Multiple sequence alignment - TraesCS2A01G109500

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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 TraesCS2A01G109500 chr2A 100.000 4530 0 0 1 4530 61387721 61383192 0.000000e+00 8366.0
1 TraesCS2A01G109500 chr2A 97.500 40 1 0 1 40 542665491 542665452 8.130000e-08 69.4
2 TraesCS2A01G109500 chr2A 89.583 48 5 0 1 48 106646506 106646553 1.360000e-05 62.1
3 TraesCS2A01G109500 chr2B 94.282 2763 81 23 1804 4530 95544194 95541473 0.000000e+00 4156.0
4 TraesCS2A01G109500 chr2B 90.529 718 33 7 815 1506 95545163 95544455 0.000000e+00 917.0
5 TraesCS2A01G109500 chr2B 86.949 590 46 9 42 610 95554258 95553679 6.390000e-178 634.0
6 TraesCS2A01G109500 chr2B 88.000 225 11 3 1510 1734 95544399 95544191 7.520000e-63 252.0
7 TraesCS2A01G109500 chr2B 90.816 98 5 4 693 789 95550849 95550755 1.320000e-25 128.0
8 TraesCS2A01G109500 chr2B 91.139 79 5 2 1733 1810 656941940 656942017 6.200000e-19 106.0
9 TraesCS2A01G109500 chr2B 85.000 60 8 1 1 60 231118268 231118326 4.890000e-05 60.2
10 TraesCS2A01G109500 chr2D 94.508 2713 75 17 1804 4487 60792482 60789815 0.000000e+00 4117.0
11 TraesCS2A01G109500 chr2D 85.649 1526 127 42 37 1506 60794230 60792741 0.000000e+00 1520.0
12 TraesCS2A01G109500 chr2D 87.556 225 12 3 1510 1734 60792687 60792479 3.500000e-61 246.0
13 TraesCS2A01G109500 chr2D 88.095 84 7 3 1727 1809 71410936 71411017 3.730000e-16 97.1
14 TraesCS2A01G109500 chr3B 87.763 760 75 7 2789 3531 775476506 775475748 0.000000e+00 872.0
15 TraesCS2A01G109500 chr3B 83.991 431 48 10 2286 2711 775477400 775476986 1.180000e-105 394.0
16 TraesCS2A01G109500 chr3B 90.909 77 7 0 1733 1809 23785907 23785831 2.230000e-18 104.0
17 TraesCS2A01G109500 chr3B 97.500 40 1 0 1 40 253094018 253094057 8.130000e-08 69.4
18 TraesCS2A01G109500 chr3B 84.127 63 7 3 1 62 823769988 823769928 1.760000e-04 58.4
19 TraesCS2A01G109500 chr3D 87.156 654 67 7 2789 3426 580331760 580331108 0.000000e+00 726.0
20 TraesCS2A01G109500 chr3D 84.527 433 46 12 2286 2713 580332860 580332444 4.220000e-110 409.0
21 TraesCS2A01G109500 chr3D 89.189 111 10 2 3423 3532 580330949 580330840 2.200000e-28 137.0
22 TraesCS2A01G109500 chr3A 83.152 825 104 16 2729 3531 715646541 715645730 0.000000e+00 721.0
23 TraesCS2A01G109500 chr3A 88.462 312 26 3 2286 2593 715647484 715647179 7.160000e-98 368.0
24 TraesCS2A01G109500 chr4A 86.680 518 33 14 987 1491 534200173 534200667 3.990000e-150 542.0
25 TraesCS2A01G109500 chr4A 87.879 396 26 7 36 410 534181375 534181769 3.220000e-121 446.0
26 TraesCS2A01G109500 chr4A 97.333 75 1 1 922 996 534182599 534182672 4.760000e-25 126.0
27 TraesCS2A01G109500 chr4A 90.698 86 4 2 1728 1809 647342584 647342499 1.330000e-20 111.0
28 TraesCS2A01G109500 chr6A 93.671 79 4 1 1733 1811 168004065 168004142 2.860000e-22 117.0
29 TraesCS2A01G109500 chr6A 93.478 46 2 1 1 45 46898996 46898951 2.920000e-07 67.6
30 TraesCS2A01G109500 chr6A 91.489 47 4 0 1 47 116606655 116606609 1.050000e-06 65.8
31 TraesCS2A01G109500 chr6A 91.489 47 3 1 1 47 282515 282560 3.780000e-06 63.9
32 TraesCS2A01G109500 chr1A 86.538 104 8 5 1732 1830 432980104 432980002 4.790000e-20 110.0
33 TraesCS2A01G109500 chr7D 89.157 83 9 0 4405 4487 18405142 18405060 2.230000e-18 104.0
34 TraesCS2A01G109500 chr6D 84.906 106 12 4 4275 4376 461497255 461497150 2.230000e-18 104.0
35 TraesCS2A01G109500 chr6D 90.000 80 7 1 1732 1810 219783642 219783721 8.020000e-18 102.0
36 TraesCS2A01G109500 chr5B 79.070 172 20 10 4211 4374 419614531 419614694 2.230000e-18 104.0
37 TraesCS2A01G109500 chr5B 83.200 125 9 6 4240 4354 484833427 484833305 2.230000e-18 104.0
38 TraesCS2A01G109500 chr5B 83.544 79 13 0 4405 4483 419614755 419614833 1.750000e-09 75.0
39 TraesCS2A01G109500 chr5A 90.123 81 6 1 1732 1810 638032981 638032901 2.230000e-18 104.0
40 TraesCS2A01G109500 chr5A 85.714 63 6 3 4273 4332 505488848 505488786 3.780000e-06 63.9
41 TraesCS2A01G109500 chr5D 87.097 93 7 4 1720 1809 438979954 438979864 2.880000e-17 100.0
42 TraesCS2A01G109500 chr7A 91.304 46 4 0 1 46 188995657 188995702 3.780000e-06 63.9


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 TraesCS2A01G109500 chr2A 61383192 61387721 4529 True 8366.0 8366 100.000000 1 4530 1 chr2A.!!$R1 4529
1 TraesCS2A01G109500 chr2B 95541473 95545163 3690 True 1775.0 4156 90.937000 815 4530 3 chr2B.!!$R1 3715
2 TraesCS2A01G109500 chr2B 95550755 95554258 3503 True 381.0 634 88.882500 42 789 2 chr2B.!!$R2 747
3 TraesCS2A01G109500 chr2D 60789815 60794230 4415 True 1961.0 4117 89.237667 37 4487 3 chr2D.!!$R1 4450
4 TraesCS2A01G109500 chr3B 775475748 775477400 1652 True 633.0 872 85.877000 2286 3531 2 chr3B.!!$R3 1245
5 TraesCS2A01G109500 chr3D 580330840 580332860 2020 True 424.0 726 86.957333 2286 3532 3 chr3D.!!$R1 1246
6 TraesCS2A01G109500 chr3A 715645730 715647484 1754 True 544.5 721 85.807000 2286 3531 2 chr3A.!!$R1 1245
7 TraesCS2A01G109500 chr4A 534181375 534182672 1297 False 286.0 446 92.606000 36 996 2 chr4A.!!$F2 960

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
136 141 0.036732 GAAGGTGCATGAGTGGGTCA 59.963 55.0 0.0 0.0 40.38 4.02 F
1357 4728 0.036765 TGACGGGGAAAATCTGGACG 60.037 55.0 0.0 0.0 0.00 4.79 F
1748 5171 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.0 0.0 0.0 0.00 4.12 F
1749 5172 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 5118 0.409092 TCCATCAACACCCCAGCATT 59.591 50.000 0.00 0.0 0.00 3.56 R
3129 7273 1.931172 ACACAAGAAAACCGAGACACG 59.069 47.619 0.00 0.0 42.18 4.49 R
3366 7515 1.453155 ATTCTTGGCCACTAAGTGCG 58.547 50.000 3.88 0.0 31.34 5.34 R
3592 7903 3.257469 GAGCATGACTCACCTTGATCA 57.743 47.619 0.00 0.0 45.49 2.92 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
39 40 9.671279 CCTTTAGGGCATATTTTCTTCATTTTT 57.329 29.630 0.00 0.00 0.00 1.94
68 69 5.557866 ACACAATGGTAGAAAGTACCCTTC 58.442 41.667 0.00 0.00 36.79 3.46
69 70 5.309806 ACACAATGGTAGAAAGTACCCTTCT 59.690 40.000 11.44 11.44 36.79 2.85
76 81 3.236896 AGAAAGTACCCTTCTCCGTTGA 58.763 45.455 2.65 0.00 0.00 3.18
115 120 1.922447 TCTTGTCATGCATAAGGGGGT 59.078 47.619 0.00 0.00 0.00 4.95
136 141 0.036732 GAAGGTGCATGAGTGGGTCA 59.963 55.000 0.00 0.00 40.38 4.02
157 162 7.917505 GGGTCAAATATTCTTATGCTTTGAGTG 59.082 37.037 0.00 0.00 36.73 3.51
307 331 5.700832 TGAGTGATGGTTGTTTCAGTATCAC 59.299 40.000 0.00 0.00 42.72 3.06
329 353 4.788617 ACTGGTATGGTAATTGGAGGTTCT 59.211 41.667 0.00 0.00 0.00 3.01
349 373 6.295349 GGTTCTAAGTGGTTCAGAGAAGATGA 60.295 42.308 0.00 0.00 0.00 2.92
357 381 4.161189 GGTTCAGAGAAGATGACTGGATGA 59.839 45.833 0.00 0.00 33.19 2.92
391 415 1.548719 TGGTACACAACGATGAGGAGG 59.451 52.381 0.00 0.00 0.00 4.30
446 470 0.737367 ACCGTGCATGATGTCGTCTG 60.737 55.000 7.72 0.00 0.00 3.51
525 1121 1.310904 GCTCGTCTCCGTTATCCTCT 58.689 55.000 0.00 0.00 35.01 3.69
526 1122 1.677052 GCTCGTCTCCGTTATCCTCTT 59.323 52.381 0.00 0.00 35.01 2.85
554 1150 7.663081 TCAAATAGCTGTTGTTTCTCTCATCTT 59.337 33.333 0.00 0.00 0.00 2.40
560 1156 5.116180 TGTTGTTTCTCTCATCTTTGTCGT 58.884 37.500 0.00 0.00 0.00 4.34
564 1160 6.745116 TGTTTCTCTCATCTTTGTCGTCTAA 58.255 36.000 0.00 0.00 0.00 2.10
587 1183 1.795286 GTCTCACCGCTCAAAGTCTTG 59.205 52.381 0.00 0.00 0.00 3.02
590 1186 2.174349 CCGCTCAAAGTCTTGCGC 59.826 61.111 0.00 0.00 45.97 6.09
596 1192 1.334869 CTCAAAGTCTTGCGCCAAACT 59.665 47.619 4.18 1.84 32.14 2.66
597 1193 1.065401 TCAAAGTCTTGCGCCAAACTG 59.935 47.619 4.18 0.00 32.14 3.16
610 3437 2.290323 GCCAAACTGACCACCTCTACAT 60.290 50.000 0.00 0.00 0.00 2.29
612 3439 3.244561 CCAAACTGACCACCTCTACATGT 60.245 47.826 2.69 2.69 0.00 3.21
620 3447 1.544246 CACCTCTACATGTGTCGACCA 59.456 52.381 14.12 11.06 0.00 4.02
622 3449 1.819288 CCTCTACATGTGTCGACCAGT 59.181 52.381 14.12 8.65 0.00 4.00
624 3451 2.488153 CTCTACATGTGTCGACCAGTCA 59.512 50.000 14.12 7.63 0.00 3.41
629 3456 2.900716 TGTGTCGACCAGTCATTCAA 57.099 45.000 14.12 0.00 0.00 2.69
640 3467 2.094906 CAGTCATTCAACGACCGTCCTA 60.095 50.000 0.00 0.00 33.70 2.94
651 3478 0.324923 ACCGTCCTATGCCAGTACCA 60.325 55.000 0.00 0.00 0.00 3.25
730 4074 0.402504 TTGGGGACGGTTTATGCAGT 59.597 50.000 0.00 0.00 0.00 4.40
734 4078 0.648958 GGACGGTTTATGCAGTACGC 59.351 55.000 0.00 3.22 42.89 4.42
735 4079 1.636988 GACGGTTTATGCAGTACGCT 58.363 50.000 10.27 1.01 43.06 5.07
736 4080 1.587034 GACGGTTTATGCAGTACGCTC 59.413 52.381 10.27 0.00 43.06 5.03
882 4228 0.234884 CACTTCTTCCGCAAACGACC 59.765 55.000 0.00 0.00 43.93 4.79
1068 4428 4.790962 TCCTCCCCGTCGTCCTCG 62.791 72.222 0.00 0.00 38.55 4.63
1215 4575 3.692406 GTCTCCGTGGGCTTCCGT 61.692 66.667 0.00 0.00 0.00 4.69
1227 4587 1.815817 GCTTCCGTGCACCCCAATTT 61.816 55.000 12.15 0.00 0.00 1.82
1319 4690 4.035792 CCGTGTTGTTCTTGTTGGTGATTA 59.964 41.667 0.00 0.00 0.00 1.75
1357 4728 0.036765 TGACGGGGAAAATCTGGACG 60.037 55.000 0.00 0.00 0.00 4.79
1479 4850 0.670162 AGCGTGCATGCTTTCTGTTT 59.330 45.000 27.72 3.15 44.46 2.83
1500 4871 1.414919 AGCAGTCGTTGTTACCCTCAA 59.585 47.619 0.00 0.00 0.00 3.02
1506 4877 6.106673 CAGTCGTTGTTACCCTCAATTAGAT 58.893 40.000 0.00 0.00 0.00 1.98
1507 4878 7.262772 CAGTCGTTGTTACCCTCAATTAGATA 58.737 38.462 0.00 0.00 0.00 1.98
1529 4952 5.848833 AATTGGGAAGCTTTCTGATCATC 57.151 39.130 4.35 0.00 0.00 2.92
1537 4960 2.863137 GCTTTCTGATCATCGACTGGTC 59.137 50.000 0.00 0.00 35.38 4.02
1606 5029 8.731275 TCCTGTATGTTTATTAAGTCACCATG 57.269 34.615 0.00 0.00 0.00 3.66
1610 5033 9.679661 TGTATGTTTATTAAGTCACCATGTCAT 57.320 29.630 0.00 0.00 0.00 3.06
1643 5066 2.430465 ACTCAAGTTGCTGCTGTATGG 58.570 47.619 0.00 0.00 0.00 2.74
1644 5067 2.224621 ACTCAAGTTGCTGCTGTATGGT 60.225 45.455 0.00 0.00 0.00 3.55
1645 5068 2.816087 CTCAAGTTGCTGCTGTATGGTT 59.184 45.455 0.00 0.00 0.00 3.67
1646 5069 2.553602 TCAAGTTGCTGCTGTATGGTTG 59.446 45.455 0.00 0.00 0.00 3.77
1647 5070 2.553602 CAAGTTGCTGCTGTATGGTTGA 59.446 45.455 0.00 0.00 0.00 3.18
1648 5071 2.430465 AGTTGCTGCTGTATGGTTGAG 58.570 47.619 0.00 0.00 0.00 3.02
1649 5072 2.154462 GTTGCTGCTGTATGGTTGAGT 58.846 47.619 0.00 0.00 0.00 3.41
1650 5073 2.554032 GTTGCTGCTGTATGGTTGAGTT 59.446 45.455 0.00 0.00 0.00 3.01
1651 5074 2.153645 TGCTGCTGTATGGTTGAGTTG 58.846 47.619 0.00 0.00 0.00 3.16
1652 5075 1.470098 GCTGCTGTATGGTTGAGTTGG 59.530 52.381 0.00 0.00 0.00 3.77
1653 5076 1.470098 CTGCTGTATGGTTGAGTTGGC 59.530 52.381 0.00 0.00 0.00 4.52
1654 5077 1.202867 TGCTGTATGGTTGAGTTGGCA 60.203 47.619 0.00 0.00 0.00 4.92
1655 5078 2.094675 GCTGTATGGTTGAGTTGGCAT 58.905 47.619 0.00 0.00 0.00 4.40
1656 5079 3.278574 GCTGTATGGTTGAGTTGGCATA 58.721 45.455 0.00 0.00 0.00 3.14
1657 5080 3.885297 GCTGTATGGTTGAGTTGGCATAT 59.115 43.478 0.00 0.00 0.00 1.78
1658 5081 4.261322 GCTGTATGGTTGAGTTGGCATATG 60.261 45.833 0.00 0.00 0.00 1.78
1659 5082 5.109500 TGTATGGTTGAGTTGGCATATGA 57.891 39.130 6.97 0.00 0.00 2.15
1660 5083 5.125356 TGTATGGTTGAGTTGGCATATGAG 58.875 41.667 6.97 0.00 0.00 2.90
1677 5100 8.355169 GGCATATGAGATGACATAAATGTGTTT 58.645 33.333 6.97 0.00 41.95 2.83
1678 5101 9.740239 GCATATGAGATGACATAAATGTGTTTT 57.260 29.630 6.97 0.00 41.95 2.43
1709 5132 3.289836 TGATGATAATGCTGGGGTGTTG 58.710 45.455 0.00 0.00 0.00 3.33
1734 5157 5.059161 TGGATCAATGAGCTATGCAAGTAC 58.941 41.667 0.00 0.00 0.00 2.73
1735 5158 5.163269 TGGATCAATGAGCTATGCAAGTACT 60.163 40.000 0.00 0.00 0.00 2.73
1736 5159 5.407995 GGATCAATGAGCTATGCAAGTACTC 59.592 44.000 0.00 0.00 0.00 2.59
1737 5160 4.697514 TCAATGAGCTATGCAAGTACTCC 58.302 43.478 0.00 0.00 0.00 3.85
1738 5161 3.760580 ATGAGCTATGCAAGTACTCCC 57.239 47.619 0.00 0.00 0.00 4.30
1739 5162 2.752030 TGAGCTATGCAAGTACTCCCT 58.248 47.619 0.00 0.00 0.00 4.20
1740 5163 2.695666 TGAGCTATGCAAGTACTCCCTC 59.304 50.000 0.00 0.00 0.00 4.30
1741 5164 2.036604 GAGCTATGCAAGTACTCCCTCC 59.963 54.545 0.00 0.00 0.00 4.30
1742 5165 1.269831 GCTATGCAAGTACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63
1743 5166 2.032620 CTATGCAAGTACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
1744 5167 0.824759 ATGCAAGTACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
1745 5168 1.255667 TGCAAGTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
1746 5169 1.957765 GCAAGTACTCCCTCCGTCCC 61.958 65.000 0.00 0.00 0.00 4.46
1747 5170 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
1748 5171 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1749 5172 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1750 5173 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1751 5174 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1752 5175 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1753 5176 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1754 5177 2.645797 ACTCCCTCCGTCCCAAAATAAA 59.354 45.455 0.00 0.00 0.00 1.40
1755 5178 3.268595 ACTCCCTCCGTCCCAAAATAAAT 59.731 43.478 0.00 0.00 0.00 1.40
1756 5179 3.626930 TCCCTCCGTCCCAAAATAAATG 58.373 45.455 0.00 0.00 0.00 2.32
1757 5180 3.010808 TCCCTCCGTCCCAAAATAAATGT 59.989 43.478 0.00 0.00 0.00 2.71
1758 5181 3.380320 CCCTCCGTCCCAAAATAAATGTC 59.620 47.826 0.00 0.00 0.00 3.06
1759 5182 4.270008 CCTCCGTCCCAAAATAAATGTCT 58.730 43.478 0.00 0.00 0.00 3.41
1760 5183 4.335594 CCTCCGTCCCAAAATAAATGTCTC 59.664 45.833 0.00 0.00 0.00 3.36
1761 5184 4.912586 TCCGTCCCAAAATAAATGTCTCA 58.087 39.130 0.00 0.00 0.00 3.27
1762 5185 5.317808 TCCGTCCCAAAATAAATGTCTCAA 58.682 37.500 0.00 0.00 0.00 3.02
1763 5186 5.182380 TCCGTCCCAAAATAAATGTCTCAAC 59.818 40.000 0.00 0.00 0.00 3.18
1764 5187 5.399013 CGTCCCAAAATAAATGTCTCAACC 58.601 41.667 0.00 0.00 0.00 3.77
1765 5188 5.183140 CGTCCCAAAATAAATGTCTCAACCT 59.817 40.000 0.00 0.00 0.00 3.50
1766 5189 6.294508 CGTCCCAAAATAAATGTCTCAACCTT 60.295 38.462 0.00 0.00 0.00 3.50
1767 5190 7.094549 CGTCCCAAAATAAATGTCTCAACCTTA 60.095 37.037 0.00 0.00 0.00 2.69
1768 5191 8.244113 GTCCCAAAATAAATGTCTCAACCTTAG 58.756 37.037 0.00 0.00 0.00 2.18
1769 5192 7.947890 TCCCAAAATAAATGTCTCAACCTTAGT 59.052 33.333 0.00 0.00 0.00 2.24
1770 5193 9.238368 CCCAAAATAAATGTCTCAACCTTAGTA 57.762 33.333 0.00 0.00 0.00 1.82
1777 5200 8.747538 AAATGTCTCAACCTTAGTACAAAGTT 57.252 30.769 0.00 0.00 0.00 2.66
1778 5201 7.730364 ATGTCTCAACCTTAGTACAAAGTTG 57.270 36.000 10.21 10.21 0.00 3.16
1779 5202 6.880484 TGTCTCAACCTTAGTACAAAGTTGA 58.120 36.000 15.47 15.47 31.66 3.18
1780 5203 6.759827 TGTCTCAACCTTAGTACAAAGTTGAC 59.240 38.462 13.46 8.65 30.50 3.18
1781 5204 6.759827 GTCTCAACCTTAGTACAAAGTTGACA 59.240 38.462 13.46 4.99 30.50 3.58
1782 5205 6.759827 TCTCAACCTTAGTACAAAGTTGACAC 59.240 38.462 13.46 0.00 30.50 3.67
1783 5206 6.408035 TCAACCTTAGTACAAAGTTGACACA 58.592 36.000 13.46 0.00 29.55 3.72
1784 5207 6.314400 TCAACCTTAGTACAAAGTTGACACAC 59.686 38.462 13.46 0.00 29.55 3.82
1785 5208 5.985911 ACCTTAGTACAAAGTTGACACACT 58.014 37.500 0.00 0.00 0.00 3.55
1786 5209 6.412214 ACCTTAGTACAAAGTTGACACACTT 58.588 36.000 0.00 0.00 38.74 3.16
1787 5210 7.558604 ACCTTAGTACAAAGTTGACACACTTA 58.441 34.615 0.00 0.00 35.87 2.24
1788 5211 8.208903 ACCTTAGTACAAAGTTGACACACTTAT 58.791 33.333 0.00 0.77 35.87 1.73
1789 5212 9.052759 CCTTAGTACAAAGTTGACACACTTATT 57.947 33.333 0.00 0.00 35.87 1.40
1793 5216 8.188139 AGTACAAAGTTGACACACTTATTTTGG 58.812 33.333 0.00 0.00 35.87 3.28
1794 5217 6.337356 ACAAAGTTGACACACTTATTTTGGG 58.663 36.000 0.00 0.00 35.87 4.12
1795 5218 6.153680 ACAAAGTTGACACACTTATTTTGGGA 59.846 34.615 0.00 0.00 35.87 4.37
1796 5219 5.767816 AGTTGACACACTTATTTTGGGAC 57.232 39.130 0.00 0.00 0.00 4.46
1797 5220 4.274950 AGTTGACACACTTATTTTGGGACG 59.725 41.667 0.00 0.00 0.00 4.79
1798 5221 3.142951 TGACACACTTATTTTGGGACGG 58.857 45.455 0.00 0.00 0.00 4.79
1799 5222 3.181453 TGACACACTTATTTTGGGACGGA 60.181 43.478 0.00 0.00 0.00 4.69
1800 5223 3.408634 ACACACTTATTTTGGGACGGAG 58.591 45.455 0.00 0.00 0.00 4.63
1801 5224 2.747446 CACACTTATTTTGGGACGGAGG 59.253 50.000 0.00 0.00 0.00 4.30
1802 5225 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1803 5226 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
1804 5227 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
1805 5228 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1806 5229 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1851 5274 9.936759 TGGAAACAAGTTGAATTTTTAGTTCTT 57.063 25.926 10.54 0.00 37.44 2.52
1882 5305 5.232838 GCAAGTTGATTTATTAGGCATGCAC 59.767 40.000 21.36 9.10 0.00 4.57
1883 5306 5.520376 AGTTGATTTATTAGGCATGCACC 57.480 39.130 21.36 2.42 0.00 5.01
1886 5309 4.285020 TGATTTATTAGGCATGCACCCAA 58.715 39.130 21.36 7.47 0.00 4.12
1917 5342 6.886459 TCCTTAAAATGCTTGTGAAGATAGCT 59.114 34.615 0.00 0.00 35.93 3.32
1918 5343 7.394359 TCCTTAAAATGCTTGTGAAGATAGCTT 59.606 33.333 0.00 0.00 35.93 3.74
1930 5355 7.865707 TGTGAAGATAGCTTTCTGTTTTTCTC 58.134 34.615 7.50 3.34 33.61 2.87
1935 5360 4.216366 AGCTTTCTGTTTTTCTCGCTTC 57.784 40.909 0.00 0.00 0.00 3.86
1939 5364 5.050023 GCTTTCTGTTTTTCTCGCTTCTACT 60.050 40.000 0.00 0.00 0.00 2.57
1969 5394 3.882288 TGCAGTCACATGTTTCTTAAGCA 59.118 39.130 0.00 1.37 0.00 3.91
2000 5425 6.713762 TTCTGGAAATTTCGCCATGAATAT 57.286 33.333 11.95 0.00 36.22 1.28
2008 5433 9.515020 GAAATTTCGCCATGAATATTTTAGACA 57.485 29.630 1.68 0.00 36.22 3.41
2014 5439 6.183360 CGCCATGAATATTTTAGACACCAAGT 60.183 38.462 0.00 0.00 0.00 3.16
2016 5441 8.682710 GCCATGAATATTTTAGACACCAAGTAA 58.317 33.333 0.00 0.00 0.00 2.24
2097 5531 6.399639 AGTGTAACAATTCCGAAAATGGTT 57.600 33.333 7.95 7.95 41.43 3.67
2100 5534 7.436970 AGTGTAACAATTCCGAAAATGGTTTTC 59.563 33.333 8.10 5.34 42.01 2.29
2164 5600 0.773644 AGCCAACTCATGTGTCCCTT 59.226 50.000 0.03 0.00 0.00 3.95
2165 5601 1.168714 GCCAACTCATGTGTCCCTTC 58.831 55.000 0.03 0.00 0.00 3.46
2166 5602 1.826385 CCAACTCATGTGTCCCTTCC 58.174 55.000 0.03 0.00 0.00 3.46
2167 5603 1.352352 CCAACTCATGTGTCCCTTCCT 59.648 52.381 0.03 0.00 0.00 3.36
2168 5604 2.224867 CCAACTCATGTGTCCCTTCCTT 60.225 50.000 0.03 0.00 0.00 3.36
2169 5605 2.816087 CAACTCATGTGTCCCTTCCTTG 59.184 50.000 0.03 0.00 0.00 3.61
2170 5606 2.338809 ACTCATGTGTCCCTTCCTTGA 58.661 47.619 0.00 0.00 0.00 3.02
2188 5624 5.488919 TCCTTGAGGAGAAATATGGAGTGTT 59.511 40.000 0.00 0.00 39.78 3.32
2232 5668 6.642131 GCAAACATAACTGCAATTCTTGAAGA 59.358 34.615 1.85 0.00 38.71 2.87
2252 5688 3.746492 AGATGTTTAGCACAAGTCCGTTC 59.254 43.478 0.00 0.00 39.50 3.95
2253 5689 3.188159 TGTTTAGCACAAGTCCGTTCT 57.812 42.857 0.00 0.00 29.87 3.01
2254 5690 3.537580 TGTTTAGCACAAGTCCGTTCTT 58.462 40.909 0.00 0.00 29.87 2.52
2255 5691 4.695396 TGTTTAGCACAAGTCCGTTCTTA 58.305 39.130 0.00 0.00 29.87 2.10
2256 5692 5.302360 TGTTTAGCACAAGTCCGTTCTTAT 58.698 37.500 0.00 0.00 29.87 1.73
2257 5693 5.761234 TGTTTAGCACAAGTCCGTTCTTATT 59.239 36.000 0.00 0.00 29.87 1.40
2258 5694 6.261381 TGTTTAGCACAAGTCCGTTCTTATTT 59.739 34.615 0.00 0.00 29.87 1.40
2259 5695 6.870971 TTAGCACAAGTCCGTTCTTATTTT 57.129 33.333 0.00 0.00 0.00 1.82
2260 5696 5.767816 AGCACAAGTCCGTTCTTATTTTT 57.232 34.783 0.00 0.00 0.00 1.94
2342 5778 3.646611 TGCAATCACTGTCCATTTGTG 57.353 42.857 0.00 0.00 0.00 3.33
2422 5858 6.425721 ACATTGCAAGACCAGATGAAAATTTG 59.574 34.615 4.94 0.00 0.00 2.32
2549 5988 3.963129 TCCCCAGGTTATGCTTTACTTG 58.037 45.455 0.00 0.00 0.00 3.16
2586 6025 7.699812 GCATGAATAGCTTTTAGTTCCTTTCTG 59.300 37.037 0.00 0.00 0.00 3.02
2596 6099 8.433421 TTTTAGTTCCTTTCTGTGTACTTCTG 57.567 34.615 0.00 0.00 0.00 3.02
3366 7515 1.358725 TAAGCCGTGCAATCGACTGC 61.359 55.000 12.77 12.77 42.95 4.40
3415 7564 4.276431 TCGACCAAAAACCAAGGTATGTTC 59.724 41.667 0.00 0.00 35.36 3.18
3592 7903 2.036733 TCTCCCTCGAATTGAAACACGT 59.963 45.455 0.00 0.00 0.00 4.49
3825 8136 5.967674 CAGAATTGCGGATAAACAGATTGTC 59.032 40.000 0.00 0.00 0.00 3.18
3916 8227 2.494530 CGTAGCTCTCTGAGGGGCC 61.495 68.421 6.69 0.00 0.00 5.80
4232 8543 4.585162 TGGTACGGATTTTTGGAACATGTT 59.415 37.500 11.78 11.78 39.30 2.71
4238 8549 5.055812 GGATTTTTGGAACATGTTTGCAGA 58.944 37.500 13.36 0.98 39.30 4.26
4255 8566 0.178068 AGACGCACCCGATTAAGCAT 59.822 50.000 0.00 0.00 38.29 3.79
4260 8571 2.598192 CGCACCCGATTAAGCATTTTTG 59.402 45.455 0.00 0.00 36.29 2.44
4320 8634 9.464714 CGACAAACATAGTCTAGCATAATACTT 57.535 33.333 0.00 0.00 33.89 2.24
4368 8699 6.585416 TGAGCTATGTCATATTCTGAGCAAA 58.415 36.000 5.94 0.00 33.51 3.68
4484 8815 3.694072 GCTAGACCATGTATGTTGCCAAA 59.306 43.478 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.671279 AAAAATGAAGAAAATATGCCCTAAAGG 57.329 29.630 0.00 0.00 39.47 3.11
68 69 1.064952 GGTGTGTTTTGGTCAACGGAG 59.935 52.381 0.00 0.00 0.00 4.63
69 70 1.096416 GGTGTGTTTTGGTCAACGGA 58.904 50.000 0.00 0.00 0.00 4.69
76 81 2.766400 CGTGCGGGTGTGTTTTGGT 61.766 57.895 0.00 0.00 0.00 3.67
115 120 0.478072 ACCCACTCATGCACCTTCAA 59.522 50.000 0.00 0.00 0.00 2.69
136 141 8.579850 TCACCACTCAAAGCATAAGAATATTT 57.420 30.769 0.00 0.00 0.00 1.40
157 162 0.179034 CAGCTATGGCCTTCCTCACC 60.179 60.000 3.32 0.00 39.73 4.02
307 331 5.373812 AGAACCTCCAATTACCATACCAG 57.626 43.478 0.00 0.00 0.00 4.00
329 353 5.047021 CCAGTCATCTTCTCTGAACCACTTA 60.047 44.000 0.00 0.00 0.00 2.24
349 373 2.450476 GTGGCAAAAGGATCATCCAGT 58.550 47.619 6.42 0.00 39.61 4.00
357 381 1.202830 TGTACCACGTGGCAAAAGGAT 60.203 47.619 34.26 14.75 39.32 3.24
391 415 4.451150 TCCACGCGCCCTGATGAC 62.451 66.667 5.73 0.00 0.00 3.06
415 439 2.180204 GCACGGTTGGGATCGATGG 61.180 63.158 0.54 0.00 0.00 3.51
446 470 3.119280 GCTAGGAGGAGAAGACAAGTGAC 60.119 52.174 0.00 0.00 0.00 3.67
525 1121 6.992123 TGAGAGAAACAACAGCTATTTGAGAA 59.008 34.615 12.96 0.00 0.00 2.87
526 1122 6.524734 TGAGAGAAACAACAGCTATTTGAGA 58.475 36.000 12.96 0.00 0.00 3.27
554 1150 2.159612 CGGTGAGACGATTAGACGACAA 60.160 50.000 0.00 0.00 37.03 3.18
560 1156 1.746470 TGAGCGGTGAGACGATTAGA 58.254 50.000 0.00 0.00 35.47 2.10
564 1160 0.603569 ACTTTGAGCGGTGAGACGAT 59.396 50.000 0.00 0.00 35.47 3.73
587 1183 2.594592 AGGTGGTCAGTTTGGCGC 60.595 61.111 0.00 0.00 0.00 6.53
590 1186 3.244561 ACATGTAGAGGTGGTCAGTTTGG 60.245 47.826 0.00 0.00 0.00 3.28
596 1192 1.544246 CGACACATGTAGAGGTGGTCA 59.456 52.381 9.61 0.00 38.23 4.02
597 1193 1.816835 TCGACACATGTAGAGGTGGTC 59.183 52.381 9.61 0.00 38.23 4.02
610 3437 2.479837 GTTGAATGACTGGTCGACACA 58.520 47.619 18.91 11.87 0.00 3.72
612 3439 1.338655 TCGTTGAATGACTGGTCGACA 59.661 47.619 18.91 2.63 0.00 4.35
620 3447 0.966920 AGGACGGTCGTTGAATGACT 59.033 50.000 16.27 0.00 34.62 3.41
622 3449 2.737359 GCATAGGACGGTCGTTGAATGA 60.737 50.000 8.79 0.00 0.00 2.57
624 3451 1.472728 GGCATAGGACGGTCGTTGAAT 60.473 52.381 8.79 0.00 0.00 2.57
629 3456 0.394762 TACTGGCATAGGACGGTCGT 60.395 55.000 0.00 8.53 36.78 4.34
640 3467 0.901827 TCATCGTGTGGTACTGGCAT 59.098 50.000 0.00 0.00 0.00 4.40
651 3478 2.844946 TCCACACATTTGTCATCGTGT 58.155 42.857 0.00 0.00 43.12 4.49
691 3518 7.984617 TCCCCAAAAACAGAACAAGATTAAAAG 59.015 33.333 0.00 0.00 0.00 2.27
809 4153 5.067805 GGTCCAGTTGAAGAAAACACATTCT 59.932 40.000 0.00 0.00 41.34 2.40
810 4154 5.281727 GGTCCAGTTGAAGAAAACACATTC 58.718 41.667 0.00 0.00 32.21 2.67
811 4155 4.202010 CGGTCCAGTTGAAGAAAACACATT 60.202 41.667 0.00 0.00 32.21 2.71
812 4156 3.315191 CGGTCCAGTTGAAGAAAACACAT 59.685 43.478 0.00 0.00 32.21 3.21
813 4157 2.680841 CGGTCCAGTTGAAGAAAACACA 59.319 45.455 0.00 0.00 32.21 3.72
841 4185 2.509336 AAAGAGCGCGATGGTCCG 60.509 61.111 12.10 0.00 46.44 4.79
852 4196 0.884514 GAAGAAGTGGCCCAAAGAGC 59.115 55.000 0.00 0.00 0.00 4.09
865 4209 0.234884 GTGGTCGTTTGCGGAAGAAG 59.765 55.000 0.00 0.00 38.89 2.85
882 4228 2.485814 GGGCTGACAGCTTAAGAAAGTG 59.514 50.000 25.92 0.00 41.99 3.16
1098 4458 2.050623 GACCTATACGCGCGGACC 60.051 66.667 35.22 9.59 0.00 4.46
1099 4459 2.050623 GGACCTATACGCGCGGAC 60.051 66.667 35.22 13.47 0.00 4.79
1100 4460 3.289834 GGGACCTATACGCGCGGA 61.290 66.667 35.22 29.30 0.00 5.54
1274 4634 2.490509 CAGCAACATGAGGCTTCAATCA 59.509 45.455 1.33 0.00 38.56 2.57
1357 4728 1.067821 CTACCCTCGAAGTCATCCAGC 59.932 57.143 0.00 0.00 0.00 4.85
1479 4850 2.241160 TGAGGGTAACAACGACTGCTA 58.759 47.619 0.00 0.00 39.74 3.49
1484 4855 8.658499 ATTATCTAATTGAGGGTAACAACGAC 57.342 34.615 0.00 0.00 39.74 4.34
1500 4871 9.294614 GATCAGAAAGCTTCCCAATTATCTAAT 57.705 33.333 0.00 0.00 0.00 1.73
1506 4877 5.528690 CGATGATCAGAAAGCTTCCCAATTA 59.471 40.000 0.00 0.00 0.00 1.40
1507 4878 4.337555 CGATGATCAGAAAGCTTCCCAATT 59.662 41.667 0.00 0.00 0.00 2.32
1537 4960 5.872617 TGTCACTAAACATCTATTGAACCCG 59.127 40.000 0.00 0.00 0.00 5.28
1610 5033 8.836413 GCAGCAACTTGAGTAAATATACCAATA 58.164 33.333 0.00 0.00 32.08 1.90
1643 5066 4.877823 TGTCATCTCATATGCCAACTCAAC 59.122 41.667 0.00 0.00 0.00 3.18
1644 5067 5.101648 TGTCATCTCATATGCCAACTCAA 57.898 39.130 0.00 0.00 0.00 3.02
1645 5068 4.758773 TGTCATCTCATATGCCAACTCA 57.241 40.909 0.00 0.00 0.00 3.41
1646 5069 7.734924 TTTATGTCATCTCATATGCCAACTC 57.265 36.000 0.00 0.00 31.58 3.01
1647 5070 7.722728 ACATTTATGTCATCTCATATGCCAACT 59.277 33.333 0.00 0.00 35.87 3.16
1648 5071 7.806487 CACATTTATGTCATCTCATATGCCAAC 59.194 37.037 0.00 0.00 39.39 3.77
1649 5072 7.503230 ACACATTTATGTCATCTCATATGCCAA 59.497 33.333 0.00 0.00 39.39 4.52
1650 5073 6.999871 ACACATTTATGTCATCTCATATGCCA 59.000 34.615 0.00 0.00 39.39 4.92
1651 5074 7.444629 ACACATTTATGTCATCTCATATGCC 57.555 36.000 0.00 0.00 39.39 4.40
1652 5075 9.740239 AAAACACATTTATGTCATCTCATATGC 57.260 29.630 0.00 0.00 39.39 3.14
1677 5100 8.361889 CCCAGCATTATCATCAACATATCAAAA 58.638 33.333 0.00 0.00 0.00 2.44
1678 5101 7.039574 CCCCAGCATTATCATCAACATATCAAA 60.040 37.037 0.00 0.00 0.00 2.69
1695 5118 0.409092 TCCATCAACACCCCAGCATT 59.591 50.000 0.00 0.00 0.00 3.56
1709 5132 4.760715 ACTTGCATAGCTCATTGATCCATC 59.239 41.667 0.00 0.00 0.00 3.51
1734 5157 3.359695 TTTATTTTGGGACGGAGGGAG 57.640 47.619 0.00 0.00 0.00 4.30
1735 5158 3.010808 ACATTTATTTTGGGACGGAGGGA 59.989 43.478 0.00 0.00 0.00 4.20
1736 5159 3.361786 ACATTTATTTTGGGACGGAGGG 58.638 45.455 0.00 0.00 0.00 4.30
1737 5160 4.270008 AGACATTTATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
1738 5161 4.941263 TGAGACATTTATTTTGGGACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
1739 5162 4.912586 TGAGACATTTATTTTGGGACGGA 58.087 39.130 0.00 0.00 0.00 4.69
1740 5163 5.399013 GTTGAGACATTTATTTTGGGACGG 58.601 41.667 0.00 0.00 0.00 4.79
1741 5164 5.183140 AGGTTGAGACATTTATTTTGGGACG 59.817 40.000 0.00 0.00 0.00 4.79
1742 5165 6.590234 AGGTTGAGACATTTATTTTGGGAC 57.410 37.500 0.00 0.00 0.00 4.46
1743 5166 7.947890 ACTAAGGTTGAGACATTTATTTTGGGA 59.052 33.333 0.00 0.00 31.38 4.37
1744 5167 8.122472 ACTAAGGTTGAGACATTTATTTTGGG 57.878 34.615 0.00 0.00 31.38 4.12
1751 5174 9.841295 AACTTTGTACTAAGGTTGAGACATTTA 57.159 29.630 19.08 0.00 31.38 1.40
1752 5175 8.621286 CAACTTTGTACTAAGGTTGAGACATTT 58.379 33.333 19.08 0.52 31.38 2.32
1753 5176 7.990886 TCAACTTTGTACTAAGGTTGAGACATT 59.009 33.333 20.87 5.37 33.77 2.71
1754 5177 7.441458 GTCAACTTTGTACTAAGGTTGAGACAT 59.559 37.037 23.18 2.26 31.82 3.06
1755 5178 6.759827 GTCAACTTTGTACTAAGGTTGAGACA 59.240 38.462 23.18 9.82 31.82 3.41
1756 5179 6.759827 TGTCAACTTTGTACTAAGGTTGAGAC 59.240 38.462 23.18 18.68 31.82 3.36
1757 5180 6.759827 GTGTCAACTTTGTACTAAGGTTGAGA 59.240 38.462 23.18 20.99 31.82 3.27
1758 5181 6.537301 TGTGTCAACTTTGTACTAAGGTTGAG 59.463 38.462 23.18 9.15 31.82 3.02
1759 5182 6.314400 GTGTGTCAACTTTGTACTAAGGTTGA 59.686 38.462 20.87 20.87 0.00 3.18
1760 5183 6.315393 AGTGTGTCAACTTTGTACTAAGGTTG 59.685 38.462 19.08 18.65 0.00 3.77
1761 5184 6.412214 AGTGTGTCAACTTTGTACTAAGGTT 58.588 36.000 19.08 9.89 0.00 3.50
1762 5185 5.985911 AGTGTGTCAACTTTGTACTAAGGT 58.014 37.500 19.08 11.48 0.00 3.50
1763 5186 6.920569 AAGTGTGTCAACTTTGTACTAAGG 57.079 37.500 19.08 4.85 37.05 2.69
1767 5190 8.188139 CCAAAATAAGTGTGTCAACTTTGTACT 58.812 33.333 0.00 0.00 40.77 2.73
1768 5191 7.434013 CCCAAAATAAGTGTGTCAACTTTGTAC 59.566 37.037 5.95 0.00 40.77 2.90
1769 5192 7.339721 TCCCAAAATAAGTGTGTCAACTTTGTA 59.660 33.333 5.95 0.00 40.77 2.41
1770 5193 6.153680 TCCCAAAATAAGTGTGTCAACTTTGT 59.846 34.615 5.95 0.00 40.77 2.83
1771 5194 6.475402 GTCCCAAAATAAGTGTGTCAACTTTG 59.525 38.462 5.95 0.00 40.77 2.77
1772 5195 6.569780 GTCCCAAAATAAGTGTGTCAACTTT 58.430 36.000 5.95 0.00 40.77 2.66
1773 5196 5.220970 CGTCCCAAAATAAGTGTGTCAACTT 60.221 40.000 0.00 0.00 42.89 2.66
1774 5197 4.274950 CGTCCCAAAATAAGTGTGTCAACT 59.725 41.667 0.00 0.00 0.00 3.16
1775 5198 4.533222 CGTCCCAAAATAAGTGTGTCAAC 58.467 43.478 0.00 0.00 0.00 3.18
1776 5199 3.566322 CCGTCCCAAAATAAGTGTGTCAA 59.434 43.478 0.00 0.00 0.00 3.18
1777 5200 3.142951 CCGTCCCAAAATAAGTGTGTCA 58.857 45.455 0.00 0.00 0.00 3.58
1778 5201 3.404899 TCCGTCCCAAAATAAGTGTGTC 58.595 45.455 0.00 0.00 0.00 3.67
1779 5202 3.408634 CTCCGTCCCAAAATAAGTGTGT 58.591 45.455 0.00 0.00 0.00 3.72
1780 5203 2.747446 CCTCCGTCCCAAAATAAGTGTG 59.253 50.000 0.00 0.00 0.00 3.82
1781 5204 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
1782 5205 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1783 5206 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1784 5207 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1785 5208 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1786 5209 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1787 5210 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1788 5211 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1789 5212 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
1790 5213 2.969950 CAATATACTCCCTCCGTCCCAA 59.030 50.000 0.00 0.00 0.00 4.12
1791 5214 2.605257 CAATATACTCCCTCCGTCCCA 58.395 52.381 0.00 0.00 0.00 4.37
1792 5215 1.275573 GCAATATACTCCCTCCGTCCC 59.724 57.143 0.00 0.00 0.00 4.46
1793 5216 2.028930 CAGCAATATACTCCCTCCGTCC 60.029 54.545 0.00 0.00 0.00 4.79
1794 5217 2.891580 TCAGCAATATACTCCCTCCGTC 59.108 50.000 0.00 0.00 0.00 4.79
1795 5218 2.958818 TCAGCAATATACTCCCTCCGT 58.041 47.619 0.00 0.00 0.00 4.69
1796 5219 3.766591 AGATCAGCAATATACTCCCTCCG 59.233 47.826 0.00 0.00 0.00 4.63
1797 5220 4.774726 TCAGATCAGCAATATACTCCCTCC 59.225 45.833 0.00 0.00 0.00 4.30
1798 5221 5.991933 TCAGATCAGCAATATACTCCCTC 57.008 43.478 0.00 0.00 0.00 4.30
1799 5222 5.189342 CCATCAGATCAGCAATATACTCCCT 59.811 44.000 0.00 0.00 0.00 4.20
1800 5223 5.046014 ACCATCAGATCAGCAATATACTCCC 60.046 44.000 0.00 0.00 0.00 4.30
1801 5224 6.047511 ACCATCAGATCAGCAATATACTCC 57.952 41.667 0.00 0.00 0.00 3.85
1802 5225 6.370994 CCAACCATCAGATCAGCAATATACTC 59.629 42.308 0.00 0.00 0.00 2.59
1803 5226 6.043590 TCCAACCATCAGATCAGCAATATACT 59.956 38.462 0.00 0.00 0.00 2.12
1804 5227 6.233434 TCCAACCATCAGATCAGCAATATAC 58.767 40.000 0.00 0.00 0.00 1.47
1805 5228 6.438186 TCCAACCATCAGATCAGCAATATA 57.562 37.500 0.00 0.00 0.00 0.86
1806 5229 5.314718 TCCAACCATCAGATCAGCAATAT 57.685 39.130 0.00 0.00 0.00 1.28
1842 5265 7.566760 TCAACTTGCTTCATCAAGAACTAAA 57.433 32.000 10.10 0.00 44.61 1.85
1843 5266 7.750229 ATCAACTTGCTTCATCAAGAACTAA 57.250 32.000 10.10 0.00 44.61 2.24
1851 5274 7.122501 TGCCTAATAAATCAACTTGCTTCATCA 59.877 33.333 0.00 0.00 0.00 3.07
1852 5275 7.483307 TGCCTAATAAATCAACTTGCTTCATC 58.517 34.615 0.00 0.00 0.00 2.92
1853 5276 7.408756 TGCCTAATAAATCAACTTGCTTCAT 57.591 32.000 0.00 0.00 0.00 2.57
1882 5305 6.486320 ACAAGCATTTTAAGGAACAATTTGGG 59.514 34.615 0.78 0.00 0.00 4.12
1883 5306 7.226325 TCACAAGCATTTTAAGGAACAATTTGG 59.774 33.333 0.78 0.00 0.00 3.28
1886 5309 8.203485 TCTTCACAAGCATTTTAAGGAACAATT 58.797 29.630 0.00 0.00 0.00 2.32
1917 5342 7.208080 AGTAGTAGAAGCGAGAAAAACAGAAA 58.792 34.615 0.00 0.00 0.00 2.52
1918 5343 6.746120 AGTAGTAGAAGCGAGAAAAACAGAA 58.254 36.000 0.00 0.00 0.00 3.02
1930 5355 1.472878 TGCAGTGGAGTAGTAGAAGCG 59.527 52.381 0.00 0.00 0.00 4.68
1935 5360 2.820197 TGTGACTGCAGTGGAGTAGTAG 59.180 50.000 27.27 0.00 34.49 2.57
1939 5364 1.970640 ACATGTGACTGCAGTGGAGTA 59.029 47.619 27.27 2.43 0.00 2.59
1978 5403 6.713762 AATATTCATGGCGAAATTTCCAGA 57.286 33.333 12.54 3.94 37.12 3.86
1980 5405 8.690884 TCTAAAATATTCATGGCGAAATTTCCA 58.309 29.630 12.54 6.83 37.12 3.53
2069 5503 6.452494 TTTTCGGAATTGTTACACTTTCCA 57.548 33.333 19.73 9.22 37.99 3.53
2092 5526 4.553330 ACCACTCATACTCGAAAACCAT 57.447 40.909 0.00 0.00 0.00 3.55
2097 5531 4.866508 ACTGAACCACTCATACTCGAAA 57.133 40.909 0.00 0.00 32.14 3.46
2100 5534 4.636648 AGTCTACTGAACCACTCATACTCG 59.363 45.833 0.00 0.00 32.14 4.18
2101 5535 5.677598 GCAGTCTACTGAACCACTCATACTC 60.678 48.000 14.21 0.00 46.59 2.59
2103 5537 4.425520 GCAGTCTACTGAACCACTCATAC 58.574 47.826 14.21 0.00 46.59 2.39
2104 5538 3.447586 GGCAGTCTACTGAACCACTCATA 59.552 47.826 14.21 0.00 46.59 2.15
2105 5539 2.234908 GGCAGTCTACTGAACCACTCAT 59.765 50.000 14.21 0.00 46.59 2.90
2106 5540 1.618837 GGCAGTCTACTGAACCACTCA 59.381 52.381 14.21 0.00 46.59 3.41
2107 5541 1.066787 GGGCAGTCTACTGAACCACTC 60.067 57.143 14.21 0.00 46.59 3.51
2108 5542 0.977395 GGGCAGTCTACTGAACCACT 59.023 55.000 14.21 0.00 46.59 4.00
2109 5543 0.977395 AGGGCAGTCTACTGAACCAC 59.023 55.000 14.21 0.00 46.59 4.16
2135 5571 3.181445 ACATGAGTTGGCTGAACACCTAA 60.181 43.478 0.00 0.00 36.98 2.69
2164 5600 5.032846 ACACTCCATATTTCTCCTCAAGGA 58.967 41.667 0.00 0.00 43.08 3.36
2165 5601 5.365021 ACACTCCATATTTCTCCTCAAGG 57.635 43.478 0.00 0.00 0.00 3.61
2220 5656 7.864379 ACTTGTGCTAAACATCTTCAAGAATTG 59.136 33.333 0.00 0.00 43.02 2.32
2232 5668 3.740115 AGAACGGACTTGTGCTAAACAT 58.260 40.909 0.00 0.00 38.99 2.71
2257 5693 7.123547 ACTCTCTTGGTGGTTATTTGACAAAAA 59.876 33.333 4.41 0.00 0.00 1.94
2258 5694 6.605594 ACTCTCTTGGTGGTTATTTGACAAAA 59.394 34.615 4.41 0.00 0.00 2.44
2259 5695 6.126409 ACTCTCTTGGTGGTTATTTGACAAA 58.874 36.000 2.48 2.48 0.00 2.83
2260 5696 5.690865 ACTCTCTTGGTGGTTATTTGACAA 58.309 37.500 0.00 0.00 0.00 3.18
2261 5697 5.304686 ACTCTCTTGGTGGTTATTTGACA 57.695 39.130 0.00 0.00 0.00 3.58
2262 5698 7.923414 ATTACTCTCTTGGTGGTTATTTGAC 57.077 36.000 0.00 0.00 0.00 3.18
2263 5699 8.383175 AGAATTACTCTCTTGGTGGTTATTTGA 58.617 33.333 0.00 0.00 0.00 2.69
2264 5700 8.567285 AGAATTACTCTCTTGGTGGTTATTTG 57.433 34.615 0.00 0.00 0.00 2.32
2265 5701 8.794335 GAGAATTACTCTCTTGGTGGTTATTT 57.206 34.615 0.00 0.00 46.32 1.40
2293 5729 5.842907 ACATAACCTGAAAGAAAGGCAAAC 58.157 37.500 0.00 0.00 38.48 2.93
2298 5734 7.917505 GCATATGAACATAACCTGAAAGAAAGG 59.082 37.037 6.97 0.00 40.93 3.11
2422 5858 5.113502 AGCTACAAGCACAAATCAAAGAC 57.886 39.130 1.22 0.00 45.56 3.01
2549 5988 5.192327 AGCTATTCATGCTTATTGGTTGC 57.808 39.130 0.00 0.00 37.52 4.17
2586 6025 3.746045 TGTCCTGGTTCAGAAGTACAC 57.254 47.619 0.00 0.00 32.44 2.90
2713 6216 5.048713 GGCATCTCCCATTTACTAAATTCCG 60.049 44.000 0.00 0.00 0.00 4.30
3129 7273 1.931172 ACACAAGAAAACCGAGACACG 59.069 47.619 0.00 0.00 42.18 4.49
3366 7515 1.453155 ATTCTTGGCCACTAAGTGCG 58.547 50.000 3.88 0.00 31.34 5.34
3415 7564 6.344500 ACATGCTAAGATTCTACTTGACCTG 58.656 40.000 0.00 0.00 0.00 4.00
3592 7903 3.257469 GAGCATGACTCACCTTGATCA 57.743 47.619 0.00 0.00 45.49 2.92
3825 8136 2.248835 AAAACAACCTCCGACGCCG 61.249 57.895 0.00 0.00 0.00 6.46
4238 8549 1.459450 AAATGCTTAATCGGGTGCGT 58.541 45.000 0.00 0.00 0.00 5.24
4373 8704 9.454585 CATTATTCACGATTTTTGTATCAGCAT 57.545 29.630 0.00 0.00 0.00 3.79
4388 8719 3.057876 AGCAAAAACGCCATTATTCACGA 60.058 39.130 0.00 0.00 0.00 4.35
4506 8837 5.525199 GCACCCGAATTTTAAGAAGTCAAA 58.475 37.500 0.00 0.00 0.00 2.69
4508 8839 4.759516 GCACCCGAATTTTAAGAAGTCA 57.240 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.