Multiple sequence alignment - TraesCS4A01G398500

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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 TraesCS4A01G398500 chr4A 100.000 3510 0 0 1 3510 673487922 673491431 0.000000e+00 6482.0
1 TraesCS4A01G398500 chr4A 89.895 762 56 15 2764 3510 646019828 646019073 0.000000e+00 961.0
2 TraesCS4A01G398500 chr4A 91.429 385 26 4 3133 3510 687922166 687922550 4.010000e-144 521.0
3 TraesCS4A01G398500 chr4A 91.169 385 26 5 3133 3510 687816324 687816707 1.870000e-142 516.0
4 TraesCS4A01G398500 chr4A 90.909 385 27 5 3133 3510 687895384 687895767 8.690000e-141 510.0
5 TraesCS4A01G398500 chr4A 88.163 245 19 8 3273 3510 688047271 688047030 2.060000e-72 283.0
6 TraesCS4A01G398500 chr4A 88.987 227 19 5 3286 3510 687816933 687817155 3.450000e-70 276.0
7 TraesCS4A01G398500 chr4A 84.980 253 22 8 2777 3024 688047983 688047742 3.500000e-60 243.0
8 TraesCS4A01G398500 chr4A 81.818 165 30 0 1082 1246 673675467 673675631 4.720000e-29 139.0
9 TraesCS4A01G398500 chr7D 97.184 1101 28 2 1517 2614 56954834 56955934 0.000000e+00 1858.0
10 TraesCS4A01G398500 chr7D 91.153 1266 95 11 252 1507 56953426 56954684 0.000000e+00 1701.0
11 TraesCS4A01G398500 chr7D 81.865 193 25 9 253 442 611009747 611009562 1.690000e-33 154.0
12 TraesCS4A01G398500 chr7D 81.481 189 29 5 254 439 484347794 484347979 2.180000e-32 150.0
13 TraesCS4A01G398500 chr7D 90.909 88 7 1 2683 2770 56955920 56956006 2.210000e-22 117.0
14 TraesCS4A01G398500 chr7A 93.465 1010 64 2 1561 2569 61434598 61435606 0.000000e+00 1498.0
15 TraesCS4A01G398500 chr7A 91.349 786 61 4 737 1517 61433675 61434458 0.000000e+00 1068.0
16 TraesCS4A01G398500 chr7A 89.474 190 16 4 2765 2954 587079750 587079565 1.630000e-58 237.0
17 TraesCS4A01G398500 chr7A 85.632 174 20 3 567 735 61431276 61431449 1.000000e-40 178.0
18 TraesCS4A01G398500 chrUn 90.810 457 28 9 3064 3510 249794611 249794159 1.800000e-167 599.0
19 TraesCS4A01G398500 chrUn 77.737 539 92 17 837 1359 369145297 369145823 4.400000e-79 305.0
20 TraesCS4A01G398500 chr2B 90.497 463 30 9 3058 3510 53931233 53931691 1.800000e-167 599.0
21 TraesCS4A01G398500 chr2B 77.310 855 147 31 837 1658 2072679 2071839 8.880000e-126 460.0
22 TraesCS4A01G398500 chr2B 82.584 178 28 3 275 451 45638261 45638086 1.690000e-33 154.0
23 TraesCS4A01G398500 chr3D 87.751 498 41 13 2899 3377 583872519 583872023 6.580000e-157 564.0
24 TraesCS4A01G398500 chr3D 92.478 226 13 4 2771 2996 583872738 583872517 1.570000e-83 320.0
25 TraesCS4A01G398500 chr3D 81.443 194 27 7 253 442 583468449 583468261 2.180000e-32 150.0
26 TraesCS4A01G398500 chr3B 88.769 463 32 14 2902 3346 775372170 775371710 1.840000e-152 549.0
27 TraesCS4A01G398500 chr3B 96.311 244 7 1 1 244 603415412 603415653 1.960000e-107 399.0
28 TraesCS4A01G398500 chr3B 95.455 242 8 1 1 242 143590860 143590622 1.980000e-102 383.0
29 TraesCS4A01G398500 chr3B 94.672 244 10 1 1 244 542689009 542689249 3.310000e-100 375.0
30 TraesCS4A01G398500 chr3B 90.323 186 16 2 2765 2949 558397212 558397028 3.500000e-60 243.0
31 TraesCS4A01G398500 chr6B 88.204 373 30 9 3152 3510 605964613 605964241 1.940000e-117 433.0
32 TraesCS4A01G398500 chr6B 82.588 425 57 11 2761 3176 26451418 26451002 3.330000e-95 359.0
33 TraesCS4A01G398500 chr6B 79.343 213 35 8 2970 3176 26451093 26450884 1.310000e-29 141.0
34 TraesCS4A01G398500 chr6B 77.600 250 43 13 2958 3199 26450747 26450503 4.720000e-29 139.0
35 TraesCS4A01G398500 chr6B 94.872 39 0 1 2616 2652 534090239 534090277 3.780000e-05 60.2
36 TraesCS4A01G398500 chr4B 97.561 246 4 2 1 244 481595971 481596216 1.510000e-113 420.0
37 TraesCS4A01G398500 chr4B 88.750 240 23 4 2758 2993 38445106 38444867 1.230000e-74 291.0
38 TraesCS4A01G398500 chr7B 97.143 245 4 1 1 245 153598350 153598109 9.070000e-111 411.0
39 TraesCS4A01G398500 chr7B 87.764 237 22 7 12 245 14901991 14901759 1.610000e-68 270.0
40 TraesCS4A01G398500 chr7B 92.350 183 12 1 2771 2951 710424621 710424803 3.480000e-65 259.0
41 TraesCS4A01G398500 chr5B 96.203 237 8 1 1 237 271021802 271021567 1.530000e-103 387.0
42 TraesCS4A01G398500 chr5B 96.020 201 8 0 1 201 578718016 578718216 9.390000e-86 327.0
43 TraesCS4A01G398500 chr5B 81.481 189 31 4 253 439 681776669 681776483 6.070000e-33 152.0
44 TraesCS4A01G398500 chr1B 95.062 243 8 1 1 243 625238255 625238017 2.560000e-101 379.0
45 TraesCS4A01G398500 chr6D 83.264 239 30 8 2768 2997 127439971 127440208 9.870000e-51 211.0
46 TraesCS4A01G398500 chr1A 82.540 189 27 4 254 439 423988216 423988401 1.010000e-35 161.0
47 TraesCS4A01G398500 chr1D 83.237 173 28 1 271 442 285562274 285562102 1.300000e-34 158.0
48 TraesCS4A01G398500 chr1D 91.489 47 3 1 2616 2661 396889992 396889946 2.920000e-06 63.9
49 TraesCS4A01G398500 chr3A 82.105 190 27 5 253 439 713221086 713220901 4.690000e-34 156.0
50 TraesCS4A01G398500 chr5D 78.486 251 42 10 2958 3199 435020450 435020203 1.690000e-33 154.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G398500 chr4A 673487922 673491431 3509 False 6482.000000 6482 100.000000 1 3510 1 chr4A.!!$F1 3509
1 TraesCS4A01G398500 chr4A 646019073 646019828 755 True 961.000000 961 89.895000 2764 3510 1 chr4A.!!$R1 746
2 TraesCS4A01G398500 chr4A 687816324 687817155 831 False 396.000000 516 90.078000 3133 3510 2 chr4A.!!$F5 377
3 TraesCS4A01G398500 chr4A 688047030 688047983 953 True 263.000000 283 86.571500 2777 3510 2 chr4A.!!$R2 733
4 TraesCS4A01G398500 chr7D 56953426 56956006 2580 False 1225.333333 1858 93.082000 252 2770 3 chr7D.!!$F2 2518
5 TraesCS4A01G398500 chr7A 61431276 61435606 4330 False 914.666667 1498 90.148667 567 2569 3 chr7A.!!$F1 2002
6 TraesCS4A01G398500 chrUn 369145297 369145823 526 False 305.000000 305 77.737000 837 1359 1 chrUn.!!$F1 522
7 TraesCS4A01G398500 chr2B 2071839 2072679 840 True 460.000000 460 77.310000 837 1658 1 chr2B.!!$R1 821
8 TraesCS4A01G398500 chr3D 583872023 583872738 715 True 442.000000 564 90.114500 2771 3377 2 chr3D.!!$R2 606
9 TraesCS4A01G398500 chr6B 26450503 26451418 915 True 213.000000 359 79.843667 2761 3199 3 chr6B.!!$R2 438

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
617 622 0.032952 AGCTTGCCACATGTTTGCAG 59.967 50.0 16.79 12.98 36.21 4.41 F
1194 3444 0.322008 GCAGGGACTTCAAGGACCAG 60.322 60.0 0.00 0.00 34.60 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 4284 1.069090 GGTCTTGCTCACCGTCACA 59.931 57.895 0.00 0.0 0.0 3.58 R
2685 5153 0.482446 TGGCCTCAACAAGTGGGAAT 59.518 50.000 3.32 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
17 18 2.125106 ATCGACCGAGCCCAAAGC 60.125 61.111 0.00 0.00 44.25 3.51
18 19 3.682292 ATCGACCGAGCCCAAAGCC 62.682 63.158 0.00 0.00 45.47 4.35
20 21 4.344865 GACCGAGCCCAAAGCCCA 62.345 66.667 0.00 0.00 45.47 5.36
24 25 1.006220 CGAGCCCAAAGCCCAAAAC 60.006 57.895 0.00 0.00 45.47 2.43
25 26 1.371183 GAGCCCAAAGCCCAAAACC 59.629 57.895 0.00 0.00 45.47 3.27
26 27 2.030412 GCCCAAAGCCCAAAACCG 59.970 61.111 0.00 0.00 34.35 4.44
27 28 2.740438 CCCAAAGCCCAAAACCGG 59.260 61.111 0.00 0.00 0.00 5.28
28 29 2.137528 CCCAAAGCCCAAAACCGGT 61.138 57.895 0.00 0.00 0.00 5.28
29 30 1.691195 CCCAAAGCCCAAAACCGGTT 61.691 55.000 15.86 15.86 0.00 4.44
30 31 1.041437 CCAAAGCCCAAAACCGGTTA 58.959 50.000 22.60 0.00 0.00 2.85
31 32 1.000394 CCAAAGCCCAAAACCGGTTAG 60.000 52.381 22.60 16.18 0.00 2.34
32 33 0.677288 AAAGCCCAAAACCGGTTAGC 59.323 50.000 22.60 20.14 0.00 3.09
33 34 1.183030 AAGCCCAAAACCGGTTAGCC 61.183 55.000 22.60 7.72 0.00 3.93
34 35 2.642254 GCCCAAAACCGGTTAGCCC 61.642 63.158 22.60 4.72 0.00 5.19
71 72 4.075793 CGGACTGGGAGGGGGAGA 62.076 72.222 0.00 0.00 0.00 3.71
72 73 2.365768 GGACTGGGAGGGGGAGAC 60.366 72.222 0.00 0.00 0.00 3.36
73 74 2.450243 GACTGGGAGGGGGAGACA 59.550 66.667 0.00 0.00 0.00 3.41
74 75 1.990614 GACTGGGAGGGGGAGACAC 60.991 68.421 0.00 0.00 0.00 3.67
75 76 3.077556 CTGGGAGGGGGAGACACG 61.078 72.222 0.00 0.00 0.00 4.49
76 77 4.715130 TGGGAGGGGGAGACACGG 62.715 72.222 0.00 0.00 0.00 4.94
78 79 4.393778 GGAGGGGGAGACACGGGA 62.394 72.222 0.00 0.00 0.00 5.14
79 80 2.760385 GAGGGGGAGACACGGGAG 60.760 72.222 0.00 0.00 0.00 4.30
80 81 4.400251 AGGGGGAGACACGGGAGG 62.400 72.222 0.00 0.00 0.00 4.30
82 83 4.393778 GGGGAGACACGGGAGGGA 62.394 72.222 0.00 0.00 36.77 4.20
83 84 2.760385 GGGAGACACGGGAGGGAG 60.760 72.222 0.00 0.00 36.77 4.30
84 85 2.760385 GGAGACACGGGAGGGAGG 60.760 72.222 0.00 0.00 36.77 4.30
85 86 2.760385 GAGACACGGGAGGGAGGG 60.760 72.222 0.00 0.00 36.77 4.30
86 87 4.400251 AGACACGGGAGGGAGGGG 62.400 72.222 0.00 0.00 36.77 4.79
131 132 3.554342 CGGAGGGAGGCATGAGGG 61.554 72.222 0.00 0.00 0.00 4.30
132 133 2.040464 GGAGGGAGGCATGAGGGA 60.040 66.667 0.00 0.00 0.00 4.20
133 134 2.146061 GGAGGGAGGCATGAGGGAG 61.146 68.421 0.00 0.00 0.00 4.30
134 135 2.040043 AGGGAGGCATGAGGGAGG 60.040 66.667 0.00 0.00 0.00 4.30
135 136 2.040464 GGGAGGCATGAGGGAGGA 60.040 66.667 0.00 0.00 0.00 3.71
136 137 1.694169 GGGAGGCATGAGGGAGGAA 60.694 63.158 0.00 0.00 0.00 3.36
137 138 1.704007 GGGAGGCATGAGGGAGGAAG 61.704 65.000 0.00 0.00 0.00 3.46
138 139 1.704007 GGAGGCATGAGGGAGGAAGG 61.704 65.000 0.00 0.00 0.00 3.46
139 140 1.695597 AGGCATGAGGGAGGAAGGG 60.696 63.158 0.00 0.00 0.00 3.95
140 141 2.761465 GGCATGAGGGAGGAAGGGG 61.761 68.421 0.00 0.00 0.00 4.79
141 142 2.003548 GCATGAGGGAGGAAGGGGT 61.004 63.158 0.00 0.00 0.00 4.95
142 143 1.988982 GCATGAGGGAGGAAGGGGTC 61.989 65.000 0.00 0.00 0.00 4.46
143 144 0.327000 CATGAGGGAGGAAGGGGTCT 60.327 60.000 0.00 0.00 0.00 3.85
144 145 0.327000 ATGAGGGAGGAAGGGGTCTG 60.327 60.000 0.00 0.00 0.00 3.51
145 146 1.690985 GAGGGAGGAAGGGGTCTGG 60.691 68.421 0.00 0.00 0.00 3.86
146 147 2.692741 GGGAGGAAGGGGTCTGGG 60.693 72.222 0.00 0.00 0.00 4.45
147 148 2.692741 GGAGGAAGGGGTCTGGGG 60.693 72.222 0.00 0.00 0.00 4.96
148 149 2.125225 GAGGAAGGGGTCTGGGGT 59.875 66.667 0.00 0.00 0.00 4.95
149 150 1.541620 GAGGAAGGGGTCTGGGGTT 60.542 63.158 0.00 0.00 0.00 4.11
150 151 1.541620 AGGAAGGGGTCTGGGGTTC 60.542 63.158 0.00 0.00 0.00 3.62
151 152 1.850755 GGAAGGGGTCTGGGGTTCA 60.851 63.158 0.00 0.00 0.00 3.18
152 153 1.379146 GAAGGGGTCTGGGGTTCAC 59.621 63.158 0.00 0.00 0.00 3.18
153 154 1.386772 AAGGGGTCTGGGGTTCACA 60.387 57.895 0.00 0.00 0.00 3.58
154 155 1.716028 AAGGGGTCTGGGGTTCACAC 61.716 60.000 0.00 0.00 0.00 3.82
155 156 2.032071 GGGTCTGGGGTTCACACG 59.968 66.667 0.00 0.00 0.00 4.49
156 157 2.513259 GGGTCTGGGGTTCACACGA 61.513 63.158 0.00 0.00 0.00 4.35
157 158 1.004918 GGTCTGGGGTTCACACGAG 60.005 63.158 0.00 0.00 0.00 4.18
158 159 1.469335 GGTCTGGGGTTCACACGAGA 61.469 60.000 0.00 0.00 31.52 4.04
159 160 0.319641 GTCTGGGGTTCACACGAGAC 60.320 60.000 8.41 8.41 45.33 3.36
160 161 0.469331 TCTGGGGTTCACACGAGACT 60.469 55.000 0.00 0.00 28.89 3.24
161 162 0.393077 CTGGGGTTCACACGAGACTT 59.607 55.000 0.00 0.00 0.00 3.01
162 163 0.105964 TGGGGTTCACACGAGACTTG 59.894 55.000 0.00 0.00 0.00 3.16
163 164 0.602905 GGGGTTCACACGAGACTTGG 60.603 60.000 0.00 0.00 0.00 3.61
164 165 0.391597 GGGTTCACACGAGACTTGGA 59.608 55.000 0.00 0.00 0.00 3.53
165 166 1.499049 GGTTCACACGAGACTTGGAC 58.501 55.000 0.00 0.00 0.00 4.02
166 167 1.129326 GTTCACACGAGACTTGGACG 58.871 55.000 0.00 0.00 0.00 4.79
167 168 0.596600 TTCACACGAGACTTGGACGC 60.597 55.000 0.00 0.00 0.00 5.19
168 169 2.022129 CACACGAGACTTGGACGCC 61.022 63.158 0.00 0.00 0.00 5.68
169 170 2.805353 CACGAGACTTGGACGCCG 60.805 66.667 0.00 0.00 0.00 6.46
170 171 2.981909 ACGAGACTTGGACGCCGA 60.982 61.111 0.00 0.00 0.00 5.54
171 172 2.504244 CGAGACTTGGACGCCGAC 60.504 66.667 0.00 0.00 0.00 4.79
173 174 3.966026 GAGACTTGGACGCCGACGG 62.966 68.421 10.29 10.29 46.04 4.79
174 175 4.047059 GACTTGGACGCCGACGGA 62.047 66.667 20.50 0.00 46.04 4.69
175 176 3.966026 GACTTGGACGCCGACGGAG 62.966 68.421 20.50 18.44 46.04 4.63
176 177 4.796231 CTTGGACGCCGACGGAGG 62.796 72.222 20.50 11.13 46.04 4.30
231 232 4.214327 GCGCGAGAGGAGGGGAAG 62.214 72.222 12.10 0.00 0.00 3.46
232 233 2.440430 CGCGAGAGGAGGGGAAGA 60.440 66.667 0.00 0.00 0.00 2.87
233 234 2.485795 CGCGAGAGGAGGGGAAGAG 61.486 68.421 0.00 0.00 0.00 2.85
234 235 1.076632 GCGAGAGGAGGGGAAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
235 236 1.106944 GCGAGAGGAGGGGAAGAGAG 61.107 65.000 0.00 0.00 0.00 3.20
236 237 1.106944 CGAGAGGAGGGGAAGAGAGC 61.107 65.000 0.00 0.00 0.00 4.09
237 238 1.076339 AGAGGAGGGGAAGAGAGCG 60.076 63.158 0.00 0.00 0.00 5.03
238 239 2.762043 AGGAGGGGAAGAGAGCGC 60.762 66.667 0.00 0.00 0.00 5.92
239 240 3.855853 GGAGGGGAAGAGAGCGCC 61.856 72.222 2.29 0.00 38.53 6.53
240 241 3.077556 GAGGGGAAGAGAGCGCCA 61.078 66.667 2.29 0.00 40.52 5.69
241 242 2.366167 AGGGGAAGAGAGCGCCAT 60.366 61.111 2.29 0.00 40.52 4.40
242 243 2.110006 GGGGAAGAGAGCGCCATC 59.890 66.667 2.29 1.70 38.18 3.51
243 244 2.110006 GGGAAGAGAGCGCCATCC 59.890 66.667 2.29 4.79 0.00 3.51
244 245 2.110006 GGAAGAGAGCGCCATCCC 59.890 66.667 2.29 0.00 0.00 3.85
245 246 2.110006 GAAGAGAGCGCCATCCCC 59.890 66.667 2.29 0.00 0.00 4.81
246 247 3.798954 GAAGAGAGCGCCATCCCCG 62.799 68.421 2.29 0.00 0.00 5.73
247 248 4.841617 AGAGAGCGCCATCCCCGA 62.842 66.667 2.29 0.00 0.00 5.14
248 249 4.593864 GAGAGCGCCATCCCCGAC 62.594 72.222 2.29 0.00 0.00 4.79
254 255 4.419921 GCCATCCCCGACCCGTTT 62.420 66.667 0.00 0.00 0.00 3.60
255 256 2.353573 CCATCCCCGACCCGTTTT 59.646 61.111 0.00 0.00 0.00 2.43
256 257 1.303806 CCATCCCCGACCCGTTTTT 60.304 57.895 0.00 0.00 0.00 1.94
285 286 5.761205 TGCCTATGAAATACTTTGGCCTTA 58.239 37.500 3.32 0.00 41.24 2.69
297 298 4.955450 ACTTTGGCCTTATATGACATTGCA 59.045 37.500 3.32 0.00 0.00 4.08
303 304 5.221501 GGCCTTATATGACATTGCAATTGGT 60.222 40.000 9.83 5.57 0.00 3.67
322 323 3.118992 TGGTTTGCTTGTTATTGTGTGCA 60.119 39.130 0.00 0.00 0.00 4.57
332 333 1.242989 ATTGTGTGCATGCGTTGGTA 58.757 45.000 14.09 0.00 0.00 3.25
335 336 1.068679 TGTGTGCATGCGTTGGTATTG 60.069 47.619 14.09 0.00 0.00 1.90
351 352 3.627577 GGTATTGGTTGTGTGCATCCTAG 59.372 47.826 0.00 0.00 35.89 3.02
357 358 2.874701 GTTGTGTGCATCCTAGCTATGG 59.125 50.000 0.00 0.00 34.99 2.74
360 361 2.366916 GTGTGCATCCTAGCTATGGAGT 59.633 50.000 14.62 4.33 36.99 3.85
364 365 1.067283 CATCCTAGCTATGGAGTGGCG 60.067 57.143 14.62 0.00 39.65 5.69
371 372 1.656652 CTATGGAGTGGCGGAGTTTG 58.343 55.000 0.00 0.00 0.00 2.93
374 375 2.617274 GGAGTGGCGGAGTTTGTGC 61.617 63.158 0.00 0.00 0.00 4.57
390 391 6.208644 AGTTTGTGCTCATTGTGTTTGTATC 58.791 36.000 0.00 0.00 0.00 2.24
408 410 7.707624 TTGTATCCTCTTGATGCTTCATTTT 57.292 32.000 2.75 0.00 37.04 1.82
413 415 4.421948 CTCTTGATGCTTCATTTTGAGCC 58.578 43.478 2.75 0.00 0.00 4.70
414 416 4.084287 TCTTGATGCTTCATTTTGAGCCT 58.916 39.130 2.75 0.00 0.00 4.58
415 417 4.525487 TCTTGATGCTTCATTTTGAGCCTT 59.475 37.500 2.75 0.00 0.00 4.35
424 426 6.650390 GCTTCATTTTGAGCCTTAAAAATCCA 59.350 34.615 0.00 0.00 34.55 3.41
425 427 7.360353 GCTTCATTTTGAGCCTTAAAAATCCAC 60.360 37.037 0.00 0.00 34.55 4.02
429 431 3.697166 TGAGCCTTAAAAATCCACCCTC 58.303 45.455 0.00 0.00 0.00 4.30
456 458 9.232082 TGTTGAAAAGAACAATAAAATGAGACG 57.768 29.630 0.00 0.00 32.84 4.18
472 474 6.621316 ATGAGACGTATTGATCTCGTAACT 57.379 37.500 0.00 0.00 43.68 2.24
509 511 9.927081 ACCTGTTAGGATCATCAAAATCTTAAT 57.073 29.630 1.13 0.00 37.67 1.40
548 552 2.738147 GTGCCTACACGTGCTACTG 58.262 57.895 17.22 0.91 36.98 2.74
556 560 0.572590 CACGTGCTACTGCGAATAGC 59.427 55.000 0.82 6.71 44.48 2.97
585 589 2.902705 TATGTCTGGGGCGTATTGAC 57.097 50.000 0.00 0.00 0.00 3.18
611 616 3.012518 GTCTTGATAGCTTGCCACATGT 58.987 45.455 0.00 0.00 0.00 3.21
617 622 0.032952 AGCTTGCCACATGTTTGCAG 59.967 50.000 16.79 12.98 36.21 4.41
621 626 1.330234 TGCCACATGTTTGCAGTCAT 58.670 45.000 14.25 0.00 0.00 3.06
623 628 3.090790 TGCCACATGTTTGCAGTCATAT 58.909 40.909 14.25 0.00 0.00 1.78
630 635 7.223193 CCACATGTTTGCAGTCATATATTTTGG 59.777 37.037 0.00 3.61 0.00 3.28
657 662 4.813161 CCAATGCCATCAACTACTCACTAG 59.187 45.833 0.00 0.00 0.00 2.57
662 667 5.656859 TGCCATCAACTACTCACTAGTATGT 59.343 40.000 0.00 0.00 37.57 2.29
720 729 7.563270 CAAATTTACAAATTGTGTGTGCCTAC 58.437 34.615 9.15 0.00 41.89 3.18
735 2968 8.893727 GTGTGTGCCTACAGATTTAGAATTAAT 58.106 33.333 0.00 0.00 37.52 1.40
793 3029 8.853077 TTATCTATTGAATGCCACCTTCATAG 57.147 34.615 0.00 0.00 32.94 2.23
826 3062 6.072728 TCCACAAAAGATGAACGGAACTATTG 60.073 38.462 0.00 0.00 0.00 1.90
830 3066 9.010029 ACAAAAGATGAACGGAACTATTGTATT 57.990 29.630 0.00 0.00 0.00 1.89
854 3090 8.586570 TTTGGTGCAAACTTAATTAGTTCATG 57.413 30.769 0.00 0.00 46.34 3.07
986 3228 2.031919 CTGGGGCGCAGTTGTGTA 59.968 61.111 22.22 0.00 0.00 2.90
994 3236 2.025418 GCAGTTGTGTACCGGACCG 61.025 63.158 9.46 6.99 0.00 4.79
1023 3265 1.675552 CGGTGAGGTTCTTGGTGTTT 58.324 50.000 0.00 0.00 0.00 2.83
1025 3267 2.032924 CGGTGAGGTTCTTGGTGTTTTC 59.967 50.000 0.00 0.00 0.00 2.29
1042 3284 3.417069 TTTCGGCCATCTTTCTCTTCA 57.583 42.857 2.24 0.00 0.00 3.02
1194 3444 0.322008 GCAGGGACTTCAAGGACCAG 60.322 60.000 0.00 0.00 34.60 4.00
1265 3515 4.401837 AGGTCGGTCAGAACCTTATTAGAC 59.598 45.833 0.00 0.00 44.04 2.59
1274 3524 6.430000 TCAGAACCTTATTAGACCTTGTTTGC 59.570 38.462 0.00 0.00 0.00 3.68
1287 3537 4.815846 ACCTTGTTTGCACAAATGGATTTC 59.184 37.500 14.99 0.00 42.53 2.17
1319 3569 7.118390 ACATTTCACATGAACTCTTAGTAGTGC 59.882 37.037 0.00 0.00 33.13 4.40
1341 3592 4.615223 GCTATGGCATGCATATCTTGTGTG 60.615 45.833 21.36 2.99 38.54 3.82
1381 3632 2.038557 TGCAGGTGAGAAACTAGGGTTC 59.961 50.000 0.00 0.00 34.14 3.62
1509 3766 7.578852 TCACGTATCTATGTAAGTACCATTCG 58.421 38.462 0.00 0.00 0.00 3.34
1512 3769 7.227314 ACGTATCTATGTAAGTACCATTCGTCA 59.773 37.037 0.00 0.00 0.00 4.35
1517 3774 2.762535 AAGTACCATTCGTCAGTGGG 57.237 50.000 0.00 0.00 39.86 4.61
1519 3776 2.253610 AGTACCATTCGTCAGTGGGAA 58.746 47.619 0.00 0.00 39.86 3.97
1537 3933 7.231467 AGTGGGAAACTGTGTATACTGAAATT 58.769 34.615 4.17 0.00 37.88 1.82
1559 3955 9.748708 AAATTTATACATGTTGCATACATCACC 57.251 29.630 2.30 0.00 45.71 4.02
1605 4071 2.099756 GTGGCAGCATGTAATCCCTTTC 59.900 50.000 0.00 0.00 39.31 2.62
1756 4222 6.182507 TCAACTACTACATCAACCCTTTGT 57.817 37.500 0.00 0.00 34.02 2.83
1818 4284 3.880490 TCGTTGGCATCTTTAACAACACT 59.120 39.130 0.00 0.00 42.35 3.55
1999 4465 0.096976 CATTGGCGATCACGGTGTTC 59.903 55.000 8.17 8.51 40.15 3.18
2086 4552 1.665916 TGCAGCTGTTGACTCGCTC 60.666 57.895 16.64 0.00 0.00 5.03
2089 4555 0.735632 CAGCTGTTGACTCGCTCTCC 60.736 60.000 5.25 0.00 0.00 3.71
2187 4653 3.619979 GCACATGGTAGGATACATAGGCC 60.620 52.174 0.00 0.00 45.43 5.19
2254 4722 5.925397 TGCATGTTTATTTTCTTGTCGCATT 59.075 32.000 0.00 0.00 0.00 3.56
2265 4733 1.448985 TGTCGCATTAACCTTGCTCC 58.551 50.000 0.00 0.00 37.96 4.70
2417 4885 3.456039 GTCCGAACGCGACGACAC 61.456 66.667 25.06 18.31 40.82 3.67
2531 4999 0.824759 CCCTGGACCTAGTACAGTGC 59.175 60.000 6.24 0.00 42.54 4.40
2608 5076 8.160765 TGTCTCAAAATAAACTGTAGATTCCCA 58.839 33.333 0.00 0.00 0.00 4.37
2611 5079 6.938030 TCAAAATAAACTGTAGATTCCCACGT 59.062 34.615 0.00 0.00 0.00 4.49
2612 5080 6.737254 AAATAAACTGTAGATTCCCACGTG 57.263 37.500 9.08 9.08 0.00 4.49
2613 5081 3.764237 AAACTGTAGATTCCCACGTGT 57.236 42.857 15.65 0.00 0.00 4.49
2614 5082 2.743636 ACTGTAGATTCCCACGTGTG 57.256 50.000 15.65 2.45 0.00 3.82
2615 5083 1.968493 ACTGTAGATTCCCACGTGTGT 59.032 47.619 15.65 0.00 0.00 3.72
2616 5084 2.367567 ACTGTAGATTCCCACGTGTGTT 59.632 45.455 15.65 0.00 0.00 3.32
2617 5085 3.181458 ACTGTAGATTCCCACGTGTGTTT 60.181 43.478 15.65 0.00 0.00 2.83
2618 5086 3.811083 TGTAGATTCCCACGTGTGTTTT 58.189 40.909 15.65 0.00 0.00 2.43
2619 5087 4.200874 TGTAGATTCCCACGTGTGTTTTT 58.799 39.130 15.65 0.00 0.00 1.94
2637 5105 3.822594 TTTTCGAATATGCACAAGCGT 57.177 38.095 0.00 0.00 46.23 5.07
2638 5106 2.804421 TTCGAATATGCACAAGCGTG 57.196 45.000 0.00 0.00 46.23 5.34
2655 5123 9.481800 CACAAGCGTGCATATCATATATTAAAG 57.518 33.333 0.00 0.00 36.06 1.85
2656 5124 9.435688 ACAAGCGTGCATATCATATATTAAAGA 57.564 29.630 0.00 0.00 0.00 2.52
2682 5150 3.658398 CAAAGAGTGCCTCCACCAT 57.342 52.632 0.00 0.00 43.09 3.55
2683 5151 2.787473 CAAAGAGTGCCTCCACCATA 57.213 50.000 0.00 0.00 43.09 2.74
2684 5152 3.287867 CAAAGAGTGCCTCCACCATAT 57.712 47.619 0.00 0.00 43.09 1.78
2685 5153 4.422073 CAAAGAGTGCCTCCACCATATA 57.578 45.455 0.00 0.00 43.09 0.86
2686 5154 4.978099 CAAAGAGTGCCTCCACCATATAT 58.022 43.478 0.00 0.00 43.09 0.86
2687 5155 5.380043 CAAAGAGTGCCTCCACCATATATT 58.620 41.667 0.00 0.00 43.09 1.28
2688 5156 4.899352 AGAGTGCCTCCACCATATATTC 57.101 45.455 0.00 0.00 43.09 1.75
2689 5157 3.584848 AGAGTGCCTCCACCATATATTCC 59.415 47.826 0.00 0.00 43.09 3.01
2690 5158 2.644798 AGTGCCTCCACCATATATTCCC 59.355 50.000 0.00 0.00 43.09 3.97
2691 5159 2.375174 GTGCCTCCACCATATATTCCCA 59.625 50.000 0.00 0.00 35.92 4.37
2692 5160 2.375174 TGCCTCCACCATATATTCCCAC 59.625 50.000 0.00 0.00 0.00 4.61
2693 5161 2.644798 GCCTCCACCATATATTCCCACT 59.355 50.000 0.00 0.00 0.00 4.00
2700 5168 5.532406 CCACCATATATTCCCACTTGTTGAG 59.468 44.000 0.00 0.00 0.00 3.02
2738 5206 7.697691 TGTGTAAGTTACCTATAAGTCGCTAC 58.302 38.462 10.51 0.00 0.00 3.58
2743 5211 7.736447 AGTTACCTATAAGTCGCTACGTATT 57.264 36.000 2.37 0.00 33.20 1.89
2762 5230 7.085116 ACGTATTTGCTACAGCTCTATGTATC 58.915 38.462 2.44 0.00 42.66 2.24
2763 5231 7.040340 ACGTATTTGCTACAGCTCTATGTATCT 60.040 37.037 2.44 0.00 42.66 1.98
2764 5232 8.451748 CGTATTTGCTACAGCTCTATGTATCTA 58.548 37.037 2.44 0.00 42.66 1.98
2873 5341 0.250989 TCGTTGATTTGGTGGACCCC 60.251 55.000 0.00 0.00 34.29 4.95
2885 5353 5.342361 TGGTGGACCCCTAATTTAAAAGT 57.658 39.130 0.00 0.00 34.29 2.66
2927 5395 2.479566 AGAGCGCTCCATCTCAAAAA 57.520 45.000 32.94 0.00 0.00 1.94
2968 5441 1.477553 CTAGGTTGTACGTGCCCCTA 58.522 55.000 15.18 15.18 0.00 3.53
3106 5793 7.121315 GCCGCTCCATCCTAAAATAAAGATTAT 59.879 37.037 0.00 0.00 0.00 1.28
3163 5853 9.120538 TCTATCTGCATGTCCCTTTAAATAAAC 57.879 33.333 0.00 0.00 0.00 2.01
3169 5859 9.921637 TGCATGTCCCTTTAAATAAACTAAAAG 57.078 29.630 0.00 0.00 0.00 2.27
3289 6319 6.972722 ACTAGATCTCACGTCCTATAAAAGC 58.027 40.000 0.00 0.00 0.00 3.51
3318 6353 8.553459 AAAACTACCACATCTCATGTTTAGAG 57.447 34.615 8.24 0.00 42.70 2.43
3493 7113 4.030913 ACGGATCTCAGGTTCCTTTATGA 58.969 43.478 0.00 0.00 31.06 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.860930 TTGGGCTTTGGGCTCGGTC 62.861 63.158 0.00 0.00 46.29 4.79
5 6 2.206536 TTTTGGGCTTTGGGCTCGG 61.207 57.895 0.00 0.00 46.29 4.63
6 7 1.006220 GTTTTGGGCTTTGGGCTCG 60.006 57.895 0.00 0.00 46.29 5.03
8 9 2.506957 CGGTTTTGGGCTTTGGGCT 61.507 57.895 0.00 0.00 41.46 5.19
9 10 2.030412 CGGTTTTGGGCTTTGGGC 59.970 61.111 0.00 0.00 40.90 5.36
10 11 1.691195 AACCGGTTTTGGGCTTTGGG 61.691 55.000 15.86 0.00 0.00 4.12
11 12 1.000394 CTAACCGGTTTTGGGCTTTGG 60.000 52.381 27.64 0.00 0.00 3.28
12 13 1.604438 GCTAACCGGTTTTGGGCTTTG 60.604 52.381 27.64 0.00 0.00 2.77
13 14 0.677288 GCTAACCGGTTTTGGGCTTT 59.323 50.000 27.64 0.00 0.00 3.51
14 15 1.183030 GGCTAACCGGTTTTGGGCTT 61.183 55.000 27.64 0.00 0.00 4.35
15 16 1.605451 GGCTAACCGGTTTTGGGCT 60.605 57.895 27.64 0.45 0.00 5.19
16 17 2.642254 GGGCTAACCGGTTTTGGGC 61.642 63.158 27.64 24.73 36.48 5.36
17 18 3.689414 GGGCTAACCGGTTTTGGG 58.311 61.111 27.64 14.16 36.48 4.12
54 55 4.075793 TCTCCCCCTCCCAGTCCG 62.076 72.222 0.00 0.00 0.00 4.79
55 56 2.365768 GTCTCCCCCTCCCAGTCC 60.366 72.222 0.00 0.00 0.00 3.85
56 57 1.990614 GTGTCTCCCCCTCCCAGTC 60.991 68.421 0.00 0.00 0.00 3.51
57 58 2.122954 GTGTCTCCCCCTCCCAGT 59.877 66.667 0.00 0.00 0.00 4.00
58 59 3.077556 CGTGTCTCCCCCTCCCAG 61.078 72.222 0.00 0.00 0.00 4.45
59 60 4.715130 CCGTGTCTCCCCCTCCCA 62.715 72.222 0.00 0.00 0.00 4.37
61 62 4.393778 TCCCGTGTCTCCCCCTCC 62.394 72.222 0.00 0.00 0.00 4.30
62 63 2.760385 CTCCCGTGTCTCCCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
63 64 4.400251 CCTCCCGTGTCTCCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
65 66 4.393778 TCCCTCCCGTGTCTCCCC 62.394 72.222 0.00 0.00 0.00 4.81
66 67 2.760385 CTCCCTCCCGTGTCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
67 68 2.760385 CCTCCCTCCCGTGTCTCC 60.760 72.222 0.00 0.00 0.00 3.71
68 69 2.760385 CCCTCCCTCCCGTGTCTC 60.760 72.222 0.00 0.00 0.00 3.36
69 70 4.400251 CCCCTCCCTCCCGTGTCT 62.400 72.222 0.00 0.00 0.00 3.41
112 113 3.554342 CTCATGCCTCCCTCCGGG 61.554 72.222 0.00 0.00 46.11 5.73
113 114 3.554342 CCTCATGCCTCCCTCCGG 61.554 72.222 0.00 0.00 0.00 5.14
114 115 3.554342 CCCTCATGCCTCCCTCCG 61.554 72.222 0.00 0.00 0.00 4.63
115 116 2.040464 TCCCTCATGCCTCCCTCC 60.040 66.667 0.00 0.00 0.00 4.30
116 117 2.146061 CCTCCCTCATGCCTCCCTC 61.146 68.421 0.00 0.00 0.00 4.30
117 118 2.040043 CCTCCCTCATGCCTCCCT 60.040 66.667 0.00 0.00 0.00 4.20
118 119 1.694169 TTCCTCCCTCATGCCTCCC 60.694 63.158 0.00 0.00 0.00 4.30
119 120 1.704007 CCTTCCTCCCTCATGCCTCC 61.704 65.000 0.00 0.00 0.00 4.30
120 121 1.704007 CCCTTCCTCCCTCATGCCTC 61.704 65.000 0.00 0.00 0.00 4.70
121 122 1.695597 CCCTTCCTCCCTCATGCCT 60.696 63.158 0.00 0.00 0.00 4.75
122 123 2.761465 CCCCTTCCTCCCTCATGCC 61.761 68.421 0.00 0.00 0.00 4.40
123 124 1.988982 GACCCCTTCCTCCCTCATGC 61.989 65.000 0.00 0.00 0.00 4.06
124 125 0.327000 AGACCCCTTCCTCCCTCATG 60.327 60.000 0.00 0.00 0.00 3.07
125 126 0.327000 CAGACCCCTTCCTCCCTCAT 60.327 60.000 0.00 0.00 0.00 2.90
126 127 1.081092 CAGACCCCTTCCTCCCTCA 59.919 63.158 0.00 0.00 0.00 3.86
127 128 1.690985 CCAGACCCCTTCCTCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
128 129 2.456840 CCAGACCCCTTCCTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
129 130 2.692741 CCCAGACCCCTTCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
130 131 2.692741 CCCCAGACCCCTTCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
131 132 1.541620 AACCCCAGACCCCTTCCTC 60.542 63.158 0.00 0.00 0.00 3.71
132 133 1.541620 GAACCCCAGACCCCTTCCT 60.542 63.158 0.00 0.00 0.00 3.36
133 134 1.850755 TGAACCCCAGACCCCTTCC 60.851 63.158 0.00 0.00 0.00 3.46
134 135 1.379146 GTGAACCCCAGACCCCTTC 59.621 63.158 0.00 0.00 0.00 3.46
135 136 1.386772 TGTGAACCCCAGACCCCTT 60.387 57.895 0.00 0.00 0.00 3.95
136 137 2.154074 GTGTGAACCCCAGACCCCT 61.154 63.158 0.00 0.00 33.32 4.79
137 138 2.434774 GTGTGAACCCCAGACCCC 59.565 66.667 0.00 0.00 33.32 4.95
138 139 2.032071 CGTGTGAACCCCAGACCC 59.968 66.667 0.00 0.00 35.80 4.46
139 140 1.004918 CTCGTGTGAACCCCAGACC 60.005 63.158 0.00 0.00 35.80 3.85
140 141 0.319641 GTCTCGTGTGAACCCCAGAC 60.320 60.000 0.00 0.00 35.86 3.51
141 142 0.469331 AGTCTCGTGTGAACCCCAGA 60.469 55.000 0.00 0.00 0.00 3.86
142 143 0.393077 AAGTCTCGTGTGAACCCCAG 59.607 55.000 0.00 0.00 0.00 4.45
143 144 0.105964 CAAGTCTCGTGTGAACCCCA 59.894 55.000 0.00 0.00 0.00 4.96
144 145 0.602905 CCAAGTCTCGTGTGAACCCC 60.603 60.000 0.00 0.00 0.00 4.95
145 146 0.391597 TCCAAGTCTCGTGTGAACCC 59.608 55.000 0.00 0.00 0.00 4.11
146 147 1.499049 GTCCAAGTCTCGTGTGAACC 58.501 55.000 0.00 0.00 0.00 3.62
147 148 1.129326 CGTCCAAGTCTCGTGTGAAC 58.871 55.000 0.00 0.00 0.00 3.18
148 149 0.596600 GCGTCCAAGTCTCGTGTGAA 60.597 55.000 0.00 0.00 0.00 3.18
149 150 1.007734 GCGTCCAAGTCTCGTGTGA 60.008 57.895 0.00 0.00 0.00 3.58
150 151 2.022129 GGCGTCCAAGTCTCGTGTG 61.022 63.158 0.00 0.00 0.00 3.82
151 152 2.338984 GGCGTCCAAGTCTCGTGT 59.661 61.111 0.00 0.00 0.00 4.49
152 153 2.805353 CGGCGTCCAAGTCTCGTG 60.805 66.667 0.00 0.00 0.00 4.35
153 154 2.981909 TCGGCGTCCAAGTCTCGT 60.982 61.111 6.85 0.00 0.00 4.18
154 155 2.504244 GTCGGCGTCCAAGTCTCG 60.504 66.667 6.85 0.00 0.00 4.04
155 156 2.504244 CGTCGGCGTCCAAGTCTC 60.504 66.667 6.85 0.00 0.00 3.36
156 157 4.052229 CCGTCGGCGTCCAAGTCT 62.052 66.667 9.28 0.00 36.15 3.24
157 158 3.966026 CTCCGTCGGCGTCCAAGTC 62.966 68.421 9.28 0.00 36.15 3.01
158 159 4.052229 CTCCGTCGGCGTCCAAGT 62.052 66.667 9.28 0.00 36.15 3.16
159 160 4.796231 CCTCCGTCGGCGTCCAAG 62.796 72.222 9.28 0.00 36.15 3.61
214 215 4.214327 CTTCCCCTCCTCTCGCGC 62.214 72.222 0.00 0.00 0.00 6.86
215 216 2.440430 TCTTCCCCTCCTCTCGCG 60.440 66.667 0.00 0.00 0.00 5.87
216 217 1.076632 TCTCTTCCCCTCCTCTCGC 60.077 63.158 0.00 0.00 0.00 5.03
217 218 1.106944 GCTCTCTTCCCCTCCTCTCG 61.107 65.000 0.00 0.00 0.00 4.04
218 219 1.106944 CGCTCTCTTCCCCTCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
219 220 1.076339 CGCTCTCTTCCCCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
220 221 2.791868 GCGCTCTCTTCCCCTCCTC 61.792 68.421 0.00 0.00 0.00 3.71
221 222 2.762043 GCGCTCTCTTCCCCTCCT 60.762 66.667 0.00 0.00 0.00 3.69
222 223 3.855853 GGCGCTCTCTTCCCCTCC 61.856 72.222 7.64 0.00 0.00 4.30
223 224 2.376228 GATGGCGCTCTCTTCCCCTC 62.376 65.000 7.64 0.00 0.00 4.30
224 225 2.366167 ATGGCGCTCTCTTCCCCT 60.366 61.111 7.64 0.00 0.00 4.79
225 226 2.110006 GATGGCGCTCTCTTCCCC 59.890 66.667 7.64 0.00 0.00 4.81
226 227 2.110006 GGATGGCGCTCTCTTCCC 59.890 66.667 7.64 0.00 0.00 3.97
227 228 2.110006 GGGATGGCGCTCTCTTCC 59.890 66.667 7.64 7.93 0.00 3.46
228 229 2.110006 GGGGATGGCGCTCTCTTC 59.890 66.667 7.64 0.00 0.00 2.87
229 230 3.854669 CGGGGATGGCGCTCTCTT 61.855 66.667 7.64 0.00 0.00 2.85
230 231 4.841617 TCGGGGATGGCGCTCTCT 62.842 66.667 7.64 0.00 0.00 3.10
231 232 4.593864 GTCGGGGATGGCGCTCTC 62.594 72.222 7.64 4.08 0.00 3.20
237 238 3.931190 AAAACGGGTCGGGGATGGC 62.931 63.158 0.00 0.00 0.00 4.40
238 239 1.303806 AAAAACGGGTCGGGGATGG 60.304 57.895 0.00 0.00 0.00 3.51
239 240 4.408378 AAAAACGGGTCGGGGATG 57.592 55.556 0.00 0.00 0.00 3.51
255 256 9.377312 GCCAAAGTATTTCATAGGCAATAAAAA 57.623 29.630 0.00 0.00 41.50 1.94
256 257 7.984617 GGCCAAAGTATTTCATAGGCAATAAAA 59.015 33.333 0.00 0.00 43.07 1.52
257 258 7.344352 AGGCCAAAGTATTTCATAGGCAATAAA 59.656 33.333 5.01 0.00 43.07 1.40
258 259 6.838612 AGGCCAAAGTATTTCATAGGCAATAA 59.161 34.615 5.01 0.00 43.07 1.40
259 260 6.372931 AGGCCAAAGTATTTCATAGGCAATA 58.627 36.000 5.01 0.00 43.07 1.90
260 261 5.211201 AGGCCAAAGTATTTCATAGGCAAT 58.789 37.500 5.01 0.00 43.07 3.56
261 262 4.609301 AGGCCAAAGTATTTCATAGGCAA 58.391 39.130 5.01 0.00 43.07 4.52
262 263 4.249638 AGGCCAAAGTATTTCATAGGCA 57.750 40.909 5.01 0.00 43.07 4.75
263 264 6.901081 ATAAGGCCAAAGTATTTCATAGGC 57.099 37.500 5.01 0.00 41.25 3.93
264 265 9.739276 TCATATAAGGCCAAAGTATTTCATAGG 57.261 33.333 5.01 0.00 35.03 2.57
267 268 8.995027 TGTCATATAAGGCCAAAGTATTTCAT 57.005 30.769 5.01 0.00 35.03 2.57
268 269 8.995027 ATGTCATATAAGGCCAAAGTATTTCA 57.005 30.769 5.01 0.00 35.03 2.69
269 270 9.683069 CAATGTCATATAAGGCCAAAGTATTTC 57.317 33.333 5.01 0.00 35.03 2.17
270 271 8.143835 GCAATGTCATATAAGGCCAAAGTATTT 58.856 33.333 5.01 0.00 40.26 1.40
271 272 7.287466 TGCAATGTCATATAAGGCCAAAGTATT 59.713 33.333 5.01 0.00 0.00 1.89
272 273 6.777091 TGCAATGTCATATAAGGCCAAAGTAT 59.223 34.615 5.01 0.00 0.00 2.12
273 274 6.125719 TGCAATGTCATATAAGGCCAAAGTA 58.874 36.000 5.01 0.00 0.00 2.24
274 275 4.955450 TGCAATGTCATATAAGGCCAAAGT 59.045 37.500 5.01 0.00 0.00 2.66
297 298 5.007528 GCACACAATAACAAGCAAACCAATT 59.992 36.000 0.00 0.00 0.00 2.32
303 304 3.493877 GCATGCACACAATAACAAGCAAA 59.506 39.130 14.21 0.00 35.45 3.68
309 310 2.606551 CCAACGCATGCACACAATAACA 60.607 45.455 19.57 0.00 0.00 2.41
313 314 1.242989 TACCAACGCATGCACACAAT 58.757 45.000 19.57 0.35 0.00 2.71
322 323 2.030363 CACACAACCAATACCAACGCAT 60.030 45.455 0.00 0.00 0.00 4.73
332 333 2.094675 GCTAGGATGCACACAACCAAT 58.905 47.619 0.00 0.00 41.12 3.16
335 336 2.691409 TAGCTAGGATGCACACAACC 57.309 50.000 0.00 0.00 39.00 3.77
351 352 0.107654 AAACTCCGCCACTCCATAGC 60.108 55.000 0.00 0.00 0.00 2.97
357 358 1.569479 GAGCACAAACTCCGCCACTC 61.569 60.000 0.00 0.00 0.00 3.51
360 361 0.537143 AATGAGCACAAACTCCGCCA 60.537 50.000 0.00 0.00 35.72 5.69
364 365 3.715628 AACACAATGAGCACAAACTCC 57.284 42.857 0.00 0.00 35.72 3.85
371 372 4.697352 AGAGGATACAAACACAATGAGCAC 59.303 41.667 0.00 0.00 41.41 4.40
374 375 7.470079 CATCAAGAGGATACAAACACAATGAG 58.530 38.462 0.00 0.00 41.41 2.90
390 391 4.421948 GCTCAAAATGAAGCATCAAGAGG 58.578 43.478 0.00 0.00 39.49 3.69
408 410 3.333680 AGAGGGTGGATTTTTAAGGCTCA 59.666 43.478 0.00 0.00 0.00 4.26
413 415 6.648879 TTCAACAGAGGGTGGATTTTTAAG 57.351 37.500 0.00 0.00 0.00 1.85
414 416 7.343316 TCTTTTCAACAGAGGGTGGATTTTTAA 59.657 33.333 0.00 0.00 0.00 1.52
415 417 6.836527 TCTTTTCAACAGAGGGTGGATTTTTA 59.163 34.615 0.00 0.00 0.00 1.52
424 426 7.654022 TTTATTGTTCTTTTCAACAGAGGGT 57.346 32.000 0.00 0.00 37.57 4.34
425 427 8.981647 CATTTTATTGTTCTTTTCAACAGAGGG 58.018 33.333 0.00 0.00 37.57 4.30
509 511 7.666804 AGGCACAGCATGAATATTGTATATTCA 59.333 33.333 19.00 19.00 44.82 2.57
512 514 8.102676 TGTAGGCACAGCATGAATATTGTATAT 58.897 33.333 0.00 0.00 39.69 0.86
539 543 0.591488 TCGCTATTCGCAGTAGCACG 60.591 55.000 11.17 0.00 43.65 5.34
548 552 6.021074 CAGACATATGATTACTCGCTATTCGC 60.021 42.308 10.38 0.00 38.27 4.70
556 560 3.589988 GCCCCAGACATATGATTACTCG 58.410 50.000 10.38 0.00 0.00 4.18
559 563 3.402628 ACGCCCCAGACATATGATTAC 57.597 47.619 10.38 0.00 0.00 1.89
562 566 3.582647 TCAATACGCCCCAGACATATGAT 59.417 43.478 10.38 0.00 0.00 2.45
563 567 2.969262 TCAATACGCCCCAGACATATGA 59.031 45.455 10.38 0.00 0.00 2.15
568 572 0.908910 ATGTCAATACGCCCCAGACA 59.091 50.000 0.00 0.00 42.62 3.41
585 589 4.082625 TGTGGCAAGCTATCAAGACAAATG 60.083 41.667 0.00 0.00 0.00 2.32
611 616 6.605194 TGGCTACCAAAATATATGACTGCAAA 59.395 34.615 0.00 0.00 0.00 3.68
630 635 3.545703 AGTAGTTGATGGCATTGGCTAC 58.454 45.455 19.40 19.40 40.87 3.58
735 2968 9.567776 TTGTATTGGTGAATTTTCTTAGTCTCA 57.432 29.630 0.00 0.00 0.00 3.27
883 3120 3.268013 AGTGCTTGCACATTACGAAAC 57.732 42.857 24.82 0.00 0.00 2.78
948 3189 2.224161 GCTAGGCTGGTCTAATGAGGTG 60.224 54.545 0.00 0.00 0.00 4.00
971 3213 3.053896 GGTACACAACTGCGCCCC 61.054 66.667 4.18 0.00 0.00 5.80
973 3215 3.419759 CCGGTACACAACTGCGCC 61.420 66.667 4.18 0.00 32.61 6.53
976 3218 2.025418 CGGTCCGGTACACAACTGC 61.025 63.158 2.34 0.00 32.61 4.40
1023 3265 3.273434 CATGAAGAGAAAGATGGCCGAA 58.727 45.455 0.00 0.00 0.00 4.30
1025 3267 1.945394 CCATGAAGAGAAAGATGGCCG 59.055 52.381 0.00 0.00 0.00 6.13
1042 3284 1.292223 CGTCTGTCGTTGGTCCCAT 59.708 57.895 0.00 0.00 34.52 4.00
1086 3328 0.250727 CACCGAACAACATGACCCCT 60.251 55.000 0.00 0.00 0.00 4.79
1194 3444 0.391263 CAAACCTCCCTGTAGCGACC 60.391 60.000 0.00 0.00 0.00 4.79
1265 3515 5.058490 AGAAATCCATTTGTGCAAACAAGG 58.942 37.500 0.00 3.50 32.51 3.61
1319 3569 4.758165 TCACACAAGATATGCATGCCATAG 59.242 41.667 16.68 5.07 39.65 2.23
1381 3632 0.183014 ATGCAGGAGGAGAGCCATTG 59.817 55.000 0.00 0.00 36.29 2.82
1512 3769 5.818678 TTCAGTATACACAGTTTCCCACT 57.181 39.130 5.50 0.00 35.35 4.00
1756 4222 5.219343 TCAGCATTCTCTGTCAAGAAGAA 57.781 39.130 0.00 0.00 38.60 2.52
1818 4284 1.069090 GGTCTTGCTCACCGTCACA 59.931 57.895 0.00 0.00 0.00 3.58
1999 4465 2.437359 CTGCTTCTCCCAAGGCCG 60.437 66.667 0.00 0.00 0.00 6.13
2086 4552 6.925718 TCTTAAGATCATTGTATCGCTTGGAG 59.074 38.462 0.00 0.00 0.00 3.86
2089 4555 7.533222 GCAATCTTAAGATCATTGTATCGCTTG 59.467 37.037 18.19 9.74 32.75 4.01
2187 4653 2.239654 TCCAAGGAGGCAAGGATTAGTG 59.760 50.000 0.00 0.00 37.29 2.74
2254 4722 4.640771 ATGAACAGAAGGAGCAAGGTTA 57.359 40.909 0.00 0.00 0.00 2.85
2265 4733 6.471976 TCAGTTCGAATCAATGAACAGAAG 57.528 37.500 0.00 0.00 45.34 2.85
2417 4885 1.302431 TGGAGTCCCAATGCACGTG 60.302 57.895 12.28 12.28 40.09 4.49
2531 4999 7.646314 AGCGTAATACTAACTGGTACATACAG 58.354 38.462 0.00 0.00 38.20 2.74
2616 5084 3.911365 CACGCTTGTGCATATTCGAAAAA 59.089 39.130 0.00 0.00 39.64 1.94
2617 5085 3.487536 CACGCTTGTGCATATTCGAAAA 58.512 40.909 0.00 0.00 39.64 2.29
2618 5086 3.116063 CACGCTTGTGCATATTCGAAA 57.884 42.857 0.00 0.00 39.64 3.46
2619 5087 2.804421 CACGCTTGTGCATATTCGAA 57.196 45.000 0.00 0.00 39.64 3.71
2629 5097 9.481800 CTTTAATATATGATATGCACGCTTGTG 57.518 33.333 0.00 0.00 46.67 3.33
2630 5098 9.435688 TCTTTAATATATGATATGCACGCTTGT 57.564 29.630 0.00 0.00 0.00 3.16
2670 5138 2.375174 TGGGAATATATGGTGGAGGCAC 59.625 50.000 0.00 0.00 0.00 5.01
2671 5139 2.375174 GTGGGAATATATGGTGGAGGCA 59.625 50.000 0.00 0.00 0.00 4.75
2672 5140 2.644798 AGTGGGAATATATGGTGGAGGC 59.355 50.000 0.00 0.00 0.00 4.70
2673 5141 4.104738 ACAAGTGGGAATATATGGTGGAGG 59.895 45.833 0.00 0.00 0.00 4.30
2674 5142 5.310409 ACAAGTGGGAATATATGGTGGAG 57.690 43.478 0.00 0.00 0.00 3.86
2675 5143 5.192722 TCAACAAGTGGGAATATATGGTGGA 59.807 40.000 0.00 0.00 0.00 4.02
2676 5144 5.445069 TCAACAAGTGGGAATATATGGTGG 58.555 41.667 0.00 0.00 0.00 4.61
2677 5145 5.532406 CCTCAACAAGTGGGAATATATGGTG 59.468 44.000 0.00 0.00 0.00 4.17
2678 5146 5.694995 CCTCAACAAGTGGGAATATATGGT 58.305 41.667 0.00 0.00 0.00 3.55
2679 5147 4.520492 GCCTCAACAAGTGGGAATATATGG 59.480 45.833 0.00 0.00 0.00 2.74
2680 5148 4.520492 GGCCTCAACAAGTGGGAATATATG 59.480 45.833 0.00 0.00 0.00 1.78
2681 5149 4.167892 TGGCCTCAACAAGTGGGAATATAT 59.832 41.667 3.32 0.00 0.00 0.86
2682 5150 3.525609 TGGCCTCAACAAGTGGGAATATA 59.474 43.478 3.32 0.00 0.00 0.86
2683 5151 2.311542 TGGCCTCAACAAGTGGGAATAT 59.688 45.455 3.32 0.00 0.00 1.28
2684 5152 1.707989 TGGCCTCAACAAGTGGGAATA 59.292 47.619 3.32 0.00 0.00 1.75
2685 5153 0.482446 TGGCCTCAACAAGTGGGAAT 59.518 50.000 3.32 0.00 0.00 3.01
2686 5154 0.482446 ATGGCCTCAACAAGTGGGAA 59.518 50.000 3.32 0.00 0.00 3.97
2687 5155 1.367346 TATGGCCTCAACAAGTGGGA 58.633 50.000 3.32 0.00 0.00 4.37
2688 5156 2.214376 TTATGGCCTCAACAAGTGGG 57.786 50.000 3.32 0.00 0.00 4.61
2689 5157 4.806640 ATTTTATGGCCTCAACAAGTGG 57.193 40.909 3.32 0.00 0.00 4.00
2690 5158 7.276218 CACATTATTTTATGGCCTCAACAAGTG 59.724 37.037 3.32 0.00 0.00 3.16
2691 5159 7.039082 ACACATTATTTTATGGCCTCAACAAGT 60.039 33.333 3.32 0.00 0.00 3.16
2692 5160 7.322664 ACACATTATTTTATGGCCTCAACAAG 58.677 34.615 3.32 0.00 0.00 3.16
2693 5161 7.238486 ACACATTATTTTATGGCCTCAACAA 57.762 32.000 3.32 0.00 0.00 2.83
2738 5206 7.309177 AGATACATAGAGCTGTAGCAAATACG 58.691 38.462 6.65 0.00 45.16 3.06
2743 5211 9.913310 ATAGATAGATACATAGAGCTGTAGCAA 57.087 33.333 6.65 0.00 45.16 3.91
2942 5415 2.537401 CACGTACAACCTAGGCTAAGC 58.463 52.381 9.30 0.00 0.00 3.09
2968 5441 8.500753 TTGCACGTAATCTTATTTTAGGATGT 57.499 30.769 0.00 0.00 0.00 3.06
3049 5688 0.758734 ACCCTAATGATAGCTGCGCA 59.241 50.000 10.98 10.98 0.00 6.09
3050 5689 1.532868 CAACCCTAATGATAGCTGCGC 59.467 52.381 0.00 0.00 0.00 6.09
3127 5817 6.159988 GGACATGCAGATAGATGTAAGGTAC 58.840 44.000 0.00 0.00 32.85 3.34
3135 5825 7.756395 ATTTAAAGGGACATGCAGATAGATG 57.244 36.000 0.00 0.00 0.00 2.90
3318 6353 5.596845 TGTTTTGTTTTAAGGGACATGAGC 58.403 37.500 0.00 0.00 0.00 4.26
3464 6513 4.079901 AGGAACCTGAGATCCGTTAGTAGA 60.080 45.833 0.00 0.00 40.78 2.59


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

AutoCloner maintained by Alex Coulton.