Multiple sequence alignment - TraesCS5D01G261900

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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 TraesCS5D01G261900 chr5D 100.000 5260 0 0 1 5260 368028897 368034156 0.000000e+00 9714.0
1 TraesCS5D01G261900 chr5D 91.394 3335 231 24 177 3485 368078219 368081523 0.000000e+00 4518.0
2 TraesCS5D01G261900 chr5D 89.169 1985 194 13 633 2603 368244606 368246583 0.000000e+00 2455.0
3 TraesCS5D01G261900 chr5D 84.734 2522 307 46 353 2829 368285770 368288258 0.000000e+00 2453.0
4 TraesCS5D01G261900 chr5D 80.706 1643 273 31 633 2252 367990886 367992507 0.000000e+00 1238.0
5 TraesCS5D01G261900 chr5D 80.589 1597 263 40 681 2248 367996363 367997941 0.000000e+00 1188.0
6 TraesCS5D01G261900 chr5D 76.812 1794 358 45 993 2765 367812249 367814005 0.000000e+00 955.0
7 TraesCS5D01G261900 chr5D 90.272 514 33 13 3935 4439 368081582 368082087 0.000000e+00 656.0
8 TraesCS5D01G261900 chr5D 89.918 367 34 3 4895 5260 488398512 488398148 2.220000e-128 470.0
9 TraesCS5D01G261900 chr5D 77.630 751 115 33 2819 3534 368288274 368289006 1.760000e-109 407.0
10 TraesCS5D01G261900 chr5D 87.218 266 26 5 196 456 368244163 368244425 3.980000e-76 296.0
11 TraesCS5D01G261900 chr5D 73.857 700 137 32 3935 4604 368289004 368289687 2.450000e-58 237.0
12 TraesCS5D01G261900 chr5D 88.889 189 16 3 4553 4738 368082553 368082739 1.470000e-55 228.0
13 TraesCS5D01G261900 chr5D 91.667 132 9 2 4425 4555 368082109 368082239 1.160000e-41 182.0
14 TraesCS5D01G261900 chr5A 96.765 3648 95 10 482 4121 470076442 470080074 0.000000e+00 6061.0
15 TraesCS5D01G261900 chr5A 83.430 3096 420 58 482 3529 470170324 470173374 0.000000e+00 2789.0
16 TraesCS5D01G261900 chr5A 78.797 2627 429 80 998 3541 469898888 469901469 0.000000e+00 1648.0
17 TraesCS5D01G261900 chr5A 95.820 311 6 3 4117 4421 470080490 470080799 3.660000e-136 496.0
18 TraesCS5D01G261900 chr5A 85.036 421 45 10 3542 3945 33127508 33127927 3.790000e-111 412.0
19 TraesCS5D01G261900 chr5A 89.883 257 24 2 4420 4675 470080903 470081158 3.930000e-86 329.0
20 TraesCS5D01G261900 chr5A 82.097 391 42 12 90 471 470076032 470076403 5.120000e-80 309.0
21 TraesCS5D01G261900 chr5A 74.363 706 133 32 3936 4604 470173378 470174072 1.880000e-64 257.0
22 TraesCS5D01G261900 chr5A 88.166 169 5 7 1 167 470075806 470075961 2.500000e-43 187.0
23 TraesCS5D01G261900 chr5A 85.938 128 18 0 353 480 470170167 470170294 2.550000e-28 137.0
24 TraesCS5D01G261900 chr5A 98.684 76 1 0 4811 4886 565775637 565775562 9.190000e-28 135.0
25 TraesCS5D01G261900 chr5A 97.368 76 2 0 4811 4886 94126022 94125947 4.270000e-26 130.0
26 TraesCS5D01G261900 chr5A 92.500 80 5 1 4737 4815 4612037 4612116 4.310000e-21 113.0
27 TraesCS5D01G261900 chr5A 97.222 36 0 1 49 83 470076002 470076037 5.690000e-05 60.2
28 TraesCS5D01G261900 chr5B 95.772 3169 101 17 177 3320 436152291 436155451 0.000000e+00 5079.0
29 TraesCS5D01G261900 chr5B 95.698 2301 72 11 2425 4712 436097688 436099974 0.000000e+00 3675.0
30 TraesCS5D01G261900 chr5B 95.312 2304 85 8 1 2294 436095403 436097693 0.000000e+00 3635.0
31 TraesCS5D01G261900 chr5B 83.178 3008 398 62 482 3413 436209055 436212030 0.000000e+00 2652.0
32 TraesCS5D01G261900 chr5B 89.018 1985 194 13 633 2603 436162916 436164890 0.000000e+00 2436.0
33 TraesCS5D01G261900 chr5B 91.696 1445 71 12 3310 4738 436156106 436157517 0.000000e+00 1958.0
34 TraesCS5D01G261900 chr5B 79.162 1862 319 45 1010 2830 435770628 435772461 0.000000e+00 1225.0
35 TraesCS5D01G261900 chr5B 86.822 258 28 3 204 456 436162165 436162421 3.100000e-72 283.0
36 TraesCS5D01G261900 chr5B 77.348 362 57 18 3935 4276 435774662 435775018 1.930000e-44 191.0
37 TraesCS5D01G261900 chr5B 77.346 309 50 13 3986 4280 436212183 436212485 1.170000e-36 165.0
38 TraesCS5D01G261900 chr5B 88.281 128 15 0 353 480 436208898 436209025 2.540000e-33 154.0
39 TraesCS5D01G261900 chr5B 92.208 77 4 2 4740 4815 528962648 528962573 2.000000e-19 108.0
40 TraesCS5D01G261900 chr1D 91.848 368 28 2 4895 5260 447335829 447335462 3.630000e-141 512.0
41 TraesCS5D01G261900 chr1D 88.919 370 37 4 4889 5256 93954765 93955132 2.230000e-123 453.0
42 TraesCS5D01G261900 chr1D 97.368 76 2 0 4811 4886 322071901 322071976 4.270000e-26 130.0
43 TraesCS5D01G261900 chr1D 97.368 76 2 0 4811 4886 378548752 378548677 4.270000e-26 130.0
44 TraesCS5D01G261900 chr1D 91.139 79 6 1 4738 4815 348996060 348996138 7.200000e-19 106.0
45 TraesCS5D01G261900 chr6D 91.553 367 28 3 4895 5260 107817325 107816961 2.190000e-138 503.0
46 TraesCS5D01G261900 chr6D 82.486 177 20 4 3764 3934 47181267 47181438 1.530000e-30 145.0
47 TraesCS5D01G261900 chr7D 89.974 379 31 4 4889 5260 51834258 51834636 2.850000e-132 483.0
48 TraesCS5D01G261900 chr7D 85.330 409 45 7 3542 3935 589510792 589511200 4.900000e-110 409.0
49 TraesCS5D01G261900 chr7D 80.094 427 52 20 3542 3951 268830815 268831225 2.400000e-73 287.0
50 TraesCS5D01G261900 chr7D 98.684 76 1 0 4811 4886 51833399 51833474 9.190000e-28 135.0
51 TraesCS5D01G261900 chr7D 98.684 76 1 0 4811 4886 204880020 204880095 9.190000e-28 135.0
52 TraesCS5D01G261900 chr7D 98.649 74 1 0 4811 4884 154205881 154205808 1.190000e-26 132.0
53 TraesCS5D01G261900 chr1A 89.918 367 34 3 4895 5260 320227988 320227624 2.220000e-128 470.0
54 TraesCS5D01G261900 chr2D 89.918 367 27 5 4895 5260 645042573 645042216 1.030000e-126 464.0
55 TraesCS5D01G261900 chr2D 86.331 417 40 9 3542 3942 640367312 640367727 6.250000e-119 438.0
56 TraesCS5D01G261900 chr2D 85.504 407 46 8 3541 3935 10300166 10300571 3.790000e-111 412.0
57 TraesCS5D01G261900 chr2D 84.804 408 47 8 3542 3935 605779617 605780023 3.820000e-106 396.0
58 TraesCS5D01G261900 chr2D 84.466 412 47 10 3541 3935 10488299 10487888 1.780000e-104 390.0
59 TraesCS5D01G261900 chr2D 97.368 76 2 0 4811 4886 498214477 498214552 4.270000e-26 130.0
60 TraesCS5D01G261900 chr2D 91.139 79 6 1 4738 4815 178524833 178524755 7.200000e-19 106.0
61 TraesCS5D01G261900 chr2D 90.123 81 6 2 4736 4815 15825429 15825508 2.590000e-18 104.0
62 TraesCS5D01G261900 chr6B 89.674 368 30 6 4895 5260 563140101 563139740 3.710000e-126 462.0
63 TraesCS5D01G261900 chr6B 93.827 81 4 1 4736 4815 230765189 230765269 2.570000e-23 121.0
64 TraesCS5D01G261900 chr6B 92.105 76 6 0 4740 4815 703137069 703136994 2.000000e-19 108.0
65 TraesCS5D01G261900 chr4D 89.431 369 31 7 4889 5256 486761471 486761832 4.800000e-125 459.0
66 TraesCS5D01G261900 chr2B 85.468 406 42 9 3542 3935 780869645 780870045 1.760000e-109 407.0
67 TraesCS5D01G261900 chr2B 79.947 379 59 13 3570 3941 453020881 453020513 4.040000e-66 263.0
68 TraesCS5D01G261900 chr6A 83.765 425 48 14 3537 3944 89598631 89599051 2.970000e-102 383.0
69 TraesCS5D01G261900 chr6A 96.774 31 1 0 159 189 85940302 85940272 1.000000e-02 52.8
70 TraesCS5D01G261900 chr6A 100.000 28 0 0 155 182 485385668 485385641 1.000000e-02 52.8
71 TraesCS5D01G261900 chr3A 82.367 431 54 14 3527 3937 641796565 641796993 6.480000e-94 355.0
72 TraesCS5D01G261900 chr2A 97.368 76 2 0 4811 4886 276258678 276258753 4.270000e-26 130.0
73 TraesCS5D01G261900 chr3B 93.750 80 4 1 4730 4808 673790144 673790223 9.250000e-23 119.0
74 TraesCS5D01G261900 chr7A 91.250 80 5 2 4737 4815 92408482 92408404 2.000000e-19 108.0
75 TraesCS5D01G261900 chr4A 100.000 28 0 0 155 182 365705459 365705486 1.000000e-02 52.8


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 TraesCS5D01G261900 chr5D 368028897 368034156 5259 False 9714.000000 9714 100.000000 1 5260 1 chr5D.!!$F2 5259
1 TraesCS5D01G261900 chr5D 368078219 368082739 4520 False 1396.000000 4518 90.555500 177 4738 4 chr5D.!!$F4 4561
2 TraesCS5D01G261900 chr5D 368244163 368246583 2420 False 1375.500000 2455 88.193500 196 2603 2 chr5D.!!$F5 2407
3 TraesCS5D01G261900 chr5D 367990886 367997941 7055 False 1213.000000 1238 80.647500 633 2252 2 chr5D.!!$F3 1619
4 TraesCS5D01G261900 chr5D 368285770 368289687 3917 False 1032.333333 2453 78.740333 353 4604 3 chr5D.!!$F6 4251
5 TraesCS5D01G261900 chr5D 367812249 367814005 1756 False 955.000000 955 76.812000 993 2765 1 chr5D.!!$F1 1772
6 TraesCS5D01G261900 chr5A 469898888 469901469 2581 False 1648.000000 1648 78.797000 998 3541 1 chr5A.!!$F3 2543
7 TraesCS5D01G261900 chr5A 470075806 470081158 5352 False 1240.366667 6061 91.658833 1 4675 6 chr5A.!!$F4 4674
8 TraesCS5D01G261900 chr5A 470170167 470174072 3905 False 1061.000000 2789 81.243667 353 4604 3 chr5A.!!$F5 4251
9 TraesCS5D01G261900 chr5B 436095403 436099974 4571 False 3655.000000 3675 95.505000 1 4712 2 chr5B.!!$F2 4711
10 TraesCS5D01G261900 chr5B 436152291 436157517 5226 False 3518.500000 5079 93.734000 177 4738 2 chr5B.!!$F3 4561
11 TraesCS5D01G261900 chr5B 436162165 436164890 2725 False 1359.500000 2436 87.920000 204 2603 2 chr5B.!!$F4 2399
12 TraesCS5D01G261900 chr5B 436208898 436212485 3587 False 990.333333 2652 82.935000 353 4280 3 chr5B.!!$F5 3927
13 TraesCS5D01G261900 chr5B 435770628 435775018 4390 False 708.000000 1225 78.255000 1010 4276 2 chr5B.!!$F1 3266
14 TraesCS5D01G261900 chr7D 51833399 51834636 1237 False 309.000000 483 94.329000 4811 5260 2 chr7D.!!$F4 449

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
273 428 0.965363 TTCCCGCCCTCAAATTGCTC 60.965 55.000 0.00 0.00 0.00 4.26 F
280 435 1.499056 CTCAAATTGCTCAGCGCGT 59.501 52.632 8.43 0.00 43.27 6.01 F
1146 6039 1.898094 TGTTTGCGAGCAGTGGCAT 60.898 52.632 0.00 0.00 44.61 4.40 F
1719 6615 0.036388 TGGTAGCTAACTGGCAGCAC 60.036 55.000 15.89 1.17 41.66 4.40 F
3072 9552 1.037579 GGCCTCCCCTGCAATACAAC 61.038 60.000 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 6096 1.488261 GCGGAAAGAATAGGACGGCG 61.488 60.000 4.80 4.8 0.00 6.46 R
1719 6615 4.183865 TGAGATCAAAGGTCATAACTGCG 58.816 43.478 0.00 0.0 0.00 5.18 R
3047 9524 2.091640 TTGCAGGGGAGGCCATTCAA 62.092 55.000 5.01 0.0 0.00 2.69 R
3535 10728 6.811170 GTCTCCATTTGGCATTTTCGAATTTA 59.189 34.615 0.00 0.0 34.44 1.40 R
4739 12855 0.032678 CGAACGGCTGGATATGCTCT 59.967 55.000 0.00 0.0 0.00 4.09 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
127 143 1.027792 GGAGACGAAGCGAGGACTCT 61.028 60.000 0.00 0.00 0.00 3.24
273 428 0.965363 TTCCCGCCCTCAAATTGCTC 60.965 55.000 0.00 0.00 0.00 4.26
280 435 1.499056 CTCAAATTGCTCAGCGCGT 59.501 52.632 8.43 0.00 43.27 6.01
351 528 2.998772 TCATTTTGTTCTGTCGCTTGC 58.001 42.857 0.00 0.00 0.00 4.01
618 842 4.514577 CGGGGCGTGTGGCTAGAG 62.515 72.222 0.00 0.00 42.94 2.43
633 857 3.306294 GGCTAGAGTTTTGCCAGCAAATT 60.306 43.478 17.80 9.93 44.14 1.82
715 5571 4.594123 TGCTTTTAGTTTTAACCCAGCC 57.406 40.909 0.00 0.00 0.00 4.85
756 5612 7.553760 TGCAGGCATCATATGTATATCGATTTT 59.446 33.333 1.71 0.00 0.00 1.82
784 5652 6.117911 TGGTTATTGATCAATAGCAACACG 57.882 37.500 31.13 0.00 36.57 4.49
932 5810 9.620259 ATCATAATCTTTACTCACTTTTCCCTC 57.380 33.333 0.00 0.00 0.00 4.30
936 5815 5.063880 TCTTTACTCACTTTTCCCTCTTGC 58.936 41.667 0.00 0.00 0.00 4.01
984 5873 2.696187 GGTACCTAGGCTTCCTCAAGAG 59.304 54.545 9.30 0.00 34.61 2.85
985 5874 2.930109 ACCTAGGCTTCCTCAAGAGA 57.070 50.000 9.30 0.00 34.61 3.10
986 5875 2.462723 ACCTAGGCTTCCTCAAGAGAC 58.537 52.381 9.30 0.00 34.61 3.36
988 5877 3.269906 ACCTAGGCTTCCTCAAGAGACTA 59.730 47.826 9.30 0.00 34.61 2.59
989 5878 3.888930 CCTAGGCTTCCTCAAGAGACTAG 59.111 52.174 0.00 6.32 34.61 2.57
990 5879 3.748645 AGGCTTCCTCAAGAGACTAGA 57.251 47.619 0.00 0.00 0.00 2.43
994 5883 4.161377 GGCTTCCTCAAGAGACTAGATTGT 59.839 45.833 0.00 0.00 0.00 2.71
1086 5979 2.503356 AGGAGAACTCATTGAGCGGATT 59.497 45.455 13.64 0.34 32.04 3.01
1146 6039 1.898094 TGTTTGCGAGCAGTGGCAT 60.898 52.632 0.00 0.00 44.61 4.40
1203 6096 3.908081 CAGGATGCGCCCCAATGC 61.908 66.667 16.75 3.92 37.37 3.56
1486 6382 4.408596 ACAACTTTGGATTTCACCCATTGT 59.591 37.500 0.00 0.00 32.57 2.71
1719 6615 0.036388 TGGTAGCTAACTGGCAGCAC 60.036 55.000 15.89 1.17 41.66 4.40
2490 7415 9.453572 GACAGGATATAGGCATGAAAATCAATA 57.546 33.333 0.00 0.00 0.00 1.90
2907 9365 5.412904 AGTGCTGTAGAAAATCAGGTAAAGC 59.587 40.000 0.00 0.00 32.94 3.51
2969 9428 4.036498 GCTATAGCTCGGTAGTTCTTGTCA 59.964 45.833 17.75 0.00 38.21 3.58
3072 9552 1.037579 GGCCTCCCCTGCAATACAAC 61.038 60.000 0.00 0.00 0.00 3.32
3125 9606 7.174772 TGCATGCACTTCTGATTTAGTTCTTTA 59.825 33.333 18.46 0.00 0.00 1.85
3757 10957 5.762179 ACTGTTCATCCTCAAAGTCCATA 57.238 39.130 0.00 0.00 0.00 2.74
3792 10993 0.179179 GCAGCTCGCAATTCAAGGTC 60.179 55.000 3.64 0.00 41.79 3.85
3796 10997 2.227388 AGCTCGCAATTCAAGGTCTTTG 59.773 45.455 0.00 0.00 38.17 2.77
3817 11018 8.690884 TCTTTGATCCTGAAATTTTACACACAA 58.309 29.630 0.00 0.00 0.00 3.33
3833 11034 8.678593 TTACACACAAACACATTACATCCTTA 57.321 30.769 0.00 0.00 0.00 2.69
4001 11208 5.502079 ACCATGGATTGATTGGTTAACGTA 58.498 37.500 21.47 0.00 40.87 3.57
4019 11226 9.983804 GTTAACGTAGAAATTTCCATTTCCTAG 57.016 33.333 14.61 0.00 46.80 3.02
4368 12041 3.991367 AGTGTTCTTTCTGAAGTACCGG 58.009 45.455 0.00 0.00 33.63 5.28
4387 12069 1.869767 GGCTGTGTGCTGCTATGTATC 59.130 52.381 0.00 0.00 42.39 2.24
4488 12279 3.686726 GCGAGACATTTGATCTGAAGGTT 59.313 43.478 0.00 0.00 0.00 3.50
4530 12325 8.246180 ACTGAATATGCTTTGAAACATTACAGG 58.754 33.333 0.00 0.00 30.88 4.00
4534 12330 4.808558 TGCTTTGAAACATTACAGGATGC 58.191 39.130 0.00 0.00 42.53 3.91
4547 12343 2.042162 ACAGGATGCTGGAAGTGGAAAT 59.958 45.455 19.22 0.00 42.53 2.17
4670 12782 6.439375 TGGAGTTTTAACTGACTGCTATAGGA 59.561 38.462 1.04 0.00 39.88 2.94
4700 12813 1.390123 AGCGTGAATGACGATTTGTCG 59.610 47.619 0.00 0.00 46.85 4.35
4729 12845 5.363939 TGTTTTTGAAAATTCGGGATTGCT 58.636 33.333 0.00 0.00 0.00 3.91
4733 12849 3.364549 TGAAAATTCGGGATTGCTGGAT 58.635 40.909 0.00 0.00 0.00 3.41
4738 12854 1.507140 TCGGGATTGCTGGATACCTT 58.493 50.000 0.00 0.00 0.00 3.50
4739 12855 2.684943 TCGGGATTGCTGGATACCTTA 58.315 47.619 0.00 0.00 0.00 2.69
4740 12856 2.632996 TCGGGATTGCTGGATACCTTAG 59.367 50.000 0.00 0.00 0.00 2.18
4741 12857 2.632996 CGGGATTGCTGGATACCTTAGA 59.367 50.000 0.00 0.00 0.00 2.10
4742 12858 3.306364 CGGGATTGCTGGATACCTTAGAG 60.306 52.174 0.00 0.00 0.00 2.43
4743 12859 3.558109 GGGATTGCTGGATACCTTAGAGC 60.558 52.174 0.00 0.00 0.00 4.09
4744 12860 3.071602 GGATTGCTGGATACCTTAGAGCA 59.928 47.826 0.00 0.00 37.88 4.26
4745 12861 4.263243 GGATTGCTGGATACCTTAGAGCAT 60.263 45.833 0.00 0.00 39.33 3.79
4746 12862 5.046304 GGATTGCTGGATACCTTAGAGCATA 60.046 44.000 0.00 0.00 39.33 3.14
4747 12863 6.352565 GGATTGCTGGATACCTTAGAGCATAT 60.353 42.308 0.00 0.00 39.33 1.78
4748 12864 5.667539 TGCTGGATACCTTAGAGCATATC 57.332 43.478 0.00 0.00 34.78 1.63
4749 12865 4.467795 TGCTGGATACCTTAGAGCATATCC 59.532 45.833 0.00 2.74 42.34 2.59
4750 12866 4.467795 GCTGGATACCTTAGAGCATATCCA 59.532 45.833 10.57 10.57 46.97 3.41
4752 12868 4.467795 TGGATACCTTAGAGCATATCCAGC 59.532 45.833 7.57 0.00 45.22 4.85
4753 12869 4.141824 GGATACCTTAGAGCATATCCAGCC 60.142 50.000 4.59 0.00 41.84 4.85
4754 12870 1.620819 ACCTTAGAGCATATCCAGCCG 59.379 52.381 0.00 0.00 0.00 5.52
4755 12871 1.620819 CCTTAGAGCATATCCAGCCGT 59.379 52.381 0.00 0.00 0.00 5.68
4756 12872 2.037772 CCTTAGAGCATATCCAGCCGTT 59.962 50.000 0.00 0.00 0.00 4.44
4757 12873 3.321497 CTTAGAGCATATCCAGCCGTTC 58.679 50.000 0.00 0.00 0.00 3.95
4758 12874 0.032678 AGAGCATATCCAGCCGTTCG 59.967 55.000 0.00 0.00 0.00 3.95
4759 12875 0.946221 GAGCATATCCAGCCGTTCGG 60.946 60.000 6.90 6.90 0.00 4.30
4778 12894 4.293671 CCCCCAGGGTGCCGAAAA 62.294 66.667 4.22 0.00 38.25 2.29
4779 12895 2.203567 CCCCAGGGTGCCGAAAAA 60.204 61.111 4.22 0.00 0.00 1.94
4780 12896 2.275380 CCCCAGGGTGCCGAAAAAG 61.275 63.158 4.22 0.00 0.00 2.27
4781 12897 1.228429 CCCAGGGTGCCGAAAAAGA 60.228 57.895 0.00 0.00 0.00 2.52
4782 12898 1.244019 CCCAGGGTGCCGAAAAAGAG 61.244 60.000 0.00 0.00 0.00 2.85
4783 12899 1.581447 CAGGGTGCCGAAAAAGAGC 59.419 57.895 0.00 0.00 0.00 4.09
4784 12900 1.966451 AGGGTGCCGAAAAAGAGCG 60.966 57.895 0.00 0.00 0.00 5.03
4790 12906 2.162716 CCGAAAAAGAGCGGTCTGG 58.837 57.895 19.39 10.75 42.49 3.86
4791 12907 1.298859 CCGAAAAAGAGCGGTCTGGG 61.299 60.000 19.39 10.72 42.49 4.45
4792 12908 1.298859 CGAAAAAGAGCGGTCTGGGG 61.299 60.000 19.39 2.58 31.37 4.96
4793 12909 0.960861 GAAAAAGAGCGGTCTGGGGG 60.961 60.000 19.39 0.00 31.37 5.40
4794 12910 3.569200 AAAAGAGCGGTCTGGGGGC 62.569 63.158 19.39 0.00 31.37 5.80
4886 13002 3.148279 GGTGATCGGGTCGAGGCT 61.148 66.667 0.00 0.00 39.91 4.58
4902 13799 4.457496 CTGGGCGACGGACATGCT 62.457 66.667 0.00 0.00 0.00 3.79
4942 13839 1.298014 CCTCGGCTTCCTCTGCTTT 59.702 57.895 0.00 0.00 0.00 3.51
4950 13847 1.719063 TTCCTCTGCTTTGGCTGGGT 61.719 55.000 0.00 0.00 36.35 4.51
5094 13997 1.248785 GGGGGAAAGCGGGAAGAAAC 61.249 60.000 0.00 0.00 0.00 2.78
5097 14000 1.209383 GAAAGCGGGAAGAAACGGC 59.791 57.895 0.00 0.00 34.78 5.68
5114 14017 0.241213 GGCGGAAAAAGGCTCTCAAC 59.759 55.000 0.00 0.00 0.00 3.18
5135 14038 4.394712 CCGACAGAGTGGCCCCAC 62.395 72.222 9.42 9.42 46.50 4.61
5151 14055 1.441311 CACGCCCCTTTTTGCTTGT 59.559 52.632 0.00 0.00 0.00 3.16
5205 14109 2.022762 GCGCCGGCTGTTATTTCG 59.977 61.111 26.68 6.32 35.83 3.46
5206 14110 2.707039 CGCCGGCTGTTATTTCGG 59.293 61.111 26.68 0.00 44.70 4.30
5225 14129 2.491022 CCCAACCCGGCGAAAAACA 61.491 57.895 9.30 0.00 0.00 2.83
5234 14138 1.214367 GGCGAAAAACAGACTCGTGA 58.786 50.000 0.00 0.00 35.06 4.35
5241 14145 4.803426 CAGACTCGTGAGGGCGCC 62.803 72.222 21.18 21.18 31.71 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 352 0.971386 CCTGCAAGCCACCAAAAGAT 59.029 50.000 0.00 0.00 0.00 2.40
280 435 5.401531 AGTAGATGGAAAACTTGCGAGTA 57.598 39.130 7.13 0.00 34.21 2.59
290 445 4.404394 TGACGGATGCTAGTAGATGGAAAA 59.596 41.667 0.00 0.00 0.00 2.29
342 519 0.029300 GAACAGCAAAGCAAGCGACA 59.971 50.000 0.00 0.00 37.01 4.35
351 528 2.252260 CGCCGTGGAACAGCAAAG 59.748 61.111 0.00 0.00 41.80 2.77
508 726 5.064441 AGACATTGGATAAAACAAGCAGC 57.936 39.130 0.00 0.00 0.00 5.25
689 5545 6.294843 GCTGGGTTAAAACTAAAAGCATGGTA 60.295 38.462 0.00 0.00 0.00 3.25
715 5571 3.054878 GCCTGCAAAGTTGAAATGACAG 58.945 45.455 0.00 0.00 0.00 3.51
784 5652 0.323360 TGTAGCAAACATGGAGCCCC 60.323 55.000 0.00 0.00 31.43 5.80
857 5732 8.565416 ACATGAAGTTAGGTAAAGTTTAACAGC 58.435 33.333 13.08 2.85 30.60 4.40
932 5810 7.805071 CCTTCTGTAGACACAATTAAAAGCAAG 59.195 37.037 0.00 0.00 33.22 4.01
984 5873 6.421202 CGGAAGCCATAGTAAACAATCTAGTC 59.579 42.308 0.00 0.00 0.00 2.59
985 5874 6.097839 TCGGAAGCCATAGTAAACAATCTAGT 59.902 38.462 0.00 0.00 0.00 2.57
986 5875 6.513180 TCGGAAGCCATAGTAAACAATCTAG 58.487 40.000 0.00 0.00 0.00 2.43
988 5877 5.353394 TCGGAAGCCATAGTAAACAATCT 57.647 39.130 0.00 0.00 0.00 2.40
989 5878 4.511826 CCTCGGAAGCCATAGTAAACAATC 59.488 45.833 0.00 0.00 0.00 2.67
990 5879 4.163458 TCCTCGGAAGCCATAGTAAACAAT 59.837 41.667 0.00 0.00 0.00 2.71
994 5883 4.510571 GTTTCCTCGGAAGCCATAGTAAA 58.489 43.478 1.51 0.00 35.38 2.01
1146 6039 3.973973 ACTGGGGATCTCGGATGATTTTA 59.026 43.478 0.00 0.00 0.00 1.52
1203 6096 1.488261 GCGGAAAGAATAGGACGGCG 61.488 60.000 4.80 4.80 0.00 6.46
1592 6488 8.729805 AGTTTTGATATCTCTCCATTTCTCAC 57.270 34.615 3.98 0.00 0.00 3.51
1719 6615 4.183865 TGAGATCAAAGGTCATAACTGCG 58.816 43.478 0.00 0.00 0.00 5.18
2097 7000 5.576563 TGTGGGGAAAGAAATCTAACAGA 57.423 39.130 0.00 0.00 0.00 3.41
2490 7415 4.934356 TCTGGAAGGCTTGGACATATTTT 58.066 39.130 3.46 0.00 0.00 1.82
2957 9416 9.654663 AAAACAGATATAGGTGACAAGAACTAC 57.345 33.333 0.00 0.00 0.00 2.73
3047 9524 2.091640 TTGCAGGGGAGGCCATTCAA 62.092 55.000 5.01 0.00 0.00 2.69
3534 10727 7.330700 GTCTCCATTTGGCATTTTCGAATTTAA 59.669 33.333 0.00 0.00 34.44 1.52
3535 10728 6.811170 GTCTCCATTTGGCATTTTCGAATTTA 59.189 34.615 0.00 0.00 34.44 1.40
3757 10957 6.992766 GCGAGCTGCACAAAATAAAAATATT 58.007 32.000 1.02 0.00 45.45 1.28
3792 10993 8.870160 TTGTGTGTAAAATTTCAGGATCAAAG 57.130 30.769 0.00 0.00 0.00 2.77
3796 10997 7.704472 TGTGTTTGTGTGTAAAATTTCAGGATC 59.296 33.333 0.00 0.00 0.00 3.36
3890 11092 3.074412 GCTCCATCGAGGACTTCAAAAA 58.926 45.455 0.00 0.00 43.07 1.94
4001 11208 7.470192 TCAGGAACTAGGAAATGGAAATTTCT 58.530 34.615 17.42 0.00 37.54 2.52
4019 11226 6.449698 TGAATTCAAAGCTCAAATCAGGAAC 58.550 36.000 5.45 0.00 0.00 3.62
4071 11281 6.808008 TCCTCAAAGAAAGATAAAGTGCAG 57.192 37.500 0.00 0.00 0.00 4.41
4368 12041 2.831333 AGATACATAGCAGCACACAGC 58.169 47.619 0.00 0.00 46.19 4.40
4488 12279 3.569194 TCAGTGGCAAGAGTTGGTTTA 57.431 42.857 0.00 0.00 0.00 2.01
4530 12325 3.760684 ACAAGATTTCCACTTCCAGCATC 59.239 43.478 0.00 0.00 0.00 3.91
4534 12330 6.095377 GCAATTACAAGATTTCCACTTCCAG 58.905 40.000 0.00 0.00 0.00 3.86
4670 12782 4.463209 CGTCATTCACGCTTTTGTAACAT 58.537 39.130 0.00 0.00 42.87 2.71
4725 12841 5.046304 GGATATGCTCTAAGGTATCCAGCAA 60.046 44.000 5.60 0.00 43.11 3.91
4729 12845 4.467795 GCTGGATATGCTCTAAGGTATCCA 59.532 45.833 11.28 11.28 46.24 3.41
4733 12849 2.826128 CGGCTGGATATGCTCTAAGGTA 59.174 50.000 0.00 0.00 0.00 3.08
4738 12854 1.269723 CGAACGGCTGGATATGCTCTA 59.730 52.381 0.00 0.00 0.00 2.43
4739 12855 0.032678 CGAACGGCTGGATATGCTCT 59.967 55.000 0.00 0.00 0.00 4.09
4740 12856 0.946221 CCGAACGGCTGGATATGCTC 60.946 60.000 0.00 0.00 0.00 4.26
4741 12857 1.069765 CCGAACGGCTGGATATGCT 59.930 57.895 0.00 0.00 0.00 3.79
4742 12858 3.642755 CCGAACGGCTGGATATGC 58.357 61.111 0.00 0.00 0.00 3.14
4762 12878 2.203567 TTTTTCGGCACCCTGGGG 60.204 61.111 18.88 7.87 42.03 4.96
4763 12879 1.228429 TCTTTTTCGGCACCCTGGG 60.228 57.895 12.28 12.28 0.00 4.45
4764 12880 1.866853 GCTCTTTTTCGGCACCCTGG 61.867 60.000 0.00 0.00 0.00 4.45
4765 12881 1.581447 GCTCTTTTTCGGCACCCTG 59.419 57.895 0.00 0.00 0.00 4.45
4766 12882 1.966451 CGCTCTTTTTCGGCACCCT 60.966 57.895 0.00 0.00 0.00 4.34
4767 12883 2.561373 CGCTCTTTTTCGGCACCC 59.439 61.111 0.00 0.00 0.00 4.61
4768 12884 2.561373 CCGCTCTTTTTCGGCACC 59.439 61.111 0.00 0.00 39.14 5.01
4773 12889 1.298859 CCCCAGACCGCTCTTTTTCG 61.299 60.000 0.00 0.00 0.00 3.46
4774 12890 0.960861 CCCCCAGACCGCTCTTTTTC 60.961 60.000 0.00 0.00 0.00 2.29
4775 12891 1.074951 CCCCCAGACCGCTCTTTTT 59.925 57.895 0.00 0.00 0.00 1.94
4776 12892 2.757077 CCCCCAGACCGCTCTTTT 59.243 61.111 0.00 0.00 0.00 2.27
4777 12893 4.035102 GCCCCCAGACCGCTCTTT 62.035 66.667 0.00 0.00 0.00 2.52
4886 13002 4.451150 GAGCATGTCCGTCGCCCA 62.451 66.667 0.00 0.00 0.00 5.36
4892 13789 4.760047 GCCACCGAGCATGTCCGT 62.760 66.667 0.00 0.00 0.00 4.69
4893 13790 3.958147 AAGCCACCGAGCATGTCCG 62.958 63.158 0.00 0.00 34.23 4.79
4927 13824 2.694760 GCCAAAGCAGAGGAAGCCG 61.695 63.158 0.00 0.00 39.53 5.52
4984 13881 0.179145 CCGCCGAAGAAGTACGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
4985 13882 1.210931 CCGCCGAAGAAGTACGTGA 59.789 57.895 0.00 0.00 0.00 4.35
5029 13927 3.878667 CCCGCCAATCTCCCTCCC 61.879 72.222 0.00 0.00 0.00 4.30
5080 13983 2.613506 CGCCGTTTCTTCCCGCTTT 61.614 57.895 0.00 0.00 0.00 3.51
5081 13984 3.047877 CGCCGTTTCTTCCCGCTT 61.048 61.111 0.00 0.00 0.00 4.68
5094 13997 1.234615 TTGAGAGCCTTTTTCCGCCG 61.235 55.000 0.00 0.00 0.00 6.46
5097 14000 1.461127 CGAGTTGAGAGCCTTTTTCCG 59.539 52.381 0.00 0.00 0.00 4.30
5100 14003 1.239347 GGCGAGTTGAGAGCCTTTTT 58.761 50.000 0.00 0.00 46.83 1.94
5135 14038 1.955663 GCACAAGCAAAAAGGGGCG 60.956 57.895 0.00 0.00 41.58 6.13
5217 14121 1.792949 CCCTCACGAGTCTGTTTTTCG 59.207 52.381 0.00 0.00 40.02 3.46
5241 14145 1.079888 GGCAAAAATCGGCCCAGTG 60.080 57.895 0.00 0.00 44.53 3.66


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

AutoCloner maintained by Alex Coulton.