Multiple sequence alignment - TraesCS1D01G106600

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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 TraesCS1D01G106600 chr1D 100.000 9503 0 0 1 9503 99413044 99403542 0.000000e+00 17549.0
1 TraesCS1D01G106600 chr1D 86.526 3926 413 67 391 4252 69499083 69502956 0.000000e+00 4213.0
2 TraesCS1D01G106600 chr1D 86.477 3838 410 65 456 4257 92323002 92319238 0.000000e+00 4111.0
3 TraesCS1D01G106600 chr1D 87.997 2541 245 35 389 2897 97554767 97557279 0.000000e+00 2948.0
4 TraesCS1D01G106600 chr1D 86.307 2629 263 38 4260 6834 69503005 69505590 0.000000e+00 2771.0
5 TraesCS1D01G106600 chr1D 87.678 2248 230 18 7264 9503 97561638 97563846 0.000000e+00 2573.0
6 TraesCS1D01G106600 chr1D 87.989 2173 225 23 2533 4678 97557267 97559430 0.000000e+00 2534.0
7 TraesCS1D01G106600 chr1D 88.689 2060 191 22 507 2540 92379522 92377479 0.000000e+00 2475.0
8 TraesCS1D01G106600 chr1D 87.243 2187 214 29 4698 6834 92267437 92265266 0.000000e+00 2433.0
9 TraesCS1D01G106600 chr1D 85.933 2225 285 15 7284 9501 69506037 69508240 0.000000e+00 2350.0
10 TraesCS1D01G106600 chr1D 84.733 2024 286 16 7497 9502 92363201 92361183 0.000000e+00 2004.0
11 TraesCS1D01G106600 chr1D 86.541 1538 197 5 7556 9089 92264530 92262999 0.000000e+00 1685.0
12 TraesCS1D01G106600 chr1D 89.415 803 79 4 6035 6833 97560181 97560981 0.000000e+00 1007.0
13 TraesCS1D01G106600 chr1D 87.647 680 64 7 6851 7523 92265199 92264533 0.000000e+00 773.0
14 TraesCS1D01G106600 chr1D 89.171 434 35 7 6842 7274 97561042 97561464 1.820000e-146 531.0
15 TraesCS1D01G106600 chr1D 87.433 374 41 3 9131 9502 92262989 92262620 8.820000e-115 425.0
16 TraesCS1D01G106600 chr1D 87.805 82 5 1 389 470 92323094 92323018 3.650000e-14 91.6
17 TraesCS1D01G106600 chr1B 91.976 9496 621 74 1 9441 152951872 152961281 0.000000e+00 13184.0
18 TraesCS1D01G106600 chr1B 85.401 3925 441 72 391 4257 103349684 103353534 0.000000e+00 3952.0
19 TraesCS1D01G106600 chr1B 85.698 2622 301 37 4258 6822 147715301 147717905 0.000000e+00 2697.0
20 TraesCS1D01G106600 chr1B 85.583 2497 307 29 6836 9317 147717973 147720431 0.000000e+00 2567.0
21 TraesCS1D01G106600 chr1B 85.549 2166 286 18 7346 9501 103356043 103358191 0.000000e+00 2241.0
22 TraesCS1D01G106600 chr1B 86.950 1885 210 22 418 2282 147711334 147713202 0.000000e+00 2085.0
23 TraesCS1D01G106600 chr1B 85.901 1986 237 28 2288 4252 147713291 147715254 0.000000e+00 2076.0
24 TraesCS1D01G106600 chr1B 86.292 1459 164 11 4258 5687 103353576 103355027 0.000000e+00 1554.0
25 TraesCS1D01G106600 chr1B 86.913 1001 103 14 5735 6709 103355037 103356035 0.000000e+00 1098.0
26 TraesCS1D01G106600 chr1A 90.257 5922 477 51 970 6834 94873954 94868076 0.000000e+00 7648.0
27 TraesCS1D01G106600 chr1A 90.644 4190 341 34 970 5133 94904566 94900402 0.000000e+00 5518.0
28 TraesCS1D01G106600 chr1A 87.588 3561 354 47 2533 6049 92613631 92617147 0.000000e+00 4047.0
29 TraesCS1D01G106600 chr1A 87.972 2544 254 36 389 2897 92611117 92613643 0.000000e+00 2955.0
30 TraesCS1D01G106600 chr1A 86.275 2725 327 33 1559 4262 88795747 88793049 0.000000e+00 2916.0
31 TraesCS1D01G106600 chr1A 85.589 2616 304 38 4267 6834 88793003 88790413 0.000000e+00 2675.0
32 TraesCS1D01G106600 chr1A 86.159 2247 254 22 7266 9503 92619948 92622146 0.000000e+00 2374.0
33 TraesCS1D01G106600 chr1A 90.283 1451 136 3 7771 9216 94867120 94865670 0.000000e+00 1893.0
34 TraesCS1D01G106600 chr1A 83.021 2026 311 28 7497 9502 88844578 88842566 0.000000e+00 1805.0
35 TraesCS1D01G106600 chr1A 82.512 1521 254 10 7498 9011 88987939 88986424 0.000000e+00 1325.0
36 TraesCS1D01G106600 chr1A 91.045 938 68 11 1 933 94905497 94904571 0.000000e+00 1253.0
37 TraesCS1D01G106600 chr1A 90.832 938 70 11 1 933 94874885 94873959 0.000000e+00 1242.0
38 TraesCS1D01G106600 chr1A 82.722 1308 189 15 7556 8834 88789675 88788376 0.000000e+00 1129.0
39 TraesCS1D01G106600 chr1A 89.219 909 62 15 6836 7722 94868020 94867126 0.000000e+00 1103.0
40 TraesCS1D01G106600 chr1A 89.415 803 79 4 6035 6833 92618491 92619291 0.000000e+00 1007.0
41 TraesCS1D01G106600 chr1A 86.782 696 68 12 6836 7523 88790357 88789678 0.000000e+00 754.0
42 TraesCS1D01G106600 chr1A 88.610 439 37 9 6836 7273 92619348 92619774 1.090000e-143 521.0
43 TraesCS1D01G106600 chr1A 84.318 491 68 7 9019 9502 88985712 88985224 1.120000e-128 472.0
44 TraesCS1D01G106600 chr1A 86.829 410 50 3 9095 9502 88614144 88613737 1.120000e-123 455.0
45 TraesCS1D01G106600 chr1A 92.361 288 22 0 9216 9503 94864648 94864361 2.470000e-110 411.0
46 TraesCS1D01G106600 chr1A 76.371 237 40 10 146 378 164146434 164146658 7.800000e-21 113.0
47 TraesCS1D01G106600 chr7D 88.071 394 38 6 1 390 240521214 240521602 8.700000e-125 459.0
48 TraesCS1D01G106600 chr7D 80.818 318 34 16 51 347 244574615 244574926 3.450000e-54 224.0
49 TraesCS1D01G106600 chr7D 80.545 257 27 17 149 390 296515164 296514916 9.810000e-40 176.0
50 TraesCS1D01G106600 chr2D 81.481 351 39 13 51 379 507362505 507362159 2.030000e-66 265.0
51 TraesCS1D01G106600 chr2B 81.176 340 42 17 51 377 79720829 79721159 4.400000e-63 254.0
52 TraesCS1D01G106600 chr2B 80.110 362 39 24 40 377 789443588 789443236 1.230000e-58 239.0
53 TraesCS1D01G106600 chr7A 78.830 359 34 25 51 378 369529334 369529681 4.500000e-48 204.0
54 TraesCS1D01G106600 chr2A 89.542 153 12 3 27 177 753533641 753533791 3.500000e-44 191.0
55 TraesCS1D01G106600 chr6D 86.127 173 21 3 216 385 42449042 42448870 5.860000e-42 183.0
56 TraesCS1D01G106600 chr6B 77.874 348 38 18 60 378 708281363 708281700 7.580000e-41 180.0


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 TraesCS1D01G106600 chr1D 99403542 99413044 9502 True 17549.000000 17549 100.000000 1 9503 1 chr1D.!!$R3 9502
1 TraesCS1D01G106600 chr1D 69499083 69508240 9157 False 3111.333333 4213 86.255333 391 9501 3 chr1D.!!$F1 9110
2 TraesCS1D01G106600 chr1D 92377479 92379522 2043 True 2475.000000 2475 88.689000 507 2540 1 chr1D.!!$R2 2033
3 TraesCS1D01G106600 chr1D 92319238 92323094 3856 True 2101.300000 4111 87.141000 389 4257 2 chr1D.!!$R5 3868
4 TraesCS1D01G106600 chr1D 92361183 92363201 2018 True 2004.000000 2004 84.733000 7497 9502 1 chr1D.!!$R1 2005
5 TraesCS1D01G106600 chr1D 97554767 97563846 9079 False 1918.600000 2948 88.450000 389 9503 5 chr1D.!!$F2 9114
6 TraesCS1D01G106600 chr1D 92262620 92267437 4817 True 1329.000000 2433 87.216000 4698 9502 4 chr1D.!!$R4 4804
7 TraesCS1D01G106600 chr1B 152951872 152961281 9409 False 13184.000000 13184 91.976000 1 9441 1 chr1B.!!$F1 9440
8 TraesCS1D01G106600 chr1B 147711334 147720431 9097 False 2356.250000 2697 86.033000 418 9317 4 chr1B.!!$F3 8899
9 TraesCS1D01G106600 chr1B 103349684 103358191 8507 False 2211.250000 3952 86.038750 391 9501 4 chr1B.!!$F2 9110
10 TraesCS1D01G106600 chr1A 94900402 94905497 5095 True 3385.500000 5518 90.844500 1 5133 2 chr1A.!!$R6 5132
11 TraesCS1D01G106600 chr1A 94864361 94874885 10524 True 2459.400000 7648 90.590400 1 9503 5 chr1A.!!$R5 9502
12 TraesCS1D01G106600 chr1A 92611117 92622146 11029 False 2180.800000 4047 87.948800 389 9503 5 chr1A.!!$F2 9114
13 TraesCS1D01G106600 chr1A 88788376 88795747 7371 True 1868.500000 2916 85.342000 1559 8834 4 chr1A.!!$R3 7275
14 TraesCS1D01G106600 chr1A 88842566 88844578 2012 True 1805.000000 1805 83.021000 7497 9502 1 chr1A.!!$R2 2005
15 TraesCS1D01G106600 chr1A 88985224 88987939 2715 True 898.500000 1325 83.415000 7498 9502 2 chr1A.!!$R4 2004

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
865 913 0.247736 ATCAAGCACAGACCCTCGAC 59.752 55.000 0.0 0.0 0.00 4.20 F
1845 1949 0.034574 TGTTCCTGCCCGCACATTAT 60.035 50.000 0.0 0.0 0.00 1.28 F
3132 4075 0.536724 GGCAATTTTAGTGCTGGGGG 59.463 55.000 0.0 0.0 41.88 5.40 F
3738 4712 0.254178 CTTACCCACTGCCATGAGCT 59.746 55.000 0.0 0.0 44.23 4.09 F
5457 6545 1.067821 CTCTAGTCCTTCCCGACATGC 59.932 57.143 0.0 0.0 35.07 4.06 F
5720 6817 0.180406 GCCTATCTTTGGGCGAGGAA 59.820 55.000 0.0 0.0 39.96 3.36 F
5994 7122 0.689080 ATCGTGGCTGGAGGACTGAT 60.689 55.000 0.0 0.0 0.00 2.90 F
6376 8885 0.950836 TGTGAGTGACCAAATTGCGG 59.049 50.000 0.0 0.0 0.00 5.69 F
7890 10685 0.608130 TTGCAGAGTACATCCGCAGT 59.392 50.000 0.0 0.0 33.48 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 2677 1.558756 CAGCCTCTCCTTCATCCAACT 59.441 52.381 0.00 0.0 0.00 3.16 R
3256 4208 1.569548 TCTCTATCTGGGGACGTTCCT 59.430 52.381 13.96 0.0 36.57 3.36 R
5059 6100 0.040204 CCCAGAAGTGGCCTTGGAAT 59.960 55.000 3.32 0.0 43.44 3.01 R
5620 6715 0.108774 TGTATGGCCACAACCGTGAA 59.891 50.000 8.16 0.0 46.80 3.18 R
6431 8940 1.072331 ACTTGAGGCAAGAACCGACAT 59.928 47.619 13.56 0.0 43.42 3.06 R
6580 9092 1.467920 CCATCCAACAAGAAGGAGGC 58.532 55.000 0.00 0.0 37.34 4.70 R
7875 10670 0.532573 CCACACTGCGGATGTACTCT 59.467 55.000 0.00 0.0 0.00 3.24 R
7963 10758 1.792757 GCCATCCCCATCTGCCCATA 61.793 60.000 0.00 0.0 0.00 2.74 R
8983 11821 2.690881 TGCCGCCTCCACCCTAAT 60.691 61.111 0.00 0.0 0.00 1.73 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
22 23 4.950050 GAGAGGAGATGAAAAATCGCCTA 58.050 43.478 10.14 0.00 46.10 3.93
66 70 4.594920 AGAAGACCATGGTGAGAAGAAAGA 59.405 41.667 25.52 0.00 0.00 2.52
100 104 4.107072 AGAAGGAAGGAGATTGATCACCA 58.893 43.478 9.60 0.00 39.63 4.17
156 160 6.440436 CGTCATGAATGAATTGATTGCCATA 58.560 36.000 0.00 0.00 38.75 2.74
193 197 5.141568 CGTTTGGTTACCTTACGTGAATTG 58.858 41.667 16.48 0.00 0.00 2.32
197 201 6.696441 TGGTTACCTTACGTGAATTGTTTT 57.304 33.333 2.07 0.00 0.00 2.43
241 245 4.412796 TGTCTGGCCAGATGAAGATAAG 57.587 45.455 37.07 6.28 39.97 1.73
244 248 3.389329 TCTGGCCAGATGAAGATAAGACC 59.611 47.826 32.00 0.00 31.41 3.85
282 286 4.407365 GGTGGAGGGAGAAAAGAAAATCA 58.593 43.478 0.00 0.00 0.00 2.57
285 289 5.536538 GTGGAGGGAGAAAAGAAAATCACTT 59.463 40.000 0.00 0.00 0.00 3.16
302 306 2.184631 TTGAGGGGAGAGGGGGTCT 61.185 63.158 0.00 0.00 38.71 3.85
324 328 1.536331 ACGAGAGAGTTGGACGAAGAC 59.464 52.381 0.00 0.00 0.00 3.01
380 385 9.970553 TCTGTTCTTTTAGGTAGTAGAGATACA 57.029 33.333 0.00 0.00 0.00 2.29
382 387 9.970553 TGTTCTTTTAGGTAGTAGAGATACAGA 57.029 33.333 0.00 0.00 0.00 3.41
590 637 3.562232 AGGCGTTCCGTTTCCCCA 61.562 61.111 0.00 0.00 37.47 4.96
591 638 2.360726 GGCGTTCCGTTTCCCCAT 60.361 61.111 0.00 0.00 0.00 4.00
719 766 4.033776 CCGGTGCACAGGGTCCAT 62.034 66.667 26.47 0.00 0.00 3.41
861 909 4.346418 CCTTCTATATCAAGCACAGACCCT 59.654 45.833 0.00 0.00 0.00 4.34
863 911 2.898729 ATATCAAGCACAGACCCTCG 57.101 50.000 0.00 0.00 0.00 4.63
864 912 1.847328 TATCAAGCACAGACCCTCGA 58.153 50.000 0.00 0.00 0.00 4.04
865 913 0.247736 ATCAAGCACAGACCCTCGAC 59.752 55.000 0.00 0.00 0.00 4.20
897 945 4.661222 TGATACAAGCATTTCTCCCACAA 58.339 39.130 0.00 0.00 0.00 3.33
927 976 5.663556 CCAAAGACTACTCCCCTTCTTCTAT 59.336 44.000 0.00 0.00 0.00 1.98
1180 1274 1.642513 GGATACCACCACCTTCCCCC 61.643 65.000 0.00 0.00 0.00 5.40
1499 1594 1.264749 CCGGGAGAGATGGGTCAACA 61.265 60.000 0.00 0.00 0.00 3.33
1578 1674 6.947464 AGTTCCTACTAGCTGCTTGATTTTA 58.053 36.000 17.66 0.00 31.21 1.52
1837 1940 1.103398 GGGATTGATGTTCCTGCCCG 61.103 60.000 0.00 0.00 33.53 6.13
1845 1949 0.034574 TGTTCCTGCCCGCACATTAT 60.035 50.000 0.00 0.00 0.00 1.28
1872 1977 1.226746 AACGTGTACAAGGCTTCTGC 58.773 50.000 13.47 0.00 38.76 4.26
1941 2046 8.774586 CAAATATGGAAATTTACTACTCCCTCG 58.225 37.037 1.27 0.00 0.00 4.63
1987 2092 7.114866 TGGATATTTCAATACGGACTACACA 57.885 36.000 0.00 0.00 0.00 3.72
2131 2242 3.531538 ACTAGATAATTGCCCGTGTGTG 58.468 45.455 0.00 0.00 0.00 3.82
2429 2627 5.948758 AGAAAAATCTGAGATGGGAGGAAAC 59.051 40.000 0.00 0.00 0.00 2.78
2452 2650 2.043992 TCAAACAGGAGAACGGAAGGA 58.956 47.619 0.00 0.00 0.00 3.36
2462 2661 2.500504 AGAACGGAAGGAGGAACCATAC 59.499 50.000 0.00 0.00 42.04 2.39
2472 2677 6.031964 AGGAGGAACCATACATAGAGAGAA 57.968 41.667 0.00 0.00 42.04 2.87
2623 3200 2.833794 TGTGAGTAGCCACAGTTTGAC 58.166 47.619 0.00 0.00 41.63 3.18
2657 3588 1.745489 GTCGATGTTCCAGCCCACC 60.745 63.158 0.00 0.00 0.00 4.61
2668 3599 1.410153 CCAGCCCACCAATTAGCATTC 59.590 52.381 0.00 0.00 0.00 2.67
2671 3602 1.956477 GCCCACCAATTAGCATTCGAT 59.044 47.619 0.00 0.00 0.00 3.59
2674 3605 4.133820 CCCACCAATTAGCATTCGATACA 58.866 43.478 0.00 0.00 0.00 2.29
2848 3782 5.271598 TCTTCATTTAGGCCACCAATTGAT 58.728 37.500 5.01 0.00 0.00 2.57
2892 3826 7.560796 AATTAGTAGGGATAGATGTTCCTGG 57.439 40.000 0.00 0.00 33.53 4.45
2929 3863 7.599998 GCATTTGAAATGTGTACAGGAATTCTT 59.400 33.333 18.12 0.00 0.00 2.52
3022 3963 9.906660 TGTGTCATAATTTTTAAATTCTTCGCT 57.093 25.926 3.85 0.00 39.24 4.93
3132 4075 0.536724 GGCAATTTTAGTGCTGGGGG 59.463 55.000 0.00 0.00 41.88 5.40
3133 4076 1.266178 GCAATTTTAGTGCTGGGGGT 58.734 50.000 0.00 0.00 39.00 4.95
3134 4077 1.623311 GCAATTTTAGTGCTGGGGGTT 59.377 47.619 0.00 0.00 39.00 4.11
3166 4112 4.701765 ACAACAACAAAAAGCATGGCATA 58.298 34.783 0.00 0.00 0.00 3.14
3289 4243 6.350277 CCCCAGATAGAGATAACATTACCGAC 60.350 46.154 0.00 0.00 0.00 4.79
3333 4295 4.394610 TCAAAGCTGCTACATATTTGCGAA 59.605 37.500 0.90 0.00 32.28 4.70
3372 4334 6.854091 ATTCCCTAAAGTAAGAGTCGTTCT 57.146 37.500 0.00 0.00 37.93 3.01
3405 4367 5.627499 TTGCATTTGAGATGTGGTACTTC 57.373 39.130 0.00 0.00 0.00 3.01
3483 4449 9.011407 CATGTTCCAAAAATTTGATGTTGTTTG 57.989 29.630 7.44 0.00 40.55 2.93
3557 4525 2.820178 TGAGTAGATGTTCCTGCTCCA 58.180 47.619 0.00 0.00 42.72 3.86
3610 4580 4.268359 GACAAAATCAAGCTCTCCTCCAT 58.732 43.478 0.00 0.00 0.00 3.41
3625 4595 0.621571 TCCATTCCCTCCAGACCAGG 60.622 60.000 0.00 0.00 0.00 4.45
3738 4712 0.254178 CTTACCCACTGCCATGAGCT 59.746 55.000 0.00 0.00 44.23 4.09
4005 4997 1.077501 CGCCCTGGTCATCCACAAT 60.078 57.895 0.00 0.00 39.03 2.71
4178 5174 5.367945 ACAAGGAAGAGGTTGACTGTTTA 57.632 39.130 0.00 0.00 31.99 2.01
4241 5237 1.600485 TCCGGACGCTTTTCAAACTTC 59.400 47.619 0.00 0.00 0.00 3.01
4252 5248 7.067116 CGCTTTTCAAACTTCACTACGATTTA 58.933 34.615 0.00 0.00 0.00 1.40
4315 5352 6.376248 AGTTCAATATGGTATCCAAGCCAAT 58.624 36.000 0.00 0.00 36.95 3.16
4351 5388 8.880750 GTTCAAGACCTTACCAACATAGTATTC 58.119 37.037 0.00 0.00 0.00 1.75
4368 5405 9.559958 CATAGTATTCAAAAAGATTTTGCGTCT 57.440 29.630 10.01 8.30 0.00 4.18
4376 5413 7.168972 TCAAAAAGATTTTGCGTCTTACATTGG 59.831 33.333 10.01 0.00 34.97 3.16
4470 5508 7.784037 TCATCAATTCGGATTTTTGGATGAAT 58.216 30.769 12.48 0.00 0.00 2.57
4605 5644 7.182060 ACCTTGGTTCACCTAATGATGTATTT 58.818 34.615 0.00 0.00 37.11 1.40
4641 5680 2.975489 AGTCACTCCCATGTTTGAGACT 59.025 45.455 10.17 6.40 32.84 3.24
4691 5731 7.062957 CCCATTGATCCTTAGGTGAAAGTAAT 58.937 38.462 0.00 0.00 0.00 1.89
4723 5763 7.422465 AGCATCTCCCTATTTAAAATTTGCA 57.578 32.000 0.00 0.00 0.00 4.08
4730 5770 8.608185 TCCCTATTTAAAATTTGCAATCCTCT 57.392 30.769 0.00 0.00 0.00 3.69
5005 6046 4.397420 TCAAGCTCAACATAAAGAAGGCA 58.603 39.130 0.00 0.00 0.00 4.75
5059 6100 6.186957 AGCAATGTAATTTAGTCACCATGGA 58.813 36.000 21.47 0.00 31.22 3.41
5079 6120 1.360393 TTCCAAGGCCACTTCTGGGT 61.360 55.000 5.01 0.00 38.13 4.51
5101 6142 1.539665 GATCTCGACCCTCCCCTCT 59.460 63.158 0.00 0.00 0.00 3.69
5303 6385 2.218603 ACCTGACGATGTGGTTGTTTC 58.781 47.619 0.00 0.00 0.00 2.78
5457 6545 1.067821 CTCTAGTCCTTCCCGACATGC 59.932 57.143 0.00 0.00 35.07 4.06
5502 6594 3.721575 ACCTTGCATTATCCCTCATGGTA 59.278 43.478 0.00 0.00 35.88 3.25
5503 6595 4.202503 ACCTTGCATTATCCCTCATGGTAG 60.203 45.833 0.00 0.00 35.88 3.18
5563 6658 2.603075 AGCCACTGGGAAATTAGCAA 57.397 45.000 0.00 0.00 35.59 3.91
5620 6715 0.321653 GATCTTGGTCAAGGCGGTGT 60.322 55.000 10.39 0.00 38.88 4.16
5642 6739 2.395360 CGGTTGTGGCCATACACCG 61.395 63.158 28.55 28.55 40.62 4.94
5720 6817 0.180406 GCCTATCTTTGGGCGAGGAA 59.820 55.000 0.00 0.00 39.96 3.36
5924 7052 8.489489 ACAATGATGAAGTGATCTATTAGTGGT 58.511 33.333 0.00 0.00 0.00 4.16
5978 7106 4.691860 AGCCAAATTTTGAGAGTCATCG 57.308 40.909 10.72 0.00 0.00 3.84
5991 7119 1.305297 TCATCGTGGCTGGAGGACT 60.305 57.895 0.00 0.00 0.00 3.85
5993 7121 1.305297 ATCGTGGCTGGAGGACTGA 60.305 57.895 0.00 0.00 0.00 3.41
5994 7122 0.689080 ATCGTGGCTGGAGGACTGAT 60.689 55.000 0.00 0.00 0.00 2.90
5996 7124 1.451028 GTGGCTGGAGGACTGATGC 60.451 63.158 0.00 0.00 0.00 3.91
6051 8558 8.960591 CATTGTGGACAAGGTTTTAAGAGATAT 58.039 33.333 0.00 0.00 39.47 1.63
6068 8575 7.259088 AGAGATATGTTTTGGGTTCTACAGT 57.741 36.000 0.00 0.00 0.00 3.55
6082 8589 5.945191 GGTTCTACAGTCTAGTAGTCAAGGT 59.055 44.000 0.00 0.00 41.68 3.50
6171 8678 3.634397 TCCAACCAGACATCCAAGATC 57.366 47.619 0.00 0.00 0.00 2.75
6186 8693 3.698040 CCAAGATCCAACCATGAGAAAGG 59.302 47.826 0.00 0.00 0.00 3.11
6376 8885 0.950836 TGTGAGTGACCAAATTGCGG 59.049 50.000 0.00 0.00 0.00 5.69
6431 8940 2.306805 AGTGGCTCACCTCATCATCAAA 59.693 45.455 2.18 0.00 34.49 2.69
6464 8973 2.293399 GCCTCAAGTTTGGAATGACGTT 59.707 45.455 0.00 0.00 0.00 3.99
6498 9007 5.876651 TGGTCTTCATGCTAGTATGATGT 57.123 39.130 25.55 0.00 36.97 3.06
6560 9072 4.046286 AGTCCTCAATAATTGGCAACCA 57.954 40.909 0.00 0.00 0.00 3.67
6580 9092 7.533426 CAACCAAGGAAATCTCTACATTCTTG 58.467 38.462 0.00 0.00 0.00 3.02
6616 9128 6.401537 TGGATGGGAGATTTCTAAGGAAAA 57.598 37.500 0.00 0.00 43.51 2.29
6636 9148 4.483476 AAGGAACGTATGTGTCTTTTGC 57.517 40.909 0.00 0.00 0.00 3.68
6651 9163 3.894427 TCTTTTGCAATAAAGTGAGGCCA 59.106 39.130 5.01 0.00 36.67 5.36
6652 9164 3.658757 TTTGCAATAAAGTGAGGCCAC 57.341 42.857 5.01 0.00 43.50 5.01
6837 9351 5.355596 TGTTCCAACAAAAATAGCACTTGG 58.644 37.500 0.00 0.00 35.67 3.61
6838 9352 5.127845 TGTTCCAACAAAAATAGCACTTGGA 59.872 36.000 0.00 0.00 36.27 3.53
6839 9353 6.183360 TGTTCCAACAAAAATAGCACTTGGAT 60.183 34.615 0.00 0.00 37.57 3.41
6840 9354 6.024552 TCCAACAAAAATAGCACTTGGATC 57.975 37.500 0.00 0.00 33.74 3.36
6897 9467 8.143835 CCTCAAATTACACAATATTGATTCCCC 58.856 37.037 22.16 0.00 30.39 4.81
6907 9477 8.694540 CACAATATTGATTCCCCAAATTGTAGA 58.305 33.333 22.16 0.00 36.64 2.59
6920 9490 7.148656 CCCCAAATTGTAGAAAACGCAAAATAG 60.149 37.037 0.00 0.00 0.00 1.73
6927 9497 7.354257 TGTAGAAAACGCAAAATAGGTGTAAC 58.646 34.615 0.00 0.00 0.00 2.50
7051 9631 4.842531 TTTCTATCAGGCTCATTCCACA 57.157 40.909 0.00 0.00 0.00 4.17
7147 9746 6.922957 CAGTAGATTCCTGAGATACTTTGAGC 59.077 42.308 0.00 0.00 31.38 4.26
7210 9813 7.636259 TCTTGGCGAATTTTATCTTGTTTTG 57.364 32.000 0.00 0.00 0.00 2.44
7211 9814 7.429633 TCTTGGCGAATTTTATCTTGTTTTGA 58.570 30.769 0.00 0.00 0.00 2.69
7229 9832 7.958674 TGTTTTGAAGTGTTGCATTAGTTTTC 58.041 30.769 0.00 0.00 0.00 2.29
7280 10067 6.290294 AGTAATGTTCCATTACGTACCAGT 57.710 37.500 16.99 1.09 38.96 4.00
7551 10346 6.089476 CACATGAGTGTTGTGTTGTGTAAAA 58.911 36.000 0.00 0.00 40.92 1.52
7711 10506 1.222766 GCTGATCGAGCTGCATCAGG 61.223 60.000 24.95 11.99 44.32 3.86
7875 10670 1.681666 CCAGCTCTCCCTTCTTGCA 59.318 57.895 0.00 0.00 0.00 4.08
7890 10685 0.608130 TTGCAGAGTACATCCGCAGT 59.392 50.000 0.00 0.00 33.48 4.40
7940 10735 1.837439 GACACCTATGATGTCCCCACA 59.163 52.381 0.00 0.00 40.56 4.17
7944 10739 3.885297 CACCTATGATGTCCCCACAATTC 59.115 47.826 0.00 0.00 35.64 2.17
7963 10758 5.627182 ATTCTATCATGACCAAGAGCACT 57.373 39.130 0.00 0.00 0.00 4.40
7964 10759 6.737720 ATTCTATCATGACCAAGAGCACTA 57.262 37.500 0.00 0.00 0.00 2.74
8060 10855 0.180406 AATCCGGCCATGACTGGTAC 59.820 55.000 6.78 0.00 45.10 3.34
8100 10895 1.315257 CCAACATGCAGTACTGGGCC 61.315 60.000 23.95 8.41 0.00 5.80
8102 10897 1.788518 AACATGCAGTACTGGGCCCA 61.789 55.000 26.67 26.67 0.00 5.36
8304 11103 1.523154 CGGCAAGCAACCTAAAGGCA 61.523 55.000 0.00 0.00 39.32 4.75
8323 11122 3.006133 TGGCAGGGATGCACCGTA 61.006 61.111 2.29 0.00 40.11 4.02
8413 11215 3.665675 GATGCCGTTGGTCCGAGCT 62.666 63.158 0.00 0.00 0.00 4.09
8522 11351 2.048503 GGTGGTCACCCTTCGACG 60.049 66.667 8.89 0.00 45.68 5.12
8602 11433 3.658709 TGAGATTGTATGTGTGTTGCGA 58.341 40.909 0.00 0.00 0.00 5.10
8734 11566 9.959749 CAGTAGATTTCAATAGAGAAGAGGTAC 57.040 37.037 0.00 0.00 0.00 3.34
8849 11684 3.773119 TGGAGGACTAACATAGGGTTGAC 59.227 47.826 0.00 0.00 40.73 3.18
8925 11763 3.017442 GTGGGAATTAGAAGGAAGGCAC 58.983 50.000 0.00 0.00 0.00 5.01
9039 12581 4.440802 CGAATGGGTCAGTTAGAAGAGGAG 60.441 50.000 0.00 0.00 0.00 3.69
9122 12671 8.706322 AATTAGATGGTCCTTACTTTGTTGTT 57.294 30.769 0.00 0.00 0.00 2.83
9208 12759 5.841810 AGTTGTGTCCCAAACATTACAATG 58.158 37.500 0.37 0.37 40.80 2.82
9213 13786 6.154192 TGTGTCCCAAACATTACAATGCATAT 59.846 34.615 0.00 0.00 40.80 1.78
9214 13787 7.340487 TGTGTCCCAAACATTACAATGCATATA 59.660 33.333 0.00 0.00 40.80 0.86
9265 13838 3.896122 AGTGCAATTAAAACACGCGATT 58.104 36.364 15.93 3.30 39.31 3.34
9266 13839 5.037015 AGTGCAATTAAAACACGCGATTA 57.963 34.783 15.93 3.62 39.31 1.75
9279 13852 5.144359 ACACGCGATTAAGTTGAAACATTC 58.856 37.500 15.93 0.00 0.00 2.67
9443 14016 6.880822 TTCACTTGTGCATATACTTACGAC 57.119 37.500 0.00 0.00 0.00 4.34
9444 14017 6.203808 TCACTTGTGCATATACTTACGACT 57.796 37.500 0.00 0.00 0.00 4.18
9450 14023 5.068067 TGTGCATATACTTACGACTTGCCTA 59.932 40.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.441572 CCCACACAGATGAAAAAGCTAGG 59.558 47.826 0.00 0.00 0.00 3.02
22 23 2.949447 ACCCACACAGATGAAAAAGCT 58.051 42.857 0.00 0.00 0.00 3.74
66 70 8.661752 ATCTCCTTCCTTCTTTCAATCAATTT 57.338 30.769 0.00 0.00 0.00 1.82
156 160 4.255833 ACCAAACGCAATCAATTCATGT 57.744 36.364 0.00 0.00 0.00 3.21
197 201 6.993902 ACAAACCGACTCTATCTTTGGTAAAA 59.006 34.615 0.00 0.00 30.36 1.52
241 245 1.674651 GGTTTTCTCCCTGCCGGTC 60.675 63.158 1.90 0.00 0.00 4.79
244 248 2.746277 CCGGTTTTCTCCCTGCCG 60.746 66.667 0.00 0.00 41.82 5.69
282 286 2.456840 CCCCCTCTCCCCTCAAGT 59.543 66.667 0.00 0.00 0.00 3.16
285 289 0.858598 TAAGACCCCCTCTCCCCTCA 60.859 60.000 0.00 0.00 0.00 3.86
302 306 3.188048 GTCTTCGTCCAACTCTCTCGTAA 59.812 47.826 0.00 0.00 0.00 3.18
327 331 2.038033 CTGTTTCCCCTCTTACGTTCCA 59.962 50.000 0.00 0.00 0.00 3.53
380 385 4.389077 GCGCGATTTTAGCCAATAGTATCT 59.611 41.667 12.10 0.00 0.00 1.98
382 387 4.315803 AGCGCGATTTTAGCCAATAGTAT 58.684 39.130 12.10 0.00 0.00 2.12
383 388 3.724374 AGCGCGATTTTAGCCAATAGTA 58.276 40.909 12.10 0.00 0.00 1.82
384 389 2.561569 AGCGCGATTTTAGCCAATAGT 58.438 42.857 12.10 0.00 0.00 2.12
385 390 3.291585 CAAGCGCGATTTTAGCCAATAG 58.708 45.455 12.10 0.00 0.00 1.73
386 391 2.540769 GCAAGCGCGATTTTAGCCAATA 60.541 45.455 12.10 0.00 0.00 1.90
387 392 1.798813 GCAAGCGCGATTTTAGCCAAT 60.799 47.619 12.10 0.00 0.00 3.16
590 637 2.616376 TGAAGGTATGCGCGCAAATTAT 59.384 40.909 39.68 23.93 0.00 1.28
591 638 2.010497 TGAAGGTATGCGCGCAAATTA 58.990 42.857 39.68 23.54 0.00 1.40
719 766 5.981315 CGACTACAGGTTTTCAAGTTCACTA 59.019 40.000 0.00 0.00 0.00 2.74
779 826 0.044092 TACCCCCAGCTCCTCATCAA 59.956 55.000 0.00 0.00 0.00 2.57
861 909 0.465097 GTATCAGAGACGGGGGTCGA 60.465 60.000 0.00 0.00 42.43 4.20
863 911 1.409427 CTTGTATCAGAGACGGGGGTC 59.591 57.143 0.00 0.00 0.00 4.46
864 912 1.486211 CTTGTATCAGAGACGGGGGT 58.514 55.000 0.00 0.00 0.00 4.95
865 913 0.105039 GCTTGTATCAGAGACGGGGG 59.895 60.000 0.00 0.00 0.00 5.40
897 945 2.306219 GGGGAGTAGTCTTTGGCTCTTT 59.694 50.000 0.00 0.00 0.00 2.52
927 976 3.435026 GGTAGATATGGGGCAAGCAAAGA 60.435 47.826 0.00 0.00 0.00 2.52
1080 1171 4.503817 GCTAGAGCACCACCATCATTATGA 60.504 45.833 0.00 0.00 41.59 2.15
1122 1216 4.467084 GCCCTTGATCCGACGCCA 62.467 66.667 0.00 0.00 0.00 5.69
1127 1221 0.404040 ACCAAAAGCCCTTGATCCGA 59.596 50.000 0.00 0.00 0.00 4.55
1257 1351 1.676006 CTTTTGAACCGTGTGAGCCTT 59.324 47.619 0.00 0.00 0.00 4.35
1293 1387 5.048504 TGGATTTTCTACGTACGTGTCTTCT 60.049 40.000 30.25 11.18 0.00 2.85
1499 1594 2.965147 CCTCAATGTTGGGGTCAAGTTT 59.035 45.455 3.40 0.00 44.04 2.66
1557 1652 5.163301 CCCTAAAATCAAGCAGCTAGTAGGA 60.163 44.000 0.00 0.00 0.00 2.94
1837 1940 6.799441 TGTACACGTTTCAAATGATAATGTGC 59.201 34.615 19.24 11.76 40.64 4.57
1845 1949 3.880490 AGCCTTGTACACGTTTCAAATGA 59.120 39.130 0.00 0.00 0.00 2.57
1941 2046 7.657336 TCCAAAACATCTTATCTTTGTGAACC 58.343 34.615 0.00 0.00 0.00 3.62
1977 2082 5.573282 CACTTATTTCAGTCTGTGTAGTCCG 59.427 44.000 0.00 0.00 0.00 4.79
1987 2092 6.715464 CGTGTTTGTTCACTTATTTCAGTCT 58.285 36.000 0.00 0.00 36.33 3.24
2131 2242 5.006746 CGAGAATGTTTATACTCCTGTTGCC 59.993 44.000 0.00 0.00 0.00 4.52
2205 2316 7.605449 ACAATTGCATACAAAGTCTTGCTAAT 58.395 30.769 5.05 0.00 39.77 1.73
2414 2608 4.656100 TTGATTGTTTCCTCCCATCTCA 57.344 40.909 0.00 0.00 0.00 3.27
2429 2627 3.189287 CCTTCCGTTCTCCTGTTTGATTG 59.811 47.826 0.00 0.00 0.00 2.67
2452 2650 6.098982 CCAACTTCTCTCTATGTATGGTTCCT 59.901 42.308 0.00 0.00 0.00 3.36
2462 2661 6.323482 TCTCCTTCATCCAACTTCTCTCTATG 59.677 42.308 0.00 0.00 0.00 2.23
2472 2677 1.558756 CAGCCTCTCCTTCATCCAACT 59.441 52.381 0.00 0.00 0.00 3.16
2623 3200 6.150396 ACATCGACTCTTACTTTAGGGATG 57.850 41.667 0.00 0.00 35.56 3.51
2657 3588 5.049198 AGTGCCATGTATCGAATGCTAATTG 60.049 40.000 0.00 0.00 0.00 2.32
2668 3599 5.991328 ACTAATGAAAGTGCCATGTATCG 57.009 39.130 0.00 0.00 0.00 2.92
2892 3826 4.931002 ACATTTCAAATGCTAATGTGTGGC 59.069 37.500 10.21 0.00 40.08 5.01
3022 3963 2.596904 GCTTGGGCGATCACTTAGTA 57.403 50.000 0.00 0.00 0.00 1.82
3256 4208 1.569548 TCTCTATCTGGGGACGTTCCT 59.430 52.381 13.96 0.00 36.57 3.36
3257 4209 2.068834 TCTCTATCTGGGGACGTTCC 57.931 55.000 3.45 3.45 35.23 3.62
3259 4211 4.543689 TGTTATCTCTATCTGGGGACGTT 58.456 43.478 0.00 0.00 0.00 3.99
3261 4213 5.730296 AATGTTATCTCTATCTGGGGACG 57.270 43.478 0.00 0.00 0.00 4.79
3333 4295 4.623863 AGGGAATACCAAATTGAGGCAAT 58.376 39.130 0.00 0.00 43.89 3.56
3413 4375 6.597672 TGTGACTTGTTTTGTCTACAGATTGT 59.402 34.615 0.00 0.00 35.63 2.71
3419 4381 4.881273 AGCATGTGACTTGTTTTGTCTACA 59.119 37.500 0.00 0.00 35.63 2.74
3420 4382 5.007626 TCAGCATGTGACTTGTTTTGTCTAC 59.992 40.000 0.00 0.00 37.40 2.59
3483 4449 5.630061 ACAAAAAGCAGCAATTTCACAAAC 58.370 33.333 0.00 0.00 0.00 2.93
3557 4525 5.824624 CACACATATCTCAAATGCTAACCCT 59.175 40.000 0.00 0.00 0.00 4.34
3610 4580 1.920325 CAGCCTGGTCTGGAGGGAA 60.920 63.158 9.43 0.00 0.00 3.97
3625 4595 3.730761 CCGCCTTGTGCAGTCAGC 61.731 66.667 0.00 0.00 45.96 4.26
4005 4997 1.807886 GCGAGCGTCTTCCTCCTTA 59.192 57.895 0.00 0.00 0.00 2.69
4050 5046 3.429043 CACACATGCATGGGCTTTC 57.571 52.632 28.81 0.00 41.91 2.62
4178 5174 2.622977 CCTCTCCTAGAACAGAGCCACT 60.623 54.545 0.00 0.00 35.69 4.00
4241 5237 5.097438 CGAACTGTCGTTAAATCGTAGTG 57.903 43.478 0.00 0.00 42.53 2.74
4351 5388 7.042791 ACCAATGTAAGACGCAAAATCTTTTTG 60.043 33.333 8.07 8.07 37.57 2.44
4368 5405 3.521937 CCTTAGGAGTGGGACCAATGTAA 59.478 47.826 0.00 0.00 0.00 2.41
4376 5413 5.695424 ATTTTAGTCCTTAGGAGTGGGAC 57.305 43.478 18.25 0.00 46.94 4.46
4470 5508 6.487668 CCATACTGTATTCATGCTCCATTCAA 59.512 38.462 0.00 0.00 0.00 2.69
4474 5512 5.280368 CCTCCATACTGTATTCATGCTCCAT 60.280 44.000 0.00 0.00 0.00 3.41
4580 5619 4.657814 ACATCATTAGGTGAACCAAGGT 57.342 40.909 1.62 0.00 40.97 3.50
4605 5644 3.643320 GAGTGACTGGGTGATGGATCATA 59.357 47.826 0.00 0.00 39.30 2.15
4691 5731 9.747898 TTTTAAATAGGGAGATGCTAAAACTCA 57.252 29.630 0.00 0.00 33.00 3.41
4723 5763 6.380079 ACCAAGTGACAAATCTAGAGGATT 57.620 37.500 0.00 0.00 45.61 3.01
5005 6046 2.359249 GCCCCACCTAAAGGAATCCAAT 60.359 50.000 0.61 0.00 38.94 3.16
5059 6100 0.040204 CCCAGAAGTGGCCTTGGAAT 59.960 55.000 3.32 0.00 43.44 3.01
5079 6120 0.114560 GGGGAGGGTCGAGATCCATA 59.885 60.000 5.08 0.00 34.62 2.74
5303 6385 1.679680 CTTGCTTGATAGGGGCACATG 59.320 52.381 0.00 0.00 35.62 3.21
5421 6509 5.770663 GGACTAGAGTATGTCATCAAGGCTA 59.229 44.000 0.00 0.00 35.11 3.93
5423 6511 4.586841 AGGACTAGAGTATGTCATCAAGGC 59.413 45.833 0.00 0.00 35.11 4.35
5457 6545 7.017651 AGGTAACATATGGGGAAGGATAAGAAG 59.982 40.741 7.80 0.00 41.41 2.85
5563 6658 3.588842 TCAACATGATTCCCTCTCCAAGT 59.411 43.478 0.00 0.00 0.00 3.16
5598 6693 1.084370 CCGCCTTGACCAAGATCGTC 61.084 60.000 11.06 0.00 40.79 4.20
5600 6695 1.079127 ACCGCCTTGACCAAGATCG 60.079 57.895 11.06 12.45 40.79 3.69
5620 6715 0.108774 TGTATGGCCACAACCGTGAA 59.891 50.000 8.16 0.00 46.80 3.18
5642 6739 1.604278 GGAGGTCAAACAGTGCAAGAC 59.396 52.381 0.00 0.00 0.00 3.01
5720 6817 0.250338 GCCTCCGGTCACTTTGTCTT 60.250 55.000 0.00 0.00 0.00 3.01
5772 6869 0.687354 GACCAGCAAACTCCTCCAGA 59.313 55.000 0.00 0.00 0.00 3.86
5924 7052 4.183223 AGCAATCATACCTAATTGGCCA 57.817 40.909 0.00 0.00 40.22 5.36
5978 7106 1.451028 GCATCAGTCCTCCAGCCAC 60.451 63.158 0.00 0.00 0.00 5.01
6051 8558 5.881923 ACTAGACTGTAGAACCCAAAACA 57.118 39.130 0.00 0.00 0.00 2.83
6068 8575 2.042569 TGAGGCCACCTTGACTACTAGA 59.957 50.000 5.01 0.00 31.76 2.43
6082 8589 0.831711 TGTGCTCTAGTGTGAGGCCA 60.832 55.000 5.01 0.00 34.82 5.36
6171 8678 2.162681 GGTCACCTTTCTCATGGTTGG 58.837 52.381 0.00 0.00 33.75 3.77
6186 8693 2.754946 TAACTCCCATCGTTGGTCAC 57.245 50.000 11.51 0.00 41.91 3.67
6431 8940 1.072331 ACTTGAGGCAAGAACCGACAT 59.928 47.619 13.56 0.00 43.42 3.06
6464 8973 7.609097 AGCATGAAGACCAAGATAAGAGATA 57.391 36.000 0.00 0.00 0.00 1.98
6498 9007 4.049546 TCGTCTCAAAACGAGGAGAAAA 57.950 40.909 0.00 0.00 46.02 2.29
6560 9072 6.072199 AGGCAAGAATGTAGAGATTTCCTT 57.928 37.500 0.00 0.00 0.00 3.36
6580 9092 1.467920 CCATCCAACAAGAAGGAGGC 58.532 55.000 0.00 0.00 37.34 4.70
6616 9128 3.472652 TGCAAAAGACACATACGTTCCT 58.527 40.909 0.00 0.00 0.00 3.36
6709 9222 9.722056 CCTACATTACATTACTCAAATTCTTGC 57.278 33.333 0.00 0.00 32.14 4.01
6828 9342 5.241403 TCCAGAAAAAGATCCAAGTGCTA 57.759 39.130 0.00 0.00 0.00 3.49
6840 9354 8.958043 CGAGATTTACAAAACTTCCAGAAAAAG 58.042 33.333 0.00 0.00 0.00 2.27
6897 9467 8.213812 CACCTATTTTGCGTTTTCTACAATTTG 58.786 33.333 0.00 0.00 0.00 2.32
6907 9477 9.583765 TTAAAAGTTACACCTATTTTGCGTTTT 57.416 25.926 0.00 0.00 0.00 2.43
7080 9660 7.885399 ACTAAGCCTCATACTCTCACAAAATTT 59.115 33.333 0.00 0.00 0.00 1.82
7097 9677 6.382608 GTGAGAAAATTTCCAACTAAGCCTC 58.617 40.000 1.57 0.00 0.00 4.70
7147 9746 8.782144 GCCAGAATCTCAAATTATCTAAGGAAG 58.218 37.037 0.00 0.00 0.00 3.46
7210 9813 8.185003 ACAAAAGAAAACTAATGCAACACTTC 57.815 30.769 0.00 0.00 0.00 3.01
7211 9814 8.546597 AACAAAAGAAAACTAATGCAACACTT 57.453 26.923 0.00 0.00 0.00 3.16
7229 9832 8.967218 CCACTATGTTACACATTGAAACAAAAG 58.033 33.333 5.49 9.64 39.88 2.27
7569 10364 6.096987 ACACCACAACACACCAAATGTAATAA 59.903 34.615 0.00 0.00 40.64 1.40
7576 10371 2.175202 ACACACCACAACACACCAAAT 58.825 42.857 0.00 0.00 0.00 2.32
7875 10670 0.532573 CCACACTGCGGATGTACTCT 59.467 55.000 0.00 0.00 0.00 3.24
7927 10722 5.651612 TGATAGAATTGTGGGGACATCAT 57.348 39.130 0.00 0.00 46.14 2.45
7940 10735 5.999044 AGTGCTCTTGGTCATGATAGAATT 58.001 37.500 0.00 0.00 0.00 2.17
7944 10739 5.236282 CCATAGTGCTCTTGGTCATGATAG 58.764 45.833 0.00 0.00 0.00 2.08
7963 10758 1.792757 GCCATCCCCATCTGCCCATA 61.793 60.000 0.00 0.00 0.00 2.74
7964 10759 3.156363 GCCATCCCCATCTGCCCAT 62.156 63.158 0.00 0.00 0.00 4.00
8060 10855 1.969589 GGGTTTGGGTGGTAGTGCG 60.970 63.158 0.00 0.00 0.00 5.34
8100 10895 4.023450 CCATCGATGACATTCAAATCCTGG 60.023 45.833 26.86 1.26 0.00 4.45
8102 10897 4.139786 CCCATCGATGACATTCAAATCCT 58.860 43.478 26.86 0.00 0.00 3.24
8522 11351 9.853555 CATATATGTCTCACTTGAATCTAGTCC 57.146 37.037 4.43 0.00 0.00 3.85
8638 11470 5.020132 CCCCAAATGGACCACATAAAGTAA 58.980 41.667 0.00 0.00 39.40 2.24
8690 11522 4.937201 ACTGAAACAATTTCCCAAGGAC 57.063 40.909 0.00 0.00 38.90 3.85
8734 11566 4.635324 ACCTTTGACATTGCCTTGTTTTTG 59.365 37.500 0.00 0.00 0.00 2.44
8849 11684 4.692625 CACACACCTCTCAATCTAAACCTG 59.307 45.833 0.00 0.00 0.00 4.00
8925 11763 3.257561 CCGATCTGTTGCCGCTCG 61.258 66.667 0.00 0.00 0.00 5.03
8983 11821 2.690881 TGCCGCCTCCACCCTAAT 60.691 61.111 0.00 0.00 0.00 1.73
9039 12581 3.432378 TGTTCTTCCTCCTCTAGTGGTC 58.568 50.000 10.56 0.00 0.00 4.02
9122 12671 6.321435 TGAACTTCAAGTGAGTCTCAACTAGA 59.679 38.462 3.51 0.00 35.28 2.43
9443 14016 7.630242 TCACCAAATCTCTAAAATAGGCAAG 57.370 36.000 0.00 0.00 0.00 4.01
9444 14017 7.362920 GCTTCACCAAATCTCTAAAATAGGCAA 60.363 37.037 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.