Multiple sequence alignment - TraesCS4B01G194000

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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 TraesCS4B01G194000 chr4B 100.000 3615 0 0 1 3615 417140460 417136846 0.000000e+00 6676.0
1 TraesCS4B01G194000 chr4B 82.011 189 30 4 360 545 124922611 124922798 1.340000e-34 158.0
2 TraesCS4B01G194000 chr4B 76.761 142 26 5 265 399 596644403 596644544 5.010000e-09 73.1
3 TraesCS4B01G194000 chr4D 95.530 2282 81 14 588 2863 337936977 337934711 0.000000e+00 3629.0
4 TraesCS4B01G194000 chr4D 95.208 480 17 4 3024 3499 337934712 337934235 0.000000e+00 754.0
5 TraesCS4B01G194000 chr4D 85.740 561 57 12 1 540 337937915 337937357 4.050000e-159 571.0
6 TraesCS4B01G194000 chr4D 81.413 269 41 7 285 545 88147936 88148203 1.020000e-50 211.0
7 TraesCS4B01G194000 chr4D 100.000 74 0 0 3541 3614 337934049 337933976 1.750000e-28 137.0
8 TraesCS4B01G194000 chr4D 98.667 75 1 0 3541 3615 40619629 40619555 2.260000e-27 134.0
9 TraesCS4B01G194000 chr4D 87.342 79 9 1 457 534 92186392 92186314 4.970000e-14 89.8
10 TraesCS4B01G194000 chr4D 100.000 43 0 0 3498 3540 337934114 337934072 2.990000e-11 80.5
11 TraesCS4B01G194000 chr4A 94.700 2264 95 9 613 2863 134207863 134210114 0.000000e+00 3493.0
12 TraesCS4B01G194000 chr4A 86.392 485 54 8 11 486 134207262 134207743 1.490000e-143 520.0
13 TraesCS4B01G194000 chr4A 94.565 184 8 2 3024 3207 134210113 134210294 2.120000e-72 283.0
14 TraesCS4B01G194000 chr4A 81.919 271 38 8 285 545 501128562 501128831 6.080000e-53 219.0
15 TraesCS4B01G194000 chr4A 78.648 281 52 7 272 545 4248257 4247978 2.870000e-41 180.0
16 TraesCS4B01G194000 chr4A 76.655 287 59 5 265 545 4479037 4478753 6.250000e-33 152.0
17 TraesCS4B01G194000 chr6A 91.729 266 15 6 3239 3499 13606013 13606276 2.650000e-96 363.0
18 TraesCS4B01G194000 chr6A 91.353 266 16 6 3239 3499 473741367 473741630 1.230000e-94 357.0
19 TraesCS4B01G194000 chr6A 96.000 75 3 0 3541 3615 473741817 473741891 4.900000e-24 122.0
20 TraesCS4B01G194000 chr6A 94.667 75 4 0 3541 3615 158468312 158468238 2.280000e-22 117.0
21 TraesCS4B01G194000 chr2A 91.729 266 15 6 3239 3499 712963997 712964260 2.650000e-96 363.0
22 TraesCS4B01G194000 chr2A 98.667 75 1 0 3541 3615 712964447 712964521 2.260000e-27 134.0
23 TraesCS4B01G194000 chr2D 90.977 266 17 6 3239 3499 584247659 584247922 5.740000e-93 351.0
24 TraesCS4B01G194000 chr2D 83.448 145 18 5 275 414 201953679 201953536 2.930000e-26 130.0
25 TraesCS4B01G194000 chr7D 90.602 266 18 6 3239 3499 9041912 9042175 2.670000e-91 346.0
26 TraesCS4B01G194000 chr7D 98.667 75 1 0 3541 3615 9042362 9042436 2.260000e-27 134.0
27 TraesCS4B01G194000 chr2B 90.875 263 17 6 3242 3499 733043712 733043452 2.670000e-91 346.0
28 TraesCS4B01G194000 chr2B 80.500 200 38 1 347 545 47370577 47370776 6.250000e-33 152.0
29 TraesCS4B01G194000 chr2B 97.333 75 2 0 3541 3615 733043265 733043191 1.050000e-25 128.0
30 TraesCS4B01G194000 chr5D 90.494 263 18 6 3242 3499 198230771 198230511 1.240000e-89 340.0
31 TraesCS4B01G194000 chr5D 98.667 75 1 0 3541 3615 198230324 198230250 2.260000e-27 134.0
32 TraesCS4B01G194000 chr1A 88.593 263 21 6 3244 3499 412554703 412554963 9.750000e-81 311.0
33 TraesCS4B01G194000 chr1A 96.000 75 3 0 3541 3615 412568974 412569048 4.900000e-24 122.0
34 TraesCS4B01G194000 chr1B 98.171 164 3 0 2862 3025 388400185 388400022 1.640000e-73 287.0
35 TraesCS4B01G194000 chr1B 96.364 165 6 0 2862 3026 453193410 453193246 4.600000e-69 272.0
36 TraesCS4B01G194000 chr1B 77.723 404 56 17 158 528 288401356 288400954 2.190000e-52 217.0
37 TraesCS4B01G194000 chr7B 97.576 165 4 0 2861 3025 460772593 460772429 2.120000e-72 283.0
38 TraesCS4B01G194000 chr3D 96.491 171 5 1 2857 3027 566545866 566546035 7.640000e-72 281.0
39 TraesCS4B01G194000 chr3B 97.006 167 5 0 2860 3026 141926587 141926421 7.640000e-72 281.0
40 TraesCS4B01G194000 chr5B 96.988 166 5 0 2861 3026 257334807 257334972 2.750000e-71 279.0
41 TraesCS4B01G194000 chr5B 95.122 164 8 0 2862 3025 253176087 253175924 3.580000e-65 259.0
42 TraesCS4B01G194000 chr6B 95.322 171 7 1 2855 3025 6040217 6040048 1.650000e-68 270.0
43 TraesCS4B01G194000 chr6B 91.160 181 14 2 2846 3026 29399869 29400047 1.000000e-60 244.0
44 TraesCS4B01G194000 chr7A 97.333 75 2 0 3541 3615 727996919 727996993 1.050000e-25 128.0


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 TraesCS4B01G194000 chr4B 417136846 417140460 3614 True 6676.0 6676 100.000000 1 3615 1 chr4B.!!$R1 3614
1 TraesCS4B01G194000 chr4D 337933976 337937915 3939 True 1034.3 3629 95.295600 1 3614 5 chr4D.!!$R3 3613
2 TraesCS4B01G194000 chr4A 134207262 134210294 3032 False 1432.0 3493 91.885667 11 3207 3 chr4A.!!$F2 3196
3 TraesCS4B01G194000 chr6A 473741367 473741891 524 False 239.5 357 93.676500 3239 3615 2 chr6A.!!$F2 376
4 TraesCS4B01G194000 chr2A 712963997 712964521 524 False 248.5 363 95.198000 3239 3615 2 chr2A.!!$F1 376
5 TraesCS4B01G194000 chr7D 9041912 9042436 524 False 240.0 346 94.634500 3239 3615 2 chr7D.!!$F1 376
6 TraesCS4B01G194000 chr2B 733043191 733043712 521 True 237.0 346 94.104000 3242 3615 2 chr2B.!!$R1 373
7 TraesCS4B01G194000 chr5D 198230250 198230771 521 True 237.0 340 94.580500 3242 3615 2 chr5D.!!$R1 373

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
222 233 1.691219 GCCCAATCTTCCACCCTCA 59.309 57.895 0.0 0.0 0.00 3.86 F
584 630 2.034842 GTGACAACGCACGAGCATATAC 60.035 50.000 5.5 0.0 42.27 1.47 F
1720 2095 0.038744 CCCAAGTTCATGGCAGAGGT 59.961 55.000 0.0 0.0 39.26 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1821 0.170561 TCGAGCGAGCTTACCACTTC 59.829 55.000 0.0 0.0 0.00 3.01 R
2383 2758 0.179018 ACTGTGGGTCAACAAGGAGC 60.179 55.000 0.0 0.0 34.62 4.70 R
3009 3384 1.639628 TCTTCTACTCCCTCCGTTCCT 59.360 52.381 0.0 0.0 0.00 3.36 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
44 45 4.739716 GCCCAATAATTGCACGAGTAAATG 59.260 41.667 0.00 0.00 0.00 2.32
74 75 1.890876 AAACTAGCATGTGCCGACAA 58.109 45.000 0.57 0.00 43.38 3.18
86 87 4.940463 TGTGCCGACAATACTATCTTACC 58.060 43.478 0.00 0.00 0.00 2.85
111 112 7.432252 CCATATATTTCAAAACGGAGAAAGCAC 59.568 37.037 0.00 0.00 37.19 4.40
115 116 3.210227 TCAAAACGGAGAAAGCACATCA 58.790 40.909 0.00 0.00 0.00 3.07
127 128 5.238432 AGAAAGCACATCACGACACATAAAA 59.762 36.000 0.00 0.00 0.00 1.52
190 201 5.798125 TCATCTTTCACTCAGTGTTCTCT 57.202 39.130 4.28 0.00 34.79 3.10
194 205 4.405680 TCTTTCACTCAGTGTTCTCTCCAA 59.594 41.667 4.28 0.00 34.79 3.53
222 233 1.691219 GCCCAATCTTCCACCCTCA 59.309 57.895 0.00 0.00 0.00 3.86
256 270 4.588528 TCTGGTTTTTCATCCCCTTTTGAG 59.411 41.667 0.00 0.00 0.00 3.02
349 367 9.315525 GGTAAAATCCAGTACTAGACATCTTTC 57.684 37.037 0.00 0.00 0.00 2.62
353 371 6.922247 TCCAGTACTAGACATCTTTCGTAG 57.078 41.667 0.00 0.00 0.00 3.51
466 485 6.942005 TCATGGGCACATACCTATTTTATCAG 59.058 38.462 0.00 0.00 34.99 2.90
553 574 8.587952 AGTTTGCACCAATATTTCTAAAACAC 57.412 30.769 0.00 0.00 0.00 3.32
556 577 8.586570 TTGCACCAATATTTCTAAAACACTTG 57.413 30.769 0.00 0.00 0.00 3.16
558 579 6.090763 GCACCAATATTTCTAAAACACTTGCC 59.909 38.462 0.00 0.00 0.00 4.52
584 630 2.034842 GTGACAACGCACGAGCATATAC 60.035 50.000 5.50 0.00 42.27 1.47
588 634 3.181484 ACAACGCACGAGCATATACCTTA 60.181 43.478 5.50 0.00 42.27 2.69
590 636 5.158494 CAACGCACGAGCATATACCTTATA 58.842 41.667 5.50 0.00 42.27 0.98
592 638 6.688637 ACGCACGAGCATATACCTTATATA 57.311 37.500 5.50 0.00 42.27 0.86
643 997 4.406648 TCACAATCCACTACTATGGCAG 57.593 45.455 0.00 0.00 39.85 4.85
678 1032 9.907229 AGTACTATTATTTTCTTCAAGGAAGGG 57.093 33.333 0.00 0.00 39.82 3.95
681 1035 9.467796 ACTATTATTTTCTTCAAGGAAGGGAAG 57.532 33.333 6.17 0.00 39.82 3.46
729 1084 3.177194 TACTTGTGCCAGCGGTGCT 62.177 57.895 9.63 0.00 40.77 4.40
1101 1469 3.812019 CCCGAGTCCGTCTCCGTG 61.812 72.222 0.00 0.00 39.84 4.94
1275 1643 2.501128 CTCATGGTGCCGGTCGAT 59.499 61.111 1.90 0.00 0.00 3.59
1490 1858 4.539870 CTCGATGCATCTTCTCTTCTCTC 58.460 47.826 23.73 0.00 0.00 3.20
1497 1865 5.599242 TGCATCTTCTCTTCTCTCTCATGAT 59.401 40.000 0.00 0.00 0.00 2.45
1568 1940 2.102578 CCGGGATGGAAATTTCTTGCT 58.897 47.619 17.42 0.75 42.00 3.91
1584 1956 9.899226 AATTTCTTGCTGTTTTGTCTAATACTC 57.101 29.630 0.00 0.00 0.00 2.59
1585 1957 7.435068 TTCTTGCTGTTTTGTCTAATACTCC 57.565 36.000 0.00 0.00 0.00 3.85
1586 1958 5.637810 TCTTGCTGTTTTGTCTAATACTCCG 59.362 40.000 0.00 0.00 0.00 4.63
1587 1959 5.142061 TGCTGTTTTGTCTAATACTCCGA 57.858 39.130 0.00 0.00 0.00 4.55
1588 1960 5.543714 TGCTGTTTTGTCTAATACTCCGAA 58.456 37.500 0.00 0.00 0.00 4.30
1589 1961 5.407387 TGCTGTTTTGTCTAATACTCCGAAC 59.593 40.000 0.00 0.00 0.00 3.95
1590 1962 5.638234 GCTGTTTTGTCTAATACTCCGAACT 59.362 40.000 0.00 0.00 0.00 3.01
1624 1999 4.309933 ACTAAACTTTCTCGTTTACCCCG 58.690 43.478 0.00 0.00 38.08 5.73
1638 2013 4.404654 CCCGAACTTTGCAGGCGC 62.405 66.667 0.00 0.00 39.24 6.53
1720 2095 0.038744 CCCAAGTTCATGGCAGAGGT 59.961 55.000 0.00 0.00 39.26 3.85
1805 2180 1.618487 AGACGGACGAAGAGTTCCTT 58.382 50.000 0.00 0.00 37.93 3.36
1979 2354 5.588246 GGATGAGAGGGAAAGAATTGAGAAC 59.412 44.000 0.00 0.00 0.00 3.01
1993 2368 8.840200 AGAATTGAGAACCTGGTAAGTAGATA 57.160 34.615 0.00 0.00 0.00 1.98
2002 2377 7.005709 ACCTGGTAAGTAGATATTGTATGCC 57.994 40.000 0.00 0.00 0.00 4.40
2005 2380 7.039011 CCTGGTAAGTAGATATTGTATGCCTCA 60.039 40.741 0.00 0.00 0.00 3.86
2014 2389 7.934457 AGATATTGTATGCCTCAAATGTGTTC 58.066 34.615 0.00 0.00 0.00 3.18
2057 2432 2.035066 AGTTTGAAGGATGTGCACTTGC 59.965 45.455 19.41 17.15 42.50 4.01
2081 2456 9.344772 TGCTAAATAAACTAGACCTTGTTTCAA 57.655 29.630 11.61 0.00 38.85 2.69
2124 2499 7.762615 TGTAGTTGTATGCAGTTAGTGGATAAC 59.237 37.037 2.87 1.69 40.81 1.89
2211 2586 9.906660 AAATTTGAGTAATCGTGAGCAAAATTA 57.093 25.926 0.00 0.00 0.00 1.40
2383 2758 1.000283 GCTGATCCAGATACCAGGACG 60.000 57.143 0.00 0.00 36.60 4.79
2422 2797 4.627467 CAGTGCGAATTCTTAGTACTTGCT 59.373 41.667 0.00 0.00 29.73 3.91
2512 2887 3.605486 GCAATGACAAAACTTCTCGCATC 59.395 43.478 0.00 0.00 0.00 3.91
2665 3040 2.097142 ACTGTAGGAAGTAGCGCTAACG 59.903 50.000 20.73 10.96 44.07 3.18
2669 3044 0.248949 GGAAGTAGCGCTAACGGAGG 60.249 60.000 20.73 0.00 40.57 4.30
2736 3111 5.982465 TTGCAAGCAAAATTTTAGGTGTC 57.018 34.783 4.79 1.70 32.44 3.67
2765 3140 2.314561 TTTTGCAAGCATTCGACTCG 57.685 45.000 0.00 0.00 0.00 4.18
2771 3146 1.719246 CAAGCATTCGACTCGTTTCGA 59.281 47.619 6.97 6.97 46.12 3.71
2846 3221 4.523168 AATGTAATAAGGCGGGGGTTAA 57.477 40.909 0.00 0.00 0.00 2.01
2863 3238 7.440198 GGGGGTTAATACTCACTTCATACTAC 58.560 42.308 0.00 0.00 0.00 2.73
2864 3239 7.289549 GGGGGTTAATACTCACTTCATACTACT 59.710 40.741 0.00 0.00 0.00 2.57
2865 3240 8.358895 GGGGTTAATACTCACTTCATACTACTC 58.641 40.741 0.00 0.00 0.00 2.59
2866 3241 8.358895 GGGTTAATACTCACTTCATACTACTCC 58.641 40.741 0.00 0.00 0.00 3.85
2867 3242 8.358895 GGTTAATACTCACTTCATACTACTCCC 58.641 40.741 0.00 0.00 0.00 4.30
2868 3243 9.134055 GTTAATACTCACTTCATACTACTCCCT 57.866 37.037 0.00 0.00 0.00 4.20
2869 3244 7.826918 AATACTCACTTCATACTACTCCCTC 57.173 40.000 0.00 0.00 0.00 4.30
2870 3245 4.538738 ACTCACTTCATACTACTCCCTCC 58.461 47.826 0.00 0.00 0.00 4.30
2871 3246 3.552875 TCACTTCATACTACTCCCTCCG 58.447 50.000 0.00 0.00 0.00 4.63
2872 3247 3.053842 TCACTTCATACTACTCCCTCCGT 60.054 47.826 0.00 0.00 0.00 4.69
2873 3248 3.700038 CACTTCATACTACTCCCTCCGTT 59.300 47.826 0.00 0.00 0.00 4.44
2874 3249 3.952967 ACTTCATACTACTCCCTCCGTTC 59.047 47.826 0.00 0.00 0.00 3.95
2875 3250 2.941480 TCATACTACTCCCTCCGTTCC 58.059 52.381 0.00 0.00 0.00 3.62
2876 3251 2.512896 TCATACTACTCCCTCCGTTCCT 59.487 50.000 0.00 0.00 0.00 3.36
2877 3252 3.718434 TCATACTACTCCCTCCGTTCCTA 59.282 47.826 0.00 0.00 0.00 2.94
2878 3253 4.166725 TCATACTACTCCCTCCGTTCCTAA 59.833 45.833 0.00 0.00 0.00 2.69
2879 3254 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2880 3255 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2881 3256 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2882 3257 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2883 3258 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2884 3259 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2885 3260 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2886 3261 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2887 3262 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2888 3263 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2889 3264 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2890 3265 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2891 3266 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2892 3267 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2910 3285 9.996554 TGTCTTTTTAGAGATATCAACAAGTGA 57.003 29.630 5.32 0.00 41.67 3.41
2919 3294 9.190317 AGAGATATCAACAAGTGACTACATACA 57.810 33.333 5.32 0.00 39.72 2.29
2920 3295 9.803315 GAGATATCAACAAGTGACTACATACAA 57.197 33.333 5.32 0.00 39.72 2.41
2923 3298 6.854496 TCAACAAGTGACTACATACAAACC 57.146 37.500 0.00 0.00 0.00 3.27
2924 3299 6.350103 TCAACAAGTGACTACATACAAACCA 58.650 36.000 0.00 0.00 0.00 3.67
2925 3300 6.824196 TCAACAAGTGACTACATACAAACCAA 59.176 34.615 0.00 0.00 0.00 3.67
2926 3301 7.337184 TCAACAAGTGACTACATACAAACCAAA 59.663 33.333 0.00 0.00 0.00 3.28
2927 3302 7.633193 ACAAGTGACTACATACAAACCAAAA 57.367 32.000 0.00 0.00 0.00 2.44
2928 3303 8.232913 ACAAGTGACTACATACAAACCAAAAT 57.767 30.769 0.00 0.00 0.00 1.82
2929 3304 8.134895 ACAAGTGACTACATACAAACCAAAATG 58.865 33.333 0.00 0.00 0.00 2.32
2930 3305 7.214467 AGTGACTACATACAAACCAAAATGG 57.786 36.000 0.00 0.00 45.02 3.16
2948 3323 9.757227 CCAAAATGGTTGAATCTACAGTTTAAA 57.243 29.630 0.00 0.00 31.09 1.52
2982 3357 7.490962 CATACATCCGTATGTTGTAACCATT 57.509 36.000 0.00 0.00 46.70 3.16
2983 3358 7.925993 CATACATCCGTATGTTGTAACCATTT 58.074 34.615 0.00 0.00 46.70 2.32
2984 3359 6.189677 ACATCCGTATGTTGTAACCATTTG 57.810 37.500 0.00 0.00 44.07 2.32
2985 3360 5.941058 ACATCCGTATGTTGTAACCATTTGA 59.059 36.000 0.00 0.00 44.07 2.69
2986 3361 6.431543 ACATCCGTATGTTGTAACCATTTGAA 59.568 34.615 0.00 0.00 44.07 2.69
2987 3362 6.879276 TCCGTATGTTGTAACCATTTGAAA 57.121 33.333 0.00 0.00 0.00 2.69
2988 3363 7.455641 TCCGTATGTTGTAACCATTTGAAAT 57.544 32.000 0.00 0.00 0.00 2.17
2989 3364 7.309177 TCCGTATGTTGTAACCATTTGAAATG 58.691 34.615 10.84 10.84 0.00 2.32
2990 3365 6.034470 CCGTATGTTGTAACCATTTGAAATGC 59.966 38.462 12.26 0.00 0.00 3.56
2991 3366 6.034470 CGTATGTTGTAACCATTTGAAATGCC 59.966 38.462 12.26 1.21 0.00 4.40
2992 3367 5.543507 TGTTGTAACCATTTGAAATGCCT 57.456 34.783 12.26 4.13 0.00 4.75
2993 3368 6.656632 TGTTGTAACCATTTGAAATGCCTA 57.343 33.333 12.26 3.23 0.00 3.93
2994 3369 6.686630 TGTTGTAACCATTTGAAATGCCTAG 58.313 36.000 12.26 1.78 0.00 3.02
2995 3370 6.491745 TGTTGTAACCATTTGAAATGCCTAGA 59.508 34.615 12.26 2.09 0.00 2.43
2996 3371 7.014711 TGTTGTAACCATTTGAAATGCCTAGAA 59.985 33.333 12.26 7.45 0.00 2.10
2997 3372 7.531857 TGTAACCATTTGAAATGCCTAGAAA 57.468 32.000 12.26 0.00 0.00 2.52
2998 3373 7.601856 TGTAACCATTTGAAATGCCTAGAAAG 58.398 34.615 12.26 0.00 0.00 2.62
2999 3374 6.916360 AACCATTTGAAATGCCTAGAAAGA 57.084 33.333 12.26 0.00 0.00 2.52
3000 3375 6.272822 ACCATTTGAAATGCCTAGAAAGAC 57.727 37.500 12.26 0.00 0.00 3.01
3001 3376 5.774690 ACCATTTGAAATGCCTAGAAAGACA 59.225 36.000 12.26 0.00 0.00 3.41
3002 3377 6.267471 ACCATTTGAAATGCCTAGAAAGACAA 59.733 34.615 12.26 0.00 0.00 3.18
3003 3378 7.153985 CCATTTGAAATGCCTAGAAAGACAAA 58.846 34.615 12.26 0.00 0.00 2.83
3004 3379 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
3005 3380 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
3012 3387 9.920946 AATGCCTAGAAAGACAAATATTTAGGA 57.079 29.630 11.79 1.09 0.00 2.94
3013 3388 9.920946 ATGCCTAGAAAGACAAATATTTAGGAA 57.079 29.630 11.79 3.74 0.00 3.36
3014 3389 9.174166 TGCCTAGAAAGACAAATATTTAGGAAC 57.826 33.333 11.79 0.00 0.00 3.62
3015 3390 8.336080 GCCTAGAAAGACAAATATTTAGGAACG 58.664 37.037 11.79 0.00 0.00 3.95
3016 3391 8.827677 CCTAGAAAGACAAATATTTAGGAACGG 58.172 37.037 0.00 0.00 0.00 4.44
3017 3392 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3018 3393 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3019 3394 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3020 3395 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3021 3396 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3022 3397 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3023 3398 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3024 3399 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3156 3531 2.035442 GTCAAGAAGCCGACAGCCC 61.035 63.158 0.00 0.00 45.47 5.19
3355 3731 5.641709 TCACAAAACTTAATGTTGACGCAA 58.358 33.333 0.00 0.00 39.13 4.85
3387 3763 1.135315 CATGAGGGAATTGGTGCAACG 60.135 52.381 0.00 0.00 38.12 4.10
3406 3785 2.353269 ACGACAGCTATTCTCAGAGACG 59.647 50.000 0.00 0.33 0.00 4.18
3439 3818 3.392431 CGGCTCACTGCAGATTCG 58.608 61.111 23.35 12.37 45.15 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.739913 GTCGGCACATGCTAGTTTACAA 59.260 45.455 3.48 0.00 41.70 2.41
58 59 2.826428 AGTATTGTCGGCACATGCTAG 58.174 47.619 3.48 0.00 41.70 3.42
60 61 2.979814 TAGTATTGTCGGCACATGCT 57.020 45.000 3.48 0.00 41.70 3.79
86 87 7.967854 TGTGCTTTCTCCGTTTTGAAATATATG 59.032 33.333 0.00 0.00 32.65 1.78
165 176 7.222872 AGAGAACACTGAGTGAAAGATGAAAT 58.777 34.615 20.97 0.00 36.96 2.17
184 195 1.608283 CGAAGGGGTGTTGGAGAGAAC 60.608 57.143 0.00 0.00 0.00 3.01
190 201 3.961414 GGGCGAAGGGGTGTTGGA 61.961 66.667 0.00 0.00 0.00 3.53
194 205 1.789576 AAGATTGGGCGAAGGGGTGT 61.790 55.000 0.00 0.00 0.00 4.16
256 270 9.113838 ACCATAGATGATGTAGTTTGATGAAAC 57.886 33.333 0.00 0.00 36.80 2.78
283 297 9.905713 ATATATGGACCGTGAATTTATTGCTAT 57.094 29.630 0.00 0.00 0.00 2.97
333 347 4.579753 GGGCTACGAAAGATGTCTAGTACT 59.420 45.833 0.00 0.00 0.00 2.73
410 428 7.505585 TCTCCTTTATTGGGTTGCCAAATATAG 59.494 37.037 0.00 6.05 33.20 1.31
433 451 5.564550 AGGTATGTGCCCATGATTTATCTC 58.435 41.667 0.00 0.00 32.29 2.75
529 550 8.587952 AGTGTTTTAGAAATATTGGTGCAAAC 57.412 30.769 0.00 0.00 0.00 2.93
536 557 6.106003 GGGGCAAGTGTTTTAGAAATATTGG 58.894 40.000 0.00 0.00 0.00 3.16
615 969 7.475015 CCATAGTAGTGGATTGTGAAACATTG 58.525 38.462 0.00 0.00 44.51 2.82
678 1032 2.931969 GTGCAATTATTGGGCAAGCTTC 59.068 45.455 7.08 0.00 39.57 3.86
681 1035 1.066286 TGGTGCAATTATTGGGCAAGC 60.066 47.619 7.08 0.00 39.57 4.01
959 1315 2.708865 GGAGACGGACGGGGTCTTC 61.709 68.421 6.71 1.80 44.41 2.87
1023 1379 1.654954 GAGAGAACACCGGCGAGCTA 61.655 60.000 9.30 0.00 0.00 3.32
1161 1529 3.219928 GCCTCCTCGCGGATCTGA 61.220 66.667 6.13 0.00 39.01 3.27
1227 1595 2.185350 CGCCTCTTCAGCACCGAT 59.815 61.111 0.00 0.00 0.00 4.18
1392 1760 1.081174 TCCATCTCCACCCTTCTCCTT 59.919 52.381 0.00 0.00 0.00 3.36
1453 1821 0.170561 TCGAGCGAGCTTACCACTTC 59.829 55.000 0.00 0.00 0.00 3.01
1490 1858 8.844441 AAAATTGTGCAAAACAAAATCATGAG 57.156 26.923 0.09 0.00 44.97 2.90
1497 1865 9.612620 ATTTCGTAAAAATTGTGCAAAACAAAA 57.387 22.222 0.00 0.00 44.97 2.44
1535 1903 1.265454 ATCCCGGGTTCAGTCAGGTC 61.265 60.000 22.86 0.00 0.00 3.85
1536 1904 1.229529 ATCCCGGGTTCAGTCAGGT 60.230 57.895 22.86 0.00 0.00 4.00
1537 1905 1.221840 CATCCCGGGTTCAGTCAGG 59.778 63.158 22.86 0.00 0.00 3.86
1538 1906 1.221840 CCATCCCGGGTTCAGTCAG 59.778 63.158 22.86 0.00 0.00 3.51
1539 1907 0.838554 TTCCATCCCGGGTTCAGTCA 60.839 55.000 22.86 0.00 34.36 3.41
1540 1908 0.326927 TTTCCATCCCGGGTTCAGTC 59.673 55.000 22.86 0.00 34.36 3.51
1541 1909 0.999712 ATTTCCATCCCGGGTTCAGT 59.000 50.000 22.86 0.00 34.36 3.41
1568 1940 7.496591 ACAAAGTTCGGAGTATTAGACAAAACA 59.503 33.333 0.00 0.00 0.00 2.83
1582 1954 5.388408 AGTACCTCTAACAAAGTTCGGAG 57.612 43.478 0.00 0.00 0.00 4.63
1583 1955 6.899393 TTAGTACCTCTAACAAAGTTCGGA 57.101 37.500 0.00 0.00 34.17 4.55
1584 1956 7.150640 AGTTTAGTACCTCTAACAAAGTTCGG 58.849 38.462 0.00 0.00 38.22 4.30
1585 1957 8.585189 AAGTTTAGTACCTCTAACAAAGTTCG 57.415 34.615 0.00 0.00 38.22 3.95
1588 1960 9.761504 GAGAAAGTTTAGTACCTCTAACAAAGT 57.238 33.333 0.00 0.00 38.22 2.66
1589 1961 8.913656 CGAGAAAGTTTAGTACCTCTAACAAAG 58.086 37.037 0.00 0.00 38.22 2.77
1590 1962 8.416329 ACGAGAAAGTTTAGTACCTCTAACAAA 58.584 33.333 0.00 0.00 38.22 2.83
1624 1999 0.249031 AAACAGCGCCTGCAAAGTTC 60.249 50.000 2.29 0.00 46.23 3.01
1638 2013 2.223340 GGCCATCGAATACAGCAAACAG 60.223 50.000 0.00 0.00 0.00 3.16
1720 2095 2.214216 CCGTCCACCTTCCTCACCA 61.214 63.158 0.00 0.00 0.00 4.17
1805 2180 1.230497 CCCGCTCTCCTCCCTCTTA 59.770 63.158 0.00 0.00 0.00 2.10
1979 2354 7.039011 TGAGGCATACAATATCTACTTACCAGG 60.039 40.741 0.00 0.00 0.00 4.45
1993 2368 4.771577 TGGAACACATTTGAGGCATACAAT 59.228 37.500 0.00 0.00 0.00 2.71
2005 2380 7.984050 TTGTCACACAAATAATGGAACACATTT 59.016 29.630 0.00 0.00 39.84 2.32
2014 2389 9.474920 AAACTACAATTGTCACACAAATAATGG 57.525 29.630 15.85 0.00 41.96 3.16
2199 2574 9.090692 ACTGAAATATTGCATAATTTTGCTCAC 57.909 29.630 19.53 6.98 43.18 3.51
2211 2586 6.883217 AGTCACAGAGAACTGAAATATTGCAT 59.117 34.615 0.00 0.00 46.03 3.96
2383 2758 0.179018 ACTGTGGGTCAACAAGGAGC 60.179 55.000 0.00 0.00 34.62 4.70
2422 2797 3.371917 CCTTATCCCACAAGCCATCAGAA 60.372 47.826 0.00 0.00 0.00 3.02
2500 2875 3.188786 GCGGCGATGCGAGAAGTT 61.189 61.111 12.98 0.00 0.00 2.66
2665 3040 3.557290 GGCCCGATACACCCCTCC 61.557 72.222 0.00 0.00 0.00 4.30
2846 3221 6.308566 GGAGGGAGTAGTATGAAGTGAGTAT 58.691 44.000 0.00 0.00 0.00 2.12
2863 3238 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2864 3239 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2865 3240 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2866 3241 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2884 3259 9.996554 TCACTTGTTGATATCTCTAAAAAGACA 57.003 29.630 9.92 0.00 0.00 3.41
2893 3268 9.190317 TGTATGTAGTCACTTGTTGATATCTCT 57.810 33.333 3.98 0.00 36.32 3.10
2894 3269 9.803315 TTGTATGTAGTCACTTGTTGATATCTC 57.197 33.333 3.98 0.00 36.32 2.75
2897 3272 9.162764 GGTTTGTATGTAGTCACTTGTTGATAT 57.837 33.333 0.00 0.00 36.32 1.63
2898 3273 8.151596 TGGTTTGTATGTAGTCACTTGTTGATA 58.848 33.333 0.00 0.00 36.32 2.15
2899 3274 6.995686 TGGTTTGTATGTAGTCACTTGTTGAT 59.004 34.615 0.00 0.00 36.32 2.57
2900 3275 6.350103 TGGTTTGTATGTAGTCACTTGTTGA 58.650 36.000 0.00 0.00 0.00 3.18
2901 3276 6.612247 TGGTTTGTATGTAGTCACTTGTTG 57.388 37.500 0.00 0.00 0.00 3.33
2902 3277 7.633193 TTTGGTTTGTATGTAGTCACTTGTT 57.367 32.000 0.00 0.00 0.00 2.83
2903 3278 7.633193 TTTTGGTTTGTATGTAGTCACTTGT 57.367 32.000 0.00 0.00 0.00 3.16
2904 3279 7.594758 CCATTTTGGTTTGTATGTAGTCACTTG 59.405 37.037 0.00 0.00 31.35 3.16
2905 3280 7.657336 CCATTTTGGTTTGTATGTAGTCACTT 58.343 34.615 0.00 0.00 31.35 3.16
2906 3281 7.214467 CCATTTTGGTTTGTATGTAGTCACT 57.786 36.000 0.00 0.00 31.35 3.41
2922 3297 9.757227 TTTAAACTGTAGATTCAACCATTTTGG 57.243 29.630 0.00 0.00 45.02 3.28
2959 3334 7.771361 TCAAATGGTTACAACATACGGATGTAT 59.229 33.333 15.10 8.21 45.93 2.29
2960 3335 7.104290 TCAAATGGTTACAACATACGGATGTA 58.896 34.615 15.10 0.00 45.93 2.29
2962 3337 6.429791 TCAAATGGTTACAACATACGGATG 57.570 37.500 5.94 5.94 39.16 3.51
2963 3338 7.455641 TTTCAAATGGTTACAACATACGGAT 57.544 32.000 0.00 0.00 0.00 4.18
2964 3339 6.879276 TTTCAAATGGTTACAACATACGGA 57.121 33.333 0.00 0.00 0.00 4.69
2965 3340 6.034470 GCATTTCAAATGGTTACAACATACGG 59.966 38.462 12.14 0.00 0.00 4.02
2966 3341 6.034470 GGCATTTCAAATGGTTACAACATACG 59.966 38.462 12.14 0.00 0.00 3.06
2967 3342 7.096551 AGGCATTTCAAATGGTTACAACATAC 58.903 34.615 12.14 0.00 0.00 2.39
2968 3343 7.238486 AGGCATTTCAAATGGTTACAACATA 57.762 32.000 12.14 0.00 0.00 2.29
2969 3344 6.112927 AGGCATTTCAAATGGTTACAACAT 57.887 33.333 12.14 0.00 0.00 2.71
2970 3345 5.543507 AGGCATTTCAAATGGTTACAACA 57.456 34.783 12.14 0.00 0.00 3.33
2971 3346 6.919721 TCTAGGCATTTCAAATGGTTACAAC 58.080 36.000 12.14 0.00 0.00 3.32
2972 3347 7.531857 TTCTAGGCATTTCAAATGGTTACAA 57.468 32.000 12.14 0.00 0.00 2.41
2973 3348 7.450014 TCTTTCTAGGCATTTCAAATGGTTACA 59.550 33.333 12.14 0.00 0.00 2.41
2974 3349 7.755373 GTCTTTCTAGGCATTTCAAATGGTTAC 59.245 37.037 12.14 0.00 0.00 2.50
2975 3350 7.450014 TGTCTTTCTAGGCATTTCAAATGGTTA 59.550 33.333 12.14 0.00 29.10 2.85
2976 3351 6.267471 TGTCTTTCTAGGCATTTCAAATGGTT 59.733 34.615 12.14 0.00 29.10 3.67
2977 3352 5.774690 TGTCTTTCTAGGCATTTCAAATGGT 59.225 36.000 12.14 0.00 29.10 3.55
2978 3353 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
2979 3354 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
2986 3361 9.920946 TCCTAAATATTTGTCTTTCTAGGCATT 57.079 29.630 11.05 0.00 35.56 3.56
2987 3362 9.920946 TTCCTAAATATTTGTCTTTCTAGGCAT 57.079 29.630 11.05 0.00 35.56 4.40
2988 3363 9.174166 GTTCCTAAATATTTGTCTTTCTAGGCA 57.826 33.333 11.05 0.00 33.22 4.75
2989 3364 8.336080 CGTTCCTAAATATTTGTCTTTCTAGGC 58.664 37.037 11.05 0.00 0.00 3.93
2990 3365 8.827677 CCGTTCCTAAATATTTGTCTTTCTAGG 58.172 37.037 11.05 6.95 0.00 3.02
2991 3366 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2992 3367 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2993 3368 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2994 3369 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2995 3370 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2996 3371 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2997 3372 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2998 3373 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2999 3374 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3000 3375 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3001 3376 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3002 3377 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
3003 3378 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3004 3379 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3005 3380 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3006 3381 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3007 3382 3.267812 TCTTCTACTCCCTCCGTTCCTAA 59.732 47.826 0.00 0.00 0.00 2.69
3008 3383 2.848694 TCTTCTACTCCCTCCGTTCCTA 59.151 50.000 0.00 0.00 0.00 2.94
3009 3384 1.639628 TCTTCTACTCCCTCCGTTCCT 59.360 52.381 0.00 0.00 0.00 3.36
3010 3385 2.025898 CTCTTCTACTCCCTCCGTTCC 58.974 57.143 0.00 0.00 0.00 3.62
3011 3386 2.684374 GTCTCTTCTACTCCCTCCGTTC 59.316 54.545 0.00 0.00 0.00 3.95
3012 3387 2.309458 AGTCTCTTCTACTCCCTCCGTT 59.691 50.000 0.00 0.00 0.00 4.44
3013 3388 1.917568 AGTCTCTTCTACTCCCTCCGT 59.082 52.381 0.00 0.00 0.00 4.69
3014 3389 2.721425 AGTCTCTTCTACTCCCTCCG 57.279 55.000 0.00 0.00 0.00 4.63
3015 3390 5.451354 ACAATAGTCTCTTCTACTCCCTCC 58.549 45.833 0.00 0.00 0.00 4.30
3016 3391 6.378848 ACAACAATAGTCTCTTCTACTCCCTC 59.621 42.308 0.00 0.00 0.00 4.30
3017 3392 6.257586 ACAACAATAGTCTCTTCTACTCCCT 58.742 40.000 0.00 0.00 0.00 4.20
3018 3393 6.532988 ACAACAATAGTCTCTTCTACTCCC 57.467 41.667 0.00 0.00 0.00 4.30
3019 3394 8.688151 ACATACAACAATAGTCTCTTCTACTCC 58.312 37.037 0.00 0.00 0.00 3.85
3024 3399 9.809096 CATGTACATACAACAATAGTCTCTTCT 57.191 33.333 8.32 0.00 39.99 2.85
3189 3564 7.123547 TGTCAACATTAAGTTTTGGAACCTTCT 59.876 33.333 0.00 0.00 38.74 2.85
3274 3649 6.348050 GCAAACTCAGTCATTCTGTTAAGAGG 60.348 42.308 0.00 0.00 43.97 3.69
3276 3651 5.470098 GGCAAACTCAGTCATTCTGTTAAGA 59.530 40.000 0.00 0.00 43.97 2.10
3277 3652 5.471456 AGGCAAACTCAGTCATTCTGTTAAG 59.529 40.000 0.00 0.00 43.97 1.85
3278 3653 5.239306 CAGGCAAACTCAGTCATTCTGTTAA 59.761 40.000 0.00 0.00 43.97 2.01
3283 3658 3.777106 TCAGGCAAACTCAGTCATTCT 57.223 42.857 0.00 0.00 0.00 2.40
3387 3763 3.003275 CCTCGTCTCTGAGAATAGCTGTC 59.997 52.174 9.31 0.00 38.28 3.51
3406 3785 3.130340 TGAGCCGCAATAAAATTTCCCTC 59.870 43.478 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.