Multiple sequence alignment - TraesCS4D01G049100

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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 TraesCS4D01G049100 chr4D 100.000 3017 0 0 1 3017 25364995 25361979 0.000000e+00 5572
1 TraesCS4D01G049100 chr4D 90.402 1344 111 8 921 2262 25321329 25320002 0.000000e+00 1751
2 TraesCS4D01G049100 chr4D 89.372 1035 100 8 983 2016 25194510 25193485 0.000000e+00 1293
3 TraesCS4D01G049100 chr4D 85.828 628 81 6 2395 3016 504188739 504188114 0.000000e+00 660
4 TraesCS4D01G049100 chr4D 77.879 877 153 29 1134 2000 25159691 25160536 9.650000e-140 507
5 TraesCS4D01G049100 chr4D 88.474 321 30 5 605 922 25338833 25338517 6.100000e-102 381
6 TraesCS4D01G049100 chr4B 92.643 2297 124 16 1 2262 37298444 37296158 0.000000e+00 3264
7 TraesCS4D01G049100 chr4B 89.372 1035 100 6 983 2016 37174481 37173456 0.000000e+00 1293
8 TraesCS4D01G049100 chr4B 77.892 873 154 24 1137 2000 36013811 36012969 9.650000e-140 507
9 TraesCS4D01G049100 chr4B 90.506 158 13 2 2103 2259 37267799 37267643 1.100000e-49 207
10 TraesCS4D01G049100 chr4A 92.290 2179 110 21 4 2150 578177191 578175039 0.000000e+00 3040
11 TraesCS4D01G049100 chr4A 90.712 2164 135 19 1 2134 578006023 578008150 0.000000e+00 2822
12 TraesCS4D01G049100 chr4A 89.952 1035 94 7 983 2016 578233566 578234591 0.000000e+00 1327
13 TraesCS4D01G049100 chr4A 85.327 627 83 7 2396 3017 1874235 1874857 9.120000e-180 640
14 TraesCS4D01G049100 chr4A 81.924 343 41 17 126 453 578104756 578104420 1.380000e-68 270
15 TraesCS4D01G049100 chr4A 85.950 121 16 1 2 121 578104934 578104814 8.780000e-26 128
16 TraesCS4D01G049100 chr3B 90.119 1680 123 18 555 2205 39544727 39546392 0.000000e+00 2143
17 TraesCS4D01G049100 chr7D 93.861 619 38 0 2399 3017 634587164 634586546 0.000000e+00 933
18 TraesCS4D01G049100 chr7D 91.304 138 11 1 2266 2403 634587341 634587205 1.430000e-43 187
19 TraesCS4D01G049100 chr7B 88.746 622 69 1 2396 3017 105939838 105940458 0.000000e+00 760
20 TraesCS4D01G049100 chr7B 91.111 135 11 1 2267 2401 716367407 716367274 6.640000e-42 182
21 TraesCS4D01G049100 chr7B 88.372 129 13 2 2273 2400 12780748 12780621 1.450000e-33 154
22 TraesCS4D01G049100 chr1D 87.923 621 71 2 2399 3017 6806800 6807418 0.000000e+00 728
23 TraesCS4D01G049100 chr6D 87.702 618 71 4 2403 3017 369666015 369665400 0.000000e+00 715
24 TraesCS4D01G049100 chr3A 88.112 572 66 1 2448 3017 741875481 741874910 0.000000e+00 678
25 TraesCS4D01G049100 chr5A 86.102 626 78 6 2399 3017 110110322 110110945 0.000000e+00 665
26 TraesCS4D01G049100 chr2D 85.256 624 89 2 2396 3017 161988294 161988916 9.120000e-180 640


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 TraesCS4D01G049100 chr4D 25361979 25364995 3016 True 5572 5572 100.0000 1 3017 1 chr4D.!!$R4 3016
1 TraesCS4D01G049100 chr4D 25320002 25321329 1327 True 1751 1751 90.4020 921 2262 1 chr4D.!!$R2 1341
2 TraesCS4D01G049100 chr4D 25193485 25194510 1025 True 1293 1293 89.3720 983 2016 1 chr4D.!!$R1 1033
3 TraesCS4D01G049100 chr4D 504188114 504188739 625 True 660 660 85.8280 2395 3016 1 chr4D.!!$R5 621
4 TraesCS4D01G049100 chr4D 25159691 25160536 845 False 507 507 77.8790 1134 2000 1 chr4D.!!$F1 866
5 TraesCS4D01G049100 chr4B 37296158 37298444 2286 True 3264 3264 92.6430 1 2262 1 chr4B.!!$R4 2261
6 TraesCS4D01G049100 chr4B 37173456 37174481 1025 True 1293 1293 89.3720 983 2016 1 chr4B.!!$R2 1033
7 TraesCS4D01G049100 chr4B 36012969 36013811 842 True 507 507 77.8920 1137 2000 1 chr4B.!!$R1 863
8 TraesCS4D01G049100 chr4A 578175039 578177191 2152 True 3040 3040 92.2900 4 2150 1 chr4A.!!$R1 2146
9 TraesCS4D01G049100 chr4A 578006023 578008150 2127 False 2822 2822 90.7120 1 2134 1 chr4A.!!$F2 2133
10 TraesCS4D01G049100 chr4A 578233566 578234591 1025 False 1327 1327 89.9520 983 2016 1 chr4A.!!$F3 1033
11 TraesCS4D01G049100 chr4A 1874235 1874857 622 False 640 640 85.3270 2396 3017 1 chr4A.!!$F1 621
12 TraesCS4D01G049100 chr3B 39544727 39546392 1665 False 2143 2143 90.1190 555 2205 1 chr3B.!!$F1 1650
13 TraesCS4D01G049100 chr7D 634586546 634587341 795 True 560 933 92.5825 2266 3017 2 chr7D.!!$R1 751
14 TraesCS4D01G049100 chr7B 105939838 105940458 620 False 760 760 88.7460 2396 3017 1 chr7B.!!$F1 621
15 TraesCS4D01G049100 chr1D 6806800 6807418 618 False 728 728 87.9230 2399 3017 1 chr1D.!!$F1 618
16 TraesCS4D01G049100 chr6D 369665400 369666015 615 True 715 715 87.7020 2403 3017 1 chr6D.!!$R1 614
17 TraesCS4D01G049100 chr3A 741874910 741875481 571 True 678 678 88.1120 2448 3017 1 chr3A.!!$R1 569
18 TraesCS4D01G049100 chr5A 110110322 110110945 623 False 665 665 86.1020 2399 3017 1 chr5A.!!$F1 618
19 TraesCS4D01G049100 chr2D 161988294 161988916 622 False 640 640 85.2560 2396 3017 1 chr2D.!!$F1 621

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
874 949 0.249699 CCGCCACATCGCCAGTATAA 60.25 55.0 0.0 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 2419 0.605589 GGAAGGAAGAACACCACCCG 60.606 60.0 0.0 0.0 0.0 5.28 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
363 396 3.559069 TGCAGTTAGGGTATAGCGTAGT 58.441 45.455 4.70 0.00 0.00 2.73
411 444 2.034685 TGAATGGAGATCTAACGGCTCG 59.965 50.000 0.00 0.00 0.00 5.03
456 489 3.815401 CTGCCTAGGCCAAATACATACAC 59.185 47.826 30.81 0.00 41.09 2.90
464 497 4.142249 GGCCAAATACATACACCAAACTCC 60.142 45.833 0.00 0.00 0.00 3.85
468 501 7.627726 GCCAAATACATACACCAAACTCCTAAC 60.628 40.741 0.00 0.00 0.00 2.34
535 570 2.910319 AGTGTATCTTACCAGCCACCAA 59.090 45.455 0.00 0.00 0.00 3.67
739 813 6.381481 TCATGAATATCCATTCTTGCACAC 57.619 37.500 0.00 0.00 42.16 3.82
740 814 5.887035 TCATGAATATCCATTCTTGCACACA 59.113 36.000 0.00 0.00 42.16 3.72
741 815 6.377712 TCATGAATATCCATTCTTGCACACAA 59.622 34.615 0.00 0.00 42.16 3.33
748 822 6.839124 TCCATTCTTGCACACAAAGATAAT 57.161 33.333 0.00 0.00 34.74 1.28
755 829 7.829725 TCTTGCACACAAAGATAATTAAGCAT 58.170 30.769 0.00 0.00 34.74 3.79
871 946 4.830765 GCCGCCACATCGCCAGTA 62.831 66.667 0.00 0.00 0.00 2.74
872 947 2.108976 CCGCCACATCGCCAGTAT 59.891 61.111 0.00 0.00 0.00 2.12
873 948 1.365999 CCGCCACATCGCCAGTATA 59.634 57.895 0.00 0.00 0.00 1.47
874 949 0.249699 CCGCCACATCGCCAGTATAA 60.250 55.000 0.00 0.00 0.00 0.98
875 950 1.577468 CGCCACATCGCCAGTATAAA 58.423 50.000 0.00 0.00 0.00 1.40
876 951 1.526887 CGCCACATCGCCAGTATAAAG 59.473 52.381 0.00 0.00 0.00 1.85
877 952 1.264288 GCCACATCGCCAGTATAAAGC 59.736 52.381 0.00 0.00 0.00 3.51
979 1064 2.860194 GCAAAACACACACACACACACA 60.860 45.455 0.00 0.00 0.00 3.72
1320 1405 4.407694 TCGCCGCACATCGTTCGA 62.408 61.111 0.00 0.00 38.34 3.71
1381 1469 0.033601 ACTCCTCGAGCTGATGGACT 60.034 55.000 6.99 0.00 32.04 3.85
1383 1471 0.323816 TCCTCGAGCTGATGGACTGT 60.324 55.000 6.99 0.00 0.00 3.55
1402 1490 2.047443 GGTTCCCTCGACTCGCTCT 61.047 63.158 0.00 0.00 0.00 4.09
2011 2100 2.125952 TGATCGAGCAGCGGTGTG 60.126 61.111 17.07 6.88 41.33 3.82
2039 2146 1.195900 ACGCGCGTGTAAATGTTGAAT 59.804 42.857 37.37 3.85 0.00 2.57
2125 2235 1.434188 TGAGCTTGGAAGGGTCTCAA 58.566 50.000 0.00 0.00 31.62 3.02
2205 2316 7.780008 AAGAAAAATCCTTAAACCGGTTTTG 57.220 32.000 35.69 26.36 34.23 2.44
2238 2349 1.220206 CAGCAGCGGAACAGATCCT 59.780 57.895 0.00 0.00 46.98 3.24
2274 2385 3.605749 AACAGATCCCGTGGTGGCG 62.606 63.158 0.00 0.00 35.87 5.69
2298 2409 2.353610 GGGTTCGACTTCGGGCCTA 61.354 63.158 0.84 0.00 40.29 3.93
2330 2441 0.605589 GTGGTGTTCTTCCTTCCCCG 60.606 60.000 0.00 0.00 0.00 5.73
2397 2553 1.985614 CAGCTCTGGATGGTGTGGA 59.014 57.895 0.00 0.00 0.00 4.02
2506 2663 4.459089 GGACGGAGGTGCAGCTCC 62.459 72.222 42.26 42.26 34.18 4.70
2556 2713 1.520192 ACTGCAACACGGTGACAGA 59.480 52.632 25.56 6.19 36.16 3.41
2685 2846 3.048475 CTGCTGACGCTGCTGCTT 61.048 61.111 14.03 3.84 36.97 3.91
2839 3001 4.514585 GGTGGTGGGTGTGTGGCA 62.515 66.667 0.00 0.00 0.00 4.92
2945 3111 3.016971 CCCCACCCATGCCTCTCA 61.017 66.667 0.00 0.00 0.00 3.27
2995 3161 2.810887 GCAGCAGCGTCGTCATCA 60.811 61.111 0.00 0.00 0.00 3.07
2996 3162 3.075998 CAGCAGCGTCGTCATCAC 58.924 61.111 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 9.956720 CACCATCATAAGTATCTCAAAATTTCC 57.043 33.333 0.00 0.00 0.00 3.13
247 256 9.284968 ACATTGTTAGACTAGCAAAGTGTTATT 57.715 29.630 16.09 0.00 39.07 1.40
305 337 1.110442 CTCGTCATTCTCCAGCTCCT 58.890 55.000 0.00 0.00 0.00 3.69
363 396 6.762333 TGTCTTGAGATCAATCTTCACTTCA 58.238 36.000 0.00 0.00 37.25 3.02
416 449 2.726241 GCAGCGGAACTTGATTTGTTTC 59.274 45.455 0.00 0.00 0.00 2.78
456 489 4.906618 TGCTTTAGGAGTTAGGAGTTTGG 58.093 43.478 0.00 0.00 0.00 3.28
464 497 7.865706 AATACACCAATGCTTTAGGAGTTAG 57.134 36.000 7.49 0.00 0.00 2.34
495 530 4.868734 ACACTTGTAAGCTTAATACCGCTC 59.131 41.667 7.99 0.00 34.96 5.03
497 532 6.700520 AGATACACTTGTAAGCTTAATACCGC 59.299 38.462 7.99 0.00 33.76 5.68
545 580 1.559368 TCCTCCATTACGTTTCCGGA 58.441 50.000 0.00 0.00 38.78 5.14
644 682 5.591067 CGAAATACCCCCTAAAACATTGCTA 59.409 40.000 0.00 0.00 0.00 3.49
748 822 9.684448 TTGAAAACGATGTGAAAATATGCTTAA 57.316 25.926 0.00 0.00 0.00 1.85
847 922 3.737172 GATGTGGCGGCGCAAGTT 61.737 61.111 34.36 13.42 41.68 2.66
867 942 5.294552 GGTGAGGTTAGCTTGCTTTATACTG 59.705 44.000 0.00 0.00 0.00 2.74
868 943 5.189934 AGGTGAGGTTAGCTTGCTTTATACT 59.810 40.000 0.00 0.00 0.00 2.12
869 944 5.429130 AGGTGAGGTTAGCTTGCTTTATAC 58.571 41.667 0.00 0.00 0.00 1.47
870 945 5.396436 GGAGGTGAGGTTAGCTTGCTTTATA 60.396 44.000 0.00 0.00 0.00 0.98
871 946 4.518249 GAGGTGAGGTTAGCTTGCTTTAT 58.482 43.478 0.00 0.00 0.00 1.40
872 947 3.307480 GGAGGTGAGGTTAGCTTGCTTTA 60.307 47.826 0.00 0.00 0.00 1.85
873 948 2.553247 GGAGGTGAGGTTAGCTTGCTTT 60.553 50.000 0.00 0.00 0.00 3.51
874 949 1.003696 GGAGGTGAGGTTAGCTTGCTT 59.996 52.381 0.00 0.00 0.00 3.91
875 950 0.615850 GGAGGTGAGGTTAGCTTGCT 59.384 55.000 0.00 0.00 0.00 3.91
876 951 0.324943 TGGAGGTGAGGTTAGCTTGC 59.675 55.000 0.00 0.00 0.00 4.01
877 952 1.347707 TGTGGAGGTGAGGTTAGCTTG 59.652 52.381 0.00 0.00 0.00 4.01
979 1064 2.100749 TGATCTTGATCGCCGTGTGTAT 59.899 45.455 6.19 0.00 0.00 2.29
1268 1353 2.082231 CAACTTCTACCTCCTCGTCGA 58.918 52.381 0.00 0.00 0.00 4.20
1320 1405 4.035843 GGGAGGACCGAGTGACAT 57.964 61.111 0.00 0.00 36.97 3.06
1623 1711 4.530857 GGGCTCATGTACGCGGCT 62.531 66.667 12.47 0.00 0.00 5.52
1872 1961 2.322081 GCAAGCGGCCACGAAACTA 61.322 57.895 2.24 0.00 44.60 2.24
1895 1984 2.747686 GCTTCCGGTGGTCCTTCA 59.252 61.111 0.00 0.00 0.00 3.02
2039 2146 2.410785 ACGATTCGAGAACGTGACAA 57.589 45.000 13.95 0.00 38.79 3.18
2125 2235 4.996793 TGGCTAGAGATGCTCTTAGAGAT 58.003 43.478 14.14 3.79 41.50 2.75
2199 2310 1.798087 CGGATGGTACCGCAAAACC 59.202 57.895 7.57 3.41 46.20 3.27
2274 2385 2.033194 CGAAGTCGAACCCCAAGCC 61.033 63.158 0.00 0.00 43.02 4.35
2277 2388 2.745037 CCCGAAGTCGAACCCCAA 59.255 61.111 1.43 0.00 43.02 4.12
2282 2393 1.515736 CGTAGGCCCGAAGTCGAAC 60.516 63.158 0.00 0.00 43.02 3.95
2308 2419 0.605589 GGAAGGAAGAACACCACCCG 60.606 60.000 0.00 0.00 0.00 5.28
2318 2429 3.755628 CGCGACGGGGAAGGAAGA 61.756 66.667 0.00 0.00 0.00 2.87
2374 2485 4.478371 CCATCCAGAGCTGCGCCA 62.478 66.667 4.18 0.00 0.00 5.69
2470 2627 2.202987 CTGGAGCCATCGCAGGTC 60.203 66.667 0.00 0.00 37.52 3.85
2731 2892 2.512515 GCCGTCTCACCATGGAGC 60.513 66.667 21.47 5.46 34.84 4.70
2945 3111 2.226315 GGGTTTCCCCCGGTACACT 61.226 63.158 0.00 0.00 45.80 3.55
2995 3161 1.004918 CTTCAGGAAGGAACGCGGT 60.005 57.895 12.47 1.91 34.87 5.68
2996 3162 3.876300 CTTCAGGAAGGAACGCGG 58.124 61.111 12.47 0.00 34.87 6.46


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

AutoCloner maintained by Alex Coulton.