Multiple sequence alignment - TraesCS5D01G492500

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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 TraesCS5D01G492500 chr5D 100.000 6302 0 0 1 6302 525667352 525661051 0.000000e+00 11638.0
1 TraesCS5D01G492500 chr5D 94.000 150 8 1 1289 1437 525665914 525665765 6.360000e-55 226.0
2 TraesCS5D01G492500 chr5D 94.000 150 8 1 1439 1588 525666064 525665916 6.360000e-55 226.0
3 TraesCS5D01G492500 chr5B 94.376 3627 147 23 504 4088 660141911 660138300 0.000000e+00 5515.0
4 TraesCS5D01G492500 chr5B 94.595 1554 54 10 4424 5963 660137744 660136207 0.000000e+00 2377.0
5 TraesCS5D01G492500 chr5B 87.013 308 22 4 6013 6302 660136202 660135895 1.310000e-86 331.0
6 TraesCS5D01G492500 chr5B 81.864 397 32 28 70 435 660142639 660142252 1.330000e-76 298.0
7 TraesCS5D01G492500 chr5B 96.026 151 5 1 1289 1438 660140978 660140828 1.750000e-60 244.0
8 TraesCS5D01G492500 chr5B 89.189 148 15 1 1442 1588 660141127 660140980 3.880000e-42 183.0
9 TraesCS5D01G492500 chr5B 89.474 114 4 5 1 107 660142741 660142629 3.060000e-28 137.0
10 TraesCS5D01G492500 chr5A 95.437 1534 61 4 924 2449 651990751 651989219 0.000000e+00 2436.0
11 TraesCS5D01G492500 chr5A 92.602 1514 59 18 4424 5930 651986777 651985310 0.000000e+00 2126.0
12 TraesCS5D01G492500 chr5A 89.408 1671 124 24 2447 4089 651988984 651987339 0.000000e+00 2056.0
13 TraesCS5D01G492500 chr5A 88.742 755 54 15 1 733 651991694 651990949 0.000000e+00 894.0
14 TraesCS5D01G492500 chr5A 95.427 328 15 0 4096 4423 552330060 552330387 2.010000e-144 523.0
15 TraesCS5D01G492500 chr5A 86.667 300 26 10 6008 6300 651985274 651984982 2.830000e-83 320.0
16 TraesCS5D01G492500 chr5A 95.364 151 6 1 1289 1438 651990228 651990078 8.170000e-59 239.0
17 TraesCS5D01G492500 chr5A 93.243 148 10 0 1441 1588 651990377 651990230 1.060000e-52 219.0
18 TraesCS5D01G492500 chr5A 87.500 96 9 3 815 908 651990900 651990806 2.400000e-19 108.0
19 TraesCS5D01G492500 chr6B 82.402 1432 193 34 2700 4089 484660565 484659151 0.000000e+00 1194.0
20 TraesCS5D01G492500 chr6B 96.308 325 12 0 4099 4423 557419293 557418969 9.300000e-148 534.0
21 TraesCS5D01G492500 chr6B 95.758 330 13 1 4096 4424 413385733 413385404 1.200000e-146 531.0
22 TraesCS5D01G492500 chr6B 87.097 62 8 0 2603 2664 20616641 20616702 3.150000e-08 71.3
23 TraesCS5D01G492500 chr7A 82.386 1425 191 37 2703 4085 14935536 14934130 0.000000e+00 1186.0
24 TraesCS5D01G492500 chr7A 95.509 334 14 1 4096 4429 102490011 102490343 3.340000e-147 532.0
25 TraesCS5D01G492500 chr7A 95.166 331 14 2 4096 4425 690045736 690045407 7.240000e-144 521.0
26 TraesCS5D01G492500 chr2B 82.386 1408 202 27 2703 4089 697569201 697570583 0.000000e+00 1184.0
27 TraesCS5D01G492500 chr2B 83.665 1206 175 16 2889 4089 239631194 239630006 0.000000e+00 1116.0
28 TraesCS5D01G492500 chr4A 82.344 1365 201 27 2720 4052 720294300 720295656 0.000000e+00 1149.0
29 TraesCS5D01G492500 chr3D 85.447 962 118 16 3141 4089 358193282 358192330 0.000000e+00 981.0
30 TraesCS5D01G492500 chr7B 85.561 935 128 7 3160 4089 641750973 641750041 0.000000e+00 972.0
31 TraesCS5D01G492500 chr4B 82.126 1035 126 29 2739 3731 215914728 215915745 0.000000e+00 832.0
32 TraesCS5D01G492500 chr2D 98.171 328 6 0 4099 4426 204145318 204144991 1.970000e-159 573.0
33 TraesCS5D01G492500 chr3A 95.706 326 13 1 4099 4423 221916052 221915727 2.010000e-144 523.0
34 TraesCS5D01G492500 chr2A 95.441 329 14 1 4096 4423 81020358 81020686 2.010000e-144 523.0
35 TraesCS5D01G492500 chr1B 94.864 331 17 0 4096 4426 389004619 389004949 9.370000e-143 518.0


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 TraesCS5D01G492500 chr5D 525661051 525667352 6301 True 4030.000000 11638 96.000000 1 6302 3 chr5D.!!$R1 6301
1 TraesCS5D01G492500 chr5B 660135895 660142741 6846 True 1297.857143 5515 90.362429 1 6302 7 chr5B.!!$R1 6301
2 TraesCS5D01G492500 chr5A 651984982 651991694 6712 True 1049.750000 2436 91.120375 1 6300 8 chr5A.!!$R1 6299
3 TraesCS5D01G492500 chr6B 484659151 484660565 1414 True 1194.000000 1194 82.402000 2700 4089 1 chr6B.!!$R2 1389
4 TraesCS5D01G492500 chr7A 14934130 14935536 1406 True 1186.000000 1186 82.386000 2703 4085 1 chr7A.!!$R1 1382
5 TraesCS5D01G492500 chr2B 697569201 697570583 1382 False 1184.000000 1184 82.386000 2703 4089 1 chr2B.!!$F1 1386
6 TraesCS5D01G492500 chr2B 239630006 239631194 1188 True 1116.000000 1116 83.665000 2889 4089 1 chr2B.!!$R1 1200
7 TraesCS5D01G492500 chr4A 720294300 720295656 1356 False 1149.000000 1149 82.344000 2720 4052 1 chr4A.!!$F1 1332
8 TraesCS5D01G492500 chr3D 358192330 358193282 952 True 981.000000 981 85.447000 3141 4089 1 chr3D.!!$R1 948
9 TraesCS5D01G492500 chr7B 641750041 641750973 932 True 972.000000 972 85.561000 3160 4089 1 chr7B.!!$R1 929
10 TraesCS5D01G492500 chr4B 215914728 215915745 1017 False 832.000000 832 82.126000 2739 3731 1 chr4B.!!$F1 992

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
596 940 0.591659 GAAACTCCCTGTTGAACCGC 59.408 55.000 0.00 0.0 39.13 5.68 F
1306 1699 0.239347 GTGTGCACCTGCTGATGTTC 59.761 55.000 15.69 0.0 42.66 3.18 F
1424 1819 0.865111 CAAGTTCACGCATCGTTGGA 59.135 50.000 0.00 0.0 38.32 3.53 F
3158 3868 0.539438 ATGCGGGGATGTGTTGTTGT 60.539 50.000 0.00 0.0 0.00 3.32 F
4097 4828 1.066752 GCGGCTTCGGTTTTGGTTT 59.933 52.632 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1983 1.065102 CAGAAGAGCGGGCAAATGATG 59.935 52.381 0.00 0.00 0.00 3.07 R
3139 3849 0.539438 ACAACAACACATCCCCGCAT 60.539 50.000 0.00 0.00 0.00 4.73 R
3386 4106 0.900182 AGCCACGACTGGTCAGATCA 60.900 55.000 4.84 0.00 40.17 2.92 R
4395 5126 0.108963 CACTTTGGAACCCGGGTGTA 59.891 55.000 31.05 14.25 0.00 2.90 R
6002 6998 0.321564 TTTCACACCATCAGGGCTCG 60.322 55.000 0.00 0.00 42.05 5.03 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
99 134 8.506168 AATTTACAGAGACAAGTTCAGTCAAA 57.494 30.769 0.00 0.00 38.46 2.69
100 135 7.915293 TTTACAGAGACAAGTTCAGTCAAAA 57.085 32.000 0.00 0.00 38.46 2.44
101 136 7.915293 TTACAGAGACAAGTTCAGTCAAAAA 57.085 32.000 0.00 0.00 38.46 1.94
126 161 2.251600 CTGCAAGTTCAGTGGCCTC 58.748 57.895 3.32 0.00 0.00 4.70
186 231 2.265904 GGGCCACGGTTTCTTCCAC 61.266 63.158 4.39 0.00 0.00 4.02
203 248 2.081462 CCACACCTTTTAACCCTAGCG 58.919 52.381 0.00 0.00 0.00 4.26
467 536 3.402681 CCCCGAGCCATGGTGAGT 61.403 66.667 14.67 0.00 0.00 3.41
489 558 4.880426 TCCCCTCCCCTGGATCGC 62.880 72.222 0.00 0.00 0.00 4.58
595 939 1.961793 TGAAACTCCCTGTTGAACCG 58.038 50.000 0.00 0.00 39.13 4.44
596 940 0.591659 GAAACTCCCTGTTGAACCGC 59.408 55.000 0.00 0.00 39.13 5.68
597 941 0.822121 AAACTCCCTGTTGAACCGCC 60.822 55.000 0.00 0.00 39.13 6.13
676 1022 6.972328 GCTAGAGTTTTGTTTGTTGATTGTCA 59.028 34.615 0.00 0.00 0.00 3.58
733 1079 3.869065 CTTATCTTGTTTCGGGGTAGCA 58.131 45.455 0.00 0.00 0.00 3.49
736 1082 2.933573 TCTTGTTTCGGGGTAGCAAAA 58.066 42.857 0.00 0.00 0.00 2.44
904 1251 5.046950 TGCCCTTTAACATGGGTGTTATTTC 60.047 40.000 0.00 0.00 46.91 2.17
908 1255 7.763985 CCCTTTAACATGGGTGTTATTTCATTC 59.236 37.037 0.00 0.00 46.91 2.67
919 1266 7.339466 GGGTGTTATTTCATTCTGTTGGTAGAT 59.661 37.037 0.00 0.00 0.00 1.98
920 1267 8.184192 GGTGTTATTTCATTCTGTTGGTAGATG 58.816 37.037 0.00 0.00 0.00 2.90
1306 1699 0.239347 GTGTGCACCTGCTGATGTTC 59.761 55.000 15.69 0.00 42.66 3.18
1324 1717 6.587990 TGATGTTCTCTTCTTAGAAGCTTTCG 59.412 38.462 16.49 3.61 36.19 3.46
1363 1757 4.728882 GCTGACTTGGATTTACATTGAGCG 60.729 45.833 0.00 0.00 0.00 5.03
1424 1819 0.865111 CAAGTTCACGCATCGTTGGA 59.135 50.000 0.00 0.00 38.32 3.53
1484 1879 7.161773 TCTTAGAAGCTTGCTTGCAAAATAT 57.838 32.000 12.92 0.00 34.99 1.28
1512 1907 4.701651 TGCTGACTTGGATTTACATTGAGG 59.298 41.667 0.00 0.00 0.00 3.86
1522 1917 7.835822 TGGATTTACATTGAGGGTTTATGTTG 58.164 34.615 0.00 0.00 34.55 3.33
1529 1924 3.420893 TGAGGGTTTATGTTGCCTGAAG 58.579 45.455 0.00 0.00 0.00 3.02
1588 1983 1.291877 CGTTGGCTGTCCAGTAGTGC 61.292 60.000 0.00 0.00 44.53 4.40
2408 2812 6.718912 TGAATGTGATGTTTCCATGTTCCTAA 59.281 34.615 0.00 0.00 0.00 2.69
2574 3215 3.004524 GCTAGTACTCCGTAATCCACTGG 59.995 52.174 0.00 0.00 0.00 4.00
2891 3600 2.095252 GCGAGTCAACGGCTTCTCC 61.095 63.158 0.00 0.00 0.00 3.71
2967 3677 1.672356 CTCAACAACGGCCCCTCTG 60.672 63.158 0.00 0.00 0.00 3.35
3087 3797 1.377725 CTCTTGAGGCCGGCATTGT 60.378 57.895 30.85 9.46 0.00 2.71
3152 3862 2.124570 GAGCATGCGGGGATGTGT 60.125 61.111 13.01 0.00 0.00 3.72
3158 3868 0.539438 ATGCGGGGATGTGTTGTTGT 60.539 50.000 0.00 0.00 0.00 3.32
3386 4106 4.988598 CTGTTGCGCGGGGTGTCT 62.989 66.667 8.83 0.00 0.00 3.41
3883 4612 2.584608 GTCGTCATGGAGGGGTGG 59.415 66.667 0.00 0.00 0.00 4.61
3885 4614 3.716195 CGTCATGGAGGGGTGGCA 61.716 66.667 0.00 0.00 0.00 4.92
3905 4634 1.228124 CATTGGTCACGTGGGTGGT 60.228 57.895 17.00 0.00 44.50 4.16
4039 4769 4.954970 CACCTGGTGTGCGGCCTT 62.955 66.667 18.76 0.00 38.34 4.35
4097 4828 1.066752 GCGGCTTCGGTTTTGGTTT 59.933 52.632 0.00 0.00 0.00 3.27
4100 4831 2.387185 CGGCTTCGGTTTTGGTTTTAC 58.613 47.619 0.00 0.00 0.00 2.01
4103 4834 2.784928 GCTTCGGTTTTGGTTTTACGTG 59.215 45.455 0.00 0.00 0.00 4.49
4104 4835 3.487209 GCTTCGGTTTTGGTTTTACGTGA 60.487 43.478 0.00 0.00 0.00 4.35
4107 4838 3.875727 TCGGTTTTGGTTTTACGTGATCA 59.124 39.130 0.00 0.00 0.00 2.92
4108 4839 4.515944 TCGGTTTTGGTTTTACGTGATCAT 59.484 37.500 0.00 0.00 0.00 2.45
4109 4840 5.699915 TCGGTTTTGGTTTTACGTGATCATA 59.300 36.000 0.00 0.00 0.00 2.15
4111 4842 6.467682 CGGTTTTGGTTTTACGTGATCATATG 59.532 38.462 0.00 0.00 0.00 1.78
4112 4843 6.750039 GGTTTTGGTTTTACGTGATCATATGG 59.250 38.462 0.00 0.00 0.00 2.74
4113 4844 7.362229 GGTTTTGGTTTTACGTGATCATATGGA 60.362 37.037 0.00 0.00 0.00 3.41
4114 4845 7.873719 TTTGGTTTTACGTGATCATATGGAT 57.126 32.000 0.00 0.00 39.53 3.41
4115 4846 6.859420 TGGTTTTACGTGATCATATGGATG 57.141 37.500 0.00 0.00 36.00 3.51
4117 4848 7.501844 TGGTTTTACGTGATCATATGGATGTA 58.498 34.615 0.00 1.26 36.00 2.29
4118 4849 8.154203 TGGTTTTACGTGATCATATGGATGTAT 58.846 33.333 0.00 0.00 36.00 2.29
4119 4850 9.647797 GGTTTTACGTGATCATATGGATGTATA 57.352 33.333 0.00 0.00 36.00 1.47
4125 4856 9.803315 ACGTGATCATATGGATGTATATTACAC 57.197 33.333 0.00 0.00 42.23 2.90
4126 4857 9.801873 CGTGATCATATGGATGTATATTACACA 57.198 33.333 0.00 0.00 42.23 3.72
4145 4876 5.771469 ACACATGTGTAATGTTTGGTGATG 58.229 37.500 29.66 0.00 42.90 3.07
4146 4877 5.534278 ACACATGTGTAATGTTTGGTGATGA 59.466 36.000 29.66 0.00 42.90 2.92
4147 4878 6.040278 ACACATGTGTAATGTTTGGTGATGAA 59.960 34.615 29.66 0.00 42.90 2.57
4148 4879 6.922407 CACATGTGTAATGTTTGGTGATGAAA 59.078 34.615 18.03 0.00 0.00 2.69
4149 4880 7.599621 CACATGTGTAATGTTTGGTGATGAAAT 59.400 33.333 18.03 0.00 0.00 2.17
4150 4881 8.801299 ACATGTGTAATGTTTGGTGATGAAATA 58.199 29.630 0.00 0.00 0.00 1.40
4152 4883 9.859427 ATGTGTAATGTTTGGTGATGAAATAAG 57.141 29.630 0.00 0.00 0.00 1.73
4153 4884 8.855110 TGTGTAATGTTTGGTGATGAAATAAGT 58.145 29.630 0.00 0.00 0.00 2.24
4161 4892 9.503427 GTTTGGTGATGAAATAAGTAACTATGC 57.497 33.333 0.00 0.00 0.00 3.14
4163 4894 7.269316 TGGTGATGAAATAAGTAACTATGCGA 58.731 34.615 0.00 0.00 0.00 5.10
4165 4896 7.307219 GGTGATGAAATAAGTAACTATGCGACC 60.307 40.741 0.00 0.00 0.00 4.79
4166 4897 7.438459 GTGATGAAATAAGTAACTATGCGACCT 59.562 37.037 0.00 0.00 0.00 3.85
4167 4898 8.635328 TGATGAAATAAGTAACTATGCGACCTA 58.365 33.333 0.00 0.00 0.00 3.08
4168 4899 9.640963 GATGAAATAAGTAACTATGCGACCTAT 57.359 33.333 0.00 0.00 0.00 2.57
4180 4911 9.772973 AACTATGCGACCTATATAAAAATGACA 57.227 29.630 0.00 0.00 0.00 3.58
4181 4912 9.772973 ACTATGCGACCTATATAAAAATGACAA 57.227 29.630 0.00 0.00 0.00 3.18
4195 4926 9.790344 ATAAAAATGACAAAATGGTGATTTCCA 57.210 25.926 0.00 0.00 34.25 3.53
4196 4927 8.517062 AAAAATGACAAAATGGTGATTTCCAA 57.483 26.923 0.00 0.00 41.09 3.53
4197 4928 8.517062 AAAATGACAAAATGGTGATTTCCAAA 57.483 26.923 0.00 0.00 41.09 3.28
4198 4929 8.694581 AAATGACAAAATGGTGATTTCCAAAT 57.305 26.923 0.00 0.00 41.09 2.32
4199 4930 9.790344 AAATGACAAAATGGTGATTTCCAAATA 57.210 25.926 0.00 0.00 41.09 1.40
4200 4931 9.439500 AATGACAAAATGGTGATTTCCAAATAG 57.561 29.630 0.00 0.00 41.09 1.73
4201 4932 7.961351 TGACAAAATGGTGATTTCCAAATAGT 58.039 30.769 0.00 0.00 41.09 2.12
4202 4933 7.871973 TGACAAAATGGTGATTTCCAAATAGTG 59.128 33.333 0.00 0.00 41.09 2.74
4204 4935 8.428063 ACAAAATGGTGATTTCCAAATAGTGAA 58.572 29.630 0.00 0.00 41.09 3.18
4205 4936 9.439500 CAAAATGGTGATTTCCAAATAGTGAAT 57.561 29.630 0.00 0.00 41.09 2.57
4210 4941 8.196771 TGGTGATTTCCAAATAGTGAATAATGC 58.803 33.333 0.00 0.00 34.24 3.56
4212 4943 9.754382 GTGATTTCCAAATAGTGAATAATGCAT 57.246 29.630 0.00 0.00 0.00 3.96
4213 4944 9.752961 TGATTTCCAAATAGTGAATAATGCATG 57.247 29.630 0.00 0.00 0.00 4.06
4215 4946 6.712179 TCCAAATAGTGAATAATGCATGCA 57.288 33.333 25.04 25.04 0.00 3.96
4216 4947 6.506147 TCCAAATAGTGAATAATGCATGCAC 58.494 36.000 25.37 10.66 42.93 4.57
4222 4953 4.735985 GTGAATAATGCATGCACTGTTCA 58.264 39.130 29.54 29.54 39.81 3.18
4224 4955 5.457799 GTGAATAATGCATGCACTGTTCATC 59.542 40.000 33.46 24.86 39.81 2.92
4225 4956 5.358725 TGAATAATGCATGCACTGTTCATCT 59.641 36.000 29.54 7.92 0.00 2.90
4226 4957 5.847111 ATAATGCATGCACTGTTCATCTT 57.153 34.783 25.37 12.49 0.00 2.40
4227 4958 4.530710 AATGCATGCACTGTTCATCTTT 57.469 36.364 25.37 6.25 0.00 2.52
4228 4959 3.564235 TGCATGCACTGTTCATCTTTC 57.436 42.857 18.46 0.00 0.00 2.62
4229 4960 3.151554 TGCATGCACTGTTCATCTTTCT 58.848 40.909 18.46 0.00 0.00 2.52
4230 4961 4.325972 TGCATGCACTGTTCATCTTTCTA 58.674 39.130 18.46 0.00 0.00 2.10
4231 4962 4.761227 TGCATGCACTGTTCATCTTTCTAA 59.239 37.500 18.46 0.00 0.00 2.10
4232 4963 5.241285 TGCATGCACTGTTCATCTTTCTAAA 59.759 36.000 18.46 0.00 0.00 1.85
4233 4964 6.151691 GCATGCACTGTTCATCTTTCTAAAA 58.848 36.000 14.21 0.00 0.00 1.52
4237 4968 7.362662 TGCACTGTTCATCTTTCTAAAATCAC 58.637 34.615 0.00 0.00 0.00 3.06
4238 4969 6.521133 GCACTGTTCATCTTTCTAAAATCACG 59.479 38.462 0.00 0.00 0.00 4.35
4239 4970 7.571244 GCACTGTTCATCTTTCTAAAATCACGA 60.571 37.037 0.00 0.00 0.00 4.35
4240 4971 8.446273 CACTGTTCATCTTTCTAAAATCACGAT 58.554 33.333 0.00 0.00 0.00 3.73
4247 4978 9.611284 CATCTTTCTAAAATCACGATTTTGTCA 57.389 29.630 22.18 6.92 46.80 3.58
4256 4987 7.769272 AATCACGATTTTGTCATTTTTGTGT 57.231 28.000 0.00 0.00 0.00 3.72
4257 4988 8.864069 AATCACGATTTTGTCATTTTTGTGTA 57.136 26.923 0.00 0.00 0.00 2.90
4258 4989 8.864069 ATCACGATTTTGTCATTTTTGTGTAA 57.136 26.923 0.00 0.00 0.00 2.41
4259 4990 8.109843 TCACGATTTTGTCATTTTTGTGTAAC 57.890 30.769 0.00 0.00 37.35 2.50
4260 4991 7.971168 TCACGATTTTGTCATTTTTGTGTAACT 59.029 29.630 0.00 0.00 38.04 2.24
4261 4992 8.259194 CACGATTTTGTCATTTTTGTGTAACTC 58.741 33.333 0.00 0.00 38.04 3.01
4262 4993 7.971168 ACGATTTTGTCATTTTTGTGTAACTCA 59.029 29.630 0.00 0.00 38.04 3.41
4263 4994 8.259194 CGATTTTGTCATTTTTGTGTAACTCAC 58.741 33.333 0.00 0.00 46.31 3.51
4279 5010 8.995220 GTGTAACTCACATGGTTACTTATTTCA 58.005 33.333 18.35 1.51 45.19 2.69
4280 5011 9.214957 TGTAACTCACATGGTTACTTATTTCAG 57.785 33.333 18.35 0.00 45.19 3.02
4281 5012 6.743575 ACTCACATGGTTACTTATTTCAGC 57.256 37.500 0.00 0.00 0.00 4.26
4284 5015 7.066284 ACTCACATGGTTACTTATTTCAGCATC 59.934 37.037 0.00 0.00 0.00 3.91
4285 5016 6.883756 TCACATGGTTACTTATTTCAGCATCA 59.116 34.615 0.00 0.00 0.00 3.07
4286 5017 7.392953 TCACATGGTTACTTATTTCAGCATCAA 59.607 33.333 0.00 0.00 0.00 2.57
4287 5018 8.028354 CACATGGTTACTTATTTCAGCATCAAA 58.972 33.333 0.00 0.00 0.00 2.69
4289 5020 7.759489 TGGTTACTTATTTCAGCATCAAAGT 57.241 32.000 0.00 0.00 0.00 2.66
4290 5021 8.177119 TGGTTACTTATTTCAGCATCAAAGTT 57.823 30.769 0.00 0.00 0.00 2.66
4291 5022 8.637986 TGGTTACTTATTTCAGCATCAAAGTTT 58.362 29.630 0.00 0.00 0.00 2.66
4296 5027 8.629158 ACTTATTTCAGCATCAAAGTTTACACA 58.371 29.630 0.00 0.00 0.00 3.72
4298 5029 7.878477 ATTTCAGCATCAAAGTTTACACATG 57.122 32.000 0.00 0.00 0.00 3.21
4299 5030 4.797471 TCAGCATCAAAGTTTACACATGC 58.203 39.130 10.74 10.74 37.50 4.06
4302 5033 4.454161 AGCATCAAAGTTTACACATGCGTA 59.546 37.500 12.04 0.00 41.25 4.42
4303 5034 5.049060 AGCATCAAAGTTTACACATGCGTAA 60.049 36.000 2.17 2.17 41.25 3.18
4306 5037 7.643764 GCATCAAAGTTTACACATGCGTAATAT 59.356 33.333 7.13 0.00 31.65 1.28
4309 5040 9.152595 TCAAAGTTTACACATGCGTAATATACA 57.847 29.630 7.13 0.00 31.65 2.29
4313 5044 9.320352 AGTTTACACATGCGTAATATACATTCA 57.680 29.630 7.13 0.00 31.65 2.57
4380 5111 3.540314 AGCATTTTGGCACAGTTCAAA 57.460 38.095 0.00 0.00 42.39 2.69
4381 5112 3.871485 AGCATTTTGGCACAGTTCAAAA 58.129 36.364 11.75 11.75 43.87 2.44
4401 5132 3.595190 AAATAGGGCTCCAATACACCC 57.405 47.619 0.00 0.00 43.17 4.61
4404 5135 2.192175 GGCTCCAATACACCCGGG 59.808 66.667 22.25 22.25 0.00 5.73
4408 5139 0.107361 CTCCAATACACCCGGGTTCC 60.107 60.000 27.83 0.00 0.00 3.62
4412 5143 1.816224 CAATACACCCGGGTTCCAAAG 59.184 52.381 27.83 14.87 0.00 2.77
4413 5144 1.069775 ATACACCCGGGTTCCAAAGT 58.930 50.000 27.83 20.47 0.00 2.66
4414 5145 0.108963 TACACCCGGGTTCCAAAGTG 59.891 55.000 27.83 13.22 0.00 3.16
4416 5147 1.149854 ACCCGGGTTCCAAAGTGAC 59.850 57.895 24.16 0.00 0.00 3.67
4417 5148 1.350310 ACCCGGGTTCCAAAGTGACT 61.350 55.000 24.16 0.00 0.00 3.41
4418 5149 0.179001 CCCGGGTTCCAAAGTGACTT 60.179 55.000 14.18 0.00 0.00 3.01
4419 5150 1.687563 CCGGGTTCCAAAGTGACTTT 58.312 50.000 4.45 4.45 33.58 2.66
4591 5571 7.065803 TCTGCTTCTACCTGCAATAATTGTAAC 59.934 37.037 0.00 0.00 38.81 2.50
4666 5646 2.560981 ACTTATTTCAACTTTGCGGGGG 59.439 45.455 0.00 0.00 0.00 5.40
4710 5690 2.603075 TGCTTGTCCCTTTTGGCTAT 57.397 45.000 0.00 0.00 38.58 2.97
5052 6032 4.090057 GCCCGCGAGTGCAAGAAC 62.090 66.667 8.23 0.00 42.97 3.01
5058 6038 1.006102 CGAGTGCAAGAACGACCCT 60.006 57.895 0.00 0.00 0.00 4.34
5070 6050 0.830444 ACGACCCTGTCTGCAACCTA 60.830 55.000 0.00 0.00 0.00 3.08
5211 6191 4.424566 CGCAACTGCATGGCCACC 62.425 66.667 8.16 2.09 42.21 4.61
5309 6290 0.461870 CGCCGGTTCTGATGGATTCA 60.462 55.000 1.90 0.00 0.00 2.57
5385 6366 3.196901 TCCTGTTTTAGATAGCTTCGGCA 59.803 43.478 0.00 0.00 44.74 5.69
5498 6483 3.809832 GCTTTGTAACTCTGCTGAACTGA 59.190 43.478 0.00 0.00 0.00 3.41
5568 6554 4.882671 ATATCATTGTGACACGCTTTCC 57.117 40.909 0.22 0.00 0.00 3.13
5672 6659 2.345876 TGGATGCATGTCGTGTTACTG 58.654 47.619 2.46 0.00 0.00 2.74
5676 6663 0.796312 GCATGTCGTGTTACTGGTGG 59.204 55.000 0.00 0.00 0.00 4.61
5677 6664 1.438651 CATGTCGTGTTACTGGTGGG 58.561 55.000 0.00 0.00 0.00 4.61
5678 6665 1.053424 ATGTCGTGTTACTGGTGGGT 58.947 50.000 0.00 0.00 0.00 4.51
5679 6666 0.831966 TGTCGTGTTACTGGTGGGTT 59.168 50.000 0.00 0.00 0.00 4.11
5680 6667 1.209990 TGTCGTGTTACTGGTGGGTTT 59.790 47.619 0.00 0.00 0.00 3.27
5681 6668 2.291365 GTCGTGTTACTGGTGGGTTTT 58.709 47.619 0.00 0.00 0.00 2.43
5682 6669 2.684374 GTCGTGTTACTGGTGGGTTTTT 59.316 45.455 0.00 0.00 0.00 1.94
5838 6825 1.704628 TCTGCAGTTGGAATGAGGGAA 59.295 47.619 14.67 0.00 0.00 3.97
5882 6869 5.577164 CAGATGTACTCGGTTTGTAGGAAAG 59.423 44.000 0.00 0.00 0.00 2.62
5936 6932 0.034574 TCCTGTGTGTTGGCAACTGT 60.035 50.000 28.71 0.00 37.61 3.55
5937 6933 0.817013 CCTGTGTGTTGGCAACTGTT 59.183 50.000 28.71 0.00 37.61 3.16
5938 6934 1.202290 CCTGTGTGTTGGCAACTGTTC 60.202 52.381 28.71 16.96 37.61 3.18
5939 6935 1.472082 CTGTGTGTTGGCAACTGTTCA 59.528 47.619 28.71 19.89 37.61 3.18
5940 6936 1.472082 TGTGTGTTGGCAACTGTTCAG 59.528 47.619 28.71 0.00 37.61 3.02
5941 6937 1.102154 TGTGTTGGCAACTGTTCAGG 58.898 50.000 28.71 0.00 37.61 3.86
5943 6939 1.065551 GTGTTGGCAACTGTTCAGGTC 59.934 52.381 28.71 1.15 37.61 3.85
5948 6944 3.030291 TGGCAACTGTTCAGGTCAAAAT 58.970 40.909 4.82 0.00 37.61 1.82
5993 6989 8.975295 TCCTAGTAGTACATTTTAGTTTCCTCC 58.025 37.037 2.52 0.00 0.00 4.30
5994 6990 8.755977 CCTAGTAGTACATTTTAGTTTCCTCCA 58.244 37.037 2.52 0.00 0.00 3.86
5997 6993 9.281371 AGTAGTACATTTTAGTTTCCTCCAAAC 57.719 33.333 2.52 0.00 44.38 2.93
6030 7026 5.186409 CCCTGATGGTGTGAAAATTGATCTT 59.814 40.000 0.00 0.00 0.00 2.40
6047 7043 3.752412 TCTTCGCAGCTTCATGATTTG 57.248 42.857 0.00 0.00 0.00 2.32
6073 7069 4.043596 TGGGAATTTTTGGAATATGGGGG 58.956 43.478 0.00 0.00 0.00 5.40
6096 7092 2.045047 AGGAATCCTCTCCTTCCTCACA 59.955 50.000 0.00 0.00 46.58 3.58
6115 7111 6.039270 CCTCACAAAATTCTTGTTGTCTGGTA 59.961 38.462 4.05 0.00 35.81 3.25
6116 7112 6.791303 TCACAAAATTCTTGTTGTCTGGTAC 58.209 36.000 4.05 0.00 35.81 3.34
6117 7113 5.977129 CACAAAATTCTTGTTGTCTGGTACC 59.023 40.000 4.43 4.43 35.81 3.34
6236 7251 0.816825 ATCATGGTCGCCATCAGCAC 60.817 55.000 8.21 0.00 43.15 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.930336 TCATGCTCTCGATGTTTCTTGT 58.070 40.909 0.00 0.00 0.00 3.16
99 134 5.523552 GCCACTGAACTTGCAGTTAAATTTT 59.476 36.000 0.00 0.00 46.42 1.82
100 135 5.049828 GCCACTGAACTTGCAGTTAAATTT 58.950 37.500 0.00 0.00 46.42 1.82
101 136 4.501400 GGCCACTGAACTTGCAGTTAAATT 60.501 41.667 0.00 0.00 46.42 1.82
102 137 3.005791 GGCCACTGAACTTGCAGTTAAAT 59.994 43.478 0.00 0.00 46.42 1.40
203 248 2.592993 TACTGTGCCAGTCCTGCCC 61.593 63.158 10.60 0.00 41.21 5.36
467 536 4.038804 CCAGGGGAGGGGAAGGGA 62.039 72.222 0.00 0.00 0.00 4.20
489 558 2.892425 GGCGTGCGAGGAATGAGG 60.892 66.667 0.00 0.00 0.00 3.86
541 882 2.368311 AGGCCTGCTACTACTACTCC 57.632 55.000 3.11 0.00 0.00 3.85
595 939 3.385755 AGCATATCCAATTCAAACCTGGC 59.614 43.478 0.00 0.00 0.00 4.85
596 940 4.202182 CCAGCATATCCAATTCAAACCTGG 60.202 45.833 0.00 0.00 0.00 4.45
597 941 4.403432 ACCAGCATATCCAATTCAAACCTG 59.597 41.667 0.00 0.00 0.00 4.00
651 997 6.972328 TGACAATCAACAAACAAAACTCTAGC 59.028 34.615 0.00 0.00 0.00 3.42
652 998 7.164171 CGTGACAATCAACAAACAAAACTCTAG 59.836 37.037 0.00 0.00 0.00 2.43
676 1022 2.422597 TGTGCACTAAATAAGCAGCGT 58.577 42.857 19.41 0.00 39.21 5.07
733 1079 3.306019 GCAACCTGGTTTCCATCGATTTT 60.306 43.478 9.90 0.00 30.82 1.82
736 1082 1.271871 TGCAACCTGGTTTCCATCGAT 60.272 47.619 9.90 0.00 30.82 3.59
904 1251 6.529125 GCAAAATCACATCTACCAACAGAATG 59.471 38.462 0.00 0.00 46.00 2.67
908 1255 4.460382 AGGCAAAATCACATCTACCAACAG 59.540 41.667 0.00 0.00 0.00 3.16
919 1266 2.517959 CAGGGAGAAGGCAAAATCACA 58.482 47.619 0.00 0.00 0.00 3.58
920 1267 1.821136 CCAGGGAGAAGGCAAAATCAC 59.179 52.381 0.00 0.00 0.00 3.06
1248 1641 4.180946 CGACGAGGAGGACTGCGG 62.181 72.222 0.00 0.00 0.00 5.69
1251 1644 2.487428 CTGCGACGAGGAGGACTG 59.513 66.667 0.00 0.00 34.34 3.51
1297 1690 5.418676 AGCTTCTAAGAAGAGAACATCAGC 58.581 41.667 1.70 2.46 32.05 4.26
1306 1699 3.990469 TGCACGAAAGCTTCTAAGAAGAG 59.010 43.478 0.00 0.00 31.96 2.85
1324 1717 4.969816 AGTCAGCATAACGTATTTTGCAC 58.030 39.130 12.49 5.12 43.09 4.57
1363 1757 8.573035 TCCAGTGAATATTTCAGGTAACAAAAC 58.427 33.333 0.00 0.00 41.01 2.43
1424 1819 2.494059 GTGCACAACACTACTGGACAT 58.506 47.619 13.17 0.00 46.41 3.06
1484 1879 7.392953 TCAATGTAAATCCAAGTCAGCATAACA 59.607 33.333 0.00 0.00 0.00 2.41
1512 1907 6.151144 AGTGAATACTTCAGGCAACATAAACC 59.849 38.462 0.00 0.00 41.01 3.27
1588 1983 1.065102 CAGAAGAGCGGGCAAATGATG 59.935 52.381 0.00 0.00 0.00 3.07
1841 2236 6.255670 GGTTTAGTTAATGCAAAGCTATTGGC 59.744 38.462 0.00 2.29 42.19 4.52
2408 2812 3.451178 AGACCTGTTATGGCGTCATACTT 59.549 43.478 9.74 0.00 35.75 2.24
2574 3215 4.084693 GCTTTGCTCTTTGATGTGCTTTTC 60.085 41.667 0.00 0.00 0.00 2.29
2606 3249 4.699735 CCAAAGATAGCACCATTGTACACA 59.300 41.667 0.00 0.00 0.00 3.72
2765 3409 2.284151 GAGAGGGAGGGAGGGGAC 59.716 72.222 0.00 0.00 0.00 4.46
2899 3608 4.776322 CCGGATCCACGCAGCCAA 62.776 66.667 13.41 0.00 0.00 4.52
3083 3793 5.454755 CGACCCCATAAAGTAGATCCACAAT 60.455 44.000 0.00 0.00 0.00 2.71
3087 3797 2.367567 GCGACCCCATAAAGTAGATCCA 59.632 50.000 0.00 0.00 0.00 3.41
3139 3849 0.539438 ACAACAACACATCCCCGCAT 60.539 50.000 0.00 0.00 0.00 4.73
3152 3862 2.412525 CCGCTGCAGCAACAACAA 59.587 55.556 36.03 0.00 42.21 2.83
3382 4102 1.541588 CACGACTGGTCAGATCAGACA 59.458 52.381 18.19 5.62 40.29 3.41
3386 4106 0.900182 AGCCACGACTGGTCAGATCA 60.900 55.000 4.84 0.00 40.17 2.92
3638 4364 2.291043 GCCTCCAAGAAGGTCCCGA 61.291 63.158 0.00 0.00 38.79 5.14
3639 4365 2.269241 GCCTCCAAGAAGGTCCCG 59.731 66.667 0.00 0.00 38.79 5.14
3640 4366 2.269241 CGCCTCCAAGAAGGTCCC 59.731 66.667 0.00 0.00 38.79 4.46
3641 4367 1.079057 GACGCCTCCAAGAAGGTCC 60.079 63.158 0.00 0.00 38.79 4.46
3744 4473 1.226746 CAAGAAGGAACACGACACCC 58.773 55.000 0.00 0.00 0.00 4.61
3810 4539 3.941188 CGAGGCCACACACCACCT 61.941 66.667 5.01 0.00 34.43 4.00
3883 4612 2.562912 CCACGTGACCAATGCTGC 59.437 61.111 19.30 0.00 0.00 5.25
3885 4614 1.600636 CACCCACGTGACCAATGCT 60.601 57.895 19.30 0.00 43.14 3.79
3905 4634 2.214216 AGGCTGGCCAACGACACTA 61.214 57.895 7.01 0.00 38.92 2.74
3937 4666 3.148279 GATCTCCACGCCGACCCT 61.148 66.667 0.00 0.00 0.00 4.34
4085 4816 3.875727 TGATCACGTAAAACCAAAACCGA 59.124 39.130 0.00 0.00 0.00 4.69
4089 4820 7.689446 TCCATATGATCACGTAAAACCAAAA 57.311 32.000 3.65 0.00 0.00 2.44
4090 4821 7.338196 ACATCCATATGATCACGTAAAACCAAA 59.662 33.333 3.65 0.00 36.54 3.28
4091 4822 6.826231 ACATCCATATGATCACGTAAAACCAA 59.174 34.615 3.65 0.00 36.54 3.67
4100 4831 9.801873 TGTGTAATATACATCCATATGATCACG 57.198 33.333 3.65 0.00 41.34 4.35
4121 4852 6.712547 TCATCACCAAACATTACACATGTGTA 59.287 34.615 30.31 30.31 44.42 2.90
4122 4853 5.534278 TCATCACCAAACATTACACATGTGT 59.466 36.000 32.47 32.47 46.87 3.72
4123 4854 6.011476 TCATCACCAAACATTACACATGTG 57.989 37.500 24.25 24.25 31.80 3.21
4124 4855 6.647334 TTCATCACCAAACATTACACATGT 57.353 33.333 0.00 0.00 0.00 3.21
4125 4856 9.636879 TTATTTCATCACCAAACATTACACATG 57.363 29.630 0.00 0.00 0.00 3.21
4126 4857 9.859427 CTTATTTCATCACCAAACATTACACAT 57.141 29.630 0.00 0.00 0.00 3.21
4127 4858 8.855110 ACTTATTTCATCACCAAACATTACACA 58.145 29.630 0.00 0.00 0.00 3.72
4135 4866 9.503427 GCATAGTTACTTATTTCATCACCAAAC 57.497 33.333 0.00 0.00 0.00 2.93
4136 4867 8.394877 CGCATAGTTACTTATTTCATCACCAAA 58.605 33.333 0.00 0.00 0.00 3.28
4137 4868 7.766738 TCGCATAGTTACTTATTTCATCACCAA 59.233 33.333 0.00 0.00 0.00 3.67
4138 4869 7.223971 GTCGCATAGTTACTTATTTCATCACCA 59.776 37.037 0.00 0.00 0.00 4.17
4139 4870 7.307219 GGTCGCATAGTTACTTATTTCATCACC 60.307 40.741 0.00 0.00 0.00 4.02
4140 4871 7.438459 AGGTCGCATAGTTACTTATTTCATCAC 59.562 37.037 0.00 0.00 0.00 3.06
4141 4872 7.497595 AGGTCGCATAGTTACTTATTTCATCA 58.502 34.615 0.00 0.00 0.00 3.07
4155 4886 9.772973 TTGTCATTTTTATATAGGTCGCATAGT 57.227 29.630 0.00 0.00 0.00 2.12
4159 4890 9.729023 CATTTTGTCATTTTTATATAGGTCGCA 57.271 29.630 0.00 0.00 0.00 5.10
4169 4900 9.790344 TGGAAATCACCATTTTGTCATTTTTAT 57.210 25.926 0.00 0.00 34.77 1.40
4170 4901 9.618890 TTGGAAATCACCATTTTGTCATTTTTA 57.381 25.926 0.00 0.00 39.82 1.52
4171 4902 8.517062 TTGGAAATCACCATTTTGTCATTTTT 57.483 26.923 0.00 0.00 39.82 1.94
4173 4904 8.694581 ATTTGGAAATCACCATTTTGTCATTT 57.305 26.923 0.00 0.00 39.82 2.32
4174 4905 9.439500 CTATTTGGAAATCACCATTTTGTCATT 57.561 29.630 0.00 0.00 39.82 2.57
4175 4906 8.596293 ACTATTTGGAAATCACCATTTTGTCAT 58.404 29.630 0.00 0.00 39.82 3.06
4178 4909 7.961351 TCACTATTTGGAAATCACCATTTTGT 58.039 30.769 0.00 0.00 39.82 2.83
4179 4910 8.830201 TTCACTATTTGGAAATCACCATTTTG 57.170 30.769 0.00 0.00 39.82 2.44
4187 4918 9.752961 CATGCATTATTCACTATTTGGAAATCA 57.247 29.630 0.00 0.00 0.00 2.57
4188 4919 8.706035 GCATGCATTATTCACTATTTGGAAATC 58.294 33.333 14.21 0.00 0.00 2.17
4189 4920 8.205512 TGCATGCATTATTCACTATTTGGAAAT 58.794 29.630 18.46 0.00 0.00 2.17
4191 4922 6.979817 GTGCATGCATTATTCACTATTTGGAA 59.020 34.615 25.64 0.00 31.32 3.53
4192 4923 6.321945 AGTGCATGCATTATTCACTATTTGGA 59.678 34.615 25.64 0.00 40.72 3.53
4193 4924 6.419710 CAGTGCATGCATTATTCACTATTTGG 59.580 38.462 25.64 0.00 40.58 3.28
4194 4925 6.976349 ACAGTGCATGCATTATTCACTATTTG 59.024 34.615 25.64 5.46 40.58 2.32
4195 4926 7.104043 ACAGTGCATGCATTATTCACTATTT 57.896 32.000 25.64 0.00 40.58 1.40
4196 4927 6.704289 ACAGTGCATGCATTATTCACTATT 57.296 33.333 25.64 1.93 40.58 1.73
4197 4928 6.319405 TGAACAGTGCATGCATTATTCACTAT 59.681 34.615 27.00 5.10 40.58 2.12
4198 4929 5.647225 TGAACAGTGCATGCATTATTCACTA 59.353 36.000 27.00 10.03 40.58 2.74
4199 4930 4.460034 TGAACAGTGCATGCATTATTCACT 59.540 37.500 27.00 14.53 42.80 3.41
4200 4931 4.735985 TGAACAGTGCATGCATTATTCAC 58.264 39.130 27.00 12.58 33.75 3.18
4201 4932 5.358725 AGATGAACAGTGCATGCATTATTCA 59.641 36.000 30.89 30.89 31.90 2.57
4202 4933 5.828747 AGATGAACAGTGCATGCATTATTC 58.171 37.500 25.64 24.08 0.00 1.75
4204 4935 5.847111 AAGATGAACAGTGCATGCATTAT 57.153 34.783 25.64 5.73 0.00 1.28
4205 4936 5.416639 AGAAAGATGAACAGTGCATGCATTA 59.583 36.000 25.64 4.62 0.00 1.90
4206 4937 4.219944 AGAAAGATGAACAGTGCATGCATT 59.780 37.500 25.64 18.02 0.00 3.56
4208 4939 3.151554 AGAAAGATGAACAGTGCATGCA 58.848 40.909 18.46 18.46 0.00 3.96
4209 4940 3.844577 AGAAAGATGAACAGTGCATGC 57.155 42.857 11.82 11.82 0.00 4.06
4210 4941 8.024865 TGATTTTAGAAAGATGAACAGTGCATG 58.975 33.333 0.00 0.00 0.00 4.06
4212 4943 7.362662 GTGATTTTAGAAAGATGAACAGTGCA 58.637 34.615 0.00 0.00 0.00 4.57
4213 4944 6.521133 CGTGATTTTAGAAAGATGAACAGTGC 59.479 38.462 0.00 0.00 0.00 4.40
4215 4946 7.962964 TCGTGATTTTAGAAAGATGAACAGT 57.037 32.000 0.00 0.00 0.00 3.55
4216 4947 9.831737 AAATCGTGATTTTAGAAAGATGAACAG 57.168 29.630 2.04 0.00 37.74 3.16
4220 4951 9.825972 GACAAAATCGTGATTTTAGAAAGATGA 57.174 29.630 17.52 0.00 46.01 2.92
4231 4962 8.195617 ACACAAAAATGACAAAATCGTGATTT 57.804 26.923 2.04 2.04 42.35 2.17
4232 4963 7.769272 ACACAAAAATGACAAAATCGTGATT 57.231 28.000 0.00 0.00 0.00 2.57
4233 4964 8.751335 GTTACACAAAAATGACAAAATCGTGAT 58.249 29.630 0.00 0.00 0.00 3.06
4237 4968 8.334016 TGAGTTACACAAAAATGACAAAATCG 57.666 30.769 0.00 0.00 0.00 3.34
4256 4987 7.880713 TGCTGAAATAAGTAACCATGTGAGTTA 59.119 33.333 0.00 0.00 0.00 2.24
4257 4988 6.714810 TGCTGAAATAAGTAACCATGTGAGTT 59.285 34.615 0.00 0.00 0.00 3.01
4258 4989 6.237901 TGCTGAAATAAGTAACCATGTGAGT 58.762 36.000 0.00 0.00 0.00 3.41
4259 4990 6.741992 TGCTGAAATAAGTAACCATGTGAG 57.258 37.500 0.00 0.00 0.00 3.51
4260 4991 6.883756 TGATGCTGAAATAAGTAACCATGTGA 59.116 34.615 0.00 0.00 0.00 3.58
4261 4992 7.087409 TGATGCTGAAATAAGTAACCATGTG 57.913 36.000 0.00 0.00 0.00 3.21
4262 4993 7.701539 TTGATGCTGAAATAAGTAACCATGT 57.298 32.000 0.00 0.00 0.00 3.21
4263 4994 8.246180 ACTTTGATGCTGAAATAAGTAACCATG 58.754 33.333 0.00 0.00 0.00 3.66
4264 4995 8.353423 ACTTTGATGCTGAAATAAGTAACCAT 57.647 30.769 0.00 0.00 0.00 3.55
4270 5001 8.629158 TGTGTAAACTTTGATGCTGAAATAAGT 58.371 29.630 0.00 0.00 0.00 2.24
4271 5002 9.630098 ATGTGTAAACTTTGATGCTGAAATAAG 57.370 29.630 0.00 0.00 0.00 1.73
4272 5003 9.409312 CATGTGTAAACTTTGATGCTGAAATAA 57.591 29.630 0.00 0.00 0.00 1.40
4274 5005 6.366877 GCATGTGTAAACTTTGATGCTGAAAT 59.633 34.615 0.00 0.00 34.64 2.17
4275 5006 5.691305 GCATGTGTAAACTTTGATGCTGAAA 59.309 36.000 0.00 0.00 34.64 2.69
4277 5008 4.613394 CGCATGTGTAAACTTTGATGCTGA 60.613 41.667 0.00 0.00 35.19 4.26
4279 5010 3.253188 ACGCATGTGTAAACTTTGATGCT 59.747 39.130 10.90 0.00 35.19 3.79
4280 5011 3.564511 ACGCATGTGTAAACTTTGATGC 58.435 40.909 10.90 0.00 34.23 3.91
4284 5015 9.929722 ATGTATATTACGCATGTGTAAACTTTG 57.070 29.630 29.81 0.00 37.81 2.77
4287 5018 9.320352 TGAATGTATATTACGCATGTGTAAACT 57.680 29.630 29.81 22.34 37.81 2.66
4357 5088 3.871485 TGAACTGTGCCAAAATGCTTTT 58.129 36.364 0.00 0.00 0.00 2.27
4358 5089 3.540314 TGAACTGTGCCAAAATGCTTT 57.460 38.095 0.00 0.00 0.00 3.51
4359 5090 3.540314 TTGAACTGTGCCAAAATGCTT 57.460 38.095 0.00 0.00 0.00 3.91
4360 5091 3.540314 TTTGAACTGTGCCAAAATGCT 57.460 38.095 6.26 0.00 30.29 3.79
4361 5092 4.612932 TTTTTGAACTGTGCCAAAATGC 57.387 36.364 16.64 0.00 40.55 3.56
4380 5111 3.687264 CGGGTGTATTGGAGCCCTATTTT 60.687 47.826 0.00 0.00 38.97 1.82
4381 5112 2.158667 CGGGTGTATTGGAGCCCTATTT 60.159 50.000 0.00 0.00 38.97 1.40
4385 5116 2.375345 CCGGGTGTATTGGAGCCCT 61.375 63.158 0.00 0.00 38.97 5.19
4390 5121 0.841158 TGGAACCCGGGTGTATTGGA 60.841 55.000 31.05 4.09 0.00 3.53
4392 5123 1.816224 CTTTGGAACCCGGGTGTATTG 59.184 52.381 31.05 12.61 0.00 1.90
4395 5126 0.108963 CACTTTGGAACCCGGGTGTA 59.891 55.000 31.05 14.25 0.00 2.90
4397 5128 1.149627 TCACTTTGGAACCCGGGTG 59.850 57.895 31.05 16.58 0.00 4.61
4401 5132 3.443976 CAAAAAGTCACTTTGGAACCCG 58.556 45.455 2.78 0.00 33.64 5.28
4408 5139 8.661352 ATTTCCATAACCAAAAAGTCACTTTG 57.339 30.769 2.78 0.00 33.64 2.77
4442 5417 7.548097 AGGACGACATATATTATGATGGTGAC 58.452 38.462 1.69 0.00 0.00 3.67
4444 5419 8.659491 CAAAGGACGACATATATTATGATGGTG 58.341 37.037 1.69 0.00 0.00 4.17
4445 5420 8.593679 TCAAAGGACGACATATATTATGATGGT 58.406 33.333 1.69 0.00 0.00 3.55
4446 5421 9.605275 ATCAAAGGACGACATATATTATGATGG 57.395 33.333 1.69 0.00 0.00 3.51
4453 5428 8.746052 TTTTCCATCAAAGGACGACATATATT 57.254 30.769 0.00 0.00 37.42 1.28
4457 5432 6.127758 CCATTTTTCCATCAAAGGACGACATA 60.128 38.462 0.00 0.00 37.42 2.29
4458 5433 5.336690 CCATTTTTCCATCAAAGGACGACAT 60.337 40.000 0.00 0.00 37.42 3.06
4591 5571 4.100279 AAGTTCACTTTACCCTGGAAGG 57.900 45.455 0.00 0.00 44.01 3.46
4666 5646 3.766676 TCGAGAGAACTGCATACTGAC 57.233 47.619 0.00 0.00 37.03 3.51
5052 6032 0.537188 ATAGGTTGCAGACAGGGTCG 59.463 55.000 0.00 0.00 37.67 4.79
5070 6050 4.634703 TGGCCCGACACGTTGCAT 62.635 61.111 0.00 0.00 0.00 3.96
5211 6191 2.447887 GCAGGTGTCGCAGATGACG 61.448 63.158 0.00 0.00 41.87 4.35
5385 6366 2.959220 AAACGGTTTCGGCGTCGTCT 62.959 55.000 10.18 0.00 41.39 4.18
5498 6483 3.870633 ATAAACGACTCTTTCTCGGCT 57.129 42.857 0.00 0.00 35.37 5.52
5547 6532 4.260985 TGGAAAGCGTGTCACAATGATAT 58.739 39.130 3.42 0.00 0.00 1.63
5548 6533 3.669536 TGGAAAGCGTGTCACAATGATA 58.330 40.909 3.42 0.00 0.00 2.15
5549 6534 2.485426 CTGGAAAGCGTGTCACAATGAT 59.515 45.455 3.42 0.00 0.00 2.45
5550 6535 1.872952 CTGGAAAGCGTGTCACAATGA 59.127 47.619 3.42 0.00 0.00 2.57
5551 6536 1.603802 ACTGGAAAGCGTGTCACAATG 59.396 47.619 3.42 0.00 0.00 2.82
5552 6537 1.967319 ACTGGAAAGCGTGTCACAAT 58.033 45.000 3.42 0.00 0.00 2.71
5553 6538 1.745232 AACTGGAAAGCGTGTCACAA 58.255 45.000 3.42 0.00 0.00 3.33
5679 6666 2.676748 ACATCTGCAACCCCAGAAAAA 58.323 42.857 0.00 0.00 44.34 1.94
5680 6667 2.364970 CAACATCTGCAACCCCAGAAAA 59.635 45.455 0.00 0.00 44.34 2.29
5681 6668 1.962807 CAACATCTGCAACCCCAGAAA 59.037 47.619 0.00 0.00 44.34 2.52
5682 6669 1.144708 TCAACATCTGCAACCCCAGAA 59.855 47.619 0.00 0.00 44.34 3.02
5764 6751 2.101249 CTCAAAGGCAGCCAACTTTTCA 59.899 45.455 15.80 0.00 34.89 2.69
5856 6843 1.710013 ACAAACCGAGTACATCTGCG 58.290 50.000 0.00 0.00 0.00 5.18
5882 6869 4.159377 TCGATGAAAATTGTTGTGCTCC 57.841 40.909 0.00 0.00 0.00 4.70
5967 6963 8.975295 GGAGGAAACTAAAATGTACTACTAGGA 58.025 37.037 0.00 0.00 44.43 2.94
5968 6964 8.755977 TGGAGGAAACTAAAATGTACTACTAGG 58.244 37.037 0.00 0.00 44.43 3.02
5971 6967 9.281371 GTTTGGAGGAAACTAAAATGTACTACT 57.719 33.333 0.00 0.00 44.43 2.57
5972 6968 8.225777 CGTTTGGAGGAAACTAAAATGTACTAC 58.774 37.037 0.00 0.00 44.43 2.73
5973 6969 7.388500 CCGTTTGGAGGAAACTAAAATGTACTA 59.612 37.037 0.00 0.00 44.43 1.82
5974 6970 6.206048 CCGTTTGGAGGAAACTAAAATGTACT 59.794 38.462 0.00 0.00 44.43 2.73
5975 6971 6.205270 TCCGTTTGGAGGAAACTAAAATGTAC 59.795 38.462 0.00 0.00 44.43 2.90
5976 6972 6.297582 TCCGTTTGGAGGAAACTAAAATGTA 58.702 36.000 0.00 0.00 44.43 2.29
5977 6973 5.134661 TCCGTTTGGAGGAAACTAAAATGT 58.865 37.500 0.00 0.00 44.43 2.71
5978 6974 5.699097 TCCGTTTGGAGGAAACTAAAATG 57.301 39.130 0.00 0.00 44.43 2.32
5991 6987 2.031465 GGGCTCGTTCCGTTTGGA 59.969 61.111 0.00 0.00 44.61 3.53
5992 6988 2.032071 AGGGCTCGTTCCGTTTGG 59.968 61.111 0.00 0.00 0.00 3.28
5993 6989 0.673644 ATCAGGGCTCGTTCCGTTTG 60.674 55.000 0.00 0.00 0.00 2.93
5994 6990 0.673644 CATCAGGGCTCGTTCCGTTT 60.674 55.000 0.00 0.00 0.00 3.60
5995 6991 1.079127 CATCAGGGCTCGTTCCGTT 60.079 57.895 0.00 0.00 0.00 4.44
5996 6992 2.579201 CATCAGGGCTCGTTCCGT 59.421 61.111 0.00 0.00 0.00 4.69
5997 6993 2.202932 CCATCAGGGCTCGTTCCG 60.203 66.667 0.00 0.00 0.00 4.30
5998 6994 1.450312 CACCATCAGGGCTCGTTCC 60.450 63.158 0.00 0.00 42.05 3.62
5999 6995 1.021390 CACACCATCAGGGCTCGTTC 61.021 60.000 0.00 0.00 42.05 3.95
6000 6996 1.003355 CACACCATCAGGGCTCGTT 60.003 57.895 0.00 0.00 42.05 3.85
6001 6997 1.480212 TTCACACCATCAGGGCTCGT 61.480 55.000 0.00 0.00 42.05 4.18
6002 6998 0.321564 TTTCACACCATCAGGGCTCG 60.322 55.000 0.00 0.00 42.05 5.03
6003 6999 1.909700 TTTTCACACCATCAGGGCTC 58.090 50.000 0.00 0.00 42.05 4.70
6004 7000 2.564062 CAATTTTCACACCATCAGGGCT 59.436 45.455 0.00 0.00 42.05 5.19
6005 7001 2.562298 TCAATTTTCACACCATCAGGGC 59.438 45.455 0.00 0.00 42.05 5.19
6006 7002 4.708421 AGATCAATTTTCACACCATCAGGG 59.292 41.667 0.00 0.00 44.81 4.45
6010 7006 4.795278 GCGAAGATCAATTTTCACACCATC 59.205 41.667 0.00 0.00 0.00 3.51
6047 7043 6.348498 CCCATATTCCAAAAATTCCCACTTC 58.652 40.000 0.00 0.00 0.00 3.01
6077 7073 4.559862 TTTGTGAGGAAGGAGAGGATTC 57.440 45.455 0.00 0.00 0.00 2.52
6087 7083 6.694411 CAGACAACAAGAATTTTGTGAGGAAG 59.306 38.462 0.00 0.00 36.06 3.46
6090 7086 5.163519 ACCAGACAACAAGAATTTTGTGAGG 60.164 40.000 0.00 3.20 36.06 3.86
6115 7111 2.713531 AATGCAGCCCTTGTTCGGGT 62.714 55.000 0.00 0.00 46.47 5.28
6117 7113 1.243342 TGAATGCAGCCCTTGTTCGG 61.243 55.000 0.00 0.00 0.00 4.30
6128 7143 0.242825 CTTGGTGCCTGTGAATGCAG 59.757 55.000 0.00 0.00 38.34 4.41
6142 7157 2.256117 ACTTTAGTGCTTCGCTTGGT 57.744 45.000 0.00 0.00 0.00 3.67
6149 7164 6.529125 TGTACGCTACATTACTTTAGTGCTTC 59.471 38.462 0.00 0.00 32.89 3.86


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

AutoCloner maintained by Alex Coulton.