Multiple sequence alignment - TraesCS4D01G172000

Loading Multiple Alignment...

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 TraesCS4D01G172000 chr4D 100.000 5468 0 0 1 5468 299175099 299169632 0.000000e+00 10098.0
1 TraesCS4D01G172000 chr4D 95.951 568 23 0 4901 5468 220802910 220802343 0.000000e+00 922.0
2 TraesCS4D01G172000 chr4D 82.903 310 51 2 21 329 313930781 313930473 1.500000e-70 278.0
3 TraesCS4D01G172000 chr4D 80.737 353 61 7 16 365 85886120 85886468 9.030000e-68 268.0
4 TraesCS4D01G172000 chr4A 94.053 4725 197 35 16 4703 185986091 185990768 0.000000e+00 7092.0
5 TraesCS4D01G172000 chr4A 90.444 450 26 4 5019 5468 630043737 630044169 1.320000e-160 577.0
6 TraesCS4D01G172000 chr4B 93.944 4739 164 58 19 4703 371382984 371378315 0.000000e+00 7047.0
7 TraesCS4D01G172000 chr4B 91.723 447 36 1 5022 5468 645071914 645071469 2.160000e-173 619.0
8 TraesCS4D01G172000 chr7D 90.444 450 36 1 5019 5468 634364626 634365068 2.190000e-163 586.0
9 TraesCS4D01G172000 chr2A 90.000 450 29 3 5019 5468 655290860 655291293 7.950000e-158 568.0
10 TraesCS4D01G172000 chr6B 88.814 447 33 6 5022 5468 485762379 485761950 2.900000e-147 532.0
11 TraesCS4D01G172000 chr6B 82.803 314 49 5 16 327 195527082 195527392 5.400000e-70 276.0
12 TraesCS4D01G172000 chr3D 92.837 363 26 0 5019 5381 160625749 160626111 1.350000e-145 527.0
13 TraesCS4D01G172000 chr3D 92.308 65 4 1 4755 4819 208844997 208844934 2.100000e-14 91.6
14 TraesCS4D01G172000 chr3B 87.213 305 37 2 4703 5006 77224374 77224677 4.050000e-91 346.0
15 TraesCS4D01G172000 chr6D 84.591 318 45 4 19 334 303029019 303028704 4.110000e-81 313.0
16 TraesCS4D01G172000 chr7B 84.053 301 43 5 36 334 379207554 379207851 8.960000e-73 285.0
17 TraesCS4D01G172000 chr7A 84.000 300 43 5 37 334 553237550 553237254 3.220000e-72 283.0
18 TraesCS4D01G172000 chr1A 83.121 314 47 6 19 330 461738232 461737923 1.160000e-71 281.0
19 TraesCS4D01G172000 chr1D 83.121 314 46 6 16 327 139138287 139138595 4.170000e-71 279.0
20 TraesCS4D01G172000 chr3A 82.278 316 51 4 21 334 144170910 144171222 9.030000e-68 268.0
21 TraesCS4D01G172000 chr1B 80.743 296 52 2 5147 5442 7479221 7479511 5.510000e-55 226.0
22 TraesCS4D01G172000 chr2B 89.726 146 15 0 4698 4843 575829064 575829209 2.600000e-43 187.0


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 TraesCS4D01G172000 chr4D 299169632 299175099 5467 True 10098 10098 100.000 1 5468 1 chr4D.!!$R2 5467
1 TraesCS4D01G172000 chr4D 220802343 220802910 567 True 922 922 95.951 4901 5468 1 chr4D.!!$R1 567
2 TraesCS4D01G172000 chr4A 185986091 185990768 4677 False 7092 7092 94.053 16 4703 1 chr4A.!!$F1 4687
3 TraesCS4D01G172000 chr4B 371378315 371382984 4669 True 7047 7047 93.944 19 4703 1 chr4B.!!$R1 4684

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
303 305 0.678366 AATCCGGCCGTGTTTGCATA 60.678 50.000 26.12 0.0 0.00 3.14 F
1126 1183 1.133637 TCTCCTAGCTCATCCGCTTCT 60.134 52.381 0.00 0.0 41.30 2.85 F
1852 1910 0.251386 TGCGAACTCTGGACCTCTCT 60.251 55.000 0.00 0.0 0.00 3.10 F
2859 2925 1.134907 GGAGCCATTCCAGCAACAATG 60.135 52.381 0.00 0.0 46.01 2.82 F
3321 3396 2.047844 GCTGCGCTGGAACTCTCA 60.048 61.111 16.47 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1239 0.600057 GCAAGAAGTGAGGGCCTTTG 59.400 55.0 7.89 8.38 0.00 2.77 R
3123 3189 0.175760 TCTGTGCTAGCGGATTGGAC 59.824 55.0 10.77 0.91 0.00 4.02 R
3608 3683 0.978667 TGGCGTCCAGTAATAGCCCA 60.979 55.0 2.14 0.00 46.67 5.36 R
3852 3927 0.744414 GCAGTAGCTTCGCCAATCCA 60.744 55.0 0.00 0.00 37.91 3.41 R
5181 5261 0.613260 TACAAGCGCTTGGGTCTCAT 59.387 50.0 43.26 27.77 44.45 2.90 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
17 18 2.750350 CTCCACGGAAGCACCCTT 59.250 61.111 0.00 0.00 34.64 3.95
29 30 4.162690 ACCCTTCGATGAGCGGCC 62.163 66.667 0.00 0.00 41.33 6.13
35 36 2.203056 CGATGAGCGGCCCAATCA 60.203 61.111 0.00 0.00 36.03 2.57
49 50 3.745797 GCCCAATCAGACATAGGGAAGAC 60.746 52.174 0.00 0.00 42.25 3.01
53 54 3.081710 TCAGACATAGGGAAGACACGA 57.918 47.619 0.00 0.00 0.00 4.35
77 78 1.807814 AGAATATGCCTCCGGGACTT 58.192 50.000 0.00 0.00 33.58 3.01
112 113 3.785859 GGGCTGGCGGACATGAGA 61.786 66.667 0.00 0.00 0.00 3.27
121 122 2.552315 GGCGGACATGAGAAAGACAAAA 59.448 45.455 0.00 0.00 0.00 2.44
122 123 3.004315 GGCGGACATGAGAAAGACAAAAA 59.996 43.478 0.00 0.00 0.00 1.94
124 125 4.787598 CGGACATGAGAAAGACAAAAAGG 58.212 43.478 0.00 0.00 0.00 3.11
125 126 4.515191 CGGACATGAGAAAGACAAAAAGGA 59.485 41.667 0.00 0.00 0.00 3.36
126 127 5.182001 CGGACATGAGAAAGACAAAAAGGAT 59.818 40.000 0.00 0.00 0.00 3.24
128 129 6.432472 GGACATGAGAAAGACAAAAAGGATCT 59.568 38.462 0.00 0.00 0.00 2.75
129 130 7.211966 ACATGAGAAAGACAAAAAGGATCTG 57.788 36.000 0.00 0.00 0.00 2.90
131 132 6.867662 TGAGAAAGACAAAAAGGATCTGTC 57.132 37.500 4.32 4.32 39.83 3.51
137 138 1.305930 AAAAAGGATCTGTCGCGGCC 61.306 55.000 8.89 0.00 0.00 6.13
138 139 2.463589 AAAAGGATCTGTCGCGGCCA 62.464 55.000 8.89 3.40 0.00 5.36
170 171 3.599343 AGTGTAGTGTATCCGTGTCGTA 58.401 45.455 0.00 0.00 0.00 3.43
171 172 4.002982 AGTGTAGTGTATCCGTGTCGTAA 58.997 43.478 0.00 0.00 0.00 3.18
191 192 2.014093 GAATGAAGCTCCGCACGACG 62.014 60.000 0.00 0.00 43.15 5.12
192 193 2.765250 AATGAAGCTCCGCACGACGT 62.765 55.000 0.00 0.00 41.42 4.34
193 194 1.929806 ATGAAGCTCCGCACGACGTA 61.930 55.000 0.00 0.00 41.42 3.57
194 195 2.126580 AAGCTCCGCACGACGTAC 60.127 61.111 0.00 0.00 41.42 3.67
259 261 1.369568 CCGTTTTTGTCCGGTTCGC 60.370 57.895 0.00 0.00 39.38 4.70
267 269 1.529226 TGTCCGGTTCGCATGAAATT 58.471 45.000 0.00 0.00 35.46 1.82
303 305 0.678366 AATCCGGCCGTGTTTGCATA 60.678 50.000 26.12 0.00 0.00 3.14
315 317 5.570973 CCGTGTTTGCATAAATTTCATTCGA 59.429 36.000 0.00 0.00 0.00 3.71
318 320 7.627949 CGTGTTTGCATAAATTTCATTCGATTG 59.372 33.333 0.00 0.78 0.00 2.67
322 324 7.522901 TGCATAAATTTCATTCGATTGGTTG 57.477 32.000 7.42 0.00 0.00 3.77
330 332 8.885494 ATTTCATTCGATTGGTTGAAAAAGAA 57.115 26.923 7.42 0.00 40.36 2.52
334 336 9.973450 TCATTCGATTGGTTGAAAAAGAATTTA 57.027 25.926 7.42 0.00 37.28 1.40
342 354 6.266558 TGGTTGAAAAAGAATTTAGGCTAGCA 59.733 34.615 18.24 0.00 37.28 3.49
371 384 1.760086 CCTCCTGCATCCGTCTCCT 60.760 63.158 0.00 0.00 0.00 3.69
373 386 1.403814 CTCCTGCATCCGTCTCCTTA 58.596 55.000 0.00 0.00 0.00 2.69
379 392 2.103094 TGCATCCGTCTCCTTAGATTGG 59.897 50.000 0.00 0.00 33.30 3.16
404 430 3.719173 AAAACGGAAGGAAATTTGCGA 57.281 38.095 3.87 0.00 43.39 5.10
407 433 1.804748 ACGGAAGGAAATTTGCGAGTC 59.195 47.619 3.87 3.69 43.39 3.36
408 434 1.201921 CGGAAGGAAATTTGCGAGTCG 60.202 52.381 8.54 8.54 43.39 4.18
432 458 1.613437 CGGTTGGAGGTGCTGATTTTT 59.387 47.619 0.00 0.00 0.00 1.94
476 502 1.817099 GCATTGACGCCTCTGGGAG 60.817 63.158 0.00 0.00 38.41 4.30
494 520 2.220313 GAGAGAATCCAATGCAGCTCC 58.780 52.381 0.00 0.00 33.66 4.70
536 563 5.517054 CGAAAAGTCCCGAGATTCTTTCTAG 59.483 44.000 0.00 0.00 33.74 2.43
546 573 1.870055 TTCTTTCTAGTCGCGCGGGT 61.870 55.000 31.69 19.73 0.00 5.28
625 654 4.689549 TCTTGGTCGGGCTCGGGA 62.690 66.667 5.94 0.00 36.95 5.14
688 719 1.139226 ACGCAGCGCACAAACTTTTG 61.139 50.000 16.61 0.00 43.62 2.44
776 820 1.141449 TGCGTTGCAGCAGCTTTTT 59.859 47.368 7.73 0.00 42.92 1.94
968 1017 2.578586 TACCCACCTCGGCTACTCCC 62.579 65.000 0.00 0.00 0.00 4.30
1126 1183 1.133637 TCTCCTAGCTCATCCGCTTCT 60.134 52.381 0.00 0.00 41.30 2.85
1182 1239 1.219393 CTCCTTCTTCCGAGCCCAC 59.781 63.158 0.00 0.00 0.00 4.61
1186 1243 1.160137 CTTCTTCCGAGCCCACAAAG 58.840 55.000 0.00 0.00 0.00 2.77
1214 1271 3.730761 CTTGCTGCCGTGCTGTCC 61.731 66.667 0.00 0.00 0.00 4.02
1289 1347 1.507174 CTCGTCCACCTCGTCTTCC 59.493 63.158 0.00 0.00 0.00 3.46
1796 1854 4.659172 CTTCCAACCGCCTGGCCA 62.659 66.667 14.12 4.71 39.70 5.36
1852 1910 0.251386 TGCGAACTCTGGACCTCTCT 60.251 55.000 0.00 0.00 0.00 3.10
1859 1917 2.292521 ACTCTGGACCTCTCTGGCAATA 60.293 50.000 0.00 0.00 40.22 1.90
2770 2830 6.682113 GCTGATATTTGGAGTTGTTCATGCAT 60.682 38.462 0.00 0.00 0.00 3.96
2829 2895 3.200605 TGTGCAGGGATCTATCACACAAT 59.799 43.478 0.00 0.00 33.94 2.71
2844 2910 1.201414 CACAATGGTTTAACCGGAGCC 59.799 52.381 9.46 0.00 42.58 4.70
2859 2925 1.134907 GGAGCCATTCCAGCAACAATG 60.135 52.381 0.00 0.00 46.01 2.82
3036 3102 2.151502 TCTCCCTCTCATCTGTGTCC 57.848 55.000 0.00 0.00 0.00 4.02
3084 3150 2.354259 CTCAACTCATCTTGTCCTGGC 58.646 52.381 0.00 0.00 0.00 4.85
3123 3189 4.703645 TGTACTGAATCCAGACTCTTCG 57.296 45.455 0.00 0.00 43.02 3.79
3246 3312 6.653020 TCTCATTGCTGTTGGTATCATAACT 58.347 36.000 0.00 0.00 0.00 2.24
3321 3396 2.047844 GCTGCGCTGGAACTCTCA 60.048 61.111 16.47 0.00 0.00 3.27
3608 3683 2.151202 CCGTAACCTTGTTGCACTCAT 58.849 47.619 0.00 0.00 0.00 2.90
3657 3732 6.093404 TCAGCTTCTTATCTACGAGTTTGTG 58.907 40.000 0.00 0.00 0.00 3.33
3693 3768 7.889469 ACTTGCATAAACAACTTCATGAATCT 58.111 30.769 8.96 0.00 0.00 2.40
3852 3927 2.006991 GGCCAAGGTGGGGGACTAT 61.007 63.158 0.00 0.00 38.19 2.12
3861 3936 1.073199 GGGGGACTATGGATTGGCG 59.927 63.158 0.00 0.00 0.00 5.69
4110 4185 2.024414 GGCAAAGTGGAAGAGTGTGTT 58.976 47.619 0.00 0.00 0.00 3.32
4115 4190 3.131709 AGTGGAAGAGTGTGTTGATGG 57.868 47.619 0.00 0.00 0.00 3.51
4445 4520 2.493713 ACGCTAGTCTTTGATAGGCG 57.506 50.000 0.00 0.00 45.31 5.52
4446 4521 1.067212 ACGCTAGTCTTTGATAGGCGG 59.933 52.381 0.00 0.00 44.34 6.13
4447 4522 1.503294 GCTAGTCTTTGATAGGCGGC 58.497 55.000 0.00 0.00 32.23 6.53
4639 4719 6.258068 AGTTGTCTGTAGTTGTTAGTTTCAGC 59.742 38.462 0.00 0.00 0.00 4.26
4703 4783 3.020984 TGGTGTCTCCTTTTCAAACCAC 58.979 45.455 0.00 0.00 37.07 4.16
4704 4784 3.288092 GGTGTCTCCTTTTCAAACCACT 58.712 45.455 0.00 0.00 0.00 4.00
4705 4785 4.080243 TGGTGTCTCCTTTTCAAACCACTA 60.080 41.667 0.00 0.00 37.07 2.74
4706 4786 4.515567 GGTGTCTCCTTTTCAAACCACTAG 59.484 45.833 0.00 0.00 0.00 2.57
4707 4787 5.365619 GTGTCTCCTTTTCAAACCACTAGA 58.634 41.667 0.00 0.00 0.00 2.43
4708 4788 5.998363 GTGTCTCCTTTTCAAACCACTAGAT 59.002 40.000 0.00 0.00 0.00 1.98
4709 4789 5.997746 TGTCTCCTTTTCAAACCACTAGATG 59.002 40.000 0.00 0.00 0.00 2.90
4710 4790 6.183361 TGTCTCCTTTTCAAACCACTAGATGA 60.183 38.462 0.00 0.00 0.00 2.92
4711 4791 6.147985 GTCTCCTTTTCAAACCACTAGATGAC 59.852 42.308 0.00 0.00 0.00 3.06
4712 4792 5.313712 TCCTTTTCAAACCACTAGATGACC 58.686 41.667 0.00 0.00 0.00 4.02
4713 4793 4.459337 CCTTTTCAAACCACTAGATGACCC 59.541 45.833 0.00 0.00 0.00 4.46
4714 4794 3.328382 TTCAAACCACTAGATGACCCG 57.672 47.619 0.00 0.00 0.00 5.28
4715 4795 1.553248 TCAAACCACTAGATGACCCGG 59.447 52.381 0.00 0.00 0.00 5.73
4716 4796 1.278127 CAAACCACTAGATGACCCGGT 59.722 52.381 0.00 0.00 0.00 5.28
4717 4797 1.652947 AACCACTAGATGACCCGGTT 58.347 50.000 0.00 0.00 31.97 4.44
4718 4798 0.902531 ACCACTAGATGACCCGGTTG 59.097 55.000 0.00 0.00 0.00 3.77
4719 4799 0.462047 CCACTAGATGACCCGGTTGC 60.462 60.000 0.00 0.00 0.00 4.17
4720 4800 0.806102 CACTAGATGACCCGGTTGCG 60.806 60.000 0.00 0.00 0.00 4.85
4721 4801 1.883084 CTAGATGACCCGGTTGCGC 60.883 63.158 0.00 0.00 0.00 6.09
4722 4802 3.379865 TAGATGACCCGGTTGCGCC 62.380 63.158 4.18 0.00 0.00 6.53
4737 4817 4.503314 GCCCATGGCGCAAGAAGC 62.503 66.667 10.83 1.83 39.62 3.86
4749 4829 3.713889 GCAAGAAGCGAGTTAGAAGTG 57.286 47.619 0.00 0.00 0.00 3.16
4750 4830 3.318017 GCAAGAAGCGAGTTAGAAGTGA 58.682 45.455 0.00 0.00 0.00 3.41
4751 4831 3.929610 GCAAGAAGCGAGTTAGAAGTGAT 59.070 43.478 0.00 0.00 0.00 3.06
4752 4832 4.201666 GCAAGAAGCGAGTTAGAAGTGATG 60.202 45.833 0.00 0.00 0.00 3.07
4753 4833 4.792521 AGAAGCGAGTTAGAAGTGATGT 57.207 40.909 0.00 0.00 0.00 3.06
4754 4834 5.140747 AGAAGCGAGTTAGAAGTGATGTT 57.859 39.130 0.00 0.00 0.00 2.71
4755 4835 6.268825 AGAAGCGAGTTAGAAGTGATGTTA 57.731 37.500 0.00 0.00 0.00 2.41
4756 4836 6.326375 AGAAGCGAGTTAGAAGTGATGTTAG 58.674 40.000 0.00 0.00 0.00 2.34
4757 4837 5.646577 AGCGAGTTAGAAGTGATGTTAGT 57.353 39.130 0.00 0.00 0.00 2.24
4758 4838 6.026947 AGCGAGTTAGAAGTGATGTTAGTT 57.973 37.500 0.00 0.00 0.00 2.24
4759 4839 5.864474 AGCGAGTTAGAAGTGATGTTAGTTG 59.136 40.000 0.00 0.00 0.00 3.16
4760 4840 5.634020 GCGAGTTAGAAGTGATGTTAGTTGT 59.366 40.000 0.00 0.00 0.00 3.32
4761 4841 6.400091 GCGAGTTAGAAGTGATGTTAGTTGTG 60.400 42.308 0.00 0.00 0.00 3.33
4762 4842 6.861572 CGAGTTAGAAGTGATGTTAGTTGTGA 59.138 38.462 0.00 0.00 0.00 3.58
4763 4843 7.061210 CGAGTTAGAAGTGATGTTAGTTGTGAG 59.939 40.741 0.00 0.00 0.00 3.51
4764 4844 7.727181 AGTTAGAAGTGATGTTAGTTGTGAGT 58.273 34.615 0.00 0.00 0.00 3.41
4765 4845 8.857098 AGTTAGAAGTGATGTTAGTTGTGAGTA 58.143 33.333 0.00 0.00 0.00 2.59
4766 4846 9.472361 GTTAGAAGTGATGTTAGTTGTGAGTAA 57.528 33.333 0.00 0.00 0.00 2.24
4767 4847 9.692749 TTAGAAGTGATGTTAGTTGTGAGTAAG 57.307 33.333 0.00 0.00 0.00 2.34
4768 4848 7.727181 AGAAGTGATGTTAGTTGTGAGTAAGT 58.273 34.615 0.00 0.00 0.00 2.24
4769 4849 8.857098 AGAAGTGATGTTAGTTGTGAGTAAGTA 58.143 33.333 0.00 0.00 0.00 2.24
4770 4850 9.130312 GAAGTGATGTTAGTTGTGAGTAAGTAG 57.870 37.037 0.00 0.00 0.00 2.57
4771 4851 7.603651 AGTGATGTTAGTTGTGAGTAAGTAGG 58.396 38.462 0.00 0.00 0.00 3.18
4772 4852 7.450634 AGTGATGTTAGTTGTGAGTAAGTAGGA 59.549 37.037 0.00 0.00 0.00 2.94
4773 4853 7.755822 GTGATGTTAGTTGTGAGTAAGTAGGAG 59.244 40.741 0.00 0.00 0.00 3.69
4774 4854 7.668469 TGATGTTAGTTGTGAGTAAGTAGGAGA 59.332 37.037 0.00 0.00 0.00 3.71
4775 4855 8.596781 ATGTTAGTTGTGAGTAAGTAGGAGAT 57.403 34.615 0.00 0.00 0.00 2.75
4776 4856 7.827701 TGTTAGTTGTGAGTAAGTAGGAGATG 58.172 38.462 0.00 0.00 0.00 2.90
4777 4857 7.450634 TGTTAGTTGTGAGTAAGTAGGAGATGT 59.549 37.037 0.00 0.00 0.00 3.06
4778 4858 8.954350 GTTAGTTGTGAGTAAGTAGGAGATGTA 58.046 37.037 0.00 0.00 0.00 2.29
4779 4859 7.633193 AGTTGTGAGTAAGTAGGAGATGTAG 57.367 40.000 0.00 0.00 0.00 2.74
4780 4860 7.403671 AGTTGTGAGTAAGTAGGAGATGTAGA 58.596 38.462 0.00 0.00 0.00 2.59
4781 4861 8.056400 AGTTGTGAGTAAGTAGGAGATGTAGAT 58.944 37.037 0.00 0.00 0.00 1.98
4782 4862 7.809546 TGTGAGTAAGTAGGAGATGTAGATG 57.190 40.000 0.00 0.00 0.00 2.90
4783 4863 7.574607 TGTGAGTAAGTAGGAGATGTAGATGA 58.425 38.462 0.00 0.00 0.00 2.92
4784 4864 8.053355 TGTGAGTAAGTAGGAGATGTAGATGAA 58.947 37.037 0.00 0.00 0.00 2.57
4785 4865 8.904834 GTGAGTAAGTAGGAGATGTAGATGAAA 58.095 37.037 0.00 0.00 0.00 2.69
4786 4866 9.475620 TGAGTAAGTAGGAGATGTAGATGAAAA 57.524 33.333 0.00 0.00 0.00 2.29
4787 4867 9.959749 GAGTAAGTAGGAGATGTAGATGAAAAG 57.040 37.037 0.00 0.00 0.00 2.27
4788 4868 9.702253 AGTAAGTAGGAGATGTAGATGAAAAGA 57.298 33.333 0.00 0.00 0.00 2.52
4794 4874 8.845413 AGGAGATGTAGATGAAAAGATAATGC 57.155 34.615 0.00 0.00 0.00 3.56
4795 4875 8.435187 AGGAGATGTAGATGAAAAGATAATGCA 58.565 33.333 0.00 0.00 0.00 3.96
4796 4876 9.060347 GGAGATGTAGATGAAAAGATAATGCAA 57.940 33.333 0.00 0.00 0.00 4.08
4801 4881 8.843262 TGTAGATGAAAAGATAATGCAATGAGG 58.157 33.333 0.00 0.00 0.00 3.86
4802 4882 9.060347 GTAGATGAAAAGATAATGCAATGAGGA 57.940 33.333 0.00 0.00 0.00 3.71
4803 4883 8.707796 AGATGAAAAGATAATGCAATGAGGAT 57.292 30.769 0.00 0.00 0.00 3.24
4804 4884 9.144298 AGATGAAAAGATAATGCAATGAGGATT 57.856 29.630 0.00 0.00 41.52 3.01
4805 4885 9.193133 GATGAAAAGATAATGCAATGAGGATTG 57.807 33.333 0.00 0.00 38.83 2.67
4806 4886 8.070034 TGAAAAGATAATGCAATGAGGATTGT 57.930 30.769 0.00 0.00 41.09 2.71
4807 4887 9.187996 TGAAAAGATAATGCAATGAGGATTGTA 57.812 29.630 0.00 0.00 41.09 2.41
4818 4898 9.407380 TGCAATGAGGATTGTATTACAAATAGT 57.593 29.630 12.96 0.00 41.96 2.12
4844 4924 8.976986 AAGATGACTTAAATTGATTTGCAGAC 57.023 30.769 0.00 0.00 34.28 3.51
4845 4925 7.246311 AGATGACTTAAATTGATTTGCAGACG 58.754 34.615 0.00 0.00 0.00 4.18
4846 4926 6.552859 TGACTTAAATTGATTTGCAGACGA 57.447 33.333 0.00 0.00 0.00 4.20
4847 4927 6.964908 TGACTTAAATTGATTTGCAGACGAA 58.035 32.000 0.00 0.00 0.00 3.85
4848 4928 7.421599 TGACTTAAATTGATTTGCAGACGAAA 58.578 30.769 0.00 0.00 0.00 3.46
4849 4929 7.918033 TGACTTAAATTGATTTGCAGACGAAAA 59.082 29.630 0.00 0.00 0.00 2.29
4850 4930 8.641499 ACTTAAATTGATTTGCAGACGAAAAA 57.359 26.923 0.00 0.00 0.00 1.94
4878 4958 7.969314 CAGAATGTTTAGAAGAGGAAGTAAGC 58.031 38.462 0.00 0.00 0.00 3.09
4879 4959 7.604164 CAGAATGTTTAGAAGAGGAAGTAAGCA 59.396 37.037 0.00 0.00 0.00 3.91
4880 4960 8.157476 AGAATGTTTAGAAGAGGAAGTAAGCAA 58.843 33.333 0.00 0.00 0.00 3.91
4881 4961 8.870075 AATGTTTAGAAGAGGAAGTAAGCAAT 57.130 30.769 0.00 0.00 0.00 3.56
4882 4962 8.870075 ATGTTTAGAAGAGGAAGTAAGCAATT 57.130 30.769 0.00 0.00 0.00 2.32
4883 4963 8.099364 TGTTTAGAAGAGGAAGTAAGCAATTG 57.901 34.615 0.00 0.00 0.00 2.32
4884 4964 7.719633 TGTTTAGAAGAGGAAGTAAGCAATTGT 59.280 33.333 7.40 0.00 0.00 2.71
4885 4965 8.568794 GTTTAGAAGAGGAAGTAAGCAATTGTT 58.431 33.333 7.40 0.00 0.00 2.83
4886 4966 6.566197 AGAAGAGGAAGTAAGCAATTGTTG 57.434 37.500 7.40 0.00 0.00 3.33
4887 4967 6.299141 AGAAGAGGAAGTAAGCAATTGTTGA 58.701 36.000 7.40 0.00 0.00 3.18
4888 4968 6.944862 AGAAGAGGAAGTAAGCAATTGTTGAT 59.055 34.615 7.40 0.00 0.00 2.57
4889 4969 8.103305 AGAAGAGGAAGTAAGCAATTGTTGATA 58.897 33.333 7.40 0.00 0.00 2.15
4890 4970 8.814038 AAGAGGAAGTAAGCAATTGTTGATAT 57.186 30.769 7.40 0.00 0.00 1.63
4891 4971 8.218338 AGAGGAAGTAAGCAATTGTTGATATG 57.782 34.615 7.40 0.00 0.00 1.78
4892 4972 8.049117 AGAGGAAGTAAGCAATTGTTGATATGA 58.951 33.333 7.40 0.00 0.00 2.15
4893 4973 8.757982 AGGAAGTAAGCAATTGTTGATATGAT 57.242 30.769 7.40 0.00 0.00 2.45
4894 4974 8.627403 AGGAAGTAAGCAATTGTTGATATGATG 58.373 33.333 7.40 0.00 0.00 3.07
4895 4975 7.864379 GGAAGTAAGCAATTGTTGATATGATGG 59.136 37.037 7.40 0.00 0.00 3.51
4896 4976 6.742109 AGTAAGCAATTGTTGATATGATGGC 58.258 36.000 7.40 0.00 0.00 4.40
4897 4977 4.233123 AGCAATTGTTGATATGATGGCG 57.767 40.909 7.40 0.00 0.00 5.69
4898 4978 3.005050 AGCAATTGTTGATATGATGGCGG 59.995 43.478 7.40 0.00 0.00 6.13
4899 4979 3.858129 GCAATTGTTGATATGATGGCGGG 60.858 47.826 7.40 0.00 0.00 6.13
4911 4991 4.967084 TGATGGCGGGTACAATAATAGT 57.033 40.909 0.00 0.00 0.00 2.12
5013 5093 7.387397 GCAATGTAAATGGATTCTTTTGGTCAA 59.613 33.333 0.00 0.00 0.00 3.18
5015 5095 9.492973 AATGTAAATGGATTCTTTTGGTCAAAG 57.507 29.630 0.00 0.00 43.15 2.77
5025 5105 5.013547 TCTTTTGGTCAAAGGTGAACTTCA 58.986 37.500 5.66 0.00 42.46 3.02
5101 5181 5.989249 GCCAAAAGCAAACAGATTTTTAGG 58.011 37.500 0.00 0.00 42.77 2.69
5139 5219 8.916654 CACATAGAACTTCATAGGCTAATTACG 58.083 37.037 0.00 0.00 0.00 3.18
5159 5239 9.617975 AATTACGTAGTTTAGTAGACTGAACAC 57.382 33.333 16.78 12.12 37.78 3.32
5174 5254 1.830587 AACACGATGCTCAGAGGGCA 61.831 55.000 0.00 0.00 44.05 5.36
5179 5259 1.537172 ATGCTCAGAGGGCATGCAT 59.463 52.632 21.36 7.26 46.85 3.96
5181 5261 1.153025 GCTCAGAGGGCATGCATGA 60.153 57.895 30.64 15.64 0.00 3.07
5213 5293 1.722751 CGCTTGTAGTTGCGCTTGAAG 60.723 52.381 9.73 3.51 45.50 3.02
5291 5371 4.096984 CAGCCTCTAGTAATTTTTGCCCTG 59.903 45.833 0.00 0.00 0.00 4.45
5352 5432 9.804977 AGGGATTTCCATCTCTAGATTTTATTG 57.195 33.333 0.00 0.00 38.63 1.90
5386 5466 1.302383 TTTGGGTCAATACAGCGGCG 61.302 55.000 0.51 0.51 0.00 6.46
5399 5479 2.364324 ACAGCGGCGGAGATATTTCTTA 59.636 45.455 9.78 0.00 30.30 2.10
5412 5492 9.032420 GGAGATATTTCTTAGTAAAACTGACCG 57.968 37.037 0.00 0.00 30.30 4.79
5428 5508 4.161565 ACTGACCGAGGAATACTGCAAATA 59.838 41.667 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.376037 GAAGGGTGCTTCCGTGGAG 60.376 63.158 0.00 0.00 37.00 3.86
1 2 2.747686 GAAGGGTGCTTCCGTGGA 59.252 61.111 0.00 0.00 37.00 4.02
2 3 2.521958 ATCGAAGGGTGCTTCCGTGG 62.522 60.000 0.00 0.00 37.00 4.94
3 4 1.079127 ATCGAAGGGTGCTTCCGTG 60.079 57.895 0.00 0.00 37.00 4.94
4 5 1.079127 CATCGAAGGGTGCTTCCGT 60.079 57.895 0.00 0.00 37.00 4.69
5 6 0.807667 CTCATCGAAGGGTGCTTCCG 60.808 60.000 0.00 0.00 37.00 4.30
6 7 1.092345 GCTCATCGAAGGGTGCTTCC 61.092 60.000 0.00 0.00 0.00 3.46
7 8 1.424493 CGCTCATCGAAGGGTGCTTC 61.424 60.000 0.00 0.00 41.67 3.86
8 9 1.448540 CGCTCATCGAAGGGTGCTT 60.449 57.895 0.00 0.00 41.67 3.91
9 10 2.185350 CGCTCATCGAAGGGTGCT 59.815 61.111 0.00 0.00 41.67 4.40
10 11 2.892425 CCGCTCATCGAAGGGTGC 60.892 66.667 0.00 0.00 41.67 5.01
11 12 2.892425 GCCGCTCATCGAAGGGTG 60.892 66.667 0.00 0.00 41.67 4.61
12 13 4.162690 GGCCGCTCATCGAAGGGT 62.163 66.667 0.00 0.00 41.67 4.34
13 14 4.918201 GGGCCGCTCATCGAAGGG 62.918 72.222 0.00 0.00 41.67 3.95
14 15 2.947938 ATTGGGCCGCTCATCGAAGG 62.948 60.000 0.00 0.00 41.67 3.46
17 18 2.108976 GATTGGGCCGCTCATCGA 59.891 61.111 0.00 0.00 41.67 3.59
29 30 4.446371 GTGTCTTCCCTATGTCTGATTGG 58.554 47.826 0.00 0.00 0.00 3.16
35 36 2.379972 CCTCGTGTCTTCCCTATGTCT 58.620 52.381 0.00 0.00 0.00 3.41
49 50 2.548920 GGAGGCATATTCTTCCCTCGTG 60.549 54.545 0.00 0.00 43.76 4.35
53 54 1.059913 CCGGAGGCATATTCTTCCCT 58.940 55.000 0.00 0.00 46.14 4.20
101 102 3.896648 TTTTGTCTTTCTCATGTCCGC 57.103 42.857 0.00 0.00 0.00 5.54
110 111 4.214332 GCGACAGATCCTTTTTGTCTTTCT 59.786 41.667 9.55 0.00 39.18 2.52
112 113 3.058914 CGCGACAGATCCTTTTTGTCTTT 60.059 43.478 0.00 0.00 39.18 2.52
121 122 3.376935 CTGGCCGCGACAGATCCTT 62.377 63.158 21.28 0.00 42.14 3.36
122 123 3.842923 CTGGCCGCGACAGATCCT 61.843 66.667 21.28 0.00 42.14 3.24
137 138 3.008330 ACACTACACTAGTCTACGGCTG 58.992 50.000 0.00 0.00 36.76 4.85
138 139 3.347077 ACACTACACTAGTCTACGGCT 57.653 47.619 0.00 0.00 36.76 5.52
191 192 3.674753 ACGGTAAAACTATGTGCACGTAC 59.325 43.478 14.85 6.75 0.00 3.67
192 193 3.911868 ACGGTAAAACTATGTGCACGTA 58.088 40.909 17.61 17.61 0.00 3.57
193 194 2.758009 ACGGTAAAACTATGTGCACGT 58.242 42.857 17.19 17.19 0.00 4.49
194 195 3.799137 AACGGTAAAACTATGTGCACG 57.201 42.857 13.13 0.00 0.00 5.34
231 233 5.517904 CCGGACAAAAACGGTTACATTTTA 58.482 37.500 0.00 0.00 44.85 1.52
267 269 4.331443 CCGGATTTCATACAAACATGACGA 59.669 41.667 0.00 0.00 34.69 4.20
303 305 9.323985 TCTTTTTCAACCAATCGAATGAAATTT 57.676 25.926 0.94 0.00 40.36 1.82
315 317 7.819415 GCTAGCCTAAATTCTTTTTCAACCAAT 59.181 33.333 2.29 0.00 0.00 3.16
318 320 6.687604 TGCTAGCCTAAATTCTTTTTCAACC 58.312 36.000 13.29 0.00 0.00 3.77
330 332 4.256920 CGCCATCTAATGCTAGCCTAAAT 58.743 43.478 13.29 0.00 0.00 1.40
334 336 0.321122 GCGCCATCTAATGCTAGCCT 60.321 55.000 13.29 0.00 0.00 4.58
342 354 1.072159 GCAGGAGGCGCCATCTAAT 59.928 57.895 31.54 6.18 40.02 1.73
367 380 5.472137 TCCGTTTTTGTTCCAATCTAAGGAG 59.528 40.000 0.00 0.00 36.33 3.69
371 384 5.828859 TCCTTCCGTTTTTGTTCCAATCTAA 59.171 36.000 0.00 0.00 0.00 2.10
373 386 4.211920 TCCTTCCGTTTTTGTTCCAATCT 58.788 39.130 0.00 0.00 0.00 2.40
379 392 5.498159 GCAAATTTCCTTCCGTTTTTGTTC 58.502 37.500 0.00 0.00 0.00 3.18
386 412 2.225727 GACTCGCAAATTTCCTTCCGTT 59.774 45.455 0.00 0.00 0.00 4.44
387 413 1.804748 GACTCGCAAATTTCCTTCCGT 59.195 47.619 0.00 0.00 0.00 4.69
410 436 3.628646 ATCAGCACCTCCAACCGCC 62.629 63.158 0.00 0.00 0.00 6.13
421 447 5.224888 TGCTTCAAGATCAAAAATCAGCAC 58.775 37.500 0.00 0.00 29.93 4.40
432 458 6.144854 CGTTTTCATCTTTGCTTCAAGATCA 58.855 36.000 0.00 0.00 0.00 2.92
472 498 1.133853 AGCTGCATTGGATTCTCTCCC 60.134 52.381 1.02 0.00 44.23 4.30
476 502 0.942962 CGGAGCTGCATTGGATTCTC 59.057 55.000 5.91 0.86 0.00 2.87
494 520 1.841663 CGGTGCTTTTGAGGTGGACG 61.842 60.000 0.00 0.00 0.00 4.79
546 573 2.281484 GAGGCTTGGTGAACCGCA 60.281 61.111 0.00 0.00 39.43 5.69
552 579 2.342279 CGGTTCGAGGCTTGGTGA 59.658 61.111 0.97 0.00 0.00 4.02
581 608 1.445716 AATAGGCTCGGAGTCGTCGG 61.446 60.000 6.90 0.00 37.69 4.79
583 610 2.580966 AAAATAGGCTCGGAGTCGTC 57.419 50.000 6.90 0.00 37.69 4.20
641 670 2.813908 CGCTTGGGCCGTGAGTAC 60.814 66.667 0.00 0.00 34.44 2.73
737 768 3.272334 GTGATCGGACGGCCATGC 61.272 66.667 8.76 0.00 0.00 4.06
853 902 2.364317 TCGGAGAGGAGCCAAGGG 60.364 66.667 0.00 0.00 0.00 3.95
858 907 3.844090 GCAGGTCGGAGAGGAGCC 61.844 72.222 0.00 0.00 36.95 4.70
968 1017 2.464865 CTGCGGAAATTCGGACTCTAG 58.535 52.381 4.67 0.00 0.00 2.43
1126 1183 1.449601 GCAAGAAGGCGATTCCGGA 60.450 57.895 0.00 0.00 38.84 5.14
1147 1204 1.000896 AGGAGACGCCCCCAAAATG 60.001 57.895 0.00 0.00 37.37 2.32
1182 1239 0.600057 GCAAGAAGTGAGGGCCTTTG 59.400 55.000 7.89 8.38 0.00 2.77
1186 1243 2.338785 GCAGCAAGAAGTGAGGGCC 61.339 63.158 0.00 0.00 0.00 5.80
1217 1275 1.530183 GGATCCCAGATGGCAAGGC 60.530 63.158 0.00 0.00 0.00 4.35
1525 1583 3.134792 GACTCGAGGCGCAGGAGA 61.135 66.667 22.92 10.40 0.00 3.71
1666 1724 2.555123 GCACTTGCCGAAGAATCCA 58.445 52.632 0.00 0.00 32.98 3.41
1771 1829 1.235281 GGCGGTTGGAAGACAGGTTC 61.235 60.000 0.00 0.00 0.00 3.62
1859 1917 2.047274 CAACTCGCCGGTGATGGT 60.047 61.111 19.93 11.35 0.00 3.55
2770 2830 9.364989 GCATACAAATACAATTAAAGGCAGAAA 57.635 29.630 0.00 0.00 0.00 2.52
2783 2843 9.456147 ACATAGTAACCAAGCATACAAATACAA 57.544 29.630 0.00 0.00 0.00 2.41
2784 2844 8.888716 CACATAGTAACCAAGCATACAAATACA 58.111 33.333 0.00 0.00 0.00 2.29
2785 2845 7.855904 GCACATAGTAACCAAGCATACAAATAC 59.144 37.037 0.00 0.00 0.00 1.89
2786 2846 7.554476 TGCACATAGTAACCAAGCATACAAATA 59.446 33.333 0.00 0.00 0.00 1.40
2787 2847 6.376864 TGCACATAGTAACCAAGCATACAAAT 59.623 34.615 0.00 0.00 0.00 2.32
2788 2848 5.707764 TGCACATAGTAACCAAGCATACAAA 59.292 36.000 0.00 0.00 0.00 2.83
2829 2895 1.614850 GGAATGGCTCCGGTTAAACCA 60.615 52.381 0.00 3.61 38.47 3.67
2844 2910 0.609151 TGGCCATTGTTGCTGGAATG 59.391 50.000 0.00 0.00 35.70 2.67
2859 2925 1.177401 GAAGGTTGGTGAGATTGGCC 58.823 55.000 0.00 0.00 0.00 5.36
3015 3081 3.748989 CGGACACAGATGAGAGGGAGATA 60.749 52.174 0.00 0.00 0.00 1.98
3018 3084 0.743688 CGGACACAGATGAGAGGGAG 59.256 60.000 0.00 0.00 0.00 4.30
3036 3102 1.508088 GCAAAGGCCAGGATTGTCG 59.492 57.895 5.01 0.00 0.00 4.35
3084 3150 6.424509 TCAGTACAATTGGTTTTGGTAGTACG 59.575 38.462 10.83 0.00 36.59 3.67
3123 3189 0.175760 TCTGTGCTAGCGGATTGGAC 59.824 55.000 10.77 0.91 0.00 4.02
3246 3312 9.199982 CGAACTTGAAGGTTAAGAACTGTAATA 57.800 33.333 0.00 0.00 0.00 0.98
3282 3348 1.010580 CAGCAGCAGCAGAATGAGAG 58.989 55.000 3.17 0.00 45.49 3.20
3321 3396 5.163001 TGGAGACTGACTGAGATATCCATCT 60.163 44.000 0.00 0.00 44.51 2.90
3608 3683 0.978667 TGGCGTCCAGTAATAGCCCA 60.979 55.000 2.14 0.00 46.67 5.36
3657 3732 3.359695 TTATGCAAGTTACCCCCAGAC 57.640 47.619 0.00 0.00 0.00 3.51
3693 3768 6.013898 TCCATGAAAGGTAATTTGCATTGGAA 60.014 34.615 0.00 0.00 0.00 3.53
3852 3927 0.744414 GCAGTAGCTTCGCCAATCCA 60.744 55.000 0.00 0.00 37.91 3.41
3861 3936 1.009829 CCAACATCGGCAGTAGCTTC 58.990 55.000 0.00 0.00 41.70 3.86
3874 3949 5.057149 GCTTAGAACATACCGATCCAACAT 58.943 41.667 0.00 0.00 0.00 2.71
4110 4185 1.552799 TTCCGCAGAGCTTCCCATCA 61.553 55.000 0.00 0.00 0.00 3.07
4115 4190 1.133216 GGAATTTTCCGCAGAGCTTCC 59.867 52.381 0.00 0.00 37.65 3.46
4371 4446 6.215495 AGCACACTAGATAGAACTTCCTTC 57.785 41.667 0.00 0.00 0.00 3.46
4445 4520 7.725251 TGGAATCCATTACATAATTTCTTGCC 58.275 34.615 0.00 0.00 0.00 4.52
4446 4521 9.034544 GTTGGAATCCATTACATAATTTCTTGC 57.965 33.333 1.39 0.00 31.53 4.01
4447 4522 9.236691 CGTTGGAATCCATTACATAATTTCTTG 57.763 33.333 1.39 0.00 31.53 3.02
4639 4719 2.007608 CTCCATCATCACACTGCACAG 58.992 52.381 0.00 0.00 0.00 3.66
4703 4783 1.883084 GCGCAACCGGGTCATCTAG 60.883 63.158 6.32 0.00 34.32 2.43
4704 4784 2.185867 GCGCAACCGGGTCATCTA 59.814 61.111 6.32 0.00 34.32 1.98
4705 4785 4.778143 GGCGCAACCGGGTCATCT 62.778 66.667 10.83 0.00 34.32 2.90
4720 4800 4.503314 GCTTCTTGCGCCATGGGC 62.503 66.667 15.13 15.60 46.75 5.36
4729 4809 3.318017 TCACTTCTAACTCGCTTCTTGC 58.682 45.455 0.00 0.00 38.57 4.01
4730 4810 4.926238 ACATCACTTCTAACTCGCTTCTTG 59.074 41.667 0.00 0.00 0.00 3.02
4731 4811 5.140747 ACATCACTTCTAACTCGCTTCTT 57.859 39.130 0.00 0.00 0.00 2.52
4732 4812 4.792521 ACATCACTTCTAACTCGCTTCT 57.207 40.909 0.00 0.00 0.00 2.85
4733 4813 6.094061 ACTAACATCACTTCTAACTCGCTTC 58.906 40.000 0.00 0.00 0.00 3.86
4734 4814 6.026947 ACTAACATCACTTCTAACTCGCTT 57.973 37.500 0.00 0.00 0.00 4.68
4735 4815 5.646577 ACTAACATCACTTCTAACTCGCT 57.353 39.130 0.00 0.00 0.00 4.93
4736 4816 5.634020 ACAACTAACATCACTTCTAACTCGC 59.366 40.000 0.00 0.00 0.00 5.03
4737 4817 6.861572 TCACAACTAACATCACTTCTAACTCG 59.138 38.462 0.00 0.00 0.00 4.18
4738 4818 7.868415 ACTCACAACTAACATCACTTCTAACTC 59.132 37.037 0.00 0.00 0.00 3.01
4739 4819 7.727181 ACTCACAACTAACATCACTTCTAACT 58.273 34.615 0.00 0.00 0.00 2.24
4740 4820 7.948278 ACTCACAACTAACATCACTTCTAAC 57.052 36.000 0.00 0.00 0.00 2.34
4741 4821 9.692749 CTTACTCACAACTAACATCACTTCTAA 57.307 33.333 0.00 0.00 0.00 2.10
4742 4822 8.857098 ACTTACTCACAACTAACATCACTTCTA 58.143 33.333 0.00 0.00 0.00 2.10
4743 4823 7.727181 ACTTACTCACAACTAACATCACTTCT 58.273 34.615 0.00 0.00 0.00 2.85
4744 4824 7.948278 ACTTACTCACAACTAACATCACTTC 57.052 36.000 0.00 0.00 0.00 3.01
4745 4825 8.088981 CCTACTTACTCACAACTAACATCACTT 58.911 37.037 0.00 0.00 0.00 3.16
4746 4826 7.450634 TCCTACTTACTCACAACTAACATCACT 59.549 37.037 0.00 0.00 0.00 3.41
4747 4827 7.600065 TCCTACTTACTCACAACTAACATCAC 58.400 38.462 0.00 0.00 0.00 3.06
4748 4828 7.668469 TCTCCTACTTACTCACAACTAACATCA 59.332 37.037 0.00 0.00 0.00 3.07
4749 4829 8.053026 TCTCCTACTTACTCACAACTAACATC 57.947 38.462 0.00 0.00 0.00 3.06
4750 4830 8.470805 CATCTCCTACTTACTCACAACTAACAT 58.529 37.037 0.00 0.00 0.00 2.71
4751 4831 7.450634 ACATCTCCTACTTACTCACAACTAACA 59.549 37.037 0.00 0.00 0.00 2.41
4752 4832 7.828712 ACATCTCCTACTTACTCACAACTAAC 58.171 38.462 0.00 0.00 0.00 2.34
4753 4833 9.175312 CTACATCTCCTACTTACTCACAACTAA 57.825 37.037 0.00 0.00 0.00 2.24
4754 4834 8.546322 TCTACATCTCCTACTTACTCACAACTA 58.454 37.037 0.00 0.00 0.00 2.24
4755 4835 7.403671 TCTACATCTCCTACTTACTCACAACT 58.596 38.462 0.00 0.00 0.00 3.16
4756 4836 7.627298 TCTACATCTCCTACTTACTCACAAC 57.373 40.000 0.00 0.00 0.00 3.32
4757 4837 8.053355 TCATCTACATCTCCTACTTACTCACAA 58.947 37.037 0.00 0.00 0.00 3.33
4758 4838 7.574607 TCATCTACATCTCCTACTTACTCACA 58.425 38.462 0.00 0.00 0.00 3.58
4759 4839 8.453238 TTCATCTACATCTCCTACTTACTCAC 57.547 38.462 0.00 0.00 0.00 3.51
4760 4840 9.475620 TTTTCATCTACATCTCCTACTTACTCA 57.524 33.333 0.00 0.00 0.00 3.41
4761 4841 9.959749 CTTTTCATCTACATCTCCTACTTACTC 57.040 37.037 0.00 0.00 0.00 2.59
4762 4842 9.702253 TCTTTTCATCTACATCTCCTACTTACT 57.298 33.333 0.00 0.00 0.00 2.24
4768 4848 9.935241 GCATTATCTTTTCATCTACATCTCCTA 57.065 33.333 0.00 0.00 0.00 2.94
4769 4849 8.435187 TGCATTATCTTTTCATCTACATCTCCT 58.565 33.333 0.00 0.00 0.00 3.69
4770 4850 8.613060 TGCATTATCTTTTCATCTACATCTCC 57.387 34.615 0.00 0.00 0.00 3.71
4775 4855 8.843262 CCTCATTGCATTATCTTTTCATCTACA 58.157 33.333 0.00 0.00 0.00 2.74
4776 4856 9.060347 TCCTCATTGCATTATCTTTTCATCTAC 57.940 33.333 0.00 0.00 0.00 2.59
4777 4857 9.803507 ATCCTCATTGCATTATCTTTTCATCTA 57.196 29.630 0.00 0.00 0.00 1.98
4778 4858 8.707796 ATCCTCATTGCATTATCTTTTCATCT 57.292 30.769 0.00 0.00 0.00 2.90
4779 4859 9.193133 CAATCCTCATTGCATTATCTTTTCATC 57.807 33.333 0.00 0.00 33.19 2.92
4780 4860 8.701895 ACAATCCTCATTGCATTATCTTTTCAT 58.298 29.630 0.00 0.00 43.03 2.57
4781 4861 8.070034 ACAATCCTCATTGCATTATCTTTTCA 57.930 30.769 0.00 0.00 43.03 2.69
4786 4866 9.797642 TGTAATACAATCCTCATTGCATTATCT 57.202 29.630 0.00 0.00 43.03 1.98
4792 4872 9.407380 ACTATTTGTAATACAATCCTCATTGCA 57.593 29.630 6.67 0.00 43.03 4.08
4819 4899 7.752239 CGTCTGCAAATCAATTTAAGTCATCTT 59.248 33.333 0.00 0.00 37.65 2.40
4820 4900 7.119699 TCGTCTGCAAATCAATTTAAGTCATCT 59.880 33.333 0.00 0.00 0.00 2.90
4821 4901 7.243487 TCGTCTGCAAATCAATTTAAGTCATC 58.757 34.615 0.00 0.00 0.00 2.92
4822 4902 7.144722 TCGTCTGCAAATCAATTTAAGTCAT 57.855 32.000 0.00 0.00 0.00 3.06
4823 4903 6.552859 TCGTCTGCAAATCAATTTAAGTCA 57.447 33.333 0.00 0.00 0.00 3.41
4824 4904 7.851822 TTTCGTCTGCAAATCAATTTAAGTC 57.148 32.000 0.00 0.00 0.00 3.01
4825 4905 8.641499 TTTTTCGTCTGCAAATCAATTTAAGT 57.359 26.923 0.00 0.00 0.00 2.24
4851 4931 9.495572 CTTACTTCCTCTTCTAAACATTCTGTT 57.504 33.333 0.00 0.00 43.41 3.16
4852 4932 7.604545 GCTTACTTCCTCTTCTAAACATTCTGT 59.395 37.037 0.00 0.00 0.00 3.41
4853 4933 7.604164 TGCTTACTTCCTCTTCTAAACATTCTG 59.396 37.037 0.00 0.00 0.00 3.02
4854 4934 7.680730 TGCTTACTTCCTCTTCTAAACATTCT 58.319 34.615 0.00 0.00 0.00 2.40
4855 4935 7.907214 TGCTTACTTCCTCTTCTAAACATTC 57.093 36.000 0.00 0.00 0.00 2.67
4856 4936 8.870075 ATTGCTTACTTCCTCTTCTAAACATT 57.130 30.769 0.00 0.00 0.00 2.71
4857 4937 8.734386 CAATTGCTTACTTCCTCTTCTAAACAT 58.266 33.333 0.00 0.00 0.00 2.71
4858 4938 7.719633 ACAATTGCTTACTTCCTCTTCTAAACA 59.280 33.333 5.05 0.00 0.00 2.83
4859 4939 8.100508 ACAATTGCTTACTTCCTCTTCTAAAC 57.899 34.615 5.05 0.00 0.00 2.01
4860 4940 8.567948 CAACAATTGCTTACTTCCTCTTCTAAA 58.432 33.333 5.05 0.00 0.00 1.85
4861 4941 7.936847 TCAACAATTGCTTACTTCCTCTTCTAA 59.063 33.333 5.05 0.00 0.00 2.10
4862 4942 7.450074 TCAACAATTGCTTACTTCCTCTTCTA 58.550 34.615 5.05 0.00 0.00 2.10
4863 4943 6.299141 TCAACAATTGCTTACTTCCTCTTCT 58.701 36.000 5.05 0.00 0.00 2.85
4864 4944 6.560253 TCAACAATTGCTTACTTCCTCTTC 57.440 37.500 5.05 0.00 0.00 2.87
4865 4945 8.680903 CATATCAACAATTGCTTACTTCCTCTT 58.319 33.333 5.05 0.00 0.00 2.85
4866 4946 8.049117 TCATATCAACAATTGCTTACTTCCTCT 58.951 33.333 5.05 0.00 0.00 3.69
4867 4947 8.213518 TCATATCAACAATTGCTTACTTCCTC 57.786 34.615 5.05 0.00 0.00 3.71
4868 4948 8.627403 CATCATATCAACAATTGCTTACTTCCT 58.373 33.333 5.05 0.00 0.00 3.36
4869 4949 7.864379 CCATCATATCAACAATTGCTTACTTCC 59.136 37.037 5.05 0.00 0.00 3.46
4870 4950 7.380602 GCCATCATATCAACAATTGCTTACTTC 59.619 37.037 5.05 0.00 0.00 3.01
4871 4951 7.205297 GCCATCATATCAACAATTGCTTACTT 58.795 34.615 5.05 0.00 0.00 2.24
4872 4952 6.513884 CGCCATCATATCAACAATTGCTTACT 60.514 38.462 5.05 0.00 0.00 2.24
4873 4953 5.626543 CGCCATCATATCAACAATTGCTTAC 59.373 40.000 5.05 0.00 0.00 2.34
4874 4954 5.278414 CCGCCATCATATCAACAATTGCTTA 60.278 40.000 5.05 0.00 0.00 3.09
4875 4955 4.500205 CCGCCATCATATCAACAATTGCTT 60.500 41.667 5.05 0.00 0.00 3.91
4876 4956 3.005050 CCGCCATCATATCAACAATTGCT 59.995 43.478 5.05 0.00 0.00 3.91
4877 4957 3.311106 CCGCCATCATATCAACAATTGC 58.689 45.455 5.05 0.00 0.00 3.56
4878 4958 3.318839 ACCCGCCATCATATCAACAATTG 59.681 43.478 3.24 3.24 0.00 2.32
4879 4959 3.565307 ACCCGCCATCATATCAACAATT 58.435 40.909 0.00 0.00 0.00 2.32
4880 4960 3.228188 ACCCGCCATCATATCAACAAT 57.772 42.857 0.00 0.00 0.00 2.71
4881 4961 2.727123 ACCCGCCATCATATCAACAA 57.273 45.000 0.00 0.00 0.00 2.83
4882 4962 2.436173 TGTACCCGCCATCATATCAACA 59.564 45.455 0.00 0.00 0.00 3.33
4883 4963 3.120321 TGTACCCGCCATCATATCAAC 57.880 47.619 0.00 0.00 0.00 3.18
4884 4964 3.847671 TTGTACCCGCCATCATATCAA 57.152 42.857 0.00 0.00 0.00 2.57
4885 4965 5.491323 TTATTGTACCCGCCATCATATCA 57.509 39.130 0.00 0.00 0.00 2.15
4886 4966 7.224753 CACTATTATTGTACCCGCCATCATATC 59.775 40.741 0.00 0.00 0.00 1.63
4887 4967 7.047891 CACTATTATTGTACCCGCCATCATAT 58.952 38.462 0.00 0.00 0.00 1.78
4888 4968 6.014070 ACACTATTATTGTACCCGCCATCATA 60.014 38.462 0.00 0.00 0.00 2.15
4889 4969 5.221843 ACACTATTATTGTACCCGCCATCAT 60.222 40.000 0.00 0.00 0.00 2.45
4890 4970 4.101898 ACACTATTATTGTACCCGCCATCA 59.898 41.667 0.00 0.00 0.00 3.07
4891 4971 4.638304 ACACTATTATTGTACCCGCCATC 58.362 43.478 0.00 0.00 0.00 3.51
4892 4972 4.699925 ACACTATTATTGTACCCGCCAT 57.300 40.909 0.00 0.00 0.00 4.40
4893 4973 4.490899 AACACTATTATTGTACCCGCCA 57.509 40.909 0.00 0.00 0.00 5.69
4894 4974 6.539826 AGTTTAACACTATTATTGTACCCGCC 59.460 38.462 0.00 0.00 31.97 6.13
4895 4975 7.543947 AGTTTAACACTATTATTGTACCCGC 57.456 36.000 0.00 0.00 31.97 6.13
4896 4976 8.392612 CCAAGTTTAACACTATTATTGTACCCG 58.607 37.037 0.00 0.00 32.94 5.28
4897 4977 9.452287 TCCAAGTTTAACACTATTATTGTACCC 57.548 33.333 0.00 0.00 32.94 3.69
5004 5084 5.930837 ATGAAGTTCACCTTTGACCAAAA 57.069 34.783 7.96 0.00 32.03 2.44
5013 5093 7.092399 ACCTAAATAGCCTATGAAGTTCACCTT 60.092 37.037 7.96 0.00 35.59 3.50
5015 5095 6.592870 ACCTAAATAGCCTATGAAGTTCACC 58.407 40.000 7.96 0.00 0.00 4.02
5087 5167 8.957466 GTATAGCTTCACCCTAAAAATCTGTTT 58.043 33.333 0.00 0.00 0.00 2.83
5101 5181 7.265673 TGAAGTTCTATGTGTATAGCTTCACC 58.734 38.462 4.17 0.00 39.01 4.02
5137 5217 5.466728 TCGTGTTCAGTCTACTAAACTACGT 59.533 40.000 14.79 0.00 33.97 3.57
5139 5219 6.250951 GCATCGTGTTCAGTCTACTAAACTAC 59.749 42.308 0.00 0.00 0.00 2.73
5174 5254 1.688772 GCTTGGGTCTCATCATGCAT 58.311 50.000 0.00 0.00 35.16 3.96
5179 5259 0.674581 CAAGCGCTTGGGTCTCATCA 60.675 55.000 36.86 0.00 36.95 3.07
5181 5261 0.613260 TACAAGCGCTTGGGTCTCAT 59.387 50.000 43.26 27.77 44.45 2.90
5213 5293 5.106515 GGAAAGAGAAATATATGCCTTCGCC 60.107 44.000 0.00 0.00 0.00 5.54
5291 5371 5.107065 CCGTCTAATCAAAGGAGTCAACAAC 60.107 44.000 0.00 0.00 0.00 3.32
5352 5432 2.562738 ACCCAAAGCTTTATGACTTGCC 59.437 45.455 12.25 0.00 0.00 4.52
5386 5466 9.032420 CGGTCAGTTTTACTAAGAAATATCTCC 57.968 37.037 0.00 0.00 33.77 3.71
5399 5479 5.721232 CAGTATTCCTCGGTCAGTTTTACT 58.279 41.667 0.00 0.00 0.00 2.24
5412 5492 8.736244 TGTTACCTTTTATTTGCAGTATTCCTC 58.264 33.333 0.00 0.00 0.00 3.71
5428 5508 7.696992 TCTTTTCTCACTGTTGTTACCTTTT 57.303 32.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.