Multiple sequence alignment - TraesCS2D01G260900

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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 TraesCS2D01G260900 chr2D 100.000 7537 0 0 1 7537 317862624 317870160 0.000000e+00 13919.0
1 TraesCS2D01G260900 chr2D 94.089 2267 96 9 3206 5444 441767380 441769636 0.000000e+00 3410.0
2 TraesCS2D01G260900 chr2A 96.589 2375 55 8 842 3205 416014029 416011670 0.000000e+00 3914.0
3 TraesCS2D01G260900 chr2A 95.663 1199 34 5 5443 6623 416011674 416010476 0.000000e+00 1910.0
4 TraesCS2D01G260900 chr2A 86.368 939 59 15 6664 7537 416010481 416009547 0.000000e+00 961.0
5 TraesCS2D01G260900 chr2A 93.993 566 34 0 284 849 22445263 22445828 0.000000e+00 857.0
6 TraesCS2D01G260900 chr2A 84.564 149 21 2 6162 6310 111429987 111429841 6.090000e-31 147.0
7 TraesCS2D01G260900 chr5B 94.381 2260 102 7 3206 5443 330740033 330742289 0.000000e+00 3446.0
8 TraesCS2D01G260900 chr5B 88.493 617 46 16 4851 5442 527042663 527042047 0.000000e+00 723.0
9 TraesCS2D01G260900 chr5B 85.841 339 37 1 5 343 304295362 304295035 4.330000e-92 350.0
10 TraesCS2D01G260900 chr1D 94.221 2267 93 17 3206 5443 98830439 98828182 0.000000e+00 3426.0
11 TraesCS2D01G260900 chr1D 94.045 2267 97 12 3217 5446 98832706 98830441 0.000000e+00 3404.0
12 TraesCS2D01G260900 chr1D 93.348 2270 108 14 3204 5442 258347735 258349992 0.000000e+00 3315.0
13 TraesCS2D01G260900 chr1D 92.421 409 20 4 1 409 470415953 470415556 2.360000e-159 573.0
14 TraesCS2D01G260900 chr4D 92.804 2265 112 10 3204 5440 274462306 274464547 0.000000e+00 3232.0
15 TraesCS2D01G260900 chr4D 93.943 974 52 1 4485 5451 390849084 390848111 0.000000e+00 1465.0
16 TraesCS2D01G260900 chr1A 91.652 2288 137 24 3206 5442 99900498 99902782 0.000000e+00 3118.0
17 TraesCS2D01G260900 chr5A 91.527 2266 132 19 3206 5443 455085171 455087404 0.000000e+00 3066.0
18 TraesCS2D01G260900 chr5A 89.718 496 33 8 1 492 534902296 534902777 1.070000e-172 617.0
19 TraesCS2D01G260900 chr5A 92.453 371 25 1 486 853 534903735 534904105 1.860000e-145 527.0
20 TraesCS2D01G260900 chr5A 97.674 43 1 0 2718 2760 549370207 549370249 2.920000e-09 75.0
21 TraesCS2D01G260900 chr3D 92.426 2086 132 7 3205 5266 606871886 606869803 0.000000e+00 2953.0
22 TraesCS2D01G260900 chr3D 90.909 55 3 1 2719 2773 611532904 611532956 1.050000e-08 73.1
23 TraesCS2D01G260900 chr6D 93.977 1959 85 11 3510 5443 211667779 211665829 0.000000e+00 2933.0
24 TraesCS2D01G260900 chr6D 93.264 1351 77 1 3205 4541 179952029 179953379 0.000000e+00 1978.0
25 TraesCS2D01G260900 chr3A 90.648 2128 175 8 3206 5309 654733850 654731723 0.000000e+00 2806.0
26 TraesCS2D01G260900 chr3A 91.138 1828 99 7 3531 5326 561094014 561095810 0.000000e+00 2420.0
27 TraesCS2D01G260900 chr6B 90.373 1610 117 19 3869 5442 159595580 159597187 0.000000e+00 2080.0
28 TraesCS2D01G260900 chr6B 95.041 484 18 3 364 843 670031791 670031310 0.000000e+00 756.0
29 TraesCS2D01G260900 chr6B 97.561 41 1 0 2720 2760 6167221 6167261 3.770000e-08 71.3
30 TraesCS2D01G260900 chr6B 90.196 51 5 0 2712 2762 7821332 7821382 4.880000e-07 67.6
31 TraesCS2D01G260900 chr6B 91.667 48 4 0 2713 2760 48674230 48674277 4.880000e-07 67.6
32 TraesCS2D01G260900 chr6B 91.667 48 4 0 2713 2760 48981425 48981472 4.880000e-07 67.6
33 TraesCS2D01G260900 chr6A 90.454 1519 129 7 3622 5132 28436841 28438351 0.000000e+00 1988.0
34 TraesCS2D01G260900 chr5D 93.358 1355 73 6 4105 5443 526248417 526249770 0.000000e+00 1988.0
35 TraesCS2D01G260900 chr4B 89.019 1448 137 12 3255 4683 140439158 140440602 0.000000e+00 1773.0
36 TraesCS2D01G260900 chr7D 97.048 847 24 1 1 846 383983395 383984241 0.000000e+00 1424.0
37 TraesCS2D01G260900 chr7D 87.534 738 78 10 14 748 402146619 402145893 0.000000e+00 841.0
38 TraesCS2D01G260900 chr7D 95.556 45 1 1 2718 2761 500925747 500925703 3.770000e-08 71.3
39 TraesCS2D01G260900 chr3B 93.499 846 52 1 1 843 78631534 78632379 0.000000e+00 1254.0
40 TraesCS2D01G260900 chr3B 93.381 846 53 1 1 843 16694534 16695379 0.000000e+00 1249.0
41 TraesCS2D01G260900 chr3B 87.034 1126 112 27 3206 4301 655318276 655319397 0.000000e+00 1240.0
42 TraesCS2D01G260900 chr1B 92.790 846 51 3 1 843 50018160 50017322 0.000000e+00 1216.0
43 TraesCS2D01G260900 chr7A 93.875 800 34 3 3205 3989 555462937 555463736 0.000000e+00 1192.0
44 TraesCS2D01G260900 chr7A 87.222 853 82 13 1 846 460114370 460113538 0.000000e+00 946.0
45 TraesCS2D01G260900 chr7B 87.264 848 100 7 1 846 411746909 411746068 0.000000e+00 961.0
46 TraesCS2D01G260900 chr4A 92.053 151 12 0 6162 6312 472961654 472961804 5.920000e-51 213.0
47 TraesCS2D01G260900 chrUn 91.667 48 4 0 2713 2760 205782104 205782151 4.880000e-07 67.6


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 TraesCS2D01G260900 chr2D 317862624 317870160 7536 False 13919.000000 13919 100.000000 1 7537 1 chr2D.!!$F1 7536
1 TraesCS2D01G260900 chr2D 441767380 441769636 2256 False 3410.000000 3410 94.089000 3206 5444 1 chr2D.!!$F2 2238
2 TraesCS2D01G260900 chr2A 416009547 416014029 4482 True 2261.666667 3914 92.873333 842 7537 3 chr2A.!!$R2 6695
3 TraesCS2D01G260900 chr2A 22445263 22445828 565 False 857.000000 857 93.993000 284 849 1 chr2A.!!$F1 565
4 TraesCS2D01G260900 chr5B 330740033 330742289 2256 False 3446.000000 3446 94.381000 3206 5443 1 chr5B.!!$F1 2237
5 TraesCS2D01G260900 chr5B 527042047 527042663 616 True 723.000000 723 88.493000 4851 5442 1 chr5B.!!$R2 591
6 TraesCS2D01G260900 chr1D 98828182 98832706 4524 True 3415.000000 3426 94.133000 3206 5446 2 chr1D.!!$R2 2240
7 TraesCS2D01G260900 chr1D 258347735 258349992 2257 False 3315.000000 3315 93.348000 3204 5442 1 chr1D.!!$F1 2238
8 TraesCS2D01G260900 chr4D 274462306 274464547 2241 False 3232.000000 3232 92.804000 3204 5440 1 chr4D.!!$F1 2236
9 TraesCS2D01G260900 chr4D 390848111 390849084 973 True 1465.000000 1465 93.943000 4485 5451 1 chr4D.!!$R1 966
10 TraesCS2D01G260900 chr1A 99900498 99902782 2284 False 3118.000000 3118 91.652000 3206 5442 1 chr1A.!!$F1 2236
11 TraesCS2D01G260900 chr5A 455085171 455087404 2233 False 3066.000000 3066 91.527000 3206 5443 1 chr5A.!!$F1 2237
12 TraesCS2D01G260900 chr5A 534902296 534904105 1809 False 572.000000 617 91.085500 1 853 2 chr5A.!!$F3 852
13 TraesCS2D01G260900 chr3D 606869803 606871886 2083 True 2953.000000 2953 92.426000 3205 5266 1 chr3D.!!$R1 2061
14 TraesCS2D01G260900 chr6D 211665829 211667779 1950 True 2933.000000 2933 93.977000 3510 5443 1 chr6D.!!$R1 1933
15 TraesCS2D01G260900 chr6D 179952029 179953379 1350 False 1978.000000 1978 93.264000 3205 4541 1 chr6D.!!$F1 1336
16 TraesCS2D01G260900 chr3A 654731723 654733850 2127 True 2806.000000 2806 90.648000 3206 5309 1 chr3A.!!$R1 2103
17 TraesCS2D01G260900 chr3A 561094014 561095810 1796 False 2420.000000 2420 91.138000 3531 5326 1 chr3A.!!$F1 1795
18 TraesCS2D01G260900 chr6B 159595580 159597187 1607 False 2080.000000 2080 90.373000 3869 5442 1 chr6B.!!$F5 1573
19 TraesCS2D01G260900 chr6A 28436841 28438351 1510 False 1988.000000 1988 90.454000 3622 5132 1 chr6A.!!$F1 1510
20 TraesCS2D01G260900 chr5D 526248417 526249770 1353 False 1988.000000 1988 93.358000 4105 5443 1 chr5D.!!$F1 1338
21 TraesCS2D01G260900 chr4B 140439158 140440602 1444 False 1773.000000 1773 89.019000 3255 4683 1 chr4B.!!$F1 1428
22 TraesCS2D01G260900 chr7D 383983395 383984241 846 False 1424.000000 1424 97.048000 1 846 1 chr7D.!!$F1 845
23 TraesCS2D01G260900 chr7D 402145893 402146619 726 True 841.000000 841 87.534000 14 748 1 chr7D.!!$R1 734
24 TraesCS2D01G260900 chr3B 78631534 78632379 845 False 1254.000000 1254 93.499000 1 843 1 chr3B.!!$F2 842
25 TraesCS2D01G260900 chr3B 16694534 16695379 845 False 1249.000000 1249 93.381000 1 843 1 chr3B.!!$F1 842
26 TraesCS2D01G260900 chr3B 655318276 655319397 1121 False 1240.000000 1240 87.034000 3206 4301 1 chr3B.!!$F3 1095
27 TraesCS2D01G260900 chr1B 50017322 50018160 838 True 1216.000000 1216 92.790000 1 843 1 chr1B.!!$R1 842
28 TraesCS2D01G260900 chr7A 555462937 555463736 799 False 1192.000000 1192 93.875000 3205 3989 1 chr7A.!!$F1 784
29 TraesCS2D01G260900 chr7A 460113538 460114370 832 True 946.000000 946 87.222000 1 846 1 chr7A.!!$R1 845
30 TraesCS2D01G260900 chr7B 411746068 411746909 841 True 961.000000 961 87.264000 1 846 1 chr7B.!!$R1 845

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
879 1859 0.981183 ACAGAGGGCGTACATGGAAA 59.019 50.0 0.00 0.0 0.00 3.13 F
1316 2304 0.269173 AGATCCGATTCCCCTTCCCT 59.731 55.0 0.00 0.0 0.00 4.20 F
1597 2585 0.679002 CTAGGGTTCGTCGACCTGGA 60.679 60.0 10.58 0.0 39.71 3.86 F
2651 3640 0.680921 GCTGAGCAAATGCCCTGGTA 60.681 55.0 0.00 0.0 43.38 3.25 F
4275 5653 0.179161 CAGACGACGCCGAGATTCTT 60.179 55.0 0.00 0.0 39.50 2.52 F
5121 8560 0.035458 GGCGGGGAGAGATGTTATGG 59.965 60.0 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2735 0.388294 CGAGATGATGCAGAGGCTGA 59.612 55.000 0.00 0.00 41.91 4.26 R
2965 3954 0.905357 ACTGGGGTCTAGACATGCAC 59.095 55.000 23.91 8.92 0.00 4.57 R
3546 4898 2.138320 CATGATCGCACCGAAGCTATT 58.862 47.619 0.00 0.00 39.99 1.73 R
4476 5878 0.171903 GCGCAAGAGGCACAAATCAT 59.828 50.000 0.30 0.00 45.17 2.45 R
6105 9553 0.250295 TCTTTGGGAACAGGCTGTCG 60.250 55.000 22.31 4.01 44.54 4.35 R
6641 10106 0.031716 CCTCCTCTGTCCCCAGATCA 60.032 60.000 0.00 0.00 46.38 2.92 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
228 233 1.056660 GACCACTGGTCCTTCCTGAA 58.943 55.000 16.54 0.00 46.19 3.02
547 1518 1.202099 TACCCAAGGAACCATCGCCA 61.202 55.000 0.00 0.00 0.00 5.69
734 1709 4.255833 TCATCCAAACAAGGATTTGTGC 57.744 40.909 0.00 0.00 46.12 4.57
812 1792 8.666580 ACTAAAACGCGTTTTGTTAAAACTAA 57.333 26.923 43.89 26.69 46.54 2.24
868 1848 3.017442 GTCTTATTTTGGGACAGAGGGC 58.983 50.000 0.00 0.00 42.39 5.19
879 1859 0.981183 ACAGAGGGCGTACATGGAAA 59.019 50.000 0.00 0.00 0.00 3.13
947 1927 4.881850 CCAGTAGCTACCACATAAAAAGGG 59.118 45.833 20.31 1.95 0.00 3.95
1215 2203 3.133721 CGATATCCTCCATTCCATCCTCC 59.866 52.174 0.00 0.00 0.00 4.30
1221 2209 1.895707 CATTCCATCCTCCTGCGCC 60.896 63.158 4.18 0.00 0.00 6.53
1316 2304 0.269173 AGATCCGATTCCCCTTCCCT 59.731 55.000 0.00 0.00 0.00 4.20
1320 2308 1.279025 CCGATTCCCCTTCCCTTCCA 61.279 60.000 0.00 0.00 0.00 3.53
1475 2463 4.243270 GCGGAGAGCTTTACTTCTACAAA 58.757 43.478 0.00 0.00 44.04 2.83
1597 2585 0.679002 CTAGGGTTCGTCGACCTGGA 60.679 60.000 10.58 0.00 39.71 3.86
1604 2592 3.827898 GTCGACCTGGAGCTCCCG 61.828 72.222 29.95 24.17 37.93 5.14
1662 2650 1.606668 TGGAACACGTGAATTTGGAGC 59.393 47.619 25.01 0.10 0.00 4.70
1691 2679 3.069980 GCTCGGCGACATGGTCTCT 62.070 63.158 4.99 0.00 0.00 3.10
1901 2889 2.101917 AGTTGCTGCCATTTATGCATCC 59.898 45.455 0.19 0.00 38.22 3.51
1949 2937 1.267732 GCATTTGATCCGAGCTTCGTG 60.268 52.381 0.00 0.00 38.40 4.35
1961 2949 2.720758 CTTCGTGCTGTTCGGCGAG 61.721 63.158 10.46 0.00 34.78 5.03
1965 2953 4.680237 TGCTGTTCGGCGAGGTGG 62.680 66.667 10.46 3.34 34.52 4.61
2039 3027 2.674796 ACGCACTCCTTCAGGATTAC 57.325 50.000 0.00 0.00 44.46 1.89
2169 3157 8.467598 TGTACTTAGTAAGAAGCTACAATCTGG 58.532 37.037 16.89 0.00 0.00 3.86
2234 3222 9.938280 TGTATACTTGCTTGTTATGACTTACTT 57.062 29.630 4.17 0.00 0.00 2.24
2319 3307 5.703130 GTCAAACTTCAGAGTTGAGGCTAAT 59.297 40.000 0.00 0.00 45.18 1.73
2331 3319 8.584157 AGAGTTGAGGCTAATACTCAGAATATG 58.416 37.037 19.20 0.00 44.91 1.78
2367 3355 7.585286 TTAGCATTGCAATTGTTCATTCTTC 57.415 32.000 9.83 0.00 0.00 2.87
2479 3468 4.270325 AGACAGTTCGCTTTGAAACTACAC 59.730 41.667 0.00 0.00 38.60 2.90
2644 3633 1.100510 TCCATCTGCTGAGCAAATGC 58.899 50.000 15.03 0.00 35.87 3.56
2651 3640 0.680921 GCTGAGCAAATGCCCTGGTA 60.681 55.000 0.00 0.00 43.38 3.25
2687 3676 9.151471 TGAAGCTGACATTACTTGATAACTTAC 57.849 33.333 0.00 0.00 0.00 2.34
2746 3735 7.235812 ACTCCCTCTGTAAAGAAATACAAGAGT 59.764 37.037 0.00 0.00 35.48 3.24
2823 3812 5.070770 TGATTGAAAAGCATTTACGCCAT 57.929 34.783 0.00 0.00 37.27 4.40
2825 3814 5.348179 TGATTGAAAAGCATTTACGCCATTG 59.652 36.000 0.00 0.00 37.27 2.82
2883 3872 9.619316 TTCTGTTGATTTAATATCGTTGGTTTG 57.381 29.630 0.00 0.00 0.00 2.93
2965 3954 2.350804 CAGTCATGCAGTCAATTCCTCG 59.649 50.000 0.00 0.00 0.00 4.63
2974 3963 2.027745 AGTCAATTCCTCGTGCATGTCT 60.028 45.455 5.68 0.00 0.00 3.41
3136 4126 9.965902 AAAACTATTGTGAAATGATCCTCTACT 57.034 29.630 0.00 0.00 0.00 2.57
3202 4193 2.502947 TGCTATGTTGAGATGGAGCAGT 59.497 45.455 0.00 0.00 35.12 4.40
3250 4241 1.074951 GCCCAGTTAGTTGTGGCCT 59.925 57.895 3.32 0.00 36.07 5.19
4027 5405 1.305465 TCTGTTACCGGCCTGGCTA 60.305 57.895 19.68 0.00 43.94 3.93
4275 5653 0.179161 CAGACGACGCCGAGATTCTT 60.179 55.000 0.00 0.00 39.50 2.52
4356 5734 2.030274 GTGACCAATTTTTCAGGGGACG 60.030 50.000 0.00 0.00 0.00 4.79
4402 5780 3.010420 CTGGATCGCCTCGTATCATCTA 58.990 50.000 0.00 0.00 34.31 1.98
4416 5802 3.465296 ATCTACGAGGAACCGCGCG 62.465 63.158 25.67 25.67 42.73 6.86
4439 5841 0.743097 GTGGTACTACGCCCTCGAAT 59.257 55.000 0.00 0.00 39.41 3.34
4644 6046 2.569134 GGCTGAGCTCTTCGTCGT 59.431 61.111 16.19 0.00 0.00 4.34
4956 8379 3.133464 CGTACCGGGCCACGTCTA 61.133 66.667 6.32 0.00 42.24 2.59
5121 8560 0.035458 GGCGGGGAGAGATGTTATGG 59.965 60.000 0.00 0.00 0.00 2.74
5401 8848 1.771255 CATCCCTCCTTTCACCCCTAG 59.229 57.143 0.00 0.00 0.00 3.02
5406 8853 1.560146 CTCCTTTCACCCCTAGAACCC 59.440 57.143 0.00 0.00 0.00 4.11
5486 8933 5.513233 AGGCCTCACACATTTGAAAGATAT 58.487 37.500 0.00 0.00 0.00 1.63
5500 8947 5.107133 TGAAAGATATTTCGAAGACCGGAC 58.893 41.667 9.46 0.10 39.14 4.79
5558 9005 2.623889 ACTGATGGTGTCTATACGAGCC 59.376 50.000 0.00 0.00 0.00 4.70
5559 9006 2.623416 CTGATGGTGTCTATACGAGCCA 59.377 50.000 0.00 0.00 0.00 4.75
5678 9125 5.757099 ACTTAGGTTTGGTGCTACTGTAT 57.243 39.130 0.00 0.00 0.00 2.29
5932 9380 3.887621 TCCGTAACTTCAGAGGATTGG 57.112 47.619 0.00 0.00 0.00 3.16
5949 9397 4.872124 GGATTGGAACATGATTTTGCCTTC 59.128 41.667 0.00 0.00 39.30 3.46
6035 9483 1.622811 CAGTCCAAGTGAGGAGCTCTT 59.377 52.381 14.64 5.66 38.64 2.85
6105 9553 3.192922 GTGTCGTATGCACCGCCC 61.193 66.667 2.85 0.00 0.00 6.13
6141 9589 0.247736 AGACTCCGGATGACTGTTGC 59.752 55.000 3.57 0.00 0.00 4.17
6157 9605 4.454161 ACTGTTGCGAATAGTAATTGTGCA 59.546 37.500 0.00 0.00 33.52 4.57
6159 9607 3.673746 TGCGAATAGTAATTGTGCAGC 57.326 42.857 0.00 0.00 32.32 5.25
6231 9679 4.166011 GAGCGGACATTGCACGGC 62.166 66.667 0.00 0.00 33.85 5.68
6264 9712 0.954452 CCCTGGCTGGATTTTATCGC 59.046 55.000 12.58 0.00 38.35 4.58
6266 9714 0.588252 CTGGCTGGATTTTATCGCCG 59.412 55.000 0.00 0.00 38.25 6.46
6362 9810 2.837498 TGATGCGGTATCTTGATGTGG 58.163 47.619 7.58 0.00 36.71 4.17
6382 9832 6.007076 TGTGGATTAGTTGCATACCTTGAAA 58.993 36.000 0.00 0.00 0.00 2.69
6385 9835 8.682710 GTGGATTAGTTGCATACCTTGAAAATA 58.317 33.333 0.00 0.00 0.00 1.40
6392 9842 9.435688 AGTTGCATACCTTGAAAATATTTTTCC 57.564 29.630 14.45 4.07 0.00 3.13
6416 9866 5.892160 TCTGAAAGAAGATCCTTGCATTG 57.108 39.130 0.00 0.00 42.31 2.82
6470 9921 3.164268 TGGATATTTGTGCCAACTTGCT 58.836 40.909 0.00 0.00 0.00 3.91
6532 9997 7.659390 AGATATGCTTCTATAAAGCTGTGTTCC 59.341 37.037 10.75 0.00 43.38 3.62
6563 10028 6.141685 GCAAATGTACAAGTTTCGTTAACCTG 59.858 38.462 0.00 1.33 37.46 4.00
6600 10065 0.678395 TGCCATGCCGTTGAAATGTT 59.322 45.000 0.00 0.00 0.00 2.71
6619 10084 9.490663 GAAATGTTGAATTATGTAGAACTTCGG 57.509 33.333 0.00 0.00 0.00 4.30
6620 10085 8.561738 AATGTTGAATTATGTAGAACTTCGGT 57.438 30.769 0.00 0.00 0.00 4.69
6621 10086 7.972832 TGTTGAATTATGTAGAACTTCGGTT 57.027 32.000 0.00 0.00 41.38 4.44
6632 10097 2.100605 ACTTCGGTTCTTCAGATGGC 57.899 50.000 0.00 0.00 0.00 4.40
6633 10098 1.339151 ACTTCGGTTCTTCAGATGGCC 60.339 52.381 0.00 0.00 0.00 5.36
6634 10099 0.690192 TTCGGTTCTTCAGATGGCCA 59.310 50.000 8.56 8.56 0.00 5.36
6635 10100 0.250234 TCGGTTCTTCAGATGGCCAG 59.750 55.000 13.05 0.00 0.00 4.85
6636 10101 0.250234 CGGTTCTTCAGATGGCCAGA 59.750 55.000 13.05 0.00 0.00 3.86
6637 10102 1.134280 CGGTTCTTCAGATGGCCAGAT 60.134 52.381 13.05 0.00 0.00 2.90
6638 10103 2.681976 CGGTTCTTCAGATGGCCAGATT 60.682 50.000 13.05 0.00 0.00 2.40
6639 10104 2.686915 GGTTCTTCAGATGGCCAGATTG 59.313 50.000 13.05 9.63 0.00 2.67
6640 10105 2.048444 TCTTCAGATGGCCAGATTGC 57.952 50.000 13.05 0.00 0.00 3.56
6641 10106 1.562942 TCTTCAGATGGCCAGATTGCT 59.437 47.619 13.05 0.00 0.00 3.91
6642 10107 1.676529 CTTCAGATGGCCAGATTGCTG 59.323 52.381 13.05 13.13 41.93 4.41
6643 10108 0.913924 TCAGATGGCCAGATTGCTGA 59.086 50.000 13.05 15.20 45.17 4.26
6644 10109 1.493446 TCAGATGGCCAGATTGCTGAT 59.507 47.619 13.05 0.00 45.17 2.90
6645 10110 1.880675 CAGATGGCCAGATTGCTGATC 59.119 52.381 13.05 0.00 45.17 2.92
6646 10111 1.775459 AGATGGCCAGATTGCTGATCT 59.225 47.619 13.05 2.18 46.12 2.75
6653 10118 1.588239 AGATTGCTGATCTGGGGACA 58.412 50.000 1.46 0.00 43.52 4.02
6663 10128 2.450243 TGGGGACAGAGGAGGGAC 59.550 66.667 0.00 0.00 35.01 4.46
6699 10164 2.284405 GTCCGGTCCTCTTCCCCA 60.284 66.667 0.00 0.00 0.00 4.96
6708 10173 1.916181 TCCTCTTCCCCATTTCACCTC 59.084 52.381 0.00 0.00 0.00 3.85
6831 10297 2.730550 GCAAGCTGCAAAAGGTATGT 57.269 45.000 1.02 0.00 44.26 2.29
6854 10320 5.850557 TGTGGAACATCACAAAGACAAAT 57.149 34.783 0.00 0.00 45.67 2.32
6863 10329 5.772825 TCACAAAGACAAATTTGCTAGCT 57.227 34.783 18.12 7.71 42.68 3.32
6864 10330 5.522456 TCACAAAGACAAATTTGCTAGCTG 58.478 37.500 18.12 7.85 42.68 4.24
6945 10411 6.705381 TCAACTTAATTGAAACCTGCCAAATG 59.295 34.615 0.00 0.00 44.59 2.32
6965 10431 0.736053 TGGCAAGTGACACGGAAAAC 59.264 50.000 0.00 0.00 0.00 2.43
7001 10467 9.317936 TGCACTGAATATACTGTCAAGAAATAG 57.682 33.333 0.00 0.00 0.00 1.73
7010 10476 3.002791 TGTCAAGAAATAGCTTCGCCAG 58.997 45.455 0.00 0.00 39.22 4.85
7012 10478 3.062774 GTCAAGAAATAGCTTCGCCAGAC 59.937 47.826 0.00 0.00 39.22 3.51
7014 10480 3.550437 AGAAATAGCTTCGCCAGACAT 57.450 42.857 0.00 0.00 39.22 3.06
7016 10482 5.023533 AGAAATAGCTTCGCCAGACATAA 57.976 39.130 0.00 0.00 39.22 1.90
7022 10510 3.624861 AGCTTCGCCAGACATAAAATCTG 59.375 43.478 0.00 0.00 42.79 2.90
7033 10521 5.297776 AGACATAAAATCTGGGCTGAATTCG 59.702 40.000 0.04 0.00 0.00 3.34
7078 10566 3.058639 GCTAAAAGCTGTGAACTGACAGG 60.059 47.826 7.51 0.00 43.17 4.00
7098 10586 3.960102 AGGAACTTGCTCCAATTTGTCAA 59.040 39.130 0.00 0.00 38.02 3.18
7099 10587 4.038402 AGGAACTTGCTCCAATTTGTCAAG 59.962 41.667 15.59 15.59 38.02 3.02
7100 10588 3.375782 ACTTGCTCCAATTTGTCAAGC 57.624 42.857 16.45 12.63 38.06 4.01
7101 10589 2.694628 ACTTGCTCCAATTTGTCAAGCA 59.305 40.909 16.45 14.36 40.96 3.91
7106 10594 5.229423 TGCTCCAATTTGTCAAGCATAAAC 58.771 37.500 11.91 0.00 38.01 2.01
7141 10629 4.454678 TCATGCAGTTCACTGAAAGAGTT 58.545 39.130 11.29 0.00 46.59 3.01
7143 10631 5.466728 TCATGCAGTTCACTGAAAGAGTTAC 59.533 40.000 11.29 0.00 46.59 2.50
7150 10638 5.723672 TCACTGAAAGAGTTACCCAGTAG 57.276 43.478 0.00 0.00 36.44 2.57
7158 10646 2.101082 GAGTTACCCAGTAGCTGTAGGC 59.899 54.545 0.00 0.00 42.19 3.93
7165 10653 3.118408 CCCAGTAGCTGTAGGCATAACAA 60.118 47.826 0.00 0.00 44.79 2.83
7177 10665 9.507280 CTGTAGGCATAACAATAACAAGAAATG 57.493 33.333 0.00 0.00 0.00 2.32
7246 10734 5.858381 TCTAGAGTGCAATCACAGAAAACT 58.142 37.500 17.53 0.00 45.49 2.66
7250 10738 5.931146 AGAGTGCAATCACAGAAAACTAGAG 59.069 40.000 17.53 0.00 45.49 2.43
7304 10809 7.510549 TGGTTAGGAAGAAAGAACTCAAATG 57.489 36.000 0.00 0.00 0.00 2.32
7311 10816 6.142958 GGAAGAAAGAACTCAAATGAAAAGCG 59.857 38.462 0.00 0.00 0.00 4.68
7315 10820 7.545615 AGAAAGAACTCAAATGAAAAGCGTTTT 59.454 29.630 0.00 0.00 33.51 2.43
7334 10839 1.960040 TATGTCCCTGCAGAGCCACG 61.960 60.000 17.39 0.00 0.00 4.94
7347 10852 1.529865 GAGCCACGACCTAACACAAAC 59.470 52.381 0.00 0.00 0.00 2.93
7348 10853 0.233848 GCCACGACCTAACACAAACG 59.766 55.000 0.00 0.00 0.00 3.60
7398 10904 7.762382 AGATTCGTTACAAAATTCTTCCCATC 58.238 34.615 0.00 0.00 0.00 3.51
7399 10905 5.539582 TCGTTACAAAATTCTTCCCATCG 57.460 39.130 0.00 0.00 0.00 3.84
7402 10908 6.649973 TCGTTACAAAATTCTTCCCATCGTTA 59.350 34.615 0.00 0.00 0.00 3.18
7451 10981 7.654022 AGGGTAAATTTGAAGAGTGTGAAAA 57.346 32.000 0.00 0.00 0.00 2.29
7462 10992 9.520204 TTGAAGAGTGTGAAAAATGAAATTCTC 57.480 29.630 0.00 0.00 33.67 2.87
7464 10994 7.496529 AGAGTGTGAAAAATGAAATTCTCGA 57.503 32.000 0.00 0.00 33.67 4.04
7495 11025 1.198408 CGCAGTTCACACATCAGCATT 59.802 47.619 0.00 0.00 0.00 3.56
7496 11026 2.592194 GCAGTTCACACATCAGCATTG 58.408 47.619 0.00 0.00 0.00 2.82
7529 11059 6.715264 ACTACCGATTTGTCTTCTCCATTTTT 59.285 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 122 1.467543 CGACGACAATGACGATGGTCT 60.468 52.381 12.41 0.00 43.79 3.85
225 230 0.033504 GTGAGAAGAGTGCCCGTTCA 59.966 55.000 0.00 0.00 0.00 3.18
228 233 2.143594 GACGTGAGAAGAGTGCCCGT 62.144 60.000 0.00 0.00 0.00 5.28
424 431 7.729124 ACAGCCAAATTACTACTAGTCCTTA 57.271 36.000 0.00 0.00 0.00 2.69
812 1792 8.403236 GTTGTTTGGATAAATAGGATTAACGCT 58.597 33.333 0.00 0.00 0.00 5.07
868 1848 5.586243 ACTGATTCTTGGATTTCCATGTACG 59.414 40.000 11.10 0.00 46.97 3.67
879 1859 6.120905 CAGGAAGATTCACTGATTCTTGGAT 58.879 40.000 17.17 4.42 34.00 3.41
890 1870 4.197750 CAGCTATTGCAGGAAGATTCACT 58.802 43.478 1.12 0.00 42.74 3.41
947 1927 0.829182 CATATTGGGCTTCCCTGGGC 60.829 60.000 8.22 0.00 45.70 5.36
1215 2203 4.785453 GGTGGAAGGGAGGCGCAG 62.785 72.222 10.83 0.00 0.00 5.18
1531 2519 2.794820 GAAGCAGGGCAGCTCGAAGT 62.795 60.000 4.11 0.00 45.89 3.01
1662 2650 3.423154 GCCGAGCTGGAAACCACG 61.423 66.667 0.00 0.00 42.00 4.94
1737 2725 2.607750 GAGGCTGACCACTCCCCA 60.608 66.667 0.00 0.00 39.06 4.96
1747 2735 0.388294 CGAGATGATGCAGAGGCTGA 59.612 55.000 0.00 0.00 41.91 4.26
1901 2889 1.197430 ACCAGAGAACCTCCAGCCTG 61.197 60.000 0.00 0.00 0.00 4.85
1949 2937 4.373116 TCCACCTCGCCGAACAGC 62.373 66.667 0.00 0.00 0.00 4.40
1965 2953 1.473080 GGTCAGCTGCTGGAGATTCTC 60.473 57.143 27.79 5.03 31.51 2.87
2169 3157 6.327279 ACTCTAAAGGTAATTTTGTGGCAC 57.673 37.500 11.55 11.55 32.01 5.01
2234 3222 5.441500 TCCTGTTGTTCCAATTGTTGAGTA 58.558 37.500 4.43 0.00 0.00 2.59
2235 3223 4.277476 TCCTGTTGTTCCAATTGTTGAGT 58.723 39.130 4.43 0.00 0.00 3.41
2236 3224 4.916983 TCCTGTTGTTCCAATTGTTGAG 57.083 40.909 4.43 0.00 0.00 3.02
2237 3225 4.464244 TGTTCCTGTTGTTCCAATTGTTGA 59.536 37.500 4.43 0.00 0.00 3.18
2290 3278 5.178996 CCTCAACTCTGAAGTTTGACATGAG 59.821 44.000 0.00 0.00 43.28 2.90
2331 3319 9.017669 CAATTGCAATGCTAATTCTCTAGAAAC 57.982 33.333 13.82 0.00 37.61 2.78
2367 3355 3.262420 CCACTGAAGATTTCCACGGTAG 58.738 50.000 0.00 0.00 0.00 3.18
2442 3430 5.005203 GCGAACTGTCTATTCATGAAGACTG 59.995 44.000 22.86 22.86 42.17 3.51
2449 3437 5.784750 TCAAAGCGAACTGTCTATTCATG 57.215 39.130 0.00 0.00 0.00 3.07
2479 3468 2.301346 AGACAGCCCAAAACTGAACAG 58.699 47.619 0.00 0.00 38.55 3.16
2644 3633 3.244044 GCTTCAGCTCTCTAATACCAGGG 60.244 52.174 0.00 0.00 38.21 4.45
2769 3758 5.003804 CACTCCAGCAATAACCAAAGTACT 58.996 41.667 0.00 0.00 0.00 2.73
2823 3812 2.369860 AGATCAAGCCTCAGTGTGACAA 59.630 45.455 0.00 0.00 0.00 3.18
2825 3814 2.344950 CAGATCAAGCCTCAGTGTGAC 58.655 52.381 0.00 0.00 0.00 3.67
2965 3954 0.905357 ACTGGGGTCTAGACATGCAC 59.095 55.000 23.91 8.92 0.00 4.57
2974 3963 4.993705 ACAAGATCAAAACTGGGGTCTA 57.006 40.909 0.00 0.00 0.00 2.59
3202 4193 5.512404 CCCTAATATGCCGGTCATAACAGAA 60.512 44.000 18.34 2.13 40.73 3.02
3546 4898 2.138320 CATGATCGCACCGAAGCTATT 58.862 47.619 0.00 0.00 39.99 1.73
3886 5264 4.746309 TGCTGCATGGTGGAGGCC 62.746 66.667 0.00 0.00 36.25 5.19
4027 5405 3.334054 GGCTCAAGGGACCCAGCT 61.334 66.667 18.27 0.00 32.14 4.24
4262 5640 0.247736 AGCTTGAAGAATCTCGGCGT 59.752 50.000 6.85 0.00 0.00 5.68
4275 5653 1.372997 GTCGCGAACTCCAGCTTGA 60.373 57.895 12.06 0.00 0.00 3.02
4336 5714 2.235016 CGTCCCCTGAAAAATTGGTCA 58.765 47.619 0.00 0.00 0.00 4.02
4439 5841 3.536917 CATGCCGCCCTCGTCCTA 61.537 66.667 0.00 0.00 0.00 2.94
4467 5869 0.803380 GCACAAATCATGGAAGCGCC 60.803 55.000 2.29 0.00 37.10 6.53
4476 5878 0.171903 GCGCAAGAGGCACAAATCAT 59.828 50.000 0.30 0.00 45.17 2.45
4741 6143 4.437587 GCCTGCTGGATGGCCACT 62.438 66.667 8.16 0.00 43.11 4.00
4886 8309 3.106407 GCGACGCTCGAGTTGCTT 61.106 61.111 13.73 0.00 45.57 3.91
4956 8379 1.451067 CAGGTAGAAGAGTCGTCGGT 58.549 55.000 0.15 0.00 0.00 4.69
4959 8382 2.018515 CCTCCAGGTAGAAGAGTCGTC 58.981 57.143 0.00 0.00 0.00 4.20
5082 8521 0.463654 TGCACAAACAGCTCGTCCTT 60.464 50.000 0.00 0.00 0.00 3.36
5121 8560 0.326927 TAAGCCCCTAATATGCCGGC 59.673 55.000 22.73 22.73 40.03 6.13
5401 8848 4.754667 GGGCGTGGTCTCGGGTTC 62.755 72.222 0.00 0.00 0.00 3.62
5486 8933 0.460722 TGTGTGTCCGGTCTTCGAAA 59.539 50.000 0.00 0.00 42.43 3.46
5500 8947 4.292599 CACCAATCTTTGTGACATGTGTG 58.707 43.478 1.15 0.00 0.00 3.82
5552 8999 1.672356 GTTGGTGCTCATGGCTCGT 60.672 57.895 7.54 0.00 42.39 4.18
5582 9029 2.550277 TGATCTGAGGCCAAGGTCTA 57.450 50.000 17.06 4.26 0.00 2.59
5585 9032 3.245371 TGAAATTGATCTGAGGCCAAGGT 60.245 43.478 5.01 0.00 0.00 3.50
5619 9066 6.061441 CACCAGTTGCCAGTTATCCATATTA 58.939 40.000 0.00 0.00 0.00 0.98
5684 9131 9.630098 CAAACATAGTGCTATGAGAAAAACATT 57.370 29.630 21.81 3.94 44.22 2.71
5932 9380 3.057596 TCCACGAAGGCAAAATCATGTTC 60.058 43.478 0.00 0.00 37.29 3.18
5949 9397 2.083774 ACACCAAACAGCATATCCACG 58.916 47.619 0.00 0.00 0.00 4.94
6094 9542 4.830765 GCTGTCGGGCGGTGCATA 62.831 66.667 0.00 0.00 0.00 3.14
6105 9553 0.250295 TCTTTGGGAACAGGCTGTCG 60.250 55.000 22.31 4.01 44.54 4.35
6141 9589 4.514545 TTCGCTGCACAATTACTATTCG 57.485 40.909 0.00 0.00 0.00 3.34
6159 9607 0.865111 TCGTGTGTGGAGCAATTTCG 59.135 50.000 0.00 0.00 0.00 3.46
6231 9679 1.952367 GCCAGGGAATCTTGTCCACAG 60.952 57.143 0.00 0.00 39.70 3.66
6339 9787 3.249320 CACATCAAGATACCGCATCAAGG 59.751 47.826 0.00 0.00 35.96 3.61
6470 9921 6.149308 GTCCTGACATGAAACATGATACAACA 59.851 38.462 16.86 7.22 0.00 3.33
6474 9925 5.643348 TGTGTCCTGACATGAAACATGATAC 59.357 40.000 16.86 8.22 43.97 2.24
6526 9991 2.888834 ACATTTGCAGTTGGGAACAC 57.111 45.000 3.40 0.00 42.67 3.32
6532 9997 4.440758 CGAAACTTGTACATTTGCAGTTGG 59.559 41.667 9.96 3.49 0.00 3.77
6563 10028 1.403249 GCATGCTCCAATTGGTGACAC 60.403 52.381 26.79 12.01 42.67 3.67
6618 10083 2.686915 CAATCTGGCCATCTGAAGAACC 59.313 50.000 5.51 0.00 0.00 3.62
6619 10084 2.098770 GCAATCTGGCCATCTGAAGAAC 59.901 50.000 5.51 0.00 0.00 3.01
6620 10085 2.025605 AGCAATCTGGCCATCTGAAGAA 60.026 45.455 5.51 0.00 0.00 2.52
6621 10086 1.562942 AGCAATCTGGCCATCTGAAGA 59.437 47.619 5.51 0.00 0.00 2.87
6622 10087 1.676529 CAGCAATCTGGCCATCTGAAG 59.323 52.381 5.51 0.00 36.68 3.02
6623 10088 1.282738 TCAGCAATCTGGCCATCTGAA 59.717 47.619 5.51 0.00 40.69 3.02
6624 10089 0.913924 TCAGCAATCTGGCCATCTGA 59.086 50.000 5.51 11.44 40.69 3.27
6625 10090 1.880675 GATCAGCAATCTGGCCATCTG 59.119 52.381 5.51 9.19 40.69 2.90
6626 10091 1.775459 AGATCAGCAATCTGGCCATCT 59.225 47.619 5.51 0.00 43.35 2.90
6627 10092 2.273538 AGATCAGCAATCTGGCCATC 57.726 50.000 5.51 0.00 43.35 3.51
6634 10099 1.489649 CTGTCCCCAGATCAGCAATCT 59.510 52.381 0.00 0.00 46.04 2.40
6635 10100 1.487976 TCTGTCCCCAGATCAGCAATC 59.512 52.381 0.00 0.00 42.80 2.67
6636 10101 1.489649 CTCTGTCCCCAGATCAGCAAT 59.510 52.381 0.00 0.00 46.38 3.56
6637 10102 0.907486 CTCTGTCCCCAGATCAGCAA 59.093 55.000 0.00 0.00 46.38 3.91
6638 10103 0.979709 CCTCTGTCCCCAGATCAGCA 60.980 60.000 0.00 0.00 46.38 4.41
6639 10104 0.689080 TCCTCTGTCCCCAGATCAGC 60.689 60.000 0.00 0.00 46.38 4.26
6640 10105 1.412079 CTCCTCTGTCCCCAGATCAG 58.588 60.000 0.00 0.00 46.38 2.90
6641 10106 0.031716 CCTCCTCTGTCCCCAGATCA 60.032 60.000 0.00 0.00 46.38 2.92
6642 10107 0.762461 CCCTCCTCTGTCCCCAGATC 60.762 65.000 0.00 0.00 46.38 2.75
6643 10108 1.231751 TCCCTCCTCTGTCCCCAGAT 61.232 60.000 0.00 0.00 46.38 2.90
6644 10109 1.862138 TCCCTCCTCTGTCCCCAGA 60.862 63.158 0.00 0.00 45.44 3.86
6645 10110 1.687493 GTCCCTCCTCTGTCCCCAG 60.687 68.421 0.00 0.00 40.25 4.45
6646 10111 2.450243 GTCCCTCCTCTGTCCCCA 59.550 66.667 0.00 0.00 0.00 4.96
6647 10112 1.687493 CTGTCCCTCCTCTGTCCCC 60.687 68.421 0.00 0.00 0.00 4.81
6648 10113 0.545548 AACTGTCCCTCCTCTGTCCC 60.546 60.000 0.00 0.00 0.00 4.46
6649 10114 0.899019 GAACTGTCCCTCCTCTGTCC 59.101 60.000 0.00 0.00 0.00 4.02
6650 10115 0.528470 CGAACTGTCCCTCCTCTGTC 59.472 60.000 0.00 0.00 0.00 3.51
6651 10116 0.900647 CCGAACTGTCCCTCCTCTGT 60.901 60.000 0.00 0.00 0.00 3.41
6652 10117 0.900647 ACCGAACTGTCCCTCCTCTG 60.901 60.000 0.00 0.00 0.00 3.35
6653 10118 0.612453 GACCGAACTGTCCCTCCTCT 60.612 60.000 0.00 0.00 0.00 3.69
6654 10119 0.612453 AGACCGAACTGTCCCTCCTC 60.612 60.000 0.00 0.00 35.83 3.71
6655 10120 0.178929 AAGACCGAACTGTCCCTCCT 60.179 55.000 0.00 0.00 35.83 3.69
6656 10121 0.685660 AAAGACCGAACTGTCCCTCC 59.314 55.000 0.00 0.00 35.83 4.30
6657 10122 2.414806 GAAAAGACCGAACTGTCCCTC 58.585 52.381 0.00 0.00 35.83 4.30
6658 10123 1.071857 GGAAAAGACCGAACTGTCCCT 59.928 52.381 0.00 0.00 35.83 4.20
6659 10124 1.071857 AGGAAAAGACCGAACTGTCCC 59.928 52.381 0.00 0.00 35.83 4.46
6660 10125 2.545537 AGGAAAAGACCGAACTGTCC 57.454 50.000 0.00 0.00 35.83 4.02
6661 10126 3.626217 ACAAAGGAAAAGACCGAACTGTC 59.374 43.478 0.00 0.00 35.43 3.51
6662 10127 3.617284 ACAAAGGAAAAGACCGAACTGT 58.383 40.909 0.00 0.00 34.73 3.55
6663 10128 3.003378 GGACAAAGGAAAAGACCGAACTG 59.997 47.826 0.00 0.00 34.73 3.16
6699 10164 5.537674 ACAAAAGAATGCAGAGAGGTGAAAT 59.462 36.000 0.00 0.00 0.00 2.17
6708 10173 9.467258 TCTTGATTTAAACAAAAGAATGCAGAG 57.533 29.630 0.00 0.00 0.00 3.35
6801 10267 3.021269 TGCAGCTTGCTGAATTTCAAG 57.979 42.857 24.67 10.05 45.31 3.02
6848 10314 4.237724 GTTTCCCAGCTAGCAAATTTGTC 58.762 43.478 18.83 11.45 0.00 3.18
6863 10329 4.221703 TGAGAAAGTTTTTGCTGTTTCCCA 59.778 37.500 0.00 0.00 30.59 4.37
6864 10330 4.754322 TGAGAAAGTTTTTGCTGTTTCCC 58.246 39.130 0.00 0.00 30.59 3.97
6879 10345 4.915667 CACATGCACACTGATTTGAGAAAG 59.084 41.667 0.00 0.00 0.00 2.62
6915 10381 5.574443 GCAGGTTTCAATTAAGTTGATGAGC 59.426 40.000 0.00 0.00 45.77 4.26
6923 10389 5.990996 CACATTTGGCAGGTTTCAATTAAGT 59.009 36.000 0.00 0.00 0.00 2.24
6945 10411 0.736053 TTTTCCGTGTCACTTGCCAC 59.264 50.000 0.65 0.00 0.00 5.01
6948 10414 3.142796 CGTTTTCCGTGTCACTTGC 57.857 52.632 0.65 0.00 0.00 4.01
6965 10431 1.808411 ATTCAGTGCAGTACCCAACG 58.192 50.000 0.00 0.00 0.00 4.10
7010 10476 5.066505 ACGAATTCAGCCCAGATTTTATGTC 59.933 40.000 6.22 0.00 0.00 3.06
7012 10478 5.505173 ACGAATTCAGCCCAGATTTTATG 57.495 39.130 6.22 0.00 0.00 1.90
7014 10480 7.012327 CAGATTACGAATTCAGCCCAGATTTTA 59.988 37.037 6.22 0.00 0.00 1.52
7016 10482 5.297776 CAGATTACGAATTCAGCCCAGATTT 59.702 40.000 6.22 0.00 0.00 2.17
7022 10510 1.261619 CGCAGATTACGAATTCAGCCC 59.738 52.381 6.22 0.00 0.00 5.19
7054 10542 4.136796 TGTCAGTTCACAGCTTTTAGCAT 58.863 39.130 1.09 0.00 45.56 3.79
7056 10544 3.058639 CCTGTCAGTTCACAGCTTTTAGC 60.059 47.826 0.00 0.00 42.29 3.09
7057 10545 4.380531 TCCTGTCAGTTCACAGCTTTTAG 58.619 43.478 0.00 0.00 42.29 1.85
7078 10566 3.737774 GCTTGACAAATTGGAGCAAGTTC 59.262 43.478 19.01 7.08 38.48 3.01
7098 10586 2.084546 GTCGGAAAGCTGGTTTATGCT 58.915 47.619 4.63 0.00 41.82 3.79
7099 10587 2.084546 AGTCGGAAAGCTGGTTTATGC 58.915 47.619 4.63 0.00 0.00 3.14
7100 10588 3.334691 TGAGTCGGAAAGCTGGTTTATG 58.665 45.455 4.63 1.25 0.00 1.90
7101 10589 3.695830 TGAGTCGGAAAGCTGGTTTAT 57.304 42.857 4.63 0.00 0.00 1.40
7106 10594 0.674581 TGCATGAGTCGGAAAGCTGG 60.675 55.000 0.00 0.00 0.00 4.85
7116 10604 4.060900 TCTTTCAGTGAACTGCATGAGTC 58.939 43.478 4.68 0.00 43.46 3.36
7141 10629 2.471815 ATGCCTACAGCTACTGGGTA 57.528 50.000 0.00 0.00 44.23 3.69
7143 10631 2.434336 TGTTATGCCTACAGCTACTGGG 59.566 50.000 0.00 0.00 44.23 4.45
7150 10638 6.677781 TCTTGTTATTGTTATGCCTACAGC 57.322 37.500 0.00 0.00 44.14 4.40
7165 10653 9.011095 CATGCATCTAGGATCATTTCTTGTTAT 57.989 33.333 0.00 0.00 0.00 1.89
7202 10690 5.883661 AGATTGTGAACTGATATTTTGCCG 58.116 37.500 0.00 0.00 0.00 5.69
7209 10697 7.117285 TGCACTCTAGATTGTGAACTGATAT 57.883 36.000 14.57 0.00 36.38 1.63
7273 10778 8.712228 AGTTCTTTCTTCCTAACCATCAAAAT 57.288 30.769 0.00 0.00 0.00 1.82
7284 10789 8.352942 GCTTTTCATTTGAGTTCTTTCTTCCTA 58.647 33.333 0.00 0.00 0.00 2.94
7297 10802 6.089417 GGGACATAAAACGCTTTTCATTTGAG 59.911 38.462 0.00 0.00 34.19 3.02
7304 10809 3.242518 GCAGGGACATAAAACGCTTTTC 58.757 45.455 0.00 0.00 34.19 2.29
7311 10816 1.745653 GGCTCTGCAGGGACATAAAAC 59.254 52.381 20.53 0.00 0.00 2.43
7315 10820 1.907739 GTGGCTCTGCAGGGACATA 59.092 57.895 28.55 0.00 0.00 2.29
7334 10839 2.159627 CAGCCATCGTTTGTGTTAGGTC 59.840 50.000 0.00 0.00 0.00 3.85
7347 10852 5.126396 TCTTGTCTGTATATCAGCCATCG 57.874 43.478 0.00 0.00 43.32 3.84
7348 10853 9.149225 CTTTATCTTGTCTGTATATCAGCCATC 57.851 37.037 0.00 0.00 43.32 3.51
7375 10881 6.150474 ACGATGGGAAGAATTTTGTAACGAAT 59.850 34.615 0.00 0.00 0.00 3.34
7379 10885 7.586747 TGTAACGATGGGAAGAATTTTGTAAC 58.413 34.615 0.00 0.00 0.00 2.50
7388 10894 4.202274 TGTCACTTGTAACGATGGGAAGAA 60.202 41.667 0.00 0.00 0.00 2.52
7395 10901 9.689075 CAAGTATAAATGTCACTTGTAACGATG 57.311 33.333 5.70 0.00 42.61 3.84
7424 10930 8.934023 TTCACACTCTTCAAATTTACCCTTAT 57.066 30.769 0.00 0.00 0.00 1.73
7441 10971 7.322222 CAGTCGAGAATTTCATTTTTCACACTC 59.678 37.037 0.00 0.00 0.00 3.51
7451 10981 3.274288 GGGAGCAGTCGAGAATTTCATT 58.726 45.455 0.00 0.00 0.00 2.57
7495 11025 6.525578 AGACAAATCGGTAGTTGAGATACA 57.474 37.500 0.00 0.00 34.79 2.29
7496 11026 7.259161 AGAAGACAAATCGGTAGTTGAGATAC 58.741 38.462 0.00 0.00 34.79 2.24


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

AutoCloner maintained by Alex Coulton.