Multiple sequence alignment - TraesCS3B01G074100

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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 TraesCS3B01G074100 chr3B 100.000 2467 0 0 495 2961 44858067 44855601 0.000000e+00 4556
1 TraesCS3B01G074100 chr3B 92.313 1353 89 11 1616 2961 45270046 45268702 0.000000e+00 1908
2 TraesCS3B01G074100 chr3B 86.478 917 98 17 727 1626 45272001 45271094 0.000000e+00 983
3 TraesCS3B01G074100 chr3B 81.348 831 120 14 759 1581 44848407 44847604 0.000000e+00 643
4 TraesCS3B01G074100 chr3B 100.000 262 0 0 1 262 44858561 44858300 4.440000e-133 484
5 TraesCS3B01G074100 chr3B 96.186 236 9 0 495 730 752497067 752496832 1.290000e-103 387
6 TraesCS3B01G074100 chr3B 95.816 239 10 0 495 733 808576506 808576268 1.290000e-103 387
7 TraesCS3B01G074100 chr3B 85.185 243 30 5 2070 2311 401805741 401805978 8.200000e-61 244
8 TraesCS3B01G074100 chr3A 90.834 1451 102 16 1518 2961 36728908 36727482 0.000000e+00 1914
9 TraesCS3B01G074100 chr3A 80.858 862 136 21 792 1637 36771065 36770217 0.000000e+00 651
10 TraesCS3B01G074100 chr3A 85.360 403 52 5 759 1158 36722380 36721982 7.640000e-111 411
11 TraesCS3B01G074100 chr3A 80.804 448 68 11 1198 1637 36678717 36678280 4.730000e-88 335
12 TraesCS3B01G074100 chr3A 86.008 243 28 5 2070 2311 410110141 410110378 3.790000e-64 255
13 TraesCS3B01G074100 chrUn 92.313 1353 89 11 1616 2961 345547948 345546604 0.000000e+00 1908
14 TraesCS3B01G074100 chrUn 92.313 1353 89 11 1616 2961 362559593 362558249 0.000000e+00 1908
15 TraesCS3B01G074100 chrUn 92.871 1024 63 4 1944 2961 38771758 38772777 0.000000e+00 1478
16 TraesCS3B01G074100 chrUn 81.818 891 139 17 759 1637 38820749 38821628 0.000000e+00 726
17 TraesCS3B01G074100 chrUn 82.557 837 131 12 759 1587 38808428 38809257 0.000000e+00 723
18 TraesCS3B01G074100 chrUn 90.000 310 18 7 1634 1942 38720310 38720607 3.580000e-104 388
19 TraesCS3B01G074100 chrUn 94.332 247 11 3 495 741 208597222 208597465 2.790000e-100 375
20 TraesCS3B01G074100 chrUn 94.332 247 11 3 495 741 211740255 211740012 2.790000e-100 375
21 TraesCS3B01G074100 chrUn 94.332 247 11 3 495 741 336652960 336652717 2.790000e-100 375
22 TraesCS3B01G074100 chrUn 94.332 247 11 3 495 741 336679530 336679287 2.790000e-100 375
23 TraesCS3B01G074100 chrUn 94.286 245 11 3 497 741 211734443 211734202 3.600000e-99 372
24 TraesCS3B01G074100 chr3D 92.439 1349 81 13 1627 2961 26640500 26639159 0.000000e+00 1906
25 TraesCS3B01G074100 chr3D 93.964 878 49 4 744 1618 26643320 26642444 0.000000e+00 1325
26 TraesCS3B01G074100 chr3D 82.019 862 125 20 792 1637 26649773 26648926 0.000000e+00 706
27 TraesCS3B01G074100 chr3D 86.022 186 25 1 759 943 26608264 26608079 6.470000e-47 198
28 TraesCS3B01G074100 chr1B 86.160 737 82 14 911 1636 636680045 636679318 0.000000e+00 778
29 TraesCS3B01G074100 chr1B 86.512 430 46 7 911 1334 636662461 636662038 2.080000e-126 462
30 TraesCS3B01G074100 chr1B 93.976 249 13 2 495 742 564196004 564196251 2.790000e-100 375
31 TraesCS3B01G074100 chr6B 96.629 267 4 4 1 262 125177112 125176846 3.500000e-119 438
32 TraesCS3B01G074100 chr6B 96.186 236 9 0 495 730 640535012 640535247 1.290000e-103 387
33 TraesCS3B01G074100 chr6B 94.758 248 12 1 495 741 36284778 36284531 4.630000e-103 385
34 TraesCS3B01G074100 chr2A 96.629 267 4 4 1 262 762706136 762705870 3.500000e-119 438
35 TraesCS3B01G074100 chr1D 96.629 267 4 4 1 262 491024794 491025060 3.500000e-119 438
36 TraesCS3B01G074100 chr1D 97.059 238 6 1 497 734 19276841 19276605 1.650000e-107 399
37 TraesCS3B01G074100 chr1D 96.596 235 8 0 497 731 37273247 37273481 9.950000e-105 390
38 TraesCS3B01G074100 chr2D 96.269 268 4 4 1 262 22406543 22406810 4.530000e-118 435
39 TraesCS3B01G074100 chr2D 96.255 267 5 4 1 262 104375116 104374850 1.630000e-117 433
40 TraesCS3B01G074100 chr2D 97.436 234 6 0 497 730 104374798 104374565 1.650000e-107 399
41 TraesCS3B01G074100 chr2D 97.009 234 7 0 497 730 623322173 623322406 7.690000e-106 394
42 TraesCS3B01G074100 chr4D 96.255 267 5 4 1 262 441103070 441103336 1.630000e-117 433
43 TraesCS3B01G074100 chr4D 95.911 269 4 4 1 262 411698349 411698617 2.110000e-116 429
44 TraesCS3B01G074100 chr5D 96.212 264 8 2 1 262 44031219 44030956 5.860000e-117 431
45 TraesCS3B01G074100 chr7D 95.911 269 4 4 1 262 593879119 593879387 2.110000e-116 429
46 TraesCS3B01G074100 chr2B 97.034 236 7 0 495 730 2051885 2051650 5.950000e-107 398
47 TraesCS3B01G074100 chr2B 93.976 249 14 1 495 743 744322273 744322026 2.790000e-100 375
48 TraesCS3B01G074100 chr4A 94.332 247 11 3 495 741 645834685 645834928 2.790000e-100 375
49 TraesCS3B01G074100 chr1A 85.470 351 44 6 1290 1636 553903113 553902766 2.810000e-95 359
50 TraesCS3B01G074100 chr5A 83.936 249 33 5 2070 2311 448610863 448611111 6.380000e-57 231


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 TraesCS3B01G074100 chr3B 44855601 44858561 2960 True 2520.0 4556 100.0000 1 2961 2 chr3B.!!$R4 2960
1 TraesCS3B01G074100 chr3B 45268702 45272001 3299 True 1445.5 1908 89.3955 727 2961 2 chr3B.!!$R5 2234
2 TraesCS3B01G074100 chr3B 44847604 44848407 803 True 643.0 643 81.3480 759 1581 1 chr3B.!!$R1 822
3 TraesCS3B01G074100 chr3A 36727482 36728908 1426 True 1914.0 1914 90.8340 1518 2961 1 chr3A.!!$R3 1443
4 TraesCS3B01G074100 chr3A 36770217 36771065 848 True 651.0 651 80.8580 792 1637 1 chr3A.!!$R4 845
5 TraesCS3B01G074100 chrUn 345546604 345547948 1344 True 1908.0 1908 92.3130 1616 2961 1 chrUn.!!$R5 1345
6 TraesCS3B01G074100 chrUn 362558249 362559593 1344 True 1908.0 1908 92.3130 1616 2961 1 chrUn.!!$R6 1345
7 TraesCS3B01G074100 chrUn 38771758 38772777 1019 False 1478.0 1478 92.8710 1944 2961 1 chrUn.!!$F2 1017
8 TraesCS3B01G074100 chrUn 38820749 38821628 879 False 726.0 726 81.8180 759 1637 1 chrUn.!!$F4 878
9 TraesCS3B01G074100 chrUn 38808428 38809257 829 False 723.0 723 82.5570 759 1587 1 chrUn.!!$F3 828
10 TraesCS3B01G074100 chr3D 26639159 26643320 4161 True 1615.5 1906 93.2015 744 2961 2 chr3D.!!$R3 2217
11 TraesCS3B01G074100 chr3D 26648926 26649773 847 True 706.0 706 82.0190 792 1637 1 chr3D.!!$R2 845
12 TraesCS3B01G074100 chr1B 636679318 636680045 727 True 778.0 778 86.1600 911 1636 1 chr1B.!!$R2 725
13 TraesCS3B01G074100 chr2D 104374565 104375116 551 True 416.0 433 96.8455 1 730 2 chr2D.!!$R1 729

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
193 199 0.387622 TACGTAGCGTCACCAAGCAC 60.388 55.000 0.00 0.0 41.54 4.40 F
706 712 2.125391 GCCCTTACGAACCGGGAC 60.125 66.667 6.32 0.0 40.55 4.46 F
1286 1324 0.037303 CCAGGCTGACAGTGACCAAT 59.963 55.000 17.94 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1128 0.251121 ACCGTGAACATCAATGGCCA 60.251 50.000 8.56 8.56 29.88 5.36 R
1543 1586 0.882042 CTGCACGATGTAGGCCATCC 60.882 60.000 5.01 0.00 46.10 3.51 R
2421 5401 2.287487 TGTTGTTGCAATCATGTGTCGG 60.287 45.455 0.59 0.00 0.00 4.79 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
63 64 3.748048 ACATGTTGTTCGACCAATCTCTG 59.252 43.478 0.00 0.00 0.00 3.35
172 177 8.046708 AGCATGTCTAGTCCTCTCTATACTATG 58.953 40.741 0.00 0.00 0.00 2.23
193 199 0.387622 TACGTAGCGTCACCAAGCAC 60.388 55.000 0.00 0.00 41.54 4.40
609 615 3.866582 GGAGGCCCATCTGTCCCG 61.867 72.222 0.00 0.00 0.00 5.14
623 629 3.071892 TCTGTCCCGGTTTGTGTAAGAAT 59.928 43.478 0.00 0.00 0.00 2.40
626 632 2.299582 TCCCGGTTTGTGTAAGAATCGA 59.700 45.455 0.00 0.00 0.00 3.59
634 640 7.508134 GGTTTGTGTAAGAATCGAGACTAAAC 58.492 38.462 0.00 0.67 0.00 2.01
706 712 2.125391 GCCCTTACGAACCGGGAC 60.125 66.667 6.32 0.00 40.55 4.46
730 736 5.632034 ATAGGCCCTTTTTCTACTAGTGG 57.368 43.478 5.39 1.87 0.00 4.00
731 737 3.527937 AGGCCCTTTTTCTACTAGTGGA 58.472 45.455 4.58 4.58 0.00 4.02
765 771 6.796705 AGTGTATGTAAAGCTGTAAACACC 57.203 37.500 16.35 5.16 37.32 4.16
810 816 4.156922 CGTATAATCCTGAGATCTTCGGCT 59.843 45.833 0.00 0.00 0.00 5.52
893 909 7.714377 GGTATGGATTTATGGAGCATATCTCAG 59.286 40.741 0.00 0.00 43.70 3.35
901 917 5.417754 TGGAGCATATCTCAGATGATTCC 57.582 43.478 0.00 0.29 43.70 3.01
991 1022 2.686835 GAGACAGGGAGGGCAGCT 60.687 66.667 0.00 0.00 0.00 4.24
1089 1127 1.324005 CCTTGTCCTCGTCCTCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
1090 1128 0.323908 CTTGTCCTCGTCCTCTCCCT 60.324 60.000 0.00 0.00 0.00 4.20
1148 1186 4.096003 CCACGTTCCCCGCTGGAT 62.096 66.667 0.00 0.00 44.66 3.41
1185 1223 2.049433 GCAGCCACTACGTCACGT 60.049 61.111 8.49 8.49 44.35 4.49
1196 1234 1.371267 CGTCACGTCGGACATGTGT 60.371 57.895 1.15 0.00 42.10 3.72
1286 1324 0.037303 CCAGGCTGACAGTGACCAAT 59.963 55.000 17.94 0.00 0.00 3.16
1288 1326 0.037303 AGGCTGACAGTGACCAATGG 59.963 55.000 3.99 0.00 0.00 3.16
1344 1382 1.973281 CATGCCAAGGACGCCAAGT 60.973 57.895 0.00 0.00 0.00 3.16
1345 1383 1.228552 ATGCCAAGGACGCCAAGTT 60.229 52.632 0.00 0.00 0.00 2.66
1660 4629 2.839486 TGGGCTGACTGAGTTTACAG 57.161 50.000 0.00 0.00 42.78 2.74
1754 4727 1.070134 AGCTGCGATTATTCGGCCTTA 59.930 47.619 0.00 0.00 45.59 2.69
1804 4777 1.753930 TGCTGGAAATGCATGATCGT 58.246 45.000 0.00 0.00 35.31 3.73
1805 4778 2.916640 TGCTGGAAATGCATGATCGTA 58.083 42.857 0.00 0.00 35.31 3.43
1820 4793 8.297426 TGCATGATCGTAGTAGTAGATTAAAGG 58.703 37.037 0.00 0.00 0.00 3.11
1826 4799 7.052873 TCGTAGTAGTAGATTAAAGGACAGCT 58.947 38.462 0.00 0.00 0.00 4.24
1843 4816 4.012374 ACAGCTAACATTCCACAATCCAG 58.988 43.478 0.00 0.00 0.00 3.86
1847 4820 3.814504 AACATTCCACAATCCAGACCT 57.185 42.857 0.00 0.00 0.00 3.85
1851 4824 3.354948 TTCCACAATCCAGACCTCATG 57.645 47.619 0.00 0.00 0.00 3.07
1865 4838 6.316390 CCAGACCTCATGTTTTTACCTCATAC 59.684 42.308 0.00 0.00 0.00 2.39
1951 4925 7.837187 TGGGGATAGTTTAACCCTAAGAAAATG 59.163 37.037 0.00 0.00 43.72 2.32
2103 5079 8.851541 TCCAAAATATAAGGTGTACTCGTTTT 57.148 30.769 8.03 3.93 0.00 2.43
2104 5080 9.287373 TCCAAAATATAAGGTGTACTCGTTTTT 57.713 29.630 8.03 1.67 0.00 1.94
2281 5261 6.801862 ACTCGTTTGACTTTTGAGAAAACAAG 59.198 34.615 0.00 0.00 31.69 3.16
2311 5291 8.386264 ACCTTATATAAAGGAATGGATGGAGTG 58.614 37.037 10.67 0.00 39.81 3.51
2471 5451 5.979517 GCCATGCACAAATATAGGAGAAAAC 59.020 40.000 0.00 0.00 0.00 2.43
2489 5469 6.007076 AGAAAACCCAACAACAAATTTTGGT 58.993 32.000 13.42 3.82 38.53 3.67
2497 5477 7.308435 CCAACAACAAATTTTGGTTAAGCAAA 58.692 30.769 24.87 24.87 35.91 3.68
2953 5949 6.640518 TGCCTAACCTAGTAGAACTTGAATG 58.359 40.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.021104 TCTCAGAGATTGGTCGAACAACAT 60.021 41.667 20.01 10.08 32.39 2.71
52 53 2.958355 CCTCTCCTCTCAGAGATTGGTC 59.042 54.545 2.09 0.00 42.44 4.02
63 64 2.642154 TATCGACCACCTCTCCTCTC 57.358 55.000 0.00 0.00 0.00 3.20
149 153 8.457585 ACCATAGTATAGAGAGGACTAGACAT 57.542 38.462 0.00 0.00 37.14 3.06
172 177 1.074872 GCTTGGTGACGCTACGTACC 61.075 60.000 0.00 0.00 41.37 3.34
193 199 4.204012 AGAAGTGTCCTCTCTTATCTCCG 58.796 47.826 0.00 0.00 0.00 4.63
494 500 1.133253 CGCGTCAGCATTTCAGGTG 59.867 57.895 0.00 0.00 45.49 4.00
495 501 1.301716 ACGCGTCAGCATTTCAGGT 60.302 52.632 5.58 0.00 45.49 4.00
609 615 7.508134 GTTTAGTCTCGATTCTTACACAAACC 58.492 38.462 0.00 0.00 0.00 3.27
634 640 2.031333 GTCGGTACTAATGCCCTAGACG 60.031 54.545 0.00 0.00 0.00 4.18
706 712 5.823045 CCACTAGTAGAAAAAGGGCCTATTG 59.177 44.000 6.41 0.00 0.00 1.90
755 761 5.184864 TCCAGCATTAAATGGGTGTTTACAG 59.815 40.000 5.24 0.00 37.19 2.74
765 771 4.142534 CGCCATATCTCCAGCATTAAATGG 60.143 45.833 0.00 0.00 37.97 3.16
893 909 2.223611 CAGCAGCTTCGATGGAATCATC 59.776 50.000 0.00 0.00 45.97 2.92
901 917 6.971184 AGAAAATAAATTCAGCAGCTTCGATG 59.029 34.615 0.00 0.00 0.00 3.84
1005 1040 1.268539 GGTGTTGGCGTGTTTTCTCTG 60.269 52.381 0.00 0.00 0.00 3.35
1011 1046 1.739049 CCATGGTGTTGGCGTGTTT 59.261 52.632 2.57 0.00 0.00 2.83
1073 1108 1.000771 CAGGGAGAGGACGAGGACA 60.001 63.158 0.00 0.00 0.00 4.02
1089 1127 0.452987 CCGTGAACATCAATGGCCAG 59.547 55.000 13.05 0.00 0.00 4.85
1090 1128 0.251121 ACCGTGAACATCAATGGCCA 60.251 50.000 8.56 8.56 29.88 5.36
1148 1186 1.372683 GAGGCTGTTGCAGAGGTCA 59.627 57.895 0.00 0.00 41.91 4.02
1196 1234 4.377708 ATGCAGAGCGCGGACACA 62.378 61.111 8.83 0.00 46.97 3.72
1218 1256 3.630013 TGCAGAGCGGCAGGAGTT 61.630 61.111 1.45 0.00 39.25 3.01
1288 1326 4.715523 TGGCCTTGGCTACCGTGC 62.716 66.667 11.71 0.00 0.00 5.34
1344 1382 1.808411 GACCGCATGACCTTCTTGAA 58.192 50.000 0.00 0.00 0.00 2.69
1345 1383 0.389817 CGACCGCATGACCTTCTTGA 60.390 55.000 0.00 0.00 0.00 3.02
1543 1586 0.882042 CTGCACGATGTAGGCCATCC 60.882 60.000 5.01 0.00 46.10 3.51
1713 4686 3.760035 ACAGCCCGGTAGCTCGTG 61.760 66.667 1.77 0.00 42.61 4.35
1740 4713 3.813724 GGTGGAACTAAGGCCGAATAATC 59.186 47.826 0.00 0.00 36.74 1.75
1741 4714 3.743269 CGGTGGAACTAAGGCCGAATAAT 60.743 47.826 0.00 0.00 44.57 1.28
1788 4761 5.276461 ACTACTACGATCATGCATTTCCA 57.724 39.130 0.00 0.00 0.00 3.53
1800 4773 7.720515 AGCTGTCCTTTAATCTACTACTACGAT 59.279 37.037 0.00 0.00 0.00 3.73
1803 4776 9.949174 GTTAGCTGTCCTTTAATCTACTACTAC 57.051 37.037 0.00 0.00 0.00 2.73
1804 4777 9.690913 TGTTAGCTGTCCTTTAATCTACTACTA 57.309 33.333 0.00 0.00 0.00 1.82
1805 4778 8.591114 TGTTAGCTGTCCTTTAATCTACTACT 57.409 34.615 0.00 0.00 0.00 2.57
1820 4793 4.009675 TGGATTGTGGAATGTTAGCTGTC 58.990 43.478 0.00 0.00 0.00 3.51
1826 4799 4.288366 TGAGGTCTGGATTGTGGAATGTTA 59.712 41.667 0.00 0.00 0.00 2.41
1843 4816 7.606456 TCTTGTATGAGGTAAAAACATGAGGTC 59.394 37.037 0.00 0.00 0.00 3.85
1851 4824 9.959749 TGTTCATTTCTTGTATGAGGTAAAAAC 57.040 29.630 0.00 0.00 33.83 2.43
2103 5079 4.462508 TTCAAATGGTTGACTTGCACAA 57.537 36.364 0.00 0.00 43.52 3.33
2104 5080 4.141981 ACATTCAAATGGTTGACTTGCACA 60.142 37.500 7.58 0.00 43.52 4.57
2281 5261 9.449719 CCATCCATTCCTTTATATAAGGTGTAC 57.550 37.037 4.13 0.00 38.55 2.90
2311 5291 9.490663 CTAGTTTACACTTGTTTATTGCATAGC 57.509 33.333 0.00 0.00 34.06 2.97
2421 5401 2.287487 TGTTGTTGCAATCATGTGTCGG 60.287 45.455 0.59 0.00 0.00 4.79
2471 5451 5.355350 TGCTTAACCAAAATTTGTTGTTGGG 59.645 36.000 9.97 2.58 45.09 4.12
2489 5469 6.820656 TGCTCCTTTTTCATGTTTTTGCTTAA 59.179 30.769 0.00 0.00 0.00 1.85
2497 5477 6.405538 TGTTTCTTGCTCCTTTTTCATGTTT 58.594 32.000 0.00 0.00 0.00 2.83
2633 5621 5.989777 ACGCGCTTAATTCATTCTACCTAAT 59.010 36.000 5.73 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.