Multiple sequence alignment - TraesCS7D01G432800

Loading Multiple Alignment...

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 TraesCS7D01G432800 chr7D 100.000 3256 0 0 1 3256 552323964 552327219 0.000000e+00 6013.0
1 TraesCS7D01G432800 chr7D 79.032 744 132 17 1268 2005 48824684 48823959 3.780000e-134 488.0
2 TraesCS7D01G432800 chr7B 92.701 2562 107 32 401 2930 597452719 597455232 0.000000e+00 3622.0
3 TraesCS7D01G432800 chr7B 88.532 218 17 5 3027 3242 597455221 597455432 1.160000e-64 257.0
4 TraesCS7D01G432800 chr7B 76.050 238 49 6 2976 3207 58715124 58714889 2.050000e-22 117.0
5 TraesCS7D01G432800 chr7A 95.103 2042 67 16 401 2415 637993676 637995711 0.000000e+00 3186.0
6 TraesCS7D01G432800 chr7A 85.023 1075 113 15 1079 2139 638132168 638133208 0.000000e+00 1050.0
7 TraesCS7D01G432800 chr7A 86.536 869 63 22 2395 3255 637996041 637996863 0.000000e+00 907.0
8 TraesCS7D01G432800 chr7A 94.972 358 17 1 1 357 219167775 219167418 7.890000e-156 560.0
9 TraesCS7D01G432800 chr7A 84.758 269 19 8 699 948 638131760 638132025 1.940000e-62 250.0
10 TraesCS7D01G432800 chr5A 84.066 1092 137 22 1082 2146 708183052 708184133 0.000000e+00 1018.0
11 TraesCS7D01G432800 chr4B 83.776 1091 143 18 1085 2146 668873284 668874369 0.000000e+00 1003.0
12 TraesCS7D01G432800 chrUn 87.432 740 81 9 1336 2069 28781714 28782447 0.000000e+00 841.0
13 TraesCS7D01G432800 chrUn 93.239 355 20 3 1 354 33762578 33762929 1.340000e-143 520.0
14 TraesCS7D01G432800 chrUn 93.239 355 20 3 1 354 33884128 33884479 1.340000e-143 520.0
15 TraesCS7D01G432800 chrUn 80.576 139 22 4 3057 3190 23170845 23170983 5.750000e-18 102.0
16 TraesCS7D01G432800 chr3A 78.314 973 151 47 1083 2019 663441808 663440860 1.010000e-159 573.0
17 TraesCS7D01G432800 chr3A 79.114 158 26 5 3069 3221 730179029 730178874 5.750000e-18 102.0
18 TraesCS7D01G432800 chr2B 96.275 349 12 1 1 348 547098496 547098844 3.640000e-159 571.0
19 TraesCS7D01G432800 chr2B 77.754 926 138 38 1108 2002 25069207 25070095 1.040000e-139 507.0
20 TraesCS7D01G432800 chr2B 79.188 197 32 7 1233 1423 41381438 41381631 9.480000e-26 128.0
21 TraesCS7D01G432800 chr2B 80.282 142 23 4 3057 3193 759651540 759651399 5.750000e-18 102.0
22 TraesCS7D01G432800 chr3D 95.014 361 17 1 1 360 55365858 55365498 1.700000e-157 566.0
23 TraesCS7D01G432800 chr3D 79.282 362 61 12 2577 2931 486789858 486789504 1.170000e-59 241.0
24 TraesCS7D01G432800 chr3D 81.126 302 37 17 2553 2841 551592339 551592633 1.180000e-54 224.0
25 TraesCS7D01G432800 chr3D 77.253 233 47 5 2982 3209 4574485 4574254 7.330000e-27 132.0
26 TraesCS7D01G432800 chr2D 95.455 352 14 1 1 350 406204418 406204769 7.890000e-156 560.0
27 TraesCS7D01G432800 chr2D 80.702 741 112 17 1267 2002 13770412 13771126 6.140000e-152 547.0
28 TraesCS7D01G432800 chr6D 94.382 356 18 2 1 354 49803999 49803644 2.210000e-151 545.0
29 TraesCS7D01G432800 chr5D 94.857 350 16 2 1 349 26523925 26523577 2.210000e-151 545.0
30 TraesCS7D01G432800 chr5D 78.108 941 127 41 1094 2002 560224906 560225799 1.040000e-144 523.0
31 TraesCS7D01G432800 chr5D 81.818 99 18 0 3103 3201 556724043 556724141 2.080000e-12 84.2
32 TraesCS7D01G432800 chr6A 94.828 348 17 1 4 350 582240554 582240207 2.860000e-150 542.0
33 TraesCS7D01G432800 chr4A 77.884 945 152 32 1097 2008 604105189 604104269 4.780000e-148 534.0
34 TraesCS7D01G432800 chr3B 77.306 965 158 40 1080 2007 700073335 700072395 2.240000e-141 512.0
35 TraesCS7D01G432800 chr3B 77.953 381 52 23 2553 2918 732164473 732164836 3.290000e-50 209.0
36 TraesCS7D01G432800 chr2A 77.155 232 45 7 2976 3201 667938803 667939032 9.480000e-26 128.0
37 TraesCS7D01G432800 chr1A 76.033 242 43 11 2970 3201 497503435 497503671 9.550000e-21 111.0
38 TraesCS7D01G432800 chr1D 94.118 34 2 0 1303 1336 84777639 84777606 6.000000e-03 52.8


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 TraesCS7D01G432800 chr7D 552323964 552327219 3255 False 6013.0 6013 100.0000 1 3256 1 chr7D.!!$F1 3255
1 TraesCS7D01G432800 chr7D 48823959 48824684 725 True 488.0 488 79.0320 1268 2005 1 chr7D.!!$R1 737
2 TraesCS7D01G432800 chr7B 597452719 597455432 2713 False 1939.5 3622 90.6165 401 3242 2 chr7B.!!$F1 2841
3 TraesCS7D01G432800 chr7A 637993676 637996863 3187 False 2046.5 3186 90.8195 401 3255 2 chr7A.!!$F1 2854
4 TraesCS7D01G432800 chr7A 638131760 638133208 1448 False 650.0 1050 84.8905 699 2139 2 chr7A.!!$F2 1440
5 TraesCS7D01G432800 chr5A 708183052 708184133 1081 False 1018.0 1018 84.0660 1082 2146 1 chr5A.!!$F1 1064
6 TraesCS7D01G432800 chr4B 668873284 668874369 1085 False 1003.0 1003 83.7760 1085 2146 1 chr4B.!!$F1 1061
7 TraesCS7D01G432800 chrUn 28781714 28782447 733 False 841.0 841 87.4320 1336 2069 1 chrUn.!!$F2 733
8 TraesCS7D01G432800 chr3A 663440860 663441808 948 True 573.0 573 78.3140 1083 2019 1 chr3A.!!$R1 936
9 TraesCS7D01G432800 chr2B 25069207 25070095 888 False 507.0 507 77.7540 1108 2002 1 chr2B.!!$F1 894
10 TraesCS7D01G432800 chr2D 13770412 13771126 714 False 547.0 547 80.7020 1267 2002 1 chr2D.!!$F1 735
11 TraesCS7D01G432800 chr5D 560224906 560225799 893 False 523.0 523 78.1080 1094 2002 1 chr5D.!!$F2 908
12 TraesCS7D01G432800 chr4A 604104269 604105189 920 True 534.0 534 77.8840 1097 2008 1 chr4A.!!$R1 911
13 TraesCS7D01G432800 chr3B 700072395 700073335 940 True 512.0 512 77.3060 1080 2007 1 chr3B.!!$R1 927

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
269 270 0.030603 GTGAGGGGAGGAAGGGATCT 60.031 60.0 0.00 0.0 0.00 2.75 F
947 1017 0.246360 CGTGCAGTACTCCACATGGA 59.754 55.0 16.97 0.0 43.08 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1293 2.847234 TTGGTGCACGGGGAGAGT 60.847 61.111 11.45 0.0 0.0 3.24 R
2367 2551 0.169009 GGCATCGGTCAGCAAAGTTC 59.831 55.000 0.00 0.0 0.0 3.01 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
31 32 3.751246 CAACCTCGACCGGCCGTA 61.751 66.667 26.12 5.43 0.00 4.02
32 33 2.990967 AACCTCGACCGGCCGTAA 60.991 61.111 26.12 5.05 0.00 3.18
33 34 3.286915 AACCTCGACCGGCCGTAAC 62.287 63.158 26.12 13.59 0.00 2.50
34 35 4.503314 CCTCGACCGGCCGTAACC 62.503 72.222 26.12 8.79 0.00 2.85
35 36 3.751246 CTCGACCGGCCGTAACCA 61.751 66.667 26.12 2.38 0.00 3.67
36 37 3.069946 TCGACCGGCCGTAACCAT 61.070 61.111 26.12 1.23 0.00 3.55
37 38 2.888534 CGACCGGCCGTAACCATG 60.889 66.667 26.12 9.27 0.00 3.66
38 39 2.512974 GACCGGCCGTAACCATGG 60.513 66.667 26.12 11.19 0.00 3.66
44 45 3.505184 CCGTAACCATGGCCGCAC 61.505 66.667 13.04 3.56 0.00 5.34
45 46 3.860125 CGTAACCATGGCCGCACG 61.860 66.667 13.04 12.33 0.00 5.34
46 47 4.174129 GTAACCATGGCCGCACGC 62.174 66.667 13.04 0.00 0.00 5.34
47 48 4.402528 TAACCATGGCCGCACGCT 62.403 61.111 13.04 0.00 37.74 5.07
58 59 3.515286 GCACGCTGCTGCATCCAT 61.515 61.111 16.29 0.00 40.96 3.41
59 60 2.407616 CACGCTGCTGCATCCATG 59.592 61.111 16.29 0.45 39.64 3.66
60 61 2.827190 ACGCTGCTGCATCCATGG 60.827 61.111 16.29 4.97 39.64 3.66
61 62 2.515290 CGCTGCTGCATCCATGGA 60.515 61.111 18.88 18.88 39.64 3.41
63 64 2.194212 GCTGCTGCATCCATGGAGG 61.194 63.158 22.10 22.10 45.11 4.30
64 65 1.226542 CTGCTGCATCCATGGAGGT 59.773 57.895 26.18 5.03 45.11 3.85
65 66 0.395311 CTGCTGCATCCATGGAGGTT 60.395 55.000 26.18 4.22 45.11 3.50
66 67 0.040058 TGCTGCATCCATGGAGGTTT 59.960 50.000 26.18 3.81 45.11 3.27
67 68 0.743097 GCTGCATCCATGGAGGTTTC 59.257 55.000 26.18 11.45 45.11 2.78
68 69 1.956636 GCTGCATCCATGGAGGTTTCA 60.957 52.381 26.18 15.25 45.11 2.69
69 70 2.022195 CTGCATCCATGGAGGTTTCAG 58.978 52.381 26.18 20.12 41.82 3.02
70 71 1.634973 TGCATCCATGGAGGTTTCAGA 59.365 47.619 26.18 0.00 39.02 3.27
71 72 2.041485 TGCATCCATGGAGGTTTCAGAA 59.959 45.455 26.18 2.77 39.02 3.02
72 73 3.091545 GCATCCATGGAGGTTTCAGAAA 58.908 45.455 26.18 0.00 39.02 2.52
73 74 3.119352 GCATCCATGGAGGTTTCAGAAAC 60.119 47.826 26.18 16.63 40.65 2.78
74 75 3.874383 TCCATGGAGGTTTCAGAAACA 57.126 42.857 24.37 7.28 43.15 2.83
75 76 3.486383 TCCATGGAGGTTTCAGAAACAC 58.514 45.455 24.37 17.44 43.15 3.32
76 77 3.117701 TCCATGGAGGTTTCAGAAACACA 60.118 43.478 24.37 19.45 43.15 3.72
77 78 3.004734 CCATGGAGGTTTCAGAAACACAC 59.995 47.826 24.37 14.68 43.15 3.82
78 79 2.285083 TGGAGGTTTCAGAAACACACG 58.715 47.619 24.37 0.00 43.15 4.49
79 80 2.093394 TGGAGGTTTCAGAAACACACGA 60.093 45.455 24.37 11.16 43.15 4.35
80 81 2.940410 GGAGGTTTCAGAAACACACGAA 59.060 45.455 24.37 0.00 43.15 3.85
81 82 3.002348 GGAGGTTTCAGAAACACACGAAG 59.998 47.826 24.37 0.00 43.15 3.79
82 83 3.869065 AGGTTTCAGAAACACACGAAGA 58.131 40.909 24.37 0.00 43.15 2.87
83 84 3.621715 AGGTTTCAGAAACACACGAAGAC 59.378 43.478 24.37 6.68 43.15 3.01
84 85 3.543460 GGTTTCAGAAACACACGAAGACG 60.543 47.826 24.37 0.00 43.15 4.18
85 86 2.855660 TCAGAAACACACGAAGACGA 57.144 45.000 0.00 0.00 42.66 4.20
86 87 2.456989 TCAGAAACACACGAAGACGAC 58.543 47.619 0.00 0.00 42.66 4.34
87 88 2.159352 TCAGAAACACACGAAGACGACA 60.159 45.455 0.00 0.00 42.66 4.35
88 89 2.794910 CAGAAACACACGAAGACGACAT 59.205 45.455 0.00 0.00 42.66 3.06
89 90 3.978855 CAGAAACACACGAAGACGACATA 59.021 43.478 0.00 0.00 42.66 2.29
90 91 4.088638 CAGAAACACACGAAGACGACATAG 59.911 45.833 0.00 0.00 42.66 2.23
91 92 2.631418 ACACACGAAGACGACATAGG 57.369 50.000 0.00 0.00 42.66 2.57
92 93 1.884579 ACACACGAAGACGACATAGGT 59.115 47.619 0.00 0.00 42.66 3.08
93 94 2.251040 CACACGAAGACGACATAGGTG 58.749 52.381 0.00 0.00 42.66 4.00
94 95 2.095415 CACACGAAGACGACATAGGTGA 60.095 50.000 0.00 0.00 42.66 4.02
95 96 2.161808 ACACGAAGACGACATAGGTGAG 59.838 50.000 0.00 0.00 42.66 3.51
96 97 1.743958 ACGAAGACGACATAGGTGAGG 59.256 52.381 0.00 0.00 42.66 3.86
97 98 1.065701 CGAAGACGACATAGGTGAGGG 59.934 57.143 0.00 0.00 42.66 4.30
98 99 0.824759 AAGACGACATAGGTGAGGGC 59.175 55.000 0.00 0.00 0.00 5.19
99 100 1.065928 GACGACATAGGTGAGGGCG 59.934 63.158 0.00 0.00 0.00 6.13
100 101 2.351336 GACGACATAGGTGAGGGCGG 62.351 65.000 0.00 0.00 0.00 6.13
101 102 2.822399 GACATAGGTGAGGGCGGG 59.178 66.667 0.00 0.00 0.00 6.13
102 103 3.462199 GACATAGGTGAGGGCGGGC 62.462 68.421 0.00 0.00 0.00 6.13
103 104 4.609018 CATAGGTGAGGGCGGGCG 62.609 72.222 0.00 0.00 0.00 6.13
104 105 4.853142 ATAGGTGAGGGCGGGCGA 62.853 66.667 0.00 0.00 0.00 5.54
173 174 4.200283 GTGAGGAGGCGAGGCGAG 62.200 72.222 0.00 0.00 0.00 5.03
224 225 3.658422 GAGGGGGCCCGTCCTTTT 61.658 66.667 30.75 4.22 41.95 2.27
225 226 3.640257 GAGGGGGCCCGTCCTTTTC 62.640 68.421 30.75 8.76 41.95 2.29
226 227 4.753662 GGGGGCCCGTCCTTTTCC 62.754 72.222 17.79 4.39 34.39 3.13
227 228 4.753662 GGGGCCCGTCCTTTTCCC 62.754 72.222 17.79 0.00 36.25 3.97
229 230 4.340246 GGCCCGTCCTTTTCCCGT 62.340 66.667 0.00 0.00 0.00 5.28
230 231 3.053896 GCCCGTCCTTTTCCCGTG 61.054 66.667 0.00 0.00 0.00 4.94
231 232 3.053896 CCCGTCCTTTTCCCGTGC 61.054 66.667 0.00 0.00 0.00 5.34
232 233 3.419759 CCGTCCTTTTCCCGTGCG 61.420 66.667 0.00 0.00 0.00 5.34
233 234 3.419759 CGTCCTTTTCCCGTGCGG 61.420 66.667 3.25 3.25 0.00 5.69
243 244 4.760047 CCGTGCGGGAGGTTGGAG 62.760 72.222 2.15 0.00 38.47 3.86
244 245 3.691342 CGTGCGGGAGGTTGGAGA 61.691 66.667 0.00 0.00 0.00 3.71
245 246 2.747686 GTGCGGGAGGTTGGAGAA 59.252 61.111 0.00 0.00 0.00 2.87
246 247 1.376037 GTGCGGGAGGTTGGAGAAG 60.376 63.158 0.00 0.00 0.00 2.85
247 248 2.269241 GCGGGAGGTTGGAGAAGG 59.731 66.667 0.00 0.00 0.00 3.46
248 249 2.291043 GCGGGAGGTTGGAGAAGGA 61.291 63.158 0.00 0.00 0.00 3.36
249 250 1.901085 CGGGAGGTTGGAGAAGGAG 59.099 63.158 0.00 0.00 0.00 3.69
250 251 1.617947 CGGGAGGTTGGAGAAGGAGG 61.618 65.000 0.00 0.00 0.00 4.30
251 252 0.547954 GGGAGGTTGGAGAAGGAGGT 60.548 60.000 0.00 0.00 0.00 3.85
252 253 0.615850 GGAGGTTGGAGAAGGAGGTG 59.384 60.000 0.00 0.00 0.00 4.00
253 254 1.645710 GAGGTTGGAGAAGGAGGTGA 58.354 55.000 0.00 0.00 0.00 4.02
254 255 1.552792 GAGGTTGGAGAAGGAGGTGAG 59.447 57.143 0.00 0.00 0.00 3.51
255 256 0.615850 GGTTGGAGAAGGAGGTGAGG 59.384 60.000 0.00 0.00 0.00 3.86
256 257 0.615850 GTTGGAGAAGGAGGTGAGGG 59.384 60.000 0.00 0.00 0.00 4.30
257 258 0.547712 TTGGAGAAGGAGGTGAGGGG 60.548 60.000 0.00 0.00 0.00 4.79
258 259 1.392534 GGAGAAGGAGGTGAGGGGA 59.607 63.158 0.00 0.00 0.00 4.81
259 260 0.689412 GGAGAAGGAGGTGAGGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
260 261 0.689412 GAGAAGGAGGTGAGGGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
261 262 1.156322 AGAAGGAGGTGAGGGGAGGA 61.156 60.000 0.00 0.00 0.00 3.71
262 263 0.252742 GAAGGAGGTGAGGGGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
263 264 0.252927 AAGGAGGTGAGGGGAGGAAG 60.253 60.000 0.00 0.00 0.00 3.46
264 265 1.690985 GGAGGTGAGGGGAGGAAGG 60.691 68.421 0.00 0.00 0.00 3.46
265 266 1.690985 GAGGTGAGGGGAGGAAGGG 60.691 68.421 0.00 0.00 0.00 3.95
266 267 2.182858 GAGGTGAGGGGAGGAAGGGA 62.183 65.000 0.00 0.00 0.00 4.20
267 268 1.004891 GGTGAGGGGAGGAAGGGAT 59.995 63.158 0.00 0.00 0.00 3.85
268 269 1.057275 GGTGAGGGGAGGAAGGGATC 61.057 65.000 0.00 0.00 0.00 3.36
269 270 0.030603 GTGAGGGGAGGAAGGGATCT 60.031 60.000 0.00 0.00 0.00 2.75
270 271 0.030705 TGAGGGGAGGAAGGGATCTG 60.031 60.000 0.00 0.00 0.00 2.90
271 272 0.266152 GAGGGGAGGAAGGGATCTGA 59.734 60.000 0.00 0.00 0.00 3.27
272 273 0.030603 AGGGGAGGAAGGGATCTGAC 60.031 60.000 0.00 0.00 0.00 3.51
273 274 1.403687 GGGGAGGAAGGGATCTGACG 61.404 65.000 0.00 0.00 0.00 4.35
274 275 0.397254 GGGAGGAAGGGATCTGACGA 60.397 60.000 0.00 0.00 0.00 4.20
275 276 1.710816 GGAGGAAGGGATCTGACGAT 58.289 55.000 0.00 0.00 0.00 3.73
276 277 1.342819 GGAGGAAGGGATCTGACGATG 59.657 57.143 0.00 0.00 0.00 3.84
277 278 0.755686 AGGAAGGGATCTGACGATGC 59.244 55.000 0.00 0.00 37.27 3.91
278 279 0.465705 GGAAGGGATCTGACGATGCA 59.534 55.000 0.00 0.00 39.50 3.96
279 280 1.539929 GGAAGGGATCTGACGATGCAG 60.540 57.143 0.00 0.00 39.50 4.41
280 281 0.467384 AAGGGATCTGACGATGCAGG 59.533 55.000 0.00 0.00 39.50 4.85
281 282 1.070445 GGGATCTGACGATGCAGGG 59.930 63.158 0.00 0.00 39.50 4.45
282 283 1.070445 GGATCTGACGATGCAGGGG 59.930 63.158 0.00 0.00 37.85 4.79
283 284 1.402896 GGATCTGACGATGCAGGGGA 61.403 60.000 0.00 0.00 37.85 4.81
284 285 0.249657 GATCTGACGATGCAGGGGAC 60.250 60.000 0.00 0.00 36.55 4.46
297 298 2.501610 GGGACCAGATCTGACGGC 59.498 66.667 24.62 10.31 0.00 5.68
298 299 2.060980 GGGACCAGATCTGACGGCT 61.061 63.158 24.62 0.58 0.00 5.52
299 300 1.142748 GGACCAGATCTGACGGCTG 59.857 63.158 24.62 8.51 0.00 4.85
301 302 2.503061 CCAGATCTGACGGCTGGG 59.497 66.667 24.62 0.21 44.24 4.45
302 303 2.503061 CAGATCTGACGGCTGGGG 59.497 66.667 18.34 0.00 0.00 4.96
303 304 3.474570 AGATCTGACGGCTGGGGC 61.475 66.667 0.00 0.00 37.82 5.80
304 305 3.474570 GATCTGACGGCTGGGGCT 61.475 66.667 0.00 0.00 38.73 5.19
320 321 3.953775 CTGGACCAGCCCAACCGT 61.954 66.667 8.99 0.00 35.47 4.83
321 322 3.491598 CTGGACCAGCCCAACCGTT 62.492 63.158 8.99 0.00 35.47 4.44
322 323 2.983592 GGACCAGCCCAACCGTTG 60.984 66.667 4.12 4.12 0.00 4.10
358 359 1.565305 CAGATCACTGCGCTAAGGAC 58.435 55.000 9.73 0.00 37.33 3.85
359 360 1.134995 CAGATCACTGCGCTAAGGACA 60.135 52.381 9.73 0.00 37.33 4.02
360 361 1.550524 AGATCACTGCGCTAAGGACAA 59.449 47.619 9.73 0.00 0.00 3.18
361 362 1.661112 GATCACTGCGCTAAGGACAAC 59.339 52.381 9.73 0.00 0.00 3.32
362 363 0.391228 TCACTGCGCTAAGGACAACA 59.609 50.000 9.73 0.00 0.00 3.33
363 364 0.512952 CACTGCGCTAAGGACAACAC 59.487 55.000 9.73 0.00 0.00 3.32
364 365 0.944311 ACTGCGCTAAGGACAACACG 60.944 55.000 9.73 0.00 0.00 4.49
365 366 2.227968 CTGCGCTAAGGACAACACGC 62.228 60.000 9.73 0.00 46.05 5.34
366 367 2.027625 GCGCTAAGGACAACACGCT 61.028 57.895 0.00 0.00 42.81 5.07
367 368 0.734942 GCGCTAAGGACAACACGCTA 60.735 55.000 0.00 0.00 42.81 4.26
368 369 1.269166 CGCTAAGGACAACACGCTAG 58.731 55.000 0.00 0.00 0.00 3.42
369 370 1.000145 GCTAAGGACAACACGCTAGC 59.000 55.000 4.06 4.06 0.00 3.42
370 371 1.404315 GCTAAGGACAACACGCTAGCT 60.404 52.381 13.93 0.00 31.23 3.32
371 372 2.159282 GCTAAGGACAACACGCTAGCTA 60.159 50.000 13.93 0.00 31.23 3.32
372 373 2.365408 AAGGACAACACGCTAGCTAC 57.635 50.000 13.93 0.00 0.00 3.58
373 374 1.546961 AGGACAACACGCTAGCTACT 58.453 50.000 13.93 0.00 0.00 2.57
374 375 2.719739 AGGACAACACGCTAGCTACTA 58.280 47.619 13.93 0.00 0.00 1.82
375 376 2.683867 AGGACAACACGCTAGCTACTAG 59.316 50.000 13.93 0.00 37.16 2.57
390 391 5.347012 GCTACTAGCTGCTAGTACTGTAC 57.653 47.826 34.30 21.36 44.35 2.90
391 392 4.084433 GCTACTAGCTGCTAGTACTGTACG 60.084 50.000 34.30 26.24 44.35 3.67
392 393 4.134379 ACTAGCTGCTAGTACTGTACGA 57.866 45.455 34.35 6.46 44.35 3.43
393 394 4.706035 ACTAGCTGCTAGTACTGTACGAT 58.294 43.478 34.35 11.21 44.35 3.73
394 395 5.851720 ACTAGCTGCTAGTACTGTACGATA 58.148 41.667 34.35 0.00 44.35 2.92
395 396 6.286758 ACTAGCTGCTAGTACTGTACGATAA 58.713 40.000 34.35 0.00 44.35 1.75
396 397 5.676532 AGCTGCTAGTACTGTACGATAAG 57.323 43.478 11.97 9.91 0.00 1.73
397 398 4.515944 AGCTGCTAGTACTGTACGATAAGG 59.484 45.833 11.97 4.46 0.00 2.69
398 399 4.514441 GCTGCTAGTACTGTACGATAAGGA 59.486 45.833 11.97 8.82 0.00 3.36
399 400 5.334260 GCTGCTAGTACTGTACGATAAGGAG 60.334 48.000 19.43 19.43 0.00 3.69
454 461 1.853963 AACTCTACCATGACTCGGCT 58.146 50.000 0.00 0.00 0.00 5.52
494 501 2.880268 CTGACTCAAATTGCCACTGACA 59.120 45.455 0.00 0.00 0.00 3.58
587 595 2.127383 CAGAAAAACCGACCGCGC 60.127 61.111 0.00 0.00 35.83 6.86
601 609 1.583451 CGCGCCATTGTCATTTCCG 60.583 57.895 0.00 0.00 0.00 4.30
631 639 0.650512 CCATACCAAACGTGCTAGCG 59.349 55.000 10.77 0.00 37.94 4.26
678 686 2.480853 TAGCACACACGTACCCGCAG 62.481 60.000 0.00 0.00 37.70 5.18
882 906 1.005097 TGGAGACAAGGCATGCAGATT 59.995 47.619 21.36 8.14 37.44 2.40
946 1016 0.740868 CCGTGCAGTACTCCACATGG 60.741 60.000 16.97 14.10 33.16 3.66
947 1017 0.246360 CGTGCAGTACTCCACATGGA 59.754 55.000 16.97 0.00 43.08 3.41
948 1018 1.134699 CGTGCAGTACTCCACATGGAT 60.135 52.381 16.97 0.00 44.46 3.41
949 1019 2.283298 GTGCAGTACTCCACATGGATG 58.717 52.381 12.21 0.00 44.46 3.51
950 1020 2.093500 GTGCAGTACTCCACATGGATGA 60.093 50.000 12.21 0.00 44.46 2.92
951 1021 2.773661 TGCAGTACTCCACATGGATGAT 59.226 45.455 0.00 0.00 44.46 2.45
952 1022 3.136763 GCAGTACTCCACATGGATGATG 58.863 50.000 0.00 0.29 44.46 3.07
953 1023 3.736720 CAGTACTCCACATGGATGATGG 58.263 50.000 0.00 0.00 44.46 3.51
954 1024 3.389002 CAGTACTCCACATGGATGATGGA 59.611 47.826 0.00 0.00 44.46 3.41
956 1026 1.893544 CTCCACATGGATGATGGAGC 58.106 55.000 14.40 0.00 44.46 4.70
957 1027 0.475475 TCCACATGGATGATGGAGCC 59.525 55.000 0.00 0.00 39.78 4.70
962 1032 2.663188 GGATGATGGAGCCGACGC 60.663 66.667 0.00 0.00 0.00 5.19
1074 1161 1.807755 CGCGTGAGTTCATCCATCCAT 60.808 52.381 0.00 0.00 0.00 3.41
1075 1162 1.869767 GCGTGAGTTCATCCATCCATC 59.130 52.381 0.00 0.00 0.00 3.51
1076 1163 2.487934 CGTGAGTTCATCCATCCATCC 58.512 52.381 0.00 0.00 0.00 3.51
1077 1164 2.487934 GTGAGTTCATCCATCCATCCG 58.512 52.381 0.00 0.00 0.00 4.18
1591 1745 3.118454 CCAAGTACACGGCGCAGG 61.118 66.667 13.26 4.07 0.00 4.85
2185 2367 0.530744 AGACGAGGCGTGAATGCTTA 59.469 50.000 0.00 0.00 41.37 3.09
2223 2405 4.275689 TGAAATGCTTGTCGATGAAGTTGT 59.724 37.500 8.46 0.00 0.00 3.32
2243 2425 2.667473 AGCCTTGCATGAATTTGCTC 57.333 45.000 0.00 0.00 43.18 4.26
2257 2439 7.223260 TGAATTTGCTCATCTTTGTCTGAAT 57.777 32.000 0.00 0.00 0.00 2.57
2319 2503 3.159472 TCATGACTTTGGAGCTTTGCAT 58.841 40.909 0.00 0.00 0.00 3.96
2469 3004 1.164662 CCATTCCGCAGATGAGGCTG 61.165 60.000 0.00 0.00 38.91 4.85
2491 3026 1.514678 TTCATGCGTTGTGTGCTCCC 61.515 55.000 0.00 0.00 0.00 4.30
2547 3082 7.664731 ACTTGTGACTAGTACTAGTAGAGCAAA 59.335 37.037 30.80 18.61 45.63 3.68
2548 3083 7.375106 TGTGACTAGTACTAGTAGAGCAAAC 57.625 40.000 30.80 18.03 45.63 2.93
2598 3134 3.942130 ATGGGTTTGCTAAAACTCTGC 57.058 42.857 3.14 0.00 45.53 4.26
2602 3138 2.488153 GGTTTGCTAAAACTCTGCCGAT 59.512 45.455 1.76 0.00 44.32 4.18
2604 3140 1.640428 TGCTAAAACTCTGCCGATCG 58.360 50.000 8.51 8.51 0.00 3.69
2613 3149 3.707793 ACTCTGCCGATCGAGATTTAAC 58.292 45.455 18.66 0.00 0.00 2.01
2626 3188 5.477291 TCGAGATTTAACCAAGTCTCAGTCT 59.523 40.000 9.60 0.00 43.96 3.24
2672 3234 3.423539 TGAAGATTTGTCCTGGACTGG 57.576 47.619 26.03 0.00 33.15 4.00
2694 3256 4.762825 CGTTCAACGGACCTCCAA 57.237 55.556 0.61 0.00 38.08 3.53
2738 3300 3.199071 ACATATCTTCCTACCGGTTGCAA 59.801 43.478 15.04 1.04 0.00 4.08
2773 3335 5.186603 ACTGATTCTAGCATCTTGTCTCACA 59.813 40.000 3.99 0.00 0.00 3.58
2780 3342 2.289320 GCATCTTGTCTCACAGGACACT 60.289 50.000 0.00 0.00 44.55 3.55
2819 3387 1.188871 TGTAGCACCCATCGGTCACA 61.189 55.000 0.00 0.00 42.04 3.58
2843 3411 1.648720 CGCCATTGATAGTTGCGGG 59.351 57.895 0.00 0.00 41.42 6.13
2864 3432 3.152341 GCTTGCAGCATATAGTCCCAAT 58.848 45.455 0.00 0.00 41.89 3.16
2927 3495 2.202295 TTTTTGTCGCTGGTTGAAGC 57.798 45.000 0.00 0.00 39.94 3.86
2928 3496 1.098869 TTTTGTCGCTGGTTGAAGCA 58.901 45.000 0.00 0.00 43.73 3.91
2929 3497 1.317613 TTTGTCGCTGGTTGAAGCAT 58.682 45.000 0.00 0.00 43.73 3.79
2930 3498 0.874390 TTGTCGCTGGTTGAAGCATC 59.126 50.000 0.00 0.00 43.73 3.91
2931 3499 0.955428 TGTCGCTGGTTGAAGCATCC 60.955 55.000 0.00 0.00 43.73 3.51
2932 3500 1.741401 TCGCTGGTTGAAGCATCCG 60.741 57.895 0.00 4.48 43.73 4.18
2933 3501 2.034879 CGCTGGTTGAAGCATCCGT 61.035 57.895 0.00 0.00 43.73 4.69
2934 3502 1.796796 GCTGGTTGAAGCATCCGTC 59.203 57.895 0.00 0.00 43.01 4.79
2935 3503 0.674895 GCTGGTTGAAGCATCCGTCT 60.675 55.000 0.00 0.00 43.01 4.18
2936 3504 1.813513 CTGGTTGAAGCATCCGTCTT 58.186 50.000 0.00 0.00 0.00 3.01
2937 3505 1.466167 CTGGTTGAAGCATCCGTCTTG 59.534 52.381 0.00 0.00 0.00 3.02
2947 3515 2.422597 CATCCGTCTTGCTGGTTGTAA 58.577 47.619 0.00 0.00 0.00 2.41
2954 3522 4.065088 GTCTTGCTGGTTGTAACATCTCA 58.935 43.478 0.00 0.00 0.00 3.27
2958 3526 4.910195 TGCTGGTTGTAACATCTCATCTT 58.090 39.130 0.00 0.00 0.00 2.40
2961 3529 5.294552 GCTGGTTGTAACATCTCATCTTACC 59.705 44.000 0.00 0.00 0.00 2.85
2979 3547 1.021390 CCGACACAACATCTGCCCTC 61.021 60.000 0.00 0.00 0.00 4.30
2984 3552 0.976641 ACAACATCTGCCCTCTTCGA 59.023 50.000 0.00 0.00 0.00 3.71
2989 3557 2.766263 ACATCTGCCCTCTTCGATTGTA 59.234 45.455 0.00 0.00 0.00 2.41
2993 3561 1.291132 GCCCTCTTCGATTGTAGCAC 58.709 55.000 0.00 0.00 0.00 4.40
3022 3590 1.511850 TCAGTCACAACATTCGCCAG 58.488 50.000 0.00 0.00 0.00 4.85
3024 3592 2.036604 TCAGTCACAACATTCGCCAGTA 59.963 45.455 0.00 0.00 0.00 2.74
3025 3593 2.413112 CAGTCACAACATTCGCCAGTAG 59.587 50.000 0.00 0.00 0.00 2.57
3130 3700 0.102481 CTAGCCGTGCCACTCGTAAT 59.898 55.000 0.00 0.00 0.00 1.89
3131 3701 0.179121 TAGCCGTGCCACTCGTAATG 60.179 55.000 0.00 0.00 0.00 1.90
3137 3707 2.550978 GTGCCACTCGTAATGCTACAT 58.449 47.619 0.00 0.00 0.00 2.29
3183 3753 4.144534 ACTTCGTTAAGTCTCAGTCGAC 57.855 45.455 7.70 7.70 42.42 4.20
3201 3771 4.322804 GTCGACTGAGTTATAAACACACCG 59.677 45.833 8.70 0.00 0.00 4.94
3205 3775 6.748658 CGACTGAGTTATAAACACACCGATTA 59.251 38.462 0.00 0.00 30.52 1.75
3206 3776 7.274033 CGACTGAGTTATAAACACACCGATTAA 59.726 37.037 0.00 0.00 30.52 1.40
3207 3777 9.095065 GACTGAGTTATAAACACACCGATTAAT 57.905 33.333 0.00 0.00 0.00 1.40
3208 3778 9.444600 ACTGAGTTATAAACACACCGATTAATT 57.555 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.285523 TTACGGCCGGTCGAGGTTG 62.286 63.158 38.47 4.83 0.00 3.77
15 16 2.990967 TTACGGCCGGTCGAGGTT 60.991 61.111 38.47 16.04 0.00 3.50
16 17 3.752339 GTTACGGCCGGTCGAGGT 61.752 66.667 38.47 16.48 0.00 3.85
17 18 4.503314 GGTTACGGCCGGTCGAGG 62.503 72.222 38.47 6.69 0.00 4.63
18 19 3.072486 ATGGTTACGGCCGGTCGAG 62.072 63.158 38.47 7.62 0.00 4.04
19 20 3.069946 ATGGTTACGGCCGGTCGA 61.070 61.111 38.47 16.59 0.00 4.20
20 21 2.888534 CATGGTTACGGCCGGTCG 60.889 66.667 29.88 29.88 0.00 4.79
21 22 2.512974 CCATGGTTACGGCCGGTC 60.513 66.667 31.76 18.32 0.00 4.79
22 23 4.789123 GCCATGGTTACGGCCGGT 62.789 66.667 31.76 17.55 42.82 5.28
27 28 3.505184 GTGCGGCCATGGTTACGG 61.505 66.667 21.28 8.79 0.00 4.02
28 29 3.860125 CGTGCGGCCATGGTTACG 61.860 66.667 14.67 16.38 0.00 3.18
29 30 4.174129 GCGTGCGGCCATGGTTAC 62.174 66.667 14.67 6.67 34.80 2.50
30 31 4.402528 AGCGTGCGGCCATGGTTA 62.403 61.111 14.67 0.00 45.17 2.85
41 42 3.515286 ATGGATGCAGCAGCGTGC 61.515 61.111 7.90 7.90 46.98 5.34
42 43 2.407616 CATGGATGCAGCAGCGTG 59.592 61.111 3.51 2.33 46.23 5.34
43 44 2.827190 CCATGGATGCAGCAGCGT 60.827 61.111 5.56 0.00 46.23 5.07
44 45 2.515290 TCCATGGATGCAGCAGCG 60.515 61.111 11.44 0.00 46.23 5.18
45 46 2.194212 CCTCCATGGATGCAGCAGC 61.194 63.158 16.63 0.62 38.76 5.25
46 47 0.395311 AACCTCCATGGATGCAGCAG 60.395 55.000 16.63 0.88 39.71 4.24
47 48 0.040058 AAACCTCCATGGATGCAGCA 59.960 50.000 16.63 0.00 39.71 4.41
48 49 0.743097 GAAACCTCCATGGATGCAGC 59.257 55.000 16.63 0.00 39.71 5.25
49 50 2.022195 CTGAAACCTCCATGGATGCAG 58.978 52.381 16.63 11.24 39.71 4.41
50 51 1.634973 TCTGAAACCTCCATGGATGCA 59.365 47.619 16.63 4.44 39.71 3.96
51 52 2.425143 TCTGAAACCTCCATGGATGC 57.575 50.000 16.63 0.00 39.71 3.91
52 53 4.081406 TGTTTCTGAAACCTCCATGGATG 58.919 43.478 25.66 15.64 40.67 3.51
53 54 4.082125 GTGTTTCTGAAACCTCCATGGAT 58.918 43.478 25.66 0.00 40.67 3.41
54 55 3.117701 TGTGTTTCTGAAACCTCCATGGA 60.118 43.478 25.66 15.27 40.67 3.41
55 56 3.004734 GTGTGTTTCTGAAACCTCCATGG 59.995 47.826 25.66 4.97 40.67 3.66
56 57 3.303990 CGTGTGTTTCTGAAACCTCCATG 60.304 47.826 25.66 20.03 40.67 3.66
57 58 2.878406 CGTGTGTTTCTGAAACCTCCAT 59.122 45.455 25.66 0.00 40.67 3.41
58 59 2.093394 TCGTGTGTTTCTGAAACCTCCA 60.093 45.455 25.66 17.82 40.67 3.86
59 60 2.557317 TCGTGTGTTTCTGAAACCTCC 58.443 47.619 25.66 15.88 40.67 4.30
60 61 3.869246 TCTTCGTGTGTTTCTGAAACCTC 59.131 43.478 25.66 19.42 40.67 3.85
61 62 3.621715 GTCTTCGTGTGTTTCTGAAACCT 59.378 43.478 25.66 0.00 40.67 3.50
62 63 3.543460 CGTCTTCGTGTGTTTCTGAAACC 60.543 47.826 25.66 18.34 40.67 3.27
63 64 3.305094 TCGTCTTCGTGTGTTTCTGAAAC 59.695 43.478 22.94 22.94 38.79 2.78
64 65 3.305094 GTCGTCTTCGTGTGTTTCTGAAA 59.695 43.478 0.00 0.00 38.33 2.69
65 66 2.855963 GTCGTCTTCGTGTGTTTCTGAA 59.144 45.455 0.00 0.00 38.33 3.02
66 67 2.159352 TGTCGTCTTCGTGTGTTTCTGA 60.159 45.455 0.00 0.00 38.33 3.27
67 68 2.190161 TGTCGTCTTCGTGTGTTTCTG 58.810 47.619 0.00 0.00 38.33 3.02
68 69 2.572191 TGTCGTCTTCGTGTGTTTCT 57.428 45.000 0.00 0.00 38.33 2.52
69 70 3.364023 CCTATGTCGTCTTCGTGTGTTTC 59.636 47.826 0.00 0.00 38.33 2.78
70 71 3.243636 ACCTATGTCGTCTTCGTGTGTTT 60.244 43.478 0.00 0.00 38.33 2.83
71 72 2.295349 ACCTATGTCGTCTTCGTGTGTT 59.705 45.455 0.00 0.00 38.33 3.32
72 73 1.884579 ACCTATGTCGTCTTCGTGTGT 59.115 47.619 0.00 0.00 38.33 3.72
73 74 2.095415 TCACCTATGTCGTCTTCGTGTG 60.095 50.000 0.00 0.00 38.33 3.82
74 75 2.156917 TCACCTATGTCGTCTTCGTGT 58.843 47.619 0.00 0.00 38.33 4.49
75 76 2.478031 CCTCACCTATGTCGTCTTCGTG 60.478 54.545 0.00 0.00 38.33 4.35
76 77 1.743958 CCTCACCTATGTCGTCTTCGT 59.256 52.381 0.00 0.00 38.33 3.85
77 78 1.065701 CCCTCACCTATGTCGTCTTCG 59.934 57.143 0.00 0.00 38.55 3.79
78 79 1.202428 GCCCTCACCTATGTCGTCTTC 60.202 57.143 0.00 0.00 0.00 2.87
79 80 0.824759 GCCCTCACCTATGTCGTCTT 59.175 55.000 0.00 0.00 0.00 3.01
80 81 1.384989 CGCCCTCACCTATGTCGTCT 61.385 60.000 0.00 0.00 0.00 4.18
81 82 1.065928 CGCCCTCACCTATGTCGTC 59.934 63.158 0.00 0.00 0.00 4.20
82 83 2.423898 CCGCCCTCACCTATGTCGT 61.424 63.158 0.00 0.00 0.00 4.34
83 84 2.417516 CCGCCCTCACCTATGTCG 59.582 66.667 0.00 0.00 0.00 4.35
84 85 2.822399 CCCGCCCTCACCTATGTC 59.178 66.667 0.00 0.00 0.00 3.06
85 86 3.480133 GCCCGCCCTCACCTATGT 61.480 66.667 0.00 0.00 0.00 2.29
86 87 4.609018 CGCCCGCCCTCACCTATG 62.609 72.222 0.00 0.00 0.00 2.23
87 88 4.853142 TCGCCCGCCCTCACCTAT 62.853 66.667 0.00 0.00 0.00 2.57
121 122 4.527157 GTCGGTCGCCTACGGTCG 62.527 72.222 0.00 0.00 40.63 4.79
122 123 4.527157 CGTCGGTCGCCTACGGTC 62.527 72.222 12.77 0.00 38.72 4.79
156 157 4.200283 CTCGCCTCGCCTCCTCAC 62.200 72.222 0.00 0.00 0.00 3.51
207 208 3.640257 GAAAAGGACGGGCCCCCTC 62.640 68.421 19.11 12.40 37.37 4.30
208 209 3.658422 GAAAAGGACGGGCCCCCT 61.658 66.667 18.66 15.85 37.37 4.79
209 210 4.753662 GGAAAAGGACGGGCCCCC 62.754 72.222 18.66 13.35 37.37 5.40
210 211 4.753662 GGGAAAAGGACGGGCCCC 62.754 72.222 18.66 1.92 37.37 5.80
212 213 4.340246 ACGGGAAAAGGACGGGCC 62.340 66.667 0.00 0.00 0.00 5.80
213 214 3.053896 CACGGGAAAAGGACGGGC 61.054 66.667 0.00 0.00 0.00 6.13
214 215 3.053896 GCACGGGAAAAGGACGGG 61.054 66.667 0.00 0.00 0.00 5.28
215 216 3.419759 CGCACGGGAAAAGGACGG 61.420 66.667 0.00 0.00 0.00 4.79
216 217 3.419759 CCGCACGGGAAAAGGACG 61.420 66.667 0.00 0.00 38.47 4.79
226 227 4.760047 CTCCAACCTCCCGCACGG 62.760 72.222 1.02 1.02 0.00 4.94
227 228 3.234630 TTCTCCAACCTCCCGCACG 62.235 63.158 0.00 0.00 0.00 5.34
228 229 1.376037 CTTCTCCAACCTCCCGCAC 60.376 63.158 0.00 0.00 0.00 5.34
229 230 2.592993 CCTTCTCCAACCTCCCGCA 61.593 63.158 0.00 0.00 0.00 5.69
230 231 2.245438 CTCCTTCTCCAACCTCCCGC 62.245 65.000 0.00 0.00 0.00 6.13
231 232 1.617947 CCTCCTTCTCCAACCTCCCG 61.618 65.000 0.00 0.00 0.00 5.14
232 233 0.547954 ACCTCCTTCTCCAACCTCCC 60.548 60.000 0.00 0.00 0.00 4.30
233 234 0.615850 CACCTCCTTCTCCAACCTCC 59.384 60.000 0.00 0.00 0.00 4.30
234 235 1.552792 CTCACCTCCTTCTCCAACCTC 59.447 57.143 0.00 0.00 0.00 3.85
235 236 1.650528 CTCACCTCCTTCTCCAACCT 58.349 55.000 0.00 0.00 0.00 3.50
236 237 0.615850 CCTCACCTCCTTCTCCAACC 59.384 60.000 0.00 0.00 0.00 3.77
237 238 0.615850 CCCTCACCTCCTTCTCCAAC 59.384 60.000 0.00 0.00 0.00 3.77
238 239 0.547712 CCCCTCACCTCCTTCTCCAA 60.548 60.000 0.00 0.00 0.00 3.53
239 240 1.081092 CCCCTCACCTCCTTCTCCA 59.919 63.158 0.00 0.00 0.00 3.86
240 241 0.689412 CTCCCCTCACCTCCTTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
241 242 0.689412 CCTCCCCTCACCTCCTTCTC 60.689 65.000 0.00 0.00 0.00 2.87
242 243 1.156322 TCCTCCCCTCACCTCCTTCT 61.156 60.000 0.00 0.00 0.00 2.85
243 244 0.252742 TTCCTCCCCTCACCTCCTTC 60.253 60.000 0.00 0.00 0.00 3.46
244 245 0.252927 CTTCCTCCCCTCACCTCCTT 60.253 60.000 0.00 0.00 0.00 3.36
245 246 1.394151 CTTCCTCCCCTCACCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
246 247 1.690985 CCTTCCTCCCCTCACCTCC 60.691 68.421 0.00 0.00 0.00 4.30
247 248 1.690985 CCCTTCCTCCCCTCACCTC 60.691 68.421 0.00 0.00 0.00 3.85
248 249 1.541168 ATCCCTTCCTCCCCTCACCT 61.541 60.000 0.00 0.00 0.00 4.00
249 250 1.004891 ATCCCTTCCTCCCCTCACC 59.995 63.158 0.00 0.00 0.00 4.02
250 251 0.030603 AGATCCCTTCCTCCCCTCAC 60.031 60.000 0.00 0.00 0.00 3.51
251 252 0.030705 CAGATCCCTTCCTCCCCTCA 60.031 60.000 0.00 0.00 0.00 3.86
252 253 0.266152 TCAGATCCCTTCCTCCCCTC 59.734 60.000 0.00 0.00 0.00 4.30
253 254 0.030603 GTCAGATCCCTTCCTCCCCT 60.031 60.000 0.00 0.00 0.00 4.79
254 255 1.403687 CGTCAGATCCCTTCCTCCCC 61.404 65.000 0.00 0.00 0.00 4.81
255 256 0.397254 TCGTCAGATCCCTTCCTCCC 60.397 60.000 0.00 0.00 0.00 4.30
256 257 1.342819 CATCGTCAGATCCCTTCCTCC 59.657 57.143 0.00 0.00 34.23 4.30
257 258 1.270041 GCATCGTCAGATCCCTTCCTC 60.270 57.143 0.00 0.00 34.23 3.71
258 259 0.755686 GCATCGTCAGATCCCTTCCT 59.244 55.000 0.00 0.00 34.23 3.36
259 260 0.465705 TGCATCGTCAGATCCCTTCC 59.534 55.000 0.00 0.00 34.23 3.46
260 261 1.539929 CCTGCATCGTCAGATCCCTTC 60.540 57.143 0.00 0.00 36.19 3.46
261 262 0.467384 CCTGCATCGTCAGATCCCTT 59.533 55.000 0.00 0.00 36.19 3.95
262 263 1.406065 CCCTGCATCGTCAGATCCCT 61.406 60.000 0.00 0.00 36.19 4.20
263 264 1.070445 CCCTGCATCGTCAGATCCC 59.930 63.158 0.00 0.00 36.19 3.85
264 265 1.070445 CCCCTGCATCGTCAGATCC 59.930 63.158 0.00 0.00 36.19 3.36
265 266 0.249657 GTCCCCTGCATCGTCAGATC 60.250 60.000 0.00 0.00 36.19 2.75
266 267 1.690219 GGTCCCCTGCATCGTCAGAT 61.690 60.000 0.00 0.00 36.19 2.90
267 268 2.359169 GGTCCCCTGCATCGTCAGA 61.359 63.158 0.00 0.00 36.19 3.27
268 269 2.187946 GGTCCCCTGCATCGTCAG 59.812 66.667 0.00 0.00 0.00 3.51
269 270 2.606213 TGGTCCCCTGCATCGTCA 60.606 61.111 0.00 0.00 0.00 4.35
270 271 1.690219 ATCTGGTCCCCTGCATCGTC 61.690 60.000 0.00 0.00 0.00 4.20
271 272 1.690219 GATCTGGTCCCCTGCATCGT 61.690 60.000 0.00 0.00 0.00 3.73
272 273 1.070445 GATCTGGTCCCCTGCATCG 59.930 63.158 0.00 0.00 0.00 3.84
273 274 0.108207 CAGATCTGGTCCCCTGCATC 59.892 60.000 15.38 0.00 0.00 3.91
274 275 0.326904 TCAGATCTGGTCCCCTGCAT 60.327 55.000 22.42 0.00 0.00 3.96
275 276 1.080907 TCAGATCTGGTCCCCTGCA 59.919 57.895 22.42 0.00 0.00 4.41
276 277 1.524482 GTCAGATCTGGTCCCCTGC 59.476 63.158 22.42 0.35 0.00 4.85
277 278 1.680522 CCGTCAGATCTGGTCCCCTG 61.681 65.000 22.42 5.09 0.00 4.45
278 279 1.381872 CCGTCAGATCTGGTCCCCT 60.382 63.158 22.42 0.00 0.00 4.79
279 280 3.095347 GCCGTCAGATCTGGTCCCC 62.095 68.421 22.42 4.48 0.00 4.81
280 281 2.060980 AGCCGTCAGATCTGGTCCC 61.061 63.158 22.42 9.16 0.00 4.46
281 282 1.142748 CAGCCGTCAGATCTGGTCC 59.857 63.158 22.42 9.90 0.00 4.46
282 283 1.142748 CCAGCCGTCAGATCTGGTC 59.857 63.158 22.42 14.32 41.76 4.02
283 284 2.362369 CCCAGCCGTCAGATCTGGT 61.362 63.158 22.42 0.00 44.41 4.00
284 285 2.503061 CCCAGCCGTCAGATCTGG 59.497 66.667 22.42 8.05 45.24 3.86
285 286 2.503061 CCCCAGCCGTCAGATCTG 59.497 66.667 17.07 17.07 0.00 2.90
286 287 3.474570 GCCCCAGCCGTCAGATCT 61.475 66.667 0.00 0.00 0.00 2.75
287 288 3.474570 AGCCCCAGCCGTCAGATC 61.475 66.667 0.00 0.00 41.25 2.75
288 289 3.790437 CAGCCCCAGCCGTCAGAT 61.790 66.667 0.00 0.00 41.25 2.90
303 304 3.491598 AACGGTTGGGCTGGTCCAG 62.492 63.158 15.15 15.15 38.17 3.86
304 305 3.494254 AACGGTTGGGCTGGTCCA 61.494 61.111 0.00 0.00 36.21 4.02
305 306 2.983592 CAACGGTTGGGCTGGTCC 60.984 66.667 13.03 0.00 0.00 4.46
339 340 1.134995 TGTCCTTAGCGCAGTGATCTG 60.135 52.381 11.47 0.00 43.87 2.90
340 341 1.186200 TGTCCTTAGCGCAGTGATCT 58.814 50.000 11.47 0.00 0.00 2.75
341 342 1.661112 GTTGTCCTTAGCGCAGTGATC 59.339 52.381 11.47 0.00 0.00 2.92
342 343 1.001974 TGTTGTCCTTAGCGCAGTGAT 59.998 47.619 11.47 0.00 0.00 3.06
343 344 0.391228 TGTTGTCCTTAGCGCAGTGA 59.609 50.000 11.47 0.00 0.00 3.41
344 345 0.512952 GTGTTGTCCTTAGCGCAGTG 59.487 55.000 11.47 0.00 0.00 3.66
345 346 0.944311 CGTGTTGTCCTTAGCGCAGT 60.944 55.000 11.47 0.00 0.00 4.40
346 347 1.781555 CGTGTTGTCCTTAGCGCAG 59.218 57.895 11.47 0.00 0.00 5.18
347 348 2.314647 GCGTGTTGTCCTTAGCGCA 61.315 57.895 11.47 0.00 43.62 6.09
348 349 0.734942 TAGCGTGTTGTCCTTAGCGC 60.735 55.000 0.00 0.00 44.36 5.92
349 350 1.269166 CTAGCGTGTTGTCCTTAGCG 58.731 55.000 0.00 0.00 0.00 4.26
350 351 1.000145 GCTAGCGTGTTGTCCTTAGC 59.000 55.000 0.00 0.00 0.00 3.09
351 352 2.656560 AGCTAGCGTGTTGTCCTTAG 57.343 50.000 9.55 0.00 0.00 2.18
352 353 3.087031 AGTAGCTAGCGTGTTGTCCTTA 58.913 45.455 9.55 0.00 0.00 2.69
353 354 1.893801 AGTAGCTAGCGTGTTGTCCTT 59.106 47.619 9.55 0.00 0.00 3.36
354 355 1.546961 AGTAGCTAGCGTGTTGTCCT 58.453 50.000 9.55 0.00 0.00 3.85
355 356 3.067721 CTAGTAGCTAGCGTGTTGTCC 57.932 52.381 9.55 0.00 0.00 4.02
368 369 4.084433 CGTACAGTACTAGCAGCTAGTAGC 60.084 50.000 33.79 27.23 46.18 3.58
369 370 5.288015 TCGTACAGTACTAGCAGCTAGTAG 58.712 45.833 33.79 26.44 46.18 2.57
370 371 5.268118 TCGTACAGTACTAGCAGCTAGTA 57.732 43.478 30.83 30.83 44.35 1.82
372 373 6.128499 CCTTATCGTACAGTACTAGCAGCTAG 60.128 46.154 25.51 25.51 39.72 3.42
373 374 5.699915 CCTTATCGTACAGTACTAGCAGCTA 59.300 44.000 9.10 1.13 0.00 3.32
374 375 4.515944 CCTTATCGTACAGTACTAGCAGCT 59.484 45.833 9.10 0.00 0.00 4.24
375 376 4.514441 TCCTTATCGTACAGTACTAGCAGC 59.486 45.833 9.10 0.00 0.00 5.25
376 377 5.759273 ACTCCTTATCGTACAGTACTAGCAG 59.241 44.000 9.10 0.54 0.00 4.24
377 378 5.678583 ACTCCTTATCGTACAGTACTAGCA 58.321 41.667 9.10 0.00 0.00 3.49
378 379 6.928492 AGTACTCCTTATCGTACAGTACTAGC 59.072 42.308 14.81 0.00 45.10 3.42
379 380 9.973450 TTAGTACTCCTTATCGTACAGTACTAG 57.027 37.037 18.74 0.00 46.38 2.57
382 383 9.103861 AGTTTAGTACTCCTTATCGTACAGTAC 57.896 37.037 0.00 0.00 39.76 2.73
383 384 9.672673 AAGTTTAGTACTCCTTATCGTACAGTA 57.327 33.333 0.00 0.00 38.69 2.74
384 385 8.572855 AAGTTTAGTACTCCTTATCGTACAGT 57.427 34.615 0.00 0.00 38.69 3.55
385 386 9.286946 CAAAGTTTAGTACTCCTTATCGTACAG 57.713 37.037 0.00 0.00 38.69 2.74
386 387 8.796475 ACAAAGTTTAGTACTCCTTATCGTACA 58.204 33.333 0.00 0.00 38.69 2.90
387 388 9.283420 GACAAAGTTTAGTACTCCTTATCGTAC 57.717 37.037 0.00 0.00 35.54 3.67
388 389 9.013229 TGACAAAGTTTAGTACTCCTTATCGTA 57.987 33.333 0.00 0.00 35.54 3.43
389 390 7.811713 GTGACAAAGTTTAGTACTCCTTATCGT 59.188 37.037 0.00 0.00 35.54 3.73
390 391 7.008086 CGTGACAAAGTTTAGTACTCCTTATCG 59.992 40.741 0.00 0.00 35.54 2.92
391 392 7.811713 ACGTGACAAAGTTTAGTACTCCTTATC 59.188 37.037 0.00 3.50 35.54 1.75
392 393 7.664758 ACGTGACAAAGTTTAGTACTCCTTAT 58.335 34.615 0.00 0.00 35.54 1.73
393 394 7.042797 ACGTGACAAAGTTTAGTACTCCTTA 57.957 36.000 0.00 0.00 35.54 2.69
394 395 5.910614 ACGTGACAAAGTTTAGTACTCCTT 58.089 37.500 0.00 0.00 35.54 3.36
395 396 5.526506 ACGTGACAAAGTTTAGTACTCCT 57.473 39.130 0.00 0.00 35.54 3.69
396 397 7.811713 AGATAACGTGACAAAGTTTAGTACTCC 59.188 37.037 0.00 0.00 35.54 3.85
397 398 8.739649 AGATAACGTGACAAAGTTTAGTACTC 57.260 34.615 0.00 0.00 35.54 2.59
398 399 9.617975 GTAGATAACGTGACAAAGTTTAGTACT 57.382 33.333 0.00 0.00 39.32 2.73
399 400 9.617975 AGTAGATAACGTGACAAAGTTTAGTAC 57.382 33.333 0.00 0.00 0.00 2.73
454 461 2.805671 CAGATTTGTGCACGTGGTCTTA 59.194 45.455 18.88 0.00 0.00 2.10
494 501 2.093500 TCTTGAGCTATGTCCGTGCAAT 60.093 45.455 0.00 0.00 0.00 3.56
587 595 0.109365 TTGCGCGGAAATGACAATGG 60.109 50.000 11.75 0.00 0.00 3.16
601 609 1.455248 TTGGTATGGGTAAGTTGCGC 58.545 50.000 0.00 0.00 0.00 6.09
631 639 3.258971 ACTATGGCAAAGAGACAGCTC 57.741 47.619 0.00 0.00 39.86 4.09
638 646 4.207891 ACCACACTACTATGGCAAAGAG 57.792 45.455 0.00 0.00 39.84 2.85
678 686 1.499056 CTGAGAACCGTGCACATGC 59.501 57.895 18.64 2.42 42.50 4.06
882 906 2.031919 GTGGACGGGTCACATGCA 59.968 61.111 0.75 0.00 35.39 3.96
955 1025 2.663188 GATGGATCCAGCGTCGGC 60.663 66.667 21.33 0.00 40.37 5.54
956 1026 1.592669 GTGATGGATCCAGCGTCGG 60.593 63.158 24.26 0.00 34.72 4.79
957 1027 1.592669 GGTGATGGATCCAGCGTCG 60.593 63.158 24.26 0.00 34.72 5.12
962 1032 1.281199 TGGGTGGGTGATGGATCCAG 61.281 60.000 21.33 0.00 0.00 3.86
993 1075 1.468520 TCACGTACTTGTACCCGTAGC 59.531 52.381 5.47 0.00 31.42 3.58
1203 1293 2.847234 TTGGTGCACGGGGAGAGT 60.847 61.111 11.45 0.00 0.00 3.24
1257 1378 4.057428 GCGACCACCTCAGAGCGT 62.057 66.667 0.00 0.00 0.00 5.07
2185 2367 4.468510 AGCATTTCATCACCATGTTCCAAT 59.531 37.500 0.00 0.00 0.00 3.16
2319 2503 4.761227 TGCATGAACAGATAAGCAAACTCA 59.239 37.500 0.00 0.00 0.00 3.41
2359 2543 2.349912 GGTCAGCAAAGTTCGCTTCTTC 60.350 50.000 0.00 0.00 37.72 2.87
2367 2551 0.169009 GGCATCGGTCAGCAAAGTTC 59.831 55.000 0.00 0.00 0.00 3.01
2469 3004 0.588252 AGCACACAACGCATGAAGAC 59.412 50.000 0.00 0.00 0.00 3.01
2579 3115 1.960689 GGCAGAGTTTTAGCAAACCCA 59.039 47.619 0.00 0.00 43.08 4.51
2598 3134 4.683832 AGACTTGGTTAAATCTCGATCGG 58.316 43.478 16.41 6.26 0.00 4.18
2602 3138 5.477291 AGACTGAGACTTGGTTAAATCTCGA 59.523 40.000 0.00 0.00 40.45 4.04
2604 3140 7.757624 CAGTAGACTGAGACTTGGTTAAATCTC 59.242 40.741 3.45 0.00 46.59 2.75
2613 3149 3.883830 ATGCAGTAGACTGAGACTTGG 57.116 47.619 13.87 0.00 46.59 3.61
2626 3188 5.289595 CAAAGATCTAACGGCTATGCAGTA 58.710 41.667 0.00 0.00 35.69 2.74
2694 3256 4.727507 TGCAAACAGTGGTACAAAATGT 57.272 36.364 0.00 0.00 44.16 2.71
2738 3300 6.782082 TGCTAGAATCAGTAAGACAGATGT 57.218 37.500 0.00 0.00 0.00 3.06
2773 3335 1.958288 AGGGCAGATGTTAGTGTCCT 58.042 50.000 0.00 0.00 44.26 3.85
2780 3342 0.454600 GTCGACGAGGGCAGATGTTA 59.545 55.000 0.00 0.00 0.00 2.41
2819 3387 2.358898 GCAACTATCAATGGCGGATGTT 59.641 45.455 0.00 0.00 0.00 2.71
2864 3432 1.134640 ACACAACAGACGCTACAACCA 60.135 47.619 0.00 0.00 0.00 3.67
2916 3484 0.674895 AGACGGATGCTTCAACCAGC 60.675 55.000 1.64 0.00 40.55 4.85
2917 3485 1.466167 CAAGACGGATGCTTCAACCAG 59.534 52.381 1.64 0.00 0.00 4.00
2918 3486 1.522668 CAAGACGGATGCTTCAACCA 58.477 50.000 1.64 0.00 0.00 3.67
2919 3487 0.169009 GCAAGACGGATGCTTCAACC 59.831 55.000 1.64 0.00 40.64 3.77
2920 3488 3.683581 GCAAGACGGATGCTTCAAC 57.316 52.632 1.64 0.00 40.64 3.18
2926 3494 1.237285 ACAACCAGCAAGACGGATGC 61.237 55.000 1.61 1.61 44.15 3.91
2927 3495 2.093306 TACAACCAGCAAGACGGATG 57.907 50.000 0.00 0.00 0.00 3.51
2928 3496 2.224426 TGTTACAACCAGCAAGACGGAT 60.224 45.455 0.00 0.00 0.00 4.18
2929 3497 1.139256 TGTTACAACCAGCAAGACGGA 59.861 47.619 0.00 0.00 0.00 4.69
2930 3498 1.588674 TGTTACAACCAGCAAGACGG 58.411 50.000 0.00 0.00 0.00 4.79
2931 3499 3.067106 AGATGTTACAACCAGCAAGACG 58.933 45.455 0.00 0.00 0.00 4.18
2932 3500 4.065088 TGAGATGTTACAACCAGCAAGAC 58.935 43.478 0.00 0.00 0.00 3.01
2933 3501 4.350368 TGAGATGTTACAACCAGCAAGA 57.650 40.909 0.00 0.00 0.00 3.02
2934 3502 4.940046 AGATGAGATGTTACAACCAGCAAG 59.060 41.667 0.00 0.00 0.00 4.01
2935 3503 4.910195 AGATGAGATGTTACAACCAGCAA 58.090 39.130 0.00 0.00 0.00 3.91
2936 3504 4.558226 AGATGAGATGTTACAACCAGCA 57.442 40.909 0.00 0.00 0.00 4.41
2937 3505 5.294552 GGTAAGATGAGATGTTACAACCAGC 59.705 44.000 6.10 0.00 39.86 4.85
2947 3515 4.021456 TGTTGTGTCGGTAAGATGAGATGT 60.021 41.667 0.00 0.00 0.00 3.06
2954 3522 3.262420 GCAGATGTTGTGTCGGTAAGAT 58.738 45.455 0.00 0.00 0.00 2.40
2958 3526 0.036765 GGGCAGATGTTGTGTCGGTA 60.037 55.000 0.00 0.00 0.00 4.02
2961 3529 0.036952 AGAGGGCAGATGTTGTGTCG 60.037 55.000 0.00 0.00 0.00 4.35
2979 3547 2.535984 GGATGACGTGCTACAATCGAAG 59.464 50.000 0.00 0.00 0.00 3.79
2984 3552 2.170397 TGATGGGATGACGTGCTACAAT 59.830 45.455 0.00 0.00 0.00 2.71
2989 3557 0.176680 GACTGATGGGATGACGTGCT 59.823 55.000 0.00 0.00 0.00 4.40
2993 3561 2.002586 GTTGTGACTGATGGGATGACG 58.997 52.381 0.00 0.00 0.00 4.35
3022 3590 4.508124 GTGACTATATGCTGCAACCACTAC 59.492 45.833 6.36 0.00 0.00 2.73
3024 3592 3.055167 TGTGACTATATGCTGCAACCACT 60.055 43.478 6.36 0.00 0.00 4.00
3025 3593 3.270027 TGTGACTATATGCTGCAACCAC 58.730 45.455 6.36 9.05 0.00 4.16
3096 3664 3.006940 CGGCTAGATGCTACAACCAAAA 58.993 45.455 0.00 0.00 42.39 2.44
3176 3746 5.345202 GGTGTGTTTATAACTCAGTCGACTG 59.655 44.000 34.76 34.76 45.08 3.51
3180 3750 4.478699 TCGGTGTGTTTATAACTCAGTCG 58.521 43.478 0.00 0.00 35.77 4.18


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

AutoCloner maintained by Alex Coulton.