Multiple sequence alignment - TraesCS6B01G233900

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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 TraesCS6B01G233900 chr6B 100.000 3126 0 0 1 3126 391687312 391684187 0.000000e+00 5773
1 TraesCS6B01G233900 chr6B 93.134 1340 63 4 1816 3126 522103408 522102069 0.000000e+00 1938
2 TraesCS6B01G233900 chr6B 93.303 657 42 2 866 1522 494394422 494393768 0.000000e+00 968
3 TraesCS6B01G233900 chr6B 89.529 764 70 6 2368 3121 596912780 596913543 0.000000e+00 959
4 TraesCS6B01G233900 chr6B 91.096 584 40 5 118 689 345156157 345156740 0.000000e+00 780
5 TraesCS6B01G233900 chr6B 97.692 390 9 0 1478 1867 494393767 494393378 0.000000e+00 671
6 TraesCS6B01G233900 chr6B 90.020 511 40 5 118 617 494396128 494395618 0.000000e+00 651
7 TraesCS6B01G233900 chr6B 90.654 214 20 0 597 810 494395110 494394897 5.100000e-73 285
8 TraesCS6B01G233900 chr3B 92.702 1521 102 4 380 1900 406612964 406614475 0.000000e+00 2185
9 TraesCS6B01G233900 chr3B 96.577 1110 34 2 1266 2371 406614479 406615588 0.000000e+00 1836
10 TraesCS6B01G233900 chr3B 89.563 824 76 6 2294 3107 286217709 286218532 0.000000e+00 1037
11 TraesCS6B01G233900 chr3B 89.853 749 65 6 2383 3121 829045972 829046719 0.000000e+00 952
12 TraesCS6B01G233900 chr3B 94.595 407 21 1 902 1308 371041777 371041372 2.050000e-176 628
13 TraesCS6B01G233900 chr3B 89.087 504 49 2 380 883 371042761 371042264 3.420000e-174 621
14 TraesCS6B01G233900 chr3B 97.189 249 6 1 1492 1740 158635616 158635863 1.340000e-113 420
15 TraesCS6B01G233900 chr3B 97.200 250 3 2 1492 1741 366553643 366553888 1.340000e-113 420
16 TraesCS6B01G233900 chr3B 91.111 225 20 0 659 883 279752283 279752507 3.920000e-79 305
17 TraesCS6B01G233900 chr3B 98.990 99 1 0 1344 1442 279756493 279756591 8.910000e-41 178
18 TraesCS6B01G233900 chr1B 93.652 1465 58 15 907 2371 148507393 148508822 0.000000e+00 2158
19 TraesCS6B01G233900 chr1B 90.544 423 24 6 461 883 148506495 148506901 2.120000e-151 545
20 TraesCS6B01G233900 chr1B 91.884 345 27 1 118 461 148506045 148506389 6.060000e-132 481
21 TraesCS6B01G233900 chr1B 90.937 331 30 0 118 448 363227666 363227336 2.210000e-121 446
22 TraesCS6B01G233900 chr1B 89.189 333 34 2 118 449 296606362 296606031 6.240000e-112 414
23 TraesCS6B01G233900 chr7B 94.924 1320 54 8 1816 3126 490185627 490184312 0.000000e+00 2054
24 TraesCS6B01G233900 chr7B 93.363 904 50 4 2233 3126 399235394 399236297 0.000000e+00 1328
25 TraesCS6B01G233900 chr7B 95.942 616 24 1 1816 2431 305465817 305466431 0.000000e+00 998
26 TraesCS6B01G233900 chr7B 95.455 616 26 2 1816 2431 195429016 195429629 0.000000e+00 981
27 TraesCS6B01G233900 chr7B 94.464 560 28 3 1260 1818 299405109 299404552 0.000000e+00 859
28 TraesCS6B01G233900 chr7B 90.588 595 43 6 107 689 356531706 356532299 0.000000e+00 776
29 TraesCS6B01G233900 chr7B 91.324 438 37 1 2671 3107 305128330 305127893 5.770000e-167 597
30 TraesCS6B01G233900 chr7B 92.878 337 23 1 924 1260 490185983 490185648 3.620000e-134 488
31 TraesCS6B01G233900 chr7B 90.286 350 32 2 2297 2645 305154905 305154557 1.020000e-124 457
32 TraesCS6B01G233900 chr7B 88.889 225 25 0 659 883 195992155 195991931 8.540000e-71 278
33 TraesCS6B01G233900 chr1A 96.123 619 20 2 1816 2431 283715114 283714497 0.000000e+00 1007
34 TraesCS6B01G233900 chr7D 95.694 627 15 4 1816 2431 301867595 301868220 0.000000e+00 998
35 TraesCS6B01G233900 chr7D 90.802 511 34 2 380 883 311616598 311617102 0.000000e+00 671
36 TraesCS6B01G233900 chr4A 90.433 763 59 7 2368 3121 116142834 116142077 0.000000e+00 992
37 TraesCS6B01G233900 chr4A 95.528 559 23 2 1260 1818 311723811 311724367 0.000000e+00 893
38 TraesCS6B01G233900 chr4B 95.779 616 23 1 1816 2431 316993730 316994342 0.000000e+00 990
39 TraesCS6B01G233900 chr4B 89.791 764 66 7 2368 3121 491011451 491010690 0.000000e+00 968
40 TraesCS6B01G233900 chr4B 95.341 558 24 2 1260 1817 401276790 401277345 0.000000e+00 885
41 TraesCS6B01G233900 chr4B 90.925 584 39 7 118 689 172472947 172473528 0.000000e+00 773
42 TraesCS6B01G233900 chr4B 93.795 419 25 1 890 1308 175311139 175310722 2.050000e-176 628
43 TraesCS6B01G233900 chr4B 93.365 422 27 1 887 1308 531337741 531338161 9.520000e-175 623
44 TraesCS6B01G233900 chr4B 94.279 402 22 1 907 1308 609107945 609107545 5.730000e-172 614
45 TraesCS6B01G233900 chr4B 91.111 315 27 1 135 449 302827941 302827628 2.880000e-115 425
46 TraesCS6B01G233900 chr4B 82.688 491 52 6 380 870 609109412 609108955 3.750000e-109 405
47 TraesCS6B01G233900 chr4B 91.111 225 20 0 659 883 338507740 338507516 3.920000e-79 305
48 TraesCS6B01G233900 chr4B 99.160 119 1 0 1 119 131856376 131856494 6.790000e-52 215
49 TraesCS6B01G233900 chr7A 90.052 764 66 5 2368 3121 266647986 266647223 0.000000e+00 981
50 TraesCS6B01G233900 chr2D 90.949 685 48 8 2445 3120 323122419 323123098 0.000000e+00 909
51 TraesCS6B01G233900 chr2D 98.319 119 2 0 1 119 610963945 610964063 3.160000e-50 209
52 TraesCS6B01G233900 chr2B 96.064 559 20 2 1260 1818 546968921 546969477 0.000000e+00 909
53 TraesCS6B01G233900 chr2B 93.182 396 25 2 913 1308 539961793 539962186 5.810000e-162 580
54 TraesCS6B01G233900 chr2B 89.529 191 13 3 380 570 546967376 546967559 5.210000e-58 235
55 TraesCS6B01G233900 chr2B 97.561 123 3 0 1696 1818 546969529 546969651 8.780000e-51 211
56 TraesCS6B01G233900 chr6A 91.522 519 34 5 2598 3107 349937405 349937922 0.000000e+00 706
57 TraesCS6B01G233900 chr6A 90.492 305 28 1 2297 2600 349934334 349934638 4.860000e-108 401
58 TraesCS6B01G233900 chr6A 91.221 262 17 1 380 641 197864991 197864736 4.960000e-93 351
59 TraesCS6B01G233900 chr3A 92.063 504 34 1 380 883 361579810 361579313 0.000000e+00 704
60 TraesCS6B01G233900 chr4D 89.881 504 27 6 380 883 366042606 366043085 7.360000e-176 627
61 TraesCS6B01G233900 chr4D 89.011 182 15 3 1 177 357305453 357305634 1.460000e-53 220
62 TraesCS6B01G233900 chr5D 91.291 333 28 1 118 449 67704657 67704325 1.320000e-123 453
63 TraesCS6B01G233900 chr5D 98.319 119 2 0 1 119 378274244 378274126 3.160000e-50 209
64 TraesCS6B01G233900 chr5B 99.160 119 1 0 1 119 326769979 326770097 6.790000e-52 215
65 TraesCS6B01G233900 chr5B 99.160 119 1 0 1 119 573288005 573287887 6.790000e-52 215
66 TraesCS6B01G233900 chr5B 87.234 188 12 4 380 567 301545667 301545492 1.470000e-48 204
67 TraesCS6B01G233900 chr3D 98.347 121 1 1 1 120 363730372 363730252 8.780000e-51 211
68 TraesCS6B01G233900 chr3D 98.319 119 2 0 1 119 41370854 41370736 3.160000e-50 209
69 TraesCS6B01G233900 chr1D 98.319 119 2 0 1 119 377316165 377316047 3.160000e-50 209


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 TraesCS6B01G233900 chr6B 391684187 391687312 3125 True 5773.000000 5773 100.000000 1 3126 1 chr6B.!!$R1 3125
1 TraesCS6B01G233900 chr6B 522102069 522103408 1339 True 1938.000000 1938 93.134000 1816 3126 1 chr6B.!!$R2 1310
2 TraesCS6B01G233900 chr6B 596912780 596913543 763 False 959.000000 959 89.529000 2368 3121 1 chr6B.!!$F2 753
3 TraesCS6B01G233900 chr6B 345156157 345156740 583 False 780.000000 780 91.096000 118 689 1 chr6B.!!$F1 571
4 TraesCS6B01G233900 chr6B 494393378 494396128 2750 True 643.750000 968 92.917250 118 1867 4 chr6B.!!$R3 1749
5 TraesCS6B01G233900 chr3B 406612964 406615588 2624 False 2010.500000 2185 94.639500 380 2371 2 chr3B.!!$F6 1991
6 TraesCS6B01G233900 chr3B 286217709 286218532 823 False 1037.000000 1037 89.563000 2294 3107 1 chr3B.!!$F2 813
7 TraesCS6B01G233900 chr3B 829045972 829046719 747 False 952.000000 952 89.853000 2383 3121 1 chr3B.!!$F4 738
8 TraesCS6B01G233900 chr3B 371041372 371042761 1389 True 624.500000 628 91.841000 380 1308 2 chr3B.!!$R1 928
9 TraesCS6B01G233900 chr3B 279752283 279756591 4308 False 241.500000 305 95.050500 659 1442 2 chr3B.!!$F5 783
10 TraesCS6B01G233900 chr1B 148506045 148508822 2777 False 1061.333333 2158 92.026667 118 2371 3 chr1B.!!$F1 2253
11 TraesCS6B01G233900 chr7B 399235394 399236297 903 False 1328.000000 1328 93.363000 2233 3126 1 chr7B.!!$F4 893
12 TraesCS6B01G233900 chr7B 490184312 490185983 1671 True 1271.000000 2054 93.901000 924 3126 2 chr7B.!!$R5 2202
13 TraesCS6B01G233900 chr7B 305465817 305466431 614 False 998.000000 998 95.942000 1816 2431 1 chr7B.!!$F2 615
14 TraesCS6B01G233900 chr7B 195429016 195429629 613 False 981.000000 981 95.455000 1816 2431 1 chr7B.!!$F1 615
15 TraesCS6B01G233900 chr7B 299404552 299405109 557 True 859.000000 859 94.464000 1260 1818 1 chr7B.!!$R2 558
16 TraesCS6B01G233900 chr7B 356531706 356532299 593 False 776.000000 776 90.588000 107 689 1 chr7B.!!$F3 582
17 TraesCS6B01G233900 chr1A 283714497 283715114 617 True 1007.000000 1007 96.123000 1816 2431 1 chr1A.!!$R1 615
18 TraesCS6B01G233900 chr7D 301867595 301868220 625 False 998.000000 998 95.694000 1816 2431 1 chr7D.!!$F1 615
19 TraesCS6B01G233900 chr7D 311616598 311617102 504 False 671.000000 671 90.802000 380 883 1 chr7D.!!$F2 503
20 TraesCS6B01G233900 chr4A 116142077 116142834 757 True 992.000000 992 90.433000 2368 3121 1 chr4A.!!$R1 753
21 TraesCS6B01G233900 chr4A 311723811 311724367 556 False 893.000000 893 95.528000 1260 1818 1 chr4A.!!$F1 558
22 TraesCS6B01G233900 chr4B 316993730 316994342 612 False 990.000000 990 95.779000 1816 2431 1 chr4B.!!$F3 615
23 TraesCS6B01G233900 chr4B 491010690 491011451 761 True 968.000000 968 89.791000 2368 3121 1 chr4B.!!$R4 753
24 TraesCS6B01G233900 chr4B 401276790 401277345 555 False 885.000000 885 95.341000 1260 1817 1 chr4B.!!$F4 557
25 TraesCS6B01G233900 chr4B 172472947 172473528 581 False 773.000000 773 90.925000 118 689 1 chr4B.!!$F2 571
26 TraesCS6B01G233900 chr4B 609107545 609109412 1867 True 509.500000 614 88.483500 380 1308 2 chr4B.!!$R5 928
27 TraesCS6B01G233900 chr7A 266647223 266647986 763 True 981.000000 981 90.052000 2368 3121 1 chr7A.!!$R1 753
28 TraesCS6B01G233900 chr2D 323122419 323123098 679 False 909.000000 909 90.949000 2445 3120 1 chr2D.!!$F1 675
29 TraesCS6B01G233900 chr2B 546967376 546969651 2275 False 451.666667 909 94.384667 380 1818 3 chr2B.!!$F2 1438
30 TraesCS6B01G233900 chr6A 349934334 349937922 3588 False 553.500000 706 91.007000 2297 3107 2 chr6A.!!$F1 810

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
152 153 0.252467 AGGCTAGCCAACTCACCTCT 60.252 55.0 34.7 7.82 38.92 3.69 F
455 456 0.323633 TCGATCCCCACAGTAACCGA 60.324 55.0 0.0 0.00 0.00 4.69 F
855 1531 0.398664 GGAGGGAAGAAGGGGATCGA 60.399 60.0 0.0 0.00 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 4345 0.321671 CAACTTCGAAGCTCCTCCCA 59.678 55.0 24.86 0.0 0.00 4.37 R
1425 5321 0.473755 TCAGCCTTCAACTCCTTGCA 59.526 50.0 0.00 0.0 0.00 4.08 R
2528 8342 0.469494 TCAGCCTGAGCAAACACTCA 59.531 50.0 0.00 0.0 44.32 3.41 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
26 27 7.234187 TCATGAAACACACTCGAATATTAGC 57.766 36.000 0.00 0.00 0.00 3.09
27 28 7.041721 TCATGAAACACACTCGAATATTAGCT 58.958 34.615 0.00 0.00 0.00 3.32
28 29 8.194769 TCATGAAACACACTCGAATATTAGCTA 58.805 33.333 0.00 0.00 0.00 3.32
29 30 7.751047 TGAAACACACTCGAATATTAGCTAC 57.249 36.000 0.00 0.00 0.00 3.58
30 31 7.317390 TGAAACACACTCGAATATTAGCTACA 58.683 34.615 0.00 0.00 0.00 2.74
31 32 7.274904 TGAAACACACTCGAATATTAGCTACAC 59.725 37.037 0.00 0.00 0.00 2.90
32 33 5.589192 ACACACTCGAATATTAGCTACACC 58.411 41.667 0.00 0.00 0.00 4.16
33 34 4.982916 CACACTCGAATATTAGCTACACCC 59.017 45.833 0.00 0.00 0.00 4.61
34 35 4.647853 ACACTCGAATATTAGCTACACCCA 59.352 41.667 0.00 0.00 0.00 4.51
35 36 5.128171 ACACTCGAATATTAGCTACACCCAA 59.872 40.000 0.00 0.00 0.00 4.12
36 37 6.183360 ACACTCGAATATTAGCTACACCCAAT 60.183 38.462 0.00 0.00 0.00 3.16
37 38 7.014905 ACACTCGAATATTAGCTACACCCAATA 59.985 37.037 0.00 0.00 0.00 1.90
38 39 7.328737 CACTCGAATATTAGCTACACCCAATAC 59.671 40.741 0.00 0.00 0.00 1.89
39 40 7.232941 ACTCGAATATTAGCTACACCCAATACT 59.767 37.037 0.00 0.00 0.00 2.12
40 41 7.959175 TCGAATATTAGCTACACCCAATACTT 58.041 34.615 0.00 0.00 0.00 2.24
41 42 9.081204 TCGAATATTAGCTACACCCAATACTTA 57.919 33.333 0.00 0.00 0.00 2.24
42 43 9.701098 CGAATATTAGCTACACCCAATACTTAA 57.299 33.333 0.00 0.00 0.00 1.85
47 48 5.899299 AGCTACACCCAATACTTAAGTACG 58.101 41.667 17.45 11.42 32.72 3.67
48 49 5.653769 AGCTACACCCAATACTTAAGTACGA 59.346 40.000 17.45 0.00 32.72 3.43
49 50 6.323225 AGCTACACCCAATACTTAAGTACGAT 59.677 38.462 17.45 4.72 32.72 3.73
50 51 6.640092 GCTACACCCAATACTTAAGTACGATC 59.360 42.308 17.45 0.00 32.72 3.69
51 52 6.534475 ACACCCAATACTTAAGTACGATCA 57.466 37.500 17.45 0.00 32.72 2.92
52 53 7.120923 ACACCCAATACTTAAGTACGATCAT 57.879 36.000 17.45 0.00 32.72 2.45
53 54 8.241497 ACACCCAATACTTAAGTACGATCATA 57.759 34.615 17.45 0.00 32.72 2.15
54 55 8.867097 ACACCCAATACTTAAGTACGATCATAT 58.133 33.333 17.45 0.00 32.72 1.78
55 56 9.706691 CACCCAATACTTAAGTACGATCATATT 57.293 33.333 17.45 4.02 32.72 1.28
56 57 9.706691 ACCCAATACTTAAGTACGATCATATTG 57.293 33.333 17.45 14.85 32.72 1.90
57 58 8.656849 CCCAATACTTAAGTACGATCATATTGC 58.343 37.037 17.45 0.00 32.72 3.56
58 59 8.656849 CCAATACTTAAGTACGATCATATTGCC 58.343 37.037 17.45 0.00 32.72 4.52
59 60 9.424319 CAATACTTAAGTACGATCATATTGCCT 57.576 33.333 17.45 0.00 32.72 4.75
60 61 9.640963 AATACTTAAGTACGATCATATTGCCTC 57.359 33.333 17.45 0.00 32.72 4.70
61 62 6.456501 ACTTAAGTACGATCATATTGCCTCC 58.543 40.000 6.26 0.00 0.00 4.30
62 63 6.267928 ACTTAAGTACGATCATATTGCCTCCT 59.732 38.462 6.26 0.00 0.00 3.69
63 64 7.450634 ACTTAAGTACGATCATATTGCCTCCTA 59.549 37.037 6.26 0.00 0.00 2.94
64 65 5.906113 AGTACGATCATATTGCCTCCTAG 57.094 43.478 0.00 0.00 0.00 3.02
65 66 5.326069 AGTACGATCATATTGCCTCCTAGT 58.674 41.667 0.00 0.00 0.00 2.57
66 67 5.775701 AGTACGATCATATTGCCTCCTAGTT 59.224 40.000 0.00 0.00 0.00 2.24
67 68 4.887748 ACGATCATATTGCCTCCTAGTTG 58.112 43.478 0.00 0.00 0.00 3.16
68 69 4.248859 CGATCATATTGCCTCCTAGTTGG 58.751 47.826 0.00 0.00 37.10 3.77
69 70 4.262635 CGATCATATTGCCTCCTAGTTGGT 60.263 45.833 0.00 0.00 37.07 3.67
70 71 4.422073 TCATATTGCCTCCTAGTTGGTG 57.578 45.455 0.00 0.00 37.07 4.17
71 72 2.710096 TATTGCCTCCTAGTTGGTGC 57.290 50.000 0.00 0.00 37.07 5.01
72 73 0.995024 ATTGCCTCCTAGTTGGTGCT 59.005 50.000 8.65 0.00 36.27 4.40
73 74 0.771127 TTGCCTCCTAGTTGGTGCTT 59.229 50.000 8.65 0.00 36.27 3.91
74 75 0.771127 TGCCTCCTAGTTGGTGCTTT 59.229 50.000 8.65 0.00 36.27 3.51
75 76 1.144913 TGCCTCCTAGTTGGTGCTTTT 59.855 47.619 8.65 0.00 36.27 2.27
76 77 2.373836 TGCCTCCTAGTTGGTGCTTTTA 59.626 45.455 8.65 0.00 36.27 1.52
77 78 3.010138 TGCCTCCTAGTTGGTGCTTTTAT 59.990 43.478 8.65 0.00 36.27 1.40
78 79 4.226394 TGCCTCCTAGTTGGTGCTTTTATA 59.774 41.667 8.65 0.00 36.27 0.98
79 80 5.190677 GCCTCCTAGTTGGTGCTTTTATAA 58.809 41.667 0.00 0.00 37.07 0.98
80 81 5.297029 GCCTCCTAGTTGGTGCTTTTATAAG 59.703 44.000 0.00 0.00 37.07 1.73
81 82 6.650120 CCTCCTAGTTGGTGCTTTTATAAGA 58.350 40.000 0.00 0.00 37.07 2.10
82 83 6.763610 CCTCCTAGTTGGTGCTTTTATAAGAG 59.236 42.308 0.00 0.00 37.07 2.85
83 84 7.364762 CCTCCTAGTTGGTGCTTTTATAAGAGA 60.365 40.741 7.19 0.00 37.07 3.10
84 85 7.556844 TCCTAGTTGGTGCTTTTATAAGAGAG 58.443 38.462 7.19 0.00 37.07 3.20
85 86 6.763610 CCTAGTTGGTGCTTTTATAAGAGAGG 59.236 42.308 7.19 0.00 32.92 3.69
86 87 6.374417 AGTTGGTGCTTTTATAAGAGAGGA 57.626 37.500 7.19 0.00 32.92 3.71
87 88 6.963322 AGTTGGTGCTTTTATAAGAGAGGAT 58.037 36.000 7.19 0.00 32.92 3.24
88 89 6.825721 AGTTGGTGCTTTTATAAGAGAGGATG 59.174 38.462 7.19 0.00 32.92 3.51
89 90 5.684704 TGGTGCTTTTATAAGAGAGGATGG 58.315 41.667 7.19 0.00 32.92 3.51
90 91 5.428457 TGGTGCTTTTATAAGAGAGGATGGA 59.572 40.000 7.19 0.00 32.92 3.41
91 92 5.994668 GGTGCTTTTATAAGAGAGGATGGAG 59.005 44.000 7.19 0.00 32.92 3.86
92 93 6.183361 GGTGCTTTTATAAGAGAGGATGGAGA 60.183 42.308 7.19 0.00 32.92 3.71
93 94 6.704050 GTGCTTTTATAAGAGAGGATGGAGAC 59.296 42.308 7.19 0.00 32.92 3.36
94 95 6.613271 TGCTTTTATAAGAGAGGATGGAGACT 59.387 38.462 7.19 0.00 32.92 3.24
95 96 7.151976 GCTTTTATAAGAGAGGATGGAGACTC 58.848 42.308 7.19 0.00 32.92 3.36
96 97 7.201956 GCTTTTATAAGAGAGGATGGAGACTCA 60.202 40.741 7.19 0.00 32.73 3.41
97 98 8.609617 TTTTATAAGAGAGGATGGAGACTCAA 57.390 34.615 4.53 0.00 36.20 3.02
98 99 8.789767 TTTATAAGAGAGGATGGAGACTCAAT 57.210 34.615 4.53 0.00 36.20 2.57
99 100 8.789767 TTATAAGAGAGGATGGAGACTCAATT 57.210 34.615 4.53 0.00 36.20 2.32
100 101 7.688918 ATAAGAGAGGATGGAGACTCAATTT 57.311 36.000 4.53 0.00 36.20 1.82
101 102 5.612725 AGAGAGGATGGAGACTCAATTTC 57.387 43.478 4.53 1.48 36.20 2.17
102 103 5.028802 AGAGAGGATGGAGACTCAATTTCA 58.971 41.667 4.53 0.00 36.20 2.69
103 104 5.486775 AGAGAGGATGGAGACTCAATTTCAA 59.513 40.000 4.53 0.00 36.20 2.69
104 105 6.013032 AGAGAGGATGGAGACTCAATTTCAAA 60.013 38.462 4.53 0.00 36.20 2.69
105 106 6.546484 AGAGGATGGAGACTCAATTTCAAAA 58.454 36.000 4.53 0.00 36.20 2.44
106 107 7.006509 AGAGGATGGAGACTCAATTTCAAAAA 58.993 34.615 4.53 0.00 36.20 1.94
107 108 7.673082 AGAGGATGGAGACTCAATTTCAAAAAT 59.327 33.333 4.53 0.00 36.20 1.82
108 109 8.884124 AGGATGGAGACTCAATTTCAAAAATA 57.116 30.769 4.53 0.00 0.00 1.40
109 110 9.312904 AGGATGGAGACTCAATTTCAAAAATAA 57.687 29.630 4.53 0.00 0.00 1.40
110 111 9.927668 GGATGGAGACTCAATTTCAAAAATAAA 57.072 29.630 4.53 0.00 0.00 1.40
152 153 0.252467 AGGCTAGCCAACTCACCTCT 60.252 55.000 34.70 7.82 38.92 3.69
155 156 1.410882 GCTAGCCAACTCACCTCTAGG 59.589 57.143 2.29 0.00 42.17 3.02
192 193 2.100252 GTCCTTCATTGGTCGTCCGATA 59.900 50.000 0.74 0.00 36.15 2.92
197 198 1.526887 CATTGGTCGTCCGATATGCAC 59.473 52.381 0.74 0.00 36.15 4.57
204 205 3.003482 GTCGTCCGATATGCACTCTAACT 59.997 47.826 0.00 0.00 0.00 2.24
230 231 2.151202 GAGCCGTTGGATCTTCACAAA 58.849 47.619 0.00 0.00 34.95 2.83
268 269 1.084370 CCTCGCGGTCATTTCCACTC 61.084 60.000 6.13 0.00 0.00 3.51
305 306 1.265635 CTCGTTTTGGGCGTTCATTGA 59.734 47.619 0.00 0.00 0.00 2.57
317 318 0.770499 TTCATTGACTGGGTCAGCCA 59.230 50.000 0.00 0.00 43.69 4.75
425 426 4.733542 GCCGCCCAAACCCTAGCA 62.734 66.667 0.00 0.00 0.00 3.49
455 456 0.323633 TCGATCCCCACAGTAACCGA 60.324 55.000 0.00 0.00 0.00 4.69
703 1364 1.548582 CCAGATCCACCTTGCAACCTT 60.549 52.381 0.00 0.00 0.00 3.50
749 1410 2.347490 GTCGTGTCAGGCCCATGT 59.653 61.111 0.00 0.00 0.00 3.21
855 1531 0.398664 GGAGGGAAGAAGGGGATCGA 60.399 60.000 0.00 0.00 0.00 3.59
872 1967 1.383803 GAGGGAGGGGAGAGCACAT 60.384 63.158 0.00 0.00 0.00 3.21
927 3158 1.077501 CCAGGCATGGTGTCGGATT 60.078 57.895 9.85 0.00 42.17 3.01
981 3212 2.052690 TGGAGTGGAGTAGCGAGGC 61.053 63.158 0.00 0.00 0.00 4.70
1001 3232 4.162690 GAAGACCGGGCAGCGGAT 62.163 66.667 11.69 0.00 0.00 4.18
1081 4340 0.460987 CCTGACGGCTGAAGATGGTC 60.461 60.000 0.00 0.00 0.00 4.02
1086 4345 1.153086 GGCTGAAGATGGTCCGCAT 60.153 57.895 0.00 0.00 30.03 4.73
1103 4362 0.539051 CATGGGAGGAGCTTCGAAGT 59.461 55.000 25.24 12.81 0.00 3.01
1174 4433 9.111613 TGCAAATTTTTCTTGTTTCAGATCATT 57.888 25.926 0.00 0.00 0.00 2.57
1210 4469 5.511234 AGTCTTATTGGCAATTGCATCTC 57.489 39.130 30.32 14.40 44.36 2.75
1217 4476 4.659111 TGGCAATTGCATCTCCTATTTG 57.341 40.909 30.32 0.00 44.36 2.32
1425 5321 0.610232 GTGATGGCTGCAGGGTCTTT 60.610 55.000 17.12 0.00 0.00 2.52
1458 5354 2.401766 GCTGAGGTCATGGTTGCCG 61.402 63.158 0.00 0.00 0.00 5.69
1536 5477 6.326583 TCTCACTTTTTCTCTTACTTCCTCCA 59.673 38.462 0.00 0.00 0.00 3.86
1537 5478 7.016661 TCTCACTTTTTCTCTTACTTCCTCCAT 59.983 37.037 0.00 0.00 0.00 3.41
1900 6086 7.041644 GCAACCTTACATGTTGACAGTAAGTTA 60.042 37.037 2.30 0.00 44.57 2.24
2098 6610 5.352569 CAGTCAAGTCGCATCCTCTAATTTT 59.647 40.000 0.00 0.00 0.00 1.82
2101 6613 5.937540 TCAAGTCGCATCCTCTAATTTTTCA 59.062 36.000 0.00 0.00 0.00 2.69
2220 6732 3.854666 CATCTACACCAGAAGACAGTGG 58.145 50.000 0.00 0.00 36.67 4.00
2356 6896 2.293399 GGTGCACTTAACTGTTTGAGGG 59.707 50.000 17.98 0.00 0.00 4.30
2381 8022 5.528043 TGCCAACTGAAAGCTAAATTCAA 57.472 34.783 1.25 0.00 37.60 2.69
2442 8256 4.174704 TGTACGACCACATAGTAGGGAT 57.825 45.455 0.00 0.00 0.00 3.85
2496 8310 0.107508 ATGAAGCTCCCATGTGGACG 60.108 55.000 0.00 0.00 38.61 4.79
2610 11585 3.181510 CGTAAGTGCTACCTTTGGCAATC 60.182 47.826 0.00 0.00 40.26 2.67
2690 11674 3.133542 TCGATTGCAGGATCAGAAGATGT 59.866 43.478 0.00 0.00 33.72 3.06
2866 11871 1.572085 CCTGACTGACTGCCGCTTTG 61.572 60.000 0.00 0.00 0.00 2.77
2889 11894 4.730949 ATGTTCATGCTTATTTGCAGCT 57.269 36.364 0.00 0.00 46.71 4.24
2892 11897 3.513680 TCATGCTTATTTGCAGCTTGG 57.486 42.857 9.81 0.00 46.71 3.61
3075 12082 3.815401 ACACAGCTTTTGGTACATCTGAC 59.185 43.478 0.00 0.00 39.30 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.239166 AGCTAATATTCGAGTGTGTTTCATG 57.761 36.000 0.00 0.00 0.00 3.07
6 7 7.254017 GGTGTAGCTAATATTCGAGTGTGTTTC 60.254 40.741 0.00 0.00 0.00 2.78
7 8 6.534079 GGTGTAGCTAATATTCGAGTGTGTTT 59.466 38.462 0.00 0.00 0.00 2.83
8 9 6.040878 GGTGTAGCTAATATTCGAGTGTGTT 58.959 40.000 0.00 0.00 0.00 3.32
9 10 5.451520 GGGTGTAGCTAATATTCGAGTGTGT 60.452 44.000 0.00 0.00 0.00 3.72
10 11 4.982916 GGGTGTAGCTAATATTCGAGTGTG 59.017 45.833 0.00 0.00 0.00 3.82
11 12 4.647853 TGGGTGTAGCTAATATTCGAGTGT 59.352 41.667 0.00 0.00 0.00 3.55
12 13 5.196341 TGGGTGTAGCTAATATTCGAGTG 57.804 43.478 0.00 0.00 0.00 3.51
13 14 5.864418 TTGGGTGTAGCTAATATTCGAGT 57.136 39.130 0.00 0.00 0.00 4.18
14 15 7.603651 AGTATTGGGTGTAGCTAATATTCGAG 58.396 38.462 0.00 0.00 0.00 4.04
15 16 7.534723 AGTATTGGGTGTAGCTAATATTCGA 57.465 36.000 0.00 0.00 0.00 3.71
16 17 9.701098 TTAAGTATTGGGTGTAGCTAATATTCG 57.299 33.333 0.00 0.00 0.00 3.34
21 22 8.139989 CGTACTTAAGTATTGGGTGTAGCTAAT 58.860 37.037 18.03 0.00 32.54 1.73
22 23 7.339212 TCGTACTTAAGTATTGGGTGTAGCTAA 59.661 37.037 18.03 0.00 32.54 3.09
23 24 6.828273 TCGTACTTAAGTATTGGGTGTAGCTA 59.172 38.462 18.03 0.00 32.54 3.32
24 25 5.653769 TCGTACTTAAGTATTGGGTGTAGCT 59.346 40.000 18.03 0.00 32.54 3.32
25 26 5.894807 TCGTACTTAAGTATTGGGTGTAGC 58.105 41.667 18.03 1.21 32.54 3.58
26 27 7.709947 TGATCGTACTTAAGTATTGGGTGTAG 58.290 38.462 18.03 3.17 32.54 2.74
27 28 7.643569 TGATCGTACTTAAGTATTGGGTGTA 57.356 36.000 18.03 0.00 32.54 2.90
28 29 6.534475 TGATCGTACTTAAGTATTGGGTGT 57.466 37.500 18.03 1.84 32.54 4.16
29 30 9.706691 AATATGATCGTACTTAAGTATTGGGTG 57.293 33.333 18.03 5.41 32.54 4.61
30 31 9.706691 CAATATGATCGTACTTAAGTATTGGGT 57.293 33.333 18.03 7.55 32.54 4.51
31 32 8.656849 GCAATATGATCGTACTTAAGTATTGGG 58.343 37.037 18.03 8.64 32.03 4.12
32 33 8.656849 GGCAATATGATCGTACTTAAGTATTGG 58.343 37.037 18.03 10.83 32.03 3.16
33 34 9.424319 AGGCAATATGATCGTACTTAAGTATTG 57.576 33.333 18.03 16.11 33.62 1.90
34 35 9.640963 GAGGCAATATGATCGTACTTAAGTATT 57.359 33.333 18.03 6.96 32.54 1.89
35 36 8.251721 GGAGGCAATATGATCGTACTTAAGTAT 58.748 37.037 18.03 3.84 32.54 2.12
36 37 7.450634 AGGAGGCAATATGATCGTACTTAAGTA 59.549 37.037 11.38 11.38 0.00 2.24
37 38 6.267928 AGGAGGCAATATGATCGTACTTAAGT 59.732 38.462 13.68 13.68 0.00 2.24
38 39 6.692486 AGGAGGCAATATGATCGTACTTAAG 58.308 40.000 0.00 0.00 0.00 1.85
39 40 6.665992 AGGAGGCAATATGATCGTACTTAA 57.334 37.500 0.00 0.00 0.00 1.85
40 41 6.946583 ACTAGGAGGCAATATGATCGTACTTA 59.053 38.462 0.00 0.00 0.00 2.24
41 42 5.775701 ACTAGGAGGCAATATGATCGTACTT 59.224 40.000 0.00 0.00 0.00 2.24
42 43 5.326069 ACTAGGAGGCAATATGATCGTACT 58.674 41.667 0.00 0.00 0.00 2.73
43 44 5.646577 ACTAGGAGGCAATATGATCGTAC 57.353 43.478 0.00 0.00 0.00 3.67
44 45 5.047306 CCAACTAGGAGGCAATATGATCGTA 60.047 44.000 0.00 0.00 41.22 3.43
45 46 4.262635 CCAACTAGGAGGCAATATGATCGT 60.263 45.833 0.00 0.00 41.22 3.73
46 47 4.248859 CCAACTAGGAGGCAATATGATCG 58.751 47.826 0.00 0.00 41.22 3.69
47 48 4.999950 CACCAACTAGGAGGCAATATGATC 59.000 45.833 2.88 0.00 41.22 2.92
48 49 4.747931 GCACCAACTAGGAGGCAATATGAT 60.748 45.833 2.88 0.00 41.22 2.45
49 50 3.433598 GCACCAACTAGGAGGCAATATGA 60.434 47.826 2.88 0.00 41.22 2.15
50 51 2.880890 GCACCAACTAGGAGGCAATATG 59.119 50.000 2.88 0.00 41.22 1.78
51 52 2.780010 AGCACCAACTAGGAGGCAATAT 59.220 45.455 2.88 0.00 41.52 1.28
52 53 2.196595 AGCACCAACTAGGAGGCAATA 58.803 47.619 2.88 0.00 41.52 1.90
53 54 0.995024 AGCACCAACTAGGAGGCAAT 59.005 50.000 2.88 0.00 41.52 3.56
54 55 0.771127 AAGCACCAACTAGGAGGCAA 59.229 50.000 2.88 0.00 41.52 4.52
55 56 0.771127 AAAGCACCAACTAGGAGGCA 59.229 50.000 2.88 0.00 41.52 4.75
56 57 1.911057 AAAAGCACCAACTAGGAGGC 58.089 50.000 2.88 0.00 41.22 4.70
57 58 6.650120 TCTTATAAAAGCACCAACTAGGAGG 58.350 40.000 0.00 0.00 35.35 4.30
58 59 7.556844 TCTCTTATAAAAGCACCAACTAGGAG 58.443 38.462 0.00 0.00 35.35 3.69
59 60 7.364762 CCTCTCTTATAAAAGCACCAACTAGGA 60.365 40.741 0.00 0.00 35.35 2.94
60 61 6.763610 CCTCTCTTATAAAAGCACCAACTAGG 59.236 42.308 0.00 0.00 36.62 3.02
61 62 7.556844 TCCTCTCTTATAAAAGCACCAACTAG 58.443 38.462 0.00 0.00 32.36 2.57
62 63 7.490657 TCCTCTCTTATAAAAGCACCAACTA 57.509 36.000 0.00 0.00 32.36 2.24
63 64 6.374417 TCCTCTCTTATAAAAGCACCAACT 57.626 37.500 0.00 0.00 32.36 3.16
64 65 6.038714 CCATCCTCTCTTATAAAAGCACCAAC 59.961 42.308 0.00 0.00 32.36 3.77
65 66 6.069673 TCCATCCTCTCTTATAAAAGCACCAA 60.070 38.462 0.00 0.00 32.36 3.67
66 67 5.428457 TCCATCCTCTCTTATAAAAGCACCA 59.572 40.000 0.00 0.00 32.36 4.17
67 68 5.930135 TCCATCCTCTCTTATAAAAGCACC 58.070 41.667 0.00 0.00 32.36 5.01
68 69 6.704050 GTCTCCATCCTCTCTTATAAAAGCAC 59.296 42.308 0.00 0.00 32.36 4.40
69 70 6.613271 AGTCTCCATCCTCTCTTATAAAAGCA 59.387 38.462 0.00 0.00 32.36 3.91
70 71 7.061566 AGTCTCCATCCTCTCTTATAAAAGC 57.938 40.000 0.00 0.00 32.36 3.51
71 72 8.243961 TGAGTCTCCATCCTCTCTTATAAAAG 57.756 38.462 0.00 0.00 0.00 2.27
72 73 8.609617 TTGAGTCTCCATCCTCTCTTATAAAA 57.390 34.615 0.00 0.00 0.00 1.52
73 74 8.789767 ATTGAGTCTCCATCCTCTCTTATAAA 57.210 34.615 0.00 0.00 0.00 1.40
74 75 8.789767 AATTGAGTCTCCATCCTCTCTTATAA 57.210 34.615 0.00 0.00 0.00 0.98
75 76 8.789767 AAATTGAGTCTCCATCCTCTCTTATA 57.210 34.615 0.00 0.00 0.00 0.98
76 77 7.346698 TGAAATTGAGTCTCCATCCTCTCTTAT 59.653 37.037 0.00 0.00 0.00 1.73
77 78 6.669591 TGAAATTGAGTCTCCATCCTCTCTTA 59.330 38.462 0.00 0.00 0.00 2.10
78 79 5.486775 TGAAATTGAGTCTCCATCCTCTCTT 59.513 40.000 0.00 0.00 0.00 2.85
79 80 5.028802 TGAAATTGAGTCTCCATCCTCTCT 58.971 41.667 0.00 0.00 0.00 3.10
80 81 5.350504 TGAAATTGAGTCTCCATCCTCTC 57.649 43.478 0.00 0.00 0.00 3.20
81 82 5.768980 TTGAAATTGAGTCTCCATCCTCT 57.231 39.130 0.00 0.00 0.00 3.69
82 83 6.824305 TTTTGAAATTGAGTCTCCATCCTC 57.176 37.500 0.00 0.00 0.00 3.71
83 84 7.787623 ATTTTTGAAATTGAGTCTCCATCCT 57.212 32.000 0.00 0.00 0.00 3.24
84 85 9.927668 TTTATTTTTGAAATTGAGTCTCCATCC 57.072 29.630 0.00 0.00 0.00 3.51
115 116 8.197439 GGCTAGCCTCATTATTGTTTTAAATGT 58.803 33.333 27.17 0.00 33.35 2.71
152 153 1.459539 CAATCGGGGGAGCCTCCTA 60.460 63.158 11.29 0.00 36.57 2.94
155 156 3.090532 ACCAATCGGGGGAGCCTC 61.091 66.667 0.00 0.00 42.91 4.70
192 193 2.886081 CTCAAGCGAGTTAGAGTGCAT 58.114 47.619 0.00 0.00 34.29 3.96
197 198 0.171455 ACGGCTCAAGCGAGTTAGAG 59.829 55.000 0.00 0.00 41.71 2.43
204 205 1.447838 GATCCAACGGCTCAAGCGA 60.448 57.895 0.00 0.00 43.26 4.93
230 231 5.689819 CGAGGTGAAAATCGAATTTGACTT 58.310 37.500 13.95 7.59 41.40 3.01
268 269 4.308526 GCCCATCCATCATAGGCG 57.691 61.111 0.00 0.00 33.18 5.52
425 426 2.364780 GGGATCGAGGGAAACGGGT 61.365 63.158 0.00 0.00 0.00 5.28
455 456 1.228552 GTGGCTGTGGATGGTGGTT 60.229 57.895 0.00 0.00 0.00 3.67
703 1364 1.150135 AGTCAGACAGGGGAGGAAGAA 59.850 52.381 2.66 0.00 0.00 2.52
855 1531 1.692042 CATGTGCTCTCCCCTCCCT 60.692 63.158 0.00 0.00 0.00 4.20
872 1967 2.088104 ATATCCCGTGCCTTCTCTCA 57.912 50.000 0.00 0.00 0.00 3.27
904 3135 1.524621 GACACCATGCCTGGATCGG 60.525 63.158 15.66 3.93 46.37 4.18
916 3147 1.186200 CTCTCTCCAATCCGACACCA 58.814 55.000 0.00 0.00 0.00 4.17
927 3158 2.366167 CCTCCCCTGCTCTCTCCA 59.634 66.667 0.00 0.00 0.00 3.86
1029 3260 3.949754 TGAAGATGCTGCTTTTCCCTATG 59.050 43.478 0.00 0.00 0.00 2.23
1081 4340 2.203126 GAAGCTCCTCCCATGCGG 60.203 66.667 0.00 0.00 0.00 5.69
1086 4345 0.321671 CAACTTCGAAGCTCCTCCCA 59.678 55.000 24.86 0.00 0.00 4.37
1103 4362 3.393089 GAGAGAAGCTCACCTTGACAA 57.607 47.619 0.00 0.00 43.38 3.18
1174 4433 8.318412 TGCCAATAAGACTATACTCACTTTCAA 58.682 33.333 0.00 0.00 0.00 2.69
1194 4453 5.129815 ACAAATAGGAGATGCAATTGCCAAT 59.870 36.000 26.94 15.12 41.18 3.16
1210 4469 7.784633 TGGAAAAAGCAAAGAAACAAATAGG 57.215 32.000 0.00 0.00 0.00 2.57
1217 4476 6.925610 AGGAAATGGAAAAAGCAAAGAAAC 57.074 33.333 0.00 0.00 0.00 2.78
1425 5321 0.473755 TCAGCCTTCAACTCCTTGCA 59.526 50.000 0.00 0.00 0.00 4.08
1536 5477 7.404671 AAGTTTAAACATTAGCGATGGGAAT 57.595 32.000 20.06 0.00 40.21 3.01
1537 5478 6.827586 AAGTTTAAACATTAGCGATGGGAA 57.172 33.333 20.06 0.00 40.21 3.97
1582 5524 2.862536 CTCAGATCTGCACACGTAATGG 59.137 50.000 18.36 0.00 0.00 3.16
1754 5920 7.331440 AGCAAAATAATCAATCGTGCATTCAAA 59.669 29.630 0.00 0.00 32.31 2.69
1900 6086 9.744468 CAAACATAAGCTTTTAAACTGGTAGTT 57.256 29.630 3.20 0.00 40.80 2.24
2098 6610 9.613428 CATAGTAGGTCCTACAAAAATCATGAA 57.387 33.333 27.35 2.45 39.22 2.57
2101 6613 9.784531 CATCATAGTAGGTCCTACAAAAATCAT 57.215 33.333 27.35 9.56 39.22 2.45
2356 6896 6.158598 TGAATTTAGCTTTCAGTTGGCATTC 58.841 36.000 0.00 0.00 0.00 2.67
2442 8256 9.149225 CAACCTAGCAAACAAATATTTATTGCA 57.851 29.630 31.60 22.84 41.11 4.08
2528 8342 0.469494 TCAGCCTGAGCAAACACTCA 59.531 50.000 0.00 0.00 44.32 3.41
2610 11585 6.402222 GGTGATTAATAGGCTGGATAGAGTG 58.598 44.000 0.00 0.00 0.00 3.51
2866 11871 5.585390 AGCTGCAAATAAGCATGAACATAC 58.415 37.500 1.02 0.00 44.68 2.39
2889 11894 3.517296 TCAGCCCAAAATCACTACCAA 57.483 42.857 0.00 0.00 0.00 3.67
2892 11897 5.904362 ATCTTTCAGCCCAAAATCACTAC 57.096 39.130 0.00 0.00 0.00 2.73
2932 11937 7.400052 AGCCATGTCAATAAGGACCTTTAAAAT 59.600 33.333 13.11 0.00 36.97 1.82
3075 12082 7.471721 TCAACAAAGATTGCCAATTCTATACG 58.528 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.