Multiple sequence alignment - TraesCS4A01G205000

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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 TraesCS4A01G205000 chr4A 100.000 3768 0 0 1 3768 497074203 497077970 0.000000e+00 6959.0
1 TraesCS4A01G205000 chr4A 83.125 160 15 7 3046 3198 40284986 40285140 6.570000e-28 135.0
2 TraesCS4A01G205000 chr4A 84.028 144 16 6 3042 3179 593825848 593825990 8.490000e-27 132.0
3 TraesCS4A01G205000 chr4D 90.466 1909 114 25 1624 3479 84302439 84304332 0.000000e+00 2455.0
4 TraesCS4A01G205000 chr4D 93.002 1629 95 14 75 1695 84300823 84302440 0.000000e+00 2359.0
5 TraesCS4A01G205000 chr4D 89.916 119 10 2 3472 3589 84306401 84306518 6.520000e-33 152.0
6 TraesCS4A01G205000 chr4D 78.523 149 18 10 3059 3197 101007951 101007807 6.710000e-13 86.1
7 TraesCS4A01G205000 chr4B 90.312 1858 117 28 1624 3437 119353369 119355207 0.000000e+00 2375.0
8 TraesCS4A01G205000 chr4B 92.558 1626 96 12 75 1695 119351765 119353370 0.000000e+00 2309.0
9 TraesCS4A01G205000 chr4B 94.574 129 7 0 3435 3563 119381003 119381131 2.300000e-47 200.0
10 TraesCS4A01G205000 chr5A 98.824 85 1 0 1 85 264112513 264112429 6.520000e-33 152.0
11 TraesCS4A01G205000 chr5A 96.703 91 3 0 1 91 512544434 512544344 6.520000e-33 152.0
12 TraesCS4A01G205000 chr5A 74.932 367 51 23 3057 3395 593504656 593505009 3.050000e-26 130.0
13 TraesCS4A01G205000 chr3A 98.824 85 1 0 1 85 89061231 89061315 6.520000e-33 152.0
14 TraesCS4A01G205000 chr3A 98.824 85 1 0 1 85 296937118 296937034 6.520000e-33 152.0
15 TraesCS4A01G205000 chr2D 91.071 112 8 2 1 112 193607800 193607691 2.340000e-32 150.0
16 TraesCS4A01G205000 chr2D 95.238 84 4 0 1 84 193080246 193080329 2.360000e-27 134.0
17 TraesCS4A01G205000 chr2A 95.699 93 3 1 1 92 680219613 680219705 8.430000e-32 148.0
18 TraesCS4A01G205000 chr1D 95.699 93 3 1 1 92 454211796 454211888 8.430000e-32 148.0
19 TraesCS4A01G205000 chr1A 95.699 93 3 1 1 92 25443614 25443522 8.430000e-32 148.0
20 TraesCS4A01G205000 chr5D 89.474 114 10 2 3654 3766 445969220 445969108 3.920000e-30 143.0
21 TraesCS4A01G205000 chr5D 96.970 33 1 0 3057 3089 23343417 23343449 5.260000e-04 56.5
22 TraesCS4A01G205000 chr3D 83.893 149 13 6 3059 3199 302295440 302295585 8.490000e-27 132.0
23 TraesCS4A01G205000 chr3D 97.826 46 1 0 3044 3089 103823962 103824007 3.120000e-11 80.5
24 TraesCS4A01G205000 chrUn 84.962 133 14 2 3636 3768 41239758 41239632 3.050000e-26 130.0
25 TraesCS4A01G205000 chr7D 86.842 114 13 2 3654 3766 598889822 598889934 3.950000e-25 126.0
26 TraesCS4A01G205000 chr6B 80.392 153 16 9 3057 3198 668971102 668971251 1.850000e-18 104.0
27 TraesCS4A01G205000 chr6B 90.244 41 3 1 3591 3630 617807967 617808007 7.000000e-03 52.8
28 TraesCS4A01G205000 chr7A 81.081 111 11 6 3081 3183 714507677 714507785 3.120000e-11 80.5
29 TraesCS4A01G205000 chr7A 81.081 111 11 6 3081 3183 714569202 714569310 3.120000e-11 80.5
30 TraesCS4A01G205000 chr3B 97.778 45 1 0 3045 3089 154454697 154454741 1.120000e-10 78.7
31 TraesCS4A01G205000 chr7B 78.462 130 16 8 3081 3200 22830706 22830833 1.450000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G205000 chr4A 497074203 497077970 3767 False 6959.000000 6959 100.000 1 3768 1 chr4A.!!$F2 3767
1 TraesCS4A01G205000 chr4D 84300823 84306518 5695 False 1655.333333 2455 91.128 75 3589 3 chr4D.!!$F1 3514
2 TraesCS4A01G205000 chr4B 119351765 119355207 3442 False 2342.000000 2375 91.435 75 3437 2 chr4B.!!$F2 3362

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
316 317 0.242017 GTCCAACAGATGCTTGGTGC 59.758 55.0 11.42 0.0 39.48 5.01 F
1020 1028 0.550914 TGCCTGTGACCAAGGTTCTT 59.449 50.0 0.00 0.0 0.00 2.52 F
2603 2692 0.322366 TGATGATGCCGCTGGTGAAA 60.322 50.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1555 0.486879 AATTTCCTTGGGCTCCACCA 59.513 50.0 0.0 0.0 42.05 4.17 R
2715 2804 1.028330 ACCAGCATCATCGCCAACAG 61.028 55.0 0.0 0.0 0.00 3.16 R
3611 5825 0.179215 GCCTCGACATTTTGACGCAG 60.179 55.0 0.0 0.0 35.65 5.18 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
21 22 4.171878 TGATATCTTCCCGTGAGTCTCT 57.828 45.455 3.98 0.00 0.00 3.10
22 23 3.885901 TGATATCTTCCCGTGAGTCTCTG 59.114 47.826 3.98 0.00 0.00 3.35
23 24 2.516227 ATCTTCCCGTGAGTCTCTGA 57.484 50.000 0.65 0.00 0.00 3.27
24 25 2.516227 TCTTCCCGTGAGTCTCTGAT 57.484 50.000 0.65 0.00 0.00 2.90
25 26 2.370349 TCTTCCCGTGAGTCTCTGATC 58.630 52.381 0.65 0.00 0.00 2.92
26 27 2.025793 TCTTCCCGTGAGTCTCTGATCT 60.026 50.000 0.65 0.00 0.00 2.75
27 28 2.516227 TCCCGTGAGTCTCTGATCTT 57.484 50.000 0.65 0.00 0.00 2.40
28 29 2.095461 TCCCGTGAGTCTCTGATCTTG 58.905 52.381 0.65 0.00 0.00 3.02
29 30 2.095461 CCCGTGAGTCTCTGATCTTGA 58.905 52.381 0.65 0.00 0.00 3.02
30 31 2.692557 CCCGTGAGTCTCTGATCTTGAT 59.307 50.000 0.65 0.00 0.00 2.57
31 32 3.243367 CCCGTGAGTCTCTGATCTTGATC 60.243 52.174 0.65 3.82 0.00 2.92
32 33 3.547813 CCGTGAGTCTCTGATCTTGATCG 60.548 52.174 0.65 2.26 0.00 3.69
33 34 3.064682 CGTGAGTCTCTGATCTTGATCGT 59.935 47.826 0.65 0.00 0.00 3.73
34 35 4.271291 CGTGAGTCTCTGATCTTGATCGTA 59.729 45.833 0.65 0.00 0.00 3.43
35 36 5.507077 GTGAGTCTCTGATCTTGATCGTAC 58.493 45.833 0.65 2.53 0.00 3.67
36 37 5.065346 GTGAGTCTCTGATCTTGATCGTACA 59.935 44.000 0.65 0.00 0.00 2.90
37 38 5.065346 TGAGTCTCTGATCTTGATCGTACAC 59.935 44.000 0.65 1.73 0.00 2.90
38 39 4.034626 AGTCTCTGATCTTGATCGTACACG 59.965 45.833 6.19 0.00 41.45 4.49
39 40 3.939592 TCTCTGATCTTGATCGTACACGT 59.060 43.478 1.19 0.00 40.80 4.49
40 41 4.395231 TCTCTGATCTTGATCGTACACGTT 59.605 41.667 1.19 0.00 40.80 3.99
41 42 5.055642 TCTGATCTTGATCGTACACGTTT 57.944 39.130 1.19 0.00 40.80 3.60
42 43 4.857037 TCTGATCTTGATCGTACACGTTTG 59.143 41.667 1.19 0.00 40.80 2.93
43 44 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
44 45 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
58 59 4.577687 CGTTTGCGTGTATGATTAGTGT 57.422 40.909 0.00 0.00 0.00 3.55
59 60 5.689927 CGTTTGCGTGTATGATTAGTGTA 57.310 39.130 0.00 0.00 0.00 2.90
60 61 5.478001 CGTTTGCGTGTATGATTAGTGTAC 58.522 41.667 0.00 0.00 0.00 2.90
61 62 5.478001 GTTTGCGTGTATGATTAGTGTACG 58.522 41.667 0.00 0.00 0.00 3.67
62 63 3.697982 TGCGTGTATGATTAGTGTACGG 58.302 45.455 0.00 0.00 0.00 4.02
63 64 3.129113 TGCGTGTATGATTAGTGTACGGT 59.871 43.478 0.00 0.00 0.00 4.83
64 65 3.727723 GCGTGTATGATTAGTGTACGGTC 59.272 47.826 0.00 0.00 0.00 4.79
65 66 4.731483 GCGTGTATGATTAGTGTACGGTCA 60.731 45.833 0.00 0.00 0.00 4.02
66 67 5.334319 CGTGTATGATTAGTGTACGGTCAA 58.666 41.667 0.00 0.00 0.00 3.18
67 68 5.801444 CGTGTATGATTAGTGTACGGTCAAA 59.199 40.000 0.00 0.00 0.00 2.69
68 69 6.474427 CGTGTATGATTAGTGTACGGTCAAAT 59.526 38.462 0.00 0.00 0.00 2.32
69 70 7.305820 CGTGTATGATTAGTGTACGGTCAAATC 60.306 40.741 0.00 0.00 0.00 2.17
70 71 6.693978 TGTATGATTAGTGTACGGTCAAATCG 59.306 38.462 0.00 0.00 0.00 3.34
71 72 4.426416 TGATTAGTGTACGGTCAAATCGG 58.574 43.478 0.00 0.00 0.00 4.18
72 73 2.945447 TAGTGTACGGTCAAATCGGG 57.055 50.000 0.00 0.00 0.00 5.14
73 74 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.000 0.00 0.00 0.00 5.73
74 75 0.741927 GTGTACGGTCAAATCGGGGG 60.742 60.000 0.00 0.00 0.00 5.40
75 76 1.816679 GTACGGTCAAATCGGGGGC 60.817 63.158 0.00 0.00 0.00 5.80
76 77 3.374012 TACGGTCAAATCGGGGGCG 62.374 63.158 0.00 0.00 0.00 6.13
77 78 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
78 79 2.822701 GGTCAAATCGGGGGCGTC 60.823 66.667 0.00 0.00 0.00 5.19
79 80 2.046700 GTCAAATCGGGGGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
121 122 8.649841 GCATATGCGTATTAAAAATGATGCATT 58.350 29.630 12.82 0.00 40.73 3.56
122 123 9.946418 CATATGCGTATTAAAAATGATGCATTG 57.054 29.630 0.00 2.17 40.73 2.82
123 124 9.695526 ATATGCGTATTAAAAATGATGCATTGT 57.304 25.926 0.00 0.00 40.73 2.71
190 191 4.370049 CAACAATGTTGCCAACTCATGAA 58.630 39.130 13.51 0.00 0.00 2.57
198 199 1.470098 GCCAACTCATGAAAGCGATGT 59.530 47.619 0.00 0.00 0.00 3.06
244 245 3.466836 ACAGTCTGACGCTTGAAATTCA 58.533 40.909 6.91 0.00 0.00 2.57
273 274 2.171448 AGTGAGATTGGATACTGTGGCC 59.829 50.000 0.00 0.00 37.61 5.36
279 280 1.195442 TGGATACTGTGGCCGACCAA 61.195 55.000 0.00 0.00 43.67 3.67
309 310 2.359850 TGGCCGTCCAACAGATGC 60.360 61.111 0.00 0.00 39.99 3.91
310 311 2.045926 GGCCGTCCAACAGATGCT 60.046 61.111 0.00 0.00 0.00 3.79
316 317 0.242017 GTCCAACAGATGCTTGGTGC 59.758 55.000 11.42 0.00 39.48 5.01
335 336 3.379372 GTGCTAGCCATGAATGATTGTGT 59.621 43.478 13.29 0.00 0.00 3.72
342 343 7.918536 AGCCATGAATGATTGTGTAGATATC 57.081 36.000 0.00 0.00 0.00 1.63
378 379 5.357032 GGTGATTTAGTACCCAAGTTCCATG 59.643 44.000 0.00 0.00 0.00 3.66
465 466 5.818136 ATGGATTGTGTGCATTGTAGTAC 57.182 39.130 0.00 0.00 34.99 2.73
519 522 9.561069 TGGATCATTATTACCTCTAAAAAGAGC 57.439 33.333 0.00 0.00 34.74 4.09
532 535 2.969628 AAAGAGCCGTGGACTATCAG 57.030 50.000 0.00 0.00 0.00 2.90
542 545 4.936411 CCGTGGACTATCAGACGAGTATAT 59.064 45.833 0.00 0.00 33.64 0.86
585 591 9.565090 CCTGACATGAGAATATCCAAAGATTTA 57.435 33.333 0.00 0.00 33.67 1.40
616 622 2.118228 TGAAAACTTGTGCATGCGTC 57.882 45.000 14.09 9.43 0.00 5.19
617 623 1.268999 TGAAAACTTGTGCATGCGTCC 60.269 47.619 14.09 3.96 0.00 4.79
763 770 6.753180 AGATGTATATGACTGACGCATTTCT 58.247 36.000 0.00 0.00 0.00 2.52
823 830 8.416329 GCATATAAAACCATTTCCATCTTGTCT 58.584 33.333 0.00 0.00 0.00 3.41
892 899 4.209288 CGAGTGCCATTTCTAGAAATACCG 59.791 45.833 26.34 20.53 38.84 4.02
963 971 5.450818 TTAATTCTAGGACCAGGCATTGT 57.549 39.130 0.00 0.00 0.00 2.71
972 980 5.930135 AGGACCAGGCATTGTAGTATAAAG 58.070 41.667 0.00 0.00 0.00 1.85
973 981 4.515567 GGACCAGGCATTGTAGTATAAAGC 59.484 45.833 0.00 0.00 0.00 3.51
998 1006 1.973281 GTGTGCATCCCACCAGGTG 60.973 63.158 13.35 13.35 44.01 4.00
1020 1028 0.550914 TGCCTGTGACCAAGGTTCTT 59.449 50.000 0.00 0.00 0.00 2.52
1021 1029 1.771854 TGCCTGTGACCAAGGTTCTTA 59.228 47.619 0.00 0.00 0.00 2.10
1027 1037 6.183360 GCCTGTGACCAAGGTTCTTATATTTC 60.183 42.308 0.00 0.00 0.00 2.17
1036 1046 8.971073 CCAAGGTTCTTATATTTCCAACAAGAT 58.029 33.333 0.00 0.00 0.00 2.40
1063 1073 6.040209 TCAACGTATGTAACAATAGGGTGT 57.960 37.500 0.00 0.00 37.07 4.16
1183 1195 4.145807 CCAGAGACCATAGGACGTATCTT 58.854 47.826 0.00 0.00 28.29 2.40
1290 1302 4.981806 TGGAAGGAAGATAAATTTGGCG 57.018 40.909 0.00 0.00 0.00 5.69
1319 1331 6.253727 CACAATAGTTATGACTCGTTGTCCTC 59.746 42.308 14.52 0.00 44.75 3.71
1535 1548 3.496331 TGGTTGGGGTCAAAAGATCTTC 58.504 45.455 8.78 0.00 34.28 2.87
1542 1555 4.082125 GGGTCAAAAGATCTTCACATGGT 58.918 43.478 8.78 0.00 0.00 3.55
1603 1616 9.722184 CTACAATCAAGATAGATCATTGACCAT 57.278 33.333 6.67 0.00 35.89 3.55
1680 1693 7.762615 TCAGTTACTAGTTGTACATATTGGTGC 59.237 37.037 0.00 0.00 0.00 5.01
1689 1772 3.498774 ACATATTGGTGCAGAGGATCC 57.501 47.619 2.48 2.48 33.66 3.36
1721 1804 9.515226 TTCATTTACTTATAGGTTGCAGACTTT 57.485 29.630 0.00 0.00 0.00 2.66
1722 1805 9.162764 TCATTTACTTATAGGTTGCAGACTTTC 57.837 33.333 0.00 0.00 0.00 2.62
1727 1810 0.779997 AGGTTGCAGACTTTCCCCAT 59.220 50.000 0.00 0.00 0.00 4.00
1805 1888 7.014711 TGTTTATGCAAGGGAATGTTTCAACTA 59.985 33.333 0.00 0.00 0.00 2.24
2016 2101 1.129437 GCTTGGCGATGAGTGAAGAAC 59.871 52.381 0.00 0.00 0.00 3.01
2031 2116 4.033358 GTGAAGAACAAGGTGCGATAGATG 59.967 45.833 0.00 0.00 39.76 2.90
2058 2143 8.144155 TGACTTCATGTTTTTGTACGATAACA 57.856 30.769 17.97 17.97 35.25 2.41
2114 2199 4.446371 CATGGGAGTGAGTTCTTGGATAC 58.554 47.826 0.00 0.00 0.00 2.24
2213 2299 5.250200 ACTAAATGTTACAGGGATTTCGCA 58.750 37.500 0.00 0.00 0.00 5.10
2284 2370 6.482835 GTGCGTGCACAATATAAATGAACTA 58.517 36.000 19.45 0.00 45.53 2.24
2436 2522 6.293190 CGTGGCATCACAAGTTTTTCTACTAA 60.293 38.462 0.00 0.00 43.79 2.24
2543 2632 1.956869 TCTGGAAGAGGGAGATGCAA 58.043 50.000 0.00 0.00 38.67 4.08
2559 2648 2.098614 TGCAAATAACGGTGATGGCAT 58.901 42.857 0.00 0.00 0.00 4.40
2561 2650 3.696548 TGCAAATAACGGTGATGGCATTA 59.303 39.130 0.00 0.00 0.00 1.90
2593 2682 2.085320 GCTGATGGAGATGATGATGCC 58.915 52.381 0.00 0.00 0.00 4.40
2603 2692 0.322366 TGATGATGCCGCTGGTGAAA 60.322 50.000 0.00 0.00 0.00 2.69
2650 2739 0.567182 AGGATGAGGGAGATGGAGCT 59.433 55.000 0.00 0.00 0.00 4.09
2671 2760 0.683973 ATGACGATGGAGATGGAGCC 59.316 55.000 0.00 0.00 0.00 4.70
2673 2762 2.341543 CGATGGAGATGGAGCCGG 59.658 66.667 0.00 0.00 0.00 6.13
2701 2790 4.888326 AGATGGAGATGGAGCTTATGAC 57.112 45.455 0.00 0.00 0.00 3.06
2715 2804 3.060873 GCTTATGACGATGAAGACGAAGC 60.061 47.826 0.00 0.00 32.88 3.86
2798 2896 2.174685 TTAGTGGCATCCAGGAGCTA 57.825 50.000 9.85 2.69 32.34 3.32
2810 2908 0.401738 AGGAGCTAACCTTGCAAGCA 59.598 50.000 21.43 7.16 38.75 3.91
2830 2928 2.268762 TGGTTGCAGTTACATGCTGA 57.731 45.000 3.29 0.00 46.63 4.26
2838 2936 6.135290 TGCAGTTACATGCTGATTAATTCC 57.865 37.500 3.29 0.00 46.63 3.01
2975 3075 7.441157 TCGCTTTTGAATATCCGAATATGTTCT 59.559 33.333 0.46 0.00 30.67 3.01
2988 3088 5.065218 CGAATATGTTCTTGAAGGAACCCTG 59.935 44.000 0.46 0.00 43.31 4.45
3012 3112 1.153249 AACCGCCCCACACATATCG 60.153 57.895 0.00 0.00 0.00 2.92
3017 3117 0.179045 GCCCCACACATATCGAAGCT 60.179 55.000 0.00 0.00 0.00 3.74
3022 3122 2.419673 CCACACATATCGAAGCTTGCAA 59.580 45.455 2.10 0.00 0.00 4.08
3044 3144 1.055849 TGCTTCTTCAGGGTAGTGCA 58.944 50.000 0.00 0.00 0.00 4.57
3162 3286 7.856145 ACATGTTTGTAAAATTTTCAAGGCA 57.144 28.000 6.72 12.97 33.16 4.75
3261 3391 7.363268 GCATTTCAAGGTATTTCATCTTGGACT 60.363 37.037 0.00 0.00 38.59 3.85
3286 3416 9.702726 CTTTTTACACACATATACCTTTCATCG 57.297 33.333 0.00 0.00 0.00 3.84
3342 3473 6.467677 TGAACCAACAAGTTTGGATTTTGAA 58.532 32.000 10.02 0.00 42.06 2.69
3346 3477 9.454859 AACCAACAAGTTTGGATTTTGAATTTA 57.545 25.926 10.02 0.00 42.06 1.40
3347 3478 9.454859 ACCAACAAGTTTGGATTTTGAATTTAA 57.545 25.926 10.02 0.00 42.06 1.52
3463 3601 5.506982 GCAAAAGTTTCTCTCTGATGTGCTT 60.507 40.000 0.00 0.00 0.00 3.91
3466 3604 4.712476 AGTTTCTCTCTGATGTGCTTGTT 58.288 39.130 0.00 0.00 0.00 2.83
3479 3617 5.499139 TGTGCTTGTTAAAGGTTTCTCTG 57.501 39.130 0.00 0.00 33.68 3.35
3481 3619 3.951037 TGCTTGTTAAAGGTTTCTCTGCA 59.049 39.130 0.00 0.00 33.68 4.41
3482 3620 4.202010 TGCTTGTTAAAGGTTTCTCTGCAC 60.202 41.667 0.00 0.00 33.68 4.57
3483 3621 4.793028 GCTTGTTAAAGGTTTCTCTGCACC 60.793 45.833 0.00 0.00 33.68 5.01
3484 3622 3.219281 TGTTAAAGGTTTCTCTGCACCC 58.781 45.455 0.00 0.00 32.92 4.61
3485 3623 3.117663 TGTTAAAGGTTTCTCTGCACCCT 60.118 43.478 0.00 0.00 32.92 4.34
3487 3625 1.986882 AAGGTTTCTCTGCACCCTTG 58.013 50.000 0.00 0.00 34.32 3.61
3488 3626 0.846693 AGGTTTCTCTGCACCCTTGT 59.153 50.000 0.00 0.00 32.92 3.16
3490 3628 1.338020 GGTTTCTCTGCACCCTTGTTG 59.662 52.381 0.00 0.00 0.00 3.33
3553 5767 6.520742 GCTTATAAGAGGCCCACTATGATGAA 60.521 42.308 16.85 0.00 0.00 2.57
3554 5768 7.574021 TTATAAGAGGCCCACTATGATGAAT 57.426 36.000 0.00 0.00 0.00 2.57
3570 5784 9.524106 CTATGATGAATTTTAAGAGCAATGCAA 57.476 29.630 8.35 0.00 0.00 4.08
3571 5785 7.585286 TGATGAATTTTAAGAGCAATGCAAC 57.415 32.000 8.35 0.71 0.00 4.17
3572 5786 7.153315 TGATGAATTTTAAGAGCAATGCAACA 58.847 30.769 8.35 0.00 0.00 3.33
3585 5799 1.225376 TGCAACAACTAACGGGAGCG 61.225 55.000 0.00 0.00 0.00 5.03
3589 5803 1.252904 ACAACTAACGGGAGCGGCTA 61.253 55.000 0.60 0.00 0.00 3.93
3590 5804 0.527817 CAACTAACGGGAGCGGCTAG 60.528 60.000 0.60 0.00 0.00 3.42
3591 5805 1.673808 AACTAACGGGAGCGGCTAGG 61.674 60.000 0.60 0.00 0.00 3.02
3592 5806 2.043652 TAACGGGAGCGGCTAGGT 60.044 61.111 0.60 0.00 0.00 3.08
3593 5807 1.673808 CTAACGGGAGCGGCTAGGTT 61.674 60.000 0.60 10.02 0.00 3.50
3594 5808 1.259840 TAACGGGAGCGGCTAGGTTT 61.260 55.000 15.06 5.25 0.00 3.27
3595 5809 2.120737 AACGGGAGCGGCTAGGTTTT 62.121 55.000 0.60 0.00 0.00 2.43
3596 5810 1.814169 CGGGAGCGGCTAGGTTTTC 60.814 63.158 0.60 0.00 0.00 2.29
3597 5811 1.451567 GGGAGCGGCTAGGTTTTCC 60.452 63.158 0.60 0.00 41.05 3.13
3611 5825 3.936661 GGTTTTCCTATTCGACGCATTC 58.063 45.455 0.00 0.00 36.94 2.67
3612 5826 3.621715 GGTTTTCCTATTCGACGCATTCT 59.378 43.478 0.00 0.00 36.94 2.40
3613 5827 4.494199 GGTTTTCCTATTCGACGCATTCTG 60.494 45.833 0.00 0.00 36.94 3.02
3614 5828 1.852942 TCCTATTCGACGCATTCTGC 58.147 50.000 0.00 0.00 40.69 4.26
3626 5840 1.906966 GCATTCTGCGTCAAAATGTCG 59.093 47.619 7.42 0.00 33.82 4.35
3627 5841 2.412716 GCATTCTGCGTCAAAATGTCGA 60.413 45.455 7.42 0.00 33.82 4.20
3628 5842 3.410850 CATTCTGCGTCAAAATGTCGAG 58.589 45.455 1.39 0.00 30.84 4.04
3629 5843 1.428448 TCTGCGTCAAAATGTCGAGG 58.572 50.000 1.39 0.00 30.84 4.63
3630 5844 0.179215 CTGCGTCAAAATGTCGAGGC 60.179 55.000 1.39 0.00 42.02 4.70
3631 5845 1.225745 GCGTCAAAATGTCGAGGCG 60.226 57.895 1.39 0.00 33.86 5.52
3632 5846 1.225745 CGTCAAAATGTCGAGGCGC 60.226 57.895 0.00 0.00 30.84 6.53
3633 5847 1.134694 GTCAAAATGTCGAGGCGCC 59.865 57.895 21.89 21.89 0.00 6.53
3634 5848 2.098298 CAAAATGTCGAGGCGCCG 59.902 61.111 23.20 10.72 0.00 6.46
3635 5849 3.799755 AAAATGTCGAGGCGCCGC 61.800 61.111 23.20 22.30 0.00 6.53
3647 5861 2.512974 CGCCGCGGAAAACCCTAT 60.513 61.111 33.48 0.00 0.00 2.57
3648 5862 2.110352 CGCCGCGGAAAACCCTATT 61.110 57.895 33.48 0.00 0.00 1.73
3649 5863 1.725665 GCCGCGGAAAACCCTATTC 59.274 57.895 33.48 1.41 0.00 1.75
3650 5864 2.011453 CCGCGGAAAACCCTATTCG 58.989 57.895 24.07 0.00 0.00 3.34
3651 5865 1.350665 CGCGGAAAACCCTATTCGC 59.649 57.895 0.00 0.00 0.00 4.70
3652 5866 1.725665 GCGGAAAACCCTATTCGCC 59.274 57.895 0.00 0.00 0.00 5.54
3653 5867 0.746923 GCGGAAAACCCTATTCGCCT 60.747 55.000 0.00 0.00 0.00 5.52
3654 5868 1.296727 CGGAAAACCCTATTCGCCTC 58.703 55.000 0.00 0.00 0.00 4.70
3655 5869 1.296727 GGAAAACCCTATTCGCCTCG 58.703 55.000 0.00 0.00 0.00 4.63
3656 5870 0.656259 GAAAACCCTATTCGCCTCGC 59.344 55.000 0.00 0.00 0.00 5.03
3657 5871 0.746923 AAAACCCTATTCGCCTCGCC 60.747 55.000 0.00 0.00 0.00 5.54
3658 5872 2.918230 AAACCCTATTCGCCTCGCCG 62.918 60.000 0.00 0.00 0.00 6.46
3660 5874 4.585526 CCTATTCGCCTCGCCGCA 62.586 66.667 0.00 0.00 0.00 5.69
3661 5875 2.356313 CTATTCGCCTCGCCGCAT 60.356 61.111 0.00 0.00 0.00 4.73
3662 5876 1.956170 CTATTCGCCTCGCCGCATT 60.956 57.895 0.00 0.00 0.00 3.56
3663 5877 1.891060 CTATTCGCCTCGCCGCATTC 61.891 60.000 0.00 0.00 0.00 2.67
3664 5878 2.363711 TATTCGCCTCGCCGCATTCT 62.364 55.000 0.00 0.00 0.00 2.40
3675 5889 4.157817 GCATTCTGCGGCAAAGTG 57.842 55.556 3.44 0.00 31.71 3.16
3676 5890 1.286880 GCATTCTGCGGCAAAGTGT 59.713 52.632 3.44 0.00 31.71 3.55
3677 5891 0.730494 GCATTCTGCGGCAAAGTGTC 60.730 55.000 3.44 0.00 31.71 3.67
3685 5899 2.828933 GGCAAAGTGTCGACCTCTC 58.171 57.895 14.12 1.12 0.00 3.20
3686 5900 1.009389 GGCAAAGTGTCGACCTCTCG 61.009 60.000 14.12 7.75 41.65 4.04
3687 5901 1.618640 GCAAAGTGTCGACCTCTCGC 61.619 60.000 14.12 13.14 39.96 5.03
3688 5902 0.318699 CAAAGTGTCGACCTCTCGCA 60.319 55.000 14.12 0.00 39.96 5.10
3689 5903 0.318784 AAAGTGTCGACCTCTCGCAC 60.319 55.000 14.12 2.27 42.41 5.34
3690 5904 1.452953 AAGTGTCGACCTCTCGCACA 61.453 55.000 14.12 6.11 43.48 4.57
3691 5905 1.729838 GTGTCGACCTCTCGCACAC 60.730 63.158 14.12 0.00 42.03 3.82
3692 5906 2.126424 GTCGACCTCTCGCACACC 60.126 66.667 3.51 0.00 39.96 4.16
3693 5907 3.371063 TCGACCTCTCGCACACCC 61.371 66.667 0.00 0.00 39.96 4.61
3694 5908 4.436998 CGACCTCTCGCACACCCC 62.437 72.222 0.00 0.00 31.91 4.95
3695 5909 3.311110 GACCTCTCGCACACCCCA 61.311 66.667 0.00 0.00 0.00 4.96
3696 5910 2.607750 ACCTCTCGCACACCCCAT 60.608 61.111 0.00 0.00 0.00 4.00
3697 5911 2.185310 GACCTCTCGCACACCCCATT 62.185 60.000 0.00 0.00 0.00 3.16
3698 5912 1.746615 CCTCTCGCACACCCCATTG 60.747 63.158 0.00 0.00 0.00 2.82
3699 5913 1.746615 CTCTCGCACACCCCATTGG 60.747 63.158 0.00 0.00 41.37 3.16
3709 5923 2.492418 CCCCATTGGTCGTTCATGG 58.508 57.895 1.20 0.00 0.00 3.66
3710 5924 2.492418 CCCATTGGTCGTTCATGGG 58.508 57.895 1.20 2.03 45.01 4.00
3711 5925 1.666209 CCCATTGGTCGTTCATGGGC 61.666 60.000 3.50 0.00 44.54 5.36
3712 5926 1.666209 CCATTGGTCGTTCATGGGCC 61.666 60.000 0.00 0.00 0.00 5.80
3713 5927 1.748879 ATTGGTCGTTCATGGGCCG 60.749 57.895 0.00 0.00 0.00 6.13
3714 5928 3.910914 TTGGTCGTTCATGGGCCGG 62.911 63.158 0.00 0.00 0.00 6.13
3715 5929 4.404098 GGTCGTTCATGGGCCGGT 62.404 66.667 1.90 0.00 0.00 5.28
3716 5930 2.818274 GTCGTTCATGGGCCGGTC 60.818 66.667 1.90 0.00 0.00 4.79
3717 5931 4.090588 TCGTTCATGGGCCGGTCC 62.091 66.667 21.35 21.35 0.00 4.46
3718 5932 4.402528 CGTTCATGGGCCGGTCCA 62.403 66.667 33.79 33.79 41.60 4.02
3723 5937 4.175337 ATGGGCCGGTCCATGACG 62.175 66.667 39.32 0.00 45.13 4.35
3726 5940 4.388499 GGCCGGTCCATGACGTGT 62.388 66.667 1.90 0.00 32.65 4.49
3727 5941 3.118454 GCCGGTCCATGACGTGTG 61.118 66.667 1.90 0.00 32.65 3.82
3728 5942 3.118454 CCGGTCCATGACGTGTGC 61.118 66.667 0.00 0.00 32.65 4.57
3729 5943 2.048222 CGGTCCATGACGTGTGCT 60.048 61.111 0.00 0.00 32.65 4.40
3730 5944 1.667830 CGGTCCATGACGTGTGCTT 60.668 57.895 0.00 0.00 32.65 3.91
3731 5945 1.626654 CGGTCCATGACGTGTGCTTC 61.627 60.000 0.00 0.00 32.65 3.86
3732 5946 1.298859 GGTCCATGACGTGTGCTTCC 61.299 60.000 0.00 0.00 32.65 3.46
3733 5947 0.320771 GTCCATGACGTGTGCTTCCT 60.321 55.000 0.00 0.00 0.00 3.36
3734 5948 1.067142 GTCCATGACGTGTGCTTCCTA 60.067 52.381 0.00 0.00 0.00 2.94
3735 5949 1.831106 TCCATGACGTGTGCTTCCTAT 59.169 47.619 0.00 0.00 0.00 2.57
3736 5950 3.028130 TCCATGACGTGTGCTTCCTATA 58.972 45.455 0.00 0.00 0.00 1.31
3737 5951 3.068165 TCCATGACGTGTGCTTCCTATAG 59.932 47.826 0.00 0.00 0.00 1.31
3738 5952 3.068165 CCATGACGTGTGCTTCCTATAGA 59.932 47.826 0.00 0.00 0.00 1.98
3739 5953 4.294232 CATGACGTGTGCTTCCTATAGAG 58.706 47.826 0.00 0.00 0.00 2.43
3740 5954 3.617284 TGACGTGTGCTTCCTATAGAGA 58.383 45.455 0.00 0.00 0.00 3.10
3741 5955 4.014406 TGACGTGTGCTTCCTATAGAGAA 58.986 43.478 0.00 2.67 0.00 2.87
3742 5956 4.461431 TGACGTGTGCTTCCTATAGAGAAA 59.539 41.667 0.00 0.00 0.00 2.52
3743 5957 5.047590 TGACGTGTGCTTCCTATAGAGAAAA 60.048 40.000 0.00 0.00 0.00 2.29
3744 5958 5.978814 ACGTGTGCTTCCTATAGAGAAAAT 58.021 37.500 0.00 0.00 0.00 1.82
3745 5959 6.407202 ACGTGTGCTTCCTATAGAGAAAATT 58.593 36.000 0.00 0.00 0.00 1.82
3746 5960 6.535508 ACGTGTGCTTCCTATAGAGAAAATTC 59.464 38.462 0.00 0.00 0.00 2.17
3747 5961 6.018669 CGTGTGCTTCCTATAGAGAAAATTCC 60.019 42.308 0.00 0.00 0.00 3.01
3748 5962 7.051000 GTGTGCTTCCTATAGAGAAAATTCCT 58.949 38.462 0.00 0.00 0.00 3.36
3749 5963 7.225734 GTGTGCTTCCTATAGAGAAAATTCCTC 59.774 40.741 0.00 0.85 0.00 3.71
3750 5964 6.422400 GTGCTTCCTATAGAGAAAATTCCTCG 59.578 42.308 0.00 0.00 35.88 4.63
3751 5965 6.323996 TGCTTCCTATAGAGAAAATTCCTCGA 59.676 38.462 0.00 0.00 35.88 4.04
3752 5966 7.147724 TGCTTCCTATAGAGAAAATTCCTCGAA 60.148 37.037 0.00 0.00 35.88 3.71
3753 5967 7.711339 GCTTCCTATAGAGAAAATTCCTCGAAA 59.289 37.037 0.00 0.00 35.88 3.46
3754 5968 9.601217 CTTCCTATAGAGAAAATTCCTCGAAAA 57.399 33.333 0.00 0.00 35.88 2.29
3755 5969 9.953565 TTCCTATAGAGAAAATTCCTCGAAAAA 57.046 29.630 0.00 0.00 35.88 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.885901 CAGAGACTCACGGGAAGATATCA 59.114 47.826 5.32 0.00 0.00 2.15
1 2 4.138290 TCAGAGACTCACGGGAAGATATC 58.862 47.826 5.02 0.00 0.00 1.63
2 3 4.171878 TCAGAGACTCACGGGAAGATAT 57.828 45.455 5.02 0.00 0.00 1.63
5 6 2.025793 AGATCAGAGACTCACGGGAAGA 60.026 50.000 5.02 0.00 0.00 2.87
6 7 2.374184 AGATCAGAGACTCACGGGAAG 58.626 52.381 5.02 0.00 0.00 3.46
7 8 2.493675 CAAGATCAGAGACTCACGGGAA 59.506 50.000 5.02 0.00 0.00 3.97
8 9 2.095461 CAAGATCAGAGACTCACGGGA 58.905 52.381 5.02 0.00 0.00 5.14
9 10 2.095461 TCAAGATCAGAGACTCACGGG 58.905 52.381 5.02 0.00 0.00 5.28
10 11 3.547813 CGATCAAGATCAGAGACTCACGG 60.548 52.174 5.02 0.00 37.69 4.94
11 12 3.064682 ACGATCAAGATCAGAGACTCACG 59.935 47.826 5.02 0.00 37.69 4.35
12 13 4.630894 ACGATCAAGATCAGAGACTCAC 57.369 45.455 5.02 0.00 37.69 3.51
13 14 5.065346 GTGTACGATCAAGATCAGAGACTCA 59.935 44.000 5.02 0.00 37.69 3.41
14 15 5.507077 GTGTACGATCAAGATCAGAGACTC 58.493 45.833 10.39 0.00 37.69 3.36
15 16 4.034626 CGTGTACGATCAAGATCAGAGACT 59.965 45.833 10.39 0.00 43.02 3.24
16 17 4.201832 ACGTGTACGATCAAGATCAGAGAC 60.202 45.833 11.79 5.07 43.02 3.36
17 18 3.939592 ACGTGTACGATCAAGATCAGAGA 59.060 43.478 11.79 0.00 43.02 3.10
18 19 4.280101 ACGTGTACGATCAAGATCAGAG 57.720 45.455 11.79 0.00 43.02 3.35
19 20 4.696899 AACGTGTACGATCAAGATCAGA 57.303 40.909 11.79 0.00 43.02 3.27
20 21 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
21 22 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
22 23 3.539592 CGCAAACGTGTACGATCAAGATC 60.540 47.826 11.79 0.00 43.02 2.75
23 24 2.344441 CGCAAACGTGTACGATCAAGAT 59.656 45.455 11.79 0.00 43.02 2.40
24 25 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
25 26 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
38 39 5.478001 CGTACACTAATCATACACGCAAAC 58.522 41.667 0.00 0.00 0.00 2.93
39 40 4.563580 CCGTACACTAATCATACACGCAAA 59.436 41.667 0.00 0.00 0.00 3.68
40 41 4.106909 CCGTACACTAATCATACACGCAA 58.893 43.478 0.00 0.00 0.00 4.85
41 42 3.129113 ACCGTACACTAATCATACACGCA 59.871 43.478 0.00 0.00 0.00 5.24
42 43 3.699067 ACCGTACACTAATCATACACGC 58.301 45.455 0.00 0.00 0.00 5.34
43 44 4.912214 TGACCGTACACTAATCATACACG 58.088 43.478 0.00 0.00 0.00 4.49
44 45 7.305820 CGATTTGACCGTACACTAATCATACAC 60.306 40.741 13.93 0.00 32.03 2.90
45 46 6.693978 CGATTTGACCGTACACTAATCATACA 59.306 38.462 13.93 0.00 32.03 2.29
46 47 6.143438 CCGATTTGACCGTACACTAATCATAC 59.857 42.308 13.93 0.00 32.03 2.39
47 48 6.210796 CCGATTTGACCGTACACTAATCATA 58.789 40.000 13.93 0.23 32.03 2.15
48 49 5.047847 CCGATTTGACCGTACACTAATCAT 58.952 41.667 13.93 0.00 32.03 2.45
49 50 4.426416 CCGATTTGACCGTACACTAATCA 58.574 43.478 13.93 0.90 32.03 2.57
50 51 3.800506 CCCGATTTGACCGTACACTAATC 59.199 47.826 0.00 2.04 0.00 1.75
51 52 3.431207 CCCCGATTTGACCGTACACTAAT 60.431 47.826 0.00 0.00 0.00 1.73
52 53 2.094078 CCCCGATTTGACCGTACACTAA 60.094 50.000 0.00 0.00 0.00 2.24
53 54 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
54 55 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
55 56 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
56 57 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
57 58 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
58 59 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
59 60 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
60 61 4.770874 ACGCCCCCGATTTGACCG 62.771 66.667 0.00 0.00 38.29 4.79
61 62 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
62 63 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
63 64 2.046700 GTGACGCCCCCGATTTGA 60.047 61.111 0.00 0.00 38.29 2.69
64 65 1.312371 AATGTGACGCCCCCGATTTG 61.312 55.000 0.00 0.00 38.29 2.32
65 66 0.610785 AAATGTGACGCCCCCGATTT 60.611 50.000 0.00 0.00 38.29 2.17
66 67 1.001393 AAATGTGACGCCCCCGATT 60.001 52.632 0.00 0.00 38.29 3.34
67 68 1.748879 CAAATGTGACGCCCCCGAT 60.749 57.895 0.00 0.00 38.29 4.18
68 69 2.359354 CAAATGTGACGCCCCCGA 60.359 61.111 0.00 0.00 38.29 5.14
69 70 1.801309 AAACAAATGTGACGCCCCCG 61.801 55.000 0.00 0.00 41.14 5.73
70 71 0.391228 AAAACAAATGTGACGCCCCC 59.609 50.000 0.00 0.00 0.00 5.40
71 72 1.067821 TGAAAACAAATGTGACGCCCC 59.932 47.619 0.00 0.00 0.00 5.80
72 73 2.500509 TGAAAACAAATGTGACGCCC 57.499 45.000 0.00 0.00 0.00 6.13
73 74 3.184178 CCAATGAAAACAAATGTGACGCC 59.816 43.478 0.00 0.00 0.00 5.68
74 75 3.362888 GCCAATGAAAACAAATGTGACGC 60.363 43.478 0.00 0.00 0.00 5.19
75 76 3.801050 TGCCAATGAAAACAAATGTGACG 59.199 39.130 0.00 0.00 0.00 4.35
76 77 5.927954 ATGCCAATGAAAACAAATGTGAC 57.072 34.783 0.00 0.00 0.00 3.67
77 78 6.092396 GCATATGCCAATGAAAACAAATGTGA 59.908 34.615 17.26 0.00 34.31 3.58
78 79 6.252281 GCATATGCCAATGAAAACAAATGTG 58.748 36.000 17.26 0.00 34.31 3.21
79 80 5.063691 CGCATATGCCAATGAAAACAAATGT 59.936 36.000 21.77 0.00 37.91 2.71
130 131 7.742767 ACCACAACCTATCAAAAACTAGTACT 58.257 34.615 0.00 0.00 0.00 2.73
145 146 7.526142 TGCATAAACATTTTACCACAACCTA 57.474 32.000 0.00 0.00 0.00 3.08
148 149 7.470289 TGTTGCATAAACATTTTACCACAAC 57.530 32.000 0.00 0.00 43.96 3.32
190 191 5.545658 AAATTTGACATACGACATCGCTT 57.454 34.783 0.14 0.00 44.43 4.68
228 229 7.752239 ACTTAATCAATGAATTTCAAGCGTCAG 59.248 33.333 2.68 0.00 0.00 3.51
244 245 9.334947 CACAGTATCCAATCTCACTTAATCAAT 57.665 33.333 0.00 0.00 0.00 2.57
266 267 0.673437 AATTTGTTGGTCGGCCACAG 59.327 50.000 9.15 0.00 46.01 3.66
287 288 0.109532 TCTGTTGGACGGCCATGAAA 59.890 50.000 13.08 0.00 45.46 2.69
295 296 0.606401 ACCAAGCATCTGTTGGACGG 60.606 55.000 8.55 0.00 46.53 4.79
309 310 2.646930 TCATTCATGGCTAGCACCAAG 58.353 47.619 18.24 3.41 44.65 3.61
310 311 2.804986 TCATTCATGGCTAGCACCAA 57.195 45.000 18.24 3.57 44.65 3.67
316 317 9.096160 GATATCTACACAATCATTCATGGCTAG 57.904 37.037 0.00 0.00 0.00 3.42
342 343 8.241367 GGGTACTAAATCACCATAGTTGTTTTG 58.759 37.037 0.00 0.00 36.48 2.44
355 356 5.944007 ACATGGAACTTGGGTACTAAATCAC 59.056 40.000 0.00 0.00 0.00 3.06
465 466 8.552034 GTTCCATGGAAGATTACTCTAATTTCG 58.448 37.037 27.73 0.00 34.49 3.46
484 485 7.886970 AGAGGTAATAATGATCCATGTTCCATG 59.113 37.037 0.00 0.00 0.00 3.66
517 520 0.393944 TCGTCTGATAGTCCACGGCT 60.394 55.000 0.00 0.00 33.02 5.52
518 521 0.029567 CTCGTCTGATAGTCCACGGC 59.970 60.000 0.00 0.00 33.02 5.68
519 522 1.380524 ACTCGTCTGATAGTCCACGG 58.619 55.000 0.00 0.00 33.02 4.94
542 545 8.097662 TCATGTCAGGTTGTGTGTTGTATTATA 58.902 33.333 0.00 0.00 0.00 0.98
585 591 8.266392 TGCACAAGTTTTCATTTCAAGAAAAT 57.734 26.923 0.00 0.00 44.10 1.82
616 622 3.117888 ACCATTTGACCTGCATACCTAGG 60.118 47.826 7.41 7.41 40.01 3.02
617 623 4.156455 ACCATTTGACCTGCATACCTAG 57.844 45.455 0.00 0.00 0.00 3.02
763 770 3.283751 CGAAAATATAAGGGTGTGGCCA 58.716 45.455 0.00 0.00 39.65 5.36
806 813 6.777580 ACACTTAAAGACAAGATGGAAATGGT 59.222 34.615 0.00 0.00 0.00 3.55
869 876 4.209288 CGGTATTTCTAGAAATGGCACTCG 59.791 45.833 31.96 23.14 40.83 4.18
892 899 5.880054 TTCAGCTTCAGCCTTGTAAATAC 57.120 39.130 0.00 0.00 43.38 1.89
998 1006 1.181098 AACCTTGGTCACAGGCATGC 61.181 55.000 9.90 9.90 0.00 4.06
1021 1029 8.964476 ACGTTGATAGATCTTGTTGGAAATAT 57.036 30.769 0.00 0.00 0.00 1.28
1027 1037 8.540492 GTTACATACGTTGATAGATCTTGTTGG 58.460 37.037 0.00 0.00 0.00 3.77
1036 1046 8.139350 CACCCTATTGTTACATACGTTGATAGA 58.861 37.037 0.00 0.00 0.00 1.98
1183 1195 4.517285 GGTACAAGAGAAGCATCCATTGA 58.483 43.478 9.83 0.00 0.00 2.57
1290 1302 6.807230 ACAACGAGTCATAACTATTGTGAGTC 59.193 38.462 11.19 11.19 43.61 3.36
1386 1399 8.492673 TCGTTGATGAAAGCTTATCTTACAAT 57.507 30.769 0.00 0.00 33.88 2.71
1464 1477 6.091305 CGGATGTTGCATTCGAACTATATGAT 59.909 38.462 0.00 0.00 0.00 2.45
1535 1548 2.361610 GGGCTCCACCACCATGTG 60.362 66.667 0.00 0.00 42.05 3.21
1542 1555 0.486879 AATTTCCTTGGGCTCCACCA 59.513 50.000 0.00 0.00 42.05 4.17
1584 1597 7.283807 TGGAAACATGGTCAATGATCTATCTTG 59.716 37.037 0.00 0.00 38.72 3.02
1664 1677 4.513442 TCCTCTGCACCAATATGTACAAC 58.487 43.478 0.00 0.00 0.00 3.32
1671 1684 3.321039 TCTGGATCCTCTGCACCAATAT 58.679 45.455 14.23 0.00 31.85 1.28
1673 1686 1.588239 TCTGGATCCTCTGCACCAAT 58.412 50.000 14.23 0.00 31.85 3.16
1680 1693 7.065120 AGTAAATGAAGATCTGGATCCTCTG 57.935 40.000 14.23 3.49 38.58 3.35
1689 1772 9.330063 TGCAACCTATAAGTAAATGAAGATCTG 57.670 33.333 0.00 0.00 0.00 2.90
2016 2101 3.987547 AGTCATCATCTATCGCACCTTG 58.012 45.455 0.00 0.00 0.00 3.61
2031 2116 9.262472 GTTATCGTACAAAAACATGAAGTCATC 57.738 33.333 0.00 0.00 33.61 2.92
2058 2143 5.523916 CGAGAAAGAAACGATAACCATCCAT 59.476 40.000 0.00 0.00 0.00 3.41
2213 2299 8.592809 AGAATGTAGATCTTCTTGACTGAAACT 58.407 33.333 0.00 0.00 0.00 2.66
2368 2454 5.418840 GGTCCAACAAACCACTGATCAATAT 59.581 40.000 0.00 0.00 36.75 1.28
2370 2456 3.573967 GGTCCAACAAACCACTGATCAAT 59.426 43.478 0.00 0.00 36.75 2.57
2371 2457 2.955660 GGTCCAACAAACCACTGATCAA 59.044 45.455 0.00 0.00 36.75 2.57
2372 2458 2.092158 TGGTCCAACAAACCACTGATCA 60.092 45.455 0.00 0.00 41.84 2.92
2373 2459 2.582052 TGGTCCAACAAACCACTGATC 58.418 47.619 0.00 0.00 41.84 2.92
2374 2460 2.693074 GTTGGTCCAACAAACCACTGAT 59.307 45.455 26.79 0.00 46.27 2.90
2497 2586 4.020307 TCCTCATTGTCTGCATGTAGTCAA 60.020 41.667 21.27 21.27 32.03 3.18
2503 2592 5.763698 CAGATATTCCTCATTGTCTGCATGT 59.236 40.000 0.00 0.00 0.00 3.21
2543 2632 3.882888 CCAGTAATGCCATCACCGTTATT 59.117 43.478 0.00 0.00 0.00 1.40
2593 2682 1.508088 GGCTCCATTTTCACCAGCG 59.492 57.895 0.00 0.00 0.00 5.18
2603 2692 3.011517 AGCGTCCAGGGCTCCATT 61.012 61.111 0.00 0.00 35.37 3.16
2650 2739 1.342496 GCTCCATCTCCATCGTCATCA 59.658 52.381 0.00 0.00 0.00 3.07
2671 2760 3.506059 ATCTCCATCTTCGCCGCCG 62.506 63.158 0.00 0.00 0.00 6.46
2673 2762 1.958205 CCATCTCCATCTTCGCCGC 60.958 63.158 0.00 0.00 0.00 6.53
2701 2790 1.391485 CCAACAGCTTCGTCTTCATCG 59.609 52.381 0.00 0.00 0.00 3.84
2715 2804 1.028330 ACCAGCATCATCGCCAACAG 61.028 55.000 0.00 0.00 0.00 3.16
2762 2860 5.828328 GCCACTAAATATTTCTGGCCTACTT 59.172 40.000 26.05 0.00 37.81 2.24
2770 2868 6.064060 TCCTGGATGCCACTAAATATTTCTG 58.936 40.000 3.39 1.69 0.00 3.02
2798 2896 3.993382 CAACCATGCTTGCAAGGTT 57.007 47.368 27.10 23.97 44.74 3.50
2810 2908 2.794103 TCAGCATGTAACTGCAACCAT 58.206 42.857 0.00 0.00 44.77 3.55
2975 3075 3.020984 GTTCACAACAGGGTTCCTTCAA 58.979 45.455 0.00 0.00 0.00 2.69
2988 3088 2.517402 TGTGGGGCGGTTCACAAC 60.517 61.111 0.00 0.00 40.43 3.32
3022 3122 2.551071 GCACTACCCTGAAGAAGCAACT 60.551 50.000 0.00 0.00 0.00 3.16
3144 3268 9.099454 ACGTATTTTGCCTTGAAAATTTTACAA 57.901 25.926 2.75 9.01 36.94 2.41
3148 3272 8.202745 TCAACGTATTTTGCCTTGAAAATTTT 57.797 26.923 2.28 2.28 36.94 1.82
3160 3284 4.683781 TGCCTTCATTTCAACGTATTTTGC 59.316 37.500 0.00 0.00 0.00 3.68
3162 3286 5.868801 CCATGCCTTCATTTCAACGTATTTT 59.131 36.000 0.00 0.00 0.00 1.82
3232 3362 6.855763 AGATGAAATACCTTGAAATGCCAA 57.144 33.333 0.00 0.00 0.00 4.52
3234 3364 6.044682 CCAAGATGAAATACCTTGAAATGCC 58.955 40.000 0.00 0.00 39.55 4.40
3261 3391 9.221933 ACGATGAAAGGTATATGTGTGTAAAAA 57.778 29.630 0.00 0.00 0.00 1.94
3319 3450 6.976636 TTCAAAATCCAAACTTGTTGGTTC 57.023 33.333 5.08 0.00 40.40 3.62
3350 3481 2.094026 GCTTCATGGAGCCCGAATTTTT 60.094 45.455 15.77 0.00 36.66 1.94
3354 3485 4.567318 GCTTCATGGAGCCCGAAT 57.433 55.556 15.77 0.00 36.66 3.34
3368 3504 1.734388 GCGTTTTGGTGACTGGGCTT 61.734 55.000 0.00 0.00 0.00 4.35
3375 3511 1.792118 GAGTGGGGCGTTTTGGTGAC 61.792 60.000 0.00 0.00 0.00 3.67
3426 3564 8.478066 AGAGAAACTTTTGCCTAAAGAAACATT 58.522 29.630 13.51 3.23 45.00 2.71
3434 3572 6.772716 ACATCAGAGAGAAACTTTTGCCTAAA 59.227 34.615 0.00 0.00 0.00 1.85
3463 3601 3.117663 AGGGTGCAGAGAAACCTTTAACA 60.118 43.478 0.00 0.00 36.64 2.41
3466 3604 3.117663 ACAAGGGTGCAGAGAAACCTTTA 60.118 43.478 0.00 0.00 39.40 1.85
3479 3617 1.373748 CTGCATGCAACAAGGGTGC 60.374 57.895 22.88 0.00 36.39 5.01
3481 3619 2.043625 CACTGCATGCAACAAGGGT 58.956 52.632 22.88 12.04 0.00 4.34
3482 3620 4.979204 CACTGCATGCAACAAGGG 57.021 55.556 22.88 11.33 0.00 3.95
3553 5767 7.114811 CGTTAGTTGTTGCATTGCTCTTAAAAT 59.885 33.333 10.49 0.22 0.00 1.82
3554 5768 6.416455 CGTTAGTTGTTGCATTGCTCTTAAAA 59.584 34.615 10.49 0.00 0.00 1.52
3570 5784 1.252904 TAGCCGCTCCCGTTAGTTGT 61.253 55.000 0.00 0.00 0.00 3.32
3571 5785 0.527817 CTAGCCGCTCCCGTTAGTTG 60.528 60.000 0.00 0.00 0.00 3.16
3572 5786 1.673808 CCTAGCCGCTCCCGTTAGTT 61.674 60.000 0.00 0.00 0.00 2.24
3585 5799 3.121544 CGTCGAATAGGAAAACCTAGCC 58.878 50.000 0.00 0.00 0.00 3.93
3589 5803 2.754946 TGCGTCGAATAGGAAAACCT 57.245 45.000 0.00 0.00 0.00 3.50
3590 5804 3.621715 AGAATGCGTCGAATAGGAAAACC 59.378 43.478 0.00 0.00 0.00 3.27
3591 5805 4.578601 CAGAATGCGTCGAATAGGAAAAC 58.421 43.478 0.00 0.00 0.00 2.43
3592 5806 4.857871 CAGAATGCGTCGAATAGGAAAA 57.142 40.909 0.00 0.00 0.00 2.29
3607 5821 3.410850 CTCGACATTTTGACGCAGAATG 58.589 45.455 16.11 16.11 40.36 2.67
3608 5822 2.416547 CCTCGACATTTTGACGCAGAAT 59.583 45.455 0.00 0.00 35.65 2.40
3609 5823 1.798223 CCTCGACATTTTGACGCAGAA 59.202 47.619 0.00 0.00 35.65 3.02
3610 5824 1.428448 CCTCGACATTTTGACGCAGA 58.572 50.000 0.00 0.00 35.65 4.26
3611 5825 0.179215 GCCTCGACATTTTGACGCAG 60.179 55.000 0.00 0.00 35.65 5.18
3612 5826 1.866237 GCCTCGACATTTTGACGCA 59.134 52.632 0.00 0.00 35.65 5.24
3613 5827 1.225745 CGCCTCGACATTTTGACGC 60.226 57.895 0.00 0.00 35.65 5.19
3614 5828 1.225745 GCGCCTCGACATTTTGACG 60.226 57.895 0.00 0.00 36.91 4.35
3615 5829 1.134694 GGCGCCTCGACATTTTGAC 59.865 57.895 22.15 0.00 33.63 3.18
3616 5830 2.387445 CGGCGCCTCGACATTTTGA 61.387 57.895 26.68 0.00 32.52 2.69
3617 5831 2.098298 CGGCGCCTCGACATTTTG 59.902 61.111 26.68 0.00 32.52 2.44
3618 5832 3.799755 GCGGCGCCTCGACATTTT 61.800 61.111 26.68 0.00 32.52 1.82
3630 5844 2.043676 GAATAGGGTTTTCCGCGGCG 62.044 60.000 23.51 16.78 41.82 6.46
3631 5845 1.725665 GAATAGGGTTTTCCGCGGC 59.274 57.895 23.51 6.01 41.82 6.53
3632 5846 2.011453 CGAATAGGGTTTTCCGCGG 58.989 57.895 22.12 22.12 41.82 6.46
3633 5847 1.350665 GCGAATAGGGTTTTCCGCG 59.649 57.895 0.00 0.00 41.82 6.46
3634 5848 0.746923 AGGCGAATAGGGTTTTCCGC 60.747 55.000 0.00 0.00 41.82 5.54
3635 5849 1.296727 GAGGCGAATAGGGTTTTCCG 58.703 55.000 0.00 0.00 41.82 4.30
3636 5850 1.296727 CGAGGCGAATAGGGTTTTCC 58.703 55.000 0.00 0.00 39.75 3.13
3637 5851 0.656259 GCGAGGCGAATAGGGTTTTC 59.344 55.000 0.00 0.00 0.00 2.29
3638 5852 0.746923 GGCGAGGCGAATAGGGTTTT 60.747 55.000 0.00 0.00 0.00 2.43
3639 5853 1.153229 GGCGAGGCGAATAGGGTTT 60.153 57.895 0.00 0.00 0.00 3.27
3640 5854 2.504519 GGCGAGGCGAATAGGGTT 59.495 61.111 0.00 0.00 0.00 4.11
3641 5855 3.912907 CGGCGAGGCGAATAGGGT 61.913 66.667 13.92 0.00 0.00 4.34
3643 5857 3.865929 ATGCGGCGAGGCGAATAGG 62.866 63.158 22.88 0.00 35.06 2.57
3644 5858 1.891060 GAATGCGGCGAGGCGAATAG 61.891 60.000 22.88 0.00 35.06 1.73
3645 5859 1.954146 GAATGCGGCGAGGCGAATA 60.954 57.895 22.88 8.23 35.06 1.75
3646 5860 3.272334 GAATGCGGCGAGGCGAAT 61.272 61.111 22.88 15.13 35.06 3.34
3647 5861 4.451150 AGAATGCGGCGAGGCGAA 62.451 61.111 22.88 13.21 35.06 4.70
3659 5873 0.453282 CGACACTTTGCCGCAGAATG 60.453 55.000 0.00 0.00 40.87 2.67
3660 5874 0.602638 TCGACACTTTGCCGCAGAAT 60.603 50.000 0.00 0.00 0.00 2.40
3661 5875 1.227409 TCGACACTTTGCCGCAGAA 60.227 52.632 0.00 0.00 0.00 3.02
3662 5876 1.954146 GTCGACACTTTGCCGCAGA 60.954 57.895 11.55 0.00 0.00 4.26
3663 5877 2.551270 GTCGACACTTTGCCGCAG 59.449 61.111 11.55 0.00 0.00 5.18
3664 5878 2.970324 GGTCGACACTTTGCCGCA 60.970 61.111 18.91 0.00 0.00 5.69
3665 5879 2.665185 AGGTCGACACTTTGCCGC 60.665 61.111 18.91 0.00 0.00 6.53
3666 5880 1.006102 AGAGGTCGACACTTTGCCG 60.006 57.895 18.91 0.00 0.00 5.69
3667 5881 2.828933 GAGAGGTCGACACTTTGCC 58.171 57.895 18.91 0.00 0.00 4.52
3678 5892 2.185310 AATGGGGTGTGCGAGAGGTC 62.185 60.000 0.00 0.00 0.00 3.85
3679 5893 2.224159 AATGGGGTGTGCGAGAGGT 61.224 57.895 0.00 0.00 0.00 3.85
3680 5894 1.746615 CAATGGGGTGTGCGAGAGG 60.747 63.158 0.00 0.00 0.00 3.69
3681 5895 1.746615 CCAATGGGGTGTGCGAGAG 60.747 63.158 0.00 0.00 0.00 3.20
3682 5896 2.350895 CCAATGGGGTGTGCGAGA 59.649 61.111 0.00 0.00 0.00 4.04
3691 5905 1.037030 CCCATGAACGACCAATGGGG 61.037 60.000 17.12 0.00 46.20 4.96
3692 5906 2.492418 CCCATGAACGACCAATGGG 58.508 57.895 3.55 13.19 45.01 4.00
3693 5907 1.666209 GGCCCATGAACGACCAATGG 61.666 60.000 0.00 0.00 0.00 3.16
3694 5908 1.809207 GGCCCATGAACGACCAATG 59.191 57.895 0.00 0.00 0.00 2.82
3695 5909 1.748879 CGGCCCATGAACGACCAAT 60.749 57.895 0.00 0.00 0.00 3.16
3696 5910 2.359354 CGGCCCATGAACGACCAA 60.359 61.111 0.00 0.00 0.00 3.67
3697 5911 4.402528 CCGGCCCATGAACGACCA 62.403 66.667 0.00 0.00 0.00 4.02
3698 5912 4.404098 ACCGGCCCATGAACGACC 62.404 66.667 0.00 0.00 0.00 4.79
3699 5913 2.818274 GACCGGCCCATGAACGAC 60.818 66.667 0.00 0.00 0.00 4.34
3700 5914 4.090588 GGACCGGCCCATGAACGA 62.091 66.667 0.00 0.00 0.00 3.85
3701 5915 3.697439 ATGGACCGGCCCATGAACG 62.697 63.158 22.96 0.00 44.77 3.95
3702 5916 2.275418 ATGGACCGGCCCATGAAC 59.725 61.111 22.96 0.00 44.77 3.18
3709 5923 4.388499 ACACGTCATGGACCGGCC 62.388 66.667 0.00 4.32 37.10 6.13
3710 5924 3.118454 CACACGTCATGGACCGGC 61.118 66.667 0.00 0.00 0.00 6.13
3711 5925 3.118454 GCACACGTCATGGACCGG 61.118 66.667 0.00 0.00 0.00 5.28
3712 5926 1.626654 GAAGCACACGTCATGGACCG 61.627 60.000 0.00 0.00 0.00 4.79
3713 5927 1.298859 GGAAGCACACGTCATGGACC 61.299 60.000 0.00 0.00 0.00 4.46
3714 5928 0.320771 AGGAAGCACACGTCATGGAC 60.321 55.000 0.00 0.00 0.00 4.02
3715 5929 1.262417 TAGGAAGCACACGTCATGGA 58.738 50.000 0.00 0.00 0.00 3.41
3716 5930 2.315925 ATAGGAAGCACACGTCATGG 57.684 50.000 0.00 0.00 0.00 3.66
3717 5931 4.036852 TCTCTATAGGAAGCACACGTCATG 59.963 45.833 0.00 0.00 0.00 3.07
3718 5932 4.207955 TCTCTATAGGAAGCACACGTCAT 58.792 43.478 0.00 0.00 0.00 3.06
3719 5933 3.617284 TCTCTATAGGAAGCACACGTCA 58.383 45.455 0.00 0.00 0.00 4.35
3720 5934 4.634184 TTCTCTATAGGAAGCACACGTC 57.366 45.455 0.00 0.00 0.00 4.34
3721 5935 5.401531 TTTTCTCTATAGGAAGCACACGT 57.598 39.130 0.00 0.00 0.00 4.49
3722 5936 6.018669 GGAATTTTCTCTATAGGAAGCACACG 60.019 42.308 0.00 0.00 0.00 4.49
3723 5937 7.051000 AGGAATTTTCTCTATAGGAAGCACAC 58.949 38.462 0.00 0.00 0.00 3.82
3724 5938 7.200434 AGGAATTTTCTCTATAGGAAGCACA 57.800 36.000 0.00 0.00 0.00 4.57
3725 5939 6.422400 CGAGGAATTTTCTCTATAGGAAGCAC 59.578 42.308 3.25 0.00 0.00 4.40
3726 5940 6.323996 TCGAGGAATTTTCTCTATAGGAAGCA 59.676 38.462 3.25 0.00 0.00 3.91
3727 5941 6.750148 TCGAGGAATTTTCTCTATAGGAAGC 58.250 40.000 3.25 0.00 0.00 3.86
3728 5942 9.601217 TTTTCGAGGAATTTTCTCTATAGGAAG 57.399 33.333 3.25 0.00 0.00 3.46
3729 5943 9.953565 TTTTTCGAGGAATTTTCTCTATAGGAA 57.046 29.630 3.25 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.