Multiple sequence alignment - TraesCS7D01G443500

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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 TraesCS7D01G443500 chr7D 100.000 5211 0 0 1 5211 563667157 563661947 0.000000e+00 9624.0
1 TraesCS7D01G443500 chr7D 82.741 394 53 9 3301 3679 563480029 563479636 2.320000e-88 337.0
2 TraesCS7D01G443500 chr7B 92.182 3722 233 29 1518 5211 613256073 613252382 0.000000e+00 5208.0
3 TraesCS7D01G443500 chr7B 92.035 2938 183 26 2298 5211 613239388 613236478 0.000000e+00 4082.0
4 TraesCS7D01G443500 chr7B 93.894 999 54 5 1119 2113 613240873 613239878 0.000000e+00 1500.0
5 TraesCS7D01G443500 chr7B 90.052 965 37 16 463 1424 613257228 613256320 0.000000e+00 1195.0
6 TraesCS7D01G443500 chr7B 92.791 430 24 6 1 424 613257653 613257225 2.670000e-172 616.0
7 TraesCS7D01G443500 chr7B 82.537 544 73 10 3187 3710 613177354 613176813 4.760000e-125 459.0
8 TraesCS7D01G443500 chr7B 81.763 329 50 10 7 330 611493959 611494282 3.090000e-67 267.0
9 TraesCS7D01G443500 chr7B 90.576 191 11 6 2112 2300 613239850 613239665 4.030000e-61 246.0
10 TraesCS7D01G443500 chr7B 76.615 449 69 19 4070 4484 613151038 613150592 1.140000e-51 215.0
11 TraesCS7D01G443500 chrUn 90.992 1210 85 14 2298 3496 332850979 332849783 0.000000e+00 1609.0
12 TraesCS7D01G443500 chrUn 93.894 999 54 5 1119 2113 332852464 332851469 0.000000e+00 1500.0
13 TraesCS7D01G443500 chrUn 89.152 1014 65 20 89 1101 455428839 455429808 0.000000e+00 1221.0
14 TraesCS7D01G443500 chrUn 81.388 317 51 7 7 320 375756866 375757177 8.660000e-63 252.0
15 TraesCS7D01G443500 chrUn 90.576 191 11 6 2112 2300 332851441 332851256 4.030000e-61 246.0
16 TraesCS7D01G443500 chrUn 84.021 194 23 7 344 534 27364343 27364531 4.150000e-41 180.0
17 TraesCS7D01G443500 chrUn 92.500 40 2 1 346 385 223353432 223353394 7.290000e-04 56.5
18 TraesCS7D01G443500 chrUn 92.500 40 2 1 346 385 397819324 397819362 7.290000e-04 56.5
19 TraesCS7D01G443500 chr7A 85.657 1241 134 23 2499 3718 649152339 649151122 0.000000e+00 1266.0
20 TraesCS7D01G443500 chr7A 87.056 873 80 17 3816 4669 649151016 649150158 0.000000e+00 955.0
21 TraesCS7D01G443500 chr7A 83.093 970 98 37 410 1350 649154610 649153678 0.000000e+00 822.0
22 TraesCS7D01G443500 chr7A 86.301 511 67 3 3220 3728 649185968 649185459 2.120000e-153 553.0
23 TraesCS7D01G443500 chr7A 81.065 507 77 6 3192 3680 649072716 649072211 2.280000e-103 387.0
24 TraesCS7D01G443500 chr7A 77.710 489 95 5 1944 2424 649191189 649190707 2.370000e-73 287.0
25 TraesCS7D01G443500 chr7A 77.586 290 33 21 4070 4334 648684335 648684053 4.200000e-31 147.0
26 TraesCS7D01G443500 chr7A 88.571 105 12 0 1654 1758 649153253 649153149 1.520000e-25 128.0
27 TraesCS7D01G443500 chr5A 86.076 316 35 9 7 320 656051311 656051619 1.080000e-86 331.0
28 TraesCS7D01G443500 chr5A 81.388 317 51 7 7 320 512785638 512785949 8.660000e-63 252.0
29 TraesCS7D01G443500 chr2A 82.067 329 52 7 7 332 757931908 757931584 1.850000e-69 274.0
30 TraesCS7D01G443500 chr2A 78.261 115 22 3 2291 2404 504328028 504327916 2.600000e-08 71.3
31 TraesCS7D01G443500 chr4B 82.812 320 40 12 7 323 296156577 296156270 6.650000e-69 272.0
32 TraesCS7D01G443500 chr6D 81.818 330 51 8 7 330 11918549 11918875 8.600000e-68 268.0
33 TraesCS7D01G443500 chr3B 82.581 310 43 10 7 312 55108248 55108550 4.000000e-66 263.0
34 TraesCS7D01G443500 chr3B 76.524 328 40 20 3402 3702 417264818 417265135 1.510000e-30 145.0
35 TraesCS7D01G443500 chr3B 95.000 40 1 1 346 385 819569109 819569147 1.570000e-05 62.1
36 TraesCS7D01G443500 chr3B 92.500 40 2 1 346 385 819586444 819586482 7.290000e-04 56.5
37 TraesCS7D01G443500 chr5B 86.842 190 22 3 344 532 62942796 62942983 5.290000e-50 209.0
38 TraesCS7D01G443500 chr5B 93.878 98 6 0 1801 1898 321130427 321130330 1.170000e-31 148.0
39 TraesCS7D01G443500 chr3D 83.981 206 29 4 332 534 365990672 365990468 1.480000e-45 195.0
40 TraesCS7D01G443500 chr3D 91.589 107 9 0 1793 1899 532994073 532994179 1.170000e-31 148.0
41 TraesCS7D01G443500 chr3D 92.424 66 3 2 2291 2355 111757552 111757488 5.560000e-15 93.5
42 TraesCS7D01G443500 chr3D 86.420 81 9 2 2291 2370 496103783 496103862 2.590000e-13 87.9
43 TraesCS7D01G443500 chr3D 90.164 61 6 0 3348 3408 304328893 304328833 4.330000e-11 80.5
44 TraesCS7D01G443500 chr5D 93.333 105 6 1 1798 1902 332584396 332584293 2.510000e-33 154.0
45 TraesCS7D01G443500 chr5D 92.308 104 7 1 1799 1901 134782108 134782211 4.200000e-31 147.0
46 TraesCS7D01G443500 chr5D 91.509 106 9 0 1796 1901 360916319 360916214 4.200000e-31 147.0
47 TraesCS7D01G443500 chr2B 93.939 99 6 0 1800 1898 382598997 382599095 3.250000e-32 150.0
48 TraesCS7D01G443500 chr2B 85.271 129 16 1 371 499 441682154 441682029 4.230000e-26 130.0
49 TraesCS7D01G443500 chr1D 80.814 172 27 6 3746 3914 403275129 403274961 4.230000e-26 130.0
50 TraesCS7D01G443500 chr3A 79.675 123 24 1 2293 2415 108463502 108463623 2.590000e-13 87.9
51 TraesCS7D01G443500 chr4A 78.704 108 23 0 2302 2409 271795259 271795152 7.240000e-09 73.1


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 TraesCS7D01G443500 chr7D 563661947 563667157 5210 True 9624.000000 9624 100.000000 1 5211 1 chr7D.!!$R2 5210
1 TraesCS7D01G443500 chr7B 613252382 613257653 5271 True 2339.666667 5208 91.675000 1 5211 3 chr7B.!!$R4 5210
2 TraesCS7D01G443500 chr7B 613236478 613240873 4395 True 1942.666667 4082 92.168333 1119 5211 3 chr7B.!!$R3 4092
3 TraesCS7D01G443500 chr7B 613176813 613177354 541 True 459.000000 459 82.537000 3187 3710 1 chr7B.!!$R2 523
4 TraesCS7D01G443500 chrUn 455428839 455429808 969 False 1221.000000 1221 89.152000 89 1101 1 chrUn.!!$F4 1012
5 TraesCS7D01G443500 chrUn 332849783 332852464 2681 True 1118.333333 1609 91.820667 1119 3496 3 chrUn.!!$R2 2377
6 TraesCS7D01G443500 chr7A 649150158 649154610 4452 True 792.750000 1266 86.094250 410 4669 4 chr7A.!!$R5 4259
7 TraesCS7D01G443500 chr7A 649185459 649185968 509 True 553.000000 553 86.301000 3220 3728 1 chr7A.!!$R3 508
8 TraesCS7D01G443500 chr7A 649072211 649072716 505 True 387.000000 387 81.065000 3192 3680 1 chr7A.!!$R2 488

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
943 970 0.541863 CGAGAAGCCCACCTACCATT 59.458 55.0 0.00 0.0 0.00 3.16 F
1398 1458 0.541863 ATTTCCCCTACCGAGCAGTG 59.458 55.0 0.00 0.0 0.00 3.66 F
1580 1863 0.798159 CGTGGTAACCGTAAAAGGGC 59.202 55.0 0.00 0.0 35.02 5.19 F
2275 2622 1.076332 GTTAAGCGTGCTTCGGATGT 58.924 50.0 10.88 0.0 40.26 3.06 F
2651 3543 0.179078 TCTCCTCGCGTCTCTACTCC 60.179 60.0 5.77 0.0 0.00 3.85 F
4129 5111 0.822164 CCTACCCGTTCGTCAAGGAT 59.178 55.0 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2083 0.104409 AGGGGACACTCCTCAAAGGT 60.104 55.0 0.00 0.0 40.36 3.50 R
2253 2600 0.249953 TCCGAAGCACGCTTAACCAA 60.250 50.0 3.85 0.0 41.07 3.67 R
2545 3431 0.387929 ACTCTGCGTCGGTTGAAAGA 59.612 50.0 0.00 0.0 0.00 2.52 R
4081 5063 0.757561 TCTGGAGGGACACGTTGACA 60.758 55.0 0.00 0.0 0.00 3.58 R
4183 5165 1.165270 CCCATGTGTCGAACTTTCCC 58.835 55.0 0.00 0.0 0.00 3.97 R
5011 5999 0.962489 ACGAGGTCAGTGAGGACAAG 59.038 55.0 0.00 0.0 39.59 3.16 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
65 66 5.977129 GTGTGTAAACTTTCAGGACCAAATG 59.023 40.000 0.00 0.00 0.00 2.32
70 71 2.034558 ACTTTCAGGACCAAATGCGTTG 59.965 45.455 0.00 0.00 36.94 4.10
77 78 3.511146 AGGACCAAATGCGTTGAAATGAT 59.489 39.130 0.00 0.00 39.87 2.45
78 79 4.704540 AGGACCAAATGCGTTGAAATGATA 59.295 37.500 0.00 0.00 39.87 2.15
86 87 3.171277 GCGTTGAAATGATAGGTTGTGC 58.829 45.455 0.00 0.00 0.00 4.57
118 121 5.240844 ACAACTCTAAGGCTTTTTAACGCAT 59.759 36.000 4.45 0.00 0.00 4.73
135 138 3.821600 ACGCATGATACTATTCGTCCTCT 59.178 43.478 0.00 0.00 0.00 3.69
138 141 5.392487 CGCATGATACTATTCGTCCTCTCAT 60.392 44.000 0.00 0.00 0.00 2.90
341 348 2.560105 GCCGTACTCGACCCCTATAAAT 59.440 50.000 0.00 0.00 39.71 1.40
342 349 3.006217 GCCGTACTCGACCCCTATAAATT 59.994 47.826 0.00 0.00 39.71 1.82
456 463 9.853555 AATCTATTCAATACGTTTGATTTGCAA 57.146 25.926 11.98 0.00 33.88 4.08
507 515 7.039504 AGTGACATTAAGATCCATGCAAACTTT 60.040 33.333 0.00 0.00 0.00 2.66
539 547 3.692791 ACGGAAGCAAAACTCTGTTTC 57.307 42.857 0.00 0.00 36.21 2.78
548 556 7.516198 AGCAAAACTCTGTTTCTCAATGTAT 57.484 32.000 0.00 0.00 0.00 2.29
575 586 1.022451 TTTGTACTGATTCCGCGCCC 61.022 55.000 0.00 0.00 0.00 6.13
589 600 2.541588 CCGCGCCCAATTATTCTTTCAG 60.542 50.000 0.00 0.00 0.00 3.02
664 682 6.503944 AGGTCTCCTAAAAGAATCTCCACTA 58.496 40.000 0.00 0.00 28.47 2.74
674 692 7.732222 AAAGAATCTCCACTATCTTCTCACT 57.268 36.000 0.00 0.00 31.20 3.41
919 946 2.037385 AAGTGGCCTCCTCTTCTTCT 57.963 50.000 3.32 0.00 32.73 2.85
943 970 0.541863 CGAGAAGCCCACCTACCATT 59.458 55.000 0.00 0.00 0.00 3.16
949 976 0.846693 GCCCACCTACCATTCTCCAT 59.153 55.000 0.00 0.00 0.00 3.41
983 1010 1.978580 GTCCTCCTCCTCTTCAACCAA 59.021 52.381 0.00 0.00 0.00 3.67
1398 1458 0.541863 ATTTCCCCTACCGAGCAGTG 59.458 55.000 0.00 0.00 0.00 3.66
1479 1609 4.220821 GGGATACACTTTGAGTCTCTGACA 59.779 45.833 0.65 0.00 34.22 3.58
1480 1610 5.105146 GGGATACACTTTGAGTCTCTGACAT 60.105 44.000 0.65 0.00 34.22 3.06
1481 1611 5.809562 GGATACACTTTGAGTCTCTGACATG 59.190 44.000 0.65 0.00 34.60 3.21
1580 1863 0.798159 CGTGGTAACCGTAAAAGGGC 59.202 55.000 0.00 0.00 35.02 5.19
1609 1892 1.202533 CCGGCCACTTGATACTAGGTG 60.203 57.143 2.24 0.00 0.00 4.00
1768 2083 7.012327 GTGGACGATGGAATATGATTCTTTTCA 59.988 37.037 0.00 0.00 0.00 2.69
1791 2107 3.566351 CTTTGAGGAGTGTCCCCTTTTT 58.434 45.455 0.00 0.00 37.19 1.94
1814 2130 5.950023 TCTATTATGTACTCCCTCCGTCTT 58.050 41.667 0.00 0.00 0.00 3.01
1885 2201 8.099364 ACAAAGTTGATACACTTATGTTGAGG 57.901 34.615 0.00 0.00 40.48 3.86
2036 2352 4.497006 GCATAACATGATTGAGCAGTGACC 60.497 45.833 0.00 0.00 0.00 4.02
2041 2357 3.049708 TGATTGAGCAGTGACCTGAAG 57.950 47.619 0.00 0.00 41.50 3.02
2073 2389 4.489771 CCCCGGCCACAGTCATCC 62.490 72.222 2.24 0.00 0.00 3.51
2153 2498 5.043248 CACTTTGTGCTTTCGGAAAAGAAT 58.957 37.500 4.53 0.00 43.90 2.40
2154 2499 5.043248 ACTTTGTGCTTTCGGAAAAGAATG 58.957 37.500 4.53 1.60 43.90 2.67
2234 2581 4.287067 AGGTGCACCTTCTCTTTCATAAGA 59.713 41.667 33.20 0.00 46.09 2.10
2253 2600 7.671819 TCATAAGATCATCTCCGAAGAACCTAT 59.328 37.037 0.00 0.00 34.49 2.57
2269 2616 3.007635 ACCTATTGGTTAAGCGTGCTTC 58.992 45.455 10.88 0.00 46.05 3.86
2275 2622 1.076332 GTTAAGCGTGCTTCGGATGT 58.924 50.000 10.88 0.00 40.26 3.06
2384 3011 9.594478 TTCAGTGAATCTATAAATTAAGCGTGA 57.406 29.630 0.08 0.00 0.00 4.35
2425 3054 1.830587 ATGAGCGACTGGCCAAGACA 61.831 55.000 7.01 6.16 45.17 3.41
2538 3424 4.385405 AGCCCTGCTGCGACTGTC 62.385 66.667 0.00 0.00 37.57 3.51
2600 3492 1.146263 GGACGGGCGATGGAAGAAT 59.854 57.895 0.00 0.00 0.00 2.40
2615 3507 4.021456 TGGAAGAATCTTGTCGCTACTTGA 60.021 41.667 0.00 0.00 0.00 3.02
2651 3543 0.179078 TCTCCTCGCGTCTCTACTCC 60.179 60.000 5.77 0.00 0.00 3.85
2675 3567 4.402155 TCTGTTCCTTGTCACAAAAGCAAT 59.598 37.500 0.00 0.00 0.00 3.56
2727 3619 3.632333 AGTGGTCCGAGATAGAATGTCA 58.368 45.455 0.00 0.00 0.00 3.58
2792 3684 9.100197 TCTATTCCACCTATCATTGCAAGTATA 57.900 33.333 4.94 4.42 0.00 1.47
2911 3812 3.686016 GGTGCTCCCTGACAAATCTAAA 58.314 45.455 0.00 0.00 0.00 1.85
2952 3853 5.941948 AGAGATACGGTTTGAAAAAGTGG 57.058 39.130 0.00 0.00 0.00 4.00
2953 3854 5.374071 AGAGATACGGTTTGAAAAAGTGGT 58.626 37.500 0.00 0.00 0.00 4.16
2954 3855 6.527423 AGAGATACGGTTTGAAAAAGTGGTA 58.473 36.000 0.00 0.00 0.00 3.25
3030 3931 1.406539 GCCTGTAAATGACATGGCAGG 59.593 52.381 20.30 20.30 44.91 4.85
3031 3932 2.026641 CCTGTAAATGACATGGCAGGG 58.973 52.381 7.63 0.00 39.65 4.45
3032 3933 1.406539 CTGTAAATGACATGGCAGGGC 59.593 52.381 7.63 0.00 37.45 5.19
3033 3934 1.272369 TGTAAATGACATGGCAGGGCA 60.272 47.619 11.34 11.34 31.20 5.36
3034 3935 1.406539 GTAAATGACATGGCAGGGCAG 59.593 52.381 15.03 0.00 0.00 4.85
3047 3948 1.905215 CAGGGCAGCTGTATATAGCCT 59.095 52.381 16.64 5.18 44.76 4.58
3067 3975 9.853177 ATAGCCTTCTATATTATTAACCATGCC 57.147 33.333 0.00 0.00 33.89 4.40
3075 3983 7.916914 ATATTATTAACCATGCCCTTACGAC 57.083 36.000 0.00 0.00 0.00 4.34
3095 4004 5.155643 CGACATCAGCACATGAAAATTTCA 58.844 37.500 11.10 11.10 42.53 2.69
3120 4029 9.209175 CATTCTTTATATTACCAGGCTGACTAC 57.791 37.037 17.94 0.00 0.00 2.73
3151 4060 6.433404 CCAAGCCATAATGAATAGCATCTCTT 59.567 38.462 0.00 0.00 35.78 2.85
3518 4441 8.530311 AGTATGTAGCTTGGATCTGAATGATAG 58.470 37.037 0.00 0.00 35.14 2.08
3687 4618 1.040339 AAAAGGTTCGCTGGCACCAA 61.040 50.000 5.17 0.00 35.25 3.67
3775 4706 8.964420 TTTTACTCTGCATATAAGTTTTGTGC 57.036 30.769 7.87 7.87 36.39 4.57
3979 4961 4.732672 ATCAACGGAGGGAGTAGTTTAC 57.267 45.455 0.00 0.00 0.00 2.01
4081 5063 2.771943 TCGTTTTCATCCATAGGAGGCT 59.228 45.455 0.00 0.00 34.05 4.58
4129 5111 0.822164 CCTACCCGTTCGTCAAGGAT 59.178 55.000 0.00 0.00 0.00 3.24
4237 5219 2.097825 CTTCCCTCCCATTGCTCAAAG 58.902 52.381 0.00 0.00 0.00 2.77
4297 5279 2.636403 TCGATCCATCCAGATGAATGCT 59.364 45.455 9.24 0.00 41.20 3.79
4300 5282 4.809958 CGATCCATCCAGATGAATGCTATC 59.190 45.833 9.24 2.46 41.20 2.08
4489 5471 9.367444 TCTTCATTAAGAGTTTACCTTTCGATC 57.633 33.333 0.00 0.00 36.80 3.69
4625 5610 3.120060 CCAGCTCTTTCTACACAACATGC 60.120 47.826 0.00 0.00 0.00 4.06
4626 5611 3.499537 CAGCTCTTTCTACACAACATGCA 59.500 43.478 0.00 0.00 0.00 3.96
4627 5612 4.155462 CAGCTCTTTCTACACAACATGCAT 59.845 41.667 0.00 0.00 0.00 3.96
4628 5613 4.155462 AGCTCTTTCTACACAACATGCATG 59.845 41.667 25.09 25.09 0.00 4.06
4633 5618 3.599343 TCTACACAACATGCATGTCCTC 58.401 45.455 31.45 0.00 40.80 3.71
4647 5633 7.009179 TGCATGTCCTCCTCCTTTATTATAG 57.991 40.000 0.00 0.00 0.00 1.31
4708 5694 6.815089 TGAGGAGATTGAGCTTTATCTCTTC 58.185 40.000 26.86 26.86 46.23 2.87
4721 5707 7.548780 AGCTTTATCTCTTCTTGTGAACTCATC 59.451 37.037 0.00 0.00 0.00 2.92
4734 5720 4.997395 GTGAACTCATCGCATATACCCAAT 59.003 41.667 0.00 0.00 38.47 3.16
4835 5822 9.752228 TTATTGCCATCATTTGCCTCTTATATA 57.248 29.630 0.00 0.00 0.00 0.86
4916 5904 4.406456 TGCTAATCAGATGGTGGTTTGTT 58.594 39.130 0.00 0.00 29.81 2.83
4965 5953 0.179004 ATGCTCACCGTTGTTTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
5011 5999 0.255890 TGCCTCCCTTGCTTCATACC 59.744 55.000 0.00 0.00 0.00 2.73
5098 6089 0.655733 CTTTTTGCACAGTCCGACGT 59.344 50.000 0.00 0.00 0.00 4.34
5152 6145 6.542821 TGGAAAGAGAAGAGAAATTTAGGCA 58.457 36.000 0.00 0.00 0.00 4.75
5153 6146 7.004086 TGGAAAGAGAAGAGAAATTTAGGCAA 58.996 34.615 0.00 0.00 0.00 4.52
5154 6147 7.671398 TGGAAAGAGAAGAGAAATTTAGGCAAT 59.329 33.333 0.00 0.00 0.00 3.56
5155 6148 7.972832 GGAAAGAGAAGAGAAATTTAGGCAATG 59.027 37.037 0.00 0.00 0.00 2.82
5156 6149 8.414629 AAAGAGAAGAGAAATTTAGGCAATGT 57.585 30.769 0.00 0.00 0.00 2.71
5157 6150 7.388460 AGAGAAGAGAAATTTAGGCAATGTG 57.612 36.000 0.00 0.00 0.00 3.21
5158 6151 5.958955 AGAAGAGAAATTTAGGCAATGTGC 58.041 37.500 0.00 0.00 44.08 4.57
5159 6152 5.713861 AGAAGAGAAATTTAGGCAATGTGCT 59.286 36.000 0.00 0.00 44.28 4.40
5160 6153 6.886459 AGAAGAGAAATTTAGGCAATGTGCTA 59.114 34.615 0.00 0.00 44.28 3.49
5181 6174 6.030849 GCTACATAGCGAGGTACATCATAAG 58.969 44.000 8.44 0.07 39.82 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.171277 GCACAACCTATCATTTCAACGC 58.829 45.455 0.00 0.00 0.00 4.84
98 101 5.545658 TCATGCGTTAAAAAGCCTTAGAG 57.454 39.130 0.00 0.00 32.21 2.43
102 105 5.897377 AGTATCATGCGTTAAAAAGCCTT 57.103 34.783 0.00 0.00 32.21 4.35
118 121 6.540083 TGGTATGAGAGGACGAATAGTATCA 58.460 40.000 0.00 0.00 0.00 2.15
158 161 2.997303 CGATTGAAATGTGACCGGTACA 59.003 45.455 7.34 13.19 0.00 2.90
163 166 5.863898 TGAAATACGATTGAAATGTGACCG 58.136 37.500 0.00 0.00 0.00 4.79
199 202 2.037144 GGATGTGACGTGTATAGGGGT 58.963 52.381 0.00 0.00 0.00 4.95
200 203 2.317040 AGGATGTGACGTGTATAGGGG 58.683 52.381 0.00 0.00 0.00 4.79
443 450 7.644945 TCATCATATTAGCTTGCAAATCAAACG 59.355 33.333 0.00 0.00 33.65 3.60
507 515 0.614812 GCTTCCGTACACCCCCTTAA 59.385 55.000 0.00 0.00 0.00 1.85
548 556 6.539324 CGCGGAATCAGTACAAAATAGAAAA 58.461 36.000 0.00 0.00 0.00 2.29
552 560 3.303132 GGCGCGGAATCAGTACAAAATAG 60.303 47.826 8.83 0.00 0.00 1.73
664 682 4.077822 CCTTTCTTTGGCAGTGAGAAGAT 58.922 43.478 0.00 0.00 31.67 2.40
674 692 4.079253 GGTGATTAGACCTTTCTTTGGCA 58.921 43.478 0.00 0.00 32.75 4.92
919 946 0.040646 TAGGTGGGCTTCTCGAGGAA 59.959 55.000 13.56 4.93 0.00 3.36
943 970 2.025226 ACAGAGACGGACCTTATGGAGA 60.025 50.000 0.81 0.00 37.04 3.71
949 976 1.340795 GGAGGACAGAGACGGACCTTA 60.341 57.143 0.00 0.00 0.00 2.69
983 1010 5.679601 GCTCCATCTTTCTATCTTCAAGGT 58.320 41.667 0.00 0.00 0.00 3.50
1103 1131 4.084328 GCTGAAGAAGACACACACATACAC 60.084 45.833 0.00 0.00 0.00 2.90
1105 1133 4.151335 CAGCTGAAGAAGACACACACATAC 59.849 45.833 8.42 0.00 0.00 2.39
1107 1135 3.136763 CAGCTGAAGAAGACACACACAT 58.863 45.455 8.42 0.00 0.00 3.21
1109 1137 2.826428 TCAGCTGAAGAAGACACACAC 58.174 47.619 15.67 0.00 0.00 3.82
1111 1139 6.734104 AATAATCAGCTGAAGAAGACACAC 57.266 37.500 22.50 0.00 0.00 3.82
1113 1141 7.548780 AGAGAAATAATCAGCTGAAGAAGACAC 59.451 37.037 22.50 9.92 0.00 3.67
1174 1202 1.761174 GTTGTCCTTGAGGGGCTCA 59.239 57.895 0.00 0.00 41.10 4.26
1282 1315 3.287867 AATCAACCAATCGCAGAGGAT 57.712 42.857 0.00 0.00 43.63 3.24
1285 1318 3.201290 AGCTAATCAACCAATCGCAGAG 58.799 45.455 0.00 0.00 43.63 3.35
1512 1642 5.448632 CCACTTTTATATCCACTTTGACGGC 60.449 44.000 0.00 0.00 0.00 5.68
1609 1892 4.636206 CCTTGGTAGTTGGTTTAGCAGATC 59.364 45.833 0.00 0.00 31.03 2.75
1648 1934 4.658063 AGTCGTTACCAATCCAATGGAAA 58.342 39.130 5.89 0.00 43.54 3.13
1768 2083 0.104409 AGGGGACACTCCTCAAAGGT 60.104 55.000 0.00 0.00 40.36 3.50
1791 2107 5.579753 AGACGGAGGGAGTACATAATAGA 57.420 43.478 0.00 0.00 0.00 1.98
1879 2195 0.831307 AATACTCCCTCCGCCTCAAC 59.169 55.000 0.00 0.00 0.00 3.18
1885 2201 3.428532 TCCTGTATAATACTCCCTCCGC 58.571 50.000 0.00 0.00 0.00 5.54
2005 2321 4.598022 TCAATCATGTTATGCCTGGAACA 58.402 39.130 0.00 0.00 39.74 3.18
2036 2352 3.191371 GGGTGTTACAAAGATGCCTTCAG 59.809 47.826 0.00 0.00 0.00 3.02
2041 2357 0.808755 CGGGGTGTTACAAAGATGCC 59.191 55.000 0.00 0.00 0.00 4.40
2153 2498 4.380339 CGGAATGATTAACAATGTGCACCA 60.380 41.667 15.69 2.61 0.00 4.17
2154 2499 4.104776 CGGAATGATTAACAATGTGCACC 58.895 43.478 15.69 0.00 0.00 5.01
2224 2571 7.170658 GGTTCTTCGGAGATGATCTTATGAAAG 59.829 40.741 0.00 0.00 40.40 2.62
2229 2576 8.310382 CAATAGGTTCTTCGGAGATGATCTTAT 58.690 37.037 0.00 0.00 40.40 1.73
2234 2581 5.220710 CCAATAGGTTCTTCGGAGATGAT 57.779 43.478 0.00 0.00 40.40 2.45
2253 2600 0.249953 TCCGAAGCACGCTTAACCAA 60.250 50.000 3.85 0.00 41.07 3.67
2269 2616 1.864711 CGCCATAAGTTACCACATCCG 59.135 52.381 0.00 0.00 0.00 4.18
2275 2622 1.208535 CCAGGACGCCATAAGTTACCA 59.791 52.381 0.00 0.00 0.00 3.25
2359 2986 9.764363 ATCACGCTTAATTTATAGATTCACTGA 57.236 29.630 0.00 0.00 0.00 3.41
2362 2989 9.599322 CCAATCACGCTTAATTTATAGATTCAC 57.401 33.333 0.00 0.00 0.00 3.18
2384 3011 8.372877 TCATTGTCAAATTACCATAACCCAAT 57.627 30.769 0.00 0.00 0.00 3.16
2425 3054 0.718408 AAAATCCCCTTCTGCCCCAT 59.282 50.000 0.00 0.00 0.00 4.00
2460 3345 4.090588 CACCCCGCACGGTATGGT 62.091 66.667 8.49 5.52 33.67 3.55
2538 3424 2.173382 CGGTTGAAAGAAGCCGCG 59.827 61.111 0.00 0.00 37.69 6.46
2539 3425 1.206831 GTCGGTTGAAAGAAGCCGC 59.793 57.895 0.00 0.00 43.45 6.53
2545 3431 0.387929 ACTCTGCGTCGGTTGAAAGA 59.612 50.000 0.00 0.00 0.00 2.52
2600 3492 3.664107 AGCAAATCAAGTAGCGACAAGA 58.336 40.909 0.00 0.00 0.00 3.02
2615 3507 5.049129 CGAGGAGAAAGAAAGACAAGCAAAT 60.049 40.000 0.00 0.00 0.00 2.32
2651 3543 3.378112 TGCTTTTGTGACAAGGAACAGAG 59.622 43.478 0.00 0.00 0.00 3.35
2675 3567 5.483937 TCAGTCTGGCAGGAGAAACTAAATA 59.516 40.000 15.73 0.00 0.00 1.40
2727 3619 1.799258 CGCTCAAGGCTGCCACTTTT 61.799 55.000 22.65 2.88 39.13 2.27
2792 3684 1.703513 GCGGGATATAAACCCCTTCCT 59.296 52.381 11.28 0.00 44.09 3.36
2864 3759 2.983229 AGCCAAGCTCTTACATGACAG 58.017 47.619 0.00 0.00 30.62 3.51
2937 3838 5.996669 ACTAGTACCACTTTTTCAAACCG 57.003 39.130 0.00 0.00 0.00 4.44
3005 3906 3.489738 GCCATGTCATTTACAGGCATCAC 60.490 47.826 6.30 0.00 44.86 3.06
3030 3931 3.971245 AGAAGGCTATATACAGCTGCC 57.029 47.619 15.27 7.32 41.50 4.85
3047 3948 9.661563 CGTAAGGGCATGGTTAATAATATAGAA 57.338 33.333 0.00 0.00 0.00 2.10
3060 3968 0.908910 TGATGTCGTAAGGGCATGGT 59.091 50.000 0.00 0.00 34.53 3.55
3067 3975 2.892374 TCATGTGCTGATGTCGTAAGG 58.108 47.619 0.00 0.00 38.47 2.69
3095 4004 9.160412 AGTAGTCAGCCTGGTAATATAAAGAAT 57.840 33.333 0.00 0.00 0.00 2.40
3106 4015 2.317040 GCCATAGTAGTCAGCCTGGTA 58.683 52.381 0.00 0.00 0.00 3.25
3151 4060 6.371548 GCACTTGATAGTTGTTGGTGATAAGA 59.628 38.462 0.00 0.00 30.26 2.10
3216 4125 5.545658 ACAAGTACTGCAAAACCGATATG 57.454 39.130 0.00 0.00 0.00 1.78
3695 4626 7.280205 AGCAAGTAAAGTAGTATACAATGGCAC 59.720 37.037 5.50 0.00 46.26 5.01
3697 4628 7.787725 AGCAAGTAAAGTAGTATACAATGGC 57.212 36.000 5.50 0.00 46.26 4.40
3788 4722 0.963962 ACGCTTGGTCGGACTCTTAA 59.036 50.000 8.23 0.00 0.00 1.85
3790 4724 1.006102 CACGCTTGGTCGGACTCTT 60.006 57.895 8.23 0.00 0.00 2.85
3944 4923 5.455525 CCTCCGTTGATTTTTATTTCGCATC 59.544 40.000 0.00 0.00 0.00 3.91
4055 5037 6.293462 GCCTCCTATGGATGAAAACGATTAAC 60.293 42.308 0.00 0.00 0.00 2.01
4081 5063 0.757561 TCTGGAGGGACACGTTGACA 60.758 55.000 0.00 0.00 0.00 3.58
4183 5165 1.165270 CCCATGTGTCGAACTTTCCC 58.835 55.000 0.00 0.00 0.00 3.97
4237 5219 8.993852 ACGTACGTATGTATATATATTTCGGC 57.006 34.615 21.41 9.88 32.11 5.54
4288 5270 6.503589 AGTAGGTACTCGATAGCATTCATC 57.496 41.667 0.00 0.00 41.75 2.92
4379 5361 7.866393 ACATAGTAGTACAATAATTCTGCGTCC 59.134 37.037 2.52 0.00 0.00 4.79
4489 5471 4.332543 GTCAAGGGAAAACAAAGCCAAAAG 59.667 41.667 0.00 0.00 0.00 2.27
4625 5610 8.317679 CCTTCTATAATAAAGGAGGAGGACATG 58.682 40.741 0.00 0.00 41.74 3.21
4626 5611 7.037945 GCCTTCTATAATAAAGGAGGAGGACAT 60.038 40.741 5.35 0.00 41.74 3.06
4627 5612 6.270231 GCCTTCTATAATAAAGGAGGAGGACA 59.730 42.308 5.35 0.00 41.74 4.02
4628 5613 6.270231 TGCCTTCTATAATAAAGGAGGAGGAC 59.730 42.308 5.35 0.00 41.74 3.85
4633 5618 9.525826 AATGAATGCCTTCTATAATAAAGGAGG 57.474 33.333 5.35 0.00 44.02 4.30
4647 5633 4.679662 CAGTGGAATGAATGAATGCCTTC 58.320 43.478 0.00 0.00 0.00 3.46
4708 5694 4.449068 GGGTATATGCGATGAGTTCACAAG 59.551 45.833 0.00 0.00 0.00 3.16
4734 5720 4.258543 GTCCAGATGTTTATTGTCCCGAA 58.741 43.478 0.00 0.00 0.00 4.30
4742 5728 7.231317 ACACATTGTCTTGTCCAGATGTTTATT 59.769 33.333 0.00 0.00 32.60 1.40
4744 5730 6.061441 ACACATTGTCTTGTCCAGATGTTTA 58.939 36.000 0.00 0.00 32.60 2.01
4746 5732 4.464008 ACACATTGTCTTGTCCAGATGTT 58.536 39.130 0.00 0.00 32.60 2.71
4862 5849 0.940126 CATGAGTGTAAGATGGCGGC 59.060 55.000 0.00 0.00 0.00 6.53
5011 5999 0.962489 ACGAGGTCAGTGAGGACAAG 59.038 55.000 0.00 0.00 39.59 3.16
5127 6120 7.004086 TGCCTAAATTTCTCTTCTCTTTCCAA 58.996 34.615 0.00 0.00 0.00 3.53
5128 6121 6.542821 TGCCTAAATTTCTCTTCTCTTTCCA 58.457 36.000 0.00 0.00 0.00 3.53
5134 6127 6.032717 GCACATTGCCTAAATTTCTCTTCTC 58.967 40.000 0.00 0.00 37.42 2.87
5157 6150 3.917329 TGATGTACCTCGCTATGTAGC 57.083 47.619 1.92 1.92 45.62 3.58
5158 6151 7.147143 ACTTATGATGTACCTCGCTATGTAG 57.853 40.000 0.00 0.00 0.00 2.74
5159 6152 7.148523 CGTACTTATGATGTACCTCGCTATGTA 60.149 40.741 0.00 0.00 37.55 2.29
5160 6153 6.348295 CGTACTTATGATGTACCTCGCTATGT 60.348 42.308 0.00 0.00 37.55 2.29


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

AutoCloner maintained by Alex Coulton.