Multiple sequence alignment - TraesCS3A01G208900

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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 TraesCS3A01G208900 chr3A 100.000 3843 0 0 1 3843 370237107 370240949 0.000000e+00 7097.0
1 TraesCS3A01G208900 chr3A 100.000 627 0 0 4217 4843 370241323 370241949 0.000000e+00 1158.0
2 TraesCS3A01G208900 chr3A 88.626 211 20 3 4254 4462 651189513 651189305 2.240000e-63 254.0
3 TraesCS3A01G208900 chr3A 88.426 216 17 6 4254 4465 712050757 712050968 2.240000e-63 254.0
4 TraesCS3A01G208900 chr3B 94.892 2506 53 42 1393 3843 377423497 377425982 0.000000e+00 3849.0
5 TraesCS3A01G208900 chr3B 94.526 1425 53 10 1 1409 377422069 377423484 0.000000e+00 2176.0
6 TraesCS3A01G208900 chr3D 96.939 2254 48 5 1606 3843 283315492 283317740 0.000000e+00 3760.0
7 TraesCS3A01G208900 chr3D 94.293 1612 58 13 1 1590 283313618 283315217 0.000000e+00 2436.0
8 TraesCS3A01G208900 chr3D 91.941 273 22 0 4571 4843 283318074 283318346 2.730000e-102 383.0
9 TraesCS3A01G208900 chr6A 78.435 1201 214 32 2344 3535 579438864 579437700 0.000000e+00 741.0
10 TraesCS3A01G208900 chr6A 87.850 214 22 3 4254 4465 471195374 471195163 1.040000e-61 248.0
11 TraesCS3A01G208900 chr6D 78.268 1201 213 35 2344 3535 433477548 433476387 0.000000e+00 728.0
12 TraesCS3A01G208900 chr6B 78.148 1199 218 32 2344 3535 654734416 654733255 0.000000e+00 723.0
13 TraesCS3A01G208900 chr7A 77.202 1215 250 23 2339 3535 108237641 108236436 0.000000e+00 684.0
14 TraesCS3A01G208900 chr7A 74.035 285 63 10 2886 3163 49047997 49047717 6.630000e-19 106.0
15 TraesCS3A01G208900 chr7D 77.119 1215 254 19 2339 3535 104091826 104090618 0.000000e+00 682.0
16 TraesCS3A01G208900 chr7B 77.037 1215 246 28 2339 3532 61910141 61908939 0.000000e+00 667.0
17 TraesCS3A01G208900 chr7B 95.000 40 1 1 2935 2974 497024959 497024921 1.460000e-05 62.1
18 TraesCS3A01G208900 chr4D 88.837 215 22 2 4251 4463 89931841 89931627 3.720000e-66 263.0
19 TraesCS3A01G208900 chr2A 89.202 213 17 5 4254 4462 576447532 576447322 1.340000e-65 261.0
20 TraesCS3A01G208900 chr5A 89.048 210 18 4 4254 4461 330283902 330283696 6.220000e-64 255.0
21 TraesCS3A01G208900 chr2D 88.263 213 21 4 4254 4462 79527849 79528061 8.050000e-63 252.0
22 TraesCS3A01G208900 chr2D 88.208 212 22 3 4254 4462 449513512 449513301 2.890000e-62 250.0
23 TraesCS3A01G208900 chr5D 88.152 211 23 2 4254 4462 537643099 537643309 2.890000e-62 250.0


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 TraesCS3A01G208900 chr3A 370237107 370241949 4842 False 4127.5 7097 100.000 1 4843 2 chr3A.!!$F2 4842
1 TraesCS3A01G208900 chr3B 377422069 377425982 3913 False 3012.5 3849 94.709 1 3843 2 chr3B.!!$F1 3842
2 TraesCS3A01G208900 chr3D 283313618 283318346 4728 False 2193.0 3760 94.391 1 4843 3 chr3D.!!$F1 4842
3 TraesCS3A01G208900 chr6A 579437700 579438864 1164 True 741.0 741 78.435 2344 3535 1 chr6A.!!$R2 1191
4 TraesCS3A01G208900 chr6D 433476387 433477548 1161 True 728.0 728 78.268 2344 3535 1 chr6D.!!$R1 1191
5 TraesCS3A01G208900 chr6B 654733255 654734416 1161 True 723.0 723 78.148 2344 3535 1 chr6B.!!$R1 1191
6 TraesCS3A01G208900 chr7A 108236436 108237641 1205 True 684.0 684 77.202 2339 3535 1 chr7A.!!$R2 1196
7 TraesCS3A01G208900 chr7D 104090618 104091826 1208 True 682.0 682 77.119 2339 3535 1 chr7D.!!$R1 1196
8 TraesCS3A01G208900 chr7B 61908939 61910141 1202 True 667.0 667 77.037 2339 3532 1 chr7B.!!$R1 1193

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
898 903 0.324943 CTTCTCCGGGAGCCAAAAGA 59.675 55.0 19.48 0.00 0.00 2.52 F
1022 1027 0.178861 AAGGAAGGGAGCAGGAGGAA 60.179 55.0 0.00 0.00 0.00 3.36 F
1549 1605 0.746659 GAATGGGGTAAGCCATGCAC 59.253 55.0 0.00 0.00 36.17 4.57 F
2302 2663 0.037160 TCCCATCCATCGATGCATGG 59.963 55.0 33.06 33.06 44.00 3.66 F
2304 2665 0.251033 CCATCCATCGATGCATGGGT 60.251 55.0 32.59 11.42 44.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 2028 0.674581 TGCTCTGGATCTTGTTGGCG 60.675 55.000 0.00 0.0 0.0 5.69 R
2078 2396 1.078759 CGTGGTGCTGTCGATCCTTC 61.079 60.000 0.00 0.0 0.0 3.46 R
3616 4030 2.360726 TCAGCCGTCGGTGAGCTA 60.361 61.111 13.94 0.0 41.5 3.32 R
3674 4088 0.037590 ACAACCCTGTGTGTGTGTGT 59.962 50.000 0.00 0.0 33.3 3.72 R
4272 4691 0.108615 CTGCTAACCGTGAGACCTGG 60.109 60.000 0.00 0.0 0.0 4.45 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
177 178 4.194640 TGCAGAATAGGAGAAATGAGCAC 58.805 43.478 0.00 0.00 0.00 4.40
182 183 5.879223 AGAATAGGAGAAATGAGCACAAGTG 59.121 40.000 0.00 0.00 0.00 3.16
299 300 6.321181 GGCCTTGATAATTCAACTGGATAACA 59.679 38.462 0.00 0.00 36.94 2.41
307 308 5.643379 TTCAACTGGATAACAAAGGCATC 57.357 39.130 0.00 0.00 0.00 3.91
319 320 5.294734 ACAAAGGCATCCAAACATTCTTT 57.705 34.783 0.00 0.00 0.00 2.52
322 323 5.549742 AAGGCATCCAAACATTCTTTGAA 57.450 34.783 0.00 0.00 0.00 2.69
324 325 5.299949 AGGCATCCAAACATTCTTTGAAAC 58.700 37.500 0.00 0.00 0.00 2.78
372 373 1.229428 CACCCGCTCGATGCATTTAT 58.771 50.000 0.00 0.00 43.06 1.40
390 391 4.864704 TTATTGCTTGTTTTCAGGTCCC 57.135 40.909 0.00 0.00 0.00 4.46
449 454 6.789457 AGGATGTGTATCTTCCCATTGATAGA 59.211 38.462 0.00 0.00 40.11 1.98
602 607 0.597118 TGCAATTGCGCCAAACACTC 60.597 50.000 24.58 0.00 45.83 3.51
687 692 5.414765 CCTACCTGACCTTGTAAAACCATTC 59.585 44.000 0.00 0.00 0.00 2.67
688 693 4.798882 ACCTGACCTTGTAAAACCATTCA 58.201 39.130 0.00 0.00 0.00 2.57
689 694 5.393866 ACCTGACCTTGTAAAACCATTCAT 58.606 37.500 0.00 0.00 0.00 2.57
691 696 6.326323 ACCTGACCTTGTAAAACCATTCATTT 59.674 34.615 0.00 0.00 0.00 2.32
692 697 6.646240 CCTGACCTTGTAAAACCATTCATTTG 59.354 38.462 0.00 0.00 0.00 2.32
693 698 7.353414 TGACCTTGTAAAACCATTCATTTGA 57.647 32.000 0.00 0.00 0.00 2.69
694 699 7.206687 TGACCTTGTAAAACCATTCATTTGAC 58.793 34.615 0.00 0.00 0.00 3.18
695 700 7.069331 TGACCTTGTAAAACCATTCATTTGACT 59.931 33.333 0.00 0.00 0.00 3.41
696 701 8.472007 ACCTTGTAAAACCATTCATTTGACTA 57.528 30.769 0.00 0.00 0.00 2.59
697 702 8.576442 ACCTTGTAAAACCATTCATTTGACTAG 58.424 33.333 0.00 0.00 0.00 2.57
698 703 7.542130 CCTTGTAAAACCATTCATTTGACTAGC 59.458 37.037 0.00 0.00 0.00 3.42
766 771 7.060383 ACATAGTTAGAGATGTTGGAGGATG 57.940 40.000 0.00 0.00 32.27 3.51
776 781 2.184020 TTGGAGGATGTCACCTGCCG 62.184 60.000 0.00 0.00 45.67 5.69
779 784 3.127533 GGATGTCACCTGCCGTGC 61.128 66.667 0.00 0.00 42.69 5.34
780 785 3.127533 GATGTCACCTGCCGTGCC 61.128 66.667 0.00 0.00 42.69 5.01
781 786 3.899981 GATGTCACCTGCCGTGCCA 62.900 63.158 0.00 0.00 42.69 4.92
782 787 3.272364 ATGTCACCTGCCGTGCCAT 62.272 57.895 0.00 0.00 42.69 4.40
783 788 3.434319 GTCACCTGCCGTGCCATG 61.434 66.667 0.00 0.00 42.69 3.66
827 832 2.180276 AGTGGAGTAAAGCGTGGATCT 58.820 47.619 0.00 0.00 0.00 2.75
898 903 0.324943 CTTCTCCGGGAGCCAAAAGA 59.675 55.000 19.48 0.00 0.00 2.52
951 956 1.223337 CTAATCTGGTACCCCCTCCCT 59.777 57.143 10.07 0.00 0.00 4.20
1007 1012 3.054361 GGATCTTTGTAGGCAAGGAAGGA 60.054 47.826 0.00 0.00 42.61 3.36
1010 1015 2.879103 TTGTAGGCAAGGAAGGAAGG 57.121 50.000 0.00 0.00 0.00 3.46
1011 1016 0.991920 TGTAGGCAAGGAAGGAAGGG 59.008 55.000 0.00 0.00 0.00 3.95
1014 1019 1.379176 GGCAAGGAAGGAAGGGAGC 60.379 63.158 0.00 0.00 0.00 4.70
1019 1024 0.620121 AGGAAGGAAGGGAGCAGGAG 60.620 60.000 0.00 0.00 0.00 3.69
1022 1027 0.178861 AAGGAAGGGAGCAGGAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
1088 1104 5.059833 TCTCCTTTCTCTTTCTCTTGTTGC 58.940 41.667 0.00 0.00 0.00 4.17
1097 1113 6.095300 TCTCTTTCTCTTGTTGCAACATTTGA 59.905 34.615 31.48 25.20 38.95 2.69
1109 1125 4.178540 GCAACATTTGACATCCATCCAAG 58.821 43.478 0.00 0.00 0.00 3.61
1381 1401 2.159707 CGTAACTTTCTTCCGCCACATG 60.160 50.000 0.00 0.00 0.00 3.21
1388 1408 2.358957 TCTTCCGCCACATGATTCTTG 58.641 47.619 0.00 0.00 0.00 3.02
1549 1605 0.746659 GAATGGGGTAAGCCATGCAC 59.253 55.000 0.00 0.00 36.17 4.57
1709 2027 4.881019 AGGCCATCATAGACTACATCAC 57.119 45.455 5.01 0.00 0.00 3.06
1710 2028 3.580458 AGGCCATCATAGACTACATCACC 59.420 47.826 5.01 0.00 0.00 4.02
2070 2388 2.860971 ACCAAGCAGCCCCTCCTT 60.861 61.111 0.00 0.00 0.00 3.36
2073 2391 1.378250 CAAGCAGCCCCTCCTTCTG 60.378 63.158 0.00 0.00 0.00 3.02
2078 2396 3.787001 GCCCCTCCTTCTGTCGGG 61.787 72.222 0.00 0.00 36.78 5.14
2153 2471 4.717629 CGACTTCGCACAGGCCGA 62.718 66.667 0.00 0.00 36.38 5.54
2294 2651 1.131638 TCCTTCCTTCCCATCCATCG 58.868 55.000 0.00 0.00 0.00 3.84
2302 2663 0.037160 TCCCATCCATCGATGCATGG 59.963 55.000 33.06 33.06 44.00 3.66
2304 2665 0.251033 CCATCCATCGATGCATGGGT 60.251 55.000 32.59 11.42 44.00 4.51
2325 2689 4.151157 GGTTTAGCTTAGTTGGTACGTGTG 59.849 45.833 0.00 0.00 0.00 3.82
2797 3190 3.144120 CTACAGCGCCAGCCTCGAT 62.144 63.158 2.29 0.00 46.67 3.59
3220 3622 2.989824 ACGCAGTACCGGCTGACT 60.990 61.111 12.73 5.89 41.94 3.41
3616 4030 2.115266 CACGGGCAGGAAAGGGTT 59.885 61.111 0.00 0.00 0.00 4.11
4240 4659 4.280677 CAGGGCAAACTATTGTTGGAAAGA 59.719 41.667 0.00 0.00 38.85 2.52
4247 4666 2.642139 ATTGTTGGAAAGATGCTGCG 57.358 45.000 0.00 0.00 0.00 5.18
4248 4667 0.039256 TTGTTGGAAAGATGCTGCGC 60.039 50.000 0.00 0.00 0.00 6.09
4249 4668 1.153958 GTTGGAAAGATGCTGCGCC 60.154 57.895 4.18 0.00 0.00 6.53
4251 4670 2.819595 GGAAAGATGCTGCGCCGA 60.820 61.111 4.18 0.00 0.00 5.54
4252 4671 2.398554 GGAAAGATGCTGCGCCGAA 61.399 57.895 4.18 0.00 0.00 4.30
4253 4672 1.061570 GAAAGATGCTGCGCCGAAG 59.938 57.895 4.18 0.00 0.00 3.79
4286 4705 4.621269 AGACCAGGTCTCACGGTT 57.379 55.556 17.31 0.00 38.71 4.44
4287 4706 3.759865 AGACCAGGTCTCACGGTTA 57.240 52.632 17.31 0.00 38.71 2.85
4288 4707 1.546961 AGACCAGGTCTCACGGTTAG 58.453 55.000 17.31 0.00 38.71 2.34
4289 4708 0.108756 GACCAGGTCTCACGGTTAGC 60.109 60.000 12.94 0.00 31.63 3.09
4290 4709 0.830444 ACCAGGTCTCACGGTTAGCA 60.830 55.000 0.00 0.00 0.00 3.49
4291 4710 0.108615 CCAGGTCTCACGGTTAGCAG 60.109 60.000 0.00 0.00 0.00 4.24
4292 4711 0.888619 CAGGTCTCACGGTTAGCAGA 59.111 55.000 0.00 0.00 0.00 4.26
4293 4712 1.478510 CAGGTCTCACGGTTAGCAGAT 59.521 52.381 0.00 0.00 0.00 2.90
4294 4713 1.478510 AGGTCTCACGGTTAGCAGATG 59.521 52.381 0.00 0.00 0.00 2.90
4295 4714 1.476891 GGTCTCACGGTTAGCAGATGA 59.523 52.381 0.00 0.00 0.00 2.92
4296 4715 2.480416 GGTCTCACGGTTAGCAGATGAG 60.480 54.545 0.00 0.00 38.51 2.90
4297 4716 2.423892 GTCTCACGGTTAGCAGATGAGA 59.576 50.000 6.10 6.10 42.63 3.27
4298 4717 2.423892 TCTCACGGTTAGCAGATGAGAC 59.576 50.000 6.10 0.00 40.59 3.36
4299 4718 1.476891 TCACGGTTAGCAGATGAGACC 59.523 52.381 0.00 0.00 0.00 3.85
4300 4719 0.824759 ACGGTTAGCAGATGAGACCC 59.175 55.000 0.00 0.00 0.00 4.46
4301 4720 0.824109 CGGTTAGCAGATGAGACCCA 59.176 55.000 0.00 0.00 0.00 4.51
4302 4721 1.414181 CGGTTAGCAGATGAGACCCAT 59.586 52.381 0.00 0.00 38.43 4.00
4303 4722 2.158900 CGGTTAGCAGATGAGACCCATT 60.159 50.000 0.00 0.00 35.17 3.16
4304 4723 3.471680 GGTTAGCAGATGAGACCCATTC 58.528 50.000 0.00 0.00 35.17 2.67
4305 4724 3.135530 GGTTAGCAGATGAGACCCATTCT 59.864 47.826 0.00 0.00 35.17 2.40
4320 4739 3.938778 CATTCTCATGGATGACACGTG 57.061 47.619 15.48 15.48 32.50 4.49
4321 4740 1.725641 TTCTCATGGATGACACGTGC 58.274 50.000 17.22 9.30 32.50 5.34
4322 4741 0.607620 TCTCATGGATGACACGTGCA 59.392 50.000 17.22 15.09 32.50 4.57
4323 4742 1.207811 TCTCATGGATGACACGTGCAT 59.792 47.619 17.22 19.21 32.50 3.96
4324 4743 2.011947 CTCATGGATGACACGTGCATT 58.988 47.619 17.22 0.00 32.50 3.56
4325 4744 2.009051 TCATGGATGACACGTGCATTC 58.991 47.619 17.22 18.15 0.00 2.67
4326 4745 1.738908 CATGGATGACACGTGCATTCA 59.261 47.619 25.79 25.79 35.81 2.57
4327 4746 2.112380 TGGATGACACGTGCATTCAT 57.888 45.000 22.22 19.95 32.53 2.57
4328 4747 3.258971 TGGATGACACGTGCATTCATA 57.741 42.857 22.22 7.59 29.93 2.15
4329 4748 3.604582 TGGATGACACGTGCATTCATAA 58.395 40.909 22.22 11.77 29.93 1.90
4330 4749 4.006319 TGGATGACACGTGCATTCATAAA 58.994 39.130 22.22 11.50 29.93 1.40
4331 4750 4.639755 TGGATGACACGTGCATTCATAAAT 59.360 37.500 22.22 4.56 29.93 1.40
4332 4751 5.207768 GGATGACACGTGCATTCATAAATC 58.792 41.667 17.22 6.46 29.93 2.17
4333 4752 4.614555 TGACACGTGCATTCATAAATCC 57.385 40.909 17.22 0.00 0.00 3.01
4334 4753 3.376859 TGACACGTGCATTCATAAATCCC 59.623 43.478 17.22 0.00 0.00 3.85
4335 4754 3.351740 ACACGTGCATTCATAAATCCCA 58.648 40.909 17.22 0.00 0.00 4.37
4336 4755 3.761218 ACACGTGCATTCATAAATCCCAA 59.239 39.130 17.22 0.00 0.00 4.12
4337 4756 4.219507 ACACGTGCATTCATAAATCCCAAA 59.780 37.500 17.22 0.00 0.00 3.28
4338 4757 4.799949 CACGTGCATTCATAAATCCCAAAG 59.200 41.667 0.82 0.00 0.00 2.77
4339 4758 3.798337 CGTGCATTCATAAATCCCAAAGC 59.202 43.478 0.00 0.00 0.00 3.51
4340 4759 4.677514 CGTGCATTCATAAATCCCAAAGCA 60.678 41.667 0.00 0.00 0.00 3.91
4341 4760 5.362263 GTGCATTCATAAATCCCAAAGCAT 58.638 37.500 0.00 0.00 0.00 3.79
4342 4761 5.464389 GTGCATTCATAAATCCCAAAGCATC 59.536 40.000 0.00 0.00 0.00 3.91
4343 4762 5.364446 TGCATTCATAAATCCCAAAGCATCT 59.636 36.000 0.00 0.00 0.00 2.90
4344 4763 6.550481 TGCATTCATAAATCCCAAAGCATCTA 59.450 34.615 0.00 0.00 0.00 1.98
4345 4764 7.069702 TGCATTCATAAATCCCAAAGCATCTAA 59.930 33.333 0.00 0.00 0.00 2.10
4346 4765 8.092687 GCATTCATAAATCCCAAAGCATCTAAT 58.907 33.333 0.00 0.00 0.00 1.73
4347 4766 9.635520 CATTCATAAATCCCAAAGCATCTAATC 57.364 33.333 0.00 0.00 0.00 1.75
4348 4767 7.765695 TCATAAATCCCAAAGCATCTAATCC 57.234 36.000 0.00 0.00 0.00 3.01
4349 4768 6.721208 TCATAAATCCCAAAGCATCTAATCCC 59.279 38.462 0.00 0.00 0.00 3.85
4350 4769 3.532641 ATCCCAAAGCATCTAATCCCC 57.467 47.619 0.00 0.00 0.00 4.81
4351 4770 1.499007 TCCCAAAGCATCTAATCCCCC 59.501 52.381 0.00 0.00 0.00 5.40
4374 4793 2.143876 CCCTATTTCAAGTGGGGGTG 57.856 55.000 0.00 0.00 36.15 4.61
4375 4794 1.341976 CCCTATTTCAAGTGGGGGTGG 60.342 57.143 0.00 0.00 36.15 4.61
4376 4795 1.638589 CCTATTTCAAGTGGGGGTGGA 59.361 52.381 0.00 0.00 0.00 4.02
4377 4796 2.042433 CCTATTTCAAGTGGGGGTGGAA 59.958 50.000 0.00 0.00 0.00 3.53
4378 4797 3.309848 CCTATTTCAAGTGGGGGTGGAAT 60.310 47.826 0.00 0.00 0.00 3.01
4379 4798 4.079443 CCTATTTCAAGTGGGGGTGGAATA 60.079 45.833 0.00 0.00 0.00 1.75
4380 4799 3.449746 TTTCAAGTGGGGGTGGAATAG 57.550 47.619 0.00 0.00 0.00 1.73
4381 4800 2.352561 TCAAGTGGGGGTGGAATAGA 57.647 50.000 0.00 0.00 0.00 1.98
4382 4801 2.858644 TCAAGTGGGGGTGGAATAGAT 58.141 47.619 0.00 0.00 0.00 1.98
4383 4802 2.509548 TCAAGTGGGGGTGGAATAGATG 59.490 50.000 0.00 0.00 0.00 2.90
4384 4803 0.846693 AGTGGGGGTGGAATAGATGC 59.153 55.000 0.00 0.00 0.00 3.91
4385 4804 0.846693 GTGGGGGTGGAATAGATGCT 59.153 55.000 0.00 0.00 0.00 3.79
4386 4805 1.215423 GTGGGGGTGGAATAGATGCTT 59.785 52.381 0.00 0.00 0.00 3.91
4387 4806 1.929494 TGGGGGTGGAATAGATGCTTT 59.071 47.619 0.00 0.00 0.00 3.51
4388 4807 2.310538 GGGGGTGGAATAGATGCTTTG 58.689 52.381 0.00 0.00 0.00 2.77
4389 4808 2.358195 GGGGGTGGAATAGATGCTTTGT 60.358 50.000 0.00 0.00 0.00 2.83
4390 4809 2.689983 GGGGTGGAATAGATGCTTTGTG 59.310 50.000 0.00 0.00 0.00 3.33
4391 4810 3.620488 GGGTGGAATAGATGCTTTGTGA 58.380 45.455 0.00 0.00 0.00 3.58
4392 4811 4.210331 GGGTGGAATAGATGCTTTGTGAT 58.790 43.478 0.00 0.00 0.00 3.06
4393 4812 4.646492 GGGTGGAATAGATGCTTTGTGATT 59.354 41.667 0.00 0.00 0.00 2.57
4394 4813 5.127682 GGGTGGAATAGATGCTTTGTGATTT 59.872 40.000 0.00 0.00 0.00 2.17
4395 4814 6.321181 GGGTGGAATAGATGCTTTGTGATTTA 59.679 38.462 0.00 0.00 0.00 1.40
4396 4815 7.014615 GGGTGGAATAGATGCTTTGTGATTTAT 59.985 37.037 0.00 0.00 0.00 1.40
4397 4816 9.066892 GGTGGAATAGATGCTTTGTGATTTATA 57.933 33.333 0.00 0.00 0.00 0.98
4405 4824 9.793252 AGATGCTTTGTGATTTATAAATGTCAC 57.207 29.630 15.39 17.42 0.00 3.67
4406 4825 8.619146 ATGCTTTGTGATTTATAAATGTCACG 57.381 30.769 15.39 7.83 30.17 4.35
4407 4826 7.589395 TGCTTTGTGATTTATAAATGTCACGT 58.411 30.769 15.39 0.00 30.17 4.49
4408 4827 7.536964 TGCTTTGTGATTTATAAATGTCACGTG 59.463 33.333 15.39 9.94 30.17 4.49
4409 4828 7.537306 GCTTTGTGATTTATAAATGTCACGTGT 59.463 33.333 15.39 0.00 30.17 4.49
4410 4829 8.942669 TTTGTGATTTATAAATGTCACGTGTC 57.057 30.769 15.39 10.98 30.17 3.67
4411 4830 7.659652 TGTGATTTATAAATGTCACGTGTCA 57.340 32.000 17.50 17.50 30.17 3.58
4412 4831 8.262715 TGTGATTTATAAATGTCACGTGTCAT 57.737 30.769 20.34 20.34 30.17 3.06
4413 4832 8.387354 TGTGATTTATAAATGTCACGTGTCATC 58.613 33.333 24.84 13.40 30.17 2.92
4414 4833 7.850982 GTGATTTATAAATGTCACGTGTCATCC 59.149 37.037 24.84 6.82 0.00 3.51
4415 4834 7.550906 TGATTTATAAATGTCACGTGTCATCCA 59.449 33.333 24.84 16.91 0.00 3.41
4416 4835 7.857734 TTTATAAATGTCACGTGTCATCCAT 57.142 32.000 24.84 21.23 0.00 3.41
4417 4836 5.991328 ATAAATGTCACGTGTCATCCATC 57.009 39.130 24.84 4.80 0.00 3.51
4418 4837 3.333029 AATGTCACGTGTCATCCATCA 57.667 42.857 24.84 9.40 0.00 3.07
4419 4838 2.368655 TGTCACGTGTCATCCATCAG 57.631 50.000 16.51 0.00 0.00 2.90
4420 4839 1.066929 TGTCACGTGTCATCCATCAGG 60.067 52.381 16.51 0.00 0.00 3.86
4434 4853 2.860009 CATCAGGATGGGTCTTGGATG 58.140 52.381 1.25 0.00 36.16 3.51
4435 4854 2.268796 TCAGGATGGGTCTTGGATGA 57.731 50.000 0.00 0.00 36.16 2.92
4436 4855 2.121948 TCAGGATGGGTCTTGGATGAG 58.878 52.381 0.00 0.00 36.16 2.90
4437 4856 2.121948 CAGGATGGGTCTTGGATGAGA 58.878 52.381 0.00 0.00 0.00 3.27
4438 4857 2.122768 AGGATGGGTCTTGGATGAGAC 58.877 52.381 0.00 0.00 44.20 3.36
4444 4863 2.682155 GTCTTGGATGAGACCTGGTC 57.318 55.000 19.20 19.20 40.10 4.02
4445 4864 2.183679 GTCTTGGATGAGACCTGGTCT 58.816 52.381 28.70 28.70 46.42 3.85
4446 4865 2.569404 GTCTTGGATGAGACCTGGTCTT 59.431 50.000 28.90 15.47 43.53 3.01
4447 4866 3.769844 GTCTTGGATGAGACCTGGTCTTA 59.230 47.826 28.90 25.26 43.53 2.10
4448 4867 4.407296 GTCTTGGATGAGACCTGGTCTTAT 59.593 45.833 28.21 28.21 43.53 1.73
4449 4868 5.598830 GTCTTGGATGAGACCTGGTCTTATA 59.401 44.000 27.99 18.98 43.53 0.98
4450 4869 5.835819 TCTTGGATGAGACCTGGTCTTATAG 59.164 44.000 27.99 22.25 43.53 1.31
4451 4870 5.403558 TGGATGAGACCTGGTCTTATAGA 57.596 43.478 27.99 17.29 43.53 1.98
4452 4871 5.777449 TGGATGAGACCTGGTCTTATAGAA 58.223 41.667 27.99 16.50 43.53 2.10
4453 4872 6.385443 TGGATGAGACCTGGTCTTATAGAAT 58.615 40.000 27.99 16.19 43.53 2.40
4454 4873 6.846505 TGGATGAGACCTGGTCTTATAGAATT 59.153 38.462 27.99 11.18 43.53 2.17
4455 4874 7.015682 TGGATGAGACCTGGTCTTATAGAATTC 59.984 40.741 27.99 17.79 43.53 2.17
4456 4875 7.234577 GGATGAGACCTGGTCTTATAGAATTCT 59.765 40.741 27.99 13.56 43.53 2.40
4457 4876 7.979786 TGAGACCTGGTCTTATAGAATTCTT 57.020 36.000 28.90 3.43 43.53 2.52
4458 4877 8.380742 TGAGACCTGGTCTTATAGAATTCTTT 57.619 34.615 28.90 8.54 43.53 2.52
4459 4878 8.826765 TGAGACCTGGTCTTATAGAATTCTTTT 58.173 33.333 28.90 4.60 43.53 2.27
4460 4879 9.320352 GAGACCTGGTCTTATAGAATTCTTTTC 57.680 37.037 28.90 8.14 43.53 2.29
4461 4880 8.268605 AGACCTGGTCTTATAGAATTCTTTTCC 58.731 37.037 23.49 8.65 40.28 3.13
4462 4881 7.048512 ACCTGGTCTTATAGAATTCTTTTCCG 58.951 38.462 14.36 0.00 0.00 4.30
4463 4882 6.017852 CCTGGTCTTATAGAATTCTTTTCCGC 60.018 42.308 14.36 1.14 0.00 5.54
4464 4883 5.522460 TGGTCTTATAGAATTCTTTTCCGCG 59.478 40.000 14.36 0.00 0.00 6.46
4465 4884 5.050295 GGTCTTATAGAATTCTTTTCCGCGG 60.050 44.000 22.12 22.12 0.00 6.46
4466 4885 4.510340 TCTTATAGAATTCTTTTCCGCGGC 59.490 41.667 23.51 2.24 0.00 6.53
4467 4886 1.375551 TAGAATTCTTTTCCGCGGCC 58.624 50.000 23.51 0.00 0.00 6.13
4468 4887 1.226295 GAATTCTTTTCCGCGGCCG 60.226 57.895 24.05 24.05 0.00 6.13
4469 4888 1.641123 GAATTCTTTTCCGCGGCCGA 61.641 55.000 33.48 4.65 36.29 5.54
4470 4889 1.238625 AATTCTTTTCCGCGGCCGAA 61.239 50.000 33.48 18.99 36.29 4.30
4471 4890 1.644786 ATTCTTTTCCGCGGCCGAAG 61.645 55.000 33.48 22.88 36.29 3.79
4472 4891 2.999739 TTCTTTTCCGCGGCCGAAGT 63.000 55.000 33.48 0.00 36.29 3.01
4485 4904 0.319405 CCGAAGTCTGTAAACGGGGT 59.681 55.000 0.00 0.00 39.92 4.95
4486 4905 1.545582 CCGAAGTCTGTAAACGGGGTA 59.454 52.381 0.00 0.00 39.92 3.69
4488 4907 2.989166 CGAAGTCTGTAAACGGGGTAAC 59.011 50.000 0.00 0.00 0.00 2.50
4489 4908 3.552684 CGAAGTCTGTAAACGGGGTAACA 60.553 47.826 0.00 0.00 39.74 2.41
4490 4909 4.379652 GAAGTCTGTAAACGGGGTAACAA 58.620 43.478 0.00 0.00 39.74 2.83
4491 4910 3.732212 AGTCTGTAAACGGGGTAACAAC 58.268 45.455 0.00 0.00 39.74 3.32
4500 4927 1.081094 GGGGTAACAACCGATGAACG 58.919 55.000 0.00 0.00 39.45 3.95
4501 4928 1.608801 GGGGTAACAACCGATGAACGT 60.609 52.381 0.00 0.00 38.39 3.99
4514 4941 2.492019 TGAACGTCATCGATGCTAGG 57.508 50.000 20.81 12.24 40.62 3.02
4516 4943 2.033424 TGAACGTCATCGATGCTAGGAG 59.967 50.000 20.81 9.67 40.62 3.69
4517 4944 0.312416 ACGTCATCGATGCTAGGAGC 59.688 55.000 20.81 0.00 40.15 4.70
4518 4945 0.727457 CGTCATCGATGCTAGGAGCG 60.727 60.000 20.81 16.29 41.19 5.03
4520 4947 1.735920 CATCGATGCTAGGAGCGGC 60.736 63.158 21.76 0.00 46.26 6.53
4521 4948 1.905843 ATCGATGCTAGGAGCGGCT 60.906 57.895 21.76 0.00 46.26 5.52
4522 4949 2.152297 ATCGATGCTAGGAGCGGCTG 62.152 60.000 21.76 0.00 46.26 4.85
4524 4951 2.765807 ATGCTAGGAGCGGCTGGT 60.766 61.111 7.50 0.00 46.26 4.00
4529 4956 3.622060 TAGGAGCGGCTGGTTTGGC 62.622 63.158 7.50 0.00 0.00 4.52
4558 4986 4.100084 CAGGGTGGCGATGCTGGA 62.100 66.667 0.00 0.00 0.00 3.86
4561 4989 2.045926 GGTGGCGATGCTGGAAGT 60.046 61.111 0.00 0.00 35.30 3.01
4574 5024 3.728373 GAAGTGGCCGGTGGGGAT 61.728 66.667 1.90 0.00 38.47 3.85
4584 5034 4.864334 GTGGGGATGCTGGGAGCG 62.864 72.222 0.00 0.00 46.26 5.03
4593 5043 4.899239 CTGGGAGCGGCCGACATC 62.899 72.222 33.48 22.40 37.63 3.06
4598 5048 4.592192 AGCGGCCGACATCGATGG 62.592 66.667 33.48 12.82 43.02 3.51
4610 5060 1.048724 ATCGATGGTGGGACCGACAT 61.049 55.000 9.04 1.53 42.58 3.06
4611 5061 1.220749 CGATGGTGGGACCGACATT 59.779 57.895 9.04 0.00 42.58 2.71
4616 5066 1.600107 GTGGGACCGACATTGCCTA 59.400 57.895 1.08 0.00 0.00 3.93
4634 5084 0.604073 TAATGCTGGAACCGACGACA 59.396 50.000 0.00 0.00 0.00 4.35
4635 5085 0.949105 AATGCTGGAACCGACGACAC 60.949 55.000 0.00 0.00 0.00 3.67
4686 5136 1.361668 CGCCTGATGTTGGAACCGAG 61.362 60.000 0.00 0.00 0.00 4.63
4693 5143 0.036164 TGTTGGAACCGAGGACATGG 59.964 55.000 0.00 0.00 0.00 3.66
4694 5144 0.323629 GTTGGAACCGAGGACATGGA 59.676 55.000 0.00 0.00 0.00 3.41
4705 5155 1.064240 AGGACATGGATTGCTGCATCA 60.064 47.619 1.84 3.17 29.89 3.07
4709 5159 2.021457 CATGGATTGCTGCATCAGACA 58.979 47.619 1.84 0.00 29.89 3.41
4751 5201 1.153765 CGCTGATTGCTGAGACCGA 60.154 57.895 0.00 0.00 40.11 4.69
4753 5203 0.390340 GCTGATTGCTGAGACCGACA 60.390 55.000 0.00 0.00 38.95 4.35
4767 5217 1.135373 ACCGACAACTCAGATGCTACG 60.135 52.381 0.00 0.00 0.00 3.51
4788 5238 1.526917 GATTGCTGGGACCGATGGG 60.527 63.158 0.00 0.00 40.11 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 1.532868 GTGGTTAGCAGCAGACACTTG 59.467 52.381 0.00 0.00 0.00 3.16
182 183 1.001406 AGACAGTGGTTAGCAGCAGAC 59.999 52.381 0.00 0.00 0.00 3.51
299 300 5.549742 TCAAAGAATGTTTGGATGCCTTT 57.450 34.783 3.00 0.00 0.00 3.11
307 308 7.471721 GGAAAAAGGTTTCAAAGAATGTTTGG 58.528 34.615 3.00 0.00 44.29 3.28
372 373 1.028905 CGGGACCTGAAAACAAGCAA 58.971 50.000 0.00 0.00 0.00 3.91
387 388 5.767277 AAAAGGAAATACTTAGTCCGGGA 57.233 39.130 0.00 0.00 36.49 5.14
414 415 2.554806 TACACATCCTTGCGTACTCG 57.445 50.000 0.00 0.00 40.37 4.18
415 416 4.308899 AGATACACATCCTTGCGTACTC 57.691 45.455 0.00 0.00 0.00 2.59
417 418 3.802685 GGAAGATACACATCCTTGCGTAC 59.197 47.826 0.00 0.00 34.02 3.67
522 527 1.944430 GCGTCGAACCAAGGAATCCTT 60.944 52.381 9.08 9.08 45.88 3.36
550 555 1.133790 GCAAACAGCATGAGATCCACC 59.866 52.381 0.00 0.00 44.79 4.61
602 607 0.994995 CTGACGAGGTTCATTCGCAG 59.005 55.000 0.00 0.70 41.57 5.18
687 692 2.299993 TCTCGCAGGCTAGTCAAATG 57.700 50.000 0.00 0.00 0.00 2.32
688 693 3.334583 TTTCTCGCAGGCTAGTCAAAT 57.665 42.857 0.00 0.00 0.00 2.32
689 694 2.831685 TTTCTCGCAGGCTAGTCAAA 57.168 45.000 0.00 0.00 0.00 2.69
691 696 2.103373 AGATTTCTCGCAGGCTAGTCA 58.897 47.619 0.00 0.00 0.00 3.41
692 697 2.880963 AGATTTCTCGCAGGCTAGTC 57.119 50.000 0.00 0.00 0.00 2.59
693 698 3.556999 TCTAGATTTCTCGCAGGCTAGT 58.443 45.455 0.00 0.00 0.00 2.57
694 699 4.576216 TTCTAGATTTCTCGCAGGCTAG 57.424 45.455 0.00 0.00 0.00 3.42
695 700 4.402793 ACTTTCTAGATTTCTCGCAGGCTA 59.597 41.667 0.00 0.00 0.00 3.93
696 701 3.196685 ACTTTCTAGATTTCTCGCAGGCT 59.803 43.478 0.00 0.00 0.00 4.58
697 702 3.308323 CACTTTCTAGATTTCTCGCAGGC 59.692 47.826 0.00 0.00 0.00 4.85
698 703 4.499183 ACACTTTCTAGATTTCTCGCAGG 58.501 43.478 0.00 0.00 0.00 4.85
779 784 0.035152 TAGGCAGAGGCAACACATGG 60.035 55.000 0.00 0.00 43.71 3.66
780 785 1.674441 CATAGGCAGAGGCAACACATG 59.326 52.381 0.00 0.00 43.71 3.21
781 786 2.020694 GCATAGGCAGAGGCAACACAT 61.021 52.381 0.00 0.00 43.71 3.21
782 787 0.677731 GCATAGGCAGAGGCAACACA 60.678 55.000 0.00 0.00 43.71 3.72
783 788 1.379642 GGCATAGGCAGAGGCAACAC 61.380 60.000 0.15 0.00 43.71 3.32
827 832 4.704540 CCATGGCCACTTCAACTATACAAA 59.295 41.667 8.16 0.00 0.00 2.83
898 903 0.462759 GCTATTCTTGCACGCTCCCT 60.463 55.000 0.00 0.00 0.00 4.20
951 956 1.137479 CGCCGTTAAATGACCTAGGGA 59.863 52.381 14.81 0.00 0.00 4.20
1007 1012 0.620121 CCTCTTCCTCCTGCTCCCTT 60.620 60.000 0.00 0.00 0.00 3.95
1010 1015 0.032615 TCTCCTCTTCCTCCTGCTCC 60.033 60.000 0.00 0.00 0.00 4.70
1011 1016 1.756538 CTTCTCCTCTTCCTCCTGCTC 59.243 57.143 0.00 0.00 0.00 4.26
1014 1019 1.007721 TCCCTTCTCCTCTTCCTCCTG 59.992 57.143 0.00 0.00 0.00 3.86
1019 1024 0.973496 AGCGTCCCTTCTCCTCTTCC 60.973 60.000 0.00 0.00 0.00 3.46
1022 1027 2.585876 GAAGCGTCCCTTCTCCTCT 58.414 57.895 0.00 0.00 45.27 3.69
1088 1104 5.047872 TCACTTGGATGGATGTCAAATGTTG 60.048 40.000 0.00 0.00 0.00 3.33
1097 1113 2.103771 CTCCGATCACTTGGATGGATGT 59.896 50.000 0.00 0.00 36.00 3.06
1381 1401 8.081025 GCTTTATGGGAGAAATCATCAAGAATC 58.919 37.037 0.00 0.00 30.41 2.52
1388 1408 6.072783 GCACTAGCTTTATGGGAGAAATCATC 60.073 42.308 0.00 0.00 37.91 2.92
1561 1617 2.629617 TGCTTGATGAGTGAGTGAGTGA 59.370 45.455 0.00 0.00 0.00 3.41
1562 1618 2.735663 GTGCTTGATGAGTGAGTGAGTG 59.264 50.000 0.00 0.00 0.00 3.51
1563 1619 2.608998 CGTGCTTGATGAGTGAGTGAGT 60.609 50.000 0.00 0.00 0.00 3.41
1590 1648 3.070159 CCTATATATGCATGCTACGCCCT 59.930 47.826 20.33 0.34 0.00 5.19
1591 1649 3.069586 TCCTATATATGCATGCTACGCCC 59.930 47.826 20.33 0.00 0.00 6.13
1592 1650 4.202161 ACTCCTATATATGCATGCTACGCC 60.202 45.833 20.33 0.00 0.00 5.68
1709 2027 1.372087 GCTCTGGATCTTGTTGGCGG 61.372 60.000 0.00 0.00 0.00 6.13
1710 2028 0.674581 TGCTCTGGATCTTGTTGGCG 60.675 55.000 0.00 0.00 0.00 5.69
2060 2378 2.685380 CCGACAGAAGGAGGGGCT 60.685 66.667 0.00 0.00 0.00 5.19
2061 2379 3.787001 CCCGACAGAAGGAGGGGC 61.787 72.222 0.00 0.00 40.18 5.80
2062 2380 1.612442 TTCCCGACAGAAGGAGGGG 60.612 63.158 0.00 0.00 43.92 4.79
2078 2396 1.078759 CGTGGTGCTGTCGATCCTTC 61.079 60.000 0.00 0.00 0.00 3.46
2294 2651 4.202050 CCAACTAAGCTAAACCCATGCATC 60.202 45.833 0.00 0.00 0.00 3.91
2302 2663 4.151157 CACACGTACCAACTAAGCTAAACC 59.849 45.833 0.00 0.00 0.00 3.27
2304 2665 3.742369 GCACACGTACCAACTAAGCTAAA 59.258 43.478 0.00 0.00 0.00 1.85
2349 2715 1.964608 CTTGAGCCGCCTCATCTCCA 61.965 60.000 0.00 0.00 46.84 3.86
3616 4030 2.360726 TCAGCCGTCGGTGAGCTA 60.361 61.111 13.94 0.00 41.50 3.32
3674 4088 0.037590 ACAACCCTGTGTGTGTGTGT 59.962 50.000 0.00 0.00 33.30 3.72
4269 4688 1.546961 CTAACCGTGAGACCTGGTCT 58.453 55.000 28.70 28.70 46.42 3.85
4270 4689 0.108756 GCTAACCGTGAGACCTGGTC 60.109 60.000 19.20 19.20 34.11 4.02
4271 4690 0.830444 TGCTAACCGTGAGACCTGGT 60.830 55.000 0.00 0.00 37.68 4.00
4272 4691 0.108615 CTGCTAACCGTGAGACCTGG 60.109 60.000 0.00 0.00 0.00 4.45
4273 4692 0.888619 TCTGCTAACCGTGAGACCTG 59.111 55.000 0.00 0.00 0.00 4.00
4274 4693 1.478510 CATCTGCTAACCGTGAGACCT 59.521 52.381 0.00 0.00 0.00 3.85
4275 4694 1.476891 TCATCTGCTAACCGTGAGACC 59.523 52.381 0.00 0.00 0.00 3.85
4276 4695 2.423892 TCTCATCTGCTAACCGTGAGAC 59.576 50.000 0.00 0.00 40.06 3.36
4277 4696 2.423892 GTCTCATCTGCTAACCGTGAGA 59.576 50.000 0.00 0.00 41.99 3.27
4278 4697 2.480416 GGTCTCATCTGCTAACCGTGAG 60.480 54.545 0.00 0.00 38.07 3.51
4279 4698 1.476891 GGTCTCATCTGCTAACCGTGA 59.523 52.381 0.00 0.00 0.00 4.35
4280 4699 1.471676 GGGTCTCATCTGCTAACCGTG 60.472 57.143 0.00 0.00 0.00 4.94
4281 4700 0.824759 GGGTCTCATCTGCTAACCGT 59.175 55.000 0.00 0.00 0.00 4.83
4282 4701 0.824109 TGGGTCTCATCTGCTAACCG 59.176 55.000 0.00 0.00 0.00 4.44
4283 4702 3.135530 AGAATGGGTCTCATCTGCTAACC 59.864 47.826 0.00 0.00 34.44 2.85
4284 4703 4.414337 AGAATGGGTCTCATCTGCTAAC 57.586 45.455 0.00 0.00 34.44 2.34
4295 4714 3.117745 TGTCATCCATGAGAATGGGTCT 58.882 45.455 4.96 0.00 41.95 3.85
4296 4715 3.209410 GTGTCATCCATGAGAATGGGTC 58.791 50.000 4.96 0.00 41.95 4.46
4297 4716 2.420547 CGTGTCATCCATGAGAATGGGT 60.421 50.000 4.96 0.00 41.95 4.51
4298 4717 2.216046 CGTGTCATCCATGAGAATGGG 58.784 52.381 4.96 0.00 41.95 4.00
4299 4718 2.610833 CACGTGTCATCCATGAGAATGG 59.389 50.000 7.58 0.00 43.01 3.16
4300 4719 2.031314 GCACGTGTCATCCATGAGAATG 59.969 50.000 18.38 0.00 37.51 2.67
4301 4720 2.283298 GCACGTGTCATCCATGAGAAT 58.717 47.619 18.38 0.00 37.51 2.40
4302 4721 1.001860 TGCACGTGTCATCCATGAGAA 59.998 47.619 18.38 0.00 37.51 2.87
4303 4722 0.607620 TGCACGTGTCATCCATGAGA 59.392 50.000 18.38 0.00 37.51 3.27
4304 4723 1.660167 ATGCACGTGTCATCCATGAG 58.340 50.000 18.38 0.00 37.51 2.90
4305 4724 2.009051 GAATGCACGTGTCATCCATGA 58.991 47.619 18.38 0.00 34.01 3.07
4306 4725 1.738908 TGAATGCACGTGTCATCCATG 59.261 47.619 18.38 0.00 36.08 3.66
4307 4726 2.112380 TGAATGCACGTGTCATCCAT 57.888 45.000 18.38 8.58 0.00 3.41
4308 4727 2.112380 ATGAATGCACGTGTCATCCA 57.888 45.000 18.38 14.95 0.00 3.41
4309 4728 4.614555 TTTATGAATGCACGTGTCATCC 57.385 40.909 19.78 11.60 34.01 3.51
4310 4729 5.207768 GGATTTATGAATGCACGTGTCATC 58.792 41.667 19.78 14.23 34.13 2.92
4311 4730 4.036734 GGGATTTATGAATGCACGTGTCAT 59.963 41.667 19.99 19.99 35.50 3.06
4312 4731 3.376859 GGGATTTATGAATGCACGTGTCA 59.623 43.478 18.38 15.67 35.50 3.58
4313 4732 3.376859 TGGGATTTATGAATGCACGTGTC 59.623 43.478 18.38 10.14 35.50 3.67
4314 4733 3.351740 TGGGATTTATGAATGCACGTGT 58.648 40.909 18.38 0.00 35.50 4.49
4315 4734 4.368874 TTGGGATTTATGAATGCACGTG 57.631 40.909 12.28 12.28 35.50 4.49
4316 4735 4.677779 GCTTTGGGATTTATGAATGCACGT 60.678 41.667 4.16 0.00 35.50 4.49
4317 4736 3.798337 GCTTTGGGATTTATGAATGCACG 59.202 43.478 4.16 0.00 35.50 5.34
4318 4737 4.757594 TGCTTTGGGATTTATGAATGCAC 58.242 39.130 4.16 0.00 35.50 4.57
4319 4738 5.364446 AGATGCTTTGGGATTTATGAATGCA 59.636 36.000 4.16 0.00 35.50 3.96
4320 4739 5.850614 AGATGCTTTGGGATTTATGAATGC 58.149 37.500 0.00 0.00 33.28 3.56
4321 4740 9.635520 GATTAGATGCTTTGGGATTTATGAATG 57.364 33.333 0.00 0.00 0.00 2.67
4322 4741 8.810041 GGATTAGATGCTTTGGGATTTATGAAT 58.190 33.333 0.00 0.00 0.00 2.57
4323 4742 7.233348 GGGATTAGATGCTTTGGGATTTATGAA 59.767 37.037 0.00 0.00 0.00 2.57
4324 4743 6.721208 GGGATTAGATGCTTTGGGATTTATGA 59.279 38.462 0.00 0.00 0.00 2.15
4325 4744 6.071165 GGGGATTAGATGCTTTGGGATTTATG 60.071 42.308 0.00 0.00 0.00 1.90
4326 4745 6.019108 GGGGATTAGATGCTTTGGGATTTAT 58.981 40.000 0.00 0.00 0.00 1.40
4327 4746 5.393866 GGGGATTAGATGCTTTGGGATTTA 58.606 41.667 0.00 0.00 0.00 1.40
4328 4747 4.226384 GGGGATTAGATGCTTTGGGATTT 58.774 43.478 0.00 0.00 0.00 2.17
4329 4748 3.438520 GGGGGATTAGATGCTTTGGGATT 60.439 47.826 0.00 0.00 0.00 3.01
4330 4749 2.110721 GGGGGATTAGATGCTTTGGGAT 59.889 50.000 0.00 0.00 0.00 3.85
4331 4750 1.499007 GGGGGATTAGATGCTTTGGGA 59.501 52.381 0.00 0.00 0.00 4.37
4332 4751 2.001076 GGGGGATTAGATGCTTTGGG 57.999 55.000 0.00 0.00 0.00 4.12
4355 4774 1.341976 CCACCCCCACTTGAAATAGGG 60.342 57.143 0.00 0.00 41.12 3.53
4356 4775 1.638589 TCCACCCCCACTTGAAATAGG 59.361 52.381 0.00 0.00 0.00 2.57
4357 4776 3.449746 TTCCACCCCCACTTGAAATAG 57.550 47.619 0.00 0.00 0.00 1.73
4358 4777 4.791334 TCTATTCCACCCCCACTTGAAATA 59.209 41.667 0.00 0.00 0.00 1.40
4359 4778 3.596046 TCTATTCCACCCCCACTTGAAAT 59.404 43.478 0.00 0.00 0.00 2.17
4360 4779 2.990284 TCTATTCCACCCCCACTTGAAA 59.010 45.455 0.00 0.00 0.00 2.69
4361 4780 2.638325 TCTATTCCACCCCCACTTGAA 58.362 47.619 0.00 0.00 0.00 2.69
4362 4781 2.352561 TCTATTCCACCCCCACTTGA 57.647 50.000 0.00 0.00 0.00 3.02
4363 4782 2.936202 CATCTATTCCACCCCCACTTG 58.064 52.381 0.00 0.00 0.00 3.16
4364 4783 1.215423 GCATCTATTCCACCCCCACTT 59.785 52.381 0.00 0.00 0.00 3.16
4365 4784 0.846693 GCATCTATTCCACCCCCACT 59.153 55.000 0.00 0.00 0.00 4.00
4366 4785 0.846693 AGCATCTATTCCACCCCCAC 59.153 55.000 0.00 0.00 0.00 4.61
4367 4786 1.607225 AAGCATCTATTCCACCCCCA 58.393 50.000 0.00 0.00 0.00 4.96
4368 4787 2.310538 CAAAGCATCTATTCCACCCCC 58.689 52.381 0.00 0.00 0.00 5.40
4369 4788 2.689983 CACAAAGCATCTATTCCACCCC 59.310 50.000 0.00 0.00 0.00 4.95
4370 4789 3.620488 TCACAAAGCATCTATTCCACCC 58.380 45.455 0.00 0.00 0.00 4.61
4371 4790 5.841957 AATCACAAAGCATCTATTCCACC 57.158 39.130 0.00 0.00 0.00 4.61
4379 4798 9.793252 GTGACATTTATAAATCACAAAGCATCT 57.207 29.630 19.94 0.00 0.00 2.90
4380 4799 8.736742 CGTGACATTTATAAATCACAAAGCATC 58.263 33.333 22.59 8.62 0.00 3.91
4381 4800 8.243426 ACGTGACATTTATAAATCACAAAGCAT 58.757 29.630 22.59 6.47 0.00 3.79
4382 4801 7.536964 CACGTGACATTTATAAATCACAAAGCA 59.463 33.333 22.59 7.76 0.00 3.91
4383 4802 7.537306 ACACGTGACATTTATAAATCACAAAGC 59.463 33.333 25.01 9.56 0.00 3.51
4384 4803 8.948853 ACACGTGACATTTATAAATCACAAAG 57.051 30.769 25.01 16.28 0.00 2.77
4385 4804 8.560374 TGACACGTGACATTTATAAATCACAAA 58.440 29.630 25.01 7.99 0.00 2.83
4386 4805 8.089115 TGACACGTGACATTTATAAATCACAA 57.911 30.769 25.01 7.76 0.00 3.33
4387 4806 7.659652 TGACACGTGACATTTATAAATCACA 57.340 32.000 25.01 16.05 0.00 3.58
4388 4807 7.850982 GGATGACACGTGACATTTATAAATCAC 59.149 37.037 29.08 16.81 31.08 3.06
4389 4808 7.550906 TGGATGACACGTGACATTTATAAATCA 59.449 33.333 29.08 15.41 31.08 2.57
4390 4809 7.915508 TGGATGACACGTGACATTTATAAATC 58.084 34.615 29.08 17.06 31.08 2.17
4391 4810 7.857734 TGGATGACACGTGACATTTATAAAT 57.142 32.000 29.08 10.11 31.08 1.40
4392 4811 7.550906 TGATGGATGACACGTGACATTTATAAA 59.449 33.333 29.08 16.64 31.08 1.40
4393 4812 7.044798 TGATGGATGACACGTGACATTTATAA 58.955 34.615 29.08 18.31 31.08 0.98
4394 4813 6.578023 TGATGGATGACACGTGACATTTATA 58.422 36.000 29.08 17.83 31.08 0.98
4395 4814 5.427378 TGATGGATGACACGTGACATTTAT 58.573 37.500 29.08 24.62 31.08 1.40
4396 4815 4.826556 TGATGGATGACACGTGACATTTA 58.173 39.130 29.08 21.84 31.08 1.40
4397 4816 3.673902 TGATGGATGACACGTGACATTT 58.326 40.909 29.08 18.96 31.08 2.32
4398 4817 3.264947 CTGATGGATGACACGTGACATT 58.735 45.455 29.08 16.96 31.08 2.71
4399 4818 2.419159 CCTGATGGATGACACGTGACAT 60.419 50.000 28.93 28.93 34.57 3.06
4400 4819 1.066929 CCTGATGGATGACACGTGACA 60.067 52.381 25.01 23.44 34.57 3.58
4401 4820 1.204704 TCCTGATGGATGACACGTGAC 59.795 52.381 25.01 17.68 37.46 3.67
4402 4821 1.555967 TCCTGATGGATGACACGTGA 58.444 50.000 25.01 0.00 37.46 4.35
4414 4833 2.440627 TCATCCAAGACCCATCCTGATG 59.559 50.000 0.00 0.00 38.51 3.07
4415 4834 2.709934 CTCATCCAAGACCCATCCTGAT 59.290 50.000 0.00 0.00 0.00 2.90
4416 4835 2.121948 CTCATCCAAGACCCATCCTGA 58.878 52.381 0.00 0.00 0.00 3.86
4417 4836 2.121948 TCTCATCCAAGACCCATCCTG 58.878 52.381 0.00 0.00 0.00 3.86
4418 4837 2.122768 GTCTCATCCAAGACCCATCCT 58.877 52.381 0.00 0.00 39.85 3.24
4419 4838 2.629336 GTCTCATCCAAGACCCATCC 57.371 55.000 0.00 0.00 39.85 3.51
4425 4844 2.183679 AGACCAGGTCTCATCCAAGAC 58.816 52.381 17.31 0.00 38.71 3.01
4426 4845 2.630889 AGACCAGGTCTCATCCAAGA 57.369 50.000 17.31 0.00 38.71 3.02
4427 4846 5.835819 TCTATAAGACCAGGTCTCATCCAAG 59.164 44.000 23.17 8.51 42.59 3.61
4428 4847 5.777449 TCTATAAGACCAGGTCTCATCCAA 58.223 41.667 23.17 4.64 42.59 3.53
4429 4848 5.403558 TCTATAAGACCAGGTCTCATCCA 57.596 43.478 23.17 6.44 42.59 3.41
4430 4849 6.926630 ATTCTATAAGACCAGGTCTCATCC 57.073 41.667 23.17 0.00 42.59 3.51
4431 4850 8.189119 AGAATTCTATAAGACCAGGTCTCATC 57.811 38.462 23.17 11.43 42.59 2.92
4432 4851 8.560124 AAGAATTCTATAAGACCAGGTCTCAT 57.440 34.615 23.17 16.61 42.59 2.90
4433 4852 7.979786 AAGAATTCTATAAGACCAGGTCTCA 57.020 36.000 23.17 9.12 42.59 3.27
4434 4853 9.320352 GAAAAGAATTCTATAAGACCAGGTCTC 57.680 37.037 23.17 7.06 42.59 3.36
4435 4854 8.268605 GGAAAAGAATTCTATAAGACCAGGTCT 58.731 37.037 17.31 17.31 45.64 3.85
4436 4855 7.224949 CGGAAAAGAATTCTATAAGACCAGGTC 59.775 40.741 12.25 12.25 0.00 3.85
4437 4856 7.048512 CGGAAAAGAATTCTATAAGACCAGGT 58.951 38.462 8.75 0.00 0.00 4.00
4438 4857 6.017852 GCGGAAAAGAATTCTATAAGACCAGG 60.018 42.308 8.75 0.00 0.00 4.45
4439 4858 6.292381 CGCGGAAAAGAATTCTATAAGACCAG 60.292 42.308 8.75 5.39 0.00 4.00
4440 4859 5.522460 CGCGGAAAAGAATTCTATAAGACCA 59.478 40.000 8.75 0.00 0.00 4.02
4441 4860 5.050295 CCGCGGAAAAGAATTCTATAAGACC 60.050 44.000 24.07 6.24 0.00 3.85
4442 4861 5.558463 GCCGCGGAAAAGAATTCTATAAGAC 60.558 44.000 33.48 0.00 0.00 3.01
4443 4862 4.510340 GCCGCGGAAAAGAATTCTATAAGA 59.490 41.667 33.48 0.00 0.00 2.10
4444 4863 4.319549 GGCCGCGGAAAAGAATTCTATAAG 60.320 45.833 33.48 1.27 0.00 1.73
4445 4864 3.562557 GGCCGCGGAAAAGAATTCTATAA 59.437 43.478 33.48 0.00 0.00 0.98
4446 4865 3.135994 GGCCGCGGAAAAGAATTCTATA 58.864 45.455 33.48 0.00 0.00 1.31
4447 4866 1.947456 GGCCGCGGAAAAGAATTCTAT 59.053 47.619 33.48 0.41 0.00 1.98
4448 4867 1.375551 GGCCGCGGAAAAGAATTCTA 58.624 50.000 33.48 0.00 0.00 2.10
4449 4868 1.644786 CGGCCGCGGAAAAGAATTCT 61.645 55.000 33.48 0.88 0.00 2.40
4450 4869 1.226295 CGGCCGCGGAAAAGAATTC 60.226 57.895 33.48 7.28 0.00 2.17
4451 4870 1.238625 TTCGGCCGCGGAAAAGAATT 61.239 50.000 33.48 0.00 0.00 2.17
4452 4871 1.644786 CTTCGGCCGCGGAAAAGAAT 61.645 55.000 33.48 0.00 0.00 2.40
4453 4872 2.280933 TTCGGCCGCGGAAAAGAA 60.281 55.556 33.48 23.17 0.00 2.52
4454 4873 2.740826 CTTCGGCCGCGGAAAAGA 60.741 61.111 33.48 18.51 0.00 2.52
4455 4874 3.023591 GACTTCGGCCGCGGAAAAG 62.024 63.158 33.48 27.63 0.00 2.27
4456 4875 3.045492 GACTTCGGCCGCGGAAAA 61.045 61.111 33.48 17.87 0.00 2.29
4457 4876 3.998672 AGACTTCGGCCGCGGAAA 61.999 61.111 33.48 18.26 0.00 3.13
4458 4877 4.735132 CAGACTTCGGCCGCGGAA 62.735 66.667 33.48 14.15 0.00 4.30
4460 4879 3.636313 TTACAGACTTCGGCCGCGG 62.636 63.158 24.05 24.05 0.00 6.46
4461 4880 1.735198 TTTACAGACTTCGGCCGCG 60.735 57.895 23.51 16.74 0.00 6.46
4462 4881 1.785951 GTTTACAGACTTCGGCCGC 59.214 57.895 23.51 6.27 0.00 6.53
4463 4882 1.349259 CCGTTTACAGACTTCGGCCG 61.349 60.000 22.12 22.12 35.01 6.13
4464 4883 1.017701 CCCGTTTACAGACTTCGGCC 61.018 60.000 0.00 0.00 39.87 6.13
4465 4884 1.017701 CCCCGTTTACAGACTTCGGC 61.018 60.000 0.00 0.00 39.87 5.54
4466 4885 0.319405 ACCCCGTTTACAGACTTCGG 59.681 55.000 0.00 0.00 40.72 4.30
4467 4886 2.989166 GTTACCCCGTTTACAGACTTCG 59.011 50.000 0.00 0.00 0.00 3.79
4468 4887 3.993920 TGTTACCCCGTTTACAGACTTC 58.006 45.455 0.00 0.00 0.00 3.01
4469 4888 4.129380 GTTGTTACCCCGTTTACAGACTT 58.871 43.478 0.00 0.00 0.00 3.01
4470 4889 3.494924 GGTTGTTACCCCGTTTACAGACT 60.495 47.826 0.00 0.00 38.60 3.24
4471 4890 2.807967 GGTTGTTACCCCGTTTACAGAC 59.192 50.000 0.00 0.00 38.60 3.51
4472 4891 2.547642 CGGTTGTTACCCCGTTTACAGA 60.548 50.000 2.93 0.00 41.75 3.41
4495 4922 2.021457 TCCTAGCATCGATGACGTTCA 58.979 47.619 29.20 4.52 40.69 3.18
4500 4927 0.387878 CCGCTCCTAGCATCGATGAC 60.388 60.000 29.20 18.88 42.58 3.06
4501 4928 1.959848 CCGCTCCTAGCATCGATGA 59.040 57.895 29.20 8.14 42.58 2.92
4520 4947 1.579429 GTTGTAGCGGCCAAACCAG 59.421 57.895 2.24 0.00 39.03 4.00
4521 4948 1.899534 GGTTGTAGCGGCCAAACCA 60.900 57.895 18.75 0.00 39.03 3.67
4522 4949 1.899534 TGGTTGTAGCGGCCAAACC 60.900 57.895 17.49 17.49 0.00 3.27
4524 4951 1.152943 TGTGGTTGTAGCGGCCAAA 60.153 52.632 2.24 0.00 33.66 3.28
4529 4956 1.671054 CACCCTGTGGTTGTAGCGG 60.671 63.158 0.00 0.00 44.75 5.52
4558 4986 4.047125 CATCCCCACCGGCCACTT 62.047 66.667 0.00 0.00 0.00 3.16
4576 5026 4.899239 GATGTCGGCCGCTCCCAG 62.899 72.222 23.51 0.00 0.00 4.45
4584 5034 2.588877 CCACCATCGATGTCGGCC 60.589 66.667 23.27 0.00 40.29 6.13
4593 5043 1.089481 CAATGTCGGTCCCACCATCG 61.089 60.000 0.00 0.00 38.47 3.84
4598 5048 0.035820 TTAGGCAATGTCGGTCCCAC 60.036 55.000 0.00 0.00 0.00 4.61
4616 5066 0.949105 GTGTCGTCGGTTCCAGCATT 60.949 55.000 0.00 0.00 0.00 3.56
4634 5084 1.672356 CTAGCTTGCAGCAACCCGT 60.672 57.895 2.83 0.00 45.56 5.28
4635 5085 2.401766 CCTAGCTTGCAGCAACCCG 61.402 63.158 2.83 0.00 45.56 5.28
4657 5107 0.036732 ACATCAGGCGTTGTCATGGT 59.963 50.000 0.00 0.00 0.00 3.55
4666 5116 1.671054 CGGTTCCAACATCAGGCGT 60.671 57.895 0.00 0.00 0.00 5.68
4686 5136 1.337071 CTGATGCAGCAATCCATGTCC 59.663 52.381 5.96 0.00 0.00 4.02
4693 5143 2.089980 ACCTTGTCTGATGCAGCAATC 58.910 47.619 5.96 2.44 31.36 2.67
4694 5144 2.089980 GACCTTGTCTGATGCAGCAAT 58.910 47.619 5.96 0.00 31.36 3.56
4705 5155 2.887152 GTTCCAGCAATTGACCTTGTCT 59.113 45.455 10.34 0.00 33.15 3.41
4709 5159 1.247567 CGGTTCCAGCAATTGACCTT 58.752 50.000 10.34 0.00 0.00 3.50
4751 5201 2.447443 TCCTCGTAGCATCTGAGTTGT 58.553 47.619 0.00 0.00 0.00 3.32
4753 5203 3.739519 GCAATCCTCGTAGCATCTGAGTT 60.740 47.826 0.00 0.00 0.00 3.01
4767 5217 0.533755 CATCGGTCCCAGCAATCCTC 60.534 60.000 0.00 0.00 0.00 3.71
4815 5265 2.031163 ACACCTTGCCGTCTCAGC 59.969 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.