Multiple sequence alignment - TraesCS6D01G194000

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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 TraesCS6D01G194000 chr6D 100.000 2353 0 0 1 2353 269237247 269234895 0.000000e+00 4346.0
1 TraesCS6D01G194000 chr6D 90.196 102 9 1 107 208 389141616 389141716 5.280000e-27 132.0
2 TraesCS6D01G194000 chr6A 95.609 1002 34 6 423 1420 383490799 383489804 0.000000e+00 1598.0
3 TraesCS6D01G194000 chr6A 92.070 227 16 1 201 425 383491462 383491236 3.770000e-83 318.0
4 TraesCS6D01G194000 chr6A 81.792 346 25 21 1450 1766 383489816 383489480 3.000000e-64 255.0
5 TraesCS6D01G194000 chr6A 87.255 102 12 1 107 208 346634107 346634207 5.310000e-22 115.0
6 TraesCS6D01G194000 chr6B 95.423 874 32 5 549 1420 417349014 417348147 0.000000e+00 1386.0
7 TraesCS6D01G194000 chr6B 89.828 698 48 10 1655 2351 417347377 417346702 0.000000e+00 874.0
8 TraesCS6D01G194000 chr6B 89.109 101 10 1 104 204 199015899 199015998 8.830000e-25 124.0
9 TraesCS6D01G194000 chr6B 88.776 98 11 0 107 204 208471205 208471108 1.140000e-23 121.0
10 TraesCS6D01G194000 chr6B 96.429 56 2 0 1457 1512 417348152 417348097 2.490000e-15 93.5
11 TraesCS6D01G194000 chr6B 96.226 53 2 0 48 100 658813724 658813776 1.160000e-13 87.9
12 TraesCS6D01G194000 chr6B 97.674 43 1 0 1611 1653 417347835 417347793 9.020000e-10 75.0
13 TraesCS6D01G194000 chr5B 81.682 535 81 8 1789 2322 232792016 232792534 1.670000e-116 429.0
14 TraesCS6D01G194000 chr5B 77.376 526 91 16 1824 2343 677519148 677518645 1.060000e-73 287.0
15 TraesCS6D01G194000 chr5B 97.917 48 1 0 49 96 27408575 27408528 1.500000e-12 84.2
16 TraesCS6D01G194000 chr1D 81.664 529 72 19 1829 2353 439725630 439726137 1.300000e-112 416.0
17 TraesCS6D01G194000 chr1D 77.931 290 43 9 1986 2275 452466012 452466280 6.730000e-36 161.0
18 TraesCS6D01G194000 chr2D 78.415 593 106 16 1765 2353 122396669 122397243 1.330000e-97 366.0
19 TraesCS6D01G194000 chr2B 79.619 525 81 20 1777 2298 510351496 510350995 1.030000e-93 353.0
20 TraesCS6D01G194000 chr2B 77.403 593 102 16 1765 2350 175413418 175413985 8.110000e-85 324.0
21 TraesCS6D01G194000 chr2B 88.660 97 9 2 117 213 749955209 749955115 1.480000e-22 117.0
22 TraesCS6D01G194000 chr7D 77.983 595 102 15 1765 2350 554368489 554369063 1.730000e-91 346.0
23 TraesCS6D01G194000 chr7D 80.095 211 35 7 2147 2353 205240740 205240533 1.460000e-32 150.0
24 TraesCS6D01G194000 chr2A 79.102 512 87 16 1818 2326 738013212 738012718 3.750000e-88 335.0
25 TraesCS6D01G194000 chr2A 74.677 387 84 11 1854 2232 678067582 678067962 2.420000e-35 159.0
26 TraesCS6D01G194000 chr2A 90.476 63 6 0 38 100 118678120 118678182 1.500000e-12 84.2
27 TraesCS6D01G194000 chr2A 94.231 52 3 0 49 100 646627039 646626988 1.940000e-11 80.5
28 TraesCS6D01G194000 chr2A 94.340 53 2 1 49 100 683715213 683715265 1.940000e-11 80.5
29 TraesCS6D01G194000 chr2A 100.000 28 0 0 2326 2353 738012728 738012701 4.000000e-03 52.8
30 TraesCS6D01G194000 chrUn 77.376 526 91 16 1824 2343 331609321 331609824 1.060000e-73 287.0
31 TraesCS6D01G194000 chr7A 76.863 510 110 7 1809 2316 68841419 68841922 4.950000e-72 281.0
32 TraesCS6D01G194000 chr7A 75.850 588 118 16 1770 2351 49470644 49470075 6.400000e-71 278.0
33 TraesCS6D01G194000 chr7A 88.776 98 10 1 107 204 103919038 103918942 4.110000e-23 119.0
34 TraesCS6D01G194000 chr7A 94.340 53 2 1 44 96 609454106 609454055 1.940000e-11 80.5
35 TraesCS6D01G194000 chr7A 94.340 53 2 1 49 100 696202659 696202607 1.940000e-11 80.5
36 TraesCS6D01G194000 chr1B 90.722 97 7 2 117 213 198131898 198131804 6.830000e-26 128.0
37 TraesCS6D01G194000 chr3D 77.232 224 43 5 2019 2239 418759968 418759750 8.830000e-25 124.0
38 TraesCS6D01G194000 chr3D 94.340 53 3 0 48 100 561491042 561491094 5.390000e-12 82.4
39 TraesCS6D01G194000 chr3A 89.691 97 8 2 107 203 731438581 731438675 3.180000e-24 122.0
40 TraesCS6D01G194000 chr3A 88.119 101 11 1 106 206 242726204 242726105 4.110000e-23 119.0
41 TraesCS6D01G194000 chr3B 87.500 64 6 2 48 110 719434139 719434077 3.240000e-09 73.1


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 TraesCS6D01G194000 chr6D 269234895 269237247 2352 True 4346.000000 4346 100.000000 1 2353 1 chr6D.!!$R1 2352
1 TraesCS6D01G194000 chr6A 383489480 383491462 1982 True 723.666667 1598 89.823667 201 1766 3 chr6A.!!$R1 1565
2 TraesCS6D01G194000 chr6B 417346702 417349014 2312 True 607.125000 1386 94.838500 549 2351 4 chr6B.!!$R2 1802
3 TraesCS6D01G194000 chr5B 232792016 232792534 518 False 429.000000 429 81.682000 1789 2322 1 chr5B.!!$F1 533
4 TraesCS6D01G194000 chr5B 677518645 677519148 503 True 287.000000 287 77.376000 1824 2343 1 chr5B.!!$R2 519
5 TraesCS6D01G194000 chr1D 439725630 439726137 507 False 416.000000 416 81.664000 1829 2353 1 chr1D.!!$F1 524
6 TraesCS6D01G194000 chr2D 122396669 122397243 574 False 366.000000 366 78.415000 1765 2353 1 chr2D.!!$F1 588
7 TraesCS6D01G194000 chr2B 510350995 510351496 501 True 353.000000 353 79.619000 1777 2298 1 chr2B.!!$R1 521
8 TraesCS6D01G194000 chr2B 175413418 175413985 567 False 324.000000 324 77.403000 1765 2350 1 chr2B.!!$F1 585
9 TraesCS6D01G194000 chr7D 554368489 554369063 574 False 346.000000 346 77.983000 1765 2350 1 chr7D.!!$F1 585
10 TraesCS6D01G194000 chrUn 331609321 331609824 503 False 287.000000 287 77.376000 1824 2343 1 chrUn.!!$F1 519
11 TraesCS6D01G194000 chr7A 68841419 68841922 503 False 281.000000 281 76.863000 1809 2316 1 chr7A.!!$F1 507
12 TraesCS6D01G194000 chr7A 49470075 49470644 569 True 278.000000 278 75.850000 1770 2351 1 chr7A.!!$R1 581

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
27 28 0.245813 AAAGGGTACGTTCCTCGAGC 59.754 55.0 11.29 0.0 42.86 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1863 0.106819 GTGGACGGAGGGAGTAGCTA 60.107 60.0 0.0 0.0 0.0 3.32 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 3.310727 CCCGACAAAAGGGTACGTT 57.689 52.632 0.00 0.00 43.89 3.99
20 21 1.150827 CCCGACAAAAGGGTACGTTC 58.849 55.000 0.00 0.00 43.89 3.95
21 22 1.150827 CCGACAAAAGGGTACGTTCC 58.849 55.000 1.96 1.96 34.32 3.62
22 23 1.270465 CCGACAAAAGGGTACGTTCCT 60.270 52.381 11.29 7.71 34.32 3.36
23 24 2.064014 CGACAAAAGGGTACGTTCCTC 58.936 52.381 11.29 1.62 34.32 3.71
24 25 2.064014 GACAAAAGGGTACGTTCCTCG 58.936 52.381 11.29 5.84 46.00 4.63
25 26 1.688197 ACAAAAGGGTACGTTCCTCGA 59.312 47.619 11.29 0.00 42.86 4.04
26 27 2.288640 ACAAAAGGGTACGTTCCTCGAG 60.289 50.000 11.29 5.13 42.86 4.04
27 28 0.245813 AAAGGGTACGTTCCTCGAGC 59.754 55.000 11.29 0.00 42.86 5.03
28 29 0.611340 AAGGGTACGTTCCTCGAGCT 60.611 55.000 11.29 0.00 42.86 4.09
29 30 1.139095 GGGTACGTTCCTCGAGCTG 59.861 63.158 11.29 0.00 42.86 4.24
30 31 1.310933 GGGTACGTTCCTCGAGCTGA 61.311 60.000 11.29 0.00 42.86 4.26
31 32 0.524862 GGTACGTTCCTCGAGCTGAA 59.475 55.000 6.99 3.24 42.86 3.02
32 33 1.615502 GTACGTTCCTCGAGCTGAAC 58.384 55.000 19.02 19.02 42.86 3.18
33 34 1.068748 GTACGTTCCTCGAGCTGAACA 60.069 52.381 24.80 10.99 40.65 3.18
34 35 0.603569 ACGTTCCTCGAGCTGAACAT 59.396 50.000 24.80 13.79 40.65 2.71
35 36 1.816835 ACGTTCCTCGAGCTGAACATA 59.183 47.619 24.80 0.00 40.65 2.29
36 37 2.159366 ACGTTCCTCGAGCTGAACATAG 60.159 50.000 24.80 15.65 40.65 2.23
37 38 2.097629 CGTTCCTCGAGCTGAACATAGA 59.902 50.000 24.80 6.73 40.65 1.98
38 39 3.427638 CGTTCCTCGAGCTGAACATAGAA 60.428 47.826 24.80 11.43 40.65 2.10
39 40 4.495422 GTTCCTCGAGCTGAACATAGAAA 58.505 43.478 22.20 0.00 40.41 2.52
40 41 5.112686 GTTCCTCGAGCTGAACATAGAAAT 58.887 41.667 22.20 0.00 40.41 2.17
41 42 4.686972 TCCTCGAGCTGAACATAGAAATG 58.313 43.478 6.99 0.00 39.17 2.32
42 43 3.806521 CCTCGAGCTGAACATAGAAATGG 59.193 47.826 6.99 0.00 37.43 3.16
43 44 4.437239 CTCGAGCTGAACATAGAAATGGT 58.563 43.478 0.00 0.00 37.43 3.55
44 45 5.451937 CCTCGAGCTGAACATAGAAATGGTA 60.452 44.000 6.99 0.00 37.43 3.25
45 46 5.592054 TCGAGCTGAACATAGAAATGGTAG 58.408 41.667 0.00 0.00 37.43 3.18
46 47 4.747108 CGAGCTGAACATAGAAATGGTAGG 59.253 45.833 0.00 0.00 37.43 3.18
47 48 4.455606 AGCTGAACATAGAAATGGTAGGC 58.544 43.478 0.00 0.00 37.43 3.93
48 49 4.164988 AGCTGAACATAGAAATGGTAGGCT 59.835 41.667 0.00 0.00 36.49 4.58
49 50 4.884164 GCTGAACATAGAAATGGTAGGCTT 59.116 41.667 0.00 0.00 37.43 4.35
50 51 5.358160 GCTGAACATAGAAATGGTAGGCTTT 59.642 40.000 0.00 0.00 37.43 3.51
51 52 6.127619 GCTGAACATAGAAATGGTAGGCTTTT 60.128 38.462 0.00 0.00 37.43 2.27
52 53 7.577616 GCTGAACATAGAAATGGTAGGCTTTTT 60.578 37.037 0.00 0.00 37.43 1.94
74 75 5.418310 TTTTGCGAGAAAACTTTCGATCT 57.582 34.783 0.00 0.00 41.92 2.75
75 76 6.533819 TTTTGCGAGAAAACTTTCGATCTA 57.466 33.333 0.00 0.00 41.92 1.98
76 77 6.721571 TTTGCGAGAAAACTTTCGATCTAT 57.278 33.333 0.00 0.00 41.92 1.98
77 78 6.721571 TTGCGAGAAAACTTTCGATCTATT 57.278 33.333 0.00 0.00 41.92 1.73
78 79 6.332504 TGCGAGAAAACTTTCGATCTATTC 57.667 37.500 0.00 0.00 41.92 1.75
79 80 5.867174 TGCGAGAAAACTTTCGATCTATTCA 59.133 36.000 0.00 0.00 41.92 2.57
80 81 6.535150 TGCGAGAAAACTTTCGATCTATTCAT 59.465 34.615 0.00 0.00 41.92 2.57
81 82 7.060422 GCGAGAAAACTTTCGATCTATTCATC 58.940 38.462 0.00 0.00 41.92 2.92
82 83 7.254117 GCGAGAAAACTTTCGATCTATTCATCA 60.254 37.037 0.00 0.00 41.92 3.07
83 84 8.595533 CGAGAAAACTTTCGATCTATTCATCAA 58.404 33.333 0.00 0.00 41.92 2.57
88 89 9.994432 AAACTTTCGATCTATTCATCAATTGTC 57.006 29.630 5.13 0.00 0.00 3.18
89 90 8.722480 ACTTTCGATCTATTCATCAATTGTCA 57.278 30.769 5.13 0.00 0.00 3.58
90 91 9.166173 ACTTTCGATCTATTCATCAATTGTCAA 57.834 29.630 5.13 0.00 0.00 3.18
91 92 9.647679 CTTTCGATCTATTCATCAATTGTCAAG 57.352 33.333 5.13 0.00 0.00 3.02
92 93 7.719778 TCGATCTATTCATCAATTGTCAAGG 57.280 36.000 5.13 0.00 0.00 3.61
93 94 7.275183 TCGATCTATTCATCAATTGTCAAGGT 58.725 34.615 5.13 0.00 0.00 3.50
94 95 8.421002 TCGATCTATTCATCAATTGTCAAGGTA 58.579 33.333 5.13 0.00 0.00 3.08
95 96 8.706936 CGATCTATTCATCAATTGTCAAGGTAG 58.293 37.037 5.13 3.39 0.00 3.18
96 97 7.792374 TCTATTCATCAATTGTCAAGGTAGC 57.208 36.000 5.13 0.00 0.00 3.58
97 98 7.337938 TCTATTCATCAATTGTCAAGGTAGCA 58.662 34.615 5.13 0.00 0.00 3.49
98 99 5.627499 TTCATCAATTGTCAAGGTAGCAC 57.373 39.130 5.13 0.00 0.00 4.40
99 100 4.650734 TCATCAATTGTCAAGGTAGCACA 58.349 39.130 5.13 0.00 0.00 4.57
100 101 4.696877 TCATCAATTGTCAAGGTAGCACAG 59.303 41.667 5.13 0.00 0.00 3.66
101 102 4.085357 TCAATTGTCAAGGTAGCACAGT 57.915 40.909 5.13 0.00 0.00 3.55
102 103 4.460263 TCAATTGTCAAGGTAGCACAGTT 58.540 39.130 5.13 0.00 0.00 3.16
103 104 5.616270 TCAATTGTCAAGGTAGCACAGTTA 58.384 37.500 5.13 0.00 0.00 2.24
104 105 6.058833 TCAATTGTCAAGGTAGCACAGTTAA 58.941 36.000 5.13 0.00 0.00 2.01
105 106 5.941948 ATTGTCAAGGTAGCACAGTTAAC 57.058 39.130 0.00 0.00 0.00 2.01
106 107 4.682778 TGTCAAGGTAGCACAGTTAACT 57.317 40.909 1.12 1.12 0.00 2.24
107 108 5.794726 TGTCAAGGTAGCACAGTTAACTA 57.205 39.130 8.04 0.00 0.00 2.24
108 109 5.535333 TGTCAAGGTAGCACAGTTAACTAC 58.465 41.667 8.04 2.24 36.40 2.73
109 110 5.303589 TGTCAAGGTAGCACAGTTAACTACT 59.696 40.000 8.04 8.79 37.14 2.57
110 111 5.862860 GTCAAGGTAGCACAGTTAACTACTC 59.137 44.000 8.04 0.10 37.14 2.59
111 112 5.047519 TCAAGGTAGCACAGTTAACTACTCC 60.048 44.000 8.04 9.41 37.14 3.85
112 113 3.768215 AGGTAGCACAGTTAACTACTCCC 59.232 47.826 8.04 6.86 37.14 4.30
113 114 3.768215 GGTAGCACAGTTAACTACTCCCT 59.232 47.826 8.04 3.63 37.14 4.20
114 115 3.963428 AGCACAGTTAACTACTCCCTG 57.037 47.619 8.04 0.00 33.85 4.45
115 116 3.240302 AGCACAGTTAACTACTCCCTGT 58.760 45.455 8.04 0.00 36.85 4.00
117 118 4.602340 CACAGTTAACTACTCCCTGTGT 57.398 45.455 8.04 0.00 44.90 3.72
118 119 4.557205 CACAGTTAACTACTCCCTGTGTC 58.443 47.826 8.04 0.00 44.90 3.67
119 120 3.577415 ACAGTTAACTACTCCCTGTGTCC 59.423 47.826 8.04 0.00 35.20 4.02
120 121 3.056035 CAGTTAACTACTCCCTGTGTCCC 60.056 52.174 8.04 0.00 33.85 4.46
121 122 2.901839 GTTAACTACTCCCTGTGTCCCA 59.098 50.000 0.00 0.00 0.00 4.37
122 123 2.112279 AACTACTCCCTGTGTCCCAA 57.888 50.000 0.00 0.00 0.00 4.12
123 124 2.112279 ACTACTCCCTGTGTCCCAAA 57.888 50.000 0.00 0.00 0.00 3.28
124 125 2.414612 ACTACTCCCTGTGTCCCAAAA 58.585 47.619 0.00 0.00 0.00 2.44
125 126 2.986728 ACTACTCCCTGTGTCCCAAAAT 59.013 45.455 0.00 0.00 0.00 1.82
126 127 4.172807 ACTACTCCCTGTGTCCCAAAATA 58.827 43.478 0.00 0.00 0.00 1.40
127 128 4.600111 ACTACTCCCTGTGTCCCAAAATAA 59.400 41.667 0.00 0.00 0.00 1.40
128 129 4.034285 ACTCCCTGTGTCCCAAAATAAG 57.966 45.455 0.00 0.00 0.00 1.73
129 130 3.397955 ACTCCCTGTGTCCCAAAATAAGT 59.602 43.478 0.00 0.00 0.00 2.24
130 131 3.758554 CTCCCTGTGTCCCAAAATAAGTG 59.241 47.826 0.00 0.00 0.00 3.16
131 132 3.396276 TCCCTGTGTCCCAAAATAAGTGA 59.604 43.478 0.00 0.00 0.00 3.41
132 133 3.506067 CCCTGTGTCCCAAAATAAGTGAC 59.494 47.826 0.00 0.00 0.00 3.67
133 134 4.398319 CCTGTGTCCCAAAATAAGTGACT 58.602 43.478 0.00 0.00 0.00 3.41
134 135 4.827284 CCTGTGTCCCAAAATAAGTGACTT 59.173 41.667 2.37 2.37 0.00 3.01
135 136 6.001460 CCTGTGTCCCAAAATAAGTGACTTA 58.999 40.000 7.60 7.60 0.00 2.24
136 137 6.488683 CCTGTGTCCCAAAATAAGTGACTTAA 59.511 38.462 9.35 0.00 29.35 1.85
137 138 7.308589 CCTGTGTCCCAAAATAAGTGACTTAAG 60.309 40.741 9.35 0.00 29.35 1.85
138 139 7.057894 TGTGTCCCAAAATAAGTGACTTAAGT 58.942 34.615 8.13 8.13 29.35 2.24
139 140 7.558444 TGTGTCCCAAAATAAGTGACTTAAGTT 59.442 33.333 10.02 4.19 29.35 2.66
140 141 8.410912 GTGTCCCAAAATAAGTGACTTAAGTTT 58.589 33.333 10.02 9.77 29.35 2.66
141 142 8.410141 TGTCCCAAAATAAGTGACTTAAGTTTG 58.590 33.333 23.94 23.94 36.22 2.93
142 143 8.410912 GTCCCAAAATAAGTGACTTAAGTTTGT 58.589 33.333 26.19 8.32 35.55 2.83
143 144 9.629878 TCCCAAAATAAGTGACTTAAGTTTGTA 57.370 29.630 26.19 18.25 35.55 2.41
144 145 9.673454 CCCAAAATAAGTGACTTAAGTTTGTAC 57.327 33.333 26.19 7.26 35.55 2.90
179 180 8.461249 ACTAACTCTAGTACAAAGTTGAGTCA 57.539 34.615 14.31 0.00 39.33 3.41
180 181 8.351461 ACTAACTCTAGTACAAAGTTGAGTCAC 58.649 37.037 14.31 0.00 39.33 3.67
181 182 6.963083 ACTCTAGTACAAAGTTGAGTCACT 57.037 37.500 0.00 0.00 36.73 3.41
182 183 7.349412 ACTCTAGTACAAAGTTGAGTCACTT 57.651 36.000 0.00 0.00 36.73 3.16
183 184 8.461249 ACTCTAGTACAAAGTTGAGTCACTTA 57.539 34.615 0.00 0.00 36.73 2.24
184 185 9.080097 ACTCTAGTACAAAGTTGAGTCACTTAT 57.920 33.333 0.00 0.00 36.73 1.73
185 186 9.915629 CTCTAGTACAAAGTTGAGTCACTTATT 57.084 33.333 0.00 0.00 35.87 1.40
192 193 9.403583 ACAAAGTTGAGTCACTTATTTTTAGGA 57.596 29.630 0.00 0.00 35.87 2.94
193 194 9.665264 CAAAGTTGAGTCACTTATTTTTAGGAC 57.335 33.333 0.00 0.00 35.87 3.85
194 195 7.653767 AGTTGAGTCACTTATTTTTAGGACG 57.346 36.000 0.00 0.00 0.00 4.79
195 196 6.649557 AGTTGAGTCACTTATTTTTAGGACGG 59.350 38.462 0.00 0.00 0.00 4.79
196 197 6.349243 TGAGTCACTTATTTTTAGGACGGA 57.651 37.500 0.00 0.00 0.00 4.69
197 198 6.395629 TGAGTCACTTATTTTTAGGACGGAG 58.604 40.000 0.00 0.00 0.00 4.63
198 199 6.209986 TGAGTCACTTATTTTTAGGACGGAGA 59.790 38.462 0.00 0.00 0.00 3.71
199 200 6.631962 AGTCACTTATTTTTAGGACGGAGAG 58.368 40.000 0.00 0.00 0.00 3.20
242 243 6.204108 AGTGTAATTTTGTGGGTTCTACTTCG 59.796 38.462 0.00 0.00 0.00 3.79
251 252 5.011329 TGTGGGTTCTACTTCGTTTCTATGT 59.989 40.000 0.00 0.00 0.00 2.29
284 285 2.322658 TGAGTACATCCGGGGTTATCC 58.677 52.381 0.00 0.00 0.00 2.59
289 290 0.687354 CATCCGGGGTTATCCTCCTG 59.313 60.000 0.00 0.00 35.33 3.86
296 297 3.646637 CGGGGTTATCCTCCTGTTCTAAT 59.353 47.826 0.00 0.00 35.33 1.73
297 298 4.102681 CGGGGTTATCCTCCTGTTCTAATT 59.897 45.833 0.00 0.00 35.33 1.40
298 299 5.397559 CGGGGTTATCCTCCTGTTCTAATTT 60.398 44.000 0.00 0.00 35.33 1.82
299 300 6.432581 GGGGTTATCCTCCTGTTCTAATTTT 58.567 40.000 0.00 0.00 35.33 1.82
300 301 6.895756 GGGGTTATCCTCCTGTTCTAATTTTT 59.104 38.462 0.00 0.00 35.33 1.94
377 380 1.876664 CGCTTGGTCTCGAGTCTCA 59.123 57.895 13.13 6.67 0.00 3.27
432 874 3.868077 GGAAGCAGCTAGTAGAACACATG 59.132 47.826 0.00 0.00 0.00 3.21
446 888 5.640147 AGAACACATGGTTAATTCAAGGGA 58.360 37.500 0.00 0.00 40.63 4.20
463 905 9.393768 ATTCAAGGGAAAACGATGCTTTCGAAT 62.394 37.037 15.03 4.32 42.68 3.34
494 936 1.804151 TGCCGATCGAAAAAGGAACAG 59.196 47.619 18.66 0.00 0.00 3.16
505 947 5.050702 CGAAAAAGGAACAGAAGTCAGAGTC 60.051 44.000 0.00 0.00 0.00 3.36
543 985 2.664851 TTGCTTCCGAGTGCGTGG 60.665 61.111 0.00 0.00 35.23 4.94
544 986 3.158537 TTGCTTCCGAGTGCGTGGA 62.159 57.895 0.00 0.00 35.23 4.02
574 1016 1.883275 TCAAGTTAAATGCCACGTGGG 59.117 47.619 34.58 17.30 40.85 4.61
772 1214 4.858140 GCAGTTCTCGGAAGACTAGTTAAC 59.142 45.833 0.00 0.00 35.39 2.01
799 1241 1.605753 AAGGGCAAAGACGTCCTTTC 58.394 50.000 13.01 0.00 42.88 2.62
819 1262 4.351874 TCTTCTTTTTGACGGGACAGAT 57.648 40.909 0.00 0.00 0.00 2.90
949 1392 1.025812 CCACCTACCTGCTCTACTCG 58.974 60.000 0.00 0.00 0.00 4.18
1033 1477 0.825010 CCTTGTGAGCCTGGTTGCTT 60.825 55.000 0.00 0.00 42.95 3.91
1044 1488 2.751806 CCTGGTTGCTTTGATCTTCCTC 59.248 50.000 0.00 0.00 0.00 3.71
1091 1535 2.409975 GCAAGTGCTCGTTGGTAAGTA 58.590 47.619 0.00 0.00 38.21 2.24
1098 1542 3.691118 TGCTCGTTGGTAAGTACGTAGAT 59.309 43.478 0.00 0.00 38.79 1.98
1100 1544 5.098211 GCTCGTTGGTAAGTACGTAGATTT 58.902 41.667 0.00 0.00 38.79 2.17
1108 1552 6.017934 TGGTAAGTACGTAGATTTAGTAGCCG 60.018 42.308 0.00 0.00 0.00 5.52
1142 1586 8.667592 ACCTTGAGTAGTTCCTAGTATCTTTT 57.332 34.615 0.00 0.00 0.00 2.27
1406 1854 1.098050 GGCGACGTAGGTCTTTCCTA 58.902 55.000 13.31 0.00 46.10 2.94
1415 1863 3.413105 AGGTCTTTCCTAGCTGATCCT 57.587 47.619 0.00 0.00 46.10 3.24
1416 1864 4.544564 AGGTCTTTCCTAGCTGATCCTA 57.455 45.455 0.00 0.00 46.10 2.94
1417 1865 4.479158 AGGTCTTTCCTAGCTGATCCTAG 58.521 47.826 0.00 0.00 46.10 3.02
1418 1866 3.006430 GGTCTTTCCTAGCTGATCCTAGC 59.994 52.174 0.00 0.00 44.01 3.42
1426 1874 2.302587 GCTGATCCTAGCTACTCCCT 57.697 55.000 0.00 0.00 40.52 4.20
1427 1875 2.167662 GCTGATCCTAGCTACTCCCTC 58.832 57.143 0.00 0.00 40.52 4.30
1428 1876 2.802719 CTGATCCTAGCTACTCCCTCC 58.197 57.143 0.00 0.00 0.00 4.30
1429 1877 1.074084 TGATCCTAGCTACTCCCTCCG 59.926 57.143 0.00 0.00 0.00 4.63
1430 1878 1.074244 GATCCTAGCTACTCCCTCCGT 59.926 57.143 0.00 0.00 0.00 4.69
1431 1879 0.473326 TCCTAGCTACTCCCTCCGTC 59.527 60.000 0.00 0.00 0.00 4.79
1432 1880 0.537828 CCTAGCTACTCCCTCCGTCC 60.538 65.000 0.00 0.00 0.00 4.79
1433 1881 0.183014 CTAGCTACTCCCTCCGTCCA 59.817 60.000 0.00 0.00 0.00 4.02
1434 1882 0.106819 TAGCTACTCCCTCCGTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
1435 1883 1.380112 GCTACTCCCTCCGTCCACT 60.380 63.158 0.00 0.00 0.00 4.00
1436 1884 1.668101 GCTACTCCCTCCGTCCACTG 61.668 65.000 0.00 0.00 0.00 3.66
1437 1885 1.000019 TACTCCCTCCGTCCACTGG 60.000 63.158 0.00 0.00 0.00 4.00
1438 1886 2.509931 TACTCCCTCCGTCCACTGGG 62.510 65.000 0.00 0.00 40.95 4.45
1439 1887 3.596799 TCCCTCCGTCCACTGGGA 61.597 66.667 0.00 0.00 45.58 4.37
1447 1895 3.596799 TCCACTGGGACGGAGGGA 61.597 66.667 0.00 0.00 45.78 4.20
1448 1896 3.077556 CCACTGGGACGGAGGGAG 61.078 72.222 0.00 0.00 41.92 4.30
1487 1937 1.619827 CAATTTGGTCCCATGTGTGCT 59.380 47.619 0.00 0.00 0.00 4.40
1497 1947 1.004595 CATGTGTGCTGTCCTGATCG 58.995 55.000 0.00 0.00 0.00 3.69
1593 2075 7.546316 GTCTCTTTTGGTAGATTCTGTAAGGAC 59.454 40.741 0.00 0.00 0.00 3.85
1595 2077 7.386851 TCTTTTGGTAGATTCTGTAAGGACTG 58.613 38.462 0.00 0.00 0.00 3.51
1596 2078 6.681729 TTTGGTAGATTCTGTAAGGACTGT 57.318 37.500 0.00 0.00 0.00 3.55
1597 2079 5.661056 TGGTAGATTCTGTAAGGACTGTG 57.339 43.478 0.00 0.00 0.00 3.66
1598 2080 5.084519 TGGTAGATTCTGTAAGGACTGTGT 58.915 41.667 0.00 0.00 0.00 3.72
1680 2707 6.744537 CACTTTGCTAATTGCTATGTCTGTTC 59.255 38.462 0.00 0.00 43.37 3.18
1681 2708 5.818136 TTGCTAATTGCTATGTCTGTTCC 57.182 39.130 0.00 0.00 43.37 3.62
1740 2767 2.277084 CGTACAAGCTGGTTCATACCC 58.723 52.381 0.00 0.00 44.35 3.69
1775 2802 2.592102 ACCTCATGGCATGTCACTTT 57.408 45.000 25.62 4.46 36.63 2.66
1811 2841 3.542676 AACCACGTCTGGCGGTCA 61.543 61.111 6.61 0.00 46.52 4.02
1827 2857 2.045926 CAGCCGGGCTAAGCACTT 60.046 61.111 23.37 0.00 36.40 3.16
1888 2918 2.046892 ATCACTGCCCACGACTGC 60.047 61.111 0.00 0.00 0.00 4.40
1921 2951 1.588674 TTCGAGCACACCGAAACATT 58.411 45.000 0.00 0.00 42.18 2.71
1922 2952 2.442212 TCGAGCACACCGAAACATTA 57.558 45.000 0.00 0.00 32.64 1.90
2141 3189 4.072131 GCTACAGATGAGACTAGAGAGGG 58.928 52.174 0.00 0.00 0.00 4.30
2142 3190 3.593442 ACAGATGAGACTAGAGAGGGG 57.407 52.381 0.00 0.00 0.00 4.79
2143 3191 3.127250 ACAGATGAGACTAGAGAGGGGA 58.873 50.000 0.00 0.00 0.00 4.81
2144 3192 3.117663 ACAGATGAGACTAGAGAGGGGAC 60.118 52.174 0.00 0.00 0.00 4.46
2145 3193 2.105821 AGATGAGACTAGAGAGGGGACG 59.894 54.545 0.00 0.00 0.00 4.79
2146 3194 0.107116 TGAGACTAGAGAGGGGACGC 60.107 60.000 0.00 0.00 0.00 5.19
2147 3195 0.181824 GAGACTAGAGAGGGGACGCT 59.818 60.000 0.00 0.00 46.12 5.07
2148 3196 1.417145 GAGACTAGAGAGGGGACGCTA 59.583 57.143 0.00 0.00 42.18 4.26
2149 3197 1.418637 AGACTAGAGAGGGGACGCTAG 59.581 57.143 0.00 0.00 42.18 3.42
2150 3198 1.417145 GACTAGAGAGGGGACGCTAGA 59.583 57.143 11.90 0.00 42.18 2.43
2151 3199 1.418637 ACTAGAGAGGGGACGCTAGAG 59.581 57.143 11.90 0.00 42.18 2.43
2152 3200 1.695242 CTAGAGAGGGGACGCTAGAGA 59.305 57.143 0.00 0.00 42.18 3.10
2153 3201 0.472471 AGAGAGGGGACGCTAGAGAG 59.528 60.000 0.00 0.00 42.18 3.20
2154 3202 0.536460 GAGAGGGGACGCTAGAGAGG 60.536 65.000 0.00 0.00 42.18 3.69
2235 3284 8.748412 AGCCAATAGAAAGCAACAACAATATAA 58.252 29.630 0.00 0.00 0.00 0.98
2245 3295 8.761575 AGCAACAACAATATAAACAATCAAGG 57.238 30.769 0.00 0.00 0.00 3.61
2268 3319 5.504665 GGCATAGACAAAACATTGATCGGAG 60.505 44.000 0.00 0.00 0.00 4.63
2346 3399 3.190744 GGTTTTCTTTGGATCGGTTCTCC 59.809 47.826 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.886043 AACGTACCCTTTTGTCGGGC 60.886 55.000 0.00 0.00 46.04 6.13
2 3 1.150827 GGAACGTACCCTTTTGTCGG 58.849 55.000 0.00 0.00 0.00 4.79
3 4 2.064014 GAGGAACGTACCCTTTTGTCG 58.936 52.381 10.34 0.00 33.36 4.35
4 5 2.064014 CGAGGAACGTACCCTTTTGTC 58.936 52.381 10.34 0.00 37.22 3.18
6 7 2.334838 CTCGAGGAACGTACCCTTTTG 58.665 52.381 3.91 5.12 43.13 2.44
7 8 1.337541 GCTCGAGGAACGTACCCTTTT 60.338 52.381 15.58 0.00 43.13 2.27
9 10 0.611340 AGCTCGAGGAACGTACCCTT 60.611 55.000 15.58 0.00 43.13 3.95
10 11 1.001145 AGCTCGAGGAACGTACCCT 60.001 57.895 15.58 8.95 43.13 4.34
11 12 1.139095 CAGCTCGAGGAACGTACCC 59.861 63.158 15.58 0.00 43.13 3.69
12 13 0.524862 TTCAGCTCGAGGAACGTACC 59.475 55.000 15.58 0.00 43.13 3.34
13 14 1.068748 TGTTCAGCTCGAGGAACGTAC 60.069 52.381 21.79 7.02 44.85 3.67
14 15 1.241165 TGTTCAGCTCGAGGAACGTA 58.759 50.000 21.79 9.19 44.85 3.57
15 16 0.603569 ATGTTCAGCTCGAGGAACGT 59.396 50.000 21.79 20.04 44.85 3.99
16 17 2.097629 TCTATGTTCAGCTCGAGGAACG 59.902 50.000 21.79 12.63 44.85 3.95
17 18 3.784701 TCTATGTTCAGCTCGAGGAAC 57.215 47.619 21.02 21.02 42.82 3.62
18 19 4.801330 TTTCTATGTTCAGCTCGAGGAA 57.199 40.909 15.58 7.30 0.00 3.36
19 20 4.442052 CCATTTCTATGTTCAGCTCGAGGA 60.442 45.833 15.58 0.22 0.00 3.71
20 21 3.806521 CCATTTCTATGTTCAGCTCGAGG 59.193 47.826 15.58 0.00 0.00 4.63
21 22 4.437239 ACCATTTCTATGTTCAGCTCGAG 58.563 43.478 8.45 8.45 0.00 4.04
22 23 4.471904 ACCATTTCTATGTTCAGCTCGA 57.528 40.909 0.00 0.00 0.00 4.04
23 24 4.747108 CCTACCATTTCTATGTTCAGCTCG 59.253 45.833 0.00 0.00 0.00 5.03
24 25 4.513318 GCCTACCATTTCTATGTTCAGCTC 59.487 45.833 0.00 0.00 0.00 4.09
25 26 4.164988 AGCCTACCATTTCTATGTTCAGCT 59.835 41.667 0.00 0.00 0.00 4.24
26 27 4.455606 AGCCTACCATTTCTATGTTCAGC 58.544 43.478 0.00 0.00 0.00 4.26
27 28 7.396540 AAAAGCCTACCATTTCTATGTTCAG 57.603 36.000 0.00 0.00 0.00 3.02
28 29 7.775053 AAAAAGCCTACCATTTCTATGTTCA 57.225 32.000 0.00 0.00 0.00 3.18
51 52 5.816919 AGATCGAAAGTTTTCTCGCAAAAA 58.183 33.333 0.00 0.00 35.07 1.94
52 53 5.418310 AGATCGAAAGTTTTCTCGCAAAA 57.582 34.783 0.00 0.00 35.07 2.44
53 54 6.721571 ATAGATCGAAAGTTTTCTCGCAAA 57.278 33.333 0.00 0.00 35.07 3.68
54 55 6.367695 TGAATAGATCGAAAGTTTTCTCGCAA 59.632 34.615 0.00 0.00 35.07 4.85
55 56 5.867174 TGAATAGATCGAAAGTTTTCTCGCA 59.133 36.000 0.00 0.00 35.07 5.10
56 57 6.332504 TGAATAGATCGAAAGTTTTCTCGC 57.667 37.500 0.00 0.00 35.07 5.03
57 58 8.120030 TGATGAATAGATCGAAAGTTTTCTCG 57.880 34.615 0.00 0.00 35.07 4.04
62 63 9.994432 GACAATTGATGAATAGATCGAAAGTTT 57.006 29.630 13.59 0.00 0.00 2.66
63 64 9.166173 TGACAATTGATGAATAGATCGAAAGTT 57.834 29.630 13.59 0.00 0.00 2.66
64 65 8.722480 TGACAATTGATGAATAGATCGAAAGT 57.278 30.769 13.59 0.00 0.00 2.66
65 66 9.647679 CTTGACAATTGATGAATAGATCGAAAG 57.352 33.333 13.59 0.00 0.00 2.62
66 67 8.615211 CCTTGACAATTGATGAATAGATCGAAA 58.385 33.333 13.59 0.00 0.00 3.46
67 68 7.770433 ACCTTGACAATTGATGAATAGATCGAA 59.230 33.333 13.59 0.00 0.00 3.71
68 69 7.275183 ACCTTGACAATTGATGAATAGATCGA 58.725 34.615 13.59 0.00 0.00 3.59
69 70 7.488187 ACCTTGACAATTGATGAATAGATCG 57.512 36.000 13.59 0.00 0.00 3.69
70 71 8.502387 GCTACCTTGACAATTGATGAATAGATC 58.498 37.037 13.59 0.00 0.00 2.75
71 72 7.994911 TGCTACCTTGACAATTGATGAATAGAT 59.005 33.333 13.59 0.00 0.00 1.98
72 73 7.280876 GTGCTACCTTGACAATTGATGAATAGA 59.719 37.037 13.59 0.00 0.00 1.98
73 74 7.066163 TGTGCTACCTTGACAATTGATGAATAG 59.934 37.037 13.59 7.57 0.00 1.73
74 75 6.883756 TGTGCTACCTTGACAATTGATGAATA 59.116 34.615 13.59 0.00 0.00 1.75
75 76 5.711506 TGTGCTACCTTGACAATTGATGAAT 59.288 36.000 13.59 0.00 0.00 2.57
76 77 5.069318 TGTGCTACCTTGACAATTGATGAA 58.931 37.500 13.59 0.64 0.00 2.57
77 78 4.650734 TGTGCTACCTTGACAATTGATGA 58.349 39.130 13.59 0.00 0.00 2.92
78 79 4.456911 ACTGTGCTACCTTGACAATTGATG 59.543 41.667 13.59 0.00 0.00 3.07
79 80 4.655963 ACTGTGCTACCTTGACAATTGAT 58.344 39.130 13.59 0.00 0.00 2.57
80 81 4.085357 ACTGTGCTACCTTGACAATTGA 57.915 40.909 13.59 0.00 0.00 2.57
81 82 4.836125 AACTGTGCTACCTTGACAATTG 57.164 40.909 3.24 3.24 0.00 2.32
82 83 6.062095 AGTTAACTGTGCTACCTTGACAATT 58.938 36.000 7.48 0.00 0.00 2.32
83 84 5.621193 AGTTAACTGTGCTACCTTGACAAT 58.379 37.500 7.48 0.00 0.00 2.71
84 85 5.031066 AGTTAACTGTGCTACCTTGACAA 57.969 39.130 7.48 0.00 0.00 3.18
85 86 4.682778 AGTTAACTGTGCTACCTTGACA 57.317 40.909 7.48 0.00 0.00 3.58
86 87 5.780984 AGTAGTTAACTGTGCTACCTTGAC 58.219 41.667 18.56 3.68 36.93 3.18
87 88 5.047519 GGAGTAGTTAACTGTGCTACCTTGA 60.048 44.000 18.56 0.00 39.07 3.02
88 89 5.169295 GGAGTAGTTAACTGTGCTACCTTG 58.831 45.833 18.56 0.00 39.07 3.61
89 90 4.222366 GGGAGTAGTTAACTGTGCTACCTT 59.778 45.833 18.56 0.00 39.07 3.50
90 91 3.768215 GGGAGTAGTTAACTGTGCTACCT 59.232 47.826 18.56 2.62 39.07 3.08
91 92 3.768215 AGGGAGTAGTTAACTGTGCTACC 59.232 47.826 18.56 20.12 39.07 3.18
92 93 4.220163 ACAGGGAGTAGTTAACTGTGCTAC 59.780 45.833 18.56 13.01 40.56 3.58
93 94 4.413760 ACAGGGAGTAGTTAACTGTGCTA 58.586 43.478 18.56 0.00 40.56 3.49
94 95 3.240302 ACAGGGAGTAGTTAACTGTGCT 58.760 45.455 18.56 12.68 40.56 4.40
95 96 3.679824 ACAGGGAGTAGTTAACTGTGC 57.320 47.619 18.56 10.15 40.56 4.57
97 98 3.577415 GGACACAGGGAGTAGTTAACTGT 59.423 47.826 18.56 5.19 42.62 3.55
98 99 3.056035 GGGACACAGGGAGTAGTTAACTG 60.056 52.174 18.56 2.86 39.07 3.16
99 100 3.171528 GGGACACAGGGAGTAGTTAACT 58.828 50.000 13.68 13.68 42.80 2.24
100 101 2.901839 TGGGACACAGGGAGTAGTTAAC 59.098 50.000 0.00 0.00 0.00 2.01
101 102 3.263369 TGGGACACAGGGAGTAGTTAA 57.737 47.619 0.00 0.00 0.00 2.01
102 103 3.263369 TTGGGACACAGGGAGTAGTTA 57.737 47.619 0.00 0.00 39.29 2.24
103 104 2.112279 TTGGGACACAGGGAGTAGTT 57.888 50.000 0.00 0.00 39.29 2.24
104 105 2.112279 TTTGGGACACAGGGAGTAGT 57.888 50.000 0.00 0.00 39.29 2.73
105 106 3.721087 ATTTTGGGACACAGGGAGTAG 57.279 47.619 0.00 0.00 39.29 2.57
106 107 4.600111 ACTTATTTTGGGACACAGGGAGTA 59.400 41.667 0.00 0.00 39.29 2.59
107 108 3.397955 ACTTATTTTGGGACACAGGGAGT 59.602 43.478 0.00 0.00 39.29 3.85
108 109 3.758554 CACTTATTTTGGGACACAGGGAG 59.241 47.826 0.00 0.00 39.29 4.30
109 110 3.396276 TCACTTATTTTGGGACACAGGGA 59.604 43.478 0.00 0.00 39.29 4.20
110 111 3.506067 GTCACTTATTTTGGGACACAGGG 59.494 47.826 0.00 0.00 39.29 4.45
111 112 4.398319 AGTCACTTATTTTGGGACACAGG 58.602 43.478 0.00 0.00 39.29 4.00
112 113 7.228706 ACTTAAGTCACTTATTTTGGGACACAG 59.771 37.037 1.12 0.00 39.29 3.66
113 114 7.057894 ACTTAAGTCACTTATTTTGGGACACA 58.942 34.615 1.12 0.00 39.29 3.72
114 115 7.506328 ACTTAAGTCACTTATTTTGGGACAC 57.494 36.000 1.12 0.00 39.29 3.67
115 116 8.410141 CAAACTTAAGTCACTTATTTTGGGACA 58.590 33.333 8.95 0.00 32.10 4.02
116 117 8.410912 ACAAACTTAAGTCACTTATTTTGGGAC 58.589 33.333 23.60 4.66 35.68 4.46
117 118 8.528044 ACAAACTTAAGTCACTTATTTTGGGA 57.472 30.769 23.60 1.52 35.68 4.37
118 119 9.673454 GTACAAACTTAAGTCACTTATTTTGGG 57.327 33.333 23.60 10.17 35.68 4.12
153 154 9.565090 TGACTCAACTTTGTACTAGAGTTAGTA 57.435 33.333 0.00 0.00 40.55 1.82
154 155 8.351461 GTGACTCAACTTTGTACTAGAGTTAGT 58.649 37.037 0.00 10.72 42.66 2.24
155 156 8.569641 AGTGACTCAACTTTGTACTAGAGTTAG 58.430 37.037 0.00 8.69 36.56 2.34
156 157 8.461249 AGTGACTCAACTTTGTACTAGAGTTA 57.539 34.615 0.00 0.00 36.56 2.24
157 158 7.349412 AGTGACTCAACTTTGTACTAGAGTT 57.651 36.000 0.00 0.00 36.56 3.01
158 159 6.963083 AGTGACTCAACTTTGTACTAGAGT 57.037 37.500 0.00 0.00 38.89 3.24
159 160 9.915629 AATAAGTGACTCAACTTTGTACTAGAG 57.084 33.333 0.00 0.00 40.77 2.43
166 167 9.403583 TCCTAAAAATAAGTGACTCAACTTTGT 57.596 29.630 0.00 0.00 40.77 2.83
167 168 9.665264 GTCCTAAAAATAAGTGACTCAACTTTG 57.335 33.333 0.00 0.00 40.77 2.77
168 169 8.557029 CGTCCTAAAAATAAGTGACTCAACTTT 58.443 33.333 0.00 0.00 40.77 2.66
169 170 7.172703 CCGTCCTAAAAATAAGTGACTCAACTT 59.827 37.037 0.00 0.00 42.89 2.66
170 171 6.649557 CCGTCCTAAAAATAAGTGACTCAACT 59.350 38.462 0.00 0.00 0.00 3.16
171 172 6.647895 TCCGTCCTAAAAATAAGTGACTCAAC 59.352 38.462 0.00 0.00 0.00 3.18
172 173 6.761312 TCCGTCCTAAAAATAAGTGACTCAA 58.239 36.000 0.00 0.00 0.00 3.02
173 174 6.209986 TCTCCGTCCTAAAAATAAGTGACTCA 59.790 38.462 0.00 0.00 0.00 3.41
174 175 6.628185 TCTCCGTCCTAAAAATAAGTGACTC 58.372 40.000 0.00 0.00 0.00 3.36
175 176 6.436532 TCTCTCCGTCCTAAAAATAAGTGACT 59.563 38.462 0.00 0.00 0.00 3.41
176 177 6.628185 TCTCTCCGTCCTAAAAATAAGTGAC 58.372 40.000 0.00 0.00 0.00 3.67
177 178 6.436532 ACTCTCTCCGTCCTAAAAATAAGTGA 59.563 38.462 0.00 0.00 0.00 3.41
178 179 6.631962 ACTCTCTCCGTCCTAAAAATAAGTG 58.368 40.000 0.00 0.00 0.00 3.16
179 180 6.854091 ACTCTCTCCGTCCTAAAAATAAGT 57.146 37.500 0.00 0.00 0.00 2.24
182 183 9.075678 CCTAATACTCTCTCCGTCCTAAAAATA 57.924 37.037 0.00 0.00 0.00 1.40
183 184 7.783596 TCCTAATACTCTCTCCGTCCTAAAAAT 59.216 37.037 0.00 0.00 0.00 1.82
184 185 7.121382 TCCTAATACTCTCTCCGTCCTAAAAA 58.879 38.462 0.00 0.00 0.00 1.94
185 186 6.666678 TCCTAATACTCTCTCCGTCCTAAAA 58.333 40.000 0.00 0.00 0.00 1.52
186 187 6.257994 TCCTAATACTCTCTCCGTCCTAAA 57.742 41.667 0.00 0.00 0.00 1.85
187 188 5.901413 TCCTAATACTCTCTCCGTCCTAA 57.099 43.478 0.00 0.00 0.00 2.69
188 189 7.565190 TTATCCTAATACTCTCTCCGTCCTA 57.435 40.000 0.00 0.00 0.00 2.94
189 190 6.451292 TTATCCTAATACTCTCTCCGTCCT 57.549 41.667 0.00 0.00 0.00 3.85
190 191 7.521871 TTTTATCCTAATACTCTCTCCGTCC 57.478 40.000 0.00 0.00 0.00 4.79
218 219 6.017687 ACGAAGTAGAACCCACAAAATTACAC 60.018 38.462 0.00 0.00 41.94 2.90
230 231 6.200475 GCATACATAGAAACGAAGTAGAACCC 59.800 42.308 0.00 0.00 45.00 4.11
234 235 7.979537 ACATTGCATACATAGAAACGAAGTAGA 59.020 33.333 0.00 0.00 45.00 2.59
242 243 8.830580 ACTCATGTACATTGCATACATAGAAAC 58.169 33.333 5.37 0.00 40.51 2.78
343 346 2.153266 AAGCGCACTTGCTGGTAACAT 61.153 47.619 11.47 0.00 46.60 2.71
390 393 1.464608 CAATGACTGTGTAGTTGCCCG 59.535 52.381 0.00 0.00 37.25 6.13
402 405 2.983229 ACTAGCTGCTTCCAATGACTG 58.017 47.619 7.79 0.00 0.00 3.51
432 874 4.862574 GCATCGTTTTCCCTTGAATTAACC 59.137 41.667 0.00 0.00 0.00 2.85
463 905 3.804786 TCGATCGGCAAAATGGTAGTA 57.195 42.857 16.41 0.00 0.00 1.82
464 906 2.684001 TCGATCGGCAAAATGGTAGT 57.316 45.000 16.41 0.00 0.00 2.73
465 907 4.349663 TTTTCGATCGGCAAAATGGTAG 57.650 40.909 16.41 0.00 0.00 3.18
494 936 1.748493 AGCGAGGATGACTCTGACTTC 59.252 52.381 0.00 0.00 44.33 3.01
544 986 5.047164 TGGCATTTAACTTGATGTCTTGCAT 60.047 36.000 0.00 0.00 41.24 3.96
574 1016 2.387125 TTTCGCGCAACCAAGCAGAC 62.387 55.000 8.75 0.00 0.00 3.51
739 1181 1.751351 CCGAGAACTGCATGTCCTAGA 59.249 52.381 0.00 0.00 0.00 2.43
799 1241 4.065088 TCATCTGTCCCGTCAAAAAGAAG 58.935 43.478 0.00 0.00 0.00 2.85
819 1262 3.390967 TCACAGATTCAGGGAACAGTTCA 59.609 43.478 15.36 0.00 0.00 3.18
827 1270 3.200825 GGAGGAATTCACAGATTCAGGGA 59.799 47.826 7.93 0.00 37.69 4.20
949 1392 2.740055 CAGTCGCAGCCTCACCAC 60.740 66.667 0.00 0.00 0.00 4.16
998 1442 1.005215 CAAGGCCAAGGAACCTCATCT 59.995 52.381 5.01 0.00 34.31 2.90
1033 1477 5.249393 ACCTGAAGCTTAAGAGGAAGATCAA 59.751 40.000 20.41 0.00 0.00 2.57
1044 1488 4.516698 TGAAGCAAAGACCTGAAGCTTAAG 59.483 41.667 3.50 3.50 44.73 1.85
1091 1535 3.442100 GCAACGGCTACTAAATCTACGT 58.558 45.455 0.00 0.00 36.96 3.57
1108 1552 4.451435 GGAACTACTCAAGGTAACAGCAAC 59.549 45.833 0.00 0.00 41.41 4.17
1142 1586 2.303890 AGACAGTGAATGGTCATGCAGA 59.696 45.455 0.00 0.00 35.80 4.26
1185 1633 0.598065 CCTTGCACGGAAGGGAAAAG 59.402 55.000 2.29 0.00 39.19 2.27
1407 1855 2.167662 GAGGGAGTAGCTAGGATCAGC 58.832 57.143 0.00 0.00 42.12 4.26
1408 1856 2.802719 GGAGGGAGTAGCTAGGATCAG 58.197 57.143 0.00 0.00 0.00 2.90
1409 1857 1.074084 CGGAGGGAGTAGCTAGGATCA 59.926 57.143 0.00 0.00 0.00 2.92
1410 1858 1.074244 ACGGAGGGAGTAGCTAGGATC 59.926 57.143 0.00 0.00 0.00 3.36
1411 1859 1.074244 GACGGAGGGAGTAGCTAGGAT 59.926 57.143 0.00 0.00 0.00 3.24
1412 1860 0.473326 GACGGAGGGAGTAGCTAGGA 59.527 60.000 0.00 0.00 0.00 2.94
1413 1861 0.537828 GGACGGAGGGAGTAGCTAGG 60.538 65.000 0.00 0.00 0.00 3.02
1414 1862 0.183014 TGGACGGAGGGAGTAGCTAG 59.817 60.000 0.00 0.00 0.00 3.42
1415 1863 0.106819 GTGGACGGAGGGAGTAGCTA 60.107 60.000 0.00 0.00 0.00 3.32
1416 1864 1.380112 GTGGACGGAGGGAGTAGCT 60.380 63.158 0.00 0.00 0.00 3.32
1417 1865 1.380112 AGTGGACGGAGGGAGTAGC 60.380 63.158 0.00 0.00 0.00 3.58
1418 1866 1.038130 CCAGTGGACGGAGGGAGTAG 61.038 65.000 1.68 0.00 0.00 2.57
1419 1867 1.000019 CCAGTGGACGGAGGGAGTA 60.000 63.158 1.68 0.00 0.00 2.59
1420 1868 2.283966 CCAGTGGACGGAGGGAGT 60.284 66.667 1.68 0.00 0.00 3.85
1421 1869 3.077556 CCCAGTGGACGGAGGGAG 61.078 72.222 11.95 0.00 44.30 4.30
1430 1878 3.596799 TCCCTCCGTCCCAGTGGA 61.597 66.667 11.95 0.00 38.75 4.02
1431 1879 2.509931 TACTCCCTCCGTCCCAGTGG 62.510 65.000 0.63 0.63 0.00 4.00
1432 1880 1.000019 TACTCCCTCCGTCCCAGTG 60.000 63.158 0.00 0.00 0.00 3.66
1433 1881 1.306970 CTACTCCCTCCGTCCCAGT 59.693 63.158 0.00 0.00 0.00 4.00
1434 1882 2.128507 GCTACTCCCTCCGTCCCAG 61.129 68.421 0.00 0.00 0.00 4.45
1435 1883 1.284111 TAGCTACTCCCTCCGTCCCA 61.284 60.000 0.00 0.00 0.00 4.37
1436 1884 0.537828 CTAGCTACTCCCTCCGTCCC 60.538 65.000 0.00 0.00 0.00 4.46
1437 1885 1.174078 GCTAGCTACTCCCTCCGTCC 61.174 65.000 7.70 0.00 0.00 4.79
1438 1886 0.179012 AGCTAGCTACTCCCTCCGTC 60.179 60.000 17.69 0.00 0.00 4.79
1439 1887 1.072648 CTAGCTAGCTACTCCCTCCGT 59.927 57.143 20.67 0.00 0.00 4.69
1440 1888 1.816074 CTAGCTAGCTACTCCCTCCG 58.184 60.000 20.67 4.73 0.00 4.63
1441 1889 1.541379 GCTAGCTAGCTACTCCCTCC 58.459 60.000 33.71 5.30 45.62 4.30
1487 1937 2.723586 TTTGCGTGCCGATCAGGACA 62.724 55.000 7.64 3.18 45.00 4.02
1497 1947 1.424403 GGGTACAAAATTTGCGTGCC 58.576 50.000 15.61 15.61 34.95 5.01
1593 2075 5.182190 TGAAGCTACAAGAGACTCTACACAG 59.818 44.000 5.14 2.55 0.00 3.66
1595 2077 5.630661 TGAAGCTACAAGAGACTCTACAC 57.369 43.478 5.14 0.00 0.00 2.90
1596 2078 5.126222 CCATGAAGCTACAAGAGACTCTACA 59.874 44.000 5.14 0.00 0.00 2.74
1597 2079 5.126384 ACCATGAAGCTACAAGAGACTCTAC 59.874 44.000 5.14 0.00 0.00 2.59
1598 2080 5.265191 ACCATGAAGCTACAAGAGACTCTA 58.735 41.667 5.14 0.00 0.00 2.43
1680 2707 5.245075 ACTTTAGAGTTCAGGAAGAGACAGG 59.755 44.000 0.00 0.00 29.87 4.00
1681 2708 6.015856 TCACTTTAGAGTTCAGGAAGAGACAG 60.016 42.308 0.00 0.00 32.54 3.51
1757 2784 2.159476 CGAAAAGTGACATGCCATGAGG 60.159 50.000 12.53 0.00 38.23 3.86
1811 2841 2.045926 CAAGTGCTTAGCCCGGCT 60.046 61.111 18.05 18.05 43.41 5.52
1820 2850 3.300765 GCTGCTGGGCAAGTGCTT 61.301 61.111 2.85 0.00 38.41 3.91
1855 2885 2.959516 GTGATCACACTTGATGACCGA 58.040 47.619 21.07 0.00 42.95 4.69
1888 2918 2.425124 CGAAACGCTGCACAACGG 60.425 61.111 0.00 0.00 0.00 4.44
1921 2951 4.498345 GCACTTGAAAAACACCCATTCGTA 60.498 41.667 0.00 0.00 0.00 3.43
1922 2952 3.736740 GCACTTGAAAAACACCCATTCGT 60.737 43.478 0.00 0.00 0.00 3.85
2123 3159 3.486383 GTCCCCTCTCTAGTCTCATCTG 58.514 54.545 0.00 0.00 0.00 2.90
2141 3189 1.654954 TTGCGTCCTCTCTAGCGTCC 61.655 60.000 0.00 0.00 0.00 4.79
2142 3190 0.382515 ATTGCGTCCTCTCTAGCGTC 59.617 55.000 0.00 0.00 0.00 5.19
2143 3191 0.101399 CATTGCGTCCTCTCTAGCGT 59.899 55.000 0.00 0.00 0.00 5.07
2144 3192 0.101399 ACATTGCGTCCTCTCTAGCG 59.899 55.000 0.00 0.00 0.00 4.26
2145 3193 2.197577 GAACATTGCGTCCTCTCTAGC 58.802 52.381 0.00 0.00 0.00 3.42
2146 3194 3.510388 TGAACATTGCGTCCTCTCTAG 57.490 47.619 0.00 0.00 0.00 2.43
2147 3195 3.258372 ACTTGAACATTGCGTCCTCTCTA 59.742 43.478 0.00 0.00 0.00 2.43
2148 3196 2.037772 ACTTGAACATTGCGTCCTCTCT 59.962 45.455 0.00 0.00 0.00 3.10
2149 3197 2.417719 ACTTGAACATTGCGTCCTCTC 58.582 47.619 0.00 0.00 0.00 3.20
2150 3198 2.550830 ACTTGAACATTGCGTCCTCT 57.449 45.000 0.00 0.00 0.00 3.69
2151 3199 3.994392 TCTTACTTGAACATTGCGTCCTC 59.006 43.478 0.00 0.00 0.00 3.71
2152 3200 3.997021 CTCTTACTTGAACATTGCGTCCT 59.003 43.478 0.00 0.00 0.00 3.85
2153 3201 3.125316 CCTCTTACTTGAACATTGCGTCC 59.875 47.826 0.00 0.00 0.00 4.79
2154 3202 3.994392 TCCTCTTACTTGAACATTGCGTC 59.006 43.478 0.00 0.00 0.00 5.19
2235 3284 6.403866 TGTTTTGTCTATGCCTTGATTGTT 57.596 33.333 0.00 0.00 0.00 2.83
2245 3295 5.065218 ACTCCGATCAATGTTTTGTCTATGC 59.935 40.000 0.00 0.00 34.32 3.14
2252 3303 6.338146 TCCTACTACTCCGATCAATGTTTTG 58.662 40.000 0.00 0.00 0.00 2.44
2268 3319 2.660670 TCCCTAGCTGCTCCTACTAC 57.339 55.000 4.91 0.00 0.00 2.73
2324 3376 3.190744 GGAGAACCGATCCAAAGAAAACC 59.809 47.826 0.00 0.00 36.79 3.27


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

AutoCloner maintained by Alex Coulton.