Multiple sequence alignment - TraesCS4A01G067700

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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 TraesCS4A01G067700 chr4A 100.000 6985 0 0 1 6985 66141078 66148062 0.000000e+00 12899.0
1 TraesCS4A01G067700 chr4B 96.320 5000 112 24 1 4961 471331136 471336102 0.000000e+00 8148.0
2 TraesCS4A01G067700 chr4B 93.888 1129 47 10 5218 6333 471336353 471337472 0.000000e+00 1683.0
3 TraesCS4A01G067700 chr4B 93.946 446 11 9 6541 6985 471337755 471338185 0.000000e+00 660.0
4 TraesCS4A01G067700 chr4B 95.604 91 4 0 5129 5219 471336149 471336239 5.650000e-31 147.0
5 TraesCS4A01G067700 chr4B 95.745 47 2 0 4635 4681 642195602 642195648 7.510000e-10 76.8
6 TraesCS4A01G067700 chr4B 97.561 41 1 0 4641 4681 12236109 12236149 3.500000e-08 71.3
7 TraesCS4A01G067700 chr4D 96.027 4984 109 25 1 4961 384263707 384268624 0.000000e+00 8024.0
8 TraesCS4A01G067700 chr4D 94.272 1222 33 12 5129 6333 384268669 384269870 0.000000e+00 1834.0
9 TraesCS4A01G067700 chr4D 84.827 692 40 31 6328 6985 384270133 384270793 2.750000e-178 636.0
10 TraesCS4A01G067700 chr4D 97.778 45 1 0 4637 4681 499394216 499394172 2.090000e-10 78.7
11 TraesCS4A01G067700 chr4D 97.619 42 1 0 4640 4681 455290474 455290433 9.720000e-09 73.1
12 TraesCS4A01G067700 chr4D 95.349 43 2 0 4640 4682 428982418 428982376 1.260000e-07 69.4
13 TraesCS4A01G067700 chr4D 89.796 49 4 1 4548 4595 440830073 440830121 2.100000e-05 62.1
14 TraesCS4A01G067700 chr1D 99.476 191 1 0 6795 6985 384844721 384844911 1.440000e-91 348.0
15 TraesCS4A01G067700 chr1D 97.561 41 1 0 4641 4681 344135258 344135218 3.500000e-08 71.3
16 TraesCS4A01G067700 chr1D 91.111 45 3 1 4551 4595 326972459 326972502 7.570000e-05 60.2
17 TraesCS4A01G067700 chr6B 97.980 198 3 1 6789 6985 679983095 679983292 6.710000e-90 342.0
18 TraesCS4A01G067700 chr6B 88.235 153 16 2 4959 5110 613584549 613584398 1.550000e-41 182.0
19 TraesCS4A01G067700 chr6B 86.709 158 17 4 4953 5109 60612782 60612936 9.310000e-39 172.0
20 TraesCS4A01G067700 chr6B 88.235 85 8 2 4551 4634 560191948 560191865 4.460000e-17 100.0
21 TraesCS4A01G067700 chr5D 98.953 191 2 0 6795 6985 405334397 405334587 6.710000e-90 342.0
22 TraesCS4A01G067700 chr5D 90.698 86 3 5 4551 4634 556009331 556009413 7.410000e-20 110.0
23 TraesCS4A01G067700 chr1A 97.980 198 3 1 6789 6985 490418640 490418443 6.710000e-90 342.0
24 TraesCS4A01G067700 chr1A 97.980 198 3 1 6789 6985 490760390 490760193 6.710000e-90 342.0
25 TraesCS4A01G067700 chr1A 97.959 196 4 0 6790 6985 62794165 62794360 2.410000e-89 340.0
26 TraesCS4A01G067700 chr1A 88.961 154 16 1 4959 5111 24075819 24075972 9.250000e-44 189.0
27 TraesCS4A01G067700 chr2D 98.947 190 2 0 6796 6985 498767300 498767111 2.410000e-89 340.0
28 TraesCS4A01G067700 chr2D 84.615 78 10 2 4555 4632 145890497 145890422 7.510000e-10 76.8
29 TraesCS4A01G067700 chr3D 88.068 176 10 2 4949 5113 375693820 375693995 1.540000e-46 198.0
30 TraesCS4A01G067700 chr3D 88.889 153 14 3 4959 5109 368346007 368346158 1.200000e-42 185.0
31 TraesCS4A01G067700 chr3D 86.905 84 11 0 4551 4634 305448565 305448648 2.070000e-15 95.3
32 TraesCS4A01G067700 chr3D 97.778 45 0 1 4549 4593 501053335 501053378 7.510000e-10 76.8
33 TraesCS4A01G067700 chr3D 94.000 50 1 2 4638 4685 448432918 448432869 2.700000e-09 75.0
34 TraesCS4A01G067700 chr3D 95.122 41 2 0 4549 4589 607070793 607070833 1.630000e-06 65.8
35 TraesCS4A01G067700 chr6D 89.441 161 7 3 4959 5109 467802431 467802271 1.990000e-45 195.0
36 TraesCS4A01G067700 chr6D 84.795 171 16 7 4944 5110 205268889 205268725 5.610000e-36 163.0
37 TraesCS4A01G067700 chr6D 95.652 46 2 0 4551 4596 34828978 34829023 2.700000e-09 75.0
38 TraesCS4A01G067700 chr6D 95.745 47 1 1 4635 4681 41640859 41640904 2.700000e-09 75.0
39 TraesCS4A01G067700 chr5B 88.816 152 12 2 4959 5106 478307176 478307326 1.550000e-41 182.0
40 TraesCS4A01G067700 chr5B 89.412 85 6 3 4551 4634 34252183 34252101 3.450000e-18 104.0
41 TraesCS4A01G067700 chr5B 85.366 82 12 0 4550 4631 544610473 544610554 1.250000e-12 86.1
42 TraesCS4A01G067700 chr5A 86.792 159 17 3 4955 5111 475527341 475527185 2.590000e-39 174.0
43 TraesCS4A01G067700 chr5A 82.432 74 7 5 5062 5132 170089666 170089736 7.570000e-05 60.2
44 TraesCS4A01G067700 chr6A 88.235 85 8 2 4551 4634 500508888 500508971 4.460000e-17 100.0
45 TraesCS4A01G067700 chr7B 85.714 84 12 0 4551 4634 539218379 539218296 9.650000e-14 89.8
46 TraesCS4A01G067700 chr7B 97.778 45 1 0 4637 4681 685247206 685247162 2.090000e-10 78.7
47 TraesCS4A01G067700 chr7B 91.071 56 5 0 4638 4693 539218327 539218272 7.510000e-10 76.8
48 TraesCS4A01G067700 chr7A 93.333 60 2 2 4959 5017 714613313 714613371 3.470000e-13 87.9
49 TraesCS4A01G067700 chr2B 97.778 45 1 0 4637 4681 206114776 206114820 2.090000e-10 78.7
50 TraesCS4A01G067700 chr2B 97.778 45 1 0 4637 4681 281874091 281874135 2.090000e-10 78.7
51 TraesCS4A01G067700 chr1B 93.617 47 3 0 4635 4681 411568742 411568788 3.500000e-08 71.3
52 TraesCS4A01G067700 chrUn 100.000 29 0 0 4653 4681 11030516 11030544 4.000000e-03 54.7


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 TraesCS4A01G067700 chr4A 66141078 66148062 6984 False 12899.0 12899 100.000000 1 6985 1 chr4A.!!$F1 6984
1 TraesCS4A01G067700 chr4B 471331136 471338185 7049 False 2659.5 8148 94.939500 1 6985 4 chr4B.!!$F3 6984
2 TraesCS4A01G067700 chr4D 384263707 384270793 7086 False 3498.0 8024 91.708667 1 6985 3 chr4D.!!$F2 6984

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
101 110 0.107831 TTGTGACGCAGGCTTAGGTT 59.892 50.000 0.00 0.0 0.00 3.50 F
382 396 0.733566 ATGTGCGCGCAGGAAAAATG 60.734 50.000 37.44 0.0 0.00 2.32 F
918 938 1.872952 TGCCTTTGTCTTGTGATCGTG 59.127 47.619 0.00 0.0 0.00 4.35 F
1254 1274 4.646572 ACTGTCTGTCCTCAAATTTCCTC 58.353 43.478 0.00 0.0 0.00 3.71 F
3131 3157 1.059098 AGTGTGACTGATGGCTCCAA 58.941 50.000 0.00 0.0 0.00 3.53 F
3807 3833 2.874086 CACAATGTTGAGAGACAGCACA 59.126 45.455 0.00 0.0 42.03 4.57 F
5357 5565 0.251916 TAAATCGGTGGCAGGAGGTG 59.748 55.000 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1508 0.250901 ACACAAGACACTCATGGGGC 60.251 55.000 0.00 0.0 0.00 5.80 R
1490 1511 1.267806 GCCAACACAAGACACTCATGG 59.732 52.381 0.00 0.0 0.00 3.66 R
1869 1895 6.109359 ACTATCATTCACTGCTGTAAGGTTC 58.891 40.000 0.00 0.0 0.00 3.62 R
3231 3257 1.378250 AGCAGCCTCAGCATCAACC 60.378 57.895 0.00 0.0 43.56 3.77 R
4121 4147 0.674895 ATTCTCGCTGGCAGACAACC 60.675 55.000 20.86 0.0 0.00 3.77 R
5708 5919 0.887933 CGGGCAACTGGTTAGCAAAT 59.112 50.000 0.00 0.0 40.24 2.32 R
6742 7271 0.326264 GGAGTGCCTGTTCATCCTGT 59.674 55.000 0.00 0.0 0.00 4.00 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
97 106 1.804151 GTGAATTGTGACGCAGGCTTA 59.196 47.619 0.00 0.00 0.00 3.09
100 109 0.324943 ATTGTGACGCAGGCTTAGGT 59.675 50.000 0.00 0.00 0.00 3.08
101 110 0.107831 TTGTGACGCAGGCTTAGGTT 59.892 50.000 0.00 0.00 0.00 3.50
130 139 5.581126 TCTTGCCAAATGGAATATGTGAC 57.419 39.130 2.98 0.00 37.39 3.67
177 186 2.815503 GGGTTTATGTTGCGTACCTTGT 59.184 45.455 0.00 0.00 0.00 3.16
306 319 1.019278 CGGTGTCCCACTGTATGTGC 61.019 60.000 0.00 0.00 44.92 4.57
317 330 4.512944 CCACTGTATGTGCATGACCTTATC 59.487 45.833 0.00 0.00 44.92 1.75
320 333 5.104776 ACTGTATGTGCATGACCTTATCTGT 60.105 40.000 0.00 0.00 0.00 3.41
326 339 5.104569 TGTGCATGACCTTATCTGTGGATTA 60.105 40.000 0.00 0.00 33.71 1.75
361 375 5.571784 AGCAGTGTGAATTATGGATGTTG 57.428 39.130 0.00 0.00 0.00 3.33
381 395 0.808125 TATGTGCGCGCAGGAAAAAT 59.192 45.000 37.44 21.67 0.00 1.82
382 396 0.733566 ATGTGCGCGCAGGAAAAATG 60.734 50.000 37.44 0.00 0.00 2.32
394 408 5.732647 CGCAGGAAAAATGTTACTGATAACG 59.267 40.000 0.00 0.00 43.23 3.18
427 441 3.822735 AGTGACAATGGTGGAGTCAAATG 59.177 43.478 0.00 0.00 43.16 2.32
466 484 3.555956 GGTTTGCTGGTCACGTATATGAG 59.444 47.826 0.00 0.00 0.00 2.90
680 700 2.775384 ACCTGAGTTGTAAGGAACACCA 59.225 45.455 0.00 0.00 38.00 4.17
912 932 3.876914 TCTACTGTTGCCTTTGTCTTGTG 59.123 43.478 0.00 0.00 0.00 3.33
918 938 1.872952 TGCCTTTGTCTTGTGATCGTG 59.127 47.619 0.00 0.00 0.00 4.35
983 1003 9.237846 CAACGCACTTGTATATGATCGATATAT 57.762 33.333 0.00 5.41 33.02 0.86
1203 1223 9.638239 TTCAGTACTATTTTGATTTGGATTTGC 57.362 29.630 0.00 0.00 0.00 3.68
1205 1225 9.079833 CAGTACTATTTTGATTTGGATTTGCTG 57.920 33.333 0.00 0.00 0.00 4.41
1254 1274 4.646572 ACTGTCTGTCCTCAAATTTCCTC 58.353 43.478 0.00 0.00 0.00 3.71
1372 1392 9.772973 TTTGTATAACCTAGATACATTGCGAAT 57.227 29.630 4.18 0.00 39.05 3.34
1487 1508 9.435688 AGCCAAATTTTTAGCTACTTATTTTGG 57.564 29.630 20.00 20.00 33.44 3.28
1490 1511 8.664798 CAAATTTTTAGCTACTTATTTTGGCCC 58.335 33.333 0.00 0.00 0.00 5.80
1831 1856 9.921637 GATCTGGGTAGAATTATTTACTCTCTG 57.078 37.037 0.00 0.00 36.32 3.35
1869 1895 5.749462 ACTAGACCTTCCTCATTTTCCATG 58.251 41.667 0.00 0.00 0.00 3.66
1902 1928 9.155975 ACAGCAGTGAATGATAGTTTACTTTAG 57.844 33.333 0.00 0.00 0.00 1.85
2397 2423 7.010160 AGTCAGGTGAAAGGGAAATAAATTCA 58.990 34.615 0.00 0.00 39.98 2.57
3111 3137 8.184304 TCAAGAAAGAGAAAGTAGCTAAGAGT 57.816 34.615 0.00 0.00 0.00 3.24
3131 3157 1.059098 AGTGTGACTGATGGCTCCAA 58.941 50.000 0.00 0.00 0.00 3.53
3223 3249 3.985279 CCATGACAATGCTGTTGACAAAG 59.015 43.478 8.99 6.58 35.30 2.77
3231 3257 6.919662 ACAATGCTGTTGACAAAGTAAAGATG 59.080 34.615 8.99 0.00 28.57 2.90
3378 3404 5.690464 AACTGCAGTCCAGATTATCTTCT 57.310 39.130 21.95 0.00 44.64 2.85
3583 3609 7.014518 CCATGGATCAAGAAGTTATAAATGCCA 59.985 37.037 5.56 0.00 0.00 4.92
3659 3685 4.500545 CCAGAGACCGTCTTCTGATTATGG 60.501 50.000 20.62 5.61 30.64 2.74
3807 3833 2.874086 CACAATGTTGAGAGACAGCACA 59.126 45.455 0.00 0.00 42.03 4.57
4134 4160 1.001641 ATCCAGGTTGTCTGCCAGC 60.002 57.895 0.00 0.00 42.05 4.85
4275 4301 2.737252 GACTTTAACAGCTGAACTCGGG 59.263 50.000 23.35 6.53 0.00 5.14
4466 4492 2.069273 CATGTGGAAGAGGTTGACGAC 58.931 52.381 0.00 0.00 0.00 4.34
4537 4566 5.163519 CCTTTTCTCAAACACACATCCAAGT 60.164 40.000 0.00 0.00 0.00 3.16
4560 4589 3.767673 GTGTGATTGTAGTACTCCCTCCA 59.232 47.826 0.00 0.00 0.00 3.86
4577 4630 4.887071 CCCTCCAATCCGAATTAATTGACA 59.113 41.667 5.17 0.00 35.35 3.58
4602 4655 5.295292 CAGCCTCTATACAATGTCAAACTGG 59.705 44.000 0.00 0.00 0.00 4.00
4614 4667 6.683974 ATGTCAAACTGGCATTGTATAGAC 57.316 37.500 1.13 0.00 40.21 2.59
4620 4673 3.118775 ACTGGCATTGTATAGACGCTTCA 60.119 43.478 0.00 0.00 0.00 3.02
4632 4685 8.325282 TGTATAGACGCTTCAACAATTAATTCG 58.675 33.333 0.00 0.00 0.00 3.34
4652 4705 6.479972 TTCGGTTGACATTGTATAGAGGAT 57.520 37.500 0.00 0.00 0.00 3.24
4681 4734 0.753262 AATTCGGATCGGAGGGAGTG 59.247 55.000 2.99 0.00 0.00 3.51
4683 4736 3.147595 CGGATCGGAGGGAGTGCA 61.148 66.667 0.00 0.00 0.00 4.57
4684 4737 2.721167 CGGATCGGAGGGAGTGCAA 61.721 63.158 0.00 0.00 0.00 4.08
4685 4738 1.144936 GGATCGGAGGGAGTGCAAG 59.855 63.158 0.00 0.00 0.00 4.01
4689 4742 0.324738 TCGGAGGGAGTGCAAGAGAT 60.325 55.000 0.00 0.00 0.00 2.75
4800 4855 4.285863 TGAATGTTGTCTTCCCTTTTGGT 58.714 39.130 0.00 0.00 38.10 3.67
4819 4874 4.765273 TGGTTCCTTTTTCTTCTTTTGGC 58.235 39.130 0.00 0.00 0.00 4.52
4830 4885 3.065648 TCTTCTTTTGGCAACGTTGTACC 59.934 43.478 27.78 21.34 42.51 3.34
4961 5018 3.940209 TGGCACAATTCCAAATCACTC 57.060 42.857 0.00 0.00 31.92 3.51
4962 5019 2.562298 TGGCACAATTCCAAATCACTCC 59.438 45.455 0.00 0.00 31.92 3.85
4963 5020 2.094026 GGCACAATTCCAAATCACTCCC 60.094 50.000 0.00 0.00 0.00 4.30
4964 5021 2.827921 GCACAATTCCAAATCACTCCCT 59.172 45.455 0.00 0.00 0.00 4.20
4965 5022 3.119352 GCACAATTCCAAATCACTCCCTC 60.119 47.826 0.00 0.00 0.00 4.30
4966 5023 3.445096 CACAATTCCAAATCACTCCCTCC 59.555 47.826 0.00 0.00 0.00 4.30
4967 5024 2.684881 CAATTCCAAATCACTCCCTCCG 59.315 50.000 0.00 0.00 0.00 4.63
4968 5025 1.358152 TTCCAAATCACTCCCTCCGT 58.642 50.000 0.00 0.00 0.00 4.69
4969 5026 1.358152 TCCAAATCACTCCCTCCGTT 58.642 50.000 0.00 0.00 0.00 4.44
4970 5027 1.278127 TCCAAATCACTCCCTCCGTTC 59.722 52.381 0.00 0.00 0.00 3.95
4971 5028 1.679032 CCAAATCACTCCCTCCGTTCC 60.679 57.143 0.00 0.00 0.00 3.62
4972 5029 1.279271 CAAATCACTCCCTCCGTTCCT 59.721 52.381 0.00 0.00 0.00 3.36
4973 5030 2.500098 CAAATCACTCCCTCCGTTCCTA 59.500 50.000 0.00 0.00 0.00 2.94
4974 5031 2.544844 ATCACTCCCTCCGTTCCTAA 57.455 50.000 0.00 0.00 0.00 2.69
4975 5032 2.314071 TCACTCCCTCCGTTCCTAAA 57.686 50.000 0.00 0.00 0.00 1.85
4976 5033 2.829023 TCACTCCCTCCGTTCCTAAAT 58.171 47.619 0.00 0.00 0.00 1.40
4977 5034 3.985127 TCACTCCCTCCGTTCCTAAATA 58.015 45.455 0.00 0.00 0.00 1.40
4978 5035 4.553678 TCACTCCCTCCGTTCCTAAATAT 58.446 43.478 0.00 0.00 0.00 1.28
4979 5036 5.708544 TCACTCCCTCCGTTCCTAAATATA 58.291 41.667 0.00 0.00 0.00 0.86
4980 5037 6.138263 TCACTCCCTCCGTTCCTAAATATAA 58.862 40.000 0.00 0.00 0.00 0.98
4981 5038 6.267014 TCACTCCCTCCGTTCCTAAATATAAG 59.733 42.308 0.00 0.00 0.00 1.73
4982 5039 6.041751 CACTCCCTCCGTTCCTAAATATAAGT 59.958 42.308 0.00 0.00 0.00 2.24
4983 5040 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4984 5041 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4985 5042 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4986 5043 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4987 5044 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4988 5045 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
5048 5105 7.972832 AGACGTATTTTAAAGTGTGGATTCA 57.027 32.000 0.00 0.00 0.00 2.57
5049 5106 7.803724 AGACGTATTTTAAAGTGTGGATTCAC 58.196 34.615 0.00 0.00 43.87 3.18
5051 5108 7.803724 ACGTATTTTAAAGTGTGGATTCACTC 58.196 34.615 5.55 1.32 46.25 3.51
5052 5109 7.442969 ACGTATTTTAAAGTGTGGATTCACTCA 59.557 33.333 5.55 0.00 46.25 3.41
5053 5110 8.450964 CGTATTTTAAAGTGTGGATTCACTCAT 58.549 33.333 5.55 0.00 46.25 2.90
5057 5114 8.870160 TTTAAAGTGTGGATTCACTCATTTTG 57.130 30.769 5.55 0.00 46.25 2.44
5058 5115 4.510038 AGTGTGGATTCACTCATTTTGC 57.490 40.909 5.55 0.00 44.07 3.68
5059 5116 4.147321 AGTGTGGATTCACTCATTTTGCT 58.853 39.130 5.55 0.00 44.07 3.91
5060 5117 4.586001 AGTGTGGATTCACTCATTTTGCTT 59.414 37.500 5.55 0.00 44.07 3.91
5061 5118 4.919754 GTGTGGATTCACTCATTTTGCTTC 59.080 41.667 5.55 0.00 43.94 3.86
5062 5119 4.161333 GTGGATTCACTCATTTTGCTTCG 58.839 43.478 0.00 0.00 40.58 3.79
5063 5120 3.820467 TGGATTCACTCATTTTGCTTCGT 59.180 39.130 0.00 0.00 0.00 3.85
5064 5121 5.000591 TGGATTCACTCATTTTGCTTCGTA 58.999 37.500 0.00 0.00 0.00 3.43
5065 5122 5.647658 TGGATTCACTCATTTTGCTTCGTAT 59.352 36.000 0.00 0.00 0.00 3.06
5066 5123 5.967674 GGATTCACTCATTTTGCTTCGTATG 59.032 40.000 0.00 0.00 0.00 2.39
5067 5124 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
5068 5125 7.201609 GGATTCACTCATTTTGCTTCGTATGTA 60.202 37.037 0.00 0.00 0.00 2.29
5069 5126 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
5070 5127 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
5071 5128 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
5072 5129 5.581085 ACTCATTTTGCTTCGTATGTAGTCC 59.419 40.000 0.00 0.00 0.00 3.85
5073 5130 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
5074 5131 6.112734 TCATTTTGCTTCGTATGTAGTCCAT 58.887 36.000 0.00 0.00 37.58 3.41
5075 5132 7.269316 TCATTTTGCTTCGTATGTAGTCCATA 58.731 34.615 0.00 0.00 34.86 2.74
5076 5133 7.931407 TCATTTTGCTTCGTATGTAGTCCATAT 59.069 33.333 0.00 0.00 38.29 1.78
5077 5134 9.203421 CATTTTGCTTCGTATGTAGTCCATATA 57.797 33.333 0.00 0.00 38.29 0.86
5078 5135 9.772973 ATTTTGCTTCGTATGTAGTCCATATAA 57.227 29.630 0.00 0.00 38.29 0.98
5079 5136 8.812147 TTTGCTTCGTATGTAGTCCATATAAG 57.188 34.615 0.00 0.00 38.29 1.73
5080 5137 7.754851 TGCTTCGTATGTAGTCCATATAAGA 57.245 36.000 0.00 0.00 38.29 2.10
5081 5138 8.173542 TGCTTCGTATGTAGTCCATATAAGAA 57.826 34.615 0.00 0.00 38.29 2.52
5082 5139 8.297426 TGCTTCGTATGTAGTCCATATAAGAAG 58.703 37.037 11.92 11.92 41.51 2.85
5083 5140 8.512956 GCTTCGTATGTAGTCCATATAAGAAGA 58.487 37.037 17.25 0.00 41.34 2.87
5084 5141 9.828852 CTTCGTATGTAGTCCATATAAGAAGAC 57.171 37.037 11.22 0.00 41.34 3.01
5085 5142 9.570468 TTCGTATGTAGTCCATATAAGAAGACT 57.430 33.333 0.00 0.00 42.13 3.24
5086 5143 9.570468 TCGTATGTAGTCCATATAAGAAGACTT 57.430 33.333 0.00 0.00 40.07 3.01
5103 5160 7.953752 AGAAGACTTATATTTAGGAACGGAGG 58.046 38.462 0.00 0.00 0.00 4.30
5104 5161 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
5105 5162 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
5106 5163 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
5127 5184 6.313905 GGGAGTACTTATGTTCATCTGTTGTG 59.686 42.308 0.00 0.00 0.00 3.33
5227 5428 6.015504 CGGCAAGCGCTAAATATGTTATAAG 58.984 40.000 12.05 0.00 38.60 1.73
5236 5437 9.760660 CGCTAAATATGTTATAAGCTCATTTCC 57.239 33.333 0.00 0.00 0.00 3.13
5239 5440 7.687941 AATATGTTATAAGCTCATTTCCGGG 57.312 36.000 0.00 0.00 0.00 5.73
5242 5443 5.991861 TGTTATAAGCTCATTTCCGGGTTA 58.008 37.500 0.00 0.00 0.00 2.85
5357 5565 0.251916 TAAATCGGTGGCAGGAGGTG 59.748 55.000 0.00 0.00 0.00 4.00
5369 5577 1.526225 GGAGGTGGAAATAGCGGCC 60.526 63.158 0.00 0.00 0.00 6.13
5581 5792 2.259917 TCAGGAAATGCTGGAGTCAGA 58.740 47.619 1.97 0.00 43.49 3.27
5632 5843 1.386533 CACATGACCCCTTCTGATGC 58.613 55.000 0.00 0.00 0.00 3.91
5648 5859 4.083862 GCGGACGGAAGCCCTTCT 62.084 66.667 7.85 0.00 39.45 2.85
5699 5910 1.135257 CATAGGTCGCGATCCTCATCC 60.135 57.143 26.39 15.79 36.60 3.51
5708 5919 2.591923 CGATCCTCATCCTCTTCCTCA 58.408 52.381 0.00 0.00 0.00 3.86
5800 6011 6.602803 TGAACATTAGCTGGATTGCAAGATTA 59.397 34.615 4.94 0.00 34.99 1.75
5837 6048 2.212652 TGATTCTTCGGCGAATGGATG 58.787 47.619 23.96 11.14 33.96 3.51
5851 6062 3.862877 ATGGATGGATGACGGATGAAA 57.137 42.857 0.00 0.00 0.00 2.69
5852 6063 3.643199 TGGATGGATGACGGATGAAAA 57.357 42.857 0.00 0.00 0.00 2.29
5907 6118 6.197096 GCGAATCTGCTTGTGTATTATTTTGG 59.803 38.462 0.00 0.00 0.00 3.28
5937 6148 1.227823 CGGTGGTTCAGTTGCTGGA 60.228 57.895 0.00 0.00 31.51 3.86
5984 6195 3.472652 GTTATGACCAGGTTGTGTGTGA 58.527 45.455 0.00 0.00 0.00 3.58
5986 6197 1.199615 TGACCAGGTTGTGTGTGAGA 58.800 50.000 0.00 0.00 0.00 3.27
5991 6202 2.288702 CCAGGTTGTGTGTGAGAGAGAG 60.289 54.545 0.00 0.00 0.00 3.20
5992 6203 2.625314 CAGGTTGTGTGTGAGAGAGAGA 59.375 50.000 0.00 0.00 0.00 3.10
5993 6204 2.890311 AGGTTGTGTGTGAGAGAGAGAG 59.110 50.000 0.00 0.00 0.00 3.20
5994 6205 2.625790 GGTTGTGTGTGAGAGAGAGAGT 59.374 50.000 0.00 0.00 0.00 3.24
5995 6206 3.551863 GGTTGTGTGTGAGAGAGAGAGTG 60.552 52.174 0.00 0.00 0.00 3.51
5996 6207 2.937519 TGTGTGTGAGAGAGAGAGTGT 58.062 47.619 0.00 0.00 0.00 3.55
5997 6208 2.620585 TGTGTGTGAGAGAGAGAGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
6023 6234 5.634020 GTGTGTTAGCTGTCGTTATCTTCTT 59.366 40.000 0.00 0.00 0.00 2.52
6082 6293 5.639506 CCTCACTAAAACCTCACTGTACATG 59.360 44.000 0.00 0.00 0.00 3.21
6138 6349 5.247507 TGTTTGTGTTCCATTCTCTTGTG 57.752 39.130 0.00 0.00 0.00 3.33
6139 6350 4.946772 TGTTTGTGTTCCATTCTCTTGTGA 59.053 37.500 0.00 0.00 0.00 3.58
6202 6413 3.581755 TGTACAGCTAAGTTAACCTGCG 58.418 45.455 0.88 4.25 0.00 5.18
6309 6523 9.469807 GTCTTCTATGTTACTCATACATCCTTG 57.530 37.037 0.00 0.00 37.42 3.61
6317 6531 1.561076 TCATACATCCTTGCTGCTGGT 59.439 47.619 0.00 0.00 0.00 4.00
6339 6833 7.047891 TGGTAAGACAGCTTATACCAATTCAG 58.952 38.462 12.09 0.00 38.94 3.02
6351 6845 9.474920 CTTATACCAATTCAGAAACAGCAAAAA 57.525 29.630 0.00 0.00 0.00 1.94
6355 6849 6.128309 ACCAATTCAGAAACAGCAAAAACAAC 60.128 34.615 0.00 0.00 0.00 3.32
6356 6850 6.128336 CCAATTCAGAAACAGCAAAAACAACA 60.128 34.615 0.00 0.00 0.00 3.33
6388 6882 9.317936 GTTTTCTTTCTCAACAATCCAGAAAAT 57.682 29.630 7.28 0.00 39.61 1.82
6394 6888 6.898041 TCTCAACAATCCAGAAAATACAACG 58.102 36.000 0.00 0.00 0.00 4.10
6403 6897 4.915085 CCAGAAAATACAACGAACGCAAAT 59.085 37.500 0.00 0.00 0.00 2.32
6405 6899 6.281056 CAGAAAATACAACGAACGCAAATTG 58.719 36.000 0.00 0.00 0.00 2.32
6406 6900 4.623122 AAATACAACGAACGCAAATTGC 57.377 36.364 8.09 8.09 40.69 3.56
6407 6901 2.757686 TACAACGAACGCAAATTGCA 57.242 40.000 18.65 0.00 45.36 4.08
6408 6902 1.914634 ACAACGAACGCAAATTGCAA 58.085 40.000 18.65 0.00 45.36 4.08
6409 6903 2.468831 ACAACGAACGCAAATTGCAAT 58.531 38.095 18.65 5.99 45.36 3.56
6411 6905 1.696988 ACGAACGCAAATTGCAATCC 58.303 45.000 18.65 3.63 45.36 3.01
6412 6906 1.269448 ACGAACGCAAATTGCAATCCT 59.731 42.857 18.65 0.00 45.36 3.24
6413 6907 1.650153 CGAACGCAAATTGCAATCCTG 59.350 47.619 18.65 13.95 45.36 3.86
6414 6908 1.994779 GAACGCAAATTGCAATCCTGG 59.005 47.619 18.65 9.61 45.36 4.45
6416 6910 1.344114 ACGCAAATTGCAATCCTGGTT 59.656 42.857 18.65 0.00 45.36 3.67
6417 6911 1.727880 CGCAAATTGCAATCCTGGTTG 59.272 47.619 18.65 13.71 45.36 3.77
6418 6912 2.769893 GCAAATTGCAATCCTGGTTGT 58.230 42.857 13.38 0.00 44.26 3.32
6419 6913 2.738314 GCAAATTGCAATCCTGGTTGTC 59.262 45.455 13.38 6.05 44.26 3.18
6420 6914 3.328505 CAAATTGCAATCCTGGTTGTCC 58.671 45.455 13.38 0.00 0.00 4.02
6421 6915 2.307496 ATTGCAATCCTGGTTGTCCA 57.693 45.000 5.99 0.00 42.05 4.02
6422 6916 2.307496 TTGCAATCCTGGTTGTCCAT 57.693 45.000 0.00 0.00 43.43 3.41
6424 6918 2.170166 TGCAATCCTGGTTGTCCATTC 58.830 47.619 9.63 0.00 43.43 2.67
6425 6919 1.478105 GCAATCCTGGTTGTCCATTCC 59.522 52.381 9.63 0.00 43.43 3.01
6426 6920 2.806434 CAATCCTGGTTGTCCATTCCA 58.194 47.619 0.00 0.00 43.43 3.53
6427 6921 3.164268 CAATCCTGGTTGTCCATTCCAA 58.836 45.455 0.00 0.00 43.43 3.53
6428 6922 2.286365 TCCTGGTTGTCCATTCCAAC 57.714 50.000 0.00 0.00 43.43 3.77
6429 6923 1.780309 TCCTGGTTGTCCATTCCAACT 59.220 47.619 0.00 0.00 43.43 3.16
6430 6924 2.983192 TCCTGGTTGTCCATTCCAACTA 59.017 45.455 0.00 0.00 43.43 2.24
6431 6925 3.396276 TCCTGGTTGTCCATTCCAACTAA 59.604 43.478 0.00 0.00 43.43 2.24
6432 6926 4.141135 TCCTGGTTGTCCATTCCAACTAAA 60.141 41.667 0.00 0.00 43.43 1.85
6433 6927 4.022329 CCTGGTTGTCCATTCCAACTAAAC 60.022 45.833 0.00 0.00 43.43 2.01
6434 6928 4.537751 TGGTTGTCCATTCCAACTAAACA 58.462 39.130 0.00 0.00 41.47 2.83
6435 6929 5.144100 TGGTTGTCCATTCCAACTAAACAT 58.856 37.500 0.00 0.00 41.47 2.71
6436 6930 5.600484 TGGTTGTCCATTCCAACTAAACATT 59.400 36.000 0.00 0.00 41.47 2.71
6460 6954 0.755327 ACAAGGGAAAAAGCACCGCT 60.755 50.000 0.00 0.00 42.56 5.52
6461 6955 1.243902 CAAGGGAAAAAGCACCGCTA 58.756 50.000 0.00 0.00 38.25 4.26
6468 6962 5.041287 GGGAAAAAGCACCGCTAATATTTC 58.959 41.667 0.00 0.00 38.25 2.17
6472 6966 5.500645 AAAGCACCGCTAATATTTCCTTC 57.499 39.130 0.00 0.00 38.25 3.46
6478 6972 3.430218 CCGCTAATATTTCCTTCTGCGAG 59.570 47.826 0.00 0.00 44.02 5.03
6506 7000 1.153588 GCGCCATCACCAATTTGGG 60.154 57.895 19.39 8.68 43.37 4.12
6509 7003 0.826062 GCCATCACCAATTTGGGAGG 59.174 55.000 19.39 14.69 43.37 4.30
6519 7035 7.185565 TCACCAATTTGGGAGGTCATAATTTA 58.814 34.615 19.39 0.00 43.37 1.40
6520 7036 7.341769 TCACCAATTTGGGAGGTCATAATTTAG 59.658 37.037 19.39 0.00 43.37 1.85
6525 7041 8.753497 ATTTGGGAGGTCATAATTTAGAGTTC 57.247 34.615 0.00 0.00 0.00 3.01
6530 7046 8.925338 GGGAGGTCATAATTTAGAGTTCTCTAA 58.075 37.037 15.58 15.58 0.00 2.10
6546 7073 4.185394 TCTCTAAAACAACACGACTGCAA 58.815 39.130 0.00 0.00 0.00 4.08
6572 7099 1.345415 AGAACCAGGGCAAAGCAATTG 59.655 47.619 0.00 0.00 42.21 2.32
6600 7127 3.569701 AGAAGAAATCAGCCGCAAAAGAA 59.430 39.130 0.00 0.00 0.00 2.52
6601 7128 3.565905 AGAAATCAGCCGCAAAAGAAG 57.434 42.857 0.00 0.00 0.00 2.85
6602 7129 3.149196 AGAAATCAGCCGCAAAAGAAGA 58.851 40.909 0.00 0.00 0.00 2.87
6693 7222 3.191371 GGATTTACTTCACTGCAACAGGG 59.809 47.826 0.00 0.00 36.00 4.45
6722 7251 2.813754 ACATCAGGAACACAACATTCGG 59.186 45.455 0.00 0.00 0.00 4.30
6736 7265 1.883275 CATTCGGCACCAAACTACCAA 59.117 47.619 0.00 0.00 0.00 3.67
6742 7271 1.751924 GCACCAAACTACCAACACCAA 59.248 47.619 0.00 0.00 0.00 3.67
6750 7279 2.708861 ACTACCAACACCAACAGGATGA 59.291 45.455 0.00 0.00 39.69 2.92
6758 7287 0.883833 CCAACAGGATGAACAGGCAC 59.116 55.000 0.00 0.00 39.69 5.01
6759 7288 1.546323 CCAACAGGATGAACAGGCACT 60.546 52.381 0.00 0.00 39.69 4.40
6760 7289 1.808945 CAACAGGATGAACAGGCACTC 59.191 52.381 0.00 0.00 39.69 3.51
6761 7290 0.326264 ACAGGATGAACAGGCACTCC 59.674 55.000 0.00 0.00 39.69 3.85
6779 7308 2.396157 CCTCCGTAAACAAGCCGCC 61.396 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.908198 CAACAAGGAGGAGGAGGAGG 59.092 60.000 0.00 0.00 0.00 4.30
18 19 0.908198 CCAACAAGGAGGAGGAGGAG 59.092 60.000 0.00 0.00 41.22 3.69
19 20 1.201429 GCCAACAAGGAGGAGGAGGA 61.201 60.000 0.00 0.00 41.22 3.71
177 186 3.340928 CAATCCACAGAACAGATCAGCA 58.659 45.455 0.00 0.00 0.00 4.41
306 319 5.307976 TCCCTAATCCACAGATAAGGTCATG 59.692 44.000 0.00 0.00 30.42 3.07
317 330 4.510167 ACCAAGAATCCCTAATCCACAG 57.490 45.455 0.00 0.00 0.00 3.66
320 333 4.044308 TGCTACCAAGAATCCCTAATCCA 58.956 43.478 0.00 0.00 0.00 3.41
326 339 2.026822 CACACTGCTACCAAGAATCCCT 60.027 50.000 0.00 0.00 0.00 4.20
361 375 0.109964 TTTTTCCTGCGCGCACATAC 60.110 50.000 33.09 0.00 0.00 2.39
394 408 6.601613 TCCACCATTGTCACTATATGGAAAAC 59.398 38.462 8.05 0.00 41.05 2.43
427 441 4.084380 GCAAACCAAATTCAGTAAGCAAGC 60.084 41.667 0.00 0.00 0.00 4.01
466 484 7.756722 AGCACAAACTATCAGACAAAATATTGC 59.243 33.333 0.00 0.00 40.34 3.56
468 486 8.246180 CCAGCACAAACTATCAGACAAAATATT 58.754 33.333 0.00 0.00 0.00 1.28
680 700 9.997172 TCACTATATGGAAGTCCTGATATGTAT 57.003 33.333 0.00 0.00 36.82 2.29
807 827 4.769488 GGAAAAGCTCTCCTTTCCTTTCAT 59.231 41.667 17.01 0.00 42.82 2.57
886 906 5.091261 AGACAAAGGCAACAGTAGATAGG 57.909 43.478 0.00 0.00 41.41 2.57
912 932 3.684103 TGTTTGTCAACAACCACGATC 57.316 42.857 0.00 0.00 40.10 3.69
937 957 8.293867 TGCGTTGCTAAATAGTAACTGAATTTT 58.706 29.630 16.02 0.00 43.73 1.82
997 1017 9.746457 TGCAACAAACTTGCCCATATATATATA 57.254 29.630 4.90 4.92 44.32 0.86
998 1018 8.648698 TGCAACAAACTTGCCCATATATATAT 57.351 30.769 0.00 0.00 44.32 0.86
999 1019 8.648698 ATGCAACAAACTTGCCCATATATATA 57.351 30.769 0.00 0.00 44.32 0.86
1000 1020 6.975196 TGCAACAAACTTGCCCATATATAT 57.025 33.333 2.73 0.00 44.32 0.86
1001 1021 6.975196 ATGCAACAAACTTGCCCATATATA 57.025 33.333 0.00 0.00 44.32 0.86
1002 1022 5.874897 ATGCAACAAACTTGCCCATATAT 57.125 34.783 0.00 0.00 44.32 0.86
1205 1225 3.733337 AGAATGACACCACTGACACTTC 58.267 45.455 0.00 0.00 0.00 3.01
1254 1274 8.470040 AACTATTTGCATTAGCTTTGTCAATG 57.530 30.769 0.00 0.00 42.74 2.82
1372 1392 7.563020 TGGAAATGGCAGCATTTTATTGATTA 58.437 30.769 0.00 0.00 35.18 1.75
1467 1487 6.442244 TGGGGCCAAAATAAGTAGCTAAAAAT 59.558 34.615 4.39 0.00 0.00 1.82
1487 1508 0.250901 ACACAAGACACTCATGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
1490 1511 1.267806 GCCAACACAAGACACTCATGG 59.732 52.381 0.00 0.00 0.00 3.66
1869 1895 6.109359 ACTATCATTCACTGCTGTAAGGTTC 58.891 40.000 0.00 0.00 0.00 3.62
1981 2007 6.569801 GCTTTCTCCCAACCTAACATAACAAC 60.570 42.308 0.00 0.00 0.00 3.32
2397 2423 7.385205 GTGACAACATGTACTTCATACTTCAGT 59.615 37.037 0.00 0.00 34.67 3.41
3111 3137 1.937191 TGGAGCCATCAGTCACACTA 58.063 50.000 0.00 0.00 0.00 2.74
3131 3157 2.505407 TCATCCATCAGTTCCAACCGAT 59.495 45.455 0.00 0.00 0.00 4.18
3223 3249 3.065925 GCCTCAGCATCAACCATCTTTAC 59.934 47.826 0.00 0.00 39.53 2.01
3231 3257 1.378250 AGCAGCCTCAGCATCAACC 60.378 57.895 0.00 0.00 43.56 3.77
3378 3404 2.106338 TGGTGATTCAGAGTCCAGCAAA 59.894 45.455 0.00 0.00 34.62 3.68
3659 3685 4.802999 CTGAATTTTCTCAGAAAGCCCAC 58.197 43.478 0.00 0.00 44.82 4.61
3693 3719 9.155975 TCATTTGATAGAACTTTCTCAACTAGC 57.844 33.333 0.00 0.00 38.70 3.42
3807 3833 9.023962 TCCAAATTATTACTGTCTGCTTCATTT 57.976 29.630 0.00 0.00 0.00 2.32
4039 4065 3.451526 TCATTTCACTGCATCTCGCTAG 58.548 45.455 0.00 0.00 43.06 3.42
4121 4147 0.674895 ATTCTCGCTGGCAGACAACC 60.675 55.000 20.86 0.00 0.00 3.77
4134 4160 2.227388 AGCCAAGCTGTTTGAATTCTCG 59.773 45.455 7.05 0.00 37.57 4.04
4161 4187 2.426522 TCAACCATACACTTCAGCTGC 58.573 47.619 9.47 0.00 0.00 5.25
4170 4196 7.865706 AATCTTGTAGGATTCAACCATACAC 57.134 36.000 0.00 0.00 31.08 2.90
4275 4301 5.248640 TCCTGATGACTTTGTCTTTCATCC 58.751 41.667 8.04 0.00 43.39 3.51
4466 4492 5.957842 TTAGTACCTGCTTTGATTTGGTG 57.042 39.130 0.00 0.00 32.74 4.17
4537 4566 3.767673 GGAGGGAGTACTACAATCACACA 59.232 47.826 7.57 0.00 0.00 3.72
4546 4575 2.941480 TCGGATTGGAGGGAGTACTAC 58.059 52.381 0.00 0.00 0.00 2.73
4560 4589 4.949856 AGGCTGTGTCAATTAATTCGGATT 59.050 37.500 0.00 0.00 0.00 3.01
4577 4630 5.877012 CAGTTTGACATTGTATAGAGGCTGT 59.123 40.000 0.00 0.00 0.00 4.40
4602 4655 4.857871 TGTTGAAGCGTCTATACAATGC 57.142 40.909 0.31 0.00 0.00 3.56
4614 4667 5.059221 GTCAACCGAATTAATTGTTGAAGCG 59.941 40.000 24.52 13.16 45.98 4.68
4632 4685 4.449068 CGCATCCTCTATACAATGTCAACC 59.551 45.833 0.00 0.00 0.00 3.77
4652 4705 2.542178 CCGATCCGAATTAATTGACGCA 59.458 45.455 5.17 0.00 0.00 5.24
4681 4734 6.974932 TGTGAATCTAAGAACATCTCTTGC 57.025 37.500 0.00 0.00 44.47 4.01
4800 4855 4.867608 CGTTGCCAAAAGAAGAAAAAGGAA 59.132 37.500 0.00 0.00 0.00 3.36
4830 4885 3.758023 TGTTGCCAGAATCCAACAGTATG 59.242 43.478 2.41 0.00 44.39 2.39
4914 4970 1.816835 ACATGCAGAATTCAGCAGTGG 59.183 47.619 26.53 20.50 41.60 4.00
4957 5014 4.957684 ATATTTAGGAACGGAGGGAGTG 57.042 45.455 0.00 0.00 0.00 3.51
4958 5015 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4959 5016 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4960 5017 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4961 5018 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4962 5019 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
5022 5079 9.661563 TGAATCCACACTTTAAAATACGTCTAT 57.338 29.630 0.00 0.00 0.00 1.98
5023 5080 8.928733 GTGAATCCACACTTTAAAATACGTCTA 58.071 33.333 0.00 0.00 42.72 2.59
5024 5081 7.803724 GTGAATCCACACTTTAAAATACGTCT 58.196 34.615 0.00 0.00 42.72 4.18
5038 5095 4.510038 AGCAAAATGAGTGAATCCACAC 57.490 40.909 0.00 0.00 45.54 3.82
5039 5096 4.320421 CGAAGCAAAATGAGTGAATCCACA 60.320 41.667 0.00 0.00 45.54 4.17
5040 5097 4.161333 CGAAGCAAAATGAGTGAATCCAC 58.839 43.478 0.00 0.00 43.50 4.02
5041 5098 3.820467 ACGAAGCAAAATGAGTGAATCCA 59.180 39.130 0.00 0.00 0.00 3.41
5042 5099 4.425577 ACGAAGCAAAATGAGTGAATCC 57.574 40.909 0.00 0.00 0.00 3.01
5043 5100 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
5044 5101 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
5045 5102 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
5046 5103 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
5047 5104 6.408858 ACTACATACGAAGCAAAATGAGTG 57.591 37.500 0.00 0.00 0.00 3.51
5048 5105 5.581085 GGACTACATACGAAGCAAAATGAGT 59.419 40.000 0.00 0.00 0.00 3.41
5049 5106 5.580691 TGGACTACATACGAAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
5050 5107 5.483811 TGGACTACATACGAAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
5051 5108 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
5052 5109 9.772973 TTATATGGACTACATACGAAGCAAAAT 57.227 29.630 0.00 0.00 44.41 1.82
5053 5110 9.256477 CTTATATGGACTACATACGAAGCAAAA 57.744 33.333 0.00 0.00 44.41 2.44
5054 5111 8.635328 TCTTATATGGACTACATACGAAGCAAA 58.365 33.333 0.00 0.00 44.41 3.68
5055 5112 8.173542 TCTTATATGGACTACATACGAAGCAA 57.826 34.615 0.00 0.00 44.41 3.91
5056 5113 7.754851 TCTTATATGGACTACATACGAAGCA 57.245 36.000 0.00 0.00 44.41 3.91
5057 5114 8.512956 TCTTCTTATATGGACTACATACGAAGC 58.487 37.037 0.00 0.00 44.41 3.86
5058 5115 9.828852 GTCTTCTTATATGGACTACATACGAAG 57.171 37.037 0.00 8.93 44.41 3.79
5059 5116 9.570468 AGTCTTCTTATATGGACTACATACGAA 57.430 33.333 0.00 0.00 44.41 3.85
5060 5117 9.570468 AAGTCTTCTTATATGGACTACATACGA 57.430 33.333 0.00 0.00 44.41 3.43
5077 5134 8.422566 CCTCCGTTCCTAAATATAAGTCTTCTT 58.577 37.037 0.00 0.00 37.65 2.52
5078 5135 7.015389 CCCTCCGTTCCTAAATATAAGTCTTCT 59.985 40.741 0.00 0.00 0.00 2.85
5079 5136 7.015001 TCCCTCCGTTCCTAAATATAAGTCTTC 59.985 40.741 0.00 0.00 0.00 2.87
5080 5137 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
5081 5138 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
5082 5139 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
5083 5140 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
5084 5141 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
5085 5142 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
5086 5143 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
5087 5144 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
5088 5145 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
5089 5146 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
5090 5147 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
5091 5148 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
5092 5149 4.079558 ACATAAGTACTCCCTCCGTTCCTA 60.080 45.833 0.00 0.00 0.00 2.94
5093 5150 3.297736 CATAAGTACTCCCTCCGTTCCT 58.702 50.000 0.00 0.00 0.00 3.36
5094 5151 3.029570 ACATAAGTACTCCCTCCGTTCC 58.970 50.000 0.00 0.00 0.00 3.62
5095 5152 4.159135 TGAACATAAGTACTCCCTCCGTTC 59.841 45.833 0.00 4.95 0.00 3.95
5096 5153 4.091549 TGAACATAAGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
5097 5154 3.705051 TGAACATAAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
5098 5155 4.585162 AGATGAACATAAGTACTCCCTCCG 59.415 45.833 0.00 0.00 0.00 4.63
5099 5156 5.364157 ACAGATGAACATAAGTACTCCCTCC 59.636 44.000 0.00 0.00 0.00 4.30
5100 5157 6.472686 ACAGATGAACATAAGTACTCCCTC 57.527 41.667 0.00 0.00 0.00 4.30
5101 5158 6.213600 ACAACAGATGAACATAAGTACTCCCT 59.786 38.462 0.00 0.00 0.00 4.20
5102 5159 6.313905 CACAACAGATGAACATAAGTACTCCC 59.686 42.308 0.00 0.00 0.00 4.30
5103 5160 6.183360 GCACAACAGATGAACATAAGTACTCC 60.183 42.308 0.00 0.00 0.00 3.85
5104 5161 6.591834 AGCACAACAGATGAACATAAGTACTC 59.408 38.462 0.00 0.00 0.00 2.59
5105 5162 6.467677 AGCACAACAGATGAACATAAGTACT 58.532 36.000 0.00 0.00 0.00 2.73
5106 5163 6.727824 AGCACAACAGATGAACATAAGTAC 57.272 37.500 0.00 0.00 0.00 2.73
5127 5184 8.976986 AAATTCTACATTCAGAAATCACAAGC 57.023 30.769 0.00 0.00 38.03 4.01
5185 5271 3.388024 TGCCGCTTGATTCTTAGTAGGAT 59.612 43.478 0.00 0.00 0.00 3.24
5227 5428 2.678336 CTGAAGTAACCCGGAAATGAGC 59.322 50.000 0.73 0.00 0.00 4.26
5236 5437 3.257624 ACAACCTAGTCTGAAGTAACCCG 59.742 47.826 0.00 0.00 0.00 5.28
5242 5443 9.841295 TTACAAATTTACAACCTAGTCTGAAGT 57.159 29.630 0.00 0.00 0.00 3.01
5329 5537 4.082245 CCTGCCACCGATTTAAACAAGAAT 60.082 41.667 0.00 0.00 0.00 2.40
5357 5565 3.953887 GCTGCGGCCGCTATTTCC 61.954 66.667 45.79 24.89 42.51 3.13
5369 5577 1.002250 CTGCAAGCTTTTCTGCTGCG 61.002 55.000 9.40 0.00 43.24 5.18
5581 5792 2.700897 CCGTTGAGGGGAGATACATTCT 59.299 50.000 0.00 0.00 34.87 2.40
5632 5843 1.889530 AAGAGAAGGGCTTCCGTCCG 61.890 60.000 0.00 0.00 40.84 4.79
5648 5859 4.674101 CGCTTGGAACTGTTTGTTGAAAGA 60.674 41.667 0.00 0.00 39.30 2.52
5699 5910 4.583871 ACTGGTTAGCAAATGAGGAAGAG 58.416 43.478 0.00 0.00 0.00 2.85
5708 5919 0.887933 CGGGCAACTGGTTAGCAAAT 59.112 50.000 0.00 0.00 40.24 2.32
5800 6011 4.525487 AGAATCAACAAGCCAACATCACAT 59.475 37.500 0.00 0.00 0.00 3.21
5837 6048 1.014352 CCCGTTTTCATCCGTCATCC 58.986 55.000 0.00 0.00 0.00 3.51
5851 6062 4.035112 TCTATAGAAACCCATGACCCGTT 58.965 43.478 0.00 0.00 0.00 4.44
5852 6063 3.641906 CTCTATAGAAACCCATGACCCGT 59.358 47.826 3.57 0.00 0.00 5.28
5984 6195 2.660572 ACACACACACACTCTCTCTCT 58.339 47.619 0.00 0.00 0.00 3.10
5986 6197 3.243569 GCTAACACACACACACTCTCTCT 60.244 47.826 0.00 0.00 0.00 3.10
5991 6202 2.540101 GACAGCTAACACACACACACTC 59.460 50.000 0.00 0.00 0.00 3.51
5992 6203 2.550978 GACAGCTAACACACACACACT 58.449 47.619 0.00 0.00 0.00 3.55
5993 6204 1.257936 CGACAGCTAACACACACACAC 59.742 52.381 0.00 0.00 0.00 3.82
5994 6205 1.134936 ACGACAGCTAACACACACACA 60.135 47.619 0.00 0.00 0.00 3.72
5995 6206 1.567504 ACGACAGCTAACACACACAC 58.432 50.000 0.00 0.00 0.00 3.82
5996 6207 2.303163 AACGACAGCTAACACACACA 57.697 45.000 0.00 0.00 0.00 3.72
5997 6208 4.235360 AGATAACGACAGCTAACACACAC 58.765 43.478 0.00 0.00 0.00 3.82
6138 6349 5.548706 ACGACATACACAGACTACTTCTC 57.451 43.478 0.00 0.00 28.96 2.87
6139 6350 5.335740 CCAACGACATACACAGACTACTTCT 60.336 44.000 0.00 0.00 33.33 2.85
6202 6413 6.970484 ACACAATGATAACCTTCAAACTGAC 58.030 36.000 0.00 0.00 0.00 3.51
6273 6484 7.390440 TGAGTAACATAGAAGACACAAAATGGG 59.610 37.037 0.00 0.00 0.00 4.00
6317 6531 9.162764 GTTTCTGAATTGGTATAAGCTGTCTTA 57.837 33.333 0.00 0.00 38.97 2.10
6331 6825 6.128336 TGTTGTTTTTGCTGTTTCTGAATTGG 60.128 34.615 0.00 0.00 0.00 3.16
6339 6833 3.261580 AGGCTGTTGTTTTTGCTGTTTC 58.738 40.909 0.00 0.00 0.00 2.78
6351 6845 5.437060 TGAGAAAGAAAACTAGGCTGTTGT 58.563 37.500 0.00 0.00 0.00 3.32
6355 6849 6.377327 TTGTTGAGAAAGAAAACTAGGCTG 57.623 37.500 0.00 0.00 0.00 4.85
6356 6850 6.207614 GGATTGTTGAGAAAGAAAACTAGGCT 59.792 38.462 0.00 0.00 0.00 4.58
6403 6897 3.837893 TGGACAACCAGGATTGCAA 57.162 47.368 0.00 0.00 41.77 4.08
6425 6919 4.582656 TCCCTTGTCACCAATGTTTAGTTG 59.417 41.667 0.00 0.00 0.00 3.16
6426 6920 4.798882 TCCCTTGTCACCAATGTTTAGTT 58.201 39.130 0.00 0.00 0.00 2.24
6427 6921 4.447138 TCCCTTGTCACCAATGTTTAGT 57.553 40.909 0.00 0.00 0.00 2.24
6428 6922 5.782893 TTTCCCTTGTCACCAATGTTTAG 57.217 39.130 0.00 0.00 0.00 1.85
6429 6923 6.546428 TTTTTCCCTTGTCACCAATGTTTA 57.454 33.333 0.00 0.00 0.00 2.01
6430 6924 5.427378 CTTTTTCCCTTGTCACCAATGTTT 58.573 37.500 0.00 0.00 0.00 2.83
6431 6925 4.683129 GCTTTTTCCCTTGTCACCAATGTT 60.683 41.667 0.00 0.00 0.00 2.71
6432 6926 3.181466 GCTTTTTCCCTTGTCACCAATGT 60.181 43.478 0.00 0.00 0.00 2.71
6433 6927 3.181467 TGCTTTTTCCCTTGTCACCAATG 60.181 43.478 0.00 0.00 0.00 2.82
6434 6928 3.037549 TGCTTTTTCCCTTGTCACCAAT 58.962 40.909 0.00 0.00 0.00 3.16
6435 6929 2.167487 GTGCTTTTTCCCTTGTCACCAA 59.833 45.455 0.00 0.00 0.00 3.67
6436 6930 1.754226 GTGCTTTTTCCCTTGTCACCA 59.246 47.619 0.00 0.00 0.00 4.17
6447 6941 5.891451 AGGAAATATTAGCGGTGCTTTTTC 58.109 37.500 0.00 2.16 40.44 2.29
6460 6954 5.368145 ACATGCTCGCAGAAGGAAATATTA 58.632 37.500 0.00 0.00 34.09 0.98
6461 6955 4.202441 ACATGCTCGCAGAAGGAAATATT 58.798 39.130 0.00 0.00 34.09 1.28
6468 6962 1.129998 CTTCAACATGCTCGCAGAAGG 59.870 52.381 9.49 0.00 34.09 3.46
6472 6966 1.225936 CGCTTCAACATGCTCGCAG 60.226 57.895 0.00 0.00 0.00 5.18
6478 6972 0.799534 GTGATGGCGCTTCAACATGC 60.800 55.000 7.64 0.00 0.00 4.06
6519 7035 5.749109 CAGTCGTGTTGTTTTAGAGAACTCT 59.251 40.000 9.33 9.33 43.40 3.24
6520 7036 5.556570 GCAGTCGTGTTGTTTTAGAGAACTC 60.557 44.000 0.00 0.00 32.96 3.01
6525 7041 4.034048 AGTTGCAGTCGTGTTGTTTTAGAG 59.966 41.667 0.00 0.00 0.00 2.43
6530 7046 1.467374 GCAGTTGCAGTCGTGTTGTTT 60.467 47.619 0.00 0.00 41.59 2.83
6546 7073 0.396974 TTTGCCCTGGTTCTTGCAGT 60.397 50.000 0.00 0.00 34.81 4.40
6560 7087 3.110447 TCTTTGGACAATTGCTTTGCC 57.890 42.857 5.05 0.36 39.03 4.52
6572 7099 2.414691 GCGGCTGATTTCTTCTTTGGAC 60.415 50.000 0.00 0.00 0.00 4.02
6600 7127 0.671781 AGAAATGCGTGCGCTTCTCT 60.672 50.000 17.49 9.94 42.51 3.10
6601 7128 0.519999 CAGAAATGCGTGCGCTTCTC 60.520 55.000 17.49 7.80 42.51 2.87
6602 7129 1.499056 CAGAAATGCGTGCGCTTCT 59.501 52.632 17.49 14.97 42.51 2.85
6693 7222 1.463444 GTGTTCCTGATGTAACCGTGC 59.537 52.381 0.00 0.00 0.00 5.34
6722 7251 1.394618 TGGTGTTGGTAGTTTGGTGC 58.605 50.000 0.00 0.00 0.00 5.01
6736 7265 1.819305 GCCTGTTCATCCTGTTGGTGT 60.819 52.381 0.00 0.00 34.23 4.16
6742 7271 0.326264 GGAGTGCCTGTTCATCCTGT 59.674 55.000 0.00 0.00 0.00 4.00
6750 7279 0.834687 TTACGGAGGGAGTGCCTGTT 60.835 55.000 8.45 0.00 0.00 3.16
6758 7287 0.739813 CGGCTTGTTTACGGAGGGAG 60.740 60.000 0.00 0.00 0.00 4.30
6759 7288 1.294138 CGGCTTGTTTACGGAGGGA 59.706 57.895 0.00 0.00 0.00 4.20
6760 7289 2.396157 GCGGCTTGTTTACGGAGGG 61.396 63.158 0.00 0.00 0.00 4.30
6761 7290 2.396157 GGCGGCTTGTTTACGGAGG 61.396 63.158 0.00 0.00 0.00 4.30
6779 7308 2.622436 CTAGGCTTTCCTTTCCTCGTG 58.378 52.381 0.00 0.00 40.66 4.35
6847 7376 2.813908 GTCACCGCCATGGACGTC 60.814 66.667 18.40 7.13 42.00 4.34


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

AutoCloner maintained by Alex Coulton.