Multiple sequence alignment - TraesCS2D01G133200

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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 TraesCS2D01G133200 chr2D 100.000 2483 0 0 1 2483 78509921 78507439 0.000000e+00 4586.0
1 TraesCS2D01G133200 chr2D 87.767 891 83 17 734 1620 78502569 78501701 0.000000e+00 1018.0
2 TraesCS2D01G133200 chr2D 86.899 832 85 14 721 1541 78406623 78405805 0.000000e+00 911.0
3 TraesCS2D01G133200 chr2D 81.977 688 79 27 1822 2481 78493052 78492382 2.170000e-150 542.0
4 TraesCS2D01G133200 chr2D 84.720 517 53 12 1001 1503 145683351 145682847 6.170000e-136 494.0
5 TraesCS2D01G133200 chr2D 91.803 183 13 2 1608 1790 78501429 78501249 1.140000e-63 254.0
6 TraesCS2D01G133200 chr2D 83.273 275 37 7 266 533 423373812 423373540 6.860000e-61 244.0
7 TraesCS2D01G133200 chr2D 90.909 44 3 1 56 99 601977433 601977391 9.590000e-05 58.4
8 TraesCS2D01G133200 chr2B 87.903 1645 90 44 855 2461 121475104 121473531 0.000000e+00 1834.0
9 TraesCS2D01G133200 chr2B 88.929 1391 105 23 272 1636 121483921 121482554 0.000000e+00 1670.0
10 TraesCS2D01G133200 chr2B 93.300 1015 51 6 646 1652 121479016 121478011 0.000000e+00 1482.0
11 TraesCS2D01G133200 chr2B 87.864 824 85 10 721 1541 121377527 121376716 0.000000e+00 953.0
12 TraesCS2D01G133200 chr2B 87.582 765 64 13 870 1633 121383280 121382546 0.000000e+00 857.0
13 TraesCS2D01G133200 chr2B 91.981 212 14 2 646 857 121475564 121475356 6.720000e-76 294.0
14 TraesCS2D01G133200 chr2A 88.214 1086 79 17 707 1774 78756645 78755591 0.000000e+00 1251.0
15 TraesCS2D01G133200 chr2A 90.899 901 46 11 1607 2482 78768738 78767849 0.000000e+00 1177.0
16 TraesCS2D01G133200 chr2A 88.557 1005 54 18 547 1535 78773534 78772575 0.000000e+00 1162.0
17 TraesCS2D01G133200 chr2A 87.653 899 77 21 723 1603 78323126 78324008 0.000000e+00 1014.0
18 TraesCS2D01G133200 chr2A 91.196 602 37 6 547 1136 78234079 78234676 0.000000e+00 804.0
19 TraesCS2D01G133200 chr2A 90.774 607 33 12 1563 2156 78255658 78256254 0.000000e+00 789.0
20 TraesCS2D01G133200 chr2A 84.082 735 72 21 1772 2481 78745983 78745269 0.000000e+00 667.0
21 TraesCS2D01G133200 chr2A 89.474 380 24 9 1127 1506 78255296 78255659 1.340000e-127 466.0
22 TraesCS2D01G133200 chr2A 83.398 518 59 14 1001 1506 156514600 156515102 2.910000e-124 455.0
23 TraesCS2D01G133200 chr2A 88.037 326 22 4 2173 2483 78256424 78256747 1.080000e-98 370.0
24 TraesCS2D01G133200 chr2A 84.249 273 36 6 267 533 65480805 65480534 2.450000e-65 259.0
25 TraesCS2D01G133200 chr4A 86.777 242 30 2 293 533 738609973 738610213 4.070000e-68 268.0
26 TraesCS2D01G133200 chr4A 74.085 355 63 19 1991 2325 192776717 192777062 4.340000e-23 119.0
27 TraesCS2D01G133200 chr5D 86.777 242 27 3 293 533 238673225 238673462 5.270000e-67 265.0
28 TraesCS2D01G133200 chr7B 86.864 236 30 1 299 533 186273701 186273466 1.890000e-66 263.0
29 TraesCS2D01G133200 chr7B 86.441 236 30 2 299 533 668357592 668357358 8.810000e-65 257.0
30 TraesCS2D01G133200 chr5A 86.364 242 32 1 293 533 458978815 458979056 1.890000e-66 263.0
31 TraesCS2D01G133200 chr7A 86.441 236 31 1 299 533 673004399 673004164 8.810000e-65 257.0
32 TraesCS2D01G133200 chr7A 96.970 33 1 0 51 83 78450090 78450122 3.450000e-04 56.5
33 TraesCS2D01G133200 chr7A 94.286 35 1 1 58 91 491579978 491579944 4.000000e-03 52.8
34 TraesCS2D01G133200 chr1B 86.008 243 31 3 293 533 664955815 664956056 8.810000e-65 257.0
35 TraesCS2D01G133200 chr1B 97.059 34 1 0 53 86 28326003 28325970 9.590000e-05 58.4
36 TraesCS2D01G133200 chr1B 100.000 29 0 0 58 86 28326053 28326025 1.000000e-03 54.7
37 TraesCS2D01G133200 chr5B 83.333 228 24 7 266 480 693988457 693988231 5.420000e-47 198.0
38 TraesCS2D01G133200 chr5B 97.143 35 0 1 122 156 10430006 10429973 9.590000e-05 58.4
39 TraesCS2D01G133200 chr6B 80.669 269 39 7 265 520 92761063 92761331 1.950000e-46 196.0
40 TraesCS2D01G133200 chr4B 75.000 352 62 19 1994 2325 366865384 366865039 3.330000e-29 139.0
41 TraesCS2D01G133200 chr1D 85.075 67 7 3 122 186 3952643 3952578 5.730000e-07 65.8
42 TraesCS2D01G133200 chr1D 90.909 44 3 1 56 99 302822556 302822514 9.590000e-05 58.4
43 TraesCS2D01G133200 chr1D 100.000 28 0 0 56 83 106959950 106959923 4.000000e-03 52.8
44 TraesCS2D01G133200 chr3A 92.500 40 3 0 53 92 112922911 112922950 9.590000e-05 58.4
45 TraesCS2D01G133200 chr6D 96.875 32 1 0 56 87 3257045 3257014 1.000000e-03 54.7


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 TraesCS2D01G133200 chr2D 78507439 78509921 2482 True 4586.000000 4586 100.000000 1 2483 1 chr2D.!!$R3 2482
1 TraesCS2D01G133200 chr2D 78405805 78406623 818 True 911.000000 911 86.899000 721 1541 1 chr2D.!!$R1 820
2 TraesCS2D01G133200 chr2D 78501249 78502569 1320 True 636.000000 1018 89.785000 734 1790 2 chr2D.!!$R7 1056
3 TraesCS2D01G133200 chr2D 78492382 78493052 670 True 542.000000 542 81.977000 1822 2481 1 chr2D.!!$R2 659
4 TraesCS2D01G133200 chr2D 145682847 145683351 504 True 494.000000 494 84.720000 1001 1503 1 chr2D.!!$R4 502
5 TraesCS2D01G133200 chr2B 121473531 121483921 10390 True 1320.000000 1834 90.528250 272 2461 4 chr2B.!!$R3 2189
6 TraesCS2D01G133200 chr2B 121376716 121377527 811 True 953.000000 953 87.864000 721 1541 1 chr2B.!!$R1 820
7 TraesCS2D01G133200 chr2B 121382546 121383280 734 True 857.000000 857 87.582000 870 1633 1 chr2B.!!$R2 763
8 TraesCS2D01G133200 chr2A 78755591 78756645 1054 True 1251.000000 1251 88.214000 707 1774 1 chr2A.!!$R3 1067
9 TraesCS2D01G133200 chr2A 78767849 78773534 5685 True 1169.500000 1177 89.728000 547 2482 2 chr2A.!!$R4 1935
10 TraesCS2D01G133200 chr2A 78323126 78324008 882 False 1014.000000 1014 87.653000 723 1603 1 chr2A.!!$F2 880
11 TraesCS2D01G133200 chr2A 78234079 78234676 597 False 804.000000 804 91.196000 547 1136 1 chr2A.!!$F1 589
12 TraesCS2D01G133200 chr2A 78745269 78745983 714 True 667.000000 667 84.082000 1772 2481 1 chr2A.!!$R2 709
13 TraesCS2D01G133200 chr2A 78255296 78256747 1451 False 541.666667 789 89.428333 1127 2483 3 chr2A.!!$F4 1356
14 TraesCS2D01G133200 chr2A 156514600 156515102 502 False 455.000000 455 83.398000 1001 1506 1 chr2A.!!$F3 505

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
267 268 0.109597 ACTTCGTCGGCGTCGTATTT 60.11 50.0 24.03 6.65 39.49 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 6116 0.843309 TGTTTCAACTCCTCCTGCCA 59.157 50.0 0.0 0.0 0.0 4.92 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.349568 ACTCAATTATAGTGTTTTCTTTCCCC 57.650 34.615 0.00 0.00 0.00 4.81
45 46 8.170730 ACTCAATTATAGTGTTTTCTTTCCCCT 58.829 33.333 0.00 0.00 0.00 4.79
46 47 8.950007 TCAATTATAGTGTTTTCTTTCCCCTT 57.050 30.769 0.00 0.00 0.00 3.95
47 48 9.374711 TCAATTATAGTGTTTTCTTTCCCCTTT 57.625 29.630 0.00 0.00 0.00 3.11
48 49 9.639601 CAATTATAGTGTTTTCTTTCCCCTTTC 57.360 33.333 0.00 0.00 0.00 2.62
49 50 9.601810 AATTATAGTGTTTTCTTTCCCCTTTCT 57.398 29.630 0.00 0.00 0.00 2.52
50 51 9.601810 ATTATAGTGTTTTCTTTCCCCTTTCTT 57.398 29.630 0.00 0.00 0.00 2.52
51 52 5.854010 AGTGTTTTCTTTCCCCTTTCTTC 57.146 39.130 0.00 0.00 0.00 2.87
52 53 5.519808 AGTGTTTTCTTTCCCCTTTCTTCT 58.480 37.500 0.00 0.00 0.00 2.85
53 54 6.669631 AGTGTTTTCTTTCCCCTTTCTTCTA 58.330 36.000 0.00 0.00 0.00 2.10
54 55 7.298374 AGTGTTTTCTTTCCCCTTTCTTCTAT 58.702 34.615 0.00 0.00 0.00 1.98
55 56 7.785028 AGTGTTTTCTTTCCCCTTTCTTCTATT 59.215 33.333 0.00 0.00 0.00 1.73
56 57 8.082852 GTGTTTTCTTTCCCCTTTCTTCTATTC 58.917 37.037 0.00 0.00 0.00 1.75
57 58 7.232737 TGTTTTCTTTCCCCTTTCTTCTATTCC 59.767 37.037 0.00 0.00 0.00 3.01
58 59 5.452341 TCTTTCCCCTTTCTTCTATTCCC 57.548 43.478 0.00 0.00 0.00 3.97
59 60 5.108752 TCTTTCCCCTTTCTTCTATTCCCT 58.891 41.667 0.00 0.00 0.00 4.20
60 61 5.191921 TCTTTCCCCTTTCTTCTATTCCCTC 59.808 44.000 0.00 0.00 0.00 4.30
61 62 3.394645 TCCCCTTTCTTCTATTCCCTCC 58.605 50.000 0.00 0.00 0.00 4.30
62 63 2.104963 CCCCTTTCTTCTATTCCCTCCG 59.895 54.545 0.00 0.00 0.00 4.63
63 64 2.772515 CCCTTTCTTCTATTCCCTCCGT 59.227 50.000 0.00 0.00 0.00 4.69
64 65 3.200165 CCCTTTCTTCTATTCCCTCCGTT 59.800 47.826 0.00 0.00 0.00 4.44
65 66 4.324331 CCCTTTCTTCTATTCCCTCCGTTT 60.324 45.833 0.00 0.00 0.00 3.60
66 67 5.254115 CCTTTCTTCTATTCCCTCCGTTTT 58.746 41.667 0.00 0.00 0.00 2.43
67 68 6.412214 CCTTTCTTCTATTCCCTCCGTTTTA 58.588 40.000 0.00 0.00 0.00 1.52
68 69 6.882678 CCTTTCTTCTATTCCCTCCGTTTTAA 59.117 38.462 0.00 0.00 0.00 1.52
69 70 7.392393 CCTTTCTTCTATTCCCTCCGTTTTAAA 59.608 37.037 0.00 0.00 0.00 1.52
70 71 8.694581 TTTCTTCTATTCCCTCCGTTTTAAAA 57.305 30.769 0.00 0.00 0.00 1.52
71 72 8.873186 TTCTTCTATTCCCTCCGTTTTAAAAT 57.127 30.769 3.52 0.00 0.00 1.82
72 73 9.962809 TTCTTCTATTCCCTCCGTTTTAAAATA 57.037 29.630 3.52 0.00 0.00 1.40
73 74 9.962809 TCTTCTATTCCCTCCGTTTTAAAATAA 57.037 29.630 3.52 0.00 0.00 1.40
75 76 9.743581 TTCTATTCCCTCCGTTTTAAAATAAGT 57.256 29.630 3.52 0.00 0.00 2.24
76 77 9.169592 TCTATTCCCTCCGTTTTAAAATAAGTG 57.830 33.333 3.52 0.00 0.00 3.16
77 78 7.770366 ATTCCCTCCGTTTTAAAATAAGTGT 57.230 32.000 3.52 0.00 0.00 3.55
78 79 6.806388 TCCCTCCGTTTTAAAATAAGTGTC 57.194 37.500 3.52 0.00 0.00 3.67
79 80 6.536447 TCCCTCCGTTTTAAAATAAGTGTCT 58.464 36.000 3.52 0.00 0.00 3.41
80 81 6.652062 TCCCTCCGTTTTAAAATAAGTGTCTC 59.348 38.462 3.52 0.00 0.00 3.36
81 82 6.428771 CCCTCCGTTTTAAAATAAGTGTCTCA 59.571 38.462 3.52 0.00 0.00 3.27
82 83 7.040961 CCCTCCGTTTTAAAATAAGTGTCTCAA 60.041 37.037 3.52 0.00 0.00 3.02
83 84 8.512138 CCTCCGTTTTAAAATAAGTGTCTCAAT 58.488 33.333 3.52 0.00 0.00 2.57
84 85 9.893305 CTCCGTTTTAAAATAAGTGTCTCAATT 57.107 29.630 3.52 0.00 0.00 2.32
117 118 9.813826 TGAAATTTTCTCTTTCTTCTATTCCCT 57.186 29.630 10.33 0.00 34.43 4.20
125 126 9.494055 TCTCTTTCTTCTATTCCCTTTATCTCA 57.506 33.333 0.00 0.00 0.00 3.27
134 135 9.273016 TCTATTCCCTTTATCTCAAAATAAGCG 57.727 33.333 0.00 0.00 0.00 4.68
135 136 7.881775 ATTCCCTTTATCTCAAAATAAGCGT 57.118 32.000 0.00 0.00 0.00 5.07
136 137 6.920569 TCCCTTTATCTCAAAATAAGCGTC 57.079 37.500 0.00 0.00 0.00 5.19
137 138 6.650120 TCCCTTTATCTCAAAATAAGCGTCT 58.350 36.000 0.00 0.00 0.00 4.18
138 139 6.761714 TCCCTTTATCTCAAAATAAGCGTCTC 59.238 38.462 0.00 0.00 0.00 3.36
139 140 6.538742 CCCTTTATCTCAAAATAAGCGTCTCA 59.461 38.462 0.00 0.00 0.00 3.27
140 141 7.065803 CCCTTTATCTCAAAATAAGCGTCTCAA 59.934 37.037 0.00 0.00 0.00 3.02
141 142 7.905493 CCTTTATCTCAAAATAAGCGTCTCAAC 59.095 37.037 0.00 0.00 0.00 3.18
142 143 8.547967 TTTATCTCAAAATAAGCGTCTCAACT 57.452 30.769 0.00 0.00 0.00 3.16
143 144 8.547967 TTATCTCAAAATAAGCGTCTCAACTT 57.452 30.769 0.00 0.00 0.00 2.66
144 145 6.861065 TCTCAAAATAAGCGTCTCAACTTT 57.139 33.333 0.00 0.00 0.00 2.66
145 146 6.658831 TCTCAAAATAAGCGTCTCAACTTTG 58.341 36.000 0.00 0.00 0.00 2.77
146 147 6.260050 TCTCAAAATAAGCGTCTCAACTTTGT 59.740 34.615 0.00 0.00 0.00 2.83
147 148 7.439955 TCTCAAAATAAGCGTCTCAACTTTGTA 59.560 33.333 0.00 0.00 0.00 2.41
148 149 7.349711 TCAAAATAAGCGTCTCAACTTTGTAC 58.650 34.615 0.00 0.00 0.00 2.90
149 150 7.225931 TCAAAATAAGCGTCTCAACTTTGTACT 59.774 33.333 0.00 0.00 0.00 2.73
150 151 6.467723 AATAAGCGTCTCAACTTTGTACTG 57.532 37.500 0.00 0.00 0.00 2.74
151 152 3.728076 AGCGTCTCAACTTTGTACTGA 57.272 42.857 0.00 0.00 0.00 3.41
152 153 4.054780 AGCGTCTCAACTTTGTACTGAA 57.945 40.909 0.00 0.00 0.00 3.02
153 154 4.632153 AGCGTCTCAACTTTGTACTGAAT 58.368 39.130 0.00 0.00 0.00 2.57
154 155 5.057149 AGCGTCTCAACTTTGTACTGAATT 58.943 37.500 0.00 0.00 0.00 2.17
155 156 5.527582 AGCGTCTCAACTTTGTACTGAATTT 59.472 36.000 0.00 0.00 0.00 1.82
156 157 6.704493 AGCGTCTCAACTTTGTACTGAATTTA 59.296 34.615 0.00 0.00 0.00 1.40
157 158 7.010023 GCGTCTCAACTTTGTACTGAATTTAG 58.990 38.462 0.00 0.00 0.00 1.85
158 159 7.307219 GCGTCTCAACTTTGTACTGAATTTAGT 60.307 37.037 8.09 8.09 34.71 2.24
159 160 9.188588 CGTCTCAACTTTGTACTGAATTTAGTA 57.811 33.333 6.01 6.01 32.19 1.82
179 180 9.706691 TTTAGTACAAGGAGTATCAAAGTTGAG 57.293 33.333 0.00 0.00 41.08 3.02
180 181 7.540474 AGTACAAGGAGTATCAAAGTTGAGA 57.460 36.000 0.00 0.00 41.08 3.27
181 182 7.379750 AGTACAAGGAGTATCAAAGTTGAGAC 58.620 38.462 10.16 10.16 46.69 3.36
190 191 7.111353 GTATCAAAGTTGAGACACTTGAGAC 57.889 40.000 12.68 0.00 45.88 3.36
191 192 5.084818 TCAAAGTTGAGACACTTGAGACA 57.915 39.130 0.00 0.00 37.07 3.41
192 193 5.111989 TCAAAGTTGAGACACTTGAGACAG 58.888 41.667 0.00 0.00 37.07 3.51
193 194 5.105351 TCAAAGTTGAGACACTTGAGACAGA 60.105 40.000 0.00 0.00 37.07 3.41
194 195 4.582701 AGTTGAGACACTTGAGACAGAG 57.417 45.455 0.00 0.00 0.00 3.35
195 196 4.211125 AGTTGAGACACTTGAGACAGAGA 58.789 43.478 0.00 0.00 0.00 3.10
196 197 4.278170 AGTTGAGACACTTGAGACAGAGAG 59.722 45.833 0.00 0.00 0.00 3.20
197 198 4.092116 TGAGACACTTGAGACAGAGAGA 57.908 45.455 0.00 0.00 0.00 3.10
198 199 4.071423 TGAGACACTTGAGACAGAGAGAG 58.929 47.826 0.00 0.00 0.00 3.20
199 200 4.072131 GAGACACTTGAGACAGAGAGAGT 58.928 47.826 0.00 0.00 0.00 3.24
200 201 5.221742 TGAGACACTTGAGACAGAGAGAGTA 60.222 44.000 0.00 0.00 0.00 2.59
201 202 5.815581 AGACACTTGAGACAGAGAGAGTAT 58.184 41.667 0.00 0.00 0.00 2.12
202 203 6.953101 AGACACTTGAGACAGAGAGAGTATA 58.047 40.000 0.00 0.00 0.00 1.47
203 204 7.573710 AGACACTTGAGACAGAGAGAGTATAT 58.426 38.462 0.00 0.00 0.00 0.86
204 205 8.052748 AGACACTTGAGACAGAGAGAGTATATT 58.947 37.037 0.00 0.00 0.00 1.28
205 206 9.332502 GACACTTGAGACAGAGAGAGTATATTA 57.667 37.037 0.00 0.00 0.00 0.98
206 207 9.116067 ACACTTGAGACAGAGAGAGTATATTAC 57.884 37.037 0.00 0.00 0.00 1.89
207 208 9.114952 CACTTGAGACAGAGAGAGTATATTACA 57.885 37.037 0.00 0.00 0.00 2.41
208 209 9.116067 ACTTGAGACAGAGAGAGTATATTACAC 57.884 37.037 0.00 0.00 0.00 2.90
209 210 7.716768 TGAGACAGAGAGAGTATATTACACG 57.283 40.000 0.00 0.00 0.00 4.49
210 211 7.498443 TGAGACAGAGAGAGTATATTACACGA 58.502 38.462 0.00 0.00 0.00 4.35
211 212 8.151596 TGAGACAGAGAGAGTATATTACACGAT 58.848 37.037 0.00 0.00 0.00 3.73
212 213 9.642327 GAGACAGAGAGAGTATATTACACGATA 57.358 37.037 0.00 0.00 0.00 2.92
215 216 8.670135 ACAGAGAGAGTATATTACACGATATGC 58.330 37.037 0.00 0.00 0.00 3.14
216 217 8.669243 CAGAGAGAGTATATTACACGATATGCA 58.331 37.037 0.00 0.00 30.01 3.96
217 218 8.670135 AGAGAGAGTATATTACACGATATGCAC 58.330 37.037 0.00 0.00 30.01 4.57
218 219 8.336801 AGAGAGTATATTACACGATATGCACA 57.663 34.615 0.00 0.00 30.01 4.57
219 220 8.237949 AGAGAGTATATTACACGATATGCACAC 58.762 37.037 0.00 0.00 30.01 3.82
220 221 8.112016 AGAGTATATTACACGATATGCACACT 57.888 34.615 0.00 0.00 30.01 3.55
221 222 8.577296 AGAGTATATTACACGATATGCACACTT 58.423 33.333 0.00 0.00 30.01 3.16
222 223 8.520835 AGTATATTACACGATATGCACACTTG 57.479 34.615 0.00 0.00 30.01 3.16
223 224 8.141909 AGTATATTACACGATATGCACACTTGT 58.858 33.333 0.00 0.00 30.01 3.16
257 258 4.379374 AAAACGTATTTCACTTCGTCGG 57.621 40.909 0.00 0.00 35.49 4.79
258 259 1.343506 ACGTATTTCACTTCGTCGGC 58.656 50.000 0.00 0.00 30.71 5.54
259 260 0.293723 CGTATTTCACTTCGTCGGCG 59.706 55.000 1.15 1.15 39.92 6.46
260 261 1.343506 GTATTTCACTTCGTCGGCGT 58.656 50.000 10.18 0.00 39.49 5.68
261 262 1.319669 GTATTTCACTTCGTCGGCGTC 59.680 52.381 10.18 0.00 39.49 5.19
262 263 1.342082 ATTTCACTTCGTCGGCGTCG 61.342 55.000 19.85 19.85 39.49 5.12
263 264 2.666715 TTTCACTTCGTCGGCGTCGT 62.667 55.000 24.03 4.75 39.49 4.34
264 265 1.840630 TTCACTTCGTCGGCGTCGTA 61.841 55.000 24.03 15.15 39.49 3.43
265 266 1.226211 CACTTCGTCGGCGTCGTAT 60.226 57.895 24.03 9.73 39.49 3.06
266 267 0.795735 CACTTCGTCGGCGTCGTATT 60.796 55.000 24.03 8.19 39.49 1.89
267 268 0.109597 ACTTCGTCGGCGTCGTATTT 60.110 50.000 24.03 6.65 39.49 1.40
268 269 0.986992 CTTCGTCGGCGTCGTATTTT 59.013 50.000 24.03 0.00 39.49 1.82
269 270 1.387756 CTTCGTCGGCGTCGTATTTTT 59.612 47.619 24.03 0.00 39.49 1.94
297 298 1.413767 AATACAGACGCAAGCGCTCG 61.414 55.000 12.06 14.49 44.19 5.03
319 320 1.299541 CACTCACCCATATGAACGCC 58.700 55.000 3.65 0.00 0.00 5.68
324 325 0.393808 ACCCATATGAACGCCCACAC 60.394 55.000 3.65 0.00 0.00 3.82
325 326 1.436195 CCCATATGAACGCCCACACG 61.436 60.000 3.65 0.00 39.50 4.49
336 337 1.070786 CCCACACGCACACCTTACT 59.929 57.895 0.00 0.00 0.00 2.24
342 343 3.129813 CACACGCACACCTTACTCCTATA 59.870 47.826 0.00 0.00 0.00 1.31
353 354 4.583489 CCTTACTCCTATAAGCACCTTCGA 59.417 45.833 0.00 0.00 31.80 3.71
365 366 0.882474 ACCTTCGAGAGACTGAACCG 59.118 55.000 0.00 0.00 41.84 4.44
366 367 0.171455 CCTTCGAGAGACTGAACCGG 59.829 60.000 0.00 0.00 41.84 5.28
372 373 2.605823 CGAGAGACTGAACCGGCATATC 60.606 54.545 0.00 0.00 0.00 1.63
375 376 3.389329 AGAGACTGAACCGGCATATCATT 59.611 43.478 0.00 0.00 0.00 2.57
377 378 5.070446 AGAGACTGAACCGGCATATCATTTA 59.930 40.000 0.00 0.00 0.00 1.40
378 379 5.680619 AGACTGAACCGGCATATCATTTAA 58.319 37.500 0.00 0.00 0.00 1.52
379 380 5.760253 AGACTGAACCGGCATATCATTTAAG 59.240 40.000 0.00 0.00 0.00 1.85
380 381 5.680619 ACTGAACCGGCATATCATTTAAGA 58.319 37.500 0.00 0.00 0.00 2.10
381 382 6.299141 ACTGAACCGGCATATCATTTAAGAT 58.701 36.000 0.00 0.00 0.00 2.40
384 385 8.684386 TGAACCGGCATATCATTTAAGATTTA 57.316 30.769 0.00 0.00 0.00 1.40
385 386 8.564574 TGAACCGGCATATCATTTAAGATTTAC 58.435 33.333 0.00 0.00 0.00 2.01
386 387 8.458573 AACCGGCATATCATTTAAGATTTACA 57.541 30.769 0.00 0.00 0.00 2.41
387 388 8.458573 ACCGGCATATCATTTAAGATTTACAA 57.541 30.769 0.00 0.00 0.00 2.41
388 389 8.908903 ACCGGCATATCATTTAAGATTTACAAA 58.091 29.630 0.00 0.00 0.00 2.83
389 390 9.398170 CCGGCATATCATTTAAGATTTACAAAG 57.602 33.333 0.00 0.00 0.00 2.77
390 391 9.950680 CGGCATATCATTTAAGATTTACAAAGT 57.049 29.630 0.00 0.00 0.00 2.66
443 444 2.497675 TCTCCTCTCACTAAAAGCGCAT 59.502 45.455 11.47 0.00 0.00 4.73
469 470 6.197096 CGCCGAAAATCTTGAAATAAATCCAG 59.803 38.462 0.00 0.00 0.00 3.86
484 485 8.652810 AATAAATCCAGAAATAATGCAAGCAC 57.347 30.769 0.00 0.00 0.00 4.40
493 494 2.584835 AATGCAAGCACCAGGACTTA 57.415 45.000 0.00 0.00 0.00 2.24
510 511 3.046374 ACTTAAATCCTGATAGGCCGGT 58.954 45.455 1.90 0.00 34.61 5.28
520 521 1.000955 GATAGGCCGGTGATACCACTG 59.999 57.143 1.90 0.00 46.66 3.66
521 522 0.324923 TAGGCCGGTGATACCACTGT 60.325 55.000 1.90 0.00 45.88 3.55
522 523 1.198759 AGGCCGGTGATACCACTGTT 61.199 55.000 1.90 0.00 45.88 3.16
523 524 0.743345 GGCCGGTGATACCACTGTTC 60.743 60.000 1.90 0.00 45.88 3.18
524 525 0.249398 GCCGGTGATACCACTGTTCT 59.751 55.000 1.90 0.00 45.88 3.01
536 543 2.413837 CACTGTTCTTCTAACCACGGG 58.586 52.381 0.00 0.00 0.00 5.28
549 556 2.440613 ACGGGTTGGTTTGCCGTT 60.441 55.556 0.00 0.00 37.67 4.44
574 581 3.181524 CGTCGCATTTGATTCCGTAGTTT 60.182 43.478 0.00 0.00 0.00 2.66
584 598 5.566469 TGATTCCGTAGTTTCTTGGGAAAT 58.434 37.500 0.00 0.00 42.45 2.17
598 612 2.307686 TGGGAAATGGGAGGAGTTGTAC 59.692 50.000 0.00 0.00 0.00 2.90
631 649 0.790207 CGTGTTGAGTTGGATGACCG 59.210 55.000 0.00 0.00 39.42 4.79
644 662 4.780815 TGGATGACCGAAATTGAGCTAAT 58.219 39.130 0.00 0.00 39.42 1.73
692 711 3.421231 CGTCGCTAAATCCATCTTACGTC 59.579 47.826 0.00 0.00 0.00 4.34
835 874 1.726791 CACGACTCAGATTTGTTCCGG 59.273 52.381 0.00 0.00 0.00 5.14
836 875 1.343465 ACGACTCAGATTTGTTCCGGT 59.657 47.619 0.00 0.00 0.00 5.28
837 876 1.993370 CGACTCAGATTTGTTCCGGTC 59.007 52.381 0.00 0.00 0.00 4.79
838 877 2.609491 CGACTCAGATTTGTTCCGGTCA 60.609 50.000 0.00 0.00 0.00 4.02
839 878 3.600388 GACTCAGATTTGTTCCGGTCAT 58.400 45.455 0.00 0.00 0.00 3.06
840 879 3.338249 ACTCAGATTTGTTCCGGTCATG 58.662 45.455 0.00 0.00 0.00 3.07
841 880 2.083774 TCAGATTTGTTCCGGTCATGC 58.916 47.619 0.00 0.00 0.00 4.06
842 881 1.086696 AGATTTGTTCCGGTCATGCG 58.913 50.000 0.00 0.00 0.00 4.73
843 882 0.802494 GATTTGTTCCGGTCATGCGT 59.198 50.000 0.00 0.00 0.00 5.24
844 883 0.521291 ATTTGTTCCGGTCATGCGTG 59.479 50.000 0.00 0.00 0.00 5.34
845 884 1.511318 TTTGTTCCGGTCATGCGTGG 61.511 55.000 5.98 0.00 0.00 4.94
846 885 3.799755 GTTCCGGTCATGCGTGGC 61.800 66.667 5.98 3.41 0.00 5.01
1137 1225 4.680237 CGCGACCACCTCAAGGCA 62.680 66.667 0.00 0.00 39.32 4.75
1483 6116 6.096001 GTCCAAGCTCCATAACAAGATTTGAT 59.904 38.462 0.00 0.00 0.00 2.57
1501 6150 2.087646 GATGGCAGGAGGAGTTGAAAC 58.912 52.381 0.00 0.00 0.00 2.78
1604 6313 9.319143 CTTGATATAAGTTGAAGAAGGTCGATT 57.681 33.333 0.00 0.00 0.00 3.34
1790 14180 1.800805 ACTTCATTGGACACTCGCAG 58.199 50.000 0.00 0.00 0.00 5.18
1840 14236 5.862845 ACTCAGTGAAAGAATGACACTCAT 58.137 37.500 0.00 0.00 41.93 2.90
1894 14290 6.436218 AGAAAACACTCAACAAAGTAGGGTTT 59.564 34.615 0.00 0.00 46.14 3.27
1895 14291 5.830000 AACACTCAACAAAGTAGGGTTTC 57.170 39.130 0.00 0.00 33.08 2.78
1931 14330 9.730420 ATACTCGGCAAACAATTATAAATCAAC 57.270 29.630 0.00 0.00 0.00 3.18
1934 14333 8.233692 TCGGCAAACAATTATAAATCAACAAC 57.766 30.769 0.00 0.00 0.00 3.32
2104 14506 1.133869 GTAATGTGTTCCACGCCGC 59.866 57.895 0.00 0.00 37.14 6.53
2105 14507 1.301795 TAATGTGTTCCACGCCGCA 60.302 52.632 0.00 0.00 37.14 5.69
2114 14516 1.240256 TCCACGCCGCAAAAATTAGT 58.760 45.000 0.00 0.00 0.00 2.24
2121 14523 4.083217 ACGCCGCAAAAATTAGTGATGTTA 60.083 37.500 0.00 0.00 0.00 2.41
2204 14780 8.825667 AATTTTAACCGCAAGTGTATGAAAAT 57.174 26.923 0.00 0.00 0.00 1.82
2243 14819 7.222031 GGGTTCAAAACTATTTGTGTTCTTGAC 59.778 37.037 1.69 0.00 45.02 3.18
2339 14917 1.590610 GAGCTCAGTCGCAGAGGACA 61.591 60.000 9.40 0.00 39.42 4.02
2342 14920 1.674221 GCTCAGTCGCAGAGGACAAAT 60.674 52.381 0.00 0.00 39.42 2.32
2344 14922 3.182967 CTCAGTCGCAGAGGACAAATAC 58.817 50.000 0.00 0.00 39.42 1.89
2345 14923 2.826128 TCAGTCGCAGAGGACAAATACT 59.174 45.455 0.00 0.00 39.42 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.803235 GGGGAAAGAAAACACTATAATTGAGTT 58.197 33.333 0.00 0.00 0.00 3.01
19 20 8.170730 AGGGGAAAGAAAACACTATAATTGAGT 58.829 33.333 0.00 0.00 0.00 3.41
20 21 8.581253 AGGGGAAAGAAAACACTATAATTGAG 57.419 34.615 0.00 0.00 0.00 3.02
21 22 8.950007 AAGGGGAAAGAAAACACTATAATTGA 57.050 30.769 0.00 0.00 0.00 2.57
22 23 9.639601 GAAAGGGGAAAGAAAACACTATAATTG 57.360 33.333 0.00 0.00 0.00 2.32
23 24 9.601810 AGAAAGGGGAAAGAAAACACTATAATT 57.398 29.630 0.00 0.00 0.00 1.40
24 25 9.601810 AAGAAAGGGGAAAGAAAACACTATAAT 57.398 29.630 0.00 0.00 0.00 1.28
25 26 9.074576 GAAGAAAGGGGAAAGAAAACACTATAA 57.925 33.333 0.00 0.00 0.00 0.98
26 27 8.445588 AGAAGAAAGGGGAAAGAAAACACTATA 58.554 33.333 0.00 0.00 0.00 1.31
27 28 7.298374 AGAAGAAAGGGGAAAGAAAACACTAT 58.702 34.615 0.00 0.00 0.00 2.12
28 29 6.669631 AGAAGAAAGGGGAAAGAAAACACTA 58.330 36.000 0.00 0.00 0.00 2.74
29 30 5.519808 AGAAGAAAGGGGAAAGAAAACACT 58.480 37.500 0.00 0.00 0.00 3.55
30 31 5.854010 AGAAGAAAGGGGAAAGAAAACAC 57.146 39.130 0.00 0.00 0.00 3.32
31 32 7.232737 GGAATAGAAGAAAGGGGAAAGAAAACA 59.767 37.037 0.00 0.00 0.00 2.83
32 33 7.309867 GGGAATAGAAGAAAGGGGAAAGAAAAC 60.310 40.741 0.00 0.00 0.00 2.43
33 34 6.724441 GGGAATAGAAGAAAGGGGAAAGAAAA 59.276 38.462 0.00 0.00 0.00 2.29
34 35 6.046762 AGGGAATAGAAGAAAGGGGAAAGAAA 59.953 38.462 0.00 0.00 0.00 2.52
35 36 5.555941 AGGGAATAGAAGAAAGGGGAAAGAA 59.444 40.000 0.00 0.00 0.00 2.52
36 37 5.108752 AGGGAATAGAAGAAAGGGGAAAGA 58.891 41.667 0.00 0.00 0.00 2.52
37 38 5.441500 GAGGGAATAGAAGAAAGGGGAAAG 58.558 45.833 0.00 0.00 0.00 2.62
38 39 4.229812 GGAGGGAATAGAAGAAAGGGGAAA 59.770 45.833 0.00 0.00 0.00 3.13
39 40 3.786450 GGAGGGAATAGAAGAAAGGGGAA 59.214 47.826 0.00 0.00 0.00 3.97
40 41 3.394645 GGAGGGAATAGAAGAAAGGGGA 58.605 50.000 0.00 0.00 0.00 4.81
41 42 2.104963 CGGAGGGAATAGAAGAAAGGGG 59.895 54.545 0.00 0.00 0.00 4.79
42 43 2.772515 ACGGAGGGAATAGAAGAAAGGG 59.227 50.000 0.00 0.00 0.00 3.95
43 44 4.489306 AACGGAGGGAATAGAAGAAAGG 57.511 45.455 0.00 0.00 0.00 3.11
44 45 7.916914 TTAAAACGGAGGGAATAGAAGAAAG 57.083 36.000 0.00 0.00 0.00 2.62
45 46 8.694581 TTTTAAAACGGAGGGAATAGAAGAAA 57.305 30.769 0.00 0.00 0.00 2.52
46 47 8.873186 ATTTTAAAACGGAGGGAATAGAAGAA 57.127 30.769 1.97 0.00 0.00 2.52
47 48 9.962809 TTATTTTAAAACGGAGGGAATAGAAGA 57.037 29.630 1.97 0.00 0.00 2.87
49 50 9.743581 ACTTATTTTAAAACGGAGGGAATAGAA 57.256 29.630 1.97 0.00 0.00 2.10
50 51 9.169592 CACTTATTTTAAAACGGAGGGAATAGA 57.830 33.333 1.97 0.00 0.00 1.98
51 52 8.953313 ACACTTATTTTAAAACGGAGGGAATAG 58.047 33.333 1.97 0.00 0.00 1.73
52 53 8.866970 ACACTTATTTTAAAACGGAGGGAATA 57.133 30.769 1.97 0.00 0.00 1.75
53 54 7.668469 AGACACTTATTTTAAAACGGAGGGAAT 59.332 33.333 1.97 0.00 0.00 3.01
54 55 6.999871 AGACACTTATTTTAAAACGGAGGGAA 59.000 34.615 1.97 0.00 0.00 3.97
55 56 6.536447 AGACACTTATTTTAAAACGGAGGGA 58.464 36.000 1.97 0.00 0.00 4.20
56 57 6.428771 TGAGACACTTATTTTAAAACGGAGGG 59.571 38.462 1.97 5.41 0.00 4.30
57 58 7.429636 TGAGACACTTATTTTAAAACGGAGG 57.570 36.000 1.97 0.00 0.00 4.30
58 59 9.893305 AATTGAGACACTTATTTTAAAACGGAG 57.107 29.630 1.97 4.41 0.00 4.63
91 92 9.813826 AGGGAATAGAAGAAAGAGAAAATTTCA 57.186 29.630 8.55 0.00 38.79 2.69
99 100 9.494055 TGAGATAAAGGGAATAGAAGAAAGAGA 57.506 33.333 0.00 0.00 0.00 3.10
108 109 9.273016 CGCTTATTTTGAGATAAAGGGAATAGA 57.727 33.333 0.00 0.00 0.00 1.98
109 110 9.057089 ACGCTTATTTTGAGATAAAGGGAATAG 57.943 33.333 4.71 0.00 0.00 1.73
110 111 8.974060 ACGCTTATTTTGAGATAAAGGGAATA 57.026 30.769 4.71 0.00 0.00 1.75
111 112 7.775561 AGACGCTTATTTTGAGATAAAGGGAAT 59.224 33.333 4.71 0.00 0.00 3.01
112 113 7.110155 AGACGCTTATTTTGAGATAAAGGGAA 58.890 34.615 4.71 0.00 0.00 3.97
113 114 6.650120 AGACGCTTATTTTGAGATAAAGGGA 58.350 36.000 4.71 0.00 0.00 4.20
114 115 6.538742 TGAGACGCTTATTTTGAGATAAAGGG 59.461 38.462 0.00 0.00 0.00 3.95
115 116 7.539712 TGAGACGCTTATTTTGAGATAAAGG 57.460 36.000 0.00 0.00 0.00 3.11
116 117 8.660373 AGTTGAGACGCTTATTTTGAGATAAAG 58.340 33.333 0.00 0.00 0.00 1.85
117 118 8.547967 AGTTGAGACGCTTATTTTGAGATAAA 57.452 30.769 0.00 0.00 0.00 1.40
118 119 8.547967 AAGTTGAGACGCTTATTTTGAGATAA 57.452 30.769 0.00 0.00 0.00 1.75
119 120 8.443160 CAAAGTTGAGACGCTTATTTTGAGATA 58.557 33.333 0.00 0.00 0.00 1.98
120 121 7.041098 ACAAAGTTGAGACGCTTATTTTGAGAT 60.041 33.333 0.00 0.00 0.00 2.75
121 122 6.260050 ACAAAGTTGAGACGCTTATTTTGAGA 59.740 34.615 0.00 0.00 0.00 3.27
122 123 6.430451 ACAAAGTTGAGACGCTTATTTTGAG 58.570 36.000 0.00 0.00 0.00 3.02
123 124 6.371809 ACAAAGTTGAGACGCTTATTTTGA 57.628 33.333 0.00 0.00 0.00 2.69
124 125 7.321271 CAGTACAAAGTTGAGACGCTTATTTTG 59.679 37.037 0.00 0.00 0.00 2.44
125 126 7.225931 TCAGTACAAAGTTGAGACGCTTATTTT 59.774 33.333 0.00 0.00 0.00 1.82
126 127 6.704493 TCAGTACAAAGTTGAGACGCTTATTT 59.296 34.615 0.00 0.00 0.00 1.40
127 128 6.220930 TCAGTACAAAGTTGAGACGCTTATT 58.779 36.000 0.00 0.00 0.00 1.40
128 129 5.779922 TCAGTACAAAGTTGAGACGCTTAT 58.220 37.500 0.00 0.00 0.00 1.73
129 130 5.190992 TCAGTACAAAGTTGAGACGCTTA 57.809 39.130 0.00 0.00 0.00 3.09
130 131 4.054780 TCAGTACAAAGTTGAGACGCTT 57.945 40.909 0.00 0.00 0.00 4.68
131 132 3.728076 TCAGTACAAAGTTGAGACGCT 57.272 42.857 0.00 0.00 0.00 5.07
132 133 4.992381 ATTCAGTACAAAGTTGAGACGC 57.008 40.909 0.00 0.00 0.00 5.19
133 134 8.073355 ACTAAATTCAGTACAAAGTTGAGACG 57.927 34.615 0.00 0.00 0.00 4.18
153 154 9.706691 CTCAACTTTGATACTCCTTGTACTAAA 57.293 33.333 0.00 0.00 36.46 1.85
154 155 9.085645 TCTCAACTTTGATACTCCTTGTACTAA 57.914 33.333 0.00 0.00 36.46 2.24
155 156 8.521176 GTCTCAACTTTGATACTCCTTGTACTA 58.479 37.037 0.00 0.00 36.46 1.82
156 157 7.015292 TGTCTCAACTTTGATACTCCTTGTACT 59.985 37.037 8.45 0.00 35.87 2.73
157 158 7.116519 GTGTCTCAACTTTGATACTCCTTGTAC 59.883 40.741 8.45 0.00 35.87 2.90
158 159 7.015292 AGTGTCTCAACTTTGATACTCCTTGTA 59.985 37.037 8.45 0.00 35.87 2.41
159 160 5.992217 GTGTCTCAACTTTGATACTCCTTGT 59.008 40.000 8.45 0.00 35.87 3.16
160 161 6.226787 AGTGTCTCAACTTTGATACTCCTTG 58.773 40.000 8.45 0.00 35.87 3.61
161 162 6.426646 AGTGTCTCAACTTTGATACTCCTT 57.573 37.500 8.45 0.00 35.87 3.36
162 163 6.042093 TCAAGTGTCTCAACTTTGATACTCCT 59.958 38.462 8.45 3.17 38.34 3.69
163 164 6.223852 TCAAGTGTCTCAACTTTGATACTCC 58.776 40.000 8.45 1.40 38.34 3.85
164 165 7.115663 GTCTCAAGTGTCTCAACTTTGATACTC 59.884 40.741 8.45 5.60 38.34 2.59
165 166 6.926272 GTCTCAAGTGTCTCAACTTTGATACT 59.074 38.462 8.45 4.30 38.34 2.12
166 167 6.701841 TGTCTCAAGTGTCTCAACTTTGATAC 59.298 38.462 1.53 1.53 38.34 2.24
167 168 6.816136 TGTCTCAAGTGTCTCAACTTTGATA 58.184 36.000 0.00 0.00 38.34 2.15
168 169 5.674525 TGTCTCAAGTGTCTCAACTTTGAT 58.325 37.500 0.00 0.00 38.34 2.57
169 170 5.084818 TGTCTCAAGTGTCTCAACTTTGA 57.915 39.130 0.00 0.00 38.34 2.69
170 171 5.111989 TCTGTCTCAAGTGTCTCAACTTTG 58.888 41.667 0.00 0.00 38.34 2.77
171 172 5.127845 TCTCTGTCTCAAGTGTCTCAACTTT 59.872 40.000 0.00 0.00 38.34 2.66
172 173 4.646945 TCTCTGTCTCAAGTGTCTCAACTT 59.353 41.667 0.00 0.00 41.08 2.66
173 174 4.211125 TCTCTGTCTCAAGTGTCTCAACT 58.789 43.478 0.00 0.00 0.00 3.16
174 175 4.277174 TCTCTCTGTCTCAAGTGTCTCAAC 59.723 45.833 0.00 0.00 0.00 3.18
175 176 4.464947 TCTCTCTGTCTCAAGTGTCTCAA 58.535 43.478 0.00 0.00 0.00 3.02
176 177 4.071423 CTCTCTCTGTCTCAAGTGTCTCA 58.929 47.826 0.00 0.00 0.00 3.27
177 178 4.072131 ACTCTCTCTGTCTCAAGTGTCTC 58.928 47.826 0.00 0.00 0.00 3.36
178 179 4.098914 ACTCTCTCTGTCTCAAGTGTCT 57.901 45.455 0.00 0.00 0.00 3.41
179 180 7.801716 ATATACTCTCTCTGTCTCAAGTGTC 57.198 40.000 0.00 0.00 0.00 3.67
180 181 9.116067 GTAATATACTCTCTCTGTCTCAAGTGT 57.884 37.037 0.00 0.00 0.00 3.55
181 182 9.114952 TGTAATATACTCTCTCTGTCTCAAGTG 57.885 37.037 0.00 0.00 0.00 3.16
182 183 9.116067 GTGTAATATACTCTCTCTGTCTCAAGT 57.884 37.037 0.00 0.00 0.00 3.16
183 184 8.279800 CGTGTAATATACTCTCTCTGTCTCAAG 58.720 40.741 0.00 0.00 0.00 3.02
184 185 7.985752 TCGTGTAATATACTCTCTCTGTCTCAA 59.014 37.037 0.00 0.00 0.00 3.02
185 186 7.498443 TCGTGTAATATACTCTCTCTGTCTCA 58.502 38.462 0.00 0.00 0.00 3.27
186 187 7.949903 TCGTGTAATATACTCTCTCTGTCTC 57.050 40.000 0.00 0.00 0.00 3.36
189 190 8.670135 GCATATCGTGTAATATACTCTCTCTGT 58.330 37.037 0.00 0.00 0.00 3.41
190 191 8.669243 TGCATATCGTGTAATATACTCTCTCTG 58.331 37.037 0.00 0.00 0.00 3.35
191 192 8.670135 GTGCATATCGTGTAATATACTCTCTCT 58.330 37.037 0.00 0.00 0.00 3.10
192 193 8.451748 TGTGCATATCGTGTAATATACTCTCTC 58.548 37.037 0.00 0.00 0.00 3.20
193 194 8.237949 GTGTGCATATCGTGTAATATACTCTCT 58.762 37.037 0.00 0.00 0.00 3.10
194 195 8.237949 AGTGTGCATATCGTGTAATATACTCTC 58.762 37.037 0.00 0.00 0.00 3.20
195 196 8.112016 AGTGTGCATATCGTGTAATATACTCT 57.888 34.615 0.00 0.00 0.00 3.24
196 197 8.639428 CAAGTGTGCATATCGTGTAATATACTC 58.361 37.037 0.00 0.00 0.00 2.59
197 198 8.141909 ACAAGTGTGCATATCGTGTAATATACT 58.858 33.333 0.00 0.00 0.00 2.12
198 199 8.214472 CACAAGTGTGCATATCGTGTAATATAC 58.786 37.037 0.00 0.00 39.39 1.47
199 200 8.138712 TCACAAGTGTGCATATCGTGTAATATA 58.861 33.333 6.56 0.00 45.25 0.86
200 201 6.983890 TCACAAGTGTGCATATCGTGTAATAT 59.016 34.615 6.56 0.00 45.25 1.28
201 202 6.334202 TCACAAGTGTGCATATCGTGTAATA 58.666 36.000 6.56 0.00 45.25 0.98
202 203 5.175127 TCACAAGTGTGCATATCGTGTAAT 58.825 37.500 6.56 0.00 45.25 1.89
203 204 4.561105 TCACAAGTGTGCATATCGTGTAA 58.439 39.130 6.56 0.00 45.25 2.41
204 205 4.082463 TCTCACAAGTGTGCATATCGTGTA 60.082 41.667 6.56 0.00 45.25 2.90
205 206 2.995939 CTCACAAGTGTGCATATCGTGT 59.004 45.455 6.56 0.00 45.25 4.49
206 207 3.253230 TCTCACAAGTGTGCATATCGTG 58.747 45.455 6.56 0.00 45.25 4.35
207 208 3.592898 TCTCACAAGTGTGCATATCGT 57.407 42.857 6.56 0.00 45.25 3.73
208 209 4.317628 CGAATCTCACAAGTGTGCATATCG 60.318 45.833 6.56 9.90 45.25 2.92
209 210 4.805719 TCGAATCTCACAAGTGTGCATATC 59.194 41.667 6.56 2.68 45.25 1.63
210 211 4.758688 TCGAATCTCACAAGTGTGCATAT 58.241 39.130 6.56 0.00 45.25 1.78
211 212 4.082245 TCTCGAATCTCACAAGTGTGCATA 60.082 41.667 6.56 0.00 45.25 3.14
212 213 2.998670 CTCGAATCTCACAAGTGTGCAT 59.001 45.455 6.56 0.00 45.25 3.96
213 214 2.035832 TCTCGAATCTCACAAGTGTGCA 59.964 45.455 6.56 0.00 45.25 4.57
214 215 2.677199 TCTCGAATCTCACAAGTGTGC 58.323 47.619 6.56 0.00 45.25 4.57
215 216 5.657470 TTTTCTCGAATCTCACAAGTGTG 57.343 39.130 5.02 5.02 46.91 3.82
249 250 0.986992 AAAATACGACGCCGACGAAG 59.013 50.000 16.72 0.00 43.93 3.79
250 251 1.417372 AAAAATACGACGCCGACGAA 58.583 45.000 16.72 0.00 43.93 3.85
251 252 3.105514 AAAAATACGACGCCGACGA 57.894 47.368 16.72 0.00 43.93 4.20
267 268 5.236655 TGCGTCTGTATTGTGTTCAAAAA 57.763 34.783 0.00 0.00 37.11 1.94
268 269 4.884458 TGCGTCTGTATTGTGTTCAAAA 57.116 36.364 0.00 0.00 37.11 2.44
269 270 4.788201 GCTTGCGTCTGTATTGTGTTCAAA 60.788 41.667 0.00 0.00 37.11 2.69
270 271 3.303725 GCTTGCGTCTGTATTGTGTTCAA 60.304 43.478 0.00 0.00 37.98 2.69
271 272 2.223144 GCTTGCGTCTGTATTGTGTTCA 59.777 45.455 0.00 0.00 0.00 3.18
272 273 2.721797 CGCTTGCGTCTGTATTGTGTTC 60.722 50.000 6.86 0.00 0.00 3.18
273 274 1.194547 CGCTTGCGTCTGTATTGTGTT 59.805 47.619 6.86 0.00 0.00 3.32
274 275 0.790207 CGCTTGCGTCTGTATTGTGT 59.210 50.000 6.86 0.00 0.00 3.72
275 276 0.519175 GCGCTTGCGTCTGTATTGTG 60.519 55.000 16.38 0.00 0.00 3.33
276 277 0.670546 AGCGCTTGCGTCTGTATTGT 60.671 50.000 16.38 0.00 45.69 2.71
277 278 0.025513 GAGCGCTTGCGTCTGTATTG 59.974 55.000 13.26 0.00 45.69 1.90
278 279 1.413767 CGAGCGCTTGCGTCTGTATT 61.414 55.000 13.26 0.00 45.69 1.89
279 280 1.874019 CGAGCGCTTGCGTCTGTAT 60.874 57.895 13.26 0.00 45.69 2.29
297 298 2.864343 GCGTTCATATGGGTGAGTGTAC 59.136 50.000 2.13 0.00 0.00 2.90
319 320 0.949105 GGAGTAAGGTGTGCGTGTGG 60.949 60.000 0.00 0.00 0.00 4.17
324 325 3.181479 TGCTTATAGGAGTAAGGTGTGCG 60.181 47.826 0.00 0.00 33.31 5.34
325 326 4.120589 GTGCTTATAGGAGTAAGGTGTGC 58.879 47.826 0.00 0.00 33.31 4.57
332 333 5.443283 TCTCGAAGGTGCTTATAGGAGTAA 58.557 41.667 0.00 0.00 0.00 2.24
336 337 3.884091 GTCTCTCGAAGGTGCTTATAGGA 59.116 47.826 0.00 0.00 0.00 2.94
342 343 1.621992 TCAGTCTCTCGAAGGTGCTT 58.378 50.000 0.00 0.00 0.00 3.91
353 354 2.388735 TGATATGCCGGTTCAGTCTCT 58.611 47.619 1.90 0.00 0.00 3.10
375 376 7.117236 CGCCTACAGTGACTTTGTAAATCTTAA 59.883 37.037 0.00 0.00 31.17 1.85
377 378 5.408604 CGCCTACAGTGACTTTGTAAATCTT 59.591 40.000 0.00 0.00 31.17 2.40
378 379 4.929808 CGCCTACAGTGACTTTGTAAATCT 59.070 41.667 0.00 0.00 31.17 2.40
379 380 4.689345 ACGCCTACAGTGACTTTGTAAATC 59.311 41.667 0.00 0.00 31.17 2.17
380 381 4.638304 ACGCCTACAGTGACTTTGTAAAT 58.362 39.130 0.00 0.00 31.17 1.40
381 382 4.053295 GACGCCTACAGTGACTTTGTAAA 58.947 43.478 0.00 0.00 31.17 2.01
384 385 1.687123 AGACGCCTACAGTGACTTTGT 59.313 47.619 0.00 0.00 0.00 2.83
385 386 2.329379 GAGACGCCTACAGTGACTTTG 58.671 52.381 0.00 0.00 30.94 2.77
386 387 1.068472 CGAGACGCCTACAGTGACTTT 60.068 52.381 0.00 0.00 30.94 2.66
387 388 0.522180 CGAGACGCCTACAGTGACTT 59.478 55.000 0.00 0.00 30.94 3.01
388 389 0.605860 ACGAGACGCCTACAGTGACT 60.606 55.000 0.00 0.00 33.56 3.41
389 390 0.179194 GACGAGACGCCTACAGTGAC 60.179 60.000 0.00 0.00 0.00 3.67
390 391 1.632948 CGACGAGACGCCTACAGTGA 61.633 60.000 0.00 0.00 0.00 3.41
391 392 1.226046 CGACGAGACGCCTACAGTG 60.226 63.158 0.00 0.00 0.00 3.66
392 393 1.633852 GACGACGAGACGCCTACAGT 61.634 60.000 0.00 0.00 36.70 3.55
393 394 1.060622 GACGACGAGACGCCTACAG 59.939 63.158 0.00 0.00 36.70 2.74
394 395 2.733671 CGACGACGAGACGCCTACA 61.734 63.158 0.00 0.00 42.66 2.74
395 396 2.021106 CGACGACGAGACGCCTAC 59.979 66.667 0.00 0.00 42.66 3.18
396 397 2.125952 TCGACGACGAGACGCCTA 60.126 61.111 5.75 0.00 43.81 3.93
417 418 4.308265 GCTTTTAGTGAGAGGAGACGTTT 58.692 43.478 0.00 0.00 0.00 3.60
423 424 2.370281 TGCGCTTTTAGTGAGAGGAG 57.630 50.000 9.73 0.00 0.00 3.69
443 444 6.127869 TGGATTTATTTCAAGATTTTCGGCGA 60.128 34.615 4.99 4.99 0.00 5.54
469 470 3.445096 AGTCCTGGTGCTTGCATTATTTC 59.555 43.478 0.00 0.00 0.00 2.17
493 494 1.507140 TCACCGGCCTATCAGGATTT 58.493 50.000 0.00 0.00 37.67 2.17
500 501 1.000955 CAGTGGTATCACCGGCCTATC 59.999 57.143 0.00 0.00 42.58 2.08
501 502 1.048601 CAGTGGTATCACCGGCCTAT 58.951 55.000 0.00 0.00 42.58 2.57
503 504 1.198759 AACAGTGGTATCACCGGCCT 61.199 55.000 0.00 0.00 42.58 5.19
510 511 5.566032 CGTGGTTAGAAGAACAGTGGTATCA 60.566 44.000 0.00 0.00 0.00 2.15
520 521 2.148768 CCAACCCGTGGTTAGAAGAAC 58.851 52.381 7.83 0.00 45.01 3.01
521 522 2.554370 CCAACCCGTGGTTAGAAGAA 57.446 50.000 7.83 0.00 45.01 2.52
549 556 1.800032 GGAATCAAATGCGACGCCA 59.200 52.632 18.69 5.87 0.00 5.69
574 581 2.041620 CAACTCCTCCCATTTCCCAAGA 59.958 50.000 0.00 0.00 0.00 3.02
584 598 0.541063 TCAGCGTACAACTCCTCCCA 60.541 55.000 0.00 0.00 0.00 4.37
609 623 1.798813 GTCATCCAACTCAACACGGAC 59.201 52.381 0.00 0.00 0.00 4.79
631 649 7.478520 ACGTACATACCATTAGCTCAATTTC 57.521 36.000 0.00 0.00 0.00 2.17
692 711 1.195448 ACGTAACGAGTGTAGTGTCCG 59.805 52.381 0.00 0.00 0.00 4.79
838 877 3.802227 TATAAAAGGCCCGCCACGCAT 62.802 52.381 8.74 0.00 38.92 4.73
839 878 2.538512 TATAAAAGGCCCGCCACGCA 62.539 55.000 8.74 0.00 38.92 5.24
840 879 1.378124 TTATAAAAGGCCCGCCACGC 61.378 55.000 8.74 0.00 38.92 5.34
841 880 0.661020 CTTATAAAAGGCCCGCCACG 59.339 55.000 8.74 0.00 38.92 4.94
842 881 0.384309 GCTTATAAAAGGCCCGCCAC 59.616 55.000 8.74 0.00 38.92 5.01
843 882 2.801859 GCTTATAAAAGGCCCGCCA 58.198 52.632 8.74 0.00 38.92 5.69
1137 1225 3.415087 GGGGCAGCCACATCTCCT 61.415 66.667 15.19 0.00 0.00 3.69
1310 1410 2.361737 GCAGCCCCACCTTCTTCC 60.362 66.667 0.00 0.00 0.00 3.46
1470 6103 4.018506 TCCTCCTGCCATCAAATCTTGTTA 60.019 41.667 0.00 0.00 0.00 2.41
1483 6116 0.843309 TGTTTCAACTCCTCCTGCCA 59.157 50.000 0.00 0.00 0.00 4.92
1580 6289 9.667107 AAAATCGACCTTCTTCAACTTATATCA 57.333 29.630 0.00 0.00 0.00 2.15
1604 6313 6.146510 ACGTCGCTATGAACAACAAAGATAAA 59.853 34.615 0.00 0.00 0.00 1.40
1708 14097 9.733556 ATTTTTCCGTAATGCTACATGGATATA 57.266 29.630 0.00 0.00 0.00 0.86
1758 14148 6.545666 TGTCCAATGAAGTACACTCAACAAAT 59.454 34.615 0.00 0.00 0.00 2.32
1790 14180 2.024414 ACACTTGGCAAAGGTCTTGTC 58.976 47.619 5.66 0.00 37.76 3.18
1840 14236 2.224426 ACTCGGCAACATACCTGTTTGA 60.224 45.455 0.00 0.00 43.05 2.69
1894 14290 8.780846 TTGTTTGCCGAGTATCTTATAAAAGA 57.219 30.769 0.00 0.00 45.63 2.52
2204 14780 2.623878 TGAACCCGTCTTTGCTAACA 57.376 45.000 0.00 0.00 0.00 2.41
2243 14819 9.778741 TCTTGTATATAAGGCCTAAACATTGAG 57.221 33.333 5.16 0.00 0.00 3.02
2342 14920 9.555727 AAACTTTTGTATGCTTTAGAGTCAGTA 57.444 29.630 0.00 0.00 0.00 2.74
2344 14922 8.559536 TCAAACTTTTGTATGCTTTAGAGTCAG 58.440 33.333 1.75 0.00 39.18 3.51
2345 14923 8.445275 TCAAACTTTTGTATGCTTTAGAGTCA 57.555 30.769 1.75 0.00 39.18 3.41


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

AutoCloner maintained by Alex Coulton.