Multiple sequence alignment - TraesCS1A01G189000

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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 TraesCS1A01G189000 chr1A 100.000 6666 0 0 1 6666 342378980 342385645 0.000000e+00 12310.0
1 TraesCS1A01G189000 chr1A 93.333 90 4 2 4709 4797 342383770 342383682 1.510000e-26 132.0
2 TraesCS1A01G189000 chr1D 97.269 2819 39 7 1916 4710 258587485 258584681 0.000000e+00 4745.0
3 TraesCS1A01G189000 chr1D 94.374 1902 52 13 4769 6666 258584682 258582832 0.000000e+00 2868.0
4 TraesCS1A01G189000 chr1D 94.959 853 24 7 881 1727 258588334 258587495 0.000000e+00 1319.0
5 TraesCS1A01G189000 chr1D 89.209 556 41 10 133 687 258589234 258588697 0.000000e+00 676.0
6 TraesCS1A01G189000 chr1D 92.754 138 8 1 1 136 369582420 369582283 1.470000e-46 198.0
7 TraesCS1A01G189000 chr1B 93.435 2239 87 17 1831 4032 354222812 354225027 0.000000e+00 3265.0
8 TraesCS1A01G189000 chr1B 89.573 1755 111 31 133 1837 354221024 354222756 0.000000e+00 2161.0
9 TraesCS1A01G189000 chr1B 88.607 1378 63 46 5307 6658 354225852 354227161 0.000000e+00 1589.0
10 TraesCS1A01G189000 chr1B 94.021 669 35 5 4040 4704 354225096 354225763 0.000000e+00 1009.0
11 TraesCS1A01G189000 chr1B 93.182 88 6 0 4790 4877 354225768 354225855 5.420000e-26 130.0
12 TraesCS1A01G189000 chr7B 83.527 862 108 20 4039 4876 547966289 547965438 0.000000e+00 774.0
13 TraesCS1A01G189000 chr7B 95.588 68 3 0 5866 5933 547965104 547965037 7.070000e-20 110.0
14 TraesCS1A01G189000 chr2D 93.468 444 25 3 4877 5316 545513086 545512643 0.000000e+00 656.0
15 TraesCS1A01G189000 chr2D 93.960 149 9 0 4875 5023 103463307 103463159 6.730000e-55 226.0
16 TraesCS1A01G189000 chr2D 94.656 131 7 0 2 132 379784701 379784571 3.150000e-48 204.0
17 TraesCS1A01G189000 chr2D 91.156 147 11 2 1 146 199475661 199475516 1.470000e-46 198.0
18 TraesCS1A01G189000 chr7A 85.156 384 50 5 2378 2759 386392593 386392971 2.920000e-103 387.0
19 TraesCS1A01G189000 chr7A 84.103 390 55 5 2372 2759 386500227 386500611 2.940000e-98 370.0
20 TraesCS1A01G189000 chr7A 87.162 148 15 3 2743 2889 386427478 386427622 1.490000e-36 165.0
21 TraesCS1A01G189000 chr7A 86.486 148 16 3 2743 2889 386500622 386500766 6.920000e-35 159.0
22 TraesCS1A01G189000 chr7D 85.338 266 23 7 2936 3185 121681640 121681375 1.840000e-65 261.0
23 TraesCS1A01G189000 chr7D 92.537 134 10 0 1 134 279184239 279184372 6.820000e-45 193.0
24 TraesCS1A01G189000 chr7D 92.029 138 10 1 1 138 346795015 346795151 6.820000e-45 193.0
25 TraesCS1A01G189000 chr7D 89.313 131 11 1 5374 5501 121672301 121672171 1.920000e-35 161.0
26 TraesCS1A01G189000 chr7D 85.714 119 10 3 5866 5978 121671415 121671298 1.170000e-22 119.0
27 TraesCS1A01G189000 chr6D 93.478 138 8 1 1 138 140587076 140586940 3.150000e-48 204.0
28 TraesCS1A01G189000 chr6D 87.195 164 17 4 2 162 96887113 96886951 4.110000e-42 183.0
29 TraesCS1A01G189000 chr4D 91.156 147 11 2 1 146 122616855 122616710 1.470000e-46 198.0
30 TraesCS1A01G189000 chr3D 92.701 137 10 0 1 137 272628924 272628788 1.470000e-46 198.0
31 TraesCS1A01G189000 chr5B 87.671 146 16 1 2743 2888 492792998 492793141 1.150000e-37 169.0
32 TraesCS1A01G189000 chr4B 87.671 146 16 1 2743 2888 560938576 560938433 1.150000e-37 169.0
33 TraesCS1A01G189000 chr4B 86.170 94 7 6 4703 4792 484771825 484771734 5.500000e-16 97.1
34 TraesCS1A01G189000 chr4B 89.333 75 8 0 2743 2817 244772555 244772481 1.980000e-15 95.3
35 TraesCS1A01G189000 chr3A 93.333 90 3 2 4709 4795 38541612 38541523 5.420000e-26 130.0
36 TraesCS1A01G189000 chr3A 91.860 86 4 2 4709 4791 38541527 38541612 4.220000e-22 117.0
37 TraesCS1A01G189000 chr6B 90.323 93 6 3 4701 4792 583192123 583192033 1.170000e-22 119.0
38 TraesCS1A01G189000 chr2B 77.542 236 27 12 4134 4360 23309564 23309782 1.170000e-22 119.0
39 TraesCS1A01G189000 chr2B 85.849 106 13 2 4598 4703 23312292 23312395 1.970000e-20 111.0
40 TraesCS1A01G189000 chr2B 86.667 90 9 2 5840 5926 23312986 23313075 5.500000e-16 97.1
41 TraesCS1A01G189000 chr4A 94.595 74 3 1 4719 4791 659496349 659496276 5.460000e-21 113.0
42 TraesCS1A01G189000 chr4A 90.588 85 6 2 4708 4791 660083380 660083297 1.970000e-20 111.0
43 TraesCS1A01G189000 chrUn 93.243 74 4 1 4719 4791 335934628 335934555 2.540000e-19 108.0


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 TraesCS1A01G189000 chr1A 342378980 342385645 6665 False 12310.0 12310 100.00000 1 6666 1 chr1A.!!$F1 6665
1 TraesCS1A01G189000 chr1D 258582832 258589234 6402 True 2402.0 4745 93.95275 133 6666 4 chr1D.!!$R2 6533
2 TraesCS1A01G189000 chr1B 354221024 354227161 6137 False 1630.8 3265 91.76360 133 6658 5 chr1B.!!$F1 6525
3 TraesCS1A01G189000 chr7B 547965037 547966289 1252 True 442.0 774 89.55750 4039 5933 2 chr7B.!!$R1 1894
4 TraesCS1A01G189000 chr7A 386500227 386500766 539 False 264.5 370 85.29450 2372 2889 2 chr7A.!!$F3 517

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
20 21 0.036010 AAATGTGGAGAGGAGTGCGG 60.036 55.0 0.00 0.00 0.00 5.69 F
188 189 0.107703 ATCCGAATCTTGGCGCAGAA 60.108 50.0 10.83 0.00 0.00 3.02 F
189 190 0.107703 TCCGAATCTTGGCGCAGAAT 60.108 50.0 10.83 0.00 0.00 2.40 F
1144 1359 0.109781 ATTTGCCGTCAATGACACGC 60.110 50.0 14.24 13.86 35.87 5.34 F
1217 1432 0.247814 CAGCATCGTGGTTCATTCGC 60.248 55.0 0.00 0.00 0.00 4.70 F
1221 1436 0.249120 ATCGTGGTTCATTCGCTGGA 59.751 50.0 0.00 0.00 0.00 3.86 F
1575 1809 0.905357 GAGCTAGGAGTTCAGGCCAA 59.095 55.0 5.01 0.00 0.00 4.52 F
2494 2795 1.012086 CTGGCCAGATCATTGTGACG 58.988 55.0 29.88 0.00 0.00 4.35 F
3532 3873 2.092538 CCCTCCTTCAATGATGACTGCT 60.093 50.0 0.00 0.00 34.61 4.24 F
4871 5320 0.107508 CATCTGTGAATCACGGCCCT 60.108 55.0 16.93 2.08 40.25 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1372 0.767687 AATCGCGCAAAAACGAAACG 59.232 45.000 8.75 0.00 42.31 3.60 R
1656 1890 0.801872 TTCGCGTGAATGACCAATGG 59.198 50.000 7.45 0.00 0.00 3.16 R
1966 2263 1.573829 TTGCAACGACGGAAGCCATC 61.574 55.000 0.00 0.00 0.00 3.51 R
2437 2738 0.958876 CAACGGTAACCCCTTCAGCC 60.959 60.000 0.00 0.00 0.00 4.85 R
2463 2764 1.228245 TGGCCAGCTTCTGTTCCAC 60.228 57.895 0.00 0.00 30.99 4.02 R
2889 3227 1.611491 ACGGCAAATTAACACACCTGG 59.389 47.619 0.00 0.00 0.00 4.45 R
3325 3663 8.772069 TGGAACAACAAACAACTTGAGGATCAT 61.772 37.037 0.00 0.00 40.44 2.45 R
4293 4731 2.051334 TAATGGTTTGGCGGGAGATG 57.949 50.000 0.00 0.00 0.00 2.90 R
4999 5448 0.253160 TGAACTATCCAGGCCAGGGT 60.253 55.000 15.24 10.31 0.00 4.34 R
6437 6918 0.107017 AAATATCGCCACTGCTGCCT 60.107 50.000 0.00 0.00 34.43 4.75 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
19 20 1.081892 CAAATGTGGAGAGGAGTGCG 58.918 55.000 0.00 0.00 0.00 5.34
20 21 0.036010 AAATGTGGAGAGGAGTGCGG 60.036 55.000 0.00 0.00 0.00 5.69
21 22 1.194781 AATGTGGAGAGGAGTGCGGT 61.195 55.000 0.00 0.00 0.00 5.68
22 23 1.194781 ATGTGGAGAGGAGTGCGGTT 61.195 55.000 0.00 0.00 0.00 4.44
23 24 0.541063 TGTGGAGAGGAGTGCGGTTA 60.541 55.000 0.00 0.00 0.00 2.85
24 25 0.606604 GTGGAGAGGAGTGCGGTTAA 59.393 55.000 0.00 0.00 0.00 2.01
25 26 1.001633 GTGGAGAGGAGTGCGGTTAAA 59.998 52.381 0.00 0.00 0.00 1.52
26 27 1.906574 TGGAGAGGAGTGCGGTTAAAT 59.093 47.619 0.00 0.00 0.00 1.40
27 28 2.304761 TGGAGAGGAGTGCGGTTAAATT 59.695 45.455 0.00 0.00 0.00 1.82
28 29 2.678336 GGAGAGGAGTGCGGTTAAATTG 59.322 50.000 0.00 0.00 0.00 2.32
29 30 3.335579 GAGAGGAGTGCGGTTAAATTGT 58.664 45.455 0.00 0.00 0.00 2.71
30 31 3.751518 AGAGGAGTGCGGTTAAATTGTT 58.248 40.909 0.00 0.00 0.00 2.83
31 32 4.901868 AGAGGAGTGCGGTTAAATTGTTA 58.098 39.130 0.00 0.00 0.00 2.41
32 33 5.497474 AGAGGAGTGCGGTTAAATTGTTAT 58.503 37.500 0.00 0.00 0.00 1.89
33 34 6.646267 AGAGGAGTGCGGTTAAATTGTTATA 58.354 36.000 0.00 0.00 0.00 0.98
34 35 6.761714 AGAGGAGTGCGGTTAAATTGTTATAG 59.238 38.462 0.00 0.00 0.00 1.31
35 36 6.412214 AGGAGTGCGGTTAAATTGTTATAGT 58.588 36.000 0.00 0.00 0.00 2.12
36 37 6.882678 AGGAGTGCGGTTAAATTGTTATAGTT 59.117 34.615 0.00 0.00 0.00 2.24
37 38 7.392393 AGGAGTGCGGTTAAATTGTTATAGTTT 59.608 33.333 0.00 0.00 0.00 2.66
38 39 8.024865 GGAGTGCGGTTAAATTGTTATAGTTTT 58.975 33.333 0.00 0.00 0.00 2.43
39 40 8.959734 AGTGCGGTTAAATTGTTATAGTTTTC 57.040 30.769 0.00 0.00 0.00 2.29
40 41 8.789762 AGTGCGGTTAAATTGTTATAGTTTTCT 58.210 29.630 0.00 0.00 0.00 2.52
41 42 9.401873 GTGCGGTTAAATTGTTATAGTTTTCTT 57.598 29.630 0.00 0.00 0.00 2.52
42 43 9.615295 TGCGGTTAAATTGTTATAGTTTTCTTC 57.385 29.630 0.00 0.00 0.00 2.87
43 44 9.069078 GCGGTTAAATTGTTATAGTTTTCTTCC 57.931 33.333 0.00 0.00 0.00 3.46
50 51 9.901172 AATTGTTATAGTTTTCTTCCTATCCGT 57.099 29.630 0.00 0.00 0.00 4.69
51 52 9.901172 ATTGTTATAGTTTTCTTCCTATCCGTT 57.099 29.630 0.00 0.00 0.00 4.44
64 65 9.409918 TCTTCCTATCCGTTAGATATAGATTGG 57.590 37.037 0.00 0.00 36.84 3.16
65 66 9.409918 CTTCCTATCCGTTAGATATAGATTGGA 57.590 37.037 0.00 0.00 36.84 3.53
66 67 8.749026 TCCTATCCGTTAGATATAGATTGGAC 57.251 38.462 0.00 0.00 36.84 4.02
67 68 7.498239 TCCTATCCGTTAGATATAGATTGGACG 59.502 40.741 0.00 0.00 36.84 4.79
68 69 7.498239 CCTATCCGTTAGATATAGATTGGACGA 59.502 40.741 0.00 0.00 36.84 4.20
69 70 6.492007 TCCGTTAGATATAGATTGGACGAC 57.508 41.667 0.00 0.00 0.00 4.34
70 71 5.413833 TCCGTTAGATATAGATTGGACGACC 59.586 44.000 0.00 0.00 0.00 4.79
71 72 5.415077 CCGTTAGATATAGATTGGACGACCT 59.585 44.000 5.33 0.00 37.04 3.85
72 73 6.596888 CCGTTAGATATAGATTGGACGACCTA 59.403 42.308 5.33 0.00 37.04 3.08
73 74 7.282675 CCGTTAGATATAGATTGGACGACCTAT 59.717 40.741 5.33 2.65 37.04 2.57
74 75 9.322773 CGTTAGATATAGATTGGACGACCTATA 57.677 37.037 5.33 0.00 37.04 1.31
78 79 8.634444 AGATATAGATTGGACGACCTATATTGC 58.366 37.037 5.33 0.00 35.87 3.56
79 80 4.955811 AGATTGGACGACCTATATTGCA 57.044 40.909 5.33 0.00 37.04 4.08
80 81 5.290493 AGATTGGACGACCTATATTGCAA 57.710 39.130 0.00 0.00 37.04 4.08
81 82 5.300752 AGATTGGACGACCTATATTGCAAG 58.699 41.667 4.94 0.00 37.04 4.01
82 83 4.746535 TTGGACGACCTATATTGCAAGA 57.253 40.909 4.94 0.00 37.04 3.02
83 84 4.955811 TGGACGACCTATATTGCAAGAT 57.044 40.909 11.88 11.88 37.04 2.40
84 85 4.631131 TGGACGACCTATATTGCAAGATG 58.369 43.478 16.68 3.43 37.04 2.90
85 86 3.997021 GGACGACCTATATTGCAAGATGG 59.003 47.826 16.68 13.36 0.00 3.51
86 87 3.403038 ACGACCTATATTGCAAGATGGC 58.597 45.455 16.68 2.00 0.00 4.40
87 88 3.181455 ACGACCTATATTGCAAGATGGCA 60.181 43.478 16.68 0.00 43.19 4.92
88 89 4.005650 CGACCTATATTGCAAGATGGCAT 58.994 43.478 16.68 0.00 44.48 4.40
89 90 4.142752 CGACCTATATTGCAAGATGGCATG 60.143 45.833 16.68 3.99 44.48 4.06
90 91 3.508793 ACCTATATTGCAAGATGGCATGC 59.491 43.478 16.68 9.90 44.48 4.06
93 94 4.098847 TGCAAGATGGCATGCACA 57.901 50.000 21.36 15.35 46.87 4.57
94 95 2.585876 TGCAAGATGGCATGCACAT 58.414 47.368 21.36 19.41 46.87 3.21
95 96 0.458260 TGCAAGATGGCATGCACATC 59.542 50.000 27.93 27.93 46.87 3.06
96 97 0.458260 GCAAGATGGCATGCACATCA 59.542 50.000 32.43 19.63 45.49 3.07
97 98 1.068588 GCAAGATGGCATGCACATCAT 59.931 47.619 32.43 24.98 45.49 2.45
98 99 2.862530 GCAAGATGGCATGCACATCATC 60.863 50.000 32.43 27.13 45.49 2.92
99 100 2.358322 AGATGGCATGCACATCATCA 57.642 45.000 32.43 18.17 45.49 3.07
100 101 2.876581 AGATGGCATGCACATCATCAT 58.123 42.857 32.43 21.16 45.49 2.45
101 102 2.820197 AGATGGCATGCACATCATCATC 59.180 45.455 32.43 25.85 45.49 2.92
102 103 2.060050 TGGCATGCACATCATCATCA 57.940 45.000 21.36 0.48 31.79 3.07
103 104 1.679153 TGGCATGCACATCATCATCAC 59.321 47.619 21.36 0.00 31.79 3.06
104 105 1.000607 GGCATGCACATCATCATCACC 60.001 52.381 21.36 0.00 31.79 4.02
105 106 1.679153 GCATGCACATCATCATCACCA 59.321 47.619 14.21 0.00 31.79 4.17
106 107 2.100087 GCATGCACATCATCATCACCAA 59.900 45.455 14.21 0.00 31.79 3.67
107 108 3.702330 CATGCACATCATCATCACCAAC 58.298 45.455 0.00 0.00 31.79 3.77
108 109 3.076079 TGCACATCATCATCACCAACT 57.924 42.857 0.00 0.00 0.00 3.16
109 110 3.011818 TGCACATCATCATCACCAACTC 58.988 45.455 0.00 0.00 0.00 3.01
110 111 3.276857 GCACATCATCATCACCAACTCT 58.723 45.455 0.00 0.00 0.00 3.24
111 112 3.064958 GCACATCATCATCACCAACTCTG 59.935 47.826 0.00 0.00 0.00 3.35
112 113 3.064958 CACATCATCATCACCAACTCTGC 59.935 47.826 0.00 0.00 0.00 4.26
113 114 3.054582 ACATCATCATCACCAACTCTGCT 60.055 43.478 0.00 0.00 0.00 4.24
114 115 3.708403 TCATCATCACCAACTCTGCTT 57.292 42.857 0.00 0.00 0.00 3.91
115 116 4.025040 TCATCATCACCAACTCTGCTTT 57.975 40.909 0.00 0.00 0.00 3.51
116 117 4.401022 TCATCATCACCAACTCTGCTTTT 58.599 39.130 0.00 0.00 0.00 2.27
117 118 4.828939 TCATCATCACCAACTCTGCTTTTT 59.171 37.500 0.00 0.00 0.00 1.94
118 119 6.003326 TCATCATCACCAACTCTGCTTTTTA 58.997 36.000 0.00 0.00 0.00 1.52
119 120 6.660521 TCATCATCACCAACTCTGCTTTTTAT 59.339 34.615 0.00 0.00 0.00 1.40
120 121 7.828717 TCATCATCACCAACTCTGCTTTTTATA 59.171 33.333 0.00 0.00 0.00 0.98
121 122 7.994425 TCATCACCAACTCTGCTTTTTATAA 57.006 32.000 0.00 0.00 0.00 0.98
122 123 8.044060 TCATCACCAACTCTGCTTTTTATAAG 57.956 34.615 0.00 0.00 0.00 1.73
123 124 7.882791 TCATCACCAACTCTGCTTTTTATAAGA 59.117 33.333 0.00 0.00 0.00 2.10
124 125 7.672983 TCACCAACTCTGCTTTTTATAAGAG 57.327 36.000 0.00 0.00 41.59 2.85
126 127 8.372459 TCACCAACTCTGCTTTTTATAAGAGTA 58.628 33.333 4.72 0.00 46.64 2.59
127 128 8.999431 CACCAACTCTGCTTTTTATAAGAGTAA 58.001 33.333 4.72 0.00 46.64 2.24
128 129 9.569122 ACCAACTCTGCTTTTTATAAGAGTAAA 57.431 29.630 4.72 0.00 46.64 2.01
186 187 1.800805 ATATCCGAATCTTGGCGCAG 58.199 50.000 10.83 0.00 0.00 5.18
188 189 0.107703 ATCCGAATCTTGGCGCAGAA 60.108 50.000 10.83 0.00 0.00 3.02
189 190 0.107703 TCCGAATCTTGGCGCAGAAT 60.108 50.000 10.83 0.00 0.00 2.40
190 191 1.138069 TCCGAATCTTGGCGCAGAATA 59.862 47.619 10.83 0.00 0.00 1.75
213 214 3.443045 CACAATCTGCGTGCCCCC 61.443 66.667 0.00 0.00 0.00 5.40
237 238 1.216175 ACATGCCTGCCACATATCCTT 59.784 47.619 0.00 0.00 0.00 3.36
247 251 2.224305 CCACATATCCTTCCCTCGAACC 60.224 54.545 0.00 0.00 0.00 3.62
267 271 2.682856 CCAATATGACCTTGGGTTCACG 59.317 50.000 0.00 0.00 39.62 4.35
268 272 2.038387 ATATGACCTTGGGTTCACGC 57.962 50.000 0.00 0.00 35.25 5.34
283 287 4.260784 GGTTCACGCCTAATGATCAACATC 60.261 45.833 0.00 0.00 38.38 3.06
285 289 5.529581 TCACGCCTAATGATCAACATCTA 57.470 39.130 0.00 0.00 38.38 1.98
289 293 5.049828 CGCCTAATGATCAACATCTACACA 58.950 41.667 0.00 0.00 38.38 3.72
290 294 5.698089 CGCCTAATGATCAACATCTACACAT 59.302 40.000 0.00 0.00 38.38 3.21
407 411 8.579682 AAAAGCACAAGTGTATGAAAGATTTC 57.420 30.769 1.79 0.00 37.69 2.17
411 415 7.172532 AGCACAAGTGTATGAAAGATTTCGTTA 59.827 33.333 5.41 0.00 40.01 3.18
415 419 9.638300 CAAGTGTATGAAAGATTTCGTTATAGC 57.362 33.333 5.41 0.00 40.01 2.97
416 420 8.942338 AGTGTATGAAAGATTTCGTTATAGCA 57.058 30.769 5.41 0.00 40.01 3.49
449 479 6.811253 TTACAGGAAGACGCAAACATAAAT 57.189 33.333 0.00 0.00 0.00 1.40
450 480 5.046910 ACAGGAAGACGCAAACATAAATG 57.953 39.130 0.00 0.00 0.00 2.32
531 561 4.578871 TGTTACATTGACTGACCCATCTG 58.421 43.478 0.00 0.00 0.00 2.90
534 564 2.238144 ACATTGACTGACCCATCTGAGG 59.762 50.000 0.00 0.00 0.00 3.86
545 575 2.045524 CCATCTGAGGGATACAGCAGT 58.954 52.381 1.22 0.00 39.46 4.40
546 576 3.234353 CCATCTGAGGGATACAGCAGTA 58.766 50.000 1.22 0.00 39.46 2.74
547 577 3.006323 CCATCTGAGGGATACAGCAGTAC 59.994 52.174 1.22 0.00 39.46 2.73
687 720 2.127708 GGAGGAGAGAGGAGAGAGAGT 58.872 57.143 0.00 0.00 0.00 3.24
688 721 2.104963 GGAGGAGAGAGGAGAGAGAGTC 59.895 59.091 0.00 0.00 0.00 3.36
692 725 3.199946 GGAGAGAGGAGAGAGAGTCAGAA 59.800 52.174 0.00 0.00 0.00 3.02
747 780 4.577246 GTAGCGAGGCGAGCCCTG 62.577 72.222 10.95 4.66 46.60 4.45
788 821 0.468400 CGTTTCCCACCCCTCCAAAA 60.468 55.000 0.00 0.00 0.00 2.44
1144 1359 0.109781 ATTTGCCGTCAATGACACGC 60.110 50.000 14.24 13.86 35.87 5.34
1184 1399 2.256445 TTTTGCGCGATTTTCCTAGC 57.744 45.000 12.10 0.00 0.00 3.42
1217 1432 0.247814 CAGCATCGTGGTTCATTCGC 60.248 55.000 0.00 0.00 0.00 4.70
1221 1436 0.249120 ATCGTGGTTCATTCGCTGGA 59.751 50.000 0.00 0.00 0.00 3.86
1358 1575 3.629855 TGACCGTTTCATTCTGCTTTTCA 59.370 39.130 0.00 0.00 0.00 2.69
1387 1604 6.467047 ACGTGTACGATGAAAACGATACTTAG 59.533 38.462 11.79 0.00 43.02 2.18
1575 1809 0.905357 GAGCTAGGAGTTCAGGCCAA 59.095 55.000 5.01 0.00 0.00 4.52
1597 1831 7.712205 GCCAAGCCATTTTATAGTTTCATGAAT 59.288 33.333 9.40 0.00 0.00 2.57
1598 1832 9.252962 CCAAGCCATTTTATAGTTTCATGAATC 57.747 33.333 9.40 8.74 0.00 2.52
1599 1833 9.806203 CAAGCCATTTTATAGTTTCATGAATCA 57.194 29.630 16.79 3.47 0.00 2.57
1656 1890 2.750948 TGTTCGGTAGCTTGTTCACTC 58.249 47.619 0.00 0.00 0.00 3.51
1729 1963 6.194285 TGGCTTACCATATAACTATTGCCA 57.806 37.500 0.00 0.00 42.67 4.92
1730 1964 6.789268 TGGCTTACCATATAACTATTGCCAT 58.211 36.000 0.00 0.00 42.67 4.40
1738 1972 7.121382 CCATATAACTATTGCCATTGGATCCT 58.879 38.462 14.23 0.00 0.00 3.24
1816 2050 3.120025 GGCAGCTTTAGAAGTCTTCTTGC 60.120 47.826 20.03 20.46 41.14 4.01
1822 2056 5.581085 GCTTTAGAAGTCTTCTTGCGGATAA 59.419 40.000 20.03 4.21 41.14 1.75
1837 2073 5.054477 TGCGGATAAGCTTTATGAGTTACC 58.946 41.667 3.20 0.00 38.13 2.85
1839 2075 5.607477 CGGATAAGCTTTATGAGTTACCCA 58.393 41.667 3.20 0.00 0.00 4.51
1840 2076 6.053005 CGGATAAGCTTTATGAGTTACCCAA 58.947 40.000 3.20 0.00 0.00 4.12
1842 2078 7.876068 CGGATAAGCTTTATGAGTTACCCAATA 59.124 37.037 3.20 0.00 0.00 1.90
1843 2079 9.220767 GGATAAGCTTTATGAGTTACCCAATAG 57.779 37.037 3.20 0.00 0.00 1.73
1851 2148 8.706492 TTATGAGTTACCCAATAGTACAAACG 57.294 34.615 0.00 0.00 0.00 3.60
1858 2155 9.597999 GTTACCCAATAGTACAAACGTTAAAAG 57.402 33.333 0.00 0.00 0.00 2.27
1859 2156 9.553064 TTACCCAATAGTACAAACGTTAAAAGA 57.447 29.630 0.00 0.00 0.00 2.52
1870 2167 7.826690 ACAAACGTTAAAAGAGGAATGCATAT 58.173 30.769 0.00 0.00 0.00 1.78
1962 2259 2.949177 TGCTTGGGACTGCTAGAAAA 57.051 45.000 0.00 0.00 0.00 2.29
1963 2260 3.439857 TGCTTGGGACTGCTAGAAAAT 57.560 42.857 0.00 0.00 0.00 1.82
1964 2261 3.084039 TGCTTGGGACTGCTAGAAAATG 58.916 45.455 0.00 0.00 0.00 2.32
1965 2262 2.424956 GCTTGGGACTGCTAGAAAATGG 59.575 50.000 0.00 0.00 0.00 3.16
1966 2263 2.806945 TGGGACTGCTAGAAAATGGG 57.193 50.000 0.00 0.00 0.00 4.00
1976 2273 1.767759 AGAAAATGGGATGGCTTCCG 58.232 50.000 12.76 0.00 46.52 4.30
2024 2321 4.150451 GTGATTGCCAAATTGAAGTTTCCG 59.850 41.667 0.00 0.00 0.00 4.30
2039 2336 6.379133 TGAAGTTTCCGTTTAGCCTCTCTATA 59.621 38.462 0.00 0.00 0.00 1.31
2197 2495 5.619132 TGCATCTAGACCAAGAATCATCA 57.381 39.130 0.00 0.00 0.00 3.07
2198 2496 6.183810 TGCATCTAGACCAAGAATCATCAT 57.816 37.500 0.00 0.00 0.00 2.45
2199 2497 6.228995 TGCATCTAGACCAAGAATCATCATC 58.771 40.000 0.00 0.00 0.00 2.92
2200 2498 6.183361 TGCATCTAGACCAAGAATCATCATCA 60.183 38.462 0.00 0.00 0.00 3.07
2201 2499 6.879993 GCATCTAGACCAAGAATCATCATCAT 59.120 38.462 0.00 0.00 0.00 2.45
2202 2500 7.064847 GCATCTAGACCAAGAATCATCATCATC 59.935 40.741 0.00 0.00 0.00 2.92
2203 2501 7.607615 TCTAGACCAAGAATCATCATCATCA 57.392 36.000 0.00 0.00 0.00 3.07
2204 2502 8.203681 TCTAGACCAAGAATCATCATCATCAT 57.796 34.615 0.00 0.00 0.00 2.45
2205 2503 8.312564 TCTAGACCAAGAATCATCATCATCATC 58.687 37.037 0.00 0.00 0.00 2.92
2278 2576 4.085357 TCCTGCTAAAGCTGAAGAAACA 57.915 40.909 10.10 0.00 41.71 2.83
2437 2738 5.988561 GTGATGGCTTTTCTGACTATAGGAG 59.011 44.000 4.43 0.00 0.00 3.69
2463 2764 1.280998 AGGGGTTACCGTTGATGGAAG 59.719 52.381 0.00 0.00 46.96 3.46
2494 2795 1.012086 CTGGCCAGATCATTGTGACG 58.988 55.000 29.88 0.00 0.00 4.35
2639 2941 3.260884 TGGTCCATGGACTGAGAGTTTAC 59.739 47.826 37.26 20.57 44.04 2.01
2731 3034 2.627515 TCCTGATGGCTGAGTATTGC 57.372 50.000 0.00 0.00 0.00 3.56
2889 3227 5.473039 ACTGGTTCGTTTGGTGTAGTATAC 58.527 41.667 0.00 0.00 43.42 1.47
2934 3272 5.601583 TTCGCCCTTGTATATCACTACAA 57.398 39.130 0.00 0.00 38.84 2.41
3325 3663 6.607735 ATTCTTTCAAACGGTTACTTTCGA 57.392 33.333 0.00 0.00 0.00 3.71
3532 3873 2.092538 CCCTCCTTCAATGATGACTGCT 60.093 50.000 0.00 0.00 34.61 4.24
3542 3883 6.500910 TCAATGATGACTGCTTGCAATATTC 58.499 36.000 0.00 0.00 0.00 1.75
3596 3937 8.523915 AATGATCAACTTACTGCAATGGATTA 57.476 30.769 0.00 0.00 0.00 1.75
3619 3960 6.776887 AATCTTCCAGGTCAATCCTCATAT 57.223 37.500 0.00 0.00 46.24 1.78
3624 3965 4.845796 TCCAGGTCAATCCTCATATGCATA 59.154 41.667 9.27 9.27 46.24 3.14
3692 4033 8.307483 TGTTTTTGTCACTTATTTTCTTGGTCA 58.693 29.630 0.00 0.00 0.00 4.02
3951 4292 5.948992 GAAGTTATGCTTCCTTGAACAGT 57.051 39.130 0.00 0.00 45.95 3.55
3952 4293 5.693814 GAAGTTATGCTTCCTTGAACAGTG 58.306 41.667 0.00 0.00 45.95 3.66
3953 4294 4.973168 AGTTATGCTTCCTTGAACAGTGA 58.027 39.130 0.00 0.00 0.00 3.41
3954 4295 5.376625 AGTTATGCTTCCTTGAACAGTGAA 58.623 37.500 0.00 0.00 0.00 3.18
4032 4397 8.212312 TGGTATTTAGTTACAAGAACAGTGGAA 58.788 33.333 0.00 0.00 0.00 3.53
4293 4731 8.495148 CAGTTGGTTGAAATTATAAAGGTTTGC 58.505 33.333 0.00 0.00 0.00 3.68
4531 4977 7.441017 TGTAACATGCTTGCCTAATTTTCTTT 58.559 30.769 0.00 0.00 0.00 2.52
4681 5127 4.085357 ACCTATGAACAAGTCAGCACAA 57.915 40.909 0.00 0.00 40.43 3.33
4717 5163 4.933505 AACGCTAAAGTATACTCCCTCC 57.066 45.455 5.70 0.00 0.00 4.30
4720 5166 3.058363 CGCTAAAGTATACTCCCTCCGTC 60.058 52.174 5.70 0.00 0.00 4.79
4721 5167 3.255395 GCTAAAGTATACTCCCTCCGTCC 59.745 52.174 5.70 0.00 0.00 4.79
4722 5168 2.378378 AAGTATACTCCCTCCGTCCC 57.622 55.000 5.70 0.00 0.00 4.46
4723 5169 1.229131 AGTATACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
4724 5170 1.787676 AGTATACTCCCTCCGTCCCAT 59.212 52.381 0.00 0.00 0.00 4.00
4729 5175 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4734 5180 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
4738 5184 7.563924 CCCTCCGTCCCATAATATAAGATCTTA 59.436 40.741 17.32 17.32 0.00 2.10
4863 5312 2.408271 TGTCCTGGCATCTGTGAATC 57.592 50.000 0.00 0.00 0.00 2.52
4864 5313 1.629861 TGTCCTGGCATCTGTGAATCA 59.370 47.619 0.00 0.00 0.00 2.57
4865 5314 2.012673 GTCCTGGCATCTGTGAATCAC 58.987 52.381 6.41 6.41 34.56 3.06
4866 5315 1.012086 CCTGGCATCTGTGAATCACG 58.988 55.000 9.00 4.08 37.14 4.35
4867 5316 1.012086 CTGGCATCTGTGAATCACGG 58.988 55.000 15.71 15.71 41.65 4.94
4868 5317 1.026182 TGGCATCTGTGAATCACGGC 61.026 55.000 16.93 12.76 40.25 5.68
4869 5318 1.718757 GGCATCTGTGAATCACGGCC 61.719 60.000 16.93 17.33 40.25 6.13
4870 5319 1.718757 GCATCTGTGAATCACGGCCC 61.719 60.000 16.93 4.41 40.25 5.80
4871 5320 0.107508 CATCTGTGAATCACGGCCCT 60.108 55.000 16.93 2.08 40.25 5.19
4872 5321 1.138859 CATCTGTGAATCACGGCCCTA 59.861 52.381 16.93 0.58 40.25 3.53
4873 5322 0.535335 TCTGTGAATCACGGCCCTAC 59.465 55.000 16.93 0.00 40.25 3.18
4874 5323 0.537188 CTGTGAATCACGGCCCTACT 59.463 55.000 9.49 0.00 37.14 2.57
4875 5324 1.754803 CTGTGAATCACGGCCCTACTA 59.245 52.381 9.49 0.00 37.14 1.82
4876 5325 2.167693 CTGTGAATCACGGCCCTACTAA 59.832 50.000 9.49 0.00 37.14 2.24
4877 5326 2.167693 TGTGAATCACGGCCCTACTAAG 59.832 50.000 9.00 0.00 37.14 2.18
4878 5327 1.760613 TGAATCACGGCCCTACTAAGG 59.239 52.381 0.00 0.00 43.25 2.69
4932 5381 2.699768 GCAATAGCGTTGCCTGGCA 61.700 57.895 19.30 19.30 39.38 4.92
4948 5397 2.559668 CTGGCATGGACACATTTTCTGT 59.440 45.455 0.00 0.00 39.20 3.41
4999 5448 0.759959 TGAGAGGCGTTTGGTTACCA 59.240 50.000 0.00 0.00 0.00 3.25
5065 5514 2.000447 GCCCATGTACGAAGAACAGTC 59.000 52.381 0.00 0.00 0.00 3.51
5069 5518 4.322049 CCCATGTACGAAGAACAGTCTCTT 60.322 45.833 0.00 0.00 38.39 2.85
5137 5586 1.017387 CTCCAATTCTTACGCCTGGC 58.983 55.000 9.11 9.11 0.00 4.85
5169 5618 1.194781 TCTCCCTGGCTTCACTGTCC 61.195 60.000 0.00 0.00 0.00 4.02
5200 5649 4.440127 GCATGCAAACCCAGGCCG 62.440 66.667 14.21 0.00 36.59 6.13
5222 5671 2.289945 GGCTATACCTGGCATCTTGAGG 60.290 54.545 0.00 0.00 34.51 3.86
5301 5750 1.106944 CCCAGGACGCAAACCAAACT 61.107 55.000 0.00 0.00 0.00 2.66
5379 5839 4.997395 TCTGACTAGACATTTTTGCAGGTC 59.003 41.667 0.00 0.00 0.00 3.85
5573 6040 3.366440 GGTACGCTTACCTGATACCTG 57.634 52.381 12.03 0.00 44.24 4.00
5574 6041 2.954318 GGTACGCTTACCTGATACCTGA 59.046 50.000 12.03 0.00 44.24 3.86
5575 6042 3.573110 GGTACGCTTACCTGATACCTGAT 59.427 47.826 12.03 0.00 44.24 2.90
5576 6043 4.763793 GGTACGCTTACCTGATACCTGATA 59.236 45.833 12.03 0.00 44.24 2.15
5577 6044 4.850347 ACGCTTACCTGATACCTGATAC 57.150 45.455 0.00 0.00 0.00 2.24
5578 6045 3.252701 ACGCTTACCTGATACCTGATACG 59.747 47.826 0.00 0.00 0.00 3.06
5669 6139 6.047870 CCTGAACATATGAGGAAGTGAAGAG 58.952 44.000 10.38 0.00 0.00 2.85
5711 6181 1.521681 GCTATTTCTCGGCGCCACT 60.522 57.895 28.98 3.08 0.00 4.00
5749 6219 1.004560 ACCGCGAGCATATCCATGG 60.005 57.895 8.23 4.97 32.36 3.66
5939 6410 2.349912 GCTCGTTTCCAGCTTTCAGAAC 60.350 50.000 0.00 0.00 33.75 3.01
5985 6456 2.921121 TGATGTCACGCTTCGTATTGAC 59.079 45.455 0.00 0.00 38.32 3.18
6095 6566 3.192844 CCATCATCAAGGCCAGCATAATC 59.807 47.826 5.01 0.00 0.00 1.75
6117 6588 6.710692 TCATACATGCATTGCTTCTATACG 57.289 37.500 10.49 0.00 0.00 3.06
6174 6648 5.708230 TGGTAGTGGTATTGACAATCAAACC 59.292 40.000 3.36 7.74 40.12 3.27
6176 6650 4.394729 AGTGGTATTGACAATCAAACCGT 58.605 39.130 3.36 0.00 40.12 4.83
6200 6675 4.479158 TCCATTTAAAACAAGAGCCTGGT 58.521 39.130 0.00 0.00 0.00 4.00
6219 6694 1.003118 GTCCACTTACATGTGCCTCCA 59.997 52.381 9.11 0.00 36.68 3.86
6222 6697 3.521531 TCCACTTACATGTGCCTCCAATA 59.478 43.478 9.11 0.00 36.68 1.90
6223 6698 4.165950 TCCACTTACATGTGCCTCCAATAT 59.834 41.667 9.11 0.00 36.68 1.28
6224 6699 4.276678 CCACTTACATGTGCCTCCAATATG 59.723 45.833 9.11 0.00 36.68 1.78
6225 6700 5.125356 CACTTACATGTGCCTCCAATATGA 58.875 41.667 9.11 0.00 0.00 2.15
6264 6739 5.106987 GCAAATTGTTTGTTTATCTGGCCAG 60.107 40.000 27.87 27.87 42.56 4.85
6265 6740 3.658757 TTGTTTGTTTATCTGGCCAGC 57.341 42.857 28.91 14.10 0.00 4.85
6266 6741 1.892474 TGTTTGTTTATCTGGCCAGCC 59.108 47.619 28.91 12.79 0.00 4.85
6267 6742 1.204704 GTTTGTTTATCTGGCCAGCCC 59.795 52.381 28.91 13.14 34.56 5.19
6268 6743 0.407528 TTGTTTATCTGGCCAGCCCA 59.592 50.000 28.91 11.93 42.79 5.36
6358 6839 1.202758 ACGAAACCTCACCAGATGCAA 60.203 47.619 0.00 0.00 0.00 4.08
6385 6866 2.671963 GACGTGTCCTTTGCCCCC 60.672 66.667 0.00 0.00 0.00 5.40
6432 6913 0.323816 TTGGTGGTGACAAGTTGGCA 60.324 50.000 7.51 7.51 46.06 4.92
6437 6918 2.124529 TGACAAGTTGGCACGGCA 60.125 55.556 7.51 0.00 24.43 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.081892 CGCACTCCTCTCCACATTTG 58.918 55.000 0.00 0.00 0.00 2.32
1 2 0.036010 CCGCACTCCTCTCCACATTT 60.036 55.000 0.00 0.00 0.00 2.32
2 3 1.194781 ACCGCACTCCTCTCCACATT 61.195 55.000 0.00 0.00 0.00 2.71
3 4 1.194781 AACCGCACTCCTCTCCACAT 61.195 55.000 0.00 0.00 0.00 3.21
4 5 0.541063 TAACCGCACTCCTCTCCACA 60.541 55.000 0.00 0.00 0.00 4.17
5 6 0.606604 TTAACCGCACTCCTCTCCAC 59.393 55.000 0.00 0.00 0.00 4.02
6 7 1.344065 TTTAACCGCACTCCTCTCCA 58.656 50.000 0.00 0.00 0.00 3.86
7 8 2.678336 CAATTTAACCGCACTCCTCTCC 59.322 50.000 0.00 0.00 0.00 3.71
8 9 3.335579 ACAATTTAACCGCACTCCTCTC 58.664 45.455 0.00 0.00 0.00 3.20
9 10 3.418684 ACAATTTAACCGCACTCCTCT 57.581 42.857 0.00 0.00 0.00 3.69
10 11 5.813080 ATAACAATTTAACCGCACTCCTC 57.187 39.130 0.00 0.00 0.00 3.71
11 12 6.412214 ACTATAACAATTTAACCGCACTCCT 58.588 36.000 0.00 0.00 0.00 3.69
12 13 6.673154 ACTATAACAATTTAACCGCACTCC 57.327 37.500 0.00 0.00 0.00 3.85
13 14 8.959734 AAAACTATAACAATTTAACCGCACTC 57.040 30.769 0.00 0.00 0.00 3.51
14 15 8.789762 AGAAAACTATAACAATTTAACCGCACT 58.210 29.630 0.00 0.00 0.00 4.40
15 16 8.959734 AGAAAACTATAACAATTTAACCGCAC 57.040 30.769 0.00 0.00 0.00 5.34
16 17 9.615295 GAAGAAAACTATAACAATTTAACCGCA 57.385 29.630 0.00 0.00 0.00 5.69
17 18 9.069078 GGAAGAAAACTATAACAATTTAACCGC 57.931 33.333 0.00 0.00 0.00 5.68
24 25 9.901172 ACGGATAGGAAGAAAACTATAACAATT 57.099 29.630 0.00 0.00 30.43 2.32
25 26 9.901172 AACGGATAGGAAGAAAACTATAACAAT 57.099 29.630 0.00 0.00 30.43 2.71
38 39 9.409918 CCAATCTATATCTAACGGATAGGAAGA 57.590 37.037 0.00 0.00 39.89 2.87
39 40 9.409918 TCCAATCTATATCTAACGGATAGGAAG 57.590 37.037 0.00 0.00 39.89 3.46
40 41 9.186837 GTCCAATCTATATCTAACGGATAGGAA 57.813 37.037 0.00 0.00 39.89 3.36
41 42 7.498239 CGTCCAATCTATATCTAACGGATAGGA 59.502 40.741 0.00 0.00 39.89 2.94
42 43 7.498239 TCGTCCAATCTATATCTAACGGATAGG 59.502 40.741 0.00 0.00 39.89 2.57
43 44 8.336806 GTCGTCCAATCTATATCTAACGGATAG 58.663 40.741 0.00 0.00 39.89 2.08
44 45 7.281774 GGTCGTCCAATCTATATCTAACGGATA 59.718 40.741 0.00 0.00 40.69 2.59
45 46 6.095160 GGTCGTCCAATCTATATCTAACGGAT 59.905 42.308 0.00 0.00 38.38 4.18
46 47 5.413833 GGTCGTCCAATCTATATCTAACGGA 59.586 44.000 0.00 0.00 0.00 4.69
47 48 5.415077 AGGTCGTCCAATCTATATCTAACGG 59.585 44.000 0.51 0.00 35.89 4.44
48 49 6.497785 AGGTCGTCCAATCTATATCTAACG 57.502 41.667 0.51 0.00 35.89 3.18
52 53 8.634444 GCAATATAGGTCGTCCAATCTATATCT 58.366 37.037 0.51 0.00 35.53 1.98
53 54 8.414003 TGCAATATAGGTCGTCCAATCTATATC 58.586 37.037 0.51 0.00 35.53 1.63
54 55 8.306313 TGCAATATAGGTCGTCCAATCTATAT 57.694 34.615 0.51 0.00 37.13 0.86
55 56 7.712204 TGCAATATAGGTCGTCCAATCTATA 57.288 36.000 0.51 0.00 35.89 1.31
56 57 6.605471 TGCAATATAGGTCGTCCAATCTAT 57.395 37.500 0.51 0.00 35.89 1.98
57 58 6.266786 TCTTGCAATATAGGTCGTCCAATCTA 59.733 38.462 0.00 0.00 35.89 1.98
58 59 4.955811 TGCAATATAGGTCGTCCAATCT 57.044 40.909 0.51 0.00 35.89 2.40
59 60 5.297547 TCTTGCAATATAGGTCGTCCAATC 58.702 41.667 0.00 0.00 35.89 2.67
60 61 5.290493 TCTTGCAATATAGGTCGTCCAAT 57.710 39.130 0.00 0.00 35.89 3.16
61 62 4.746535 TCTTGCAATATAGGTCGTCCAA 57.253 40.909 0.00 0.00 35.89 3.53
62 63 4.503123 CCATCTTGCAATATAGGTCGTCCA 60.503 45.833 0.00 0.00 35.89 4.02
63 64 3.997021 CCATCTTGCAATATAGGTCGTCC 59.003 47.826 0.00 0.00 0.00 4.79
64 65 3.433615 GCCATCTTGCAATATAGGTCGTC 59.566 47.826 0.00 0.00 0.00 4.20
65 66 3.181455 TGCCATCTTGCAATATAGGTCGT 60.181 43.478 0.00 0.00 38.56 4.34
66 67 3.402110 TGCCATCTTGCAATATAGGTCG 58.598 45.455 0.00 0.00 38.56 4.79
67 68 4.380233 GCATGCCATCTTGCAATATAGGTC 60.380 45.833 6.36 1.46 45.84 3.85
68 69 3.508793 GCATGCCATCTTGCAATATAGGT 59.491 43.478 6.36 0.00 45.84 3.08
69 70 3.508402 TGCATGCCATCTTGCAATATAGG 59.492 43.478 16.68 4.45 46.23 2.57
70 71 4.776795 TGCATGCCATCTTGCAATATAG 57.223 40.909 16.68 0.00 46.23 1.31
76 77 0.458260 GATGTGCATGCCATCTTGCA 59.542 50.000 27.90 13.27 46.78 4.08
77 78 0.458260 TGATGTGCATGCCATCTTGC 59.542 50.000 31.46 17.68 41.96 4.01
78 79 2.360801 TGATGATGTGCATGCCATCTTG 59.639 45.455 31.46 0.00 39.54 3.02
79 80 2.661718 TGATGATGTGCATGCCATCTT 58.338 42.857 31.46 28.02 39.54 2.40
80 81 2.358322 TGATGATGTGCATGCCATCT 57.642 45.000 31.46 23.02 39.54 2.90
81 82 2.556622 TGATGATGATGTGCATGCCATC 59.443 45.455 28.22 28.22 38.10 3.51
82 83 2.296190 GTGATGATGATGTGCATGCCAT 59.704 45.455 16.68 17.49 37.34 4.40
83 84 1.679153 GTGATGATGATGTGCATGCCA 59.321 47.619 16.68 13.21 37.34 4.92
84 85 1.000607 GGTGATGATGATGTGCATGCC 60.001 52.381 16.68 7.25 37.34 4.40
85 86 1.679153 TGGTGATGATGATGTGCATGC 59.321 47.619 11.82 11.82 37.34 4.06
86 87 3.380320 AGTTGGTGATGATGATGTGCATG 59.620 43.478 0.00 0.00 37.34 4.06
87 88 3.628008 AGTTGGTGATGATGATGTGCAT 58.372 40.909 0.00 0.00 40.77 3.96
88 89 3.011818 GAGTTGGTGATGATGATGTGCA 58.988 45.455 0.00 0.00 0.00 4.57
89 90 3.064958 CAGAGTTGGTGATGATGATGTGC 59.935 47.826 0.00 0.00 0.00 4.57
90 91 3.064958 GCAGAGTTGGTGATGATGATGTG 59.935 47.826 0.00 0.00 0.00 3.21
91 92 3.054582 AGCAGAGTTGGTGATGATGATGT 60.055 43.478 0.00 0.00 32.86 3.06
92 93 3.542648 AGCAGAGTTGGTGATGATGATG 58.457 45.455 0.00 0.00 32.86 3.07
93 94 3.928005 AGCAGAGTTGGTGATGATGAT 57.072 42.857 0.00 0.00 32.86 2.45
94 95 3.708403 AAGCAGAGTTGGTGATGATGA 57.292 42.857 0.00 0.00 34.72 2.92
95 96 4.778534 AAAAGCAGAGTTGGTGATGATG 57.221 40.909 0.00 0.00 34.72 3.07
96 97 8.579850 TTATAAAAAGCAGAGTTGGTGATGAT 57.420 30.769 0.00 0.00 34.72 2.45
97 98 7.882791 TCTTATAAAAAGCAGAGTTGGTGATGA 59.117 33.333 0.00 0.00 34.72 2.92
98 99 8.044060 TCTTATAAAAAGCAGAGTTGGTGATG 57.956 34.615 0.00 0.00 34.72 3.07
99 100 7.885399 ACTCTTATAAAAAGCAGAGTTGGTGAT 59.115 33.333 0.00 0.00 42.79 3.06
100 101 7.224297 ACTCTTATAAAAAGCAGAGTTGGTGA 58.776 34.615 0.00 0.00 42.79 4.02
101 102 7.440523 ACTCTTATAAAAAGCAGAGTTGGTG 57.559 36.000 0.00 0.00 42.79 4.17
102 103 9.569122 TTTACTCTTATAAAAAGCAGAGTTGGT 57.431 29.630 7.61 0.00 42.79 3.67
160 161 4.446385 CGCCAAGATTCGGATATTCGTTTA 59.554 41.667 2.72 0.00 0.00 2.01
165 166 2.143122 TGCGCCAAGATTCGGATATTC 58.857 47.619 4.18 0.00 0.00 1.75
213 214 1.033202 TATGTGGCAGGCATGTGCAG 61.033 55.000 10.16 0.03 45.93 4.41
237 238 2.759355 AGGTCATATTGGTTCGAGGGA 58.241 47.619 0.00 0.00 0.00 4.20
247 251 2.097466 GCGTGAACCCAAGGTCATATTG 59.903 50.000 0.00 0.00 33.12 1.90
260 264 3.006940 TGTTGATCATTAGGCGTGAACC 58.993 45.455 0.00 0.00 0.00 3.62
267 271 7.657354 TGTATGTGTAGATGTTGATCATTAGGC 59.343 37.037 0.00 0.00 36.83 3.93
268 272 9.546428 TTGTATGTGTAGATGTTGATCATTAGG 57.454 33.333 0.00 0.00 36.83 2.69
289 293 8.920174 GGGGCCAAAGTAGTATTTTATTTGTAT 58.080 33.333 4.39 0.00 0.00 2.29
290 294 7.342541 GGGGGCCAAAGTAGTATTTTATTTGTA 59.657 37.037 4.39 0.00 0.00 2.41
399 403 8.296713 TCTGCTTTTTGCTATAACGAAATCTTT 58.703 29.630 0.00 0.00 43.37 2.52
406 410 7.201609 CCTGTAATCTGCTTTTTGCTATAACGA 60.202 37.037 0.00 0.00 43.37 3.85
407 411 6.907212 CCTGTAATCTGCTTTTTGCTATAACG 59.093 38.462 0.00 0.00 43.37 3.18
411 415 6.886459 TCTTCCTGTAATCTGCTTTTTGCTAT 59.114 34.615 0.00 0.00 43.37 2.97
415 419 5.385617 CGTCTTCCTGTAATCTGCTTTTTG 58.614 41.667 0.00 0.00 0.00 2.44
416 420 4.083271 GCGTCTTCCTGTAATCTGCTTTTT 60.083 41.667 0.00 0.00 0.00 1.94
429 459 5.046910 ACATTTATGTTTGCGTCTTCCTG 57.953 39.130 0.00 0.00 37.90 3.86
493 523 5.483685 TGTAACATGGAGTAGCAGAAACT 57.516 39.130 0.00 0.00 0.00 2.66
531 561 4.021894 CCATGTAGTACTGCTGTATCCCTC 60.022 50.000 12.42 0.00 0.00 4.30
534 564 3.069586 TGCCATGTAGTACTGCTGTATCC 59.930 47.826 12.42 0.00 0.00 2.59
543 573 2.118679 TGCCAGATGCCATGTAGTACT 58.881 47.619 0.00 0.00 40.16 2.73
545 575 3.862877 AATGCCAGATGCCATGTAGTA 57.137 42.857 0.00 0.00 40.16 1.82
546 576 2.742428 AATGCCAGATGCCATGTAGT 57.258 45.000 0.00 0.00 40.16 2.73
547 577 5.466819 CATTTAATGCCAGATGCCATGTAG 58.533 41.667 0.00 0.00 40.16 2.74
715 748 2.159240 TCGCTACACCACTAGATTGCTG 60.159 50.000 0.00 0.00 0.00 4.41
788 821 0.966179 GGGGCGTGAGGTGAATTTTT 59.034 50.000 0.00 0.00 0.00 1.94
844 877 3.775654 AAGCCTCCGGGAGCTTCG 61.776 66.667 21.68 6.11 46.11 3.79
1066 1281 2.105128 CGGGGACAGATCGAGCAC 59.895 66.667 2.38 0.00 0.00 4.40
1144 1359 2.802106 AAACGGCACCACGGTTTG 59.198 55.556 1.24 0.00 46.49 2.93
1157 1372 0.767687 AATCGCGCAAAAACGAAACG 59.232 45.000 8.75 0.00 42.31 3.60
1159 1374 2.216714 GGAAAATCGCGCAAAAACGAAA 59.783 40.909 8.75 0.00 42.31 3.46
1217 1432 5.278660 GCCCAATAGCAACTAATCAATCCAG 60.279 44.000 0.00 0.00 0.00 3.86
1221 1436 4.460263 TCGCCCAATAGCAACTAATCAAT 58.540 39.130 0.00 0.00 0.00 2.57
1358 1575 3.982701 TCGTTTTCATCGTACACGTCAAT 59.017 39.130 1.19 0.00 40.80 2.57
1440 1660 7.566569 TGAACCTATAAAATGGATGAACCGTA 58.433 34.615 0.00 0.00 42.61 4.02
1546 1778 1.546476 ACTCCTAGCTCGTTCTTGTGG 59.454 52.381 0.00 0.00 0.00 4.17
1548 1780 2.891580 TGAACTCCTAGCTCGTTCTTGT 59.108 45.455 14.89 0.00 38.23 3.16
1602 1836 9.282569 GAGTAGAAATGGAGCATCAAATATCTT 57.717 33.333 0.00 0.00 36.25 2.40
1603 1837 7.882271 GGAGTAGAAATGGAGCATCAAATATCT 59.118 37.037 0.00 0.00 36.25 1.98
1656 1890 0.801872 TTCGCGTGAATGACCAATGG 59.198 50.000 7.45 0.00 0.00 3.16
1746 1980 7.508977 TCTTTGAAAAGAAGGTTGGAACCATAT 59.491 33.333 11.14 0.00 44.32 1.78
1749 1983 5.020132 TCTTTGAAAAGAAGGTTGGAACCA 58.980 37.500 11.14 0.00 44.32 3.67
1790 2024 1.918957 AGACTTCTAAAGCTGCCCCAT 59.081 47.619 0.00 0.00 0.00 4.00
1794 2028 3.120025 GCAAGAAGACTTCTAAAGCTGCC 60.120 47.826 20.86 8.90 39.61 4.85
1816 2050 5.607477 TGGGTAACTCATAAAGCTTATCCG 58.393 41.667 0.00 0.00 30.44 4.18
1822 2056 8.086143 TGTACTATTGGGTAACTCATAAAGCT 57.914 34.615 0.00 0.00 0.00 3.74
1837 2073 8.314143 TCCTCTTTTAACGTTTGTACTATTGG 57.686 34.615 5.91 0.00 0.00 3.16
1840 2076 8.448615 GCATTCCTCTTTTAACGTTTGTACTAT 58.551 33.333 5.91 0.00 0.00 2.12
1842 2078 6.261381 TGCATTCCTCTTTTAACGTTTGTACT 59.739 34.615 5.91 0.00 0.00 2.73
1843 2079 6.432107 TGCATTCCTCTTTTAACGTTTGTAC 58.568 36.000 5.91 0.00 0.00 2.90
1908 2205 4.529377 ACTGCATCCATCAAACTTTTCCAT 59.471 37.500 0.00 0.00 0.00 3.41
1962 2259 1.910580 AACGACGGAAGCCATCCCAT 61.911 55.000 0.00 0.00 46.39 4.00
1963 2260 2.589157 AACGACGGAAGCCATCCCA 61.589 57.895 0.00 0.00 46.39 4.37
1964 2261 2.106683 CAACGACGGAAGCCATCCC 61.107 63.158 0.00 0.00 46.39 3.85
1965 2262 2.750888 GCAACGACGGAAGCCATCC 61.751 63.158 0.00 0.00 45.57 3.51
1966 2263 1.573829 TTGCAACGACGGAAGCCATC 61.574 55.000 0.00 0.00 0.00 3.51
1976 2273 8.391106 ACAGAAATTAATAGATCTTGCAACGAC 58.609 33.333 0.00 0.00 0.00 4.34
2024 2321 5.048294 GCTGGAGAGTATAGAGAGGCTAAAC 60.048 48.000 0.00 0.00 31.66 2.01
2039 2336 6.552445 AATAAGTATTCACAGCTGGAGAGT 57.448 37.500 19.93 14.28 0.00 3.24
2076 2374 2.289694 CCAGAGTCACCACCCTAACAAG 60.290 54.545 0.00 0.00 0.00 3.16
2197 2495 9.995003 CTATGAGATGATGATGATGATGATGAT 57.005 33.333 0.00 0.00 0.00 2.45
2198 2496 9.201989 TCTATGAGATGATGATGATGATGATGA 57.798 33.333 0.00 0.00 0.00 2.92
2199 2497 9.474920 CTCTATGAGATGATGATGATGATGATG 57.525 37.037 0.00 0.00 0.00 3.07
2200 2498 9.427821 TCTCTATGAGATGATGATGATGATGAT 57.572 33.333 0.00 0.00 33.35 2.45
2201 2499 8.824756 TCTCTATGAGATGATGATGATGATGA 57.175 34.615 0.00 0.00 33.35 2.92
2278 2576 1.065854 CCTTTCGGAAGATCTGCACCT 60.066 52.381 4.56 0.00 41.60 4.00
2437 2738 0.958876 CAACGGTAACCCCTTCAGCC 60.959 60.000 0.00 0.00 0.00 4.85
2463 2764 1.228245 TGGCCAGCTTCTGTTCCAC 60.228 57.895 0.00 0.00 30.99 4.02
2494 2795 4.855340 TCCCATTTTGACCTCCTATTGTC 58.145 43.478 0.00 0.00 0.00 3.18
2731 3034 3.134458 CCCAGAGAATAGCTTTAAGCCG 58.866 50.000 13.84 0.00 43.77 5.52
2889 3227 1.611491 ACGGCAAATTAACACACCTGG 59.389 47.619 0.00 0.00 0.00 4.45
3325 3663 8.772069 TGGAACAACAAACAACTTGAGGATCAT 61.772 37.037 0.00 0.00 40.44 2.45
3619 3960 8.763356 CAAAATCACAAAGCTTAAGTTTATGCA 58.237 29.630 4.89 0.00 36.57 3.96
3624 3965 6.883744 TCCCAAAATCACAAAGCTTAAGTTT 58.116 32.000 0.00 0.86 0.00 2.66
4293 4731 2.051334 TAATGGTTTGGCGGGAGATG 57.949 50.000 0.00 0.00 0.00 2.90
4531 4977 3.391965 CTTACCAAAAAGCTGCATGCAA 58.608 40.909 22.88 5.74 45.94 4.08
4744 5190 7.946219 ATAAGATCTTATTGCATCCAATGTGGA 59.054 33.333 20.20 0.00 40.67 4.02
4745 5191 6.401047 AAGATCTTATTGCATCCAATGTGG 57.599 37.500 6.06 0.00 41.58 4.17
4755 5201 9.599866 CGTCCCATAATATAAGATCTTATTGCA 57.400 33.333 28.39 14.49 37.07 4.08
4759 5205 9.148879 CCTCCGTCCCATAATATAAGATCTTAT 57.851 37.037 26.87 26.87 39.02 1.73
4763 5209 5.897824 TCCCTCCGTCCCATAATATAAGATC 59.102 44.000 0.00 0.00 0.00 2.75
4764 5210 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
4869 5318 1.633945 ACCAAACTGGCCCTTAGTAGG 59.366 52.381 0.00 5.95 42.67 3.18
4870 5319 3.081804 CAACCAAACTGGCCCTTAGTAG 58.918 50.000 0.00 0.00 42.67 2.57
4871 5320 2.224917 CCAACCAAACTGGCCCTTAGTA 60.225 50.000 0.00 0.00 42.67 1.82
4872 5321 1.480498 CCAACCAAACTGGCCCTTAGT 60.480 52.381 0.00 0.00 42.67 2.24
4873 5322 1.256812 CCAACCAAACTGGCCCTTAG 58.743 55.000 0.00 0.00 42.67 2.18
4874 5323 0.558712 ACCAACCAAACTGGCCCTTA 59.441 50.000 0.00 0.00 42.67 2.69
4875 5324 1.048160 CACCAACCAAACTGGCCCTT 61.048 55.000 0.00 0.00 42.67 3.95
4876 5325 1.457455 CACCAACCAAACTGGCCCT 60.457 57.895 0.00 0.00 42.67 5.19
4877 5326 1.744320 GACACCAACCAAACTGGCCC 61.744 60.000 0.00 0.00 42.67 5.80
4878 5327 1.739667 GACACCAACCAAACTGGCC 59.260 57.895 0.00 0.00 42.67 5.36
4879 5328 1.040339 TGGACACCAACCAAACTGGC 61.040 55.000 0.00 0.00 42.67 4.85
4932 5381 6.183360 GCAAAACAAACAGAAAATGTGTCCAT 60.183 34.615 0.00 0.00 43.00 3.41
4948 5397 1.136695 CTGACCAGGCAGCAAAACAAA 59.863 47.619 0.00 0.00 0.00 2.83
4999 5448 0.253160 TGAACTATCCAGGCCAGGGT 60.253 55.000 15.24 10.31 0.00 4.34
5069 5518 8.977412 CCTGGGCTCCTTTAATTCTTTAATTAA 58.023 33.333 0.00 0.00 42.87 1.40
5137 5586 1.974236 CAGGGAGATAGTTAGCCTGGG 59.026 57.143 0.00 0.00 0.00 4.45
5169 5618 1.746787 TGCATGCAAGTGATTAGCCTG 59.253 47.619 20.30 0.00 0.00 4.85
5200 5649 1.699634 TCAAGATGCCAGGTATAGCCC 59.300 52.381 0.00 0.00 38.26 5.19
5222 5671 4.036380 CCTGTAAGTTGTTTGGTTCAGGTC 59.964 45.833 0.00 0.00 37.16 3.85
5379 5839 2.827051 CGGATGGGCACAAGCATCG 61.827 63.158 0.00 0.00 44.61 3.84
5554 6021 4.850347 ATCAGGTATCAGGTAAGCGTAC 57.150 45.455 0.63 0.63 0.00 3.67
5571 6038 3.118920 TGTCCATGGGTTGTACGTATCAG 60.119 47.826 13.02 0.00 0.00 2.90
5572 6039 2.832733 TGTCCATGGGTTGTACGTATCA 59.167 45.455 13.02 0.00 0.00 2.15
5573 6040 3.530265 TGTCCATGGGTTGTACGTATC 57.470 47.619 13.02 0.00 0.00 2.24
5574 6041 3.199071 ACATGTCCATGGGTTGTACGTAT 59.801 43.478 13.02 0.00 42.91 3.06
5575 6042 2.568062 ACATGTCCATGGGTTGTACGTA 59.432 45.455 13.02 0.00 42.91 3.57
5576 6043 1.349688 ACATGTCCATGGGTTGTACGT 59.650 47.619 13.02 0.05 42.91 3.57
5577 6044 1.737236 CACATGTCCATGGGTTGTACG 59.263 52.381 13.02 0.00 42.91 3.67
5578 6045 1.472480 GCACATGTCCATGGGTTGTAC 59.528 52.381 13.02 2.34 43.92 2.90
5669 6139 1.227497 CTTCTCCAGCCGCCATCTC 60.227 63.158 0.00 0.00 0.00 2.75
5749 6219 1.590238 CAGATCAAATCCACGACGAGC 59.410 52.381 0.00 0.00 0.00 5.03
5939 6410 6.675026 TCATTTTCATGCTTCACTGAGAAAG 58.325 36.000 0.00 0.00 35.40 2.62
6057 6528 0.447801 ATGGTCGAAAACGCATCTGC 59.552 50.000 0.00 0.00 37.78 4.26
6076 6547 3.581265 TGATTATGCTGGCCTTGATGA 57.419 42.857 3.32 0.00 0.00 2.92
6077 6548 4.763279 TGTATGATTATGCTGGCCTTGATG 59.237 41.667 3.32 0.00 0.00 3.07
6078 6549 4.989277 TGTATGATTATGCTGGCCTTGAT 58.011 39.130 3.32 0.00 0.00 2.57
6095 6566 6.367149 ACTCGTATAGAAGCAATGCATGTATG 59.633 38.462 8.35 0.00 0.00 2.39
6115 6586 3.189910 TGTAGTACTTCGATTGCACTCGT 59.810 43.478 23.46 9.43 39.62 4.18
6117 6588 4.982999 TCTGTAGTACTTCGATTGCACTC 58.017 43.478 0.00 0.00 0.00 3.51
6174 6648 4.455877 AGGCTCTTGTTTTAAATGGAGACG 59.544 41.667 9.73 0.00 34.40 4.18
6176 6650 4.766891 CCAGGCTCTTGTTTTAAATGGAGA 59.233 41.667 9.73 4.17 0.00 3.71
6200 6675 1.357137 TGGAGGCACATGTAAGTGGA 58.643 50.000 0.00 0.00 39.87 4.02
6222 6697 9.996554 ACAATTTGCATCATCATATTCATTCAT 57.003 25.926 0.00 0.00 0.00 2.57
6223 6698 9.825109 AACAATTTGCATCATCATATTCATTCA 57.175 25.926 0.00 0.00 0.00 2.57
6265 6740 3.546714 AACGGAAGCCTCGGTTGGG 62.547 63.158 7.40 0.00 41.91 4.12
6266 6741 2.032071 AACGGAAGCCTCGGTTGG 59.968 61.111 7.40 0.00 41.91 3.77
6267 6742 2.033194 GGAACGGAAGCCTCGGTTG 61.033 63.158 12.47 0.00 43.09 3.77
6268 6743 2.346365 GGAACGGAAGCCTCGGTT 59.654 61.111 7.89 7.89 45.02 4.44
6303 6778 2.057922 ACACTTGTCACCCATCTTCCT 58.942 47.619 0.00 0.00 0.00 3.36
6306 6781 3.391296 ACACTACACTTGTCACCCATCTT 59.609 43.478 0.00 0.00 0.00 2.40
6358 6839 1.814527 GGACACGTCCTCGGCTATT 59.185 57.895 9.04 0.00 46.16 1.73
6385 6866 2.613691 ACCTTGCACGTAAAGTATCCG 58.386 47.619 8.79 0.00 0.00 4.18
6436 6917 0.816825 AATATCGCCACTGCTGCCTG 60.817 55.000 0.00 0.00 34.43 4.85
6437 6918 0.107017 AAATATCGCCACTGCTGCCT 60.107 50.000 0.00 0.00 34.43 4.75


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

AutoCloner maintained by Alex Coulton.