Multiple sequence alignment - TraesCS3D01G429100

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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 TraesCS3D01G429100 chr3D 100.000 2776 0 0 1 2776 543768146 543765371 0.000000e+00 5127.0
1 TraesCS3D01G429100 chr3B 95.113 1412 42 12 1 1398 719422897 719421499 0.000000e+00 2200.0
2 TraesCS3D01G429100 chr3B 89.943 1233 47 18 1588 2774 719420709 719419508 0.000000e+00 1519.0
3 TraesCS3D01G429100 chr3B 95.833 168 7 0 1388 1555 719420881 719420714 3.520000e-69 272.0
4 TraesCS3D01G429100 chr4D 91.335 1131 54 15 1503 2618 426852949 426854050 0.000000e+00 1506.0
5 TraesCS3D01G429100 chr4D 92.109 773 44 14 636 1398 426851606 426852371 0.000000e+00 1074.0
6 TraesCS3D01G429100 chr3A 95.904 708 19 7 676 1380 680732395 680731695 0.000000e+00 1138.0
7 TraesCS3D01G429100 chr3A 94.637 634 22 3 1 623 680733025 680732393 0.000000e+00 972.0
8 TraesCS3D01G429100 chr3A 92.101 633 26 6 1973 2604 680728560 680727951 0.000000e+00 870.0
9 TraesCS3D01G429100 chr3A 93.701 381 18 2 1566 1944 680728937 680728561 1.440000e-157 566.0
10 TraesCS3D01G429100 chr3A 93.333 120 4 2 2658 2774 680727432 680727314 1.020000e-39 174.0
11 TraesCS3D01G429100 chr3A 96.190 105 2 2 1383 1486 680731208 680731105 1.320000e-38 171.0
12 TraesCS3D01G429100 chr3A 94.545 110 5 1 1476 1585 680729057 680728949 4.750000e-38 169.0
13 TraesCS3D01G429100 chr3A 94.521 73 2 2 636 707 680732411 680732482 8.130000e-21 111.0
14 TraesCS3D01G429100 chr3A 95.745 47 1 1 2615 2660 680727498 680727452 1.070000e-09 75.0
15 TraesCS3D01G429100 chr4A 91.677 793 43 11 1383 2159 38695119 38694334 0.000000e+00 1077.0
16 TraesCS3D01G429100 chr4A 93.202 559 23 9 848 1398 38696121 38695570 0.000000e+00 808.0
17 TraesCS3D01G429100 chr4A 90.419 334 12 6 2299 2621 38694337 38694013 3.310000e-114 422.0
18 TraesCS3D01G429100 chr4A 91.919 297 17 4 1 293 154317935 154317642 2.570000e-110 409.0
19 TraesCS3D01G429100 chr4B 91.332 773 45 19 636 1398 522522399 522523159 0.000000e+00 1037.0
20 TraesCS3D01G429100 chr4B 90.256 585 44 9 1850 2431 522532916 522533490 0.000000e+00 752.0
21 TraesCS3D01G429100 chr4B 92.744 317 20 2 1500 1816 522532604 522532917 3.260000e-124 455.0
22 TraesCS3D01G429100 chr4B 95.735 211 7 2 2420 2628 522533595 522533805 3.420000e-89 339.0
23 TraesCS3D01G429100 chr4B 88.070 285 30 2 197 481 474384383 474384103 4.430000e-88 335.0
24 TraesCS3D01G429100 chr4B 79.646 113 17 4 2665 2774 522533878 522533987 2.960000e-10 76.8
25 TraesCS3D01G429100 chr2D 94.533 439 17 6 1 435 31398074 31398509 0.000000e+00 671.0
26 TraesCS3D01G429100 chr2D 94.050 437 20 5 3 435 74518594 74518160 0.000000e+00 658.0
27 TraesCS3D01G429100 chr2D 92.711 439 25 4 1 435 9184810 9184375 6.530000e-176 627.0
28 TraesCS3D01G429100 chr6D 90.726 248 18 4 1 244 319288975 319289221 2.670000e-85 326.0
29 TraesCS3D01G429100 chr6A 89.960 249 18 4 1 244 457094198 457094444 5.770000e-82 315.0
30 TraesCS3D01G429100 chr2B 83.650 263 22 12 1 244 197992831 197992571 7.730000e-56 228.0


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 TraesCS3D01G429100 chr3D 543765371 543768146 2775 True 5127.000000 5127 100.000000 1 2776 1 chr3D.!!$R1 2775
1 TraesCS3D01G429100 chr3B 719419508 719422897 3389 True 1330.333333 2200 93.629667 1 2774 3 chr3B.!!$R1 2773
2 TraesCS3D01G429100 chr4D 426851606 426854050 2444 False 1290.000000 1506 91.722000 636 2618 2 chr4D.!!$F1 1982
3 TraesCS3D01G429100 chr3A 680727314 680733025 5711 True 516.875000 1138 94.519500 1 2774 8 chr3A.!!$R1 2773
4 TraesCS3D01G429100 chr4A 38694013 38696121 2108 True 769.000000 1077 91.766000 848 2621 3 chr4A.!!$R2 1773
5 TraesCS3D01G429100 chr4B 522522399 522523159 760 False 1037.000000 1037 91.332000 636 1398 1 chr4B.!!$F1 762
6 TraesCS3D01G429100 chr4B 522532604 522533987 1383 False 405.700000 752 89.595250 1500 2774 4 chr4B.!!$F2 1274

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
101 102 2.472029 AGGTCCCTGGATGACAGTAAG 58.528 52.381 0.0 0.0 46.06 2.34 F
212 217 2.951229 ACGGTTGGTTCCTTCTTCAT 57.049 45.000 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1382 1.612676 AATTCAGAACAGCAGCAGCA 58.387 45.0 3.17 0.0 45.49 4.41 R
2195 5016 0.040425 CCAGGTTTTCCAAAGCGACG 60.040 55.0 0.00 0.0 43.73 5.12 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
41 42 8.450578 TGAACAATGTTCAGTTTTATCTGTCT 57.549 30.769 23.28 0.00 36.85 3.41
101 102 2.472029 AGGTCCCTGGATGACAGTAAG 58.528 52.381 0.00 0.00 46.06 2.34
192 193 2.967887 GCCCCTTTGCTTCAATGGATAT 59.032 45.455 11.60 0.00 39.91 1.63
193 194 4.151883 GCCCCTTTGCTTCAATGGATATA 58.848 43.478 11.60 0.00 39.91 0.86
194 195 4.021981 GCCCCTTTGCTTCAATGGATATAC 60.022 45.833 11.60 0.00 39.91 1.47
195 196 4.216257 CCCCTTTGCTTCAATGGATATACG 59.784 45.833 11.60 0.00 39.91 3.06
212 217 2.951229 ACGGTTGGTTCCTTCTTCAT 57.049 45.000 0.00 0.00 0.00 2.57
250 255 3.454082 TCCCCATCCATAAATTTGCAACC 59.546 43.478 0.00 0.00 0.00 3.77
367 372 7.087007 TCTAGAGCAATTAAGCATATCAGTCG 58.913 38.462 0.00 0.00 36.85 4.18
583 596 6.910290 ACCCAATTAGTTAGACTAACCCCATA 59.090 38.462 19.55 5.11 42.78 2.74
823 844 3.095912 TCTCGTCTATTTCTGGACCCA 57.904 47.619 0.00 0.00 29.47 4.51
922 946 4.668138 TTGCAGGGAGGGTATAAAGTTT 57.332 40.909 0.00 0.00 0.00 2.66
1350 1382 6.682861 GCTTCTTCCAAAGGTACATTGTTGTT 60.683 38.462 0.00 0.00 34.98 2.83
1351 1383 6.142818 TCTTCCAAAGGTACATTGTTGTTG 57.857 37.500 0.00 0.00 34.98 3.33
1352 1384 4.314740 TCCAAAGGTACATTGTTGTTGC 57.685 40.909 0.00 0.00 34.98 4.17
1563 4337 5.562298 AAAGCCTACTTTCTCCACTTACA 57.438 39.130 0.00 0.00 42.59 2.41
1600 4405 8.537728 TCATGAACTTAGGCCATAAATGAAAT 57.462 30.769 5.01 0.00 0.00 2.17
1606 4411 7.716612 ACTTAGGCCATAAATGAAATGCTTAC 58.283 34.615 5.01 0.00 0.00 2.34
1851 4656 3.728845 TGAATAGCAACCGATCTTAGGC 58.271 45.455 0.00 0.00 0.00 3.93
1906 4716 3.667497 TGTCTCAGTTCCAGCAGTTAG 57.333 47.619 0.00 0.00 0.00 2.34
1907 4717 2.965831 TGTCTCAGTTCCAGCAGTTAGT 59.034 45.455 0.00 0.00 0.00 2.24
1909 4719 4.587262 TGTCTCAGTTCCAGCAGTTAGTTA 59.413 41.667 0.00 0.00 0.00 2.24
1932 4742 5.838529 AGTTTCCCTGTAATTTTCCAAACG 58.161 37.500 0.00 0.00 0.00 3.60
1979 4789 6.095377 GCTATTGTTCTGTGAGGAATTTTGG 58.905 40.000 0.00 0.00 0.00 3.28
2127 4947 5.992217 CAGCTGACTAGTCTGTTTTACCTTT 59.008 40.000 25.19 3.94 0.00 3.11
2195 5016 3.059800 GTCGTGCTACTTGTTTGTTCCTC 60.060 47.826 0.00 0.00 0.00 3.71
2283 5104 4.794762 CAGTGGACGCAATATGAAATGTTG 59.205 41.667 0.00 0.00 46.68 3.33
2354 5177 2.026879 GGAGCAGGCGAGACGATC 59.973 66.667 0.00 0.00 0.00 3.69
2355 5178 2.775856 GGAGCAGGCGAGACGATCA 61.776 63.158 0.00 0.00 0.00 2.92
2356 5179 1.587613 GAGCAGGCGAGACGATCAC 60.588 63.158 0.00 0.00 0.00 3.06
2357 5180 2.951745 GCAGGCGAGACGATCACG 60.952 66.667 0.00 0.00 45.75 4.35
2358 5181 2.791927 CAGGCGAGACGATCACGA 59.208 61.111 8.46 0.00 42.66 4.35
2359 5182 1.356979 CAGGCGAGACGATCACGAT 59.643 57.895 8.46 0.00 42.66 3.73
2388 5211 1.443194 CTGCATTGCAACGCTGGAC 60.443 57.895 19.28 0.00 38.41 4.02
2503 5442 6.513806 TGCATGTTAGCATTATGACAAAGT 57.486 33.333 0.00 0.00 40.11 2.66
2538 5477 6.419710 GCACATGTGTTATCGTAGCTACAATA 59.580 38.462 26.01 12.42 0.00 1.90
2540 5479 8.978539 CACATGTGTTATCGTAGCTACAATAAT 58.021 33.333 23.21 12.57 0.00 1.28
2660 6068 1.214062 GCTCAGACGGTCAGACCTG 59.786 63.158 17.95 13.07 35.66 4.00
2722 6137 5.412526 TGTTATTCCGGCGAATTATGTTC 57.587 39.130 9.30 0.00 39.49 3.18
2741 6156 4.162320 TGTTCATAGGTGAGAAGATGACCC 59.838 45.833 0.00 0.00 35.39 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 3.742983 GGACCTTGCTTCTAGTCCG 57.257 57.895 0.00 0.00 39.47 4.79
192 193 4.360951 AATGAAGAAGGAACCAACCGTA 57.639 40.909 0.00 0.00 34.73 4.02
193 194 2.951229 ATGAAGAAGGAACCAACCGT 57.049 45.000 0.00 0.00 34.73 4.83
194 195 4.438744 GCATAATGAAGAAGGAACCAACCG 60.439 45.833 0.00 0.00 34.73 4.44
195 196 4.706962 AGCATAATGAAGAAGGAACCAACC 59.293 41.667 0.00 0.00 0.00 3.77
250 255 3.928992 AGTGTACAATGAGTTCTGCATCG 59.071 43.478 0.00 0.00 0.00 3.84
367 372 3.412386 AGTAACCTCAGTGACAAATGGC 58.588 45.455 0.00 0.00 28.30 4.40
583 596 4.090090 AGGTATGCTGTAGTGACTGTCTT 58.910 43.478 9.51 0.24 0.00 3.01
745 762 5.583495 ACGATACTTGAGTCTCATGCTTAC 58.417 41.667 14.12 4.85 0.00 2.34
790 807 8.800332 AGAAATAGACGAGAACCAGTACTAAAA 58.200 33.333 0.00 0.00 0.00 1.52
823 844 7.731235 ACATACTGTAAATTTACCAAAAGGGGT 59.269 33.333 22.47 11.33 45.10 4.95
922 946 3.435026 CCACCCCTCTTGACAGAAGAAAA 60.435 47.826 0.00 0.00 0.00 2.29
1268 1300 6.623767 GCATGATTGTTTCCTCTTCAACCTAC 60.624 42.308 0.00 0.00 0.00 3.18
1350 1382 1.612676 AATTCAGAACAGCAGCAGCA 58.387 45.000 3.17 0.00 45.49 4.41
1351 1383 2.325761 CAAATTCAGAACAGCAGCAGC 58.674 47.619 0.00 0.00 42.56 5.25
1352 1384 2.555325 TCCAAATTCAGAACAGCAGCAG 59.445 45.455 0.00 0.00 0.00 4.24
1600 4405 7.224297 AGACAGAAAAATGGACTAAGTAAGCA 58.776 34.615 0.00 0.00 0.00 3.91
1606 4411 6.655003 TGCCTAAGACAGAAAAATGGACTAAG 59.345 38.462 0.00 0.00 0.00 2.18
1727 4532 1.836166 CTTGATTCCCCTGCTCTCTCA 59.164 52.381 0.00 0.00 0.00 3.27
1765 4570 4.334481 CACGGTTAACATTCTATGGTTCCC 59.666 45.833 8.10 0.00 33.60 3.97
1906 4716 7.380333 CGTTTGGAAAATTACAGGGAAACTAAC 59.620 37.037 0.00 0.00 0.00 2.34
1907 4717 7.427214 CGTTTGGAAAATTACAGGGAAACTAA 58.573 34.615 0.00 0.00 0.00 2.24
1909 4719 5.221362 CCGTTTGGAAAATTACAGGGAAACT 60.221 40.000 0.00 0.00 37.49 2.66
1932 4742 4.441079 CCAGATTCAAGATTCCATTGTGCC 60.441 45.833 0.00 0.00 0.00 5.01
1979 4789 1.970640 ACAAGGCTTTGAAACCCATCC 59.029 47.619 16.36 0.00 37.73 3.51
2140 4961 9.297586 CCAATCTCAAAACACAAGATTATCATG 57.702 33.333 0.00 0.00 37.59 3.07
2145 4966 8.141268 GGAAACCAATCTCAAAACACAAGATTA 58.859 33.333 0.00 0.00 37.59 1.75
2195 5016 0.040425 CCAGGTTTTCCAAAGCGACG 60.040 55.000 0.00 0.00 43.73 5.12
2238 5059 7.872993 CACTGTCCAAGAATCTACTAACTTCAA 59.127 37.037 0.00 0.00 0.00 2.69
2283 5104 8.814235 CAATGATGAAAATTATCTTGCCTGTTC 58.186 33.333 0.00 0.00 0.00 3.18
2354 5177 4.560136 ATGCAGAGTAGTCAGTATCGTG 57.440 45.455 0.00 0.00 0.00 4.35
2355 5178 4.734989 GCAATGCAGAGTAGTCAGTATCGT 60.735 45.833 0.00 0.00 0.00 3.73
2356 5179 3.733224 GCAATGCAGAGTAGTCAGTATCG 59.267 47.826 0.00 0.00 0.00 2.92
2357 5180 4.686972 TGCAATGCAGAGTAGTCAGTATC 58.313 43.478 2.72 0.00 33.32 2.24
2358 5181 4.743057 TGCAATGCAGAGTAGTCAGTAT 57.257 40.909 2.72 0.00 33.32 2.12
2359 5182 4.245660 GTTGCAATGCAGAGTAGTCAGTA 58.754 43.478 8.31 0.00 40.61 2.74
2388 5211 0.452987 CCCAATGGACACTGAATGCG 59.547 55.000 0.00 0.00 0.00 4.73
2494 5433 6.935741 TGTGCTGTTAGTTTACTTTGTCAT 57.064 33.333 0.00 0.00 0.00 3.06
2503 5442 6.647481 ACGATAACACATGTGCTGTTAGTTTA 59.353 34.615 25.68 13.68 37.48 2.01
2538 5477 2.224769 CCCGATTATGGGCACACCTATT 60.225 50.000 0.00 0.00 43.70 1.73
2540 5479 0.762418 CCCGATTATGGGCACACCTA 59.238 55.000 0.00 0.00 43.70 3.08
2660 6068 5.181748 AGATCAGAGTGAACACCTAAATGC 58.818 41.667 0.00 0.00 0.00 3.56
2722 6137 2.036475 CCGGGTCATCTTCTCACCTATG 59.964 54.545 0.00 0.00 0.00 2.23
2741 6156 0.811219 TGAAGATCTTGCATCGCCCG 60.811 55.000 14.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.