2201 2353 2.506438 GACGCAGGGTGTCTACGC 60.506 66.667 0.00 0.00 39.62 4.42
2271 2423 0.666913 AGTTGTGTCTCGTGTAGCGT 59.333 50.000 0.00 0.00 42.13 5.07
2303 3220 7.013178 TCGGTATTCATGACAATTGCACATAAT 59.987 33.333 15.16 15.45 0.00 1.28
2535 3456 3.131933 TGCCATACAATACAAACATGGGC 59.868 43.478 0.00 0.00 37.27 5.36
2826 3747 7.957484 CGCACAACTAAATTCATATATGGCTAC 59.043 37.037 12.78 0.00 0.00 3.58
2885 3807 8.690203 TTTTGAACCATTTCATCTCAGTTCTA 57.310 30.769 0.00 0.00 41.50 2.10
2912 3835 6.966534 ACCTCTTCAGAATTTGACAATGTT 57.033 33.333 0.00 0.00 34.94 2.71
3058 3981 7.696992 TTTGATACCAAATTCCCACTAGTTC 57.303 36.000 0.00 0.00 37.36 3.01
3327 4295 7.732996 AGAAACTAGCTAACTTGTAACAAGGA 58.267 34.615 0.00 0.00 31.28 3.36
3574 4586 8.062448 GCGCGTAAAACTTAGATGAATATTCTT 58.938 33.333 16.24 10.10 0.00 2.52
3608 4620 1.339727 GGGCTCGTAACCCTGTGAAAT 60.340 52.381 3.34 0.00 44.68 2.17
3672 4684 1.865865 AGTGTGTCGTGGATGTGTTC 58.134 50.000 0.00 0.00 0.00 3.18
3746 4758 6.073548 CCTCTAGTGACTTTGTTTTGCTGTAG 60.074 42.308 0.00 0.00 0.00 2.74
3748 4760 3.066760 AGTGACTTTGTTTTGCTGTAGGC 59.933 43.478 0.00 0.00 42.22 3.93
3788 4800 3.782889 AAGCAAGTCTTGTTGTTGGTC 57.217 42.857 14.03 0.00 32.79 4.02
3884 4896 7.291182 AGTGTGGCCTTCTTATAAGAGTATGAT 59.709 37.037 14.63 0.00 36.22 2.45
3892 4904 7.559335 TCTTATAAGAGTATGATGGCACCAT 57.441 36.000 11.24 0.00 39.69 3.55
3913 4925 1.381872 GCAGTAGCCAGAGGAGGGA 60.382 63.158 0.00 0.00 33.58 4.20
4031 5043 8.584157 TGTATTTGCATTGGTATGAAAAGTCTT 58.416 29.630 0.00 0.00 41.50 3.01
4109 5121 2.825836 CCCAGCTCAACGCCCATC 60.826 66.667 0.00 0.00 40.39 3.51
4127 5139 0.902984 TCTCACCGGCATGTACACCT 60.903 55.000 0.00 0.00 0.00 4.00
4247 5266 0.677288 TCGTGGACGAGGACACATTT 59.323 50.000 0.00 0.00 44.22 2.32
4249 5268 1.872237 CGTGGACGAGGACACATTTGT 60.872 52.381 0.00 0.00 43.02 2.83
4303 5322 1.107538 TCCCGCCTCTTCATCTACGG 61.108 60.000 0.00 0.00 40.30 4.02
4379 5410 2.844654 TCATCTCTCCCTCTGCTCTT 57.155 50.000 0.00 0.00 0.00 2.85
4435 5466 1.566298 AAAATCGCAGGGAGGAGCCT 61.566 55.000 0.00 0.00 36.66 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.876156 AGTTTTGAAGCAAGGCGAGAG 59.124 47.619 0.00 0.00 0.00 3.20
122 125 3.270027 TCAACAGATTCCCACGCATTAG 58.730 45.455 0.00 0.00 0.00 1.73
156 159 5.067805 ACGCTTTGAACTTTCTTCAGGATTT 59.932 36.000 0.00 0.00 0.00 2.17
277 280 1.051812 CTGGGTTGTGTCTCAGTCCT 58.948 55.000 0.00 0.00 0.00 3.85
394 398 1.794785 CGCGCACTCGACGTAAGAA 60.795 57.895 8.75 0.00 37.46 2.52
438 442 4.382320 GGCACGCAGTTACCGGGA 62.382 66.667 6.32 0.00 41.61 5.14
520 525 1.520787 CCCGATTCACCGCCTACAC 60.521 63.158 0.00 0.00 0.00 2.90
712 721 2.867368 GTTGTGTGTCCACGTGTTCATA 59.133 45.455 15.65 8.52 44.92 2.15
861 874 1.040339 GGCTCACGAGGGTCTCTCAT 61.040 60.000 0.00 0.00 42.55 2.90
1250 1294 2.814269 CATCAGGATGTCGATGTCGTT 58.186 47.619 2.04 0.00 37.40 3.85
1455 1501 8.616076 CATAGAGTTAAAAATAAGCAGGTGGAG 58.384 37.037 0.00 0.00 0.00 3.86
1498 1552 6.174451 AGATTTGAATCACACGACATTGAG 57.826 37.500 6.50 0.00 37.89 3.02
1522 1576 9.520515 AAGAATCATTCGCCCAGTATAATAAAT 57.479 29.630 0.00 0.00 34.02 1.40
1574 1628 9.852091 AACTAAACTCGATTCTTCTAATTACGT 57.148 29.630 0.00 0.00 0.00 3.57
1671 1735 9.678260 GCAGATCATTAATACCAGGAATATTCT 57.322 33.333 14.95 0.00 0.00 2.40
1781 1850 0.321210 ACAACATCGATGCCGTGGAA 60.321 50.000 25.11 0.00 37.05 3.53
1865 1934 1.007336 CGGCACCTGTAGAACGACAC 61.007 60.000 0.00 0.00 0.00 3.67
1996 2065 8.132362 TGATAGTAGAACAAACGTTTGCAAAAT 58.868 29.630 34.70 21.08 41.79 1.82
2022 2171 2.086869 CATTGCCCGAAGAACAGACAT 58.913 47.619 0.00 0.00 0.00 3.06
2158 2309 9.376075 CTGACATATCTGAATAGAAACAACACT 57.624 33.333 0.00 0.00 36.32 3.55
2178 2329 1.188219 AGACACCCTGCGTCTGACAT 61.188 55.000 8.73 0.00 42.12 3.06
2201 2353 1.089481 CACCCGAATCACGTCCATGG 61.089 60.000 4.97 4.97 40.78 3.66
2461 3382 0.386476 CACTTGCTGTGCACCAACAT 59.614 50.000 15.69 0.00 38.71 2.71
2486 3407 3.057548 CCGAAGTGCATGCAGGCA 61.058 61.111 24.07 24.07 42.53 4.75
2665 3586 7.284489 AGCAAATCAGGTTACTTCTTAACAACA 59.716 33.333 0.00 0.00 41.87 3.33
2885 3807 9.082313 ACATTGTCAAATTCTGAAGAGGTTAAT 57.918 29.630 0.00 0.00 35.22 1.40
2912 3835 8.584157 AGACACCTGAAATAATGCAAAAATACA 58.416 29.630 0.00 0.00 0.00 2.29
3209 4176 3.208594 TGTGCATCTACCAAGCATGATC 58.791 45.455 0.00 0.00 40.78 2.92
3245 4213 7.610580 TGGGAAACAAAGAATTTCTACCAAT 57.389 32.000 0.00 0.00 35.03 3.16
3246 4214 6.462347 GCTGGGAAACAAAGAATTTCTACCAA 60.462 38.462 0.00 0.00 35.03 3.67
3327 4295 4.894784 AGTCACGTGGTTTCACTAATCAT 58.105 39.130 17.00 0.00 41.53 2.45
3416 4411 2.202797 GCCGCGATCTGCTCTTCA 60.203 61.111 8.23 0.00 43.27 3.02
3574 4586 0.534203 GAGCCCAAAGTTCCGACACA 60.534 55.000 0.00 0.00 0.00 3.72
3608 4620 7.224949 TGACATCAACACACGACAATAGTTTTA 59.775 33.333 0.00 0.00 0.00 1.52
3714 4726 6.726490 AACAAAGTCACTAGAGGACTAACA 57.274 37.500 17.82 0.00 44.50 2.41
3746 4758 6.490566 TTATAGAGAAAAACAAACCGAGCC 57.509 37.500 0.00 0.00 0.00 4.70
3748 4760 7.129109 TGCTTATAGAGAAAAACAAACCGAG 57.871 36.000 0.00 0.00 0.00 4.63
3788 4800 1.403780 GGCTACACTCTGGGTACAACG 60.404 57.143 0.00 0.00 0.00 4.10
3860 4872 7.445121 CATCATACTCTTATAAGAAGGCCACA 58.555 38.462 15.85 0.00 34.03 4.17
3884 4896 1.078214 GCTACTGCTCATGGTGCCA 60.078 57.895 8.67 0.00 36.03 4.92
3892 4904 0.685785 CCTCCTCTGGCTACTGCTCA 60.686 60.000 0.00 0.00 39.59 4.26
4071 5083 3.181434 GGCCCTATGGTATGATGTTCCAA 60.181 47.826 0.00 0.00 34.80 3.53
4109 5121 0.821517 TAGGTGTACATGCCGGTGAG 59.178 55.000 1.90 0.00 0.00 3.51
4247 5266 2.523168 TCGTCCCACAGCTCCACA 60.523 61.111 0.00 0.00 0.00 4.17
4249 5268 2.997315 CCTCGTCCCACAGCTCCA 60.997 66.667 0.00 0.00 0.00 3.86
4303 5322 2.429907 CGATGATCTCGGAGGCGC 60.430 66.667 0.00 0.00 43.82 6.53
4346 5377 0.188587 AGATGATAGAGGGCGTGGGA 59.811 55.000 0.00 0.00 0.00 4.37
4379 5410 3.687125 AGATGAGTCAGTACCGAGACAA 58.313 45.455 11.73 2.48 37.23 3.18


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

AutoCloner maintained by Alex Coulton.