Multiple sequence alignment - TraesCS7A01G365300

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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 TraesCS7A01G365300 chr7A 100.000 4505 0 0 1 4505 539327169 539322665 0.000000e+00 8320.0
1 TraesCS7A01G365300 chr7A 82.375 2105 350 20 2139 4232 539928023 539930117 0.000000e+00 1812.0
2 TraesCS7A01G365300 chr7A 75.181 3179 710 67 1356 4505 539449485 539446357 0.000000e+00 1426.0
3 TraesCS7A01G365300 chr7A 85.757 1011 135 7 1093 2103 539926865 539927866 0.000000e+00 1061.0
4 TraesCS7A01G365300 chr7A 85.956 413 47 6 4094 4505 539403676 539403274 8.950000e-117 431.0
5 TraesCS7A01G365300 chr7A 86.061 165 22 1 4342 4505 539930158 539930322 4.630000e-40 176.0
6 TraesCS7A01G365300 chr7D 97.519 3950 79 9 564 4505 460279090 460283028 0.000000e+00 6734.0
7 TraesCS7A01G365300 chr7D 84.076 3165 477 23 1084 4238 459752908 459749761 0.000000e+00 3027.0
8 TraesCS7A01G365300 chr7D 82.903 3217 505 32 1053 4238 459790384 459787182 0.000000e+00 2852.0
9 TraesCS7A01G365300 chr7D 80.690 1362 243 12 3149 4505 460108978 460110324 0.000000e+00 1040.0
10 TraesCS7A01G365300 chr7D 89.855 552 39 10 1 543 460278494 460279037 0.000000e+00 693.0
11 TraesCS7A01G365300 chr7D 83.144 528 71 8 1203 1724 460273364 460273879 2.450000e-127 466.0
12 TraesCS7A01G365300 chr7D 87.273 165 20 1 4342 4505 459749724 459749560 2.140000e-43 187.0
13 TraesCS7A01G365300 chr7D 100.000 48 0 0 564 611 460279038 460279085 6.210000e-14 89.8
14 TraesCS7A01G365300 chr7D 90.566 53 4 1 434 485 244560855 244560907 8.090000e-08 69.4
15 TraesCS7A01G365300 chr7D 89.583 48 5 0 438 485 636764522 636764475 1.350000e-05 62.1
16 TraesCS7A01G365300 chr7B 95.706 4192 146 14 166 4347 482683349 482687516 0.000000e+00 6713.0
17 TraesCS7A01G365300 chr7B 83.876 3194 478 32 1053 4232 481857188 481854018 0.000000e+00 3011.0
18 TraesCS7A01G365300 chr7B 83.050 2885 463 22 1364 4238 482078294 482075426 0.000000e+00 2595.0
19 TraesCS7A01G365300 chr7B 85.546 339 45 2 1386 1724 482664453 482664787 7.170000e-93 351.0
20 TraesCS7A01G365300 chr7B 98.137 161 3 0 4345 4505 482687597 482687757 9.540000e-72 281.0
21 TraesCS7A01G365300 chr7B 87.931 174 12 4 1 171 482682551 482682718 3.560000e-46 196.0
22 TraesCS7A01G365300 chr7B 87.879 165 19 1 4342 4505 481853976 481853812 4.600000e-45 193.0
23 TraesCS7A01G365300 chr7B 100.000 35 0 0 437 471 92325135 92325169 1.050000e-06 65.8
24 TraesCS7A01G365300 chr2B 81.603 3256 546 37 1291 4505 784188703 784191946 0.000000e+00 2645.0
25 TraesCS7A01G365300 chr2B 80.527 3266 551 54 1291 4505 798128351 798131582 0.000000e+00 2429.0
26 TraesCS7A01G365300 chr2B 79.087 416 79 6 1760 2168 780594011 780594425 3.430000e-71 279.0
27 TraesCS7A01G365300 chr2A 80.320 3252 565 49 1291 4505 764309067 764312280 0.000000e+00 2390.0
28 TraesCS7A01G365300 chr2A 96.129 775 23 3 689 1459 208166413 208167184 0.000000e+00 1258.0
29 TraesCS7A01G365300 chr3D 91.837 49 2 2 437 484 50538350 50538397 2.910000e-07 67.6
30 TraesCS7A01G365300 chr6D 88.235 51 6 0 434 484 386649856 386649906 1.350000e-05 62.1
31 TraesCS7A01G365300 chr2D 88.235 51 5 1 436 485 647824717 647824767 4.870000e-05 60.2
32 TraesCS7A01G365300 chr6A 88.000 50 4 2 437 485 594822833 594822785 1.750000e-04 58.4


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 TraesCS7A01G365300 chr7A 539322665 539327169 4504 True 8320.000000 8320 100.000000 1 4505 1 chr7A.!!$R1 4504
1 TraesCS7A01G365300 chr7A 539446357 539449485 3128 True 1426.000000 1426 75.181000 1356 4505 1 chr7A.!!$R3 3149
2 TraesCS7A01G365300 chr7A 539926865 539930322 3457 False 1016.333333 1812 84.731000 1093 4505 3 chr7A.!!$F1 3412
3 TraesCS7A01G365300 chr7D 459787182 459790384 3202 True 2852.000000 2852 82.903000 1053 4238 1 chr7D.!!$R1 3185
4 TraesCS7A01G365300 chr7D 460278494 460283028 4534 False 2505.600000 6734 95.791333 1 4505 3 chr7D.!!$F4 4504
5 TraesCS7A01G365300 chr7D 459749560 459752908 3348 True 1607.000000 3027 85.674500 1084 4505 2 chr7D.!!$R3 3421
6 TraesCS7A01G365300 chr7D 460108978 460110324 1346 False 1040.000000 1040 80.690000 3149 4505 1 chr7D.!!$F2 1356
7 TraesCS7A01G365300 chr7D 460273364 460273879 515 False 466.000000 466 83.144000 1203 1724 1 chr7D.!!$F3 521
8 TraesCS7A01G365300 chr7B 482075426 482078294 2868 True 2595.000000 2595 83.050000 1364 4238 1 chr7B.!!$R1 2874
9 TraesCS7A01G365300 chr7B 482682551 482687757 5206 False 2396.666667 6713 93.924667 1 4505 3 chr7B.!!$F3 4504
10 TraesCS7A01G365300 chr7B 481853812 481857188 3376 True 1602.000000 3011 85.877500 1053 4505 2 chr7B.!!$R2 3452
11 TraesCS7A01G365300 chr2B 784188703 784191946 3243 False 2645.000000 2645 81.603000 1291 4505 1 chr2B.!!$F2 3214
12 TraesCS7A01G365300 chr2B 798128351 798131582 3231 False 2429.000000 2429 80.527000 1291 4505 1 chr2B.!!$F3 3214
13 TraesCS7A01G365300 chr2A 764309067 764312280 3213 False 2390.000000 2390 80.320000 1291 4505 1 chr2A.!!$F2 3214
14 TraesCS7A01G365300 chr2A 208166413 208167184 771 False 1258.000000 1258 96.129000 689 1459 1 chr2A.!!$F1 770

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
239 881 0.179062 AGTCTGCATGGATCTTCGCC 60.179 55.000 0.0 0.0 0.00 5.54 F
253 895 0.672401 TTCGCCAAGTTAAGAGCCCG 60.672 55.000 0.0 0.0 0.00 6.13 F
480 1127 1.026718 CAAACCTCCCGCATCAGTCC 61.027 60.000 0.0 0.0 0.00 3.85 F
644 1328 1.261619 GTGCTCACCGAGTTTGAACTG 59.738 52.381 0.3 0.0 39.88 3.16 F
1582 2300 3.245264 ACTTGGGCAACTAAATAGGCTGT 60.245 43.478 0.0 0.0 36.22 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 3023 1.743252 CAAGAGCCAGCGAAGGGAC 60.743 63.158 0.00 0.0 0.0 4.46 R
2188 3060 3.933861 ACTCATGGGGATGTTACCTTC 57.066 47.619 0.00 0.0 0.0 3.46 R
2401 3273 0.544120 GGGATTTGGCCTTGGAACCA 60.544 55.000 3.32 0.0 0.0 3.67 R
2440 3312 2.019984 GTTGATCACCTGGAGATTGGC 58.980 52.381 8.06 0.0 0.0 4.52 R
3612 4491 9.672673 ATCAGCATATGTAAACTTCTGTAACTT 57.327 29.630 4.29 0.0 0.0 2.66 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
48 49 6.874134 AGCACCTATATATAACGCTCCAAAAG 59.126 38.462 4.98 0.00 0.00 2.27
49 50 6.092259 GCACCTATATATAACGCTCCAAAAGG 59.908 42.308 0.00 0.00 0.00 3.11
69 73 2.760650 GGTATGCCTTTCTTTCTTGGGG 59.239 50.000 0.00 0.00 0.00 4.96
82 86 3.939740 TCTTGGGGGAGAAAGATCATG 57.060 47.619 0.00 0.00 0.00 3.07
87 91 3.787577 TGGGGGAGAAAGATCATGATGAA 59.212 43.478 14.30 0.00 0.00 2.57
116 120 2.388890 CTGGGGCGGCCAGAAGATAG 62.389 65.000 30.95 11.28 37.47 2.08
176 817 2.325484 TGAGAGTGACTTAGGGTGCAA 58.675 47.619 0.00 0.00 0.00 4.08
213 855 1.672737 CGCCTCTTATCGCATATGGCA 60.673 52.381 4.56 0.00 45.17 4.92
239 881 0.179062 AGTCTGCATGGATCTTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
253 895 0.672401 TTCGCCAAGTTAAGAGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
279 922 2.309528 TGCTTCTGTCGACTGTTGTT 57.690 45.000 17.92 0.00 0.00 2.83
295 938 4.459330 TGTTGTTCAGTCCACATCATTCA 58.541 39.130 0.00 0.00 0.00 2.57
297 940 5.535783 TGTTGTTCAGTCCACATCATTCATT 59.464 36.000 0.00 0.00 0.00 2.57
299 942 6.990341 TGTTCAGTCCACATCATTCATTAG 57.010 37.500 0.00 0.00 0.00 1.73
321 965 4.450419 AGAAATGTCTCTTTCGCTCTTGTG 59.550 41.667 0.00 0.00 39.57 3.33
345 992 5.568685 TCTATTCGTTCCAAGTCTCAGAG 57.431 43.478 0.00 0.00 0.00 3.35
402 1049 1.133976 GGATTCCCTGTCCTGGATGTG 60.134 57.143 0.00 0.00 32.85 3.21
422 1069 5.911752 TGTGCAATTTGGTTCAATAGTTGT 58.088 33.333 0.00 0.00 0.00 3.32
457 1104 2.203070 GGCATCTCCAACGCCGAT 60.203 61.111 0.00 0.00 35.79 4.18
480 1127 1.026718 CAAACCTCCCGCATCAGTCC 61.027 60.000 0.00 0.00 0.00 3.85
498 1152 2.204029 GGACACCACCCCCACCTA 60.204 66.667 0.00 0.00 0.00 3.08
499 1153 1.848895 GGACACCACCCCCACCTAA 60.849 63.158 0.00 0.00 0.00 2.69
500 1154 1.377612 GACACCACCCCCACCTAAC 59.622 63.158 0.00 0.00 0.00 2.34
501 1155 2.133359 GACACCACCCCCACCTAACC 62.133 65.000 0.00 0.00 0.00 2.85
502 1156 2.533492 ACCACCCCCACCTAACCC 60.533 66.667 0.00 0.00 0.00 4.11
518 1172 1.536174 CCCAACCCAATGGCTGGTT 60.536 57.895 14.95 2.82 45.08 3.67
524 1178 1.427368 ACCCAATGGCTGGTTGTTCTA 59.573 47.619 0.00 0.00 44.76 2.10
644 1328 1.261619 GTGCTCACCGAGTTTGAACTG 59.738 52.381 0.30 0.00 39.88 3.16
648 1332 3.724374 CTCACCGAGTTTGAACTGGTAA 58.276 45.455 13.74 4.10 39.88 2.85
677 1361 7.814107 TGCAGCTTGTTGGAAGATTATTTTTAG 59.186 33.333 0.00 0.00 0.00 1.85
767 1451 7.606135 TTGGATTCCTTAATTCATGCATCAT 57.394 32.000 0.00 0.00 30.44 2.45
768 1452 7.606135 TGGATTCCTTAATTCATGCATCATT 57.394 32.000 0.00 0.69 0.00 2.57
769 1453 8.709272 TGGATTCCTTAATTCATGCATCATTA 57.291 30.769 0.00 0.00 0.00 1.90
1192 1895 7.222031 GCGTGTGTGATAGAAATTACATGTCTA 59.778 37.037 0.00 0.00 34.49 2.59
1582 2300 3.245264 ACTTGGGCAACTAAATAGGCTGT 60.245 43.478 0.00 0.00 36.22 4.40
2151 3023 6.178324 ACCTTCCTTTATAGGGAACTTTTCG 58.822 40.000 0.00 0.00 42.26 3.46
2188 3060 7.074502 GCTCTTGCTTGGAGATAATAATTTCG 58.925 38.462 5.58 0.00 36.03 3.46
2222 3094 7.631510 TCCCCATGAGTATAGATGAAATTCA 57.368 36.000 0.00 0.00 0.00 2.57
2302 3174 4.960938 TCTTTACAACATGTCAGCACTCT 58.039 39.130 0.00 0.00 0.00 3.24
2440 3312 2.549754 CCCACTTCACTAGCAAACACAG 59.450 50.000 0.00 0.00 0.00 3.66
2618 3490 2.224426 TGGTGAACTTACGCTTGGATGT 60.224 45.455 0.00 0.00 0.00 3.06
2622 3494 5.049267 GGTGAACTTACGCTTGGATGTAAAA 60.049 40.000 0.00 0.00 30.75 1.52
3612 4491 2.756760 GCAGCTCATCCATCCTTTGAAA 59.243 45.455 0.00 0.00 0.00 2.69
3818 4701 0.951040 GTGAGGCCCTGAGAAACACG 60.951 60.000 0.00 0.00 0.00 4.49
3990 4876 7.573968 AGGCCATTGAGTTTATATTCAAGAC 57.426 36.000 5.01 0.00 36.81 3.01
4097 4983 4.096984 CCCAGCAATGTCCTTCTAAATGAC 59.903 45.833 0.00 0.00 0.00 3.06
4166 5055 6.593978 ACGCAATTATTCTTATTCGAGCATC 58.406 36.000 0.00 0.00 0.00 3.91
4235 5130 4.846779 TGCACCAGGTAACAATTTTCTC 57.153 40.909 0.00 0.00 41.41 2.87
4279 5174 5.651530 TCGAGAATAACTTGTAGGCTCTTG 58.348 41.667 0.00 0.00 0.00 3.02
4482 5477 0.179062 AGCGCCCAACTGATGAGATC 60.179 55.000 2.29 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.868253 GGCATACCTTTTGGAGCGT 58.132 52.632 0.00 0.00 44.07 5.07
48 49 2.760650 CCCCAAGAAAGAAAGGCATACC 59.239 50.000 0.00 0.00 0.00 2.73
49 50 2.760650 CCCCCAAGAAAGAAAGGCATAC 59.239 50.000 0.00 0.00 0.00 2.39
69 73 5.236911 GCAGAGTTCATCATGATCTTTCTCC 59.763 44.000 4.86 0.00 0.00 3.71
82 86 1.406614 CCCCAGTCAGCAGAGTTCATC 60.407 57.143 0.00 0.00 0.00 2.92
87 91 3.699894 CGCCCCAGTCAGCAGAGT 61.700 66.667 0.00 0.00 0.00 3.24
116 120 7.094762 ACAGTCAACGAAGATTTTAATTCTCCC 60.095 37.037 0.00 0.00 0.00 4.30
196 838 1.995484 CCGTGCCATATGCGATAAGAG 59.005 52.381 0.00 0.00 45.60 2.85
213 855 2.026822 AGATCCATGCAGACTTTTCCGT 60.027 45.455 0.00 0.00 0.00 4.69
239 881 3.810310 AGATCTCGGGCTCTTAACTTG 57.190 47.619 0.00 0.00 0.00 3.16
253 895 3.178267 CAGTCGACAGAAGCAAGATCTC 58.822 50.000 19.50 0.00 0.00 2.75
279 922 7.830697 ACATTTCTAATGAATGATGTGGACTGA 59.169 33.333 6.42 0.00 34.32 3.41
295 938 6.876257 ACAAGAGCGAAAGAGACATTTCTAAT 59.124 34.615 0.00 0.00 37.10 1.73
297 940 5.635280 CACAAGAGCGAAAGAGACATTTCTA 59.365 40.000 0.00 0.00 37.10 2.10
299 942 4.449068 TCACAAGAGCGAAAGAGACATTTC 59.551 41.667 0.00 0.00 36.11 2.17
321 965 6.137794 TCTGAGACTTGGAACGAATAGATC 57.862 41.667 0.00 0.00 0.00 2.75
402 1049 7.938563 TTGTACAACTATTGAACCAAATTGC 57.061 32.000 3.59 0.00 0.00 3.56
422 1069 0.179067 CCCTAAGGCGCCGATTTGTA 60.179 55.000 23.20 6.80 0.00 2.41
457 1104 1.198094 TGATGCGGGAGGTTTGAGGA 61.198 55.000 0.00 0.00 0.00 3.71
498 1152 4.213630 CAGCCATTGGGTTGGGTT 57.786 55.556 4.22 0.00 44.96 4.11
518 1172 5.152623 AGCTAAACTCTGTGCATAGAACA 57.847 39.130 14.54 0.00 0.00 3.18
524 1178 2.038952 TGTGGAGCTAAACTCTGTGCAT 59.961 45.455 0.00 0.00 45.48 3.96
644 1328 4.640201 TCTTCCAACAAGCTGCATATTACC 59.360 41.667 1.02 0.00 0.00 2.85
648 1332 7.592885 AATAATCTTCCAACAAGCTGCATAT 57.407 32.000 1.02 0.00 0.00 1.78
700 1384 7.038587 TCAGTCACTTAAACTCCCTAAATGCTA 60.039 37.037 0.00 0.00 0.00 3.49
701 1385 5.940470 CAGTCACTTAAACTCCCTAAATGCT 59.060 40.000 0.00 0.00 0.00 3.79
720 1404 7.040478 CCAAATAAGACCATTTCAACTCAGTCA 60.040 37.037 0.00 0.00 0.00 3.41
767 1451 6.183361 TGGAAGTTGGAGTCCAAACTACATAA 60.183 38.462 26.19 5.08 45.91 1.90
768 1452 5.308497 TGGAAGTTGGAGTCCAAACTACATA 59.692 40.000 26.19 7.23 45.91 2.29
769 1453 4.104102 TGGAAGTTGGAGTCCAAACTACAT 59.896 41.667 26.19 7.68 45.91 2.29
1192 1895 2.203907 AGTGCCCAGAGCCTGAGT 60.204 61.111 4.00 0.00 42.71 3.41
1582 2300 2.331166 TGTGCTGAGGTTAAGGTACCA 58.669 47.619 15.94 0.00 40.82 3.25
2151 3023 1.743252 CAAGAGCCAGCGAAGGGAC 60.743 63.158 0.00 0.00 0.00 4.46
2188 3060 3.933861 ACTCATGGGGATGTTACCTTC 57.066 47.619 0.00 0.00 0.00 3.46
2222 3094 7.690256 AGTGATGTCTAGTATTTCCAGGTTTT 58.310 34.615 0.00 0.00 0.00 2.43
2302 3174 1.843206 TGTAGCCATGCCAAGGTATGA 59.157 47.619 17.31 0.00 39.96 2.15
2401 3273 0.544120 GGGATTTGGCCTTGGAACCA 60.544 55.000 3.32 0.00 0.00 3.67
2440 3312 2.019984 GTTGATCACCTGGAGATTGGC 58.980 52.381 8.06 0.00 0.00 4.52
3612 4491 9.672673 ATCAGCATATGTAAACTTCTGTAACTT 57.327 29.630 4.29 0.00 0.00 2.66
3651 4530 6.739112 AGTTGTCTAAAGAGAAACCATTTGC 58.261 36.000 0.00 0.00 31.96 3.68
3818 4701 2.466571 CCGTACAAGATTACGATGACGC 59.533 50.000 4.30 0.00 46.37 5.19
3990 4876 3.993081 GCTATGTCCACTGCTATTGCTAG 59.007 47.826 0.00 0.00 40.48 3.42
4166 5055 2.993899 CACTAAGCTTGTAGAACCACCG 59.006 50.000 9.86 0.00 0.00 4.94
4235 5130 4.853196 CGAAAAATGTACCATGCTCAGTTG 59.147 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.