Multiple sequence alignment - TraesCS5D01G019400

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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 TraesCS5D01G019400 chr5D 100.000 5045 0 0 1 5045 11953687 11948643 0.000000e+00 9317
1 TraesCS5D01G019400 chr5B 93.590 4259 231 22 1 4238 11775486 11771249 0.000000e+00 6314
2 TraesCS5D01G019400 chr5B 79.545 396 30 22 4612 5001 11770725 11770375 8.440000e-58 235
3 TraesCS5D01G019400 chr5B 85.500 200 16 3 4409 4603 11770886 11770695 3.980000e-46 196
4 TraesCS5D01G019400 chr1A 93.503 3694 180 28 578 4238 99871528 99867862 0.000000e+00 5437
5 TraesCS5D01G019400 chr1A 87.903 248 24 3 4289 4536 99867749 99867508 2.300000e-73 287
6 TraesCS5D01G019400 chr1A 82.937 252 19 9 4624 4856 99867505 99867259 6.620000e-49 206
7 TraesCS5D01G019400 chr1A 83.761 117 9 9 3668 3776 592529379 592529265 8.940000e-18 102
8 TraesCS5D01G019400 chr1B 88.542 96 7 4 3668 3761 687276772 687276679 4.130000e-21 113
9 TraesCS5D01G019400 chr4D 87.368 95 10 2 3668 3761 397094309 397094216 1.920000e-19 108
10 TraesCS5D01G019400 chr7D 84.821 112 9 6 3640 3747 407071755 407071648 6.910000e-19 106
11 TraesCS5D01G019400 chr7B 84.821 112 9 6 3640 3747 418049155 418049048 6.910000e-19 106
12 TraesCS5D01G019400 chr7A 84.821 112 9 6 3640 3747 464572761 464572654 6.910000e-19 106
13 TraesCS5D01G019400 chr4A 82.759 116 15 3 3668 3779 54107181 54107067 1.160000e-16 99


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 TraesCS5D01G019400 chr5D 11948643 11953687 5044 True 9317.000000 9317 100.000000 1 5045 1 chr5D.!!$R1 5044
1 TraesCS5D01G019400 chr5B 11770375 11775486 5111 True 2248.333333 6314 86.211667 1 5001 3 chr5B.!!$R1 5000
2 TraesCS5D01G019400 chr1A 99867259 99871528 4269 True 1976.666667 5437 88.114333 578 4856 3 chr1A.!!$R2 4278

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
79 82 0.532573 TCTCGCCTTGGATCACAGTC 59.467 55.0 0.00 0.0 0.00 3.51 F
145 148 1.079503 GGCAATCAGGAGAACGACAC 58.920 55.0 0.00 0.0 0.00 3.67 F
1783 1811 0.179124 GCTCTACAACTGCTCCCTCG 60.179 60.0 0.00 0.0 0.00 4.63 F
2442 2470 0.179026 AGCTCTACGGCGAGATACCA 60.179 55.0 16.62 0.0 37.29 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1774 0.031994 GCTCGAGGCTCTGGAGATTC 59.968 60.000 19.63 2.74 38.34 2.52 R
1953 1981 0.250513 GGTTGACGAGCTCCCTGAAT 59.749 55.000 8.47 0.00 0.00 2.57 R
2688 2719 0.953960 GCCGATTGTCCGACAGGTTT 60.954 55.000 0.64 0.00 39.05 3.27 R
4141 4181 1.000843 ACATGCTCTACACACGCTTGA 59.999 47.619 0.00 0.00 34.24 3.02 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
30 32 1.632589 TGAGAAGTCAGGTGCTAGCA 58.367 50.000 14.93 14.93 0.00 3.49
32 34 1.548269 GAGAAGTCAGGTGCTAGCAGT 59.452 52.381 20.03 5.55 0.00 4.40
43 45 0.972983 GCTAGCAGTCTCCACCTCCA 60.973 60.000 10.63 0.00 0.00 3.86
65 68 2.436824 GGGCCCTTTCACTCTCGC 60.437 66.667 17.04 0.00 0.00 5.03
67 70 2.665603 GCCCTTTCACTCTCGCCT 59.334 61.111 0.00 0.00 0.00 5.52
70 73 0.674895 CCCTTTCACTCTCGCCTTGG 60.675 60.000 0.00 0.00 0.00 3.61
79 82 0.532573 TCTCGCCTTGGATCACAGTC 59.467 55.000 0.00 0.00 0.00 3.51
94 97 2.743928 GTCAGCAAGGTGGAGCCG 60.744 66.667 0.00 0.00 43.70 5.52
95 98 4.704833 TCAGCAAGGTGGAGCCGC 62.705 66.667 0.00 0.00 43.70 6.53
116 119 3.411446 CCAACCTAAGAGCACACATGAA 58.589 45.455 0.00 0.00 0.00 2.57
117 120 3.189287 CCAACCTAAGAGCACACATGAAC 59.811 47.826 0.00 0.00 0.00 3.18
122 125 1.888215 AGAGCACACATGAACACTGG 58.112 50.000 0.00 0.00 0.00 4.00
145 148 1.079503 GGCAATCAGGAGAACGACAC 58.920 55.000 0.00 0.00 0.00 3.67
190 193 2.508526 CAAACTTCCTGAGGACCCAAG 58.491 52.381 0.00 0.00 0.00 3.61
192 195 1.301293 CTTCCTGAGGACCCAAGCC 59.699 63.158 0.00 0.00 0.00 4.35
206 209 2.053865 AAGCCATCGCCCCACAATG 61.054 57.895 0.00 0.00 34.57 2.82
241 244 2.839486 TTCGACACTCAGAGGCAAAT 57.161 45.000 1.53 0.00 0.00 2.32
242 245 2.370281 TCGACACTCAGAGGCAAATC 57.630 50.000 1.53 0.00 0.00 2.17
243 246 1.618343 TCGACACTCAGAGGCAAATCA 59.382 47.619 1.53 0.00 0.00 2.57
244 247 2.234661 TCGACACTCAGAGGCAAATCAT 59.765 45.455 1.53 0.00 0.00 2.45
279 284 8.729805 ATTTCAAAATGGCAAGTCACTAAAAA 57.270 26.923 0.00 0.00 0.00 1.94
475 480 2.247358 TCCCTTCCACAAAAATCAGCC 58.753 47.619 0.00 0.00 0.00 4.85
483 488 2.564062 CACAAAAATCAGCCTGGGTCAT 59.436 45.455 0.00 0.00 0.00 3.06
517 522 1.369091 CGTCCGATTTTGGAGGCCTG 61.369 60.000 12.00 0.00 39.14 4.85
518 523 1.378514 TCCGATTTTGGAGGCCTGC 60.379 57.895 18.95 18.95 33.05 4.85
533 538 1.674764 CCTGCGGCTGAGATCTCTGT 61.675 60.000 25.16 0.00 0.00 3.41
568 573 2.053244 ACCTGATAGGCCTCAATCCAG 58.947 52.381 9.68 10.51 39.63 3.86
571 576 2.702478 CTGATAGGCCTCAATCCAGACA 59.298 50.000 9.68 0.00 0.00 3.41
574 579 1.225704 GGCCTCAATCCAGACAGGG 59.774 63.158 0.00 0.00 38.24 4.45
599 604 2.267324 GGCACTCCAGCAGGTCTC 59.733 66.667 0.00 0.00 35.83 3.36
765 770 8.655935 ATTTGGAGGTTAGAAATCACTGAAAT 57.344 30.769 0.00 0.00 0.00 2.17
771 776 9.185192 GAGGTTAGAAATCACTGAAATTTTGTG 57.815 33.333 15.01 15.01 0.00 3.33
848 854 5.766670 TGTCTCTTGCATGAATCAAAGAGTT 59.233 36.000 17.66 0.00 0.00 3.01
851 857 7.332926 GTCTCTTGCATGAATCAAAGAGTTCTA 59.667 37.037 17.66 2.26 0.00 2.10
866 872 8.599774 CAAAGAGTTCTAAAGCTAAGCACTATC 58.400 37.037 2.07 0.00 0.00 2.08
880 886 6.387041 AAGCACTATCGTTAGCACACTATA 57.613 37.500 0.30 0.00 0.00 1.31
1063 1091 4.465446 CCGCCCTCCTCCTCTCCA 62.465 72.222 0.00 0.00 0.00 3.86
1066 1094 2.041405 CCCTCCTCCTCTCCACCC 60.041 72.222 0.00 0.00 0.00 4.61
1254 1282 2.408022 GCGCTCTCCGTACACGAT 59.592 61.111 0.00 0.00 43.02 3.73
1629 1657 1.439644 CAAGCTCTACCTCTCCGCC 59.560 63.158 0.00 0.00 0.00 6.13
1722 1750 3.470888 CCCCTCACCGGCGAGATT 61.471 66.667 21.15 0.00 34.79 2.40
1725 1753 2.427245 CCTCACCGGCGAGATTCCT 61.427 63.158 21.15 0.00 34.79 3.36
1783 1811 0.179124 GCTCTACAACTGCTCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
1985 2013 1.335597 CGTCAACCTGTCGCTCTACAA 60.336 52.381 0.00 0.00 0.00 2.41
1991 2019 2.061773 CCTGTCGCTCTACAACAACAG 58.938 52.381 0.00 0.00 35.13 3.16
2062 2090 1.005394 ATCGACGTGTCCACCAACC 60.005 57.895 0.00 0.00 0.00 3.77
2063 2091 1.469335 ATCGACGTGTCCACCAACCT 61.469 55.000 0.00 0.00 0.00 3.50
2173 2201 4.746951 CGACGTACGCGACCTGCA 62.747 66.667 21.80 0.00 46.97 4.41
2247 2275 2.272146 GGAATCTGGGCGCTTCCA 59.728 61.111 17.74 12.13 38.64 3.53
2249 2277 1.657751 GGAATCTGGGCGCTTCCAAC 61.658 60.000 17.74 5.70 38.64 3.77
2250 2278 0.960364 GAATCTGGGCGCTTCCAACA 60.960 55.000 7.64 0.00 36.21 3.33
2289 2317 2.203294 GGCAACCAGTTCACCGGT 60.203 61.111 0.00 0.00 36.98 5.28
2296 2324 2.047274 AGTTCACCGGTGGCATCG 60.047 61.111 33.40 14.40 0.00 3.84
2370 2398 2.710724 AATTCTCCGGCGCGATACCC 62.711 60.000 12.10 0.00 0.00 3.69
2442 2470 0.179026 AGCTCTACGGCGAGATACCA 60.179 55.000 16.62 0.00 37.29 3.25
2443 2471 0.238817 GCTCTACGGCGAGATACCAG 59.761 60.000 16.62 1.34 32.74 4.00
2465 2493 2.046023 CATCGGCAAGCTGGTCCA 60.046 61.111 0.37 0.00 0.00 4.02
2472 2500 0.809241 GCAAGCTGGTCCATCTCGAG 60.809 60.000 5.93 5.93 0.00 4.04
2484 2512 1.000385 CATCTCGAGAGCCTGGACATC 60.000 57.143 21.52 0.00 0.00 3.06
2561 2589 2.885644 CACGATGAACCTCGCCGG 60.886 66.667 0.00 0.00 42.35 6.13
2572 2600 3.589654 CTCGCCGGGAACAAGCTCA 62.590 63.158 2.18 0.00 0.00 4.26
2615 2646 3.249687 GGGGCACGAGTCTGAATTT 57.750 52.632 0.00 0.00 0.00 1.82
2620 2651 2.350772 GGCACGAGTCTGAATTTGTTGG 60.351 50.000 0.00 0.00 0.00 3.77
2634 2665 4.582701 TTTGTTGGACATTTCGAGCAAT 57.417 36.364 0.00 0.00 32.20 3.56
2643 2674 3.686726 ACATTTCGAGCAATGAACTCTCC 59.313 43.478 15.09 0.00 37.55 3.71
2698 2729 1.822990 TGAGCTACCTAAACCTGTCGG 59.177 52.381 0.00 0.00 0.00 4.79
2700 2731 1.823610 AGCTACCTAAACCTGTCGGAC 59.176 52.381 0.00 0.00 0.00 4.79
2703 2734 3.369157 GCTACCTAAACCTGTCGGACAAT 60.369 47.826 12.54 0.40 0.00 2.71
2793 2824 3.276091 CTGTGCGCCAACAACGGA 61.276 61.111 4.18 0.00 0.00 4.69
3592 3623 2.202932 CCAAGATCCTGGACGCCG 60.203 66.667 4.10 0.00 38.96 6.46
3593 3624 2.202932 CAAGATCCTGGACGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
4071 4111 7.406553 CGTTCAAAGTTATTTCAGTGTCTGAA 58.593 34.615 7.92 7.92 46.93 3.02
4088 4128 5.827267 TGTCTGAACTGAACATTTTGGATCA 59.173 36.000 0.00 0.00 0.00 2.92
4089 4129 6.016860 TGTCTGAACTGAACATTTTGGATCAG 60.017 38.462 0.00 9.60 39.66 2.90
4092 4132 2.095059 ACTGAACATTTTGGATCAGCGC 60.095 45.455 0.00 0.00 38.31 5.92
4133 4173 2.755876 ACGGCCGAGATCTGAGCA 60.756 61.111 35.90 0.00 0.00 4.26
4141 4181 2.510238 GATCTGAGCAGGCGCGTT 60.510 61.111 8.43 0.00 45.49 4.84
4185 4225 5.860611 AGCATGTGGTGTGTTAGTAGTAAA 58.139 37.500 0.00 0.00 0.00 2.01
4186 4226 5.932303 AGCATGTGGTGTGTTAGTAGTAAAG 59.068 40.000 0.00 0.00 0.00 1.85
4188 4228 6.594159 GCATGTGGTGTGTTAGTAGTAAAGAT 59.406 38.462 0.00 0.00 0.00 2.40
4189 4229 7.762615 GCATGTGGTGTGTTAGTAGTAAAGATA 59.237 37.037 0.00 0.00 0.00 1.98
4238 4278 3.882888 CCAACCAATCTTGTGTGTGTACT 59.117 43.478 0.00 0.00 0.00 2.73
4239 4279 4.024048 CCAACCAATCTTGTGTGTGTACTC 60.024 45.833 0.00 0.00 0.00 2.59
4257 4320 4.467198 ACTCGTAGGAAATTACCAGTGG 57.533 45.455 7.91 7.91 0.00 4.00
4354 4507 5.128919 GGCCAAACATACATTCTCTCTGAT 58.871 41.667 0.00 0.00 0.00 2.90
4384 4537 1.562942 TCTCAGCCTGGATTTCTGCAT 59.437 47.619 0.00 0.00 0.00 3.96
4435 4693 4.397103 TGAGCATCTCCATTTTGCTTACTG 59.603 41.667 0.00 0.00 46.21 2.74
4447 4705 7.703621 CCATTTTGCTTACTGAATCCATAGTTG 59.296 37.037 0.00 0.00 0.00 3.16
4479 4737 1.871039 GGTCGTCAAAGCAAAGCAGTA 59.129 47.619 0.00 0.00 0.00 2.74
4551 4809 9.719355 TTTCTGCAGAGAAACATACATTAGTAA 57.281 29.630 17.43 0.00 42.23 2.24
4552 4810 9.719355 TTCTGCAGAGAAACATACATTAGTAAA 57.281 29.630 17.43 0.00 35.14 2.01
4553 4811 9.719355 TCTGCAGAGAAACATACATTAGTAAAA 57.281 29.630 13.74 0.00 33.13 1.52
4554 4812 9.979270 CTGCAGAGAAACATACATTAGTAAAAG 57.021 33.333 8.42 0.00 33.13 2.27
4555 4813 9.719355 TGCAGAGAAACATACATTAGTAAAAGA 57.281 29.630 0.00 0.00 33.13 2.52
4566 4824 7.617041 ACATTAGTAAAAGAGCAAGATGACC 57.383 36.000 0.00 0.00 0.00 4.02
4571 4829 3.795688 AAAGAGCAAGATGACCCTTGA 57.204 42.857 7.72 0.00 44.66 3.02
4579 4837 3.030873 AGATGACCCTTGAGAGAGAGG 57.969 52.381 0.00 0.00 0.00 3.69
4587 4845 2.754552 CCTTGAGAGAGAGGTGAGACAG 59.245 54.545 0.00 0.00 0.00 3.51
4594 4852 2.642311 AGAGAGGTGAGACAGTGAGAGA 59.358 50.000 0.00 0.00 0.00 3.10
4595 4853 3.009723 GAGAGGTGAGACAGTGAGAGAG 58.990 54.545 0.00 0.00 0.00 3.20
4596 4854 2.642311 AGAGGTGAGACAGTGAGAGAGA 59.358 50.000 0.00 0.00 0.00 3.10
4597 4855 3.009723 GAGGTGAGACAGTGAGAGAGAG 58.990 54.545 0.00 0.00 0.00 3.20
4598 4856 2.642311 AGGTGAGACAGTGAGAGAGAGA 59.358 50.000 0.00 0.00 0.00 3.10
4599 4857 3.009723 GGTGAGACAGTGAGAGAGAGAG 58.990 54.545 0.00 0.00 0.00 3.20
4600 4858 3.307410 GGTGAGACAGTGAGAGAGAGAGA 60.307 52.174 0.00 0.00 0.00 3.10
4601 4859 3.935203 GTGAGACAGTGAGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
4602 4860 3.837731 TGAGACAGTGAGAGAGAGAGAGA 59.162 47.826 0.00 0.00 0.00 3.10
4603 4861 4.081476 TGAGACAGTGAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
4604 4862 4.096681 AGACAGTGAGAGAGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
4605 4863 4.161189 AGACAGTGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
4606 4864 4.096681 ACAGTGAGAGAGAGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
4607 4865 4.161189 ACAGTGAGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
4608 4866 4.403752 CAGTGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
4609 4867 4.648762 AGTGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
4610 4868 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
4611 4869 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
4612 4870 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
4613 4871 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4614 4872 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4615 4873 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4616 4874 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4617 4875 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4618 4876 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4619 4877 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4620 4878 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4621 4879 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4622 4880 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4643 4901 3.812053 GAGAGAGAGAGAGACAGAGATGC 59.188 52.174 0.00 0.00 0.00 3.91
4671 4938 0.317269 GCTGACACACACACACATGC 60.317 55.000 0.00 0.00 0.00 4.06
4676 4943 2.281414 CACACACACATGCCCGGA 60.281 61.111 0.73 0.00 0.00 5.14
4705 4980 4.214332 TGCTTCCAAACAAACAAACAAACC 59.786 37.500 0.00 0.00 0.00 3.27
4706 4981 4.667922 GCTTCCAAACAAACAAACAAACCG 60.668 41.667 0.00 0.00 0.00 4.44
4707 4982 2.737252 TCCAAACAAACAAACAAACCGC 59.263 40.909 0.00 0.00 0.00 5.68
4708 4983 2.473049 CCAAACAAACAAACAAACCGCG 60.473 45.455 0.00 0.00 0.00 6.46
4768 5043 4.499023 TACGTACGTCGCCGTCGC 62.499 66.667 26.53 0.00 46.28 5.19
4802 5081 2.032634 GCCAACTGTCCGCGAATCA 61.033 57.895 8.23 2.35 0.00 2.57
4803 5082 1.970917 GCCAACTGTCCGCGAATCAG 61.971 60.000 8.23 15.11 35.60 2.90
4807 5086 1.737735 CTGTCCGCGAATCAGTGCA 60.738 57.895 8.23 0.00 0.00 4.57
4811 5090 1.153765 CCGCGAATCAGTGCAGAGA 60.154 57.895 8.23 0.00 0.00 3.10
4812 5091 0.529337 CCGCGAATCAGTGCAGAGAT 60.529 55.000 8.23 0.00 0.00 2.75
4856 5136 1.194772 GCAAGCGCGTAGACTTTCTTT 59.805 47.619 8.43 0.00 0.00 2.52
4857 5137 2.349532 GCAAGCGCGTAGACTTTCTTTT 60.350 45.455 8.43 0.00 0.00 2.27
4858 5138 3.848554 GCAAGCGCGTAGACTTTCTTTTT 60.849 43.478 8.43 0.00 0.00 1.94
4878 5158 4.994220 TTTTGAATGTTAAGCGCGTAGA 57.006 36.364 8.43 0.00 0.00 2.59
4879 5159 3.984018 TTGAATGTTAAGCGCGTAGAC 57.016 42.857 8.43 5.32 0.00 2.59
4880 5160 3.226346 TGAATGTTAAGCGCGTAGACT 57.774 42.857 8.43 0.00 0.00 3.24
4881 5161 3.581755 TGAATGTTAAGCGCGTAGACTT 58.418 40.909 8.43 4.82 0.00 3.01
4882 5162 3.991773 TGAATGTTAAGCGCGTAGACTTT 59.008 39.130 8.43 8.72 0.00 2.66
4883 5163 4.090930 TGAATGTTAAGCGCGTAGACTTTC 59.909 41.667 21.50 21.50 0.00 2.62
4884 5164 3.293311 TGTTAAGCGCGTAGACTTTCT 57.707 42.857 8.43 0.00 0.00 2.52
4885 5165 3.645884 TGTTAAGCGCGTAGACTTTCTT 58.354 40.909 8.43 1.98 0.00 2.52
4899 5179 3.758300 ACTTTCTTGCACGTTTGAACAG 58.242 40.909 0.00 0.00 0.00 3.16
4905 5185 1.002576 TGCACGTTTGAACAGCATCAG 60.003 47.619 6.83 0.00 35.53 2.90
4909 5189 1.664016 CGTTTGAACAGCATCAGCACC 60.664 52.381 0.00 0.00 45.49 5.01
4910 5190 0.592637 TTTGAACAGCATCAGCACCG 59.407 50.000 0.00 0.00 45.49 4.94
4913 5193 3.848301 AACAGCATCAGCACCGGCA 62.848 57.895 0.00 0.00 45.49 5.69
4949 5234 2.108157 GTGGTGCCTCGTGTGACA 59.892 61.111 0.00 0.00 0.00 3.58
4968 5253 3.679389 ACATGGCACTTTTGTCTCCTAG 58.321 45.455 0.00 0.00 0.00 3.02
4970 5255 4.286032 ACATGGCACTTTTGTCTCCTAGTA 59.714 41.667 0.00 0.00 0.00 1.82
4983 5268 8.789825 TTGTCTCCTAGTATCGTATCTTATCC 57.210 38.462 0.00 0.00 0.00 2.59
5001 5286 1.101331 CCTGTCCACCGACCTACTAC 58.899 60.000 0.00 0.00 38.32 2.73
5002 5287 1.101331 CTGTCCACCGACCTACTACC 58.899 60.000 0.00 0.00 38.32 3.18
5003 5288 0.700564 TGTCCACCGACCTACTACCT 59.299 55.000 0.00 0.00 38.32 3.08
5004 5289 1.340405 TGTCCACCGACCTACTACCTC 60.340 57.143 0.00 0.00 38.32 3.85
5005 5290 1.064832 GTCCACCGACCTACTACCTCT 60.065 57.143 0.00 0.00 32.40 3.69
5006 5291 1.064906 TCCACCGACCTACTACCTCTG 60.065 57.143 0.00 0.00 0.00 3.35
5007 5292 1.340795 CCACCGACCTACTACCTCTGT 60.341 57.143 0.00 0.00 0.00 3.41
5008 5293 2.015587 CACCGACCTACTACCTCTGTC 58.984 57.143 0.00 0.00 0.00 3.51
5009 5294 1.064832 ACCGACCTACTACCTCTGTCC 60.065 57.143 0.00 0.00 0.00 4.02
5010 5295 1.064906 CCGACCTACTACCTCTGTCCA 60.065 57.143 0.00 0.00 0.00 4.02
5011 5296 2.423088 CCGACCTACTACCTCTGTCCAT 60.423 54.545 0.00 0.00 0.00 3.41
5012 5297 3.288964 CGACCTACTACCTCTGTCCATT 58.711 50.000 0.00 0.00 0.00 3.16
5013 5298 3.315749 CGACCTACTACCTCTGTCCATTC 59.684 52.174 0.00 0.00 0.00 2.67
5014 5299 4.279145 GACCTACTACCTCTGTCCATTCA 58.721 47.826 0.00 0.00 0.00 2.57
5015 5300 4.684724 ACCTACTACCTCTGTCCATTCAA 58.315 43.478 0.00 0.00 0.00 2.69
5016 5301 5.091552 ACCTACTACCTCTGTCCATTCAAA 58.908 41.667 0.00 0.00 0.00 2.69
5017 5302 5.187967 ACCTACTACCTCTGTCCATTCAAAG 59.812 44.000 0.00 0.00 0.00 2.77
5018 5303 5.187967 CCTACTACCTCTGTCCATTCAAAGT 59.812 44.000 0.00 0.00 0.00 2.66
5019 5304 6.380274 CCTACTACCTCTGTCCATTCAAAGTA 59.620 42.308 0.00 0.00 0.00 2.24
5020 5305 6.875972 ACTACCTCTGTCCATTCAAAGTAT 57.124 37.500 0.00 0.00 0.00 2.12
5021 5306 7.973048 ACTACCTCTGTCCATTCAAAGTATA 57.027 36.000 0.00 0.00 0.00 1.47
5022 5307 8.554490 ACTACCTCTGTCCATTCAAAGTATAT 57.446 34.615 0.00 0.00 0.00 0.86
5023 5308 8.424918 ACTACCTCTGTCCATTCAAAGTATATG 58.575 37.037 0.00 0.00 0.00 1.78
5024 5309 6.058183 ACCTCTGTCCATTCAAAGTATATGC 58.942 40.000 0.00 0.00 0.00 3.14
5025 5310 6.057533 CCTCTGTCCATTCAAAGTATATGCA 58.942 40.000 0.00 0.00 0.00 3.96
5026 5311 6.713903 CCTCTGTCCATTCAAAGTATATGCAT 59.286 38.462 3.79 3.79 0.00 3.96
5027 5312 7.094890 CCTCTGTCCATTCAAAGTATATGCATC 60.095 40.741 0.19 0.00 0.00 3.91
5028 5313 6.712095 TCTGTCCATTCAAAGTATATGCATCC 59.288 38.462 0.19 0.00 0.00 3.51
5029 5314 6.363882 TGTCCATTCAAAGTATATGCATCCA 58.636 36.000 0.19 0.00 0.00 3.41
5030 5315 6.487668 TGTCCATTCAAAGTATATGCATCCAG 59.512 38.462 0.19 0.00 0.00 3.86
5031 5316 5.474532 TCCATTCAAAGTATATGCATCCAGC 59.525 40.000 0.19 0.00 45.96 4.85
5032 5317 5.475909 CCATTCAAAGTATATGCATCCAGCT 59.524 40.000 0.19 0.00 45.94 4.24
5033 5318 6.349115 CCATTCAAAGTATATGCATCCAGCTC 60.349 42.308 0.19 0.00 45.94 4.09
5034 5319 4.309933 TCAAAGTATATGCATCCAGCTCG 58.690 43.478 0.19 0.00 45.94 5.03
5035 5320 4.060900 CAAAGTATATGCATCCAGCTCGT 58.939 43.478 0.19 0.00 45.94 4.18
5036 5321 3.309961 AGTATATGCATCCAGCTCGTG 57.690 47.619 0.19 0.00 45.94 4.35
5037 5322 1.728971 GTATATGCATCCAGCTCGTGC 59.271 52.381 0.19 0.07 45.94 5.34
5038 5323 0.604780 ATATGCATCCAGCTCGTGCC 60.605 55.000 0.19 0.00 45.94 5.01
5039 5324 2.665008 TATGCATCCAGCTCGTGCCC 62.665 60.000 0.19 0.00 45.94 5.36
5040 5325 4.479993 GCATCCAGCTCGTGCCCT 62.480 66.667 5.73 0.00 41.15 5.19
5041 5326 3.094062 GCATCCAGCTCGTGCCCTA 62.094 63.158 5.73 0.00 41.15 3.53
5042 5327 1.522092 CATCCAGCTCGTGCCCTAA 59.478 57.895 5.73 0.00 40.80 2.69
5043 5328 0.531532 CATCCAGCTCGTGCCCTAAG 60.532 60.000 5.73 0.00 40.80 2.18
5044 5329 0.978146 ATCCAGCTCGTGCCCTAAGT 60.978 55.000 5.73 0.00 40.80 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.019501 AGCACCTGACTTCTCATTCTCAAT 60.020 41.667 0.00 0.00 0.00 2.57
13 14 1.548269 GACTGCTAGCACCTGACTTCT 59.452 52.381 14.93 0.00 0.00 2.85
21 22 1.219393 GGTGGAGACTGCTAGCACC 59.781 63.158 14.93 14.25 0.00 5.01
43 45 1.352687 GAGAGTGAAAGGGCCCTCTTT 59.647 52.381 28.84 18.03 39.41 2.52
54 56 1.623311 TGATCCAAGGCGAGAGTGAAA 59.377 47.619 0.00 0.00 0.00 2.69
55 57 1.066858 GTGATCCAAGGCGAGAGTGAA 60.067 52.381 0.00 0.00 0.00 3.18
65 68 2.082231 CTTGCTGACTGTGATCCAAGG 58.918 52.381 0.00 0.00 0.00 3.61
67 70 1.421268 ACCTTGCTGACTGTGATCCAA 59.579 47.619 0.00 0.00 0.00 3.53
70 73 1.002430 TCCACCTTGCTGACTGTGATC 59.998 52.381 0.00 0.00 0.00 2.92
94 97 1.470098 CATGTGTGCTCTTAGGTTGGC 59.530 52.381 0.00 0.00 0.00 4.52
95 98 3.057969 TCATGTGTGCTCTTAGGTTGG 57.942 47.619 0.00 0.00 0.00 3.77
97 100 3.815401 GTGTTCATGTGTGCTCTTAGGTT 59.185 43.478 0.00 0.00 0.00 3.50
98 101 3.071602 AGTGTTCATGTGTGCTCTTAGGT 59.928 43.478 0.00 0.00 0.00 3.08
116 119 1.355381 TCCTGATTGCCAATCCAGTGT 59.645 47.619 14.58 0.00 37.09 3.55
117 120 2.022195 CTCCTGATTGCCAATCCAGTG 58.978 52.381 14.58 3.72 37.09 3.66
122 125 2.352960 GTCGTTCTCCTGATTGCCAATC 59.647 50.000 10.53 10.53 38.40 2.67
190 193 2.440065 TCATTGTGGGGCGATGGC 60.440 61.111 0.00 0.00 39.06 4.40
192 195 1.066002 GATTGTCATTGTGGGGCGATG 59.934 52.381 0.00 0.00 39.76 3.84
206 209 6.381801 AGTGTCGAATCAAATTTGGATTGTC 58.618 36.000 17.90 9.21 35.23 3.18
241 244 9.645059 TGCCATTTTGAAATACGATTTTAATGA 57.355 25.926 0.00 0.00 0.00 2.57
244 247 9.482627 ACTTGCCATTTTGAAATACGATTTTAA 57.517 25.926 0.00 0.00 0.00 1.52
263 268 6.811253 AATACGATTTTTAGTGACTTGCCA 57.189 33.333 0.00 0.00 0.00 4.92
374 379 9.872684 AGTTATGGATTTGTGATTATGAGGATT 57.127 29.630 0.00 0.00 0.00 3.01
378 383 8.162878 AGCAGTTATGGATTTGTGATTATGAG 57.837 34.615 0.00 0.00 0.00 2.90
471 476 3.129502 CGTGCATGACCCAGGCTG 61.130 66.667 7.75 7.75 41.96 4.85
475 480 1.003355 AGGTTCGTGCATGACCCAG 60.003 57.895 23.00 0.00 0.00 4.45
483 488 3.858868 GACGCCTGAGGTTCGTGCA 62.859 63.158 8.87 0.00 36.50 4.57
517 522 0.248990 CAGACAGAGATCTCAGCCGC 60.249 60.000 24.39 9.78 0.00 6.53
518 523 1.387539 TCAGACAGAGATCTCAGCCG 58.612 55.000 24.39 11.86 0.00 5.52
533 538 3.808834 TCAGGTAGGTCTTCACTCAGA 57.191 47.619 0.00 0.00 0.00 3.27
563 568 1.207791 CACTTAGGCCCTGTCTGGAT 58.792 55.000 0.00 0.00 38.35 3.41
599 604 1.073923 ACCTTGGCCTACAAACCTGAG 59.926 52.381 3.32 0.00 38.91 3.35
787 792 7.093727 TGTGGGAATAAACTGTTTTCTGTGAAA 60.094 33.333 11.48 0.00 32.46 2.69
827 832 6.497785 AGAACTCTTTGATTCATGCAAGAG 57.502 37.500 18.61 18.61 32.15 2.85
832 837 6.850555 AGCTTTAGAACTCTTTGATTCATGC 58.149 36.000 0.00 0.00 0.00 4.06
880 886 2.295349 CACGGTACTGTCCTACACTGTT 59.705 50.000 3.76 0.00 38.15 3.16
1066 1094 4.247380 GGAGGCGGCATGGAGGAG 62.247 72.222 13.08 0.00 0.00 3.69
1743 1771 0.103937 CGAGGCTCTGGAGATTCACC 59.896 60.000 13.50 0.00 0.00 4.02
1746 1774 0.031994 GCTCGAGGCTCTGGAGATTC 59.968 60.000 19.63 2.74 38.34 2.52
1953 1981 0.250513 GGTTGACGAGCTCCCTGAAT 59.749 55.000 8.47 0.00 0.00 2.57
2004 2032 3.741476 CCCAGTTTCTGCGGCAGC 61.741 66.667 24.78 11.32 45.41 5.25
2012 2040 1.831652 CGACCAGCTCCCCAGTTTCT 61.832 60.000 0.00 0.00 0.00 2.52
2033 2061 0.363512 CACGTCGATGAAGTTGAGCG 59.636 55.000 12.58 0.00 0.00 5.03
2035 2063 1.986378 GGACACGTCGATGAAGTTGAG 59.014 52.381 12.58 0.00 0.00 3.02
2062 2090 2.105128 GATCGGACCCGTGAGCAG 59.895 66.667 8.42 0.00 40.74 4.24
2063 2091 3.458163 GGATCGGACCCGTGAGCA 61.458 66.667 8.42 0.00 40.74 4.26
2173 2201 2.049063 GAACCTCTGCAGCGTCGT 60.049 61.111 9.47 0.00 0.00 4.34
2233 2261 1.377725 CTGTTGGAAGCGCCCAGAT 60.378 57.895 2.29 0.00 37.53 2.90
2429 2457 2.827190 TCGCTGGTATCTCGCCGT 60.827 61.111 0.00 0.00 0.00 5.68
2442 2470 4.463879 AGCTTGCCGATGCTCGCT 62.464 61.111 0.72 0.00 38.82 4.93
2443 2471 4.233635 CAGCTTGCCGATGCTCGC 62.234 66.667 0.00 0.00 38.82 5.03
2465 2493 1.327303 GATGTCCAGGCTCTCGAGAT 58.673 55.000 17.03 0.00 0.00 2.75
2472 2500 4.899239 CCCGCGATGTCCAGGCTC 62.899 72.222 8.23 0.00 0.00 4.70
2484 2512 4.891727 CTGATCCCGTTCCCCGCG 62.892 72.222 0.00 0.00 34.38 6.46
2561 2589 3.423154 CGCCGGTGAGCTTGTTCC 61.423 66.667 10.20 0.00 0.00 3.62
2598 2626 1.523758 ACAAATTCAGACTCGTGCCC 58.476 50.000 0.00 0.00 0.00 5.36
2605 2636 5.530915 TCGAAATGTCCAACAAATTCAGACT 59.469 36.000 8.66 0.00 31.50 3.24
2607 2638 5.562696 GCTCGAAATGTCCAACAAATTCAGA 60.563 40.000 0.00 6.59 31.50 3.27
2615 2646 3.145286 TCATTGCTCGAAATGTCCAACA 58.855 40.909 9.14 0.00 38.46 3.33
2620 2651 4.201763 GGAGAGTTCATTGCTCGAAATGTC 60.202 45.833 9.14 1.67 38.46 3.06
2688 2719 0.953960 GCCGATTGTCCGACAGGTTT 60.954 55.000 0.64 0.00 39.05 3.27
2698 2729 2.582498 CCCGTCGAGCCGATTGTC 60.582 66.667 0.00 0.00 38.42 3.18
2976 3007 1.292223 CCCCTTCTTCGCGAACAGA 59.708 57.895 19.38 12.36 0.00 3.41
3573 3604 2.514824 GCGTCCAGGATCTTGGCC 60.515 66.667 18.84 6.94 38.16 5.36
4071 4111 2.095059 GCGCTGATCCAAAATGTTCAGT 60.095 45.455 0.00 0.00 38.26 3.41
4076 4116 1.672881 GCTAGCGCTGATCCAAAATGT 59.327 47.619 22.90 0.00 0.00 2.71
4088 4128 3.967335 GATCGGACGGCTAGCGCT 61.967 66.667 17.26 17.26 36.09 5.92
4141 4181 1.000843 ACATGCTCTACACACGCTTGA 59.999 47.619 0.00 0.00 34.24 3.02
4185 4225 6.934645 TCTTCACCAACGAACAATCTTTATCT 59.065 34.615 0.00 0.00 0.00 1.98
4186 4226 7.129109 TCTTCACCAACGAACAATCTTTATC 57.871 36.000 0.00 0.00 0.00 1.75
4188 4228 6.928979 TTCTTCACCAACGAACAATCTTTA 57.071 33.333 0.00 0.00 0.00 1.85
4189 4229 5.828299 TTCTTCACCAACGAACAATCTTT 57.172 34.783 0.00 0.00 0.00 2.52
4238 4278 2.568062 TGCCACTGGTAATTTCCTACGA 59.432 45.455 2.53 0.00 0.00 3.43
4239 4279 2.980568 TGCCACTGGTAATTTCCTACG 58.019 47.619 2.53 0.00 0.00 3.51
4257 4320 2.029623 ACCAAGCAGAATGGATGATGC 58.970 47.619 0.00 0.00 40.56 3.91
4320 4422 3.508845 ATGTTTGGCCAAGAGTACTGT 57.491 42.857 19.48 4.66 0.00 3.55
4326 4428 4.946157 AGAGAATGTATGTTTGGCCAAGAG 59.054 41.667 19.48 0.00 0.00 2.85
4384 4537 9.709495 TTTTGCTCTTAGTACCGTAATTTTCTA 57.291 29.630 0.00 0.00 0.00 2.10
4391 4544 6.091713 GCTCATTTTTGCTCTTAGTACCGTAA 59.908 38.462 0.00 0.00 0.00 3.18
4394 4547 4.391830 TGCTCATTTTTGCTCTTAGTACCG 59.608 41.667 0.00 0.00 0.00 4.02
4395 4548 5.880054 TGCTCATTTTTGCTCTTAGTACC 57.120 39.130 0.00 0.00 0.00 3.34
4396 4549 7.313951 AGATGCTCATTTTTGCTCTTAGTAC 57.686 36.000 0.00 0.00 0.00 2.73
4447 4705 3.941657 GACGACCTGCCTGACTGCC 62.942 68.421 0.00 0.00 0.00 4.85
4460 4718 3.602390 TTACTGCTTTGCTTTGACGAC 57.398 42.857 0.00 0.00 0.00 4.34
4461 4719 4.624336 TTTTACTGCTTTGCTTTGACGA 57.376 36.364 0.00 0.00 0.00 4.20
4543 4801 6.825721 AGGGTCATCTTGCTCTTTTACTAATG 59.174 38.462 0.00 0.00 0.00 1.90
4544 4802 6.963322 AGGGTCATCTTGCTCTTTTACTAAT 58.037 36.000 0.00 0.00 0.00 1.73
4545 4803 6.374417 AGGGTCATCTTGCTCTTTTACTAA 57.626 37.500 0.00 0.00 0.00 2.24
4546 4804 6.013725 TCAAGGGTCATCTTGCTCTTTTACTA 60.014 38.462 0.00 0.00 42.68 1.82
4548 4806 5.003804 TCAAGGGTCATCTTGCTCTTTTAC 58.996 41.667 0.00 0.00 42.68 2.01
4549 4807 5.013079 TCTCAAGGGTCATCTTGCTCTTTTA 59.987 40.000 0.00 0.00 42.68 1.52
4550 4808 4.077822 CTCAAGGGTCATCTTGCTCTTTT 58.922 43.478 0.00 0.00 42.68 2.27
4551 4809 3.328931 TCTCAAGGGTCATCTTGCTCTTT 59.671 43.478 0.00 0.00 42.68 2.52
4552 4810 2.909006 TCTCAAGGGTCATCTTGCTCTT 59.091 45.455 0.00 0.00 42.68 2.85
4553 4811 2.500910 CTCTCAAGGGTCATCTTGCTCT 59.499 50.000 0.00 0.00 42.68 4.09
4554 4812 2.499289 TCTCTCAAGGGTCATCTTGCTC 59.501 50.000 0.00 0.00 42.68 4.26
4555 4813 2.500910 CTCTCTCAAGGGTCATCTTGCT 59.499 50.000 0.00 0.00 42.68 3.91
4566 4824 2.754552 CTGTCTCACCTCTCTCTCAAGG 59.245 54.545 0.00 0.00 38.70 3.61
4571 4829 2.642311 TCTCACTGTCTCACCTCTCTCT 59.358 50.000 0.00 0.00 0.00 3.10
4579 4837 3.935203 CTCTCTCTCTCTCACTGTCTCAC 59.065 52.174 0.00 0.00 0.00 3.51
4587 4845 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
4594 4852 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4595 4853 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4596 4854 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4597 4855 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4598 4856 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4599 4857 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4600 4858 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4601 4859 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4602 4860 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4603 4861 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4604 4862 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4605 4863 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4606 4864 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4607 4865 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4608 4866 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4609 4867 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4610 4868 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4611 4869 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
4612 4870 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
4613 4871 4.646945 TGTCTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
4614 4872 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
4615 4873 4.646945 TCTGTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
4616 4874 4.614475 TCTGTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
4617 4875 4.646945 TCTCTGTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
4618 4876 4.614475 TCTCTGTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
4619 4877 5.295950 CATCTCTGTCTCTCTCTCTCTCTC 58.704 50.000 0.00 0.00 0.00 3.20
4620 4878 4.444022 GCATCTCTGTCTCTCTCTCTCTCT 60.444 50.000 0.00 0.00 0.00 3.10
4621 4879 3.812053 GCATCTCTGTCTCTCTCTCTCTC 59.188 52.174 0.00 0.00 0.00 3.20
4622 4880 3.742327 CGCATCTCTGTCTCTCTCTCTCT 60.742 52.174 0.00 0.00 0.00 3.10
4676 4943 3.037549 TGTTTGTTTGGAAGCATCCCTT 58.962 40.909 5.34 0.00 45.95 3.95
4796 5075 1.579698 CCCATCTCTGCACTGATTCG 58.420 55.000 0.00 0.00 0.00 3.34
4802 5081 1.445095 GATCGCCCATCTCTGCACT 59.555 57.895 0.00 0.00 0.00 4.40
4803 5082 1.596477 GGATCGCCCATCTCTGCAC 60.596 63.158 0.00 0.00 34.14 4.57
4856 5136 5.049954 AGTCTACGCGCTTAACATTCAAAAA 60.050 36.000 5.73 0.00 0.00 1.94
4857 5137 4.449743 AGTCTACGCGCTTAACATTCAAAA 59.550 37.500 5.73 0.00 0.00 2.44
4858 5138 3.991773 AGTCTACGCGCTTAACATTCAAA 59.008 39.130 5.73 0.00 0.00 2.69
4859 5139 3.581755 AGTCTACGCGCTTAACATTCAA 58.418 40.909 5.73 0.00 0.00 2.69
4860 5140 3.226346 AGTCTACGCGCTTAACATTCA 57.774 42.857 5.73 0.00 0.00 2.57
4861 5141 4.326548 AGAAAGTCTACGCGCTTAACATTC 59.673 41.667 5.73 8.56 0.00 2.67
4862 5142 4.243270 AGAAAGTCTACGCGCTTAACATT 58.757 39.130 5.73 0.00 0.00 2.71
4863 5143 3.846360 AGAAAGTCTACGCGCTTAACAT 58.154 40.909 5.73 0.00 0.00 2.71
4864 5144 3.293311 AGAAAGTCTACGCGCTTAACA 57.707 42.857 5.73 0.00 0.00 2.41
4865 5145 3.721210 GCAAGAAAGTCTACGCGCTTAAC 60.721 47.826 5.73 0.00 0.00 2.01
4866 5146 2.410730 GCAAGAAAGTCTACGCGCTTAA 59.589 45.455 5.73 0.00 0.00 1.85
4867 5147 1.990563 GCAAGAAAGTCTACGCGCTTA 59.009 47.619 5.73 0.00 0.00 3.09
4868 5148 0.790814 GCAAGAAAGTCTACGCGCTT 59.209 50.000 5.73 0.00 0.00 4.68
4869 5149 0.319555 TGCAAGAAAGTCTACGCGCT 60.320 50.000 5.73 0.00 30.25 5.92
4870 5150 0.179248 GTGCAAGAAAGTCTACGCGC 60.179 55.000 5.73 0.00 31.47 6.86
4871 5151 0.091344 CGTGCAAGAAAGTCTACGCG 59.909 55.000 3.53 3.53 32.91 6.01
4872 5152 1.137513 ACGTGCAAGAAAGTCTACGC 58.862 50.000 6.65 0.00 35.17 4.42
4873 5153 3.244345 TCAAACGTGCAAGAAAGTCTACG 59.756 43.478 6.65 0.00 37.54 3.51
4874 5154 4.789095 TCAAACGTGCAAGAAAGTCTAC 57.211 40.909 6.65 0.00 0.00 2.59
4875 5155 4.632251 TGTTCAAACGTGCAAGAAAGTCTA 59.368 37.500 6.65 0.00 0.00 2.59
4876 5156 3.438781 TGTTCAAACGTGCAAGAAAGTCT 59.561 39.130 6.65 0.00 0.00 3.24
4877 5157 3.753842 TGTTCAAACGTGCAAGAAAGTC 58.246 40.909 6.65 0.00 0.00 3.01
4878 5158 3.758300 CTGTTCAAACGTGCAAGAAAGT 58.242 40.909 6.65 0.00 0.00 2.66
4879 5159 2.531508 GCTGTTCAAACGTGCAAGAAAG 59.468 45.455 6.65 0.00 33.32 2.62
4880 5160 2.095008 TGCTGTTCAAACGTGCAAGAAA 60.095 40.909 6.65 0.00 37.79 2.52
4881 5161 1.470494 TGCTGTTCAAACGTGCAAGAA 59.530 42.857 6.65 0.00 37.79 2.52
4882 5162 1.090728 TGCTGTTCAAACGTGCAAGA 58.909 45.000 6.65 0.00 37.79 3.02
4883 5163 2.046313 GATGCTGTTCAAACGTGCAAG 58.954 47.619 14.23 0.00 41.62 4.01
4884 5164 1.403323 TGATGCTGTTCAAACGTGCAA 59.597 42.857 14.23 1.22 41.62 4.08
4885 5165 1.002576 CTGATGCTGTTCAAACGTGCA 60.003 47.619 13.13 13.13 42.16 4.57
4899 5179 3.807538 CAGTGCCGGTGCTGATGC 61.808 66.667 18.46 0.00 38.71 3.91
4949 5234 5.675538 GATACTAGGAGACAAAAGTGCCAT 58.324 41.667 0.00 0.00 0.00 4.40
4968 5253 5.391736 CGGTGGACAGGATAAGATACGATAC 60.392 48.000 0.00 0.00 0.00 2.24
4970 5255 3.506455 CGGTGGACAGGATAAGATACGAT 59.494 47.826 0.00 0.00 0.00 3.73
4983 5268 1.101331 GGTAGTAGGTCGGTGGACAG 58.899 60.000 0.00 0.00 45.28 3.51
5001 5286 6.057533 TGCATATACTTTGAATGGACAGAGG 58.942 40.000 0.00 0.00 0.00 3.69
5002 5287 7.094890 GGATGCATATACTTTGAATGGACAGAG 60.095 40.741 0.00 0.00 0.00 3.35
5003 5288 6.712095 GGATGCATATACTTTGAATGGACAGA 59.288 38.462 0.00 0.00 0.00 3.41
5004 5289 6.487668 TGGATGCATATACTTTGAATGGACAG 59.512 38.462 0.00 0.00 0.00 3.51
5005 5290 6.363882 TGGATGCATATACTTTGAATGGACA 58.636 36.000 0.00 0.00 0.00 4.02
5006 5291 6.569226 GCTGGATGCATATACTTTGAATGGAC 60.569 42.308 0.00 0.00 42.31 4.02
5007 5292 5.474532 GCTGGATGCATATACTTTGAATGGA 59.525 40.000 0.00 0.00 42.31 3.41
5008 5293 5.475909 AGCTGGATGCATATACTTTGAATGG 59.524 40.000 0.00 0.00 45.94 3.16
5009 5294 6.570672 AGCTGGATGCATATACTTTGAATG 57.429 37.500 0.00 0.00 45.94 2.67
5010 5295 5.410746 CGAGCTGGATGCATATACTTTGAAT 59.589 40.000 0.00 0.00 45.94 2.57
5011 5296 4.751600 CGAGCTGGATGCATATACTTTGAA 59.248 41.667 0.00 0.00 45.94 2.69
5012 5297 4.202253 ACGAGCTGGATGCATATACTTTGA 60.202 41.667 1.44 0.00 45.94 2.69
5013 5298 4.060900 ACGAGCTGGATGCATATACTTTG 58.939 43.478 1.44 0.00 45.94 2.77
5014 5299 4.060900 CACGAGCTGGATGCATATACTTT 58.939 43.478 1.44 0.00 45.94 2.66
5015 5300 3.657634 CACGAGCTGGATGCATATACTT 58.342 45.455 1.44 0.00 45.94 2.24
5016 5301 2.611473 GCACGAGCTGGATGCATATACT 60.611 50.000 14.89 0.00 45.94 2.12
5017 5302 1.728971 GCACGAGCTGGATGCATATAC 59.271 52.381 14.89 0.00 45.94 1.47
5018 5303 1.338105 GGCACGAGCTGGATGCATATA 60.338 52.381 19.13 0.00 45.94 0.86
5019 5304 0.604780 GGCACGAGCTGGATGCATAT 60.605 55.000 19.13 0.00 45.94 1.78
5020 5305 1.227645 GGCACGAGCTGGATGCATA 60.228 57.895 19.13 0.00 45.94 3.14
5021 5306 2.515523 GGCACGAGCTGGATGCAT 60.516 61.111 19.13 0.00 45.94 3.96
5022 5307 4.783621 GGGCACGAGCTGGATGCA 62.784 66.667 19.13 0.00 45.94 3.96
5023 5308 2.593468 TTAGGGCACGAGCTGGATGC 62.593 60.000 1.44 8.61 41.70 3.91
5024 5309 0.531532 CTTAGGGCACGAGCTGGATG 60.532 60.000 1.44 0.00 41.70 3.51
5025 5310 0.978146 ACTTAGGGCACGAGCTGGAT 60.978 55.000 1.44 0.00 41.70 3.41
5026 5311 1.609501 ACTTAGGGCACGAGCTGGA 60.610 57.895 1.44 0.00 41.70 3.86
5027 5312 2.982130 ACTTAGGGCACGAGCTGG 59.018 61.111 4.48 0.00 41.70 4.85


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

AutoCloner maintained by Alex Coulton.