Multiple sequence alignment - TraesCS7B01G493300

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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 TraesCS7B01G493300 chr7B 100.000 2399 0 0 688 3086 744892407 744894805 0.000000e+00 4431.0
1 TraesCS7B01G493300 chr7B 95.098 1224 55 3 884 2106 749066823 749065604 0.000000e+00 1923.0
2 TraesCS7B01G493300 chr7B 94.733 1234 61 2 879 2108 746970228 746971461 0.000000e+00 1916.0
3 TraesCS7B01G493300 chr7B 100.000 473 0 0 1 473 744891720 744892192 0.000000e+00 874.0
4 TraesCS7B01G493300 chr7B 96.875 32 1 0 1803 1834 747363510 747363541 2.000000e-03 54.7
5 TraesCS7B01G493300 chr7A 92.651 2218 139 13 885 3086 734637376 734639585 0.000000e+00 3171.0
6 TraesCS7B01G493300 chr7A 88.468 633 48 12 2116 2738 164634058 164634675 0.000000e+00 741.0
7 TraesCS7B01G493300 chr7A 87.874 635 50 11 2114 2738 707808645 707809262 0.000000e+00 721.0
8 TraesCS7B01G493300 chr7A 88.654 520 45 9 2114 2629 710494662 710494153 3.380000e-174 621.0
9 TraesCS7B01G493300 chr7A 87.119 427 49 6 45 468 174272012 174272435 2.150000e-131 479.0
10 TraesCS7B01G493300 chr7D 92.900 1000 45 16 694 1692 632838237 632839211 0.000000e+00 1430.0
11 TraesCS7B01G493300 chr7D 86.543 431 53 4 45 472 238938996 238938568 1.300000e-128 470.0
12 TraesCS7B01G493300 chr7D 87.345 403 49 2 50 452 632837582 632837982 7.800000e-126 460.0
13 TraesCS7B01G493300 chr7D 86.588 425 45 9 50 468 635087436 635087854 2.800000e-125 459.0
14 TraesCS7B01G493300 chr5D 94.268 628 30 6 2114 2738 398637550 398636926 0.000000e+00 955.0
15 TraesCS7B01G493300 chr5D 94.524 347 19 0 2740 3086 97248617 97248963 1.260000e-148 536.0
16 TraesCS7B01G493300 chr5D 93.103 348 23 1 2740 3086 208186034 208185687 2.750000e-140 508.0
17 TraesCS7B01G493300 chr5D 86.374 433 55 4 45 473 391292581 391293013 1.300000e-128 470.0
18 TraesCS7B01G493300 chr5B 88.697 637 54 8 2114 2738 705964300 705963670 0.000000e+00 761.0
19 TraesCS7B01G493300 chr3D 93.660 347 22 0 2740 3086 588324651 588324305 1.270000e-143 520.0
20 TraesCS7B01G493300 chr3D 93.084 347 24 0 2740 3086 599499929 599500275 2.750000e-140 508.0
21 TraesCS7B01G493300 chr3D 86.512 430 50 4 45 473 103673983 103673561 1.680000e-127 466.0
22 TraesCS7B01G493300 chr6D 93.275 342 23 0 2745 3086 91177846 91177505 3.550000e-139 505.0
23 TraesCS7B01G493300 chr4D 92.795 347 25 0 2740 3086 77132575 77132229 1.280000e-138 503.0
24 TraesCS7B01G493300 chr4D 77.888 303 35 20 2108 2392 338549120 338549408 3.190000e-35 159.0
25 TraesCS7B01G493300 chr3A 93.023 344 24 0 2740 3083 647340421 647340764 1.280000e-138 503.0
26 TraesCS7B01G493300 chr1D 93.064 346 21 3 2740 3084 360373751 360374094 1.280000e-138 503.0
27 TraesCS7B01G493300 chr1D 85.349 430 61 2 45 472 216045268 216044839 7.850000e-121 444.0
28 TraesCS7B01G493300 chr3B 88.000 425 50 1 50 473 772706862 772706438 4.590000e-138 501.0
29 TraesCS7B01G493300 chr1A 85.480 427 57 5 51 473 494310197 494309772 1.020000e-119 440.0
30 TraesCS7B01G493300 chr6A 94.982 279 12 2 2462 2738 52465090 52465368 1.310000e-118 436.0
31 TraesCS7B01G493300 chr6A 94.286 210 11 1 2255 2464 52407113 52407321 1.380000e-83 320.0
32 TraesCS7B01G493300 chr6A 89.855 138 13 1 2108 2245 52406859 52406995 3.160000e-40 176.0
33 TraesCS7B01G493300 chr1B 79.814 431 63 15 2108 2524 540368298 540368718 3.010000e-75 292.0
34 TraesCS7B01G493300 chr2D 90.355 197 12 4 2518 2712 12938411 12938602 5.110000e-63 252.0
35 TraesCS7B01G493300 chr6B 77.151 337 64 10 53 380 64778591 64778259 1.890000e-42 183.0
36 TraesCS7B01G493300 chr4A 78.099 242 38 13 2159 2393 713990909 713991142 4.150000e-29 139.0


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 TraesCS7B01G493300 chr7B 744891720 744894805 3085 False 2652.5 4431 100.0000 1 3086 2 chr7B.!!$F3 3085
1 TraesCS7B01G493300 chr7B 749065604 749066823 1219 True 1923.0 1923 95.0980 884 2106 1 chr7B.!!$R1 1222
2 TraesCS7B01G493300 chr7B 746970228 746971461 1233 False 1916.0 1916 94.7330 879 2108 1 chr7B.!!$F1 1229
3 TraesCS7B01G493300 chr7A 734637376 734639585 2209 False 3171.0 3171 92.6510 885 3086 1 chr7A.!!$F4 2201
4 TraesCS7B01G493300 chr7A 164634058 164634675 617 False 741.0 741 88.4680 2116 2738 1 chr7A.!!$F1 622
5 TraesCS7B01G493300 chr7A 707808645 707809262 617 False 721.0 721 87.8740 2114 2738 1 chr7A.!!$F3 624
6 TraesCS7B01G493300 chr7A 710494153 710494662 509 True 621.0 621 88.6540 2114 2629 1 chr7A.!!$R1 515
7 TraesCS7B01G493300 chr7D 632837582 632839211 1629 False 945.0 1430 90.1225 50 1692 2 chr7D.!!$F2 1642
8 TraesCS7B01G493300 chr5D 398636926 398637550 624 True 955.0 955 94.2680 2114 2738 1 chr5D.!!$R2 624
9 TraesCS7B01G493300 chr5B 705963670 705964300 630 True 761.0 761 88.6970 2114 2738 1 chr5B.!!$R1 624

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
465 466 0.036164 GGCCCAAACATGGTTTTCCC 59.964 55.0 0.0 0.0 39.73 3.97 F
777 791 0.037232 GCAGAGTCCGGCTACAAGTT 60.037 55.0 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1933 0.249238 GAGCCAGCTCCATCGTAGTG 60.249 60.0 8.51 0.0 37.11 2.74 R
2773 2839 1.659262 CGTCGTCGCGTACCTCAAAC 61.659 60.0 5.77 0.0 0.00 2.93 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
19 20 1.683943 GCATGCAATAGCCTTCCAGA 58.316 50.000 14.21 0.00 41.13 3.86
20 21 1.336125 GCATGCAATAGCCTTCCAGAC 59.664 52.381 14.21 0.00 41.13 3.51
21 22 1.600957 CATGCAATAGCCTTCCAGACG 59.399 52.381 0.00 0.00 41.13 4.18
22 23 0.901827 TGCAATAGCCTTCCAGACGA 59.098 50.000 0.00 0.00 41.13 4.20
23 24 1.486310 TGCAATAGCCTTCCAGACGAT 59.514 47.619 0.00 0.00 41.13 3.73
24 25 1.869767 GCAATAGCCTTCCAGACGATG 59.130 52.381 0.00 0.00 33.58 3.84
25 26 2.483714 GCAATAGCCTTCCAGACGATGA 60.484 50.000 0.00 0.00 33.58 2.92
26 27 3.805108 GCAATAGCCTTCCAGACGATGAT 60.805 47.826 0.00 0.00 33.58 2.45
27 28 3.674528 ATAGCCTTCCAGACGATGATG 57.325 47.619 0.00 0.00 0.00 3.07
28 29 0.467384 AGCCTTCCAGACGATGATGG 59.533 55.000 0.00 0.00 37.97 3.51
29 30 0.179000 GCCTTCCAGACGATGATGGT 59.821 55.000 0.00 0.00 37.84 3.55
30 31 1.407437 GCCTTCCAGACGATGATGGTT 60.407 52.381 0.00 0.00 37.84 3.67
31 32 2.555199 CCTTCCAGACGATGATGGTTC 58.445 52.381 0.00 0.00 37.84 3.62
32 33 2.169352 CCTTCCAGACGATGATGGTTCT 59.831 50.000 0.00 0.00 37.84 3.01
33 34 3.452474 CTTCCAGACGATGATGGTTCTC 58.548 50.000 0.00 0.00 37.84 2.87
34 35 2.739943 TCCAGACGATGATGGTTCTCT 58.260 47.619 0.00 0.00 37.84 3.10
35 36 2.428530 TCCAGACGATGATGGTTCTCTG 59.571 50.000 0.00 0.00 37.84 3.35
36 37 2.200067 CAGACGATGATGGTTCTCTGC 58.800 52.381 0.00 0.00 0.00 4.26
37 38 2.106566 AGACGATGATGGTTCTCTGCT 58.893 47.619 0.00 0.00 0.00 4.24
38 39 2.499289 AGACGATGATGGTTCTCTGCTT 59.501 45.455 0.00 0.00 0.00 3.91
39 40 3.055530 AGACGATGATGGTTCTCTGCTTT 60.056 43.478 0.00 0.00 0.00 3.51
40 41 3.265791 ACGATGATGGTTCTCTGCTTTC 58.734 45.455 0.00 0.00 0.00 2.62
41 42 3.264947 CGATGATGGTTCTCTGCTTTCA 58.735 45.455 0.00 0.00 0.00 2.69
42 43 3.309138 CGATGATGGTTCTCTGCTTTCAG 59.691 47.826 0.00 0.00 41.67 3.02
43 44 2.430465 TGATGGTTCTCTGCTTTCAGC 58.570 47.619 0.00 0.00 42.82 4.26
44 45 1.742268 GATGGTTCTCTGCTTTCAGCC 59.258 52.381 0.00 0.00 41.51 4.85
45 46 0.603707 TGGTTCTCTGCTTTCAGCCG 60.604 55.000 0.00 0.00 41.51 5.52
46 47 1.499502 GTTCTCTGCTTTCAGCCGC 59.500 57.895 0.00 0.00 41.51 6.53
47 48 1.672356 TTCTCTGCTTTCAGCCGCC 60.672 57.895 0.00 0.00 41.51 6.13
48 49 2.046507 CTCTGCTTTCAGCCGCCT 60.047 61.111 0.00 0.00 41.51 5.52
98 99 4.489771 GGGCGGTGAGGACCATGG 62.490 72.222 11.19 11.19 43.33 3.66
105 106 0.257039 GTGAGGACCATGGGATGCTT 59.743 55.000 18.09 0.00 0.00 3.91
168 169 4.838486 GAGCGCCTCCTCGTCGTG 62.838 72.222 2.29 0.00 0.00 4.35
187 188 2.279120 GAGTCCATCGCCGAGCAG 60.279 66.667 0.00 0.00 0.00 4.24
190 191 3.068064 TCCATCGCCGAGCAGACA 61.068 61.111 0.00 0.00 0.00 3.41
196 197 2.094659 CGCCGAGCAGACAAATCGT 61.095 57.895 0.00 0.00 34.71 3.73
208 209 1.134220 ACAAATCGTCACACACCTGGT 60.134 47.619 0.00 0.00 0.00 4.00
222 223 3.610619 CTGGTGAGCGTGATGGGCA 62.611 63.158 0.00 0.00 0.00 5.36
274 275 1.578206 GAGCACTGGAAAACTCGCCC 61.578 60.000 0.00 0.00 0.00 6.13
276 277 1.452145 GCACTGGAAAACTCGCCCAA 61.452 55.000 0.00 0.00 0.00 4.12
282 283 1.605753 GAAAACTCGCCCAAGAAGGT 58.394 50.000 0.00 0.00 34.66 3.50
284 285 0.537371 AAACTCGCCCAAGAAGGTGG 60.537 55.000 0.00 0.00 38.02 4.61
292 293 1.352083 CCAAGAAGGTGGTGGAGAGA 58.648 55.000 0.00 0.00 34.05 3.10
296 297 2.625639 AGAAGGTGGTGGAGAGATTGT 58.374 47.619 0.00 0.00 0.00 2.71
301 302 1.215647 GGTGGAGAGATTGTCGCGT 59.784 57.895 5.77 0.00 0.00 6.01
302 303 1.078759 GGTGGAGAGATTGTCGCGTG 61.079 60.000 5.77 0.00 0.00 5.34
321 322 1.822506 GGAAACCCCTCTCTTTTCCG 58.177 55.000 0.00 0.00 39.10 4.30
343 344 1.202582 CGGGGAATGACCTATCTAGCG 59.797 57.143 0.00 0.00 38.98 4.26
346 347 2.028930 GGGAATGACCTATCTAGCGGTG 60.029 54.545 0.00 0.00 38.98 4.94
349 350 1.399714 TGACCTATCTAGCGGTGGTG 58.600 55.000 0.00 0.00 32.62 4.17
382 383 2.825836 CTGGATCGGCAAGGTGGC 60.826 66.667 0.00 0.00 39.85 5.01
416 417 4.115199 GTGGGGGCGAATCTGGCT 62.115 66.667 0.00 0.00 34.31 4.75
423 424 0.598065 GGCGAATCTGGCTGTTTGTT 59.402 50.000 0.00 0.00 0.00 2.83
440 441 3.414549 TGTTTTGACTTTTCGCCTGAC 57.585 42.857 0.00 0.00 0.00 3.51
452 453 2.515398 CCTGACAGTGTGGCCCAA 59.485 61.111 0.00 0.00 0.00 4.12
453 454 1.152777 CCTGACAGTGTGGCCCAAA 60.153 57.895 0.00 0.00 0.00 3.28
454 455 1.455383 CCTGACAGTGTGGCCCAAAC 61.455 60.000 0.00 0.00 0.00 2.93
455 456 0.751277 CTGACAGTGTGGCCCAAACA 60.751 55.000 6.86 0.00 0.00 2.83
456 457 0.106268 TGACAGTGTGGCCCAAACAT 60.106 50.000 6.86 0.00 0.00 2.71
457 458 0.314935 GACAGTGTGGCCCAAACATG 59.685 55.000 6.86 4.52 0.00 3.21
458 459 1.114722 ACAGTGTGGCCCAAACATGG 61.115 55.000 6.86 0.00 0.00 3.66
459 460 1.114722 CAGTGTGGCCCAAACATGGT 61.115 55.000 6.86 0.00 0.00 3.55
460 461 0.398381 AGTGTGGCCCAAACATGGTT 60.398 50.000 6.86 0.00 0.00 3.67
461 462 0.467804 GTGTGGCCCAAACATGGTTT 59.532 50.000 0.00 0.00 0.00 3.27
462 463 1.134250 GTGTGGCCCAAACATGGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
463 464 1.139853 TGTGGCCCAAACATGGTTTTC 59.860 47.619 0.00 0.00 0.00 2.29
464 465 0.761802 TGGCCCAAACATGGTTTTCC 59.238 50.000 0.00 0.00 41.14 3.13
465 466 0.036164 GGCCCAAACATGGTTTTCCC 59.964 55.000 0.00 0.00 39.73 3.97
466 467 1.055849 GCCCAAACATGGTTTTCCCT 58.944 50.000 0.00 0.00 39.73 4.20
467 468 1.419762 GCCCAAACATGGTTTTCCCTT 59.580 47.619 0.00 0.00 39.73 3.95
468 469 2.635427 GCCCAAACATGGTTTTCCCTTA 59.365 45.455 0.00 0.00 39.73 2.69
469 470 3.556213 GCCCAAACATGGTTTTCCCTTAC 60.556 47.826 0.00 0.00 39.73 2.34
470 471 3.305744 CCCAAACATGGTTTTCCCTTACG 60.306 47.826 0.00 0.00 39.73 3.18
471 472 3.313690 CAAACATGGTTTTCCCTTACGC 58.686 45.455 0.00 0.00 39.73 4.42
472 473 1.541379 ACATGGTTTTCCCTTACGCC 58.459 50.000 0.00 0.00 39.73 5.68
751 765 0.527817 CGCGGCGGAAGATACTCTTT 60.528 55.000 15.84 0.00 36.73 2.52
759 773 3.799420 CGGAAGATACTCTTTGCTGTAGC 59.201 47.826 0.00 0.00 36.73 3.58
777 791 0.037232 GCAGAGTCCGGCTACAAGTT 60.037 55.000 0.00 0.00 0.00 2.66
781 795 3.018149 AGAGTCCGGCTACAAGTTCTAG 58.982 50.000 0.00 0.00 0.00 2.43
807 821 5.181056 TGTTAGAACATTCCGTGTACGTAGA 59.819 40.000 0.00 0.00 41.14 2.59
825 839 5.184096 ACGTAGAGAGGCCATACATATTCAG 59.816 44.000 5.01 0.00 0.00 3.02
837 851 6.712095 CCATACATATTCAGCCAACTATGTGT 59.288 38.462 8.39 0.00 35.98 3.72
846 860 3.133003 AGCCAACTATGTGTCGATAAGCT 59.867 43.478 0.00 0.00 0.00 3.74
854 868 7.640852 ACTATGTGTCGATAAGCTTGTACTAG 58.359 38.462 9.86 0.00 0.00 2.57
855 869 6.694877 ATGTGTCGATAAGCTTGTACTAGA 57.305 37.500 9.86 0.00 0.00 2.43
856 870 6.120378 TGTGTCGATAAGCTTGTACTAGAG 57.880 41.667 9.86 0.00 0.00 2.43
857 871 5.878669 TGTGTCGATAAGCTTGTACTAGAGA 59.121 40.000 9.86 0.00 0.00 3.10
858 872 6.037281 TGTGTCGATAAGCTTGTACTAGAGAG 59.963 42.308 9.86 0.00 0.00 3.20
859 873 5.527951 TGTCGATAAGCTTGTACTAGAGAGG 59.472 44.000 9.86 0.00 0.00 3.69
860 874 5.528320 GTCGATAAGCTTGTACTAGAGAGGT 59.472 44.000 9.86 0.00 0.00 3.85
861 875 6.038492 GTCGATAAGCTTGTACTAGAGAGGTT 59.962 42.308 9.86 6.11 34.58 3.50
862 876 6.038382 TCGATAAGCTTGTACTAGAGAGGTTG 59.962 42.308 9.86 0.00 32.69 3.77
863 877 6.183360 CGATAAGCTTGTACTAGAGAGGTTGT 60.183 42.308 9.86 2.50 32.69 3.32
864 878 7.012138 CGATAAGCTTGTACTAGAGAGGTTGTA 59.988 40.741 9.86 0.00 32.69 2.41
865 879 5.900865 AGCTTGTACTAGAGAGGTTGTAC 57.099 43.478 8.60 0.00 36.69 2.90
866 880 5.572252 AGCTTGTACTAGAGAGGTTGTACT 58.428 41.667 8.60 0.00 36.98 2.73
867 881 6.011481 AGCTTGTACTAGAGAGGTTGTACTT 58.989 40.000 8.60 0.00 36.98 2.24
868 882 7.173722 AGCTTGTACTAGAGAGGTTGTACTTA 58.826 38.462 8.60 0.00 36.98 2.24
869 883 7.835181 AGCTTGTACTAGAGAGGTTGTACTTAT 59.165 37.037 8.60 0.00 36.98 1.73
870 884 9.118300 GCTTGTACTAGAGAGGTTGTACTTATA 57.882 37.037 8.60 0.00 36.98 0.98
872 886 8.654230 TGTACTAGAGAGGTTGTACTTATACG 57.346 38.462 0.00 0.00 36.98 3.06
873 887 8.478066 TGTACTAGAGAGGTTGTACTTATACGA 58.522 37.037 0.00 0.00 36.98 3.43
874 888 8.977505 GTACTAGAGAGGTTGTACTTATACGAG 58.022 40.741 0.00 0.00 34.27 4.18
875 889 5.754543 AGAGAGGTTGTACTTATACGAGC 57.245 43.478 0.00 0.00 41.68 5.03
876 890 4.579753 AGAGAGGTTGTACTTATACGAGCC 59.420 45.833 0.00 0.00 42.13 4.70
877 891 3.314635 AGAGGTTGTACTTATACGAGCCG 59.685 47.826 0.00 0.00 42.13 5.52
934 951 1.141053 GGGGTGATGGTAGCCTTGTAG 59.859 57.143 0.00 0.00 38.29 2.74
1357 1388 0.672342 ACCAGCAGACTACGAAACGT 59.328 50.000 1.91 1.91 44.35 3.99
1366 1397 0.801251 CTACGAAACGTCCGGACTCT 59.199 55.000 30.92 15.73 41.54 3.24
1509 1540 1.863662 GCAGTCCGACTCCGACTCAA 61.864 60.000 0.00 0.00 38.22 3.02
1569 1600 2.660064 GGACGAGGTGCCCACTGAT 61.660 63.158 0.00 0.00 0.00 2.90
1662 1693 2.397413 CTGCCTTGTTCACGGGGTCT 62.397 60.000 0.00 0.00 0.00 3.85
1899 1933 1.034838 TCAACACAACCACAGTGGCC 61.035 55.000 20.48 0.00 42.67 5.36
1906 1940 1.404479 AACCACAGTGGCCACTACGA 61.404 55.000 37.27 0.00 42.67 3.43
1935 1969 2.438975 CACCGGCATGGCTGTCAT 60.439 61.111 18.09 0.00 43.94 3.06
1936 1970 1.153188 CACCGGCATGGCTGTCATA 60.153 57.895 18.09 0.00 43.94 2.15
2081 2115 3.256960 GGTTGCTCCCTCACCCCA 61.257 66.667 0.00 0.00 0.00 4.96
2111 2151 9.826574 ACTTCAAACTTAATTATACATAGGCGA 57.173 29.630 0.00 0.00 0.00 5.54
2306 2352 3.807622 AGGTCAATAATTCCACATACGCG 59.192 43.478 3.53 3.53 0.00 6.01
2507 2556 7.822334 TGTGTTGTCAAATTACATACCTAGAGG 59.178 37.037 0.00 0.00 42.17 3.69
2576 2634 2.186826 GCTGGTTGTCGTTGGCAGT 61.187 57.895 0.00 0.00 0.00 4.40
2578 2636 0.813610 CTGGTTGTCGTTGGCAGTCA 60.814 55.000 0.00 0.00 0.00 3.41
2594 2652 3.308866 GCAGTCACGTAATAACCATCACC 59.691 47.826 0.00 0.00 0.00 4.02
2673 2733 1.054406 TGGGTGCCTATGACCTAGCC 61.054 60.000 0.00 0.00 33.58 3.93
2764 2830 2.011947 CTTCAGCTTCATCATTCGGCA 58.988 47.619 0.00 0.00 0.00 5.69
2773 2839 1.938577 CATCATTCGGCACTCCTCAAG 59.061 52.381 0.00 0.00 0.00 3.02
2777 2843 1.593196 TTCGGCACTCCTCAAGTTTG 58.407 50.000 0.00 0.00 35.45 2.93
2810 2876 3.741476 CGCTGGAAAGTGGGCTGC 61.741 66.667 0.00 0.00 0.00 5.25
2872 2938 3.892104 TAAGACCGGCGGTGAGGGT 62.892 63.158 39.41 18.17 35.25 4.34
2878 2944 4.101448 GGCGGTGAGGGTGCTCAT 62.101 66.667 0.00 0.00 35.65 2.90
2890 2956 1.406069 GGTGCTCATCATGAGGTCGTT 60.406 52.381 16.70 0.00 44.43 3.85
2938 3004 2.226896 CGTCGGCGAGCATCTTGAG 61.227 63.158 11.20 0.00 41.33 3.02
2970 3036 0.243907 CTCGTCGATGGTGGAGTTGT 59.756 55.000 4.48 0.00 0.00 3.32
2993 3059 1.509703 GGTGACAACCGAAGAACTCC 58.490 55.000 0.00 0.00 36.51 3.85
2997 3063 0.250338 ACAACCGAAGAACTCCTGCC 60.250 55.000 0.00 0.00 0.00 4.85
3016 3082 1.372128 GCAAGGAAACAAGGCGCTG 60.372 57.895 7.64 0.00 0.00 5.18
3030 3096 1.262166 GCGCTGAAGTTTGTTGTCGC 61.262 55.000 0.00 0.00 34.61 5.19
3047 3113 1.346538 GCTGAAGAGCGCGTTGATC 59.653 57.895 8.43 2.55 34.87 2.92
3060 3126 0.251341 GTTGATCTTGGCCCACAGGT 60.251 55.000 0.00 0.00 34.57 4.00
3061 3127 0.482446 TTGATCTTGGCCCACAGGTT 59.518 50.000 0.00 0.00 34.57 3.50
3062 3128 1.367346 TGATCTTGGCCCACAGGTTA 58.633 50.000 0.00 0.00 34.57 2.85
3079 3145 0.390124 TTACAGGCGTTGTCGTCCTT 59.610 50.000 0.00 0.00 43.20 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.336125 GTCTGGAAGGCTATTGCATGC 59.664 52.381 11.82 11.82 41.91 4.06
1 2 1.600957 CGTCTGGAAGGCTATTGCATG 59.399 52.381 0.66 0.00 35.43 4.06
2 3 1.486310 TCGTCTGGAAGGCTATTGCAT 59.514 47.619 0.66 0.00 35.43 3.96
3 4 0.901827 TCGTCTGGAAGGCTATTGCA 59.098 50.000 0.66 0.00 35.43 4.08
4 5 1.869767 CATCGTCTGGAAGGCTATTGC 59.130 52.381 0.00 0.00 35.43 3.56
5 6 3.459232 TCATCGTCTGGAAGGCTATTG 57.541 47.619 0.00 0.00 35.43 1.90
6 7 3.244353 CCATCATCGTCTGGAAGGCTATT 60.244 47.826 0.00 0.00 35.43 1.73
7 8 2.301296 CCATCATCGTCTGGAAGGCTAT 59.699 50.000 0.00 0.00 35.43 2.97
8 9 1.688735 CCATCATCGTCTGGAAGGCTA 59.311 52.381 0.00 0.00 35.43 3.93
9 10 0.467384 CCATCATCGTCTGGAAGGCT 59.533 55.000 0.00 0.00 35.43 4.58
10 11 0.179000 ACCATCATCGTCTGGAAGGC 59.821 55.000 0.00 0.00 36.35 4.35
11 12 2.169352 AGAACCATCATCGTCTGGAAGG 59.831 50.000 0.00 0.00 36.35 3.46
12 13 3.131933 AGAGAACCATCATCGTCTGGAAG 59.868 47.826 0.00 0.00 36.35 3.46
13 14 3.099905 AGAGAACCATCATCGTCTGGAA 58.900 45.455 0.00 0.00 36.35 3.53
14 15 2.428530 CAGAGAACCATCATCGTCTGGA 59.571 50.000 0.00 0.00 36.35 3.86
15 16 2.819115 CAGAGAACCATCATCGTCTGG 58.181 52.381 0.00 0.00 38.55 3.86
16 17 2.159128 AGCAGAGAACCATCATCGTCTG 60.159 50.000 0.00 0.00 35.54 3.51
17 18 2.106566 AGCAGAGAACCATCATCGTCT 58.893 47.619 0.00 0.00 0.00 4.18
18 19 2.593346 AGCAGAGAACCATCATCGTC 57.407 50.000 0.00 0.00 0.00 4.20
19 20 3.265791 GAAAGCAGAGAACCATCATCGT 58.734 45.455 0.00 0.00 0.00 3.73
20 21 3.264947 TGAAAGCAGAGAACCATCATCG 58.735 45.455 0.00 0.00 0.00 3.84
21 22 4.879104 CTGAAAGCAGAGAACCATCATC 57.121 45.455 0.00 0.00 45.17 2.92
45 46 2.507769 GCAATGCAAAGCCGAGGC 60.508 61.111 5.89 5.89 42.33 4.70
46 47 1.138247 GAGCAATGCAAAGCCGAGG 59.862 57.895 8.35 0.00 0.00 4.63
47 48 1.226211 CGAGCAATGCAAAGCCGAG 60.226 57.895 8.35 0.00 0.00 4.63
48 49 2.869646 CGAGCAATGCAAAGCCGA 59.130 55.556 8.35 0.00 0.00 5.54
98 99 1.087501 GTCCAGGACGAAAAGCATCC 58.912 55.000 3.05 0.00 0.00 3.51
179 180 1.710339 GACGATTTGTCTGCTCGGC 59.290 57.895 0.00 0.00 44.58 5.54
187 188 5.133678 CACCAGGTGTGTGACGATTTGTC 62.134 52.174 11.99 0.00 41.16 3.18
190 191 1.140052 TCACCAGGTGTGTGACGATTT 59.860 47.619 19.65 0.00 45.61 2.17
196 197 2.421314 CGCTCACCAGGTGTGTGA 59.579 61.111 25.02 4.08 45.61 3.58
199 200 1.004560 ATCACGCTCACCAGGTGTG 60.005 57.895 19.65 17.83 46.88 3.82
248 249 4.704833 TTCCAGTGCTCCTGCCGC 62.705 66.667 0.00 0.00 40.06 6.53
253 254 0.603975 GCGAGTTTTCCAGTGCTCCT 60.604 55.000 0.00 0.00 0.00 3.69
259 260 0.472471 TCTTGGGCGAGTTTTCCAGT 59.528 50.000 0.00 0.00 31.59 4.00
261 262 1.604604 CTTCTTGGGCGAGTTTTCCA 58.395 50.000 0.00 0.00 0.00 3.53
265 266 0.537371 CCACCTTCTTGGGCGAGTTT 60.537 55.000 0.00 0.00 41.11 2.66
274 275 3.244700 ACAATCTCTCCACCACCTTCTTG 60.245 47.826 0.00 0.00 0.00 3.02
276 277 2.569404 GACAATCTCTCCACCACCTTCT 59.431 50.000 0.00 0.00 0.00 2.85
282 283 1.215382 CGCGACAATCTCTCCACCA 59.785 57.895 0.00 0.00 0.00 4.17
284 285 1.078759 CCACGCGACAATCTCTCCAC 61.079 60.000 15.93 0.00 0.00 4.02
292 293 1.969589 GGGGTTTCCACGCGACAAT 60.970 57.895 15.93 0.00 36.70 2.71
296 297 2.920912 AGAGGGGTTTCCACGCGA 60.921 61.111 15.93 0.00 36.70 5.87
301 302 2.971901 GGAAAAGAGAGGGGTTTCCA 57.028 50.000 9.06 0.00 46.37 3.53
302 303 1.613520 CCGGAAAAGAGAGGGGTTTCC 60.614 57.143 0.00 4.63 44.54 3.13
321 322 1.550976 CTAGATAGGTCATTCCCCGCC 59.449 57.143 0.00 0.00 36.75 6.13
332 333 0.759436 CCCACCACCGCTAGATAGGT 60.759 60.000 0.00 0.00 42.34 3.08
364 365 2.124570 CCACCTTGCCGATCCAGG 60.125 66.667 0.00 0.00 0.00 4.45
366 367 4.776322 CGCCACCTTGCCGATCCA 62.776 66.667 0.00 0.00 0.00 3.41
401 402 3.645268 AACAGCCAGATTCGCCCCC 62.645 63.158 0.00 0.00 0.00 5.40
416 417 3.923461 CAGGCGAAAAGTCAAAACAAACA 59.077 39.130 0.00 0.00 0.00 2.83
423 424 2.354510 CACTGTCAGGCGAAAAGTCAAA 59.645 45.455 4.53 0.00 0.00 2.69
440 441 1.667151 CCATGTTTGGGCCACACTG 59.333 57.895 22.42 16.78 39.56 3.66
452 453 1.890489 GGCGTAAGGGAAAACCATGTT 59.110 47.619 0.00 0.00 43.89 2.71
453 454 1.541379 GGCGTAAGGGAAAACCATGT 58.459 50.000 0.00 0.00 43.89 3.21
690 691 3.624831 GACCTTTTTCGCGCCGACG 62.625 63.158 0.00 0.00 44.07 5.12
692 693 3.408020 CGACCTTTTTCGCGCCGA 61.408 61.111 0.00 0.00 31.03 5.54
759 773 1.546476 AGAACTTGTAGCCGGACTCTG 59.454 52.381 5.05 0.00 0.00 3.35
777 791 6.092955 ACACGGAATGTTCTAACAACTAGA 57.907 37.500 0.00 0.00 43.03 2.43
781 795 4.445385 ACGTACACGGAATGTTCTAACAAC 59.555 41.667 6.72 0.00 43.19 3.32
807 821 2.981784 TGGCTGAATATGTATGGCCTCT 59.018 45.455 3.32 0.00 40.15 3.69
825 839 3.458189 AGCTTATCGACACATAGTTGGC 58.542 45.455 0.00 0.00 32.09 4.52
837 851 5.682659 ACCTCTCTAGTACAAGCTTATCGA 58.317 41.667 0.00 0.00 0.00 3.59
846 860 9.102757 CGTATAAGTACAACCTCTCTAGTACAA 57.897 37.037 0.00 0.00 39.33 2.41
854 868 4.554330 CGGCTCGTATAAGTACAACCTCTC 60.554 50.000 0.00 0.00 0.00 3.20
855 869 3.314635 CGGCTCGTATAAGTACAACCTCT 59.685 47.826 0.00 0.00 0.00 3.69
856 870 3.549625 CCGGCTCGTATAAGTACAACCTC 60.550 52.174 0.00 0.00 0.00 3.85
857 871 2.360165 CCGGCTCGTATAAGTACAACCT 59.640 50.000 0.00 0.00 0.00 3.50
858 872 2.358898 TCCGGCTCGTATAAGTACAACC 59.641 50.000 0.00 0.00 0.00 3.77
859 873 3.625938 CTCCGGCTCGTATAAGTACAAC 58.374 50.000 0.00 0.00 0.00 3.32
860 874 2.033801 GCTCCGGCTCGTATAAGTACAA 59.966 50.000 0.00 0.00 35.22 2.41
861 875 1.605710 GCTCCGGCTCGTATAAGTACA 59.394 52.381 0.00 0.00 35.22 2.90
862 876 1.068679 GGCTCCGGCTCGTATAAGTAC 60.069 57.143 0.00 0.00 38.73 2.73
863 877 1.242076 GGCTCCGGCTCGTATAAGTA 58.758 55.000 0.00 0.00 38.73 2.24
864 878 1.793134 CGGCTCCGGCTCGTATAAGT 61.793 60.000 0.00 0.00 38.73 2.24
865 879 1.081376 CGGCTCCGGCTCGTATAAG 60.081 63.158 0.00 0.00 38.73 1.73
866 880 3.036577 CGGCTCCGGCTCGTATAA 58.963 61.111 0.00 0.00 38.73 0.98
1074 1105 2.403252 AGATTTTGGTGGCCGAGTAG 57.597 50.000 0.00 0.00 0.00 2.57
1116 1147 3.732212 GGCAAGAAAGTTGGCTGATTTT 58.268 40.909 4.19 0.00 41.17 1.82
1578 1609 2.413765 GTCTCATCGCCGACCTCC 59.586 66.667 0.00 0.00 0.00 4.30
1640 1671 4.389576 CCGTGAACAAGGCAGCGC 62.390 66.667 0.00 0.00 0.00 5.92
1662 1693 1.335132 GGGCGGTGTTCTCCCTCATA 61.335 60.000 0.00 0.00 37.08 2.15
1793 1827 3.501062 CACAAGCAGATGTTGAGTCATGT 59.499 43.478 0.00 0.00 0.00 3.21
1899 1933 0.249238 GAGCCAGCTCCATCGTAGTG 60.249 60.000 8.51 0.00 37.11 2.74
1906 1940 3.790437 CCGGTGAGCCAGCTCCAT 61.790 66.667 16.69 0.00 42.09 3.41
1935 1969 1.809619 GCATGCGTCCTTGAGCGTA 60.810 57.895 0.00 0.00 35.87 4.42
1936 1970 2.225791 TAGCATGCGTCCTTGAGCGT 62.226 55.000 13.01 0.00 35.87 5.07
2111 2151 3.852578 CCCCTATATCTAAACCCTGGCAT 59.147 47.826 0.00 0.00 0.00 4.40
2112 2152 3.256704 CCCCTATATCTAAACCCTGGCA 58.743 50.000 0.00 0.00 0.00 4.92
2306 2352 8.045176 AGTAGTTTGAATATCAACTTCTTGGC 57.955 34.615 0.00 0.00 35.89 4.52
2344 2390 3.382865 TGTTTTGTAGCAAGGCATGTCAA 59.617 39.130 0.00 0.00 0.00 3.18
2451 2497 8.560374 CAACTTTTCCTAAAACAACAACCAAAA 58.440 29.630 0.00 0.00 0.00 2.44
2464 2510 7.338196 TGACAACACAGATCAACTTTTCCTAAA 59.662 33.333 0.00 0.00 0.00 1.85
2474 2522 9.329913 GTATGTAATTTGACAACACAGATCAAC 57.670 33.333 0.00 0.00 32.21 3.18
2507 2556 3.450096 ACGGTGAGGGTCTAGGTTTTATC 59.550 47.826 0.00 0.00 0.00 1.75
2576 2634 2.166870 AGCGGTGATGGTTATTACGTGA 59.833 45.455 0.00 0.00 0.00 4.35
2578 2636 2.973694 AGCGGTGATGGTTATTACGT 57.026 45.000 0.00 0.00 0.00 3.57
2594 2652 2.398554 ACGGCTGCATTGGTAAGCG 61.399 57.895 0.50 0.00 37.83 4.68
2616 2674 1.743772 CGGACCGATCAATGCTTCCTT 60.744 52.381 8.64 0.00 0.00 3.36
2673 2733 2.927477 GTGATTTGTGATGCATTGCCAG 59.073 45.455 6.12 0.00 0.00 4.85
2724 2790 2.492088 AGCAGCGACATCTTGTAGTGTA 59.508 45.455 0.00 0.00 0.00 2.90
2773 2839 1.659262 CGTCGTCGCGTACCTCAAAC 61.659 60.000 5.77 0.00 0.00 2.93
2810 2876 4.335647 AACCTCACCCTGCTGCCG 62.336 66.667 0.00 0.00 0.00 5.69
2872 2938 3.023832 TCTAACGACCTCATGATGAGCA 58.976 45.455 16.81 0.00 42.98 4.26
2890 2956 2.950309 GACATCGGTGCTAAGGTCTCTA 59.050 50.000 0.00 0.00 0.00 2.43
2921 2987 2.520904 GCTCAAGATGCTCGCCGAC 61.521 63.158 0.00 0.00 0.00 4.79
2938 3004 0.867753 CGACGAGTACAGCATGAGGC 60.868 60.000 0.00 0.00 39.69 4.70
2947 3013 1.092348 CTCCACCATCGACGAGTACA 58.908 55.000 3.01 0.00 0.00 2.90
2970 3036 1.124780 TTCTTCGGTTGTCACCAGGA 58.875 50.000 0.00 0.00 44.53 3.86
2981 3047 2.657237 CGGCAGGAGTTCTTCGGT 59.343 61.111 0.00 0.00 0.00 4.69
2993 3059 1.286880 CCTTGTTTCCTTGCGGCAG 59.713 57.895 1.67 0.00 0.00 4.85
3006 3072 1.102978 AACAAACTTCAGCGCCTTGT 58.897 45.000 2.29 1.65 0.00 3.16
3010 3076 0.657368 CGACAACAAACTTCAGCGCC 60.657 55.000 2.29 0.00 0.00 6.53
3012 3078 0.304705 AGCGACAACAAACTTCAGCG 59.695 50.000 0.00 0.00 0.00 5.18
3016 3082 3.846383 GCTCTTCAGCGACAACAAACTTC 60.846 47.826 0.00 0.00 35.39 3.01
3030 3096 1.060266 CAAGATCAACGCGCTCTTCAG 59.940 52.381 5.73 0.00 0.00 3.02
3047 3113 0.609131 CCTGTAACCTGTGGGCCAAG 60.609 60.000 8.40 8.32 35.63 3.61
3060 3126 0.390124 AAGGACGACAACGCCTGTAA 59.610 50.000 0.00 0.00 42.01 2.41
3061 3127 0.319211 CAAGGACGACAACGCCTGTA 60.319 55.000 0.00 0.00 42.01 2.74
3062 3128 1.594293 CAAGGACGACAACGCCTGT 60.594 57.895 0.00 0.00 42.01 4.00


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

AutoCloner maintained by Alex Coulton.