Multiple sequence alignment - TraesCS4A01G346600

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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 TraesCS4A01G346600 chr4A 100.000 2426 0 0 1 2426 625248115 625250540 0.000000e+00 4481.0
1 TraesCS4A01G346600 chr4A 85.876 1416 159 12 12 1427 625176736 625178110 0.000000e+00 1469.0
2 TraesCS4A01G346600 chr4A 85.337 1439 174 16 3 1430 624982278 624983690 0.000000e+00 1454.0
3 TraesCS4A01G346600 chr5B 96.019 1482 56 2 3 1483 685648712 685650191 0.000000e+00 2407.0
4 TraesCS4A01G346600 chr5B 95.622 1439 62 1 3 1440 685992951 685991513 0.000000e+00 2307.0
5 TraesCS4A01G346600 chr5B 86.310 1439 182 10 1 1430 685951351 685949919 0.000000e+00 1552.0
6 TraesCS4A01G346600 chr5B 82.546 1673 207 38 18 1659 686051002 686049384 0.000000e+00 1393.0
7 TraesCS4A01G346600 chr5B 83.462 1421 190 14 18 1436 686212196 686210819 0.000000e+00 1280.0
8 TraesCS4A01G346600 chr5B 91.979 561 35 5 1510 2061 685650269 685650828 0.000000e+00 778.0
9 TraesCS4A01G346600 chr5B 84.518 633 41 21 1510 2129 685991359 685990771 7.520000e-160 573.0
10 TraesCS4A01G346600 chr5B 95.161 124 6 0 2220 2343 685990535 685990412 1.900000e-46 196.0
11 TraesCS4A01G346600 chr5B 96.154 52 1 1 1435 1485 685991486 685991435 1.550000e-12 84.2
12 TraesCS4A01G346600 chr5D 95.296 1318 59 1 123 1440 543840022 543838708 0.000000e+00 2087.0
13 TraesCS4A01G346600 chr5D 85.444 1429 173 15 11 1430 544286226 544284824 0.000000e+00 1454.0
14 TraesCS4A01G346600 chr5D 84.734 1428 168 15 1 1426 543858650 543857271 0.000000e+00 1384.0
15 TraesCS4A01G346600 chr5D 84.942 518 33 19 1715 2225 543838400 543837921 1.300000e-132 483.0
16 TraesCS4A01G346600 chr5D 93.720 207 13 0 2220 2426 543837887 543837681 6.510000e-81 311.0
17 TraesCS4A01G346600 chr5D 98.462 130 2 0 1 130 543840734 543840605 1.880000e-56 230.0
18 TraesCS4A01G346600 chr5D 93.464 153 8 1 1510 1662 543838554 543838404 2.430000e-55 226.0
19 TraesCS4A01G346600 chr5D 100.000 37 0 0 1443 1479 543838672 543838636 4.330000e-08 69.4


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 TraesCS4A01G346600 chr4A 625248115 625250540 2425 False 4481.000000 4481 100.00000 1 2426 1 chr4A.!!$F3 2425
1 TraesCS4A01G346600 chr4A 625176736 625178110 1374 False 1469.000000 1469 85.87600 12 1427 1 chr4A.!!$F2 1415
2 TraesCS4A01G346600 chr4A 624982278 624983690 1412 False 1454.000000 1454 85.33700 3 1430 1 chr4A.!!$F1 1427
3 TraesCS4A01G346600 chr5B 685648712 685650828 2116 False 1592.500000 2407 93.99900 3 2061 2 chr5B.!!$F1 2058
4 TraesCS4A01G346600 chr5B 685949919 685951351 1432 True 1552.000000 1552 86.31000 1 1430 1 chr5B.!!$R1 1429
5 TraesCS4A01G346600 chr5B 686049384 686051002 1618 True 1393.000000 1393 82.54600 18 1659 1 chr5B.!!$R2 1641
6 TraesCS4A01G346600 chr5B 686210819 686212196 1377 True 1280.000000 1280 83.46200 18 1436 1 chr5B.!!$R3 1418
7 TraesCS4A01G346600 chr5B 685990412 685992951 2539 True 790.050000 2307 92.86375 3 2343 4 chr5B.!!$R4 2340
8 TraesCS4A01G346600 chr5D 544284824 544286226 1402 True 1454.000000 1454 85.44400 11 1430 1 chr5D.!!$R2 1419
9 TraesCS4A01G346600 chr5D 543857271 543858650 1379 True 1384.000000 1384 84.73400 1 1426 1 chr5D.!!$R1 1425
10 TraesCS4A01G346600 chr5D 543837681 543840734 3053 True 567.733333 2087 94.31400 1 2426 6 chr5D.!!$R3 2425

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
719 1326 1.519408 CCCAAACTCCCACGTAACAG 58.481 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 3204 1.208052 TCTTCTGTATGTGCCCTGCTC 59.792 52.381 0.0 0.0 0.0 4.26 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
364 971 7.934855 ATTATTGCTCTGTTTGACTCATTCT 57.065 32.000 0.00 0.00 0.00 2.40
567 1174 6.597280 GTGATCCTAGCAAGAAAAACTCATCT 59.403 38.462 0.00 0.00 0.00 2.90
719 1326 1.519408 CCCAAACTCCCACGTAACAG 58.481 55.000 0.00 0.00 0.00 3.16
764 1371 1.600916 GCATCCTTACGGCCCCATC 60.601 63.158 0.00 0.00 0.00 3.51
865 1472 4.160439 CAGAGCACACCCTTACTCTTGATA 59.840 45.833 0.00 0.00 37.40 2.15
1089 1699 0.249120 TGGGTGGCTCATCTAACACG 59.751 55.000 0.00 0.00 34.78 4.49
1333 1952 2.661566 CCAGACAGTGCAGTTCGCG 61.662 63.158 0.00 0.00 46.97 5.87
1519 2225 7.692460 TGATTAATCTGTATGGGATTGCATC 57.308 36.000 16.24 0.00 35.40 3.91
1536 2242 0.251354 ATCTGTCATCTGGTTGCGCT 59.749 50.000 9.73 0.00 0.00 5.92
1642 2348 5.048991 GGGTACTATTGTGGACAAACTTGTG 60.049 44.000 0.00 0.00 42.43 3.33
1664 2370 5.047235 GTGGTGTATTCAACTGTACCTCTCT 60.047 44.000 0.00 0.00 31.63 3.10
1673 2379 5.987347 TCAACTGTACCTCTCTTAAAAACGG 59.013 40.000 0.00 0.00 0.00 4.44
1691 2397 1.335810 CGGCACCTTGGATCATTCATG 59.664 52.381 0.00 0.00 0.00 3.07
1699 2405 5.107133 CCTTGGATCATTCATGTGCTTTTC 58.893 41.667 0.00 0.00 0.00 2.29
1758 2488 8.267183 ACTGAATGAATGTACTGATTATGGTGA 58.733 33.333 0.00 0.00 0.00 4.02
1779 2509 7.440856 TGGTGATTTTCTTGCCATTTTTAGTTC 59.559 33.333 0.00 0.00 0.00 3.01
1788 2518 8.034215 TCTTGCCATTTTTAGTTCATAATGTGG 58.966 33.333 0.00 0.00 0.00 4.17
1792 2522 7.981225 GCCATTTTTAGTTCATAATGTGGTGAT 59.019 33.333 0.00 0.00 0.00 3.06
1796 2526 8.642935 TTTTAGTTCATAATGTGGTGATGGAA 57.357 30.769 0.00 0.00 0.00 3.53
1851 2581 0.514691 GTCTTGCGCTTTCCTCTGTG 59.485 55.000 9.73 0.00 0.00 3.66
1869 2599 6.072618 CCTCTGTGATCAAATCATAGGAATGC 60.073 42.308 9.45 0.00 45.29 3.56
1890 2625 1.974236 ACTGTCCTCTCCTCCAGTTTG 59.026 52.381 0.00 0.00 34.64 2.93
1898 2633 4.714308 CCTCTCCTCCAGTTTGTTATCTCT 59.286 45.833 0.00 0.00 0.00 3.10
2068 2806 6.989659 GGATGTATAGAATCCAACGGTCTTA 58.010 40.000 8.82 0.00 42.79 2.10
2069 2807 7.091443 GGATGTATAGAATCCAACGGTCTTAG 58.909 42.308 8.82 0.00 42.79 2.18
2071 2809 7.273320 TGTATAGAATCCAACGGTCTTAGAG 57.727 40.000 0.00 0.00 0.00 2.43
2073 2811 7.724506 TGTATAGAATCCAACGGTCTTAGAGAT 59.275 37.037 0.00 0.00 0.00 2.75
2075 2813 4.342665 AGAATCCAACGGTCTTAGAGATCC 59.657 45.833 0.00 0.00 0.00 3.36
2104 2848 6.748333 ACTCATAAACACACATTCAGGATG 57.252 37.500 0.00 0.00 41.71 3.51
2149 2998 9.708092 ACTACTTTTCAGGAACATAAACTCTAC 57.292 33.333 0.00 0.00 0.00 2.59
2155 3004 7.311092 TCAGGAACATAAACTCTACCAGAAA 57.689 36.000 0.00 0.00 0.00 2.52
2168 3017 8.954950 ACTCTACCAGAAATGTTTCTATGATG 57.045 34.615 7.62 0.00 45.23 3.07
2290 3179 8.707938 TCACATCACAGTTTACATCATCTAAG 57.292 34.615 0.00 0.00 0.00 2.18
2315 3204 6.595794 CAAACAAAAAGGCAGAAATATGCTG 58.404 36.000 0.00 2.31 45.75 4.41
2329 3218 0.465097 ATGCTGAGCAGGGCACATAC 60.465 55.000 14.36 0.00 43.65 2.39
2344 3233 4.440802 GGCACATACAGAAGAGTCAGGTAG 60.441 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 971 4.098349 GCCAATGAATGCAAGGAAGTCATA 59.902 41.667 0.00 0.00 0.00 2.15
567 1174 0.391228 TAGGCACTGAACACGCAAGA 59.609 50.000 0.00 0.00 41.52 3.02
719 1326 3.057526 GCCACAAAAGTACCCAAGATCAC 60.058 47.826 0.00 0.00 0.00 3.06
764 1371 0.721718 GCGAGAGTTGGGTGAAATCG 59.278 55.000 0.00 0.00 33.73 3.34
865 1472 5.819379 ACACAATCTGATAGATGCGTTCATT 59.181 36.000 0.00 0.00 34.65 2.57
1089 1699 2.295070 GAGGCGAGAGACCCTAAAGATC 59.705 54.545 0.00 0.00 43.69 2.75
1333 1952 4.565962 CGACATATCATAGAAGAGCATGGC 59.434 45.833 0.00 0.00 0.00 4.40
1495 2159 7.692460 GATGCAATCCCATACAGATTAATCA 57.308 36.000 17.56 0.00 37.38 2.57
1519 2225 1.642037 CCAGCGCAACCAGATGACAG 61.642 60.000 11.47 0.00 0.00 3.51
1536 2242 3.181462 CCATTCTACTGCTGCATCTACCA 60.181 47.826 1.31 0.00 0.00 3.25
1642 2348 5.662674 AGAGAGGTACAGTTGAATACACC 57.337 43.478 0.00 0.00 0.00 4.16
1664 2370 3.223435 TGATCCAAGGTGCCGTTTTTAA 58.777 40.909 0.00 0.00 0.00 1.52
1673 2379 2.480759 GCACATGAATGATCCAAGGTGC 60.481 50.000 0.00 11.75 39.68 5.01
1691 2397 1.526464 CCCGCAAACAATGAAAAGCAC 59.474 47.619 0.00 0.00 0.00 4.40
1699 2405 2.166050 TGATCCAATCCCGCAAACAATG 59.834 45.455 0.00 0.00 0.00 2.82
1779 2509 4.525996 TCCTGTTCCATCACCACATTATG 58.474 43.478 0.00 0.00 0.00 1.90
1788 2518 3.425162 AGGTTTCTCCTGTTCCATCAC 57.575 47.619 0.00 0.00 46.19 3.06
1807 2537 6.138761 GTCATTTGCAGAGTAAACAGACAAG 58.861 40.000 8.81 0.00 31.30 3.16
1851 2581 6.293845 GGACAGTGCATTCCTATGATTTGATC 60.294 42.308 0.00 0.00 33.37 2.92
1869 2599 1.638529 AACTGGAGGAGAGGACAGTG 58.361 55.000 0.00 0.00 42.85 3.66
1890 2625 8.780249 CAAGAGTAGTCTTAGGCTAGAGATAAC 58.220 40.741 12.50 9.60 41.40 1.89
1898 2633 3.954904 CTGCCAAGAGTAGTCTTAGGCTA 59.045 47.826 31.64 23.54 46.51 3.93
2026 2764 3.518992 TCCAGGTTTAAAGTTGAGGGG 57.481 47.619 0.00 0.00 0.00 4.79
2059 2797 1.757699 GGCAGGATCTCTAAGACCGTT 59.242 52.381 0.00 0.00 0.00 4.44
2060 2798 1.342076 TGGCAGGATCTCTAAGACCGT 60.342 52.381 0.00 0.00 0.00 4.83
2061 2799 1.403814 TGGCAGGATCTCTAAGACCG 58.596 55.000 0.00 0.00 0.00 4.79
2062 2800 2.769095 AGTTGGCAGGATCTCTAAGACC 59.231 50.000 0.00 0.00 0.00 3.85
2063 2801 3.449018 TGAGTTGGCAGGATCTCTAAGAC 59.551 47.826 0.00 0.00 0.00 3.01
2064 2802 3.713003 TGAGTTGGCAGGATCTCTAAGA 58.287 45.455 0.00 0.00 0.00 2.10
2065 2803 4.686191 ATGAGTTGGCAGGATCTCTAAG 57.314 45.455 0.00 0.00 0.00 2.18
2068 2806 4.225942 TGTTTATGAGTTGGCAGGATCTCT 59.774 41.667 0.00 0.00 0.00 3.10
2069 2807 4.333926 GTGTTTATGAGTTGGCAGGATCTC 59.666 45.833 0.00 0.00 0.00 2.75
2071 2809 4.009675 TGTGTTTATGAGTTGGCAGGATC 58.990 43.478 0.00 0.00 0.00 3.36
2073 2811 3.146066 GTGTGTTTATGAGTTGGCAGGA 58.854 45.455 0.00 0.00 0.00 3.86
2075 2813 4.771590 ATGTGTGTTTATGAGTTGGCAG 57.228 40.909 0.00 0.00 0.00 4.85
2104 2848 1.541588 GTTGGTCAGTTCTCCAATGGC 59.458 52.381 0.00 0.00 44.03 4.40
2149 2998 7.337689 TGTTCTCCATCATAGAAACATTTCTGG 59.662 37.037 15.62 9.46 46.34 3.86
2155 3004 6.942005 TGTGTTGTTCTCCATCATAGAAACAT 59.058 34.615 0.00 0.00 34.86 2.71
2290 3179 5.179929 AGCATATTTCTGCCTTTTTGTTTGC 59.820 36.000 0.00 0.00 43.33 3.68
2315 3204 1.208052 TCTTCTGTATGTGCCCTGCTC 59.792 52.381 0.00 0.00 0.00 4.26
2329 3218 5.606348 AATAAGCCTACCTGACTCTTCTG 57.394 43.478 0.00 0.00 0.00 3.02
2344 3233 8.931385 TTTCTATTGAGAATTGCAAATAAGCC 57.069 30.769 1.71 0.00 41.40 4.35
2383 3272 6.263168 GGAGCTGTTATGTACCAGCAAATAAT 59.737 38.462 19.68 2.70 42.60 1.28


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

AutoCloner maintained by Alex Coulton.