Multiple sequence alignment - TraesCS7D01G191100

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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 TraesCS7D01G191100 chr7D 100.000 4421 0 0 1 4421 146391561 146387141 0.000000e+00 8165.0
1 TraesCS7D01G191100 chr7D 93.182 44 2 1 4025 4068 621127310 621127352 3.690000e-06 63.9
2 TraesCS7D01G191100 chr7B 92.376 1902 93 27 524 2382 108730170 108728278 0.000000e+00 2662.0
3 TraesCS7D01G191100 chr7B 92.914 1623 54 20 2378 3950 108728237 108726626 0.000000e+00 2303.0
4 TraesCS7D01G191100 chr7B 93.529 170 5 5 3989 4154 108726627 108726460 9.500000e-62 248.0
5 TraesCS7D01G191100 chr7B 94.737 38 2 0 4025 4062 120391278 120391241 4.780000e-05 60.2
6 TraesCS7D01G191100 chr7A 92.886 1715 75 23 688 2382 147071777 147070090 0.000000e+00 2447.0
7 TraesCS7D01G191100 chr7A 94.521 1442 59 13 2885 4312 147069563 147068128 0.000000e+00 2207.0
8 TraesCS7D01G191100 chr7A 89.655 493 16 13 2378 2843 147070049 147069565 2.940000e-166 595.0
9 TraesCS7D01G191100 chr7A 82.477 662 77 18 4 646 147072423 147071782 1.080000e-150 544.0
10 TraesCS7D01G191100 chr1B 84.810 79 12 0 4111 4189 174981725 174981803 3.670000e-11 80.5


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 TraesCS7D01G191100 chr7D 146387141 146391561 4420 True 8165.000000 8165 100.000000 1 4421 1 chr7D.!!$R1 4420
1 TraesCS7D01G191100 chr7B 108726460 108730170 3710 True 1737.666667 2662 92.939667 524 4154 3 chr7B.!!$R2 3630
2 TraesCS7D01G191100 chr7A 147068128 147072423 4295 True 1448.250000 2447 89.884750 4 4312 4 chr7A.!!$R1 4308

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
249 254 0.107456 ACTGGGATGATGATGGCGAC 59.893 55.0 0.0 0.0 0.00 5.19 F
786 819 0.110056 CAGCAGCACAAAAGCGTAGG 60.110 55.0 0.0 0.0 40.15 3.18 F
1875 1930 0.326264 AGCTCCTTCATGCTCGGTTT 59.674 50.0 0.0 0.0 33.90 3.27 F
2459 2575 0.179234 TTGTCTGGCTGAACGGTTCA 59.821 50.0 21.3 21.3 38.17 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1930 1.595993 GCTCGTACTGCTCTCCCACA 61.596 60.000 0.0 0.0 0.00 4.17 R
2254 2326 1.770658 TGAGAGCCCATCGGATGAAAT 59.229 47.619 19.3 4.2 0.00 2.17 R
2881 3024 0.319211 TAACGTGAGGGCGACAAGTG 60.319 55.000 0.0 0.0 35.59 3.16 R
4174 4383 1.805428 CGTTTCAACTGCCAAGGGGG 61.805 60.000 0.0 0.0 40.85 5.40 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
20 21 2.014010 ACCAGTGCCAATTGGTTCAT 57.986 45.000 25.19 7.04 43.51 2.57
21 22 3.168035 ACCAGTGCCAATTGGTTCATA 57.832 42.857 25.19 5.06 43.51 2.15
22 23 3.091545 ACCAGTGCCAATTGGTTCATAG 58.908 45.455 25.19 12.55 43.51 2.23
59 60 5.940192 TTTGTTGTTATCAGACGCATTCT 57.060 34.783 0.00 0.00 33.33 2.40
66 67 5.062183 TGTTATCAGACGCATTCTTCTTTCG 59.938 40.000 0.00 0.00 28.96 3.46
69 70 2.736721 CAGACGCATTCTTCTTTCGGAA 59.263 45.455 0.00 0.00 28.96 4.30
84 85 7.884816 TCTTTCGGAAGTAACATAGAAACTG 57.115 36.000 2.72 0.00 34.41 3.16
131 132 9.618890 AACTATTCATACATATGCAACAAGAGT 57.381 29.630 1.58 1.53 33.76 3.24
135 136 9.783081 ATTCATACATATGCAACAAGAGTATCA 57.217 29.630 1.58 0.00 33.35 2.15
137 138 8.424133 TCATACATATGCAACAAGAGTATCAGT 58.576 33.333 1.58 0.00 33.35 3.41
182 184 6.174049 ACTCATAAGCTTGTTCTTACCTTCC 58.826 40.000 9.86 0.00 32.02 3.46
211 216 0.884514 GGAGCAAGGAAGTTTCAGCC 59.115 55.000 0.00 0.00 0.00 4.85
218 223 1.677552 GAAGTTTCAGCCGAGGGGA 59.322 57.895 0.00 0.00 34.06 4.81
227 232 3.227276 CCGAGGGGATGGAGACGG 61.227 72.222 0.00 0.00 34.06 4.79
246 251 1.271271 GGAGACTGGGATGATGATGGC 60.271 57.143 0.00 0.00 0.00 4.40
249 254 0.107456 ACTGGGATGATGATGGCGAC 59.893 55.000 0.00 0.00 0.00 5.19
278 295 4.699522 GGTGCGGGTGAGGTCCAC 62.700 72.222 0.00 0.00 44.95 4.02
295 312 3.607987 CGAATCGTCGGCAGCGAC 61.608 66.667 5.54 5.54 43.81 5.19
302 319 3.440415 TCGGCAGCGACGACAGAT 61.440 61.111 0.00 0.00 38.55 2.90
305 322 1.939785 GGCAGCGACGACAGATACG 60.940 63.158 0.00 0.00 0.00 3.06
317 334 3.722147 GACAGATACGCATGAGGTCAAT 58.278 45.455 0.00 0.00 0.00 2.57
330 347 1.353103 GTCAATGAATCGGCAGCGG 59.647 57.895 0.00 0.00 0.00 5.52
331 348 1.819208 TCAATGAATCGGCAGCGGG 60.819 57.895 0.00 0.00 0.00 6.13
332 349 2.516930 AATGAATCGGCAGCGGGG 60.517 61.111 0.00 0.00 0.00 5.73
336 353 4.489771 AATCGGCAGCGGGGAAGG 62.490 66.667 0.00 0.00 0.00 3.46
347 364 2.526110 GGGAAGGGGTGCAAGGTT 59.474 61.111 0.00 0.00 0.00 3.50
348 365 1.152333 GGGAAGGGGTGCAAGGTTT 60.152 57.895 0.00 0.00 0.00 3.27
389 406 2.048503 GAGCACGCGGTTGTAGGT 60.049 61.111 12.47 0.00 0.00 3.08
425 442 1.375523 GATTTGGCACGAGGTCGGT 60.376 57.895 4.13 0.00 44.95 4.69
435 452 2.283676 AGGTCGGTGGATCACGGT 60.284 61.111 0.00 0.00 36.35 4.83
437 454 1.035932 AGGTCGGTGGATCACGGTAG 61.036 60.000 0.00 0.00 36.35 3.18
439 456 1.679641 TCGGTGGATCACGGTAGCA 60.680 57.895 0.00 0.00 36.35 3.49
500 519 3.813166 TGGGAACAACGAGTCTTTCATTC 59.187 43.478 0.00 0.00 37.44 2.67
509 528 7.910683 ACAACGAGTCTTTCATTCTTTCTTTTC 59.089 33.333 0.00 0.00 0.00 2.29
510 529 7.793927 ACGAGTCTTTCATTCTTTCTTTTCT 57.206 32.000 0.00 0.00 0.00 2.52
513 532 7.796197 CGAGTCTTTCATTCTTTCTTTTCTGAC 59.204 37.037 0.00 0.00 0.00 3.51
514 533 7.935520 AGTCTTTCATTCTTTCTTTTCTGACC 58.064 34.615 0.00 0.00 0.00 4.02
523 542 2.317040 TCTTTTCTGACCTGGACGAGT 58.683 47.619 0.00 0.00 0.00 4.18
524 543 2.035961 TCTTTTCTGACCTGGACGAGTG 59.964 50.000 0.00 0.00 0.00 3.51
566 585 1.982226 TCGGTTTTCCTGAAGGGATGA 59.018 47.619 0.00 0.00 44.66 2.92
567 586 2.027192 TCGGTTTTCCTGAAGGGATGAG 60.027 50.000 0.00 0.00 44.66 2.90
576 595 0.462759 GAAGGGATGAGAAGCCGTGG 60.463 60.000 0.00 0.00 0.00 4.94
601 620 6.239430 GCATCTCTCCACAATGTTAGAGGATA 60.239 42.308 17.52 4.57 36.85 2.59
670 689 2.993471 GCCCTTGCACCAATGTCGG 61.993 63.158 0.00 0.00 37.47 4.79
681 700 3.009723 ACCAATGTCGGCTCAGTATTTG 58.990 45.455 0.00 0.00 0.00 2.32
683 702 2.332063 ATGTCGGCTCAGTATTTGGG 57.668 50.000 0.00 0.00 0.00 4.12
697 716 6.385759 TCAGTATTTGGGAGGTGCTTATAGAA 59.614 38.462 0.00 0.00 0.00 2.10
733 754 4.092237 TGTGAGTATTTGCGATTTGTACCG 59.908 41.667 0.00 0.00 0.00 4.02
780 813 5.869753 AGTAGTAATCAGCAGCACAAAAG 57.130 39.130 0.00 0.00 0.00 2.27
786 819 0.110056 CAGCAGCACAAAAGCGTAGG 60.110 55.000 0.00 0.00 40.15 3.18
1008 1048 1.826024 GTGGATCGTGATGGAGGCT 59.174 57.895 0.00 0.00 0.00 4.58
1261 1301 0.796312 CCATTTCTTGGTCCGACACG 59.204 55.000 0.00 0.00 40.99 4.49
1262 1302 2.538345 CCATTTCTTGGTCCGACACGG 61.538 57.143 3.66 3.66 42.00 4.94
1584 1633 9.897744 CTTCAGCAAATCAGTCTACAAAATTTA 57.102 29.630 0.00 0.00 0.00 1.40
1590 1639 9.897744 CAAATCAGTCTACAAAATTTAGCAGAA 57.102 29.630 0.00 0.00 0.00 3.02
1798 1853 4.984785 AGATGACACGTTATTGATCCATCG 59.015 41.667 0.00 0.00 35.60 3.84
1800 1855 4.944048 TGACACGTTATTGATCCATCGAT 58.056 39.130 0.00 0.00 35.21 3.59
1811 1866 4.392047 TGATCCATCGATTGAGGATTTGG 58.608 43.478 14.95 3.71 42.03 3.28
1825 1880 7.595819 TGAGGATTTGGTTACAGAAAATGTT 57.404 32.000 0.00 0.00 39.96 2.71
1831 1886 9.092876 GATTTGGTTACAGAAAATGTTTGTTCA 57.907 29.630 0.00 0.00 39.96 3.18
1875 1930 0.326264 AGCTCCTTCATGCTCGGTTT 59.674 50.000 0.00 0.00 33.90 3.27
1890 1945 1.809684 GGTTTGTGGGAGAGCAGTAC 58.190 55.000 0.00 0.00 0.00 2.73
2023 2078 7.071698 TCTCTTCATGCTTCCTACTAATTGGAT 59.928 37.037 0.00 0.00 31.76 3.41
2034 2104 5.652014 CCTACTAATTGGATGGTTCTTGCAA 59.348 40.000 0.00 0.00 0.00 4.08
2052 2122 4.475028 TGCAATTGCTCATTTTAGTGACG 58.525 39.130 29.37 0.00 42.66 4.35
2053 2123 4.023279 TGCAATTGCTCATTTTAGTGACGT 60.023 37.500 29.37 0.00 42.66 4.34
2123 2195 5.435686 TGTATGGTGAGGTCAGCTAAAAT 57.564 39.130 10.35 0.00 44.12 1.82
2162 2234 5.562298 AGTGAAGTTTCTACCCTTTGCTA 57.438 39.130 0.00 0.00 0.00 3.49
2254 2326 6.493458 TGATCCGTATGATATCACTGGAGAAA 59.507 38.462 20.70 10.72 32.41 2.52
2402 2518 9.337396 GTAACATTCACCATCCAATCTGTAATA 57.663 33.333 0.00 0.00 0.00 0.98
2459 2575 0.179234 TTGTCTGGCTGAACGGTTCA 59.821 50.000 21.30 21.30 38.17 3.18
2497 2613 3.386726 TGATTGGTATAACGGAGGTGAGG 59.613 47.826 0.00 0.00 0.00 3.86
2505 2621 1.424638 ACGGAGGTGAGGATTATGGG 58.575 55.000 0.00 0.00 0.00 4.00
2672 2813 6.013379 TGCTTTTTGAAGGTGGGTAATCATA 58.987 36.000 0.00 0.00 0.00 2.15
2787 2930 6.938698 TTACCCAGACCTGTGTTATTTCTA 57.061 37.500 0.00 0.00 0.00 2.10
2837 2980 6.534475 TCTCGGGAGCAAATTAGTTAGTAA 57.466 37.500 0.00 0.00 0.00 2.24
2881 3024 1.379642 GCCATGTTGCTGTAGGCTCC 61.380 60.000 0.00 0.00 42.01 4.70
2889 3032 0.737715 GCTGTAGGCTCCACTTGTCG 60.738 60.000 0.00 0.00 38.06 4.35
2980 3123 6.753279 TCTGCTTTCTTTGAAATTGTGAGTTG 59.247 34.615 0.00 0.00 0.00 3.16
2981 3124 6.629128 TGCTTTCTTTGAAATTGTGAGTTGA 58.371 32.000 0.00 0.00 0.00 3.18
2984 3127 9.248291 GCTTTCTTTGAAATTGTGAGTTGATTA 57.752 29.630 0.00 0.00 0.00 1.75
3013 3156 7.986085 ATGCATGGGAGTTTAATATGTACTC 57.014 36.000 0.00 0.00 38.02 2.59
3055 3198 7.305474 ACACAATTTCGATATTTGAACTGTCC 58.695 34.615 13.37 0.00 0.00 4.02
3161 3304 5.221422 ACCAAATGTCGGAATCACAATTGTT 60.221 36.000 8.77 0.00 34.22 2.83
3170 3313 7.744715 GTCGGAATCACAATTGTTAGTACTTTG 59.255 37.037 8.77 1.26 0.00 2.77
3276 3419 2.288458 TGAACTTTGTTTCTTACGCCCG 59.712 45.455 0.00 0.00 0.00 6.13
3454 3597 7.600375 TGTCTTGTTTGTGCTATCTTCTTAGAG 59.400 37.037 0.00 0.00 32.92 2.43
3614 3757 5.760253 TCTTTTTCCACTCAGTTGAGATGTC 59.240 40.000 15.63 0.00 44.74 3.06
3638 3781 2.152016 GTGACCTAAGTTTGACCTGCC 58.848 52.381 0.00 0.00 0.00 4.85
3775 3918 5.721000 TCTTGGTTGCCCTTATGAATGATTT 59.279 36.000 0.00 0.00 0.00 2.17
3813 3958 8.632906 ATCAATGATTTAGGCCTCTTTATCTG 57.367 34.615 9.68 0.61 0.00 2.90
3841 3986 2.225019 GCTGTCATGAGAACTGGTTGTG 59.775 50.000 0.00 0.00 0.00 3.33
3851 3996 6.074648 TGAGAACTGGTTGTGGGATAATTTT 58.925 36.000 0.00 0.00 0.00 1.82
3950 4156 5.189342 TGGGTTGATTATGGAGGTTAACGTA 59.811 40.000 0.00 0.00 0.00 3.57
3951 4157 6.126710 TGGGTTGATTATGGAGGTTAACGTAT 60.127 38.462 0.00 0.00 0.00 3.06
3952 4158 6.769341 GGGTTGATTATGGAGGTTAACGTATT 59.231 38.462 0.00 0.00 0.00 1.89
3954 4160 7.496591 GGTTGATTATGGAGGTTAACGTATTGA 59.503 37.037 0.00 0.00 0.00 2.57
3955 4161 9.052759 GTTGATTATGGAGGTTAACGTATTGAT 57.947 33.333 0.00 0.00 0.00 2.57
3956 4162 9.621629 TTGATTATGGAGGTTAACGTATTGATT 57.378 29.630 0.00 0.00 0.00 2.57
3957 4163 9.621629 TGATTATGGAGGTTAACGTATTGATTT 57.378 29.630 0.00 0.00 0.00 2.17
3963 4169 8.185505 TGGAGGTTAACGTATTGATTTAAATGC 58.814 33.333 5.17 0.00 0.00 3.56
3964 4170 8.403236 GGAGGTTAACGTATTGATTTAAATGCT 58.597 33.333 5.17 0.00 0.00 3.79
3965 4171 9.783256 GAGGTTAACGTATTGATTTAAATGCTT 57.217 29.630 5.17 0.00 0.00 3.91
3966 4172 9.783256 AGGTTAACGTATTGATTTAAATGCTTC 57.217 29.630 5.17 0.00 0.00 3.86
3967 4173 9.783256 GGTTAACGTATTGATTTAAATGCTTCT 57.217 29.630 5.17 0.00 0.00 2.85
3970 4176 8.895932 AACGTATTGATTTAAATGCTTCTGTC 57.104 30.769 5.17 0.00 0.00 3.51
3971 4177 8.039603 ACGTATTGATTTAAATGCTTCTGTCA 57.960 30.769 5.17 0.00 0.00 3.58
3972 4178 8.511321 ACGTATTGATTTAAATGCTTCTGTCAA 58.489 29.630 5.17 2.39 0.00 3.18
3973 4179 9.340695 CGTATTGATTTAAATGCTTCTGTCAAA 57.659 29.630 5.17 0.00 0.00 2.69
3977 4183 8.975410 TGATTTAAATGCTTCTGTCAAATCTG 57.025 30.769 5.17 0.00 33.92 2.90
3978 4184 8.795513 TGATTTAAATGCTTCTGTCAAATCTGA 58.204 29.630 5.17 0.00 33.92 3.27
3979 4185 9.798994 GATTTAAATGCTTCTGTCAAATCTGAT 57.201 29.630 5.17 0.00 33.05 2.90
3980 4186 9.798994 ATTTAAATGCTTCTGTCAAATCTGATC 57.201 29.630 0.00 0.00 33.05 2.92
3981 4187 8.571461 TTAAATGCTTCTGTCAAATCTGATCT 57.429 30.769 0.00 0.00 33.05 2.75
3982 4188 6.680874 AATGCTTCTGTCAAATCTGATCTC 57.319 37.500 0.00 0.00 33.05 2.75
3983 4189 4.511527 TGCTTCTGTCAAATCTGATCTCC 58.488 43.478 0.00 0.00 33.05 3.71
3984 4190 4.224594 TGCTTCTGTCAAATCTGATCTCCT 59.775 41.667 0.00 0.00 33.05 3.69
3985 4191 4.571580 GCTTCTGTCAAATCTGATCTCCTG 59.428 45.833 0.00 0.00 33.05 3.86
3986 4192 4.134379 TCTGTCAAATCTGATCTCCTGC 57.866 45.455 0.00 0.00 33.05 4.85
3987 4193 2.864946 CTGTCAAATCTGATCTCCTGCG 59.135 50.000 0.00 0.00 33.05 5.18
3988 4194 2.208431 GTCAAATCTGATCTCCTGCGG 58.792 52.381 0.00 0.00 33.05 5.69
3989 4195 1.833630 TCAAATCTGATCTCCTGCGGT 59.166 47.619 0.00 0.00 0.00 5.68
3990 4196 1.938577 CAAATCTGATCTCCTGCGGTG 59.061 52.381 0.00 0.00 0.00 4.94
3991 4197 0.179062 AATCTGATCTCCTGCGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
3992 4198 1.332889 ATCTGATCTCCTGCGGTGCA 61.333 55.000 0.00 0.00 36.92 4.57
4101 4308 2.088104 AGATGAGCATTCGACCCCTA 57.912 50.000 0.00 0.00 0.00 3.53
4169 4378 3.568538 GATGCATTCTTGAAACAGCGTT 58.431 40.909 0.00 0.00 0.00 4.84
4174 4383 3.398954 TTCTTGAAACAGCGTTCACAC 57.601 42.857 0.70 0.00 37.24 3.82
4200 4409 1.673920 TGGCAGTTGAAACGAGTTTCC 59.326 47.619 21.52 10.38 46.15 3.13
4215 4435 6.109359 ACGAGTTTCCTTTATTCCATCTCTG 58.891 40.000 0.00 0.00 0.00 3.35
4217 4437 5.196695 AGTTTCCTTTATTCCATCTCTGGC 58.803 41.667 0.00 0.00 42.80 4.85
4219 4439 4.860802 TCCTTTATTCCATCTCTGGCAA 57.139 40.909 0.00 0.00 42.80 4.52
4225 4445 7.147776 CCTTTATTCCATCTCTGGCAATTTTCT 60.148 37.037 0.00 0.00 42.80 2.52
4245 4465 6.554334 TTCTAAACAAACTTCCTCCATTCG 57.446 37.500 0.00 0.00 0.00 3.34
4246 4466 5.617252 TCTAAACAAACTTCCTCCATTCGT 58.383 37.500 0.00 0.00 0.00 3.85
4264 4484 6.073058 CCATTCGTGTTGGTTCCATATATGAG 60.073 42.308 14.54 4.74 0.00 2.90
4298 4518 5.922546 TCACAAATATTTCTGTGTACACGC 58.077 37.500 20.61 0.00 42.86 5.34
4312 4532 0.320771 ACACGCGATGCTTCCTTTCT 60.321 50.000 15.93 0.00 0.00 2.52
4313 4533 0.798776 CACGCGATGCTTCCTTTCTT 59.201 50.000 15.93 0.00 0.00 2.52
4314 4534 1.197721 CACGCGATGCTTCCTTTCTTT 59.802 47.619 15.93 0.00 0.00 2.52
4315 4535 1.197721 ACGCGATGCTTCCTTTCTTTG 59.802 47.619 15.93 0.00 0.00 2.77
4316 4536 1.197721 CGCGATGCTTCCTTTCTTTGT 59.802 47.619 0.00 0.00 0.00 2.83
4317 4537 2.415168 CGCGATGCTTCCTTTCTTTGTA 59.585 45.455 0.00 0.00 0.00 2.41
4318 4538 3.063997 CGCGATGCTTCCTTTCTTTGTAT 59.936 43.478 0.00 0.00 0.00 2.29
4319 4539 4.270084 CGCGATGCTTCCTTTCTTTGTATA 59.730 41.667 0.00 0.00 0.00 1.47
4320 4540 5.502606 GCGATGCTTCCTTTCTTTGTATAC 58.497 41.667 0.00 0.00 0.00 1.47
4321 4541 5.294552 GCGATGCTTCCTTTCTTTGTATACT 59.705 40.000 4.17 0.00 0.00 2.12
4322 4542 6.183360 GCGATGCTTCCTTTCTTTGTATACTT 60.183 38.462 4.17 0.00 0.00 2.24
4323 4543 7.182761 CGATGCTTCCTTTCTTTGTATACTTG 58.817 38.462 4.17 0.00 0.00 3.16
4324 4544 7.148407 CGATGCTTCCTTTCTTTGTATACTTGT 60.148 37.037 4.17 0.00 0.00 3.16
4325 4545 7.435068 TGCTTCCTTTCTTTGTATACTTGTC 57.565 36.000 4.17 0.00 0.00 3.18
4326 4546 6.430000 TGCTTCCTTTCTTTGTATACTTGTCC 59.570 38.462 4.17 0.00 0.00 4.02
4327 4547 6.430000 GCTTCCTTTCTTTGTATACTTGTCCA 59.570 38.462 4.17 0.00 0.00 4.02
4328 4548 7.121315 GCTTCCTTTCTTTGTATACTTGTCCAT 59.879 37.037 4.17 0.00 0.00 3.41
4329 4549 8.561738 TTCCTTTCTTTGTATACTTGTCCATC 57.438 34.615 4.17 0.00 0.00 3.51
4330 4550 7.685481 TCCTTTCTTTGTATACTTGTCCATCA 58.315 34.615 4.17 0.00 0.00 3.07
4331 4551 8.328758 TCCTTTCTTTGTATACTTGTCCATCAT 58.671 33.333 4.17 0.00 0.00 2.45
4332 4552 9.613428 CCTTTCTTTGTATACTTGTCCATCATA 57.387 33.333 4.17 0.00 0.00 2.15
4343 4563 7.414222 ACTTGTCCATCATATGAAAAATGCT 57.586 32.000 9.99 0.00 0.00 3.79
4344 4564 7.844009 ACTTGTCCATCATATGAAAAATGCTT 58.156 30.769 9.99 0.00 0.00 3.91
4345 4565 8.316214 ACTTGTCCATCATATGAAAAATGCTTT 58.684 29.630 9.99 0.00 0.00 3.51
4346 4566 8.706492 TTGTCCATCATATGAAAAATGCTTTC 57.294 30.769 9.99 0.00 0.00 2.62
4347 4567 7.838884 TGTCCATCATATGAAAAATGCTTTCA 58.161 30.769 9.99 2.48 41.91 2.69
4348 4568 8.312564 TGTCCATCATATGAAAAATGCTTTCAA 58.687 29.630 9.99 0.00 41.16 2.69
4349 4569 8.598075 GTCCATCATATGAAAAATGCTTTCAAC 58.402 33.333 9.99 0.00 41.16 3.18
4350 4570 8.312564 TCCATCATATGAAAAATGCTTTCAACA 58.687 29.630 9.99 0.00 41.16 3.33
4351 4571 8.385111 CCATCATATGAAAAATGCTTTCAACAC 58.615 33.333 9.99 0.00 41.16 3.32
4352 4572 9.146984 CATCATATGAAAAATGCTTTCAACACT 57.853 29.630 9.99 0.00 41.16 3.55
4363 4583 9.956720 AAATGCTTTCAACACTATAAGATATGC 57.043 29.630 0.00 0.00 0.00 3.14
4364 4584 8.915057 ATGCTTTCAACACTATAAGATATGCT 57.085 30.769 0.00 0.00 0.00 3.79
4365 4585 8.737168 TGCTTTCAACACTATAAGATATGCTT 57.263 30.769 0.00 0.00 40.68 3.91
4366 4586 8.830580 TGCTTTCAACACTATAAGATATGCTTC 58.169 33.333 0.00 0.00 38.05 3.86
4367 4587 8.830580 GCTTTCAACACTATAAGATATGCTTCA 58.169 33.333 0.00 0.00 38.05 3.02
4394 4614 8.816640 AATTAATCACATTTTTCTCCACACAC 57.183 30.769 0.00 0.00 0.00 3.82
4395 4615 7.581213 TTAATCACATTTTTCTCCACACACT 57.419 32.000 0.00 0.00 0.00 3.55
4396 4616 8.684386 TTAATCACATTTTTCTCCACACACTA 57.316 30.769 0.00 0.00 0.00 2.74
4397 4617 7.765695 AATCACATTTTTCTCCACACACTAT 57.234 32.000 0.00 0.00 0.00 2.12
4398 4618 6.801539 TCACATTTTTCTCCACACACTATC 57.198 37.500 0.00 0.00 0.00 2.08
4399 4619 6.295249 TCACATTTTTCTCCACACACTATCA 58.705 36.000 0.00 0.00 0.00 2.15
4400 4620 6.204688 TCACATTTTTCTCCACACACTATCAC 59.795 38.462 0.00 0.00 0.00 3.06
4401 4621 5.179368 ACATTTTTCTCCACACACTATCACG 59.821 40.000 0.00 0.00 0.00 4.35
4402 4622 4.594123 TTTTCTCCACACACTATCACGA 57.406 40.909 0.00 0.00 0.00 4.35
4403 4623 4.801330 TTTCTCCACACACTATCACGAT 57.199 40.909 0.00 0.00 0.00 3.73
4404 4624 4.801330 TTCTCCACACACTATCACGATT 57.199 40.909 0.00 0.00 0.00 3.34
4405 4625 4.371855 TCTCCACACACTATCACGATTC 57.628 45.455 0.00 0.00 0.00 2.52
4406 4626 3.761752 TCTCCACACACTATCACGATTCA 59.238 43.478 0.00 0.00 0.00 2.57
4407 4627 4.402474 TCTCCACACACTATCACGATTCAT 59.598 41.667 0.00 0.00 0.00 2.57
4408 4628 5.084818 TCCACACACTATCACGATTCATT 57.915 39.130 0.00 0.00 0.00 2.57
4409 4629 5.487433 TCCACACACTATCACGATTCATTT 58.513 37.500 0.00 0.00 0.00 2.32
4410 4630 5.937540 TCCACACACTATCACGATTCATTTT 59.062 36.000 0.00 0.00 0.00 1.82
4411 4631 6.023435 CCACACACTATCACGATTCATTTTG 58.977 40.000 0.00 0.00 0.00 2.44
4412 4632 6.348458 CCACACACTATCACGATTCATTTTGT 60.348 38.462 0.00 0.00 0.00 2.83
4413 4633 6.520790 CACACACTATCACGATTCATTTTGTG 59.479 38.462 0.00 0.00 37.29 3.33
4414 4634 5.509272 CACACTATCACGATTCATTTTGTGC 59.491 40.000 0.00 0.00 32.48 4.57
4415 4635 5.030295 CACTATCACGATTCATTTTGTGCC 58.970 41.667 0.00 0.00 32.48 5.01
4416 4636 4.699735 ACTATCACGATTCATTTTGTGCCA 59.300 37.500 0.00 0.00 32.48 4.92
4417 4637 4.724074 ATCACGATTCATTTTGTGCCAT 57.276 36.364 0.00 0.00 32.48 4.40
4418 4638 5.833406 ATCACGATTCATTTTGTGCCATA 57.167 34.783 0.00 0.00 32.48 2.74
4419 4639 5.833406 TCACGATTCATTTTGTGCCATAT 57.167 34.783 0.00 0.00 32.48 1.78
4420 4640 6.934048 TCACGATTCATTTTGTGCCATATA 57.066 33.333 0.00 0.00 32.48 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.355378 TCTATGAACCAATTGGCACTGG 58.645 45.455 24.79 12.25 39.32 4.00
46 47 2.932614 CCGAAAGAAGAATGCGTCTGAT 59.067 45.455 0.00 0.00 36.40 2.90
59 60 8.145767 TCAGTTTCTATGTTACTTCCGAAAGAA 58.854 33.333 0.00 0.00 36.30 2.52
66 67 7.964604 AGTGTTCAGTTTCTATGTTACTTCC 57.035 36.000 0.00 0.00 0.00 3.46
76 77 9.677567 GATTGCAATTTTAGTGTTCAGTTTCTA 57.322 29.630 14.33 0.00 0.00 2.10
78 79 7.167468 ACGATTGCAATTTTAGTGTTCAGTTTC 59.833 33.333 14.33 0.00 0.00 2.78
84 85 9.769093 ATAGTTACGATTGCAATTTTAGTGTTC 57.231 29.630 14.33 0.00 0.00 3.18
182 184 1.153289 CCTTGCTCCATCACCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
211 216 2.123854 TCCGTCTCCATCCCCTCG 60.124 66.667 0.00 0.00 0.00 4.63
218 223 0.263172 ATCCCAGTCTCCGTCTCCAT 59.737 55.000 0.00 0.00 0.00 3.41
227 232 1.607509 CGCCATCATCATCCCAGTCTC 60.608 57.143 0.00 0.00 0.00 3.36
294 311 1.065701 GACCTCATGCGTATCTGTCGT 59.934 52.381 0.00 0.00 0.00 4.34
295 312 1.065551 TGACCTCATGCGTATCTGTCG 59.934 52.381 0.00 0.00 0.00 4.35
296 313 2.871182 TGACCTCATGCGTATCTGTC 57.129 50.000 0.00 0.00 0.00 3.51
297 314 3.132824 TCATTGACCTCATGCGTATCTGT 59.867 43.478 0.00 0.00 0.00 3.41
302 319 3.123050 CGATTCATTGACCTCATGCGTA 58.877 45.455 0.00 0.00 0.00 4.42
305 322 1.002033 GCCGATTCATTGACCTCATGC 60.002 52.381 0.00 0.00 0.00 4.06
308 325 2.013563 GCTGCCGATTCATTGACCTCA 61.014 52.381 0.00 0.00 0.00 3.86
309 326 0.659957 GCTGCCGATTCATTGACCTC 59.340 55.000 0.00 0.00 0.00 3.85
317 334 3.680620 CTTCCCCGCTGCCGATTCA 62.681 63.158 0.00 0.00 36.29 2.57
330 347 1.152333 AAACCTTGCACCCCTTCCC 60.152 57.895 0.00 0.00 0.00 3.97
331 348 0.759060 ACAAACCTTGCACCCCTTCC 60.759 55.000 0.00 0.00 0.00 3.46
332 349 0.389025 CACAAACCTTGCACCCCTTC 59.611 55.000 0.00 0.00 0.00 3.46
336 353 2.421314 GCCACAAACCTTGCACCC 59.579 61.111 0.00 0.00 0.00 4.61
339 356 3.910490 GCCGCCACAAACCTTGCA 61.910 61.111 0.00 0.00 0.00 4.08
372 389 2.048503 ACCTACAACCGCGTGCTC 60.049 61.111 4.92 0.00 0.00 4.26
376 393 2.256461 GACGACCTACAACCGCGT 59.744 61.111 4.92 0.00 37.97 6.01
379 396 1.636988 GATTGGACGACCTACAACCG 58.363 55.000 5.33 0.00 37.04 4.44
383 400 1.138036 CGCGATTGGACGACCTACA 59.862 57.895 0.00 0.00 37.04 2.74
415 432 2.697761 CGTGATCCACCGACCTCGT 61.698 63.158 0.00 0.00 37.74 4.18
425 442 1.807226 CTCGTGCTACCGTGATCCA 59.193 57.895 0.00 0.00 0.00 3.41
466 483 4.388499 TTCCCAGCCGGACTTCGC 62.388 66.667 5.05 0.00 41.83 4.70
467 484 2.434359 GTTCCCAGCCGGACTTCG 60.434 66.667 5.05 0.00 41.83 3.79
468 485 1.072505 TTGTTCCCAGCCGGACTTC 59.927 57.895 5.05 0.00 41.83 3.01
469 486 1.228154 GTTGTTCCCAGCCGGACTT 60.228 57.895 5.05 0.00 41.83 3.01
470 487 2.430367 GTTGTTCCCAGCCGGACT 59.570 61.111 5.05 0.00 41.83 3.85
471 488 3.047877 CGTTGTTCCCAGCCGGAC 61.048 66.667 5.05 0.00 41.83 4.79
472 489 3.234630 CTCGTTGTTCCCAGCCGGA 62.235 63.158 5.05 0.00 39.68 5.14
473 490 2.742372 CTCGTTGTTCCCAGCCGG 60.742 66.667 0.00 0.00 0.00 6.13
474 491 2.027625 GACTCGTTGTTCCCAGCCG 61.028 63.158 0.00 0.00 0.00 5.52
475 492 0.250338 AAGACTCGTTGTTCCCAGCC 60.250 55.000 0.00 0.00 0.00 4.85
476 493 1.531578 GAAAGACTCGTTGTTCCCAGC 59.468 52.381 0.00 0.00 0.00 4.85
477 494 2.833794 TGAAAGACTCGTTGTTCCCAG 58.166 47.619 0.00 0.00 0.00 4.45
478 495 2.992124 TGAAAGACTCGTTGTTCCCA 57.008 45.000 0.00 0.00 0.00 4.37
488 505 8.073167 GGTCAGAAAAGAAAGAATGAAAGACTC 58.927 37.037 0.00 0.00 0.00 3.36
500 519 3.728845 TCGTCCAGGTCAGAAAAGAAAG 58.271 45.455 0.00 0.00 0.00 2.62
509 528 0.962489 AACTCACTCGTCCAGGTCAG 59.038 55.000 0.00 0.00 0.00 3.51
510 529 1.410004 AAACTCACTCGTCCAGGTCA 58.590 50.000 0.00 0.00 0.00 4.02
534 553 1.152989 AAAACCGACGCGTTGTGCTA 61.153 50.000 24.28 0.00 43.27 3.49
543 562 1.574702 CCCTTCAGGAAAACCGACGC 61.575 60.000 0.00 0.00 38.24 5.19
567 586 1.522580 GGAGAGATGCCACGGCTTC 60.523 63.158 14.47 14.47 43.07 3.86
576 595 4.125703 CCTCTAACATTGTGGAGAGATGC 58.874 47.826 22.00 0.00 35.07 3.91
652 671 2.568090 CGACATTGGTGCAAGGGC 59.432 61.111 0.00 0.00 41.68 5.19
653 672 2.993471 GCCGACATTGGTGCAAGGG 61.993 63.158 0.00 0.00 28.83 3.95
654 673 1.926511 GAGCCGACATTGGTGCAAGG 61.927 60.000 0.00 0.00 0.00 3.61
659 678 2.315925 ATACTGAGCCGACATTGGTG 57.684 50.000 0.00 0.00 0.00 4.17
661 680 2.355756 CCAAATACTGAGCCGACATTGG 59.644 50.000 0.00 0.00 0.00 3.16
662 681 2.355756 CCCAAATACTGAGCCGACATTG 59.644 50.000 0.00 0.00 0.00 2.82
664 683 1.837439 TCCCAAATACTGAGCCGACAT 59.163 47.619 0.00 0.00 0.00 3.06
670 689 1.065126 AGCACCTCCCAAATACTGAGC 60.065 52.381 0.00 0.00 0.00 4.26
681 700 7.389053 CACATCTTATTTCTATAAGCACCTCCC 59.611 40.741 0.00 0.00 41.92 4.30
683 702 8.894768 ACACATCTTATTTCTATAAGCACCTC 57.105 34.615 0.00 0.00 41.92 3.85
697 716 8.551205 CGCAAATACTCACATACACATCTTATT 58.449 33.333 0.00 0.00 0.00 1.40
714 735 3.998341 ACACGGTACAAATCGCAAATACT 59.002 39.130 0.00 0.00 0.00 2.12
719 740 4.808077 TTTAACACGGTACAAATCGCAA 57.192 36.364 0.00 0.00 0.00 4.85
756 777 6.673316 GCTTTTGTGCTGCTGATTACTACTAC 60.673 42.308 0.00 0.00 0.00 2.73
757 778 5.351465 GCTTTTGTGCTGCTGATTACTACTA 59.649 40.000 0.00 0.00 0.00 1.82
763 796 1.879380 ACGCTTTTGTGCTGCTGATTA 59.121 42.857 0.00 0.00 0.00 1.75
765 798 1.466167 CTACGCTTTTGTGCTGCTGAT 59.534 47.619 0.00 0.00 0.00 2.90
767 800 0.110056 CCTACGCTTTTGTGCTGCTG 60.110 55.000 0.00 0.00 0.00 4.41
769 802 0.591170 TTCCTACGCTTTTGTGCTGC 59.409 50.000 0.00 0.00 0.00 5.25
780 813 3.500680 TGTTTCTGTTCCATTTCCTACGC 59.499 43.478 0.00 0.00 0.00 4.42
786 819 7.922811 AGATTTTCTGTGTTTCTGTTCCATTTC 59.077 33.333 0.00 0.00 0.00 2.17
799 832 6.980397 CCTGTTGCTTAAAGATTTTCTGTGTT 59.020 34.615 0.00 0.00 0.00 3.32
1077 1117 3.674050 GAGCCTGGGGAGGTACGGA 62.674 68.421 0.00 0.00 0.00 4.69
1261 1301 6.073980 TGCTATCGCTACGAAATTATTTGACC 60.074 38.462 0.00 0.00 39.99 4.02
1262 1302 6.873656 TGCTATCGCTACGAAATTATTTGAC 58.126 36.000 0.00 0.00 39.99 3.18
1263 1303 7.471657 TTGCTATCGCTACGAAATTATTTGA 57.528 32.000 0.00 0.00 39.99 2.69
1265 1305 9.730420 AAATTTGCTATCGCTACGAAATTATTT 57.270 25.926 0.00 0.00 39.99 1.40
1266 1306 9.169468 CAAATTTGCTATCGCTACGAAATTATT 57.831 29.630 5.01 0.00 39.99 1.40
1270 1310 6.358118 TCAAATTTGCTATCGCTACGAAAT 57.642 33.333 13.54 0.00 39.99 2.17
1495 1544 1.743623 CCTGTCGGCGCACCAATAA 60.744 57.895 10.83 0.00 34.57 1.40
1556 1605 7.750229 TTTTGTAGACTGATTTGCTGAAGAT 57.250 32.000 0.00 0.00 0.00 2.40
1721 1771 7.449934 AACGCACTTTAAAAACAATGAAGAG 57.550 32.000 0.00 0.00 0.00 2.85
1775 1830 4.984785 CGATGGATCAATAACGTGTCATCT 59.015 41.667 0.00 0.00 0.00 2.90
1798 1853 8.306761 ACATTTTCTGTAACCAAATCCTCAATC 58.693 33.333 0.00 0.00 35.91 2.67
1800 1855 7.595819 ACATTTTCTGTAACCAAATCCTCAA 57.404 32.000 0.00 0.00 35.91 3.02
1811 1866 9.914923 GGAAATTGAACAAACATTTTCTGTAAC 57.085 29.630 0.00 0.00 38.76 2.50
1825 1880 3.558608 ATCCCCCTGGAAATTGAACAA 57.441 42.857 0.00 0.00 45.98 2.83
1831 1886 2.456577 CACGAAATCCCCCTGGAAATT 58.543 47.619 0.00 0.00 45.98 1.82
1875 1930 1.595993 GCTCGTACTGCTCTCCCACA 61.596 60.000 0.00 0.00 0.00 4.17
1890 1945 4.243007 TGACATATACACTGATGGCTCG 57.757 45.455 0.00 0.00 31.86 5.03
1976 2031 7.349598 AGAGAATAACTATCATTTGGGCACTT 58.650 34.615 0.00 0.00 0.00 3.16
2023 2078 4.339872 AAATGAGCAATTGCAAGAACCA 57.660 36.364 30.89 17.63 45.16 3.67
2068 2140 5.897377 AACACACTATGAAATGGGTTAGC 57.103 39.130 0.00 0.00 40.66 3.09
2162 2234 8.149973 ACTTCAGTACGAAAAATTATGTGTGT 57.850 30.769 0.00 0.00 31.71 3.72
2193 2265 5.565509 TCTGCAATACCAACCTGTTGAATA 58.434 37.500 11.47 4.40 42.93 1.75
2254 2326 1.770658 TGAGAGCCCATCGGATGAAAT 59.229 47.619 19.30 4.20 0.00 2.17
2402 2518 7.401493 ACCAGACTATCTATTAAGGCAGCATAT 59.599 37.037 0.00 0.00 0.00 1.78
2632 2773 5.574891 AAAAGCACATTATCGCATACCAA 57.425 34.783 0.00 0.00 0.00 3.67
2634 2775 5.577835 TCAAAAAGCACATTATCGCATACC 58.422 37.500 0.00 0.00 0.00 2.73
2635 2776 6.197096 CCTTCAAAAAGCACATTATCGCATAC 59.803 38.462 0.00 0.00 0.00 2.39
2636 2777 6.127758 ACCTTCAAAAAGCACATTATCGCATA 60.128 34.615 0.00 0.00 0.00 3.14
2637 2778 5.104374 CCTTCAAAAAGCACATTATCGCAT 58.896 37.500 0.00 0.00 0.00 4.73
2638 2779 4.022416 ACCTTCAAAAAGCACATTATCGCA 60.022 37.500 0.00 0.00 0.00 5.10
2639 2780 4.324402 CACCTTCAAAAAGCACATTATCGC 59.676 41.667 0.00 0.00 0.00 4.58
2640 2781 4.858692 CCACCTTCAAAAAGCACATTATCG 59.141 41.667 0.00 0.00 0.00 2.92
2787 2930 8.720562 GCTGGTCAACAAATTTGCTAAATATTT 58.279 29.630 18.12 5.89 0.00 1.40
2837 2980 0.726827 CGCGCTGGTGTTATTCATGT 59.273 50.000 5.56 0.00 0.00 3.21
2881 3024 0.319211 TAACGTGAGGGCGACAAGTG 60.319 55.000 0.00 0.00 35.59 3.16
2889 3032 6.261381 TGGAAAATAACATATAACGTGAGGGC 59.739 38.462 0.00 0.00 0.00 5.19
2984 3127 8.253867 ACATATTAAACTCCCATGCATTCATT 57.746 30.769 0.00 0.00 0.00 2.57
3036 3179 4.823157 TCCGGACAGTTCAAATATCGAAA 58.177 39.130 0.00 0.00 0.00 3.46
3037 3180 4.459390 TCCGGACAGTTCAAATATCGAA 57.541 40.909 0.00 0.00 0.00 3.71
3055 3198 8.726988 CCAATTAAAATACACCCTACATATCCG 58.273 37.037 0.00 0.00 0.00 4.18
3124 3267 5.124776 CCGACATTTGGTACCACATAAACAT 59.875 40.000 16.04 0.00 0.00 2.71
3125 3268 4.456222 CCGACATTTGGTACCACATAAACA 59.544 41.667 16.04 0.00 0.00 2.83
3467 3610 4.229876 GAGAACAAGCATTTTACACAGCC 58.770 43.478 0.00 0.00 0.00 4.85
3614 3757 4.691216 GCAGGTCAAACTTAGGTCACTTAG 59.309 45.833 0.00 0.00 0.00 2.18
3638 3781 9.935241 ATAGTACTGGTTATTTATGCATCAGAG 57.065 33.333 14.26 0.22 0.00 3.35
3813 3958 3.072944 AGTTCTCATGACAGCAAGAAGC 58.927 45.455 0.00 0.00 46.19 3.86
3841 3986 8.962884 AATGCCAACTATTTCAAAATTATCCC 57.037 30.769 0.00 0.00 0.00 3.85
3851 3996 5.538053 TCTGTCCAAAATGCCAACTATTTCA 59.462 36.000 0.00 0.00 0.00 2.69
3951 4157 9.414295 CAGATTTGACAGAAGCATTTAAATCAA 57.586 29.630 0.00 0.00 36.20 2.57
3952 4158 8.795513 TCAGATTTGACAGAAGCATTTAAATCA 58.204 29.630 0.00 0.00 36.20 2.57
3954 4160 9.798994 GATCAGATTTGACAGAAGCATTTAAAT 57.201 29.630 0.00 0.00 35.83 1.40
3955 4161 9.017509 AGATCAGATTTGACAGAAGCATTTAAA 57.982 29.630 0.00 0.00 35.83 1.52
3956 4162 8.571461 AGATCAGATTTGACAGAAGCATTTAA 57.429 30.769 0.00 0.00 35.83 1.52
3957 4163 7.281774 GGAGATCAGATTTGACAGAAGCATTTA 59.718 37.037 0.00 0.00 35.83 1.40
3958 4164 6.095160 GGAGATCAGATTTGACAGAAGCATTT 59.905 38.462 0.00 0.00 35.83 2.32
3959 4165 5.589452 GGAGATCAGATTTGACAGAAGCATT 59.411 40.000 0.00 0.00 35.83 3.56
3960 4166 5.104444 AGGAGATCAGATTTGACAGAAGCAT 60.104 40.000 0.00 0.00 35.83 3.79
3961 4167 4.224594 AGGAGATCAGATTTGACAGAAGCA 59.775 41.667 0.00 0.00 35.83 3.91
3962 4168 4.571580 CAGGAGATCAGATTTGACAGAAGC 59.428 45.833 0.00 0.00 35.83 3.86
3963 4169 4.571580 GCAGGAGATCAGATTTGACAGAAG 59.428 45.833 0.00 0.00 35.83 2.85
3964 4170 4.511527 GCAGGAGATCAGATTTGACAGAA 58.488 43.478 0.00 0.00 35.83 3.02
3965 4171 3.429960 CGCAGGAGATCAGATTTGACAGA 60.430 47.826 0.00 0.00 35.83 3.41
3966 4172 2.864946 CGCAGGAGATCAGATTTGACAG 59.135 50.000 0.00 0.00 35.83 3.51
3967 4173 2.897436 CGCAGGAGATCAGATTTGACA 58.103 47.619 0.00 0.00 35.83 3.58
4109 4316 7.329717 ACTTTTTGATCGAACACTCATCTACTC 59.670 37.037 0.00 0.00 0.00 2.59
4169 4378 2.391130 AACTGCCAAGGGGGTGTGA 61.391 57.895 0.00 0.00 39.65 3.58
4174 4383 1.805428 CGTTTCAACTGCCAAGGGGG 61.805 60.000 0.00 0.00 40.85 5.40
4200 4409 7.779073 AGAAAATTGCCAGAGATGGAATAAAG 58.221 34.615 0.00 0.00 0.00 1.85
4215 4435 6.423905 GGAGGAAGTTTGTTTAGAAAATTGCC 59.576 38.462 1.64 0.00 33.35 4.52
4217 4437 9.546428 AATGGAGGAAGTTTGTTTAGAAAATTG 57.454 29.630 0.00 0.00 0.00 2.32
4219 4439 8.082242 CGAATGGAGGAAGTTTGTTTAGAAAAT 58.918 33.333 0.00 0.00 0.00 1.82
4225 4445 5.127491 ACACGAATGGAGGAAGTTTGTTTA 58.873 37.500 0.00 0.00 0.00 2.01
4245 4465 5.531287 GGAACCTCATATATGGAACCAACAC 59.469 44.000 12.78 0.00 0.00 3.32
4246 4466 5.431731 AGGAACCTCATATATGGAACCAACA 59.568 40.000 12.78 0.00 0.00 3.33
4264 4484 8.739972 ACAGAAATATTTGTGATTGTAGGAACC 58.260 33.333 26.90 0.00 35.27 3.62
4298 4518 6.910536 AGTATACAAAGAAAGGAAGCATCG 57.089 37.500 5.50 0.00 0.00 3.84
4317 4537 9.139734 AGCATTTTTCATATGATGGACAAGTAT 57.860 29.630 6.17 0.00 0.00 2.12
4318 4538 8.523915 AGCATTTTTCATATGATGGACAAGTA 57.476 30.769 6.17 0.00 0.00 2.24
4319 4539 7.414222 AGCATTTTTCATATGATGGACAAGT 57.586 32.000 6.17 0.00 0.00 3.16
4320 4540 8.712285 AAAGCATTTTTCATATGATGGACAAG 57.288 30.769 6.17 0.00 31.62 3.16
4321 4541 8.312564 TGAAAGCATTTTTCATATGATGGACAA 58.687 29.630 6.17 0.00 39.27 3.18
4322 4542 7.838884 TGAAAGCATTTTTCATATGATGGACA 58.161 30.769 6.17 0.00 39.27 4.02
4323 4543 8.598075 GTTGAAAGCATTTTTCATATGATGGAC 58.402 33.333 6.17 0.00 39.27 4.02
4324 4544 8.312564 TGTTGAAAGCATTTTTCATATGATGGA 58.687 29.630 6.17 0.00 39.27 3.41
4325 4545 8.385111 GTGTTGAAAGCATTTTTCATATGATGG 58.615 33.333 6.17 0.00 39.27 3.51
4326 4546 9.146984 AGTGTTGAAAGCATTTTTCATATGATG 57.853 29.630 6.17 2.90 39.27 3.07
4337 4557 9.956720 GCATATCTTATAGTGTTGAAAGCATTT 57.043 29.630 0.00 0.00 43.98 2.32
4338 4558 9.347240 AGCATATCTTATAGTGTTGAAAGCATT 57.653 29.630 0.00 0.00 0.00 3.56
4339 4559 8.915057 AGCATATCTTATAGTGTTGAAAGCAT 57.085 30.769 0.00 0.00 0.00 3.79
4340 4560 8.737168 AAGCATATCTTATAGTGTTGAAAGCA 57.263 30.769 0.00 0.00 32.10 3.91
4341 4561 8.830580 TGAAGCATATCTTATAGTGTTGAAAGC 58.169 33.333 0.00 0.00 34.56 3.51
4368 4588 9.906660 GTGTGTGGAGAAAAATGTGATTAATTA 57.093 29.630 0.00 0.00 0.00 1.40
4369 4589 8.641541 AGTGTGTGGAGAAAAATGTGATTAATT 58.358 29.630 0.00 0.00 0.00 1.40
4370 4590 8.181904 AGTGTGTGGAGAAAAATGTGATTAAT 57.818 30.769 0.00 0.00 0.00 1.40
4371 4591 7.581213 AGTGTGTGGAGAAAAATGTGATTAA 57.419 32.000 0.00 0.00 0.00 1.40
4372 4592 8.862325 ATAGTGTGTGGAGAAAAATGTGATTA 57.138 30.769 0.00 0.00 0.00 1.75
4373 4593 7.448161 TGATAGTGTGTGGAGAAAAATGTGATT 59.552 33.333 0.00 0.00 0.00 2.57
4374 4594 6.942005 TGATAGTGTGTGGAGAAAAATGTGAT 59.058 34.615 0.00 0.00 0.00 3.06
4375 4595 6.204688 GTGATAGTGTGTGGAGAAAAATGTGA 59.795 38.462 0.00 0.00 0.00 3.58
4376 4596 6.373779 GTGATAGTGTGTGGAGAAAAATGTG 58.626 40.000 0.00 0.00 0.00 3.21
4377 4597 5.179368 CGTGATAGTGTGTGGAGAAAAATGT 59.821 40.000 0.00 0.00 0.00 2.71
4378 4598 5.408299 TCGTGATAGTGTGTGGAGAAAAATG 59.592 40.000 0.00 0.00 0.00 2.32
4379 4599 5.547465 TCGTGATAGTGTGTGGAGAAAAAT 58.453 37.500 0.00 0.00 0.00 1.82
4380 4600 4.951254 TCGTGATAGTGTGTGGAGAAAAA 58.049 39.130 0.00 0.00 0.00 1.94
4381 4601 4.594123 TCGTGATAGTGTGTGGAGAAAA 57.406 40.909 0.00 0.00 0.00 2.29
4382 4602 4.801330 ATCGTGATAGTGTGTGGAGAAA 57.199 40.909 0.00 0.00 0.00 2.52
4383 4603 4.219725 TGAATCGTGATAGTGTGTGGAGAA 59.780 41.667 0.00 0.00 0.00 2.87
4384 4604 3.761752 TGAATCGTGATAGTGTGTGGAGA 59.238 43.478 0.00 0.00 0.00 3.71
4385 4605 4.110036 TGAATCGTGATAGTGTGTGGAG 57.890 45.455 0.00 0.00 0.00 3.86
4386 4606 4.736126 ATGAATCGTGATAGTGTGTGGA 57.264 40.909 0.00 0.00 0.00 4.02
4387 4607 5.801350 AAATGAATCGTGATAGTGTGTGG 57.199 39.130 0.00 0.00 0.00 4.17
4388 4608 6.520790 CACAAAATGAATCGTGATAGTGTGTG 59.479 38.462 0.00 0.00 0.00 3.82
4389 4609 6.602179 CACAAAATGAATCGTGATAGTGTGT 58.398 36.000 0.00 0.00 0.00 3.72
4390 4610 5.509272 GCACAAAATGAATCGTGATAGTGTG 59.491 40.000 0.00 0.00 36.57 3.82
4391 4611 5.391950 GGCACAAAATGAATCGTGATAGTGT 60.392 40.000 0.00 0.00 0.00 3.55
4392 4612 5.030295 GGCACAAAATGAATCGTGATAGTG 58.970 41.667 0.00 0.00 0.00 2.74
4393 4613 4.699735 TGGCACAAAATGAATCGTGATAGT 59.300 37.500 0.00 0.00 31.92 2.12
4394 4614 5.233957 TGGCACAAAATGAATCGTGATAG 57.766 39.130 0.00 0.00 31.92 2.08


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

AutoCloner maintained by Alex Coulton.