Multiple sequence alignment - TraesCS4B01G295400

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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 TraesCS4B01G295400 chr4B 100.000 3093 0 0 1 3093 581074198 581071106 0.000000e+00 5712.0
1 TraesCS4B01G295400 chr4B 100.000 34 0 0 1019 1052 581073144 581073111 2.570000e-06 63.9
2 TraesCS4B01G295400 chr4B 100.000 34 0 0 1055 1088 581073180 581073147 2.570000e-06 63.9
3 TraesCS4B01G295400 chr4A 90.985 1564 107 11 1506 3062 616871180 616869644 0.000000e+00 2076.0
4 TraesCS4B01G295400 chr4A 85.925 746 88 11 1079 1823 616876356 616875627 0.000000e+00 780.0
5 TraesCS4B01G295400 chr4A 85.931 462 43 8 573 1028 616876816 616876371 1.000000e-129 473.0
6 TraesCS4B01G295400 chr4A 85.142 424 44 9 637 1055 616871851 616871442 1.720000e-112 416.0
7 TraesCS4B01G295400 chr4A 89.024 246 12 9 2855 3093 616868405 616868168 1.090000e-74 291.0
8 TraesCS4B01G295400 chr4A 82.353 204 30 3 1055 1258 616871478 616871281 4.100000e-39 172.0
9 TraesCS4B01G295400 chr5B 91.687 1203 73 9 1870 3065 703497877 703499059 0.000000e+00 1642.0
10 TraesCS4B01G295400 chr5B 92.796 819 55 3 1055 1870 699384148 699384965 0.000000e+00 1182.0
11 TraesCS4B01G295400 chr5B 85.093 1127 150 14 1055 2178 685499886 685500997 0.000000e+00 1134.0
12 TraesCS4B01G295400 chr5B 96.672 631 19 1 1199 1827 703497233 703497863 0.000000e+00 1048.0
13 TraesCS4B01G295400 chr5B 95.341 558 13 8 558 1102 703496677 703497234 0.000000e+00 874.0
14 TraesCS4B01G295400 chr5B 92.480 492 25 5 572 1052 699383691 699384181 0.000000e+00 693.0
15 TraesCS4B01G295400 chr5B 89.146 562 44 11 2176 2732 685501159 685501708 0.000000e+00 684.0
16 TraesCS4B01G295400 chr5B 87.276 503 55 2 553 1052 685499423 685499919 1.610000e-157 566.0
17 TraesCS4B01G295400 chr5B 89.583 336 19 6 1805 2139 699386092 699386412 2.220000e-111 412.0
18 TraesCS4B01G295400 chr5B 91.633 251 16 3 2848 3093 703499545 703499795 2.950000e-90 342.0
19 TraesCS4B01G295400 chr5B 78.801 467 88 8 1405 1869 700007709 700008166 1.390000e-78 303.0
20 TraesCS4B01G295400 chr5B 82.971 276 32 12 541 806 685323156 685322886 5.160000e-58 235.0
21 TraesCS4B01G295400 chr5B 82.971 276 32 12 541 806 685503687 685503957 5.160000e-58 235.0
22 TraesCS4B01G295400 chr5B 74.099 444 99 12 1484 1916 700040294 700040732 5.300000e-38 169.0
23 TraesCS4B01G295400 chr5B 79.688 192 27 6 78 269 586624689 586624510 9.000000e-26 128.0
24 TraesCS4B01G295400 chr5B 100.000 34 0 0 1055 1088 703497149 703497182 2.570000e-06 63.9
25 TraesCS4B01G295400 chr5D 84.038 1278 160 25 1086 2333 543508352 543507089 0.000000e+00 1190.0
26 TraesCS4B01G295400 chr5D 85.657 495 61 7 562 1048 543508852 543508360 2.130000e-141 512.0
27 TraesCS4B01G295400 chr5D 81.718 454 65 12 611 1052 552422800 552422353 2.270000e-96 363.0
28 TraesCS4B01G295400 chr5D 89.680 281 18 6 573 845 551081060 551081337 6.350000e-92 348.0
29 TraesCS4B01G295400 chr5D 84.146 328 42 7 1055 1380 551082021 551082340 3.000000e-80 309.0
30 TraesCS4B01G295400 chr5D 81.039 385 58 9 582 958 552458418 552458041 3.020000e-75 292.0
31 TraesCS4B01G295400 chr5D 76.243 543 108 14 1405 1935 551337560 551338093 5.080000e-68 268.0
32 TraesCS4B01G295400 chr5D 77.435 421 91 3 1405 1823 552032985 552032567 6.620000e-62 248.0
33 TraesCS4B01G295400 chr5D 82.095 296 36 11 1794 2089 552456809 552456531 1.430000e-58 237.0
34 TraesCS4B01G295400 chr5D 85.463 227 20 5 2849 3062 551083562 551083788 1.120000e-54 224.0
35 TraesCS4B01G295400 chr5D 84.348 230 27 7 583 804 543465677 543465449 1.870000e-52 217.0
36 TraesCS4B01G295400 chr5D 85.535 159 18 4 263 416 551080699 551080857 8.880000e-36 161.0
37 TraesCS4B01G295400 chr5D 86.607 112 15 0 941 1052 551081943 551082054 1.160000e-24 124.0
38 TraesCS4B01G295400 chr5D 80.220 182 12 8 2627 2806 543506528 543506369 7.010000e-22 115.0
39 TraesCS4B01G295400 chr6A 94.796 269 11 3 2 269 55018642 55018908 1.720000e-112 416.0
40 TraesCS4B01G295400 chr5A 94.424 269 12 3 2 269 576614401 576614135 7.980000e-111 411.0
41 TraesCS4B01G295400 chr2A 94.052 269 13 3 2 269 751746613 751746879 3.710000e-109 405.0
42 TraesCS4B01G295400 chr2A 87.407 270 30 4 1 269 4118590 4118856 1.080000e-79 307.0
43 TraesCS4B01G295400 chr7B 82.129 498 61 17 570 1052 854276 854760 4.800000e-108 401.0
44 TraesCS4B01G295400 chr7B 76.281 527 70 22 1055 1560 854727 855219 2.400000e-56 230.0
45 TraesCS4B01G295400 chr2B 93.333 270 16 2 1 269 71190870 71190602 6.210000e-107 398.0
46 TraesCS4B01G295400 chr1A 81.340 418 65 9 1405 1817 24151604 24151195 8.270000e-86 327.0
47 TraesCS4B01G295400 chr1A 77.228 202 37 5 2347 2540 519418021 519417821 3.260000e-20 110.0
48 TraesCS4B01G295400 chr3B 86.989 269 31 4 1 269 561746954 561746690 1.800000e-77 300.0
49 TraesCS4B01G295400 chr3B 86.667 270 23 8 1 269 573477386 573477643 1.400000e-73 287.0
50 TraesCS4B01G295400 chr3B 100.000 36 0 0 2708 2743 809422901 809422936 1.990000e-07 67.6
51 TraesCS4B01G295400 chr1B 79.235 183 26 6 87 269 599325241 599325411 1.950000e-22 117.0


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 TraesCS4B01G295400 chr4B 581071106 581074198 3092 True 1946.600000 5712 100.000000 1 3093 3 chr4B.!!$R1 3092
1 TraesCS4B01G295400 chr4A 616868168 616876816 8648 True 701.333333 2076 86.560000 573 3093 6 chr4A.!!$R1 2520
2 TraesCS4B01G295400 chr5B 703496677 703499795 3118 False 793.980000 1642 95.066600 558 3093 5 chr5B.!!$F5 2535
3 TraesCS4B01G295400 chr5B 699383691 699386412 2721 False 762.333333 1182 91.619667 572 2139 3 chr5B.!!$F4 1567
4 TraesCS4B01G295400 chr5B 685499423 685503957 4534 False 654.750000 1134 86.121500 541 2732 4 chr5B.!!$F3 2191
5 TraesCS4B01G295400 chr5D 543506369 543508852 2483 True 605.666667 1190 83.305000 562 2806 3 chr5D.!!$R4 2244
6 TraesCS4B01G295400 chr5D 551337560 551338093 533 False 268.000000 268 76.243000 1405 1935 1 chr5D.!!$F1 530
7 TraesCS4B01G295400 chr5D 552456531 552458418 1887 True 264.500000 292 81.567000 582 2089 2 chr5D.!!$R5 1507
8 TraesCS4B01G295400 chr5D 551080699 551083788 3089 False 233.200000 348 86.286200 263 3062 5 chr5D.!!$F2 2799
9 TraesCS4B01G295400 chr7B 854276 855219 943 False 315.500000 401 79.205000 570 1560 2 chr7B.!!$F1 990

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
47 48 0.184933 TTGTCCCACCACTCCCTTTG 59.815 55.0 0.0 0.0 0.0 2.77 F
49 50 0.185175 GTCCCACCACTCCCTTTGTT 59.815 55.0 0.0 0.0 0.0 2.83 F
517 523 0.766131 TACAGAAAAACGAGGCCCCA 59.234 50.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 1775 0.305922 CCGCCATCTTCTTCAATCGC 59.694 55.0 0.00 0.0 0.0 4.58 R
1196 1797 0.986992 GCATGCGCTCACAAAACATC 59.013 50.0 9.73 0.0 34.3 3.06 R
2148 7829 0.108138 CGAGGACCCTTGTAGCCTTG 60.108 60.0 0.00 0.0 0.0 3.61 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
43 44 3.524346 TTTTTGTCCCACCACTCCC 57.476 52.632 0.00 0.00 0.00 4.30
44 45 0.930726 TTTTTGTCCCACCACTCCCT 59.069 50.000 0.00 0.00 0.00 4.20
45 46 0.930726 TTTTGTCCCACCACTCCCTT 59.069 50.000 0.00 0.00 0.00 3.95
46 47 0.930726 TTTGTCCCACCACTCCCTTT 59.069 50.000 0.00 0.00 0.00 3.11
47 48 0.184933 TTGTCCCACCACTCCCTTTG 59.815 55.000 0.00 0.00 0.00 2.77
48 49 0.991355 TGTCCCACCACTCCCTTTGT 60.991 55.000 0.00 0.00 0.00 2.83
49 50 0.185175 GTCCCACCACTCCCTTTGTT 59.815 55.000 0.00 0.00 0.00 2.83
50 51 0.930726 TCCCACCACTCCCTTTGTTT 59.069 50.000 0.00 0.00 0.00 2.83
51 52 1.039856 CCCACCACTCCCTTTGTTTG 58.960 55.000 0.00 0.00 0.00 2.93
52 53 1.687996 CCCACCACTCCCTTTGTTTGT 60.688 52.381 0.00 0.00 0.00 2.83
53 54 2.423660 CCCACCACTCCCTTTGTTTGTA 60.424 50.000 0.00 0.00 0.00 2.41
54 55 2.884639 CCACCACTCCCTTTGTTTGTAG 59.115 50.000 0.00 0.00 0.00 2.74
55 56 2.293399 CACCACTCCCTTTGTTTGTAGC 59.707 50.000 0.00 0.00 0.00 3.58
56 57 2.174854 ACCACTCCCTTTGTTTGTAGCT 59.825 45.455 0.00 0.00 0.00 3.32
57 58 3.222603 CCACTCCCTTTGTTTGTAGCTT 58.777 45.455 0.00 0.00 0.00 3.74
58 59 3.253432 CCACTCCCTTTGTTTGTAGCTTC 59.747 47.826 0.00 0.00 0.00 3.86
59 60 3.253432 CACTCCCTTTGTTTGTAGCTTCC 59.747 47.826 0.00 0.00 0.00 3.46
60 61 2.820197 CTCCCTTTGTTTGTAGCTTCCC 59.180 50.000 0.00 0.00 0.00 3.97
61 62 2.445525 TCCCTTTGTTTGTAGCTTCCCT 59.554 45.455 0.00 0.00 0.00 4.20
62 63 2.558359 CCCTTTGTTTGTAGCTTCCCTG 59.442 50.000 0.00 0.00 0.00 4.45
63 64 2.029918 CCTTTGTTTGTAGCTTCCCTGC 60.030 50.000 0.00 0.00 0.00 4.85
64 65 2.356665 TTGTTTGTAGCTTCCCTGCA 57.643 45.000 0.00 0.00 34.14 4.41
65 66 2.584835 TGTTTGTAGCTTCCCTGCAT 57.415 45.000 0.00 0.00 36.02 3.96
66 67 2.161855 TGTTTGTAGCTTCCCTGCATG 58.838 47.619 0.00 0.00 36.02 4.06
67 68 2.224744 TGTTTGTAGCTTCCCTGCATGA 60.225 45.455 0.00 0.00 36.02 3.07
68 69 3.019564 GTTTGTAGCTTCCCTGCATGAT 58.980 45.455 0.00 0.00 36.02 2.45
69 70 4.199310 GTTTGTAGCTTCCCTGCATGATA 58.801 43.478 0.00 0.00 36.02 2.15
70 71 4.502105 TTGTAGCTTCCCTGCATGATAA 57.498 40.909 0.00 0.00 36.02 1.75
71 72 4.712051 TGTAGCTTCCCTGCATGATAAT 57.288 40.909 0.00 0.00 30.75 1.28
72 73 4.645535 TGTAGCTTCCCTGCATGATAATC 58.354 43.478 0.00 0.00 30.75 1.75
73 74 3.870538 AGCTTCCCTGCATGATAATCA 57.129 42.857 0.00 0.00 34.99 2.57
74 75 4.174704 AGCTTCCCTGCATGATAATCAA 57.825 40.909 0.00 0.00 34.99 2.57
75 76 4.737578 AGCTTCCCTGCATGATAATCAAT 58.262 39.130 0.00 0.00 34.99 2.57
76 77 4.765856 AGCTTCCCTGCATGATAATCAATC 59.234 41.667 0.00 0.00 34.99 2.67
108 109 8.563123 ACTTACTTACCTTCTAAAGCAATTCC 57.437 34.615 0.00 0.00 0.00 3.01
109 110 7.610692 ACTTACTTACCTTCTAAAGCAATTCCC 59.389 37.037 0.00 0.00 0.00 3.97
110 111 5.262009 ACTTACCTTCTAAAGCAATTCCCC 58.738 41.667 0.00 0.00 0.00 4.81
111 112 3.101643 ACCTTCTAAAGCAATTCCCCC 57.898 47.619 0.00 0.00 0.00 5.40
112 113 2.654896 ACCTTCTAAAGCAATTCCCCCT 59.345 45.455 0.00 0.00 0.00 4.79
113 114 3.077543 ACCTTCTAAAGCAATTCCCCCTT 59.922 43.478 0.00 0.00 0.00 3.95
114 115 4.293901 ACCTTCTAAAGCAATTCCCCCTTA 59.706 41.667 0.00 0.00 0.00 2.69
115 116 5.222463 ACCTTCTAAAGCAATTCCCCCTTAA 60.222 40.000 0.00 0.00 0.00 1.85
116 117 5.899547 CCTTCTAAAGCAATTCCCCCTTAAT 59.100 40.000 0.00 0.00 0.00 1.40
117 118 6.384015 CCTTCTAAAGCAATTCCCCCTTAATT 59.616 38.462 0.00 0.00 0.00 1.40
118 119 7.092891 CCTTCTAAAGCAATTCCCCCTTAATTT 60.093 37.037 0.00 0.00 0.00 1.82
119 120 8.903059 TTCTAAAGCAATTCCCCCTTAATTTA 57.097 30.769 0.00 0.00 0.00 1.40
120 121 8.903059 TCTAAAGCAATTCCCCCTTAATTTAA 57.097 30.769 0.00 0.00 0.00 1.52
121 122 9.500701 TCTAAAGCAATTCCCCCTTAATTTAAT 57.499 29.630 0.00 0.00 0.00 1.40
126 127 9.445973 AGCAATTCCCCCTTAATTTAATTATCA 57.554 29.630 0.00 0.00 0.00 2.15
150 151 9.581099 TCAAAATTTTACTCCAAACTTCTTGTC 57.419 29.630 2.44 0.00 0.00 3.18
151 152 9.364989 CAAAATTTTACTCCAAACTTCTTGTCA 57.635 29.630 2.44 0.00 0.00 3.58
152 153 9.936759 AAAATTTTACTCCAAACTTCTTGTCAA 57.063 25.926 0.37 0.00 0.00 3.18
153 154 9.586435 AAATTTTACTCCAAACTTCTTGTCAAG 57.414 29.630 6.21 6.21 0.00 3.02
154 155 5.751243 TTACTCCAAACTTCTTGTCAAGC 57.249 39.130 7.78 0.00 0.00 4.01
155 156 3.891049 ACTCCAAACTTCTTGTCAAGCT 58.109 40.909 7.78 0.00 0.00 3.74
156 157 5.036117 ACTCCAAACTTCTTGTCAAGCTA 57.964 39.130 7.78 0.00 0.00 3.32
157 158 5.437060 ACTCCAAACTTCTTGTCAAGCTAA 58.563 37.500 7.78 0.00 0.00 3.09
158 159 6.064717 ACTCCAAACTTCTTGTCAAGCTAAT 58.935 36.000 7.78 0.00 0.00 1.73
159 160 6.547510 ACTCCAAACTTCTTGTCAAGCTAATT 59.452 34.615 7.78 0.00 0.00 1.40
160 161 7.719633 ACTCCAAACTTCTTGTCAAGCTAATTA 59.280 33.333 7.78 0.00 0.00 1.40
161 162 8.458573 TCCAAACTTCTTGTCAAGCTAATTAA 57.541 30.769 7.78 0.00 0.00 1.40
162 163 8.908903 TCCAAACTTCTTGTCAAGCTAATTAAA 58.091 29.630 7.78 0.00 0.00 1.52
163 164 9.185192 CCAAACTTCTTGTCAAGCTAATTAAAG 57.815 33.333 7.78 6.98 0.00 1.85
164 165 9.185192 CAAACTTCTTGTCAAGCTAATTAAAGG 57.815 33.333 7.78 0.00 0.00 3.11
165 166 8.691661 AACTTCTTGTCAAGCTAATTAAAGGA 57.308 30.769 7.78 0.00 0.00 3.36
166 167 8.691661 ACTTCTTGTCAAGCTAATTAAAGGAA 57.308 30.769 7.78 0.00 0.00 3.36
167 168 9.131791 ACTTCTTGTCAAGCTAATTAAAGGAAA 57.868 29.630 7.78 0.00 0.00 3.13
168 169 9.965824 CTTCTTGTCAAGCTAATTAAAGGAAAA 57.034 29.630 7.78 0.00 0.00 2.29
220 221 4.654091 ACACACTTGCATTTATATGGGC 57.346 40.909 0.00 0.00 32.15 5.36
221 222 4.022603 ACACACTTGCATTTATATGGGCA 58.977 39.130 0.00 0.00 32.15 5.36
222 223 4.465660 ACACACTTGCATTTATATGGGCAA 59.534 37.500 0.00 0.00 43.32 4.52
231 232 9.757227 TTGCATTTATATGGGCAAGTAAATTAC 57.243 29.630 0.00 0.00 40.94 1.89
232 233 8.079203 TGCATTTATATGGGCAAGTAAATTACG 58.921 33.333 0.00 0.00 32.54 3.18
233 234 8.293867 GCATTTATATGGGCAAGTAAATTACGA 58.706 33.333 0.00 0.00 32.15 3.43
234 235 9.825972 CATTTATATGGGCAAGTAAATTACGAG 57.174 33.333 0.00 0.00 0.00 4.18
235 236 5.941948 ATATGGGCAAGTAAATTACGAGC 57.058 39.130 12.23 12.23 34.24 5.03
236 237 3.343941 TGGGCAAGTAAATTACGAGCT 57.656 42.857 17.42 0.00 34.99 4.09
237 238 4.475051 TGGGCAAGTAAATTACGAGCTA 57.525 40.909 17.42 8.52 34.99 3.32
238 239 4.834534 TGGGCAAGTAAATTACGAGCTAA 58.165 39.130 17.42 7.77 34.99 3.09
239 240 4.632688 TGGGCAAGTAAATTACGAGCTAAC 59.367 41.667 17.42 11.32 34.99 2.34
240 241 4.632688 GGGCAAGTAAATTACGAGCTAACA 59.367 41.667 17.42 0.00 34.99 2.41
241 242 5.446875 GGGCAAGTAAATTACGAGCTAACAC 60.447 44.000 17.42 5.64 34.99 3.32
242 243 5.121142 GGCAAGTAAATTACGAGCTAACACA 59.879 40.000 17.42 0.00 34.99 3.72
243 244 6.013689 GCAAGTAAATTACGAGCTAACACAC 58.986 40.000 13.01 0.00 32.93 3.82
244 245 6.128634 GCAAGTAAATTACGAGCTAACACACT 60.129 38.462 13.01 0.00 32.93 3.55
245 246 7.062605 GCAAGTAAATTACGAGCTAACACACTA 59.937 37.037 13.01 0.00 32.93 2.74
246 247 8.584600 CAAGTAAATTACGAGCTAACACACTAG 58.415 37.037 0.00 0.00 0.00 2.57
247 248 8.048534 AGTAAATTACGAGCTAACACACTAGA 57.951 34.615 0.00 0.00 0.00 2.43
248 249 7.967303 AGTAAATTACGAGCTAACACACTAGAC 59.033 37.037 0.00 0.00 0.00 2.59
249 250 6.512342 AATTACGAGCTAACACACTAGACT 57.488 37.500 0.00 0.00 0.00 3.24
250 251 7.621428 AATTACGAGCTAACACACTAGACTA 57.379 36.000 0.00 0.00 0.00 2.59
251 252 7.804843 ATTACGAGCTAACACACTAGACTAT 57.195 36.000 0.00 0.00 0.00 2.12
252 253 7.621428 TTACGAGCTAACACACTAGACTATT 57.379 36.000 0.00 0.00 0.00 1.73
253 254 6.512342 ACGAGCTAACACACTAGACTATTT 57.488 37.500 0.00 0.00 0.00 1.40
254 255 7.621428 ACGAGCTAACACACTAGACTATTTA 57.379 36.000 0.00 0.00 0.00 1.40
255 256 8.223177 ACGAGCTAACACACTAGACTATTTAT 57.777 34.615 0.00 0.00 0.00 1.40
256 257 9.334947 ACGAGCTAACACACTAGACTATTTATA 57.665 33.333 0.00 0.00 0.00 0.98
277 278 6.978343 ATATCTCGTTGACAAAAATCCGAA 57.022 33.333 0.00 0.00 0.00 4.30
284 285 5.513495 CGTTGACAAAAATCCGAAGAAAACA 59.487 36.000 0.00 0.00 0.00 2.83
285 286 6.034044 CGTTGACAAAAATCCGAAGAAAACAA 59.966 34.615 0.00 0.00 0.00 2.83
391 397 4.810790 ACAATCGTGTTGTTGGTTTTTGA 58.189 34.783 3.67 0.00 32.58 2.69
392 398 4.862018 ACAATCGTGTTGTTGGTTTTTGAG 59.138 37.500 3.67 0.00 32.58 3.02
416 422 7.799784 AGCAACATTAATTGAAACTGCAAATC 58.200 30.769 0.00 0.00 0.00 2.17
417 423 7.658575 AGCAACATTAATTGAAACTGCAAATCT 59.341 29.630 0.00 0.00 0.00 2.40
421 427 8.702438 ACATTAATTGAAACTGCAAATCTTTCG 58.298 29.630 0.00 0.00 0.00 3.46
422 428 5.580911 AATTGAAACTGCAAATCTTTCGC 57.419 34.783 0.00 0.00 0.00 4.70
423 429 3.706802 TGAAACTGCAAATCTTTCGCA 57.293 38.095 0.00 0.00 0.00 5.10
426 432 4.867047 TGAAACTGCAAATCTTTCGCAAAA 59.133 33.333 0.00 0.00 34.75 2.44
454 460 6.544038 AAATTTGAAACTGCAAATGCTACC 57.456 33.333 6.97 0.00 45.09 3.18
455 461 2.987413 TGAAACTGCAAATGCTACCG 57.013 45.000 6.97 0.00 42.66 4.02
456 462 2.226330 TGAAACTGCAAATGCTACCGT 58.774 42.857 6.97 0.00 42.66 4.83
457 463 2.225491 TGAAACTGCAAATGCTACCGTC 59.775 45.455 6.97 0.00 42.66 4.79
458 464 1.890876 AACTGCAAATGCTACCGTCA 58.109 45.000 6.97 0.00 42.66 4.35
459 465 2.113860 ACTGCAAATGCTACCGTCAT 57.886 45.000 6.97 0.00 42.66 3.06
460 466 3.260475 ACTGCAAATGCTACCGTCATA 57.740 42.857 6.97 0.00 42.66 2.15
461 467 3.808728 ACTGCAAATGCTACCGTCATAT 58.191 40.909 6.97 0.00 42.66 1.78
462 468 4.199310 ACTGCAAATGCTACCGTCATATT 58.801 39.130 6.97 0.00 42.66 1.28
463 469 4.035558 ACTGCAAATGCTACCGTCATATTG 59.964 41.667 6.97 0.00 42.66 1.90
464 470 3.243035 TGCAAATGCTACCGTCATATTGC 60.243 43.478 6.97 0.00 42.66 3.56
465 471 3.853307 GCAAATGCTACCGTCATATTGCC 60.853 47.826 0.00 0.00 35.04 4.52
466 472 2.928801 ATGCTACCGTCATATTGCCA 57.071 45.000 0.00 0.00 0.00 4.92
467 473 1.948104 TGCTACCGTCATATTGCCAC 58.052 50.000 0.00 0.00 0.00 5.01
468 474 1.208293 TGCTACCGTCATATTGCCACA 59.792 47.619 0.00 0.00 0.00 4.17
469 475 2.285083 GCTACCGTCATATTGCCACAA 58.715 47.619 0.00 0.00 0.00 3.33
470 476 2.878406 GCTACCGTCATATTGCCACAAT 59.122 45.455 0.00 0.00 0.00 2.71
500 506 5.684550 AAAAAGTTCGGGACACTGATTAC 57.315 39.130 0.00 0.00 0.00 1.89
503 509 3.162666 AGTTCGGGACACTGATTACAGA 58.837 45.455 0.00 0.00 46.03 3.41
505 511 4.039973 AGTTCGGGACACTGATTACAGAAA 59.960 41.667 0.00 0.00 46.03 2.52
506 512 4.610605 TCGGGACACTGATTACAGAAAA 57.389 40.909 0.00 0.00 46.03 2.29
509 515 4.377022 CGGGACACTGATTACAGAAAAACG 60.377 45.833 0.00 0.00 46.03 3.60
510 516 4.753107 GGGACACTGATTACAGAAAAACGA 59.247 41.667 0.00 0.00 46.03 3.85
511 517 5.107065 GGGACACTGATTACAGAAAAACGAG 60.107 44.000 0.00 0.00 46.03 4.18
512 518 5.107065 GGACACTGATTACAGAAAAACGAGG 60.107 44.000 0.00 0.00 46.03 4.63
514 520 3.751698 ACTGATTACAGAAAAACGAGGCC 59.248 43.478 0.00 0.00 46.03 5.19
515 521 3.078837 TGATTACAGAAAAACGAGGCCC 58.921 45.455 0.00 0.00 0.00 5.80
516 522 1.900245 TTACAGAAAAACGAGGCCCC 58.100 50.000 0.00 0.00 0.00 5.80
517 523 0.766131 TACAGAAAAACGAGGCCCCA 59.234 50.000 0.00 0.00 0.00 4.96
518 524 0.822121 ACAGAAAAACGAGGCCCCAC 60.822 55.000 0.00 0.00 0.00 4.61
519 525 1.228459 AGAAAAACGAGGCCCCACC 60.228 57.895 0.00 0.00 39.61 4.61
520 526 2.203582 AAAAACGAGGCCCCACCC 60.204 61.111 0.00 0.00 40.58 4.61
521 527 4.653888 AAAACGAGGCCCCACCCG 62.654 66.667 0.00 0.00 40.58 5.28
529 535 4.851179 GCCCCACCCGTCGGATTC 62.851 72.222 14.39 0.00 0.00 2.52
531 537 4.171103 CCCACCCGTCGGATTCCC 62.171 72.222 14.39 0.00 0.00 3.97
532 538 4.171103 CCACCCGTCGGATTCCCC 62.171 72.222 14.39 0.00 0.00 4.81
533 539 3.395702 CACCCGTCGGATTCCCCA 61.396 66.667 14.39 0.00 34.14 4.96
534 540 3.081409 ACCCGTCGGATTCCCCAG 61.081 66.667 14.39 0.00 34.14 4.45
538 544 2.190578 GTCGGATTCCCCAGCAGG 59.809 66.667 0.00 0.00 34.14 4.85
549 645 3.362797 CAGCAGGCCAGCACACAG 61.363 66.667 23.38 2.64 36.85 3.66
852 976 3.456277 GTGAGGTGGAAGATAACATCCCT 59.544 47.826 0.00 0.00 33.49 4.20
902 1026 1.067846 GCGCATACCCGATGATGACTA 60.068 52.381 0.30 0.00 37.82 2.59
1171 1769 1.046472 CCAGGTGGCCTACATCGGTA 61.046 60.000 3.32 0.00 34.56 4.02
1196 1797 0.305922 GCGATTGAAGAAGATGGCGG 59.694 55.000 0.00 0.00 0.00 6.13
1393 2009 7.285629 TCAATCTCGTGTACTATCAGGAAGATT 59.714 37.037 0.00 0.00 38.19 2.40
1403 2019 9.988815 GTACTATCAGGAAGATTATCACATTGT 57.011 33.333 0.00 0.00 38.19 2.71
1450 2068 5.923114 TCTAACTGCTTATCGCTGATTGATC 59.077 40.000 0.00 0.00 40.42 2.92
1785 2413 5.363580 AGAAAAGCTTCTTGGTTTGATTCCA 59.636 36.000 0.00 0.00 44.50 3.53
1801 2429 8.398665 GTTTGATTCCATACATGAGTTTCTACC 58.601 37.037 0.00 0.00 0.00 3.18
1930 7596 7.792374 TGCCTTATCAGATTGAAAGTCATAC 57.208 36.000 0.00 0.00 0.00 2.39
1957 7624 3.882025 GCCCGAGCAAACTCTGAG 58.118 61.111 2.45 2.45 41.09 3.35
1958 7625 1.004440 GCCCGAGCAAACTCTGAGT 60.004 57.895 4.06 4.06 41.09 3.41
1959 7626 1.294659 GCCCGAGCAAACTCTGAGTG 61.295 60.000 11.71 0.74 41.09 3.51
1960 7627 1.294659 CCCGAGCAAACTCTGAGTGC 61.295 60.000 11.71 11.40 41.09 4.40
2135 7806 0.399233 GGGTAGGAGGCCACTCTCAT 60.399 60.000 5.01 0.00 43.46 2.90
2142 7813 2.489722 GGAGGCCACTCTCATCAAAAAC 59.510 50.000 5.01 0.00 43.46 2.43
2148 7829 5.406477 GGCCACTCTCATCAAAAACAAATTC 59.594 40.000 0.00 0.00 0.00 2.17
2164 7845 2.808906 ATTCAAGGCTACAAGGGTCC 57.191 50.000 0.00 0.00 0.00 4.46
2192 8052 6.581166 GCTATTTAGTAGTTGGTTTTGTGCAC 59.419 38.462 10.75 10.75 32.72 4.57
2351 8245 3.070878 TGTTGTCAGTAGCCATGAACTCA 59.929 43.478 0.00 0.00 0.00 3.41
2519 8416 9.277783 GCTGATGTGTCCTAATTAATCTTGTAT 57.722 33.333 0.00 0.00 0.00 2.29
2618 9120 4.202050 ACTGACTTGAACATTGCAGGTTTC 60.202 41.667 7.20 2.52 0.00 2.78
2765 9272 0.977108 AGCTCTCCTCTTCAGGCAGG 60.977 60.000 0.00 0.00 40.12 4.85
2810 9317 3.502211 ACTGAGGTTGCAAAATTAGTCCG 59.498 43.478 0.00 0.00 0.00 4.79
2878 11038 5.457778 CCCCCTCTGCTTACTGTACTAGATA 60.458 48.000 0.00 0.00 0.00 1.98
2902 11065 0.393402 CAGCTCACAGGGCTATGCAA 60.393 55.000 0.00 0.00 38.03 4.08
2938 11101 2.295349 CAGGCTGAGCAACTTTGTTCAT 59.705 45.455 9.42 0.00 45.25 2.57
2947 11110 3.803778 GCAACTTTGTTCATTGGGACTTG 59.196 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.930726 AGGGAGTGGTGGGACAAAAA 59.069 50.000 0.00 0.00 44.16 1.94
26 27 0.930726 AAGGGAGTGGTGGGACAAAA 59.069 50.000 0.00 0.00 44.16 2.44
27 28 0.930726 AAAGGGAGTGGTGGGACAAA 59.069 50.000 0.00 0.00 44.16 2.83
28 29 0.184933 CAAAGGGAGTGGTGGGACAA 59.815 55.000 0.00 0.00 44.16 3.18
29 30 0.991355 ACAAAGGGAGTGGTGGGACA 60.991 55.000 0.00 0.00 0.00 4.02
30 31 0.185175 AACAAAGGGAGTGGTGGGAC 59.815 55.000 0.00 0.00 0.00 4.46
31 32 0.930726 AAACAAAGGGAGTGGTGGGA 59.069 50.000 0.00 0.00 0.00 4.37
32 33 1.039856 CAAACAAAGGGAGTGGTGGG 58.960 55.000 0.00 0.00 0.00 4.61
33 34 1.775385 ACAAACAAAGGGAGTGGTGG 58.225 50.000 0.00 0.00 0.00 4.61
34 35 2.293399 GCTACAAACAAAGGGAGTGGTG 59.707 50.000 0.00 0.00 0.00 4.17
35 36 2.174854 AGCTACAAACAAAGGGAGTGGT 59.825 45.455 0.00 0.00 0.00 4.16
36 37 2.863809 AGCTACAAACAAAGGGAGTGG 58.136 47.619 0.00 0.00 0.00 4.00
37 38 3.253432 GGAAGCTACAAACAAAGGGAGTG 59.747 47.826 0.00 0.00 0.00 3.51
38 39 3.487372 GGAAGCTACAAACAAAGGGAGT 58.513 45.455 0.00 0.00 0.00 3.85
39 40 2.820197 GGGAAGCTACAAACAAAGGGAG 59.180 50.000 0.00 0.00 0.00 4.30
40 41 2.445525 AGGGAAGCTACAAACAAAGGGA 59.554 45.455 0.00 0.00 0.00 4.20
41 42 2.558359 CAGGGAAGCTACAAACAAAGGG 59.442 50.000 0.00 0.00 0.00 3.95
42 43 2.029918 GCAGGGAAGCTACAAACAAAGG 60.030 50.000 0.00 0.00 0.00 3.11
43 44 2.622942 TGCAGGGAAGCTACAAACAAAG 59.377 45.455 0.00 0.00 34.99 2.77
44 45 2.660572 TGCAGGGAAGCTACAAACAAA 58.339 42.857 0.00 0.00 34.99 2.83
45 46 2.356665 TGCAGGGAAGCTACAAACAA 57.643 45.000 0.00 0.00 34.99 2.83
46 47 2.161855 CATGCAGGGAAGCTACAAACA 58.838 47.619 0.00 0.00 34.99 2.83
47 48 2.436417 TCATGCAGGGAAGCTACAAAC 58.564 47.619 0.00 0.00 34.99 2.93
48 49 2.877097 TCATGCAGGGAAGCTACAAA 57.123 45.000 0.00 0.00 34.99 2.83
49 50 4.502105 TTATCATGCAGGGAAGCTACAA 57.498 40.909 0.00 0.00 34.99 2.41
50 51 4.102996 TGATTATCATGCAGGGAAGCTACA 59.897 41.667 0.00 0.00 34.99 2.74
51 52 4.645535 TGATTATCATGCAGGGAAGCTAC 58.354 43.478 0.00 0.00 34.99 3.58
52 53 4.980339 TGATTATCATGCAGGGAAGCTA 57.020 40.909 0.00 0.00 34.99 3.32
53 54 3.870538 TGATTATCATGCAGGGAAGCT 57.129 42.857 0.00 0.00 34.99 3.74
54 55 4.521639 TGATTGATTATCATGCAGGGAAGC 59.478 41.667 0.00 0.00 38.35 3.86
82 83 9.011095 GGAATTGCTTTAGAAGGTAAGTAAGTT 57.989 33.333 0.00 0.00 31.22 2.66
83 84 7.610692 GGGAATTGCTTTAGAAGGTAAGTAAGT 59.389 37.037 0.00 0.00 31.22 2.24
84 85 7.067129 GGGGAATTGCTTTAGAAGGTAAGTAAG 59.933 40.741 0.00 0.00 31.22 2.34
85 86 6.888088 GGGGAATTGCTTTAGAAGGTAAGTAA 59.112 38.462 0.00 0.00 32.03 2.24
86 87 6.420638 GGGGAATTGCTTTAGAAGGTAAGTA 58.579 40.000 0.00 0.00 0.00 2.24
87 88 5.262009 GGGGAATTGCTTTAGAAGGTAAGT 58.738 41.667 0.00 0.00 0.00 2.24
88 89 4.645136 GGGGGAATTGCTTTAGAAGGTAAG 59.355 45.833 0.00 0.00 0.00 2.34
89 90 4.293901 AGGGGGAATTGCTTTAGAAGGTAA 59.706 41.667 0.00 0.00 0.00 2.85
90 91 3.856206 AGGGGGAATTGCTTTAGAAGGTA 59.144 43.478 0.00 0.00 0.00 3.08
91 92 2.654896 AGGGGGAATTGCTTTAGAAGGT 59.345 45.455 0.00 0.00 0.00 3.50
92 93 3.388552 AGGGGGAATTGCTTTAGAAGG 57.611 47.619 0.00 0.00 0.00 3.46
93 94 7.423844 AATTAAGGGGGAATTGCTTTAGAAG 57.576 36.000 0.00 0.00 0.00 2.85
94 95 7.806680 AAATTAAGGGGGAATTGCTTTAGAA 57.193 32.000 0.00 0.00 0.00 2.10
95 96 8.903059 TTAAATTAAGGGGGAATTGCTTTAGA 57.097 30.769 0.00 0.00 0.00 2.10
100 101 9.445973 TGATAATTAAATTAAGGGGGAATTGCT 57.554 29.630 0.00 0.00 0.00 3.91
124 125 9.581099 GACAAGAAGTTTGGAGTAAAATTTTGA 57.419 29.630 13.76 0.00 36.76 2.69
125 126 9.364989 TGACAAGAAGTTTGGAGTAAAATTTTG 57.635 29.630 13.76 0.00 36.76 2.44
126 127 9.936759 TTGACAAGAAGTTTGGAGTAAAATTTT 57.063 25.926 8.75 8.75 36.76 1.82
127 128 9.586435 CTTGACAAGAAGTTTGGAGTAAAATTT 57.414 29.630 9.76 0.00 36.76 1.82
128 129 7.706607 GCTTGACAAGAAGTTTGGAGTAAAATT 59.293 33.333 19.51 0.00 39.08 1.82
129 130 7.068716 AGCTTGACAAGAAGTTTGGAGTAAAAT 59.931 33.333 19.51 0.00 0.00 1.82
130 131 6.377146 AGCTTGACAAGAAGTTTGGAGTAAAA 59.623 34.615 19.51 0.00 0.00 1.52
131 132 5.885912 AGCTTGACAAGAAGTTTGGAGTAAA 59.114 36.000 19.51 0.00 0.00 2.01
132 133 5.437060 AGCTTGACAAGAAGTTTGGAGTAA 58.563 37.500 19.51 0.00 0.00 2.24
133 134 5.036117 AGCTTGACAAGAAGTTTGGAGTA 57.964 39.130 19.51 0.00 0.00 2.59
134 135 3.891049 AGCTTGACAAGAAGTTTGGAGT 58.109 40.909 19.51 0.00 0.00 3.85
135 136 6.566197 ATTAGCTTGACAAGAAGTTTGGAG 57.434 37.500 19.51 0.00 0.00 3.86
136 137 6.959639 AATTAGCTTGACAAGAAGTTTGGA 57.040 33.333 19.51 0.00 0.00 3.53
137 138 9.185192 CTTTAATTAGCTTGACAAGAAGTTTGG 57.815 33.333 19.51 0.00 0.00 3.28
138 139 9.185192 CCTTTAATTAGCTTGACAAGAAGTTTG 57.815 33.333 19.51 0.50 0.00 2.93
139 140 9.131791 TCCTTTAATTAGCTTGACAAGAAGTTT 57.868 29.630 19.51 8.79 0.00 2.66
140 141 8.691661 TCCTTTAATTAGCTTGACAAGAAGTT 57.308 30.769 19.51 10.74 0.00 2.66
141 142 8.691661 TTCCTTTAATTAGCTTGACAAGAAGT 57.308 30.769 19.51 7.05 0.00 3.01
142 143 9.965824 TTTTCCTTTAATTAGCTTGACAAGAAG 57.034 29.630 19.51 10.73 0.00 2.85
194 195 8.356657 GCCCATATAAATGCAAGTGTGTAAATA 58.643 33.333 0.00 0.00 0.00 1.40
195 196 7.147759 TGCCCATATAAATGCAAGTGTGTAAAT 60.148 33.333 0.00 0.00 0.00 1.40
196 197 6.153510 TGCCCATATAAATGCAAGTGTGTAAA 59.846 34.615 0.00 0.00 0.00 2.01
197 198 5.654209 TGCCCATATAAATGCAAGTGTGTAA 59.346 36.000 0.00 0.00 0.00 2.41
198 199 5.196695 TGCCCATATAAATGCAAGTGTGTA 58.803 37.500 0.00 0.00 0.00 2.90
199 200 4.022603 TGCCCATATAAATGCAAGTGTGT 58.977 39.130 0.00 0.00 0.00 3.72
200 201 4.652421 TGCCCATATAAATGCAAGTGTG 57.348 40.909 0.00 0.00 0.00 3.82
205 206 9.757227 GTAATTTACTTGCCCATATAAATGCAA 57.243 29.630 0.00 0.00 41.08 4.08
206 207 8.079203 CGTAATTTACTTGCCCATATAAATGCA 58.921 33.333 5.11 0.00 29.79 3.96
207 208 8.293867 TCGTAATTTACTTGCCCATATAAATGC 58.706 33.333 5.11 0.00 29.79 3.56
208 209 9.825972 CTCGTAATTTACTTGCCCATATAAATG 57.174 33.333 5.11 0.00 29.79 2.32
209 210 8.512138 GCTCGTAATTTACTTGCCCATATAAAT 58.488 33.333 5.11 0.00 0.00 1.40
210 211 7.717875 AGCTCGTAATTTACTTGCCCATATAAA 59.282 33.333 13.36 0.00 0.00 1.40
211 212 7.221450 AGCTCGTAATTTACTTGCCCATATAA 58.779 34.615 13.36 0.00 0.00 0.98
212 213 6.765403 AGCTCGTAATTTACTTGCCCATATA 58.235 36.000 13.36 0.00 0.00 0.86
213 214 5.621193 AGCTCGTAATTTACTTGCCCATAT 58.379 37.500 13.36 0.00 0.00 1.78
214 215 5.031066 AGCTCGTAATTTACTTGCCCATA 57.969 39.130 13.36 0.00 0.00 2.74
215 216 3.886123 AGCTCGTAATTTACTTGCCCAT 58.114 40.909 13.36 0.00 0.00 4.00
216 217 3.343941 AGCTCGTAATTTACTTGCCCA 57.656 42.857 13.36 0.00 0.00 5.36
217 218 4.632688 TGTTAGCTCGTAATTTACTTGCCC 59.367 41.667 13.36 6.44 0.00 5.36
218 219 5.121142 TGTGTTAGCTCGTAATTTACTTGCC 59.879 40.000 13.36 4.15 0.00 4.52
219 220 6.013689 GTGTGTTAGCTCGTAATTTACTTGC 58.986 40.000 5.11 8.30 0.00 4.01
220 221 7.347508 AGTGTGTTAGCTCGTAATTTACTTG 57.652 36.000 5.11 0.00 0.00 3.16
221 222 8.517878 TCTAGTGTGTTAGCTCGTAATTTACTT 58.482 33.333 5.11 0.00 0.00 2.24
222 223 7.967303 GTCTAGTGTGTTAGCTCGTAATTTACT 59.033 37.037 5.11 0.00 0.00 2.24
223 224 7.967303 AGTCTAGTGTGTTAGCTCGTAATTTAC 59.033 37.037 0.00 0.00 0.00 2.01
224 225 8.048534 AGTCTAGTGTGTTAGCTCGTAATTTA 57.951 34.615 0.00 0.00 0.00 1.40
225 226 6.921914 AGTCTAGTGTGTTAGCTCGTAATTT 58.078 36.000 0.00 0.00 0.00 1.82
226 227 6.512342 AGTCTAGTGTGTTAGCTCGTAATT 57.488 37.500 0.00 0.00 0.00 1.40
227 228 7.804843 ATAGTCTAGTGTGTTAGCTCGTAAT 57.195 36.000 0.00 0.00 0.00 1.89
228 229 7.621428 AATAGTCTAGTGTGTTAGCTCGTAA 57.379 36.000 0.00 0.00 0.00 3.18
229 230 7.621428 AAATAGTCTAGTGTGTTAGCTCGTA 57.379 36.000 0.00 0.00 0.00 3.43
230 231 6.512342 AAATAGTCTAGTGTGTTAGCTCGT 57.488 37.500 0.00 0.00 0.00 4.18
250 251 9.104965 TCGGATTTTTGTCAACGAGATATAAAT 57.895 29.630 0.00 0.00 33.84 1.40
251 252 8.481974 TCGGATTTTTGTCAACGAGATATAAA 57.518 30.769 0.00 0.00 0.00 1.40
252 253 8.481974 TTCGGATTTTTGTCAACGAGATATAA 57.518 30.769 0.00 0.00 0.00 0.98
253 254 7.977293 TCTTCGGATTTTTGTCAACGAGATATA 59.023 33.333 0.00 0.00 0.00 0.86
254 255 6.816640 TCTTCGGATTTTTGTCAACGAGATAT 59.183 34.615 0.00 0.00 0.00 1.63
255 256 6.160684 TCTTCGGATTTTTGTCAACGAGATA 58.839 36.000 0.00 0.00 0.00 1.98
256 257 4.994852 TCTTCGGATTTTTGTCAACGAGAT 59.005 37.500 0.00 0.00 0.00 2.75
257 258 4.373527 TCTTCGGATTTTTGTCAACGAGA 58.626 39.130 0.00 0.00 0.00 4.04
258 259 4.725556 TCTTCGGATTTTTGTCAACGAG 57.274 40.909 0.00 0.00 0.00 4.18
259 260 5.487153 TTTCTTCGGATTTTTGTCAACGA 57.513 34.783 0.00 0.00 0.00 3.85
260 261 5.513495 TGTTTTCTTCGGATTTTTGTCAACG 59.487 36.000 0.00 0.00 0.00 4.10
261 262 6.879188 TGTTTTCTTCGGATTTTTGTCAAC 57.121 33.333 0.00 0.00 0.00 3.18
336 339 5.989551 AAATGCAAACCTTGTGATTTCAC 57.010 34.783 3.72 3.72 46.59 3.18
337 340 6.347696 AGAAAATGCAAACCTTGTGATTTCA 58.652 32.000 0.00 0.00 33.71 2.69
338 341 6.849588 AGAAAATGCAAACCTTGTGATTTC 57.150 33.333 0.00 0.00 32.61 2.17
339 342 8.729805 TTTAGAAAATGCAAACCTTGTGATTT 57.270 26.923 0.00 0.00 0.00 2.17
342 345 9.823647 TTATTTTAGAAAATGCAAACCTTGTGA 57.176 25.926 9.92 0.00 38.90 3.58
391 397 7.658575 AGATTTGCAGTTTCAATTAATGTTGCT 59.341 29.630 0.00 0.00 0.00 3.91
392 398 7.799784 AGATTTGCAGTTTCAATTAATGTTGC 58.200 30.769 0.00 0.00 0.00 4.17
428 434 8.720562 GGTAGCATTTGCAGTTTCAAATTTATT 58.279 29.630 5.20 0.00 42.21 1.40
429 435 7.063308 CGGTAGCATTTGCAGTTTCAAATTTAT 59.937 33.333 5.20 0.00 42.21 1.40
430 436 6.364706 CGGTAGCATTTGCAGTTTCAAATTTA 59.635 34.615 5.20 0.00 42.21 1.40
431 437 5.177327 CGGTAGCATTTGCAGTTTCAAATTT 59.823 36.000 5.20 0.00 42.21 1.82
432 438 4.685628 CGGTAGCATTTGCAGTTTCAAATT 59.314 37.500 5.20 0.00 42.21 1.82
433 439 4.236935 CGGTAGCATTTGCAGTTTCAAAT 58.763 39.130 5.20 0.00 44.77 2.32
434 440 3.067461 ACGGTAGCATTTGCAGTTTCAAA 59.933 39.130 5.20 0.00 45.16 2.69
435 441 2.621055 ACGGTAGCATTTGCAGTTTCAA 59.379 40.909 5.20 0.00 45.16 2.69
436 442 2.225491 GACGGTAGCATTTGCAGTTTCA 59.775 45.455 5.20 0.00 45.16 2.69
437 443 2.225491 TGACGGTAGCATTTGCAGTTTC 59.775 45.455 5.20 0.00 45.16 2.78
438 444 2.226330 TGACGGTAGCATTTGCAGTTT 58.774 42.857 5.20 0.00 45.16 2.66
439 445 1.890876 TGACGGTAGCATTTGCAGTT 58.109 45.000 5.20 0.00 45.16 3.16
440 446 2.113860 ATGACGGTAGCATTTGCAGT 57.886 45.000 5.20 0.00 45.16 4.40
441 447 4.530388 CAATATGACGGTAGCATTTGCAG 58.470 43.478 5.20 0.00 45.16 4.41
442 448 3.243035 GCAATATGACGGTAGCATTTGCA 60.243 43.478 5.20 0.00 45.16 4.08
443 449 3.300009 GCAATATGACGGTAGCATTTGC 58.700 45.455 0.00 0.00 42.49 3.68
444 450 3.314913 TGGCAATATGACGGTAGCATTTG 59.685 43.478 0.00 0.00 0.00 2.32
445 451 3.315191 GTGGCAATATGACGGTAGCATTT 59.685 43.478 0.00 0.00 0.00 2.32
446 452 2.878406 GTGGCAATATGACGGTAGCATT 59.122 45.455 0.00 0.00 0.00 3.56
447 453 2.158827 TGTGGCAATATGACGGTAGCAT 60.159 45.455 0.00 0.00 0.00 3.79
448 454 1.208293 TGTGGCAATATGACGGTAGCA 59.792 47.619 0.00 0.00 0.00 3.49
449 455 1.948104 TGTGGCAATATGACGGTAGC 58.052 50.000 0.00 0.00 0.00 3.58
450 456 6.260050 AGTTTATTGTGGCAATATGACGGTAG 59.740 38.462 0.00 0.00 0.00 3.18
451 457 6.037720 CAGTTTATTGTGGCAATATGACGGTA 59.962 38.462 0.00 0.00 0.00 4.02
452 458 4.947388 AGTTTATTGTGGCAATATGACGGT 59.053 37.500 0.00 0.00 0.00 4.83
453 459 5.065859 TCAGTTTATTGTGGCAATATGACGG 59.934 40.000 0.00 6.23 0.00 4.79
454 460 6.117911 TCAGTTTATTGTGGCAATATGACG 57.882 37.500 0.00 0.00 0.00 4.35
455 461 8.755696 TTTTCAGTTTATTGTGGCAATATGAC 57.244 30.769 0.00 5.52 0.00 3.06
491 497 4.378459 GGCCTCGTTTTTCTGTAATCAGTG 60.378 45.833 0.00 0.00 41.91 3.66
497 503 1.143277 TGGGGCCTCGTTTTTCTGTAA 59.857 47.619 0.84 0.00 0.00 2.41
498 504 0.766131 TGGGGCCTCGTTTTTCTGTA 59.234 50.000 0.84 0.00 0.00 2.74
499 505 0.822121 GTGGGGCCTCGTTTTTCTGT 60.822 55.000 0.84 0.00 0.00 3.41
500 506 1.524008 GGTGGGGCCTCGTTTTTCTG 61.524 60.000 0.84 0.00 0.00 3.02
502 508 2.273179 GGGTGGGGCCTCGTTTTTC 61.273 63.158 0.84 0.00 37.43 2.29
503 509 2.203582 GGGTGGGGCCTCGTTTTT 60.204 61.111 0.84 0.00 37.43 1.94
512 518 4.851179 GAATCCGACGGGTGGGGC 62.851 72.222 15.25 0.00 33.83 5.80
514 520 4.171103 GGGAATCCGACGGGTGGG 62.171 72.222 15.25 0.00 33.83 4.61
515 521 4.171103 GGGGAATCCGACGGGTGG 62.171 72.222 15.25 0.00 33.83 4.61
516 522 3.385749 CTGGGGAATCCGACGGGTG 62.386 68.421 15.25 0.00 38.76 4.61
517 523 3.081409 CTGGGGAATCCGACGGGT 61.081 66.667 15.25 2.96 38.76 5.28
518 524 4.547367 GCTGGGGAATCCGACGGG 62.547 72.222 15.25 0.00 38.76 5.28
519 525 3.740128 CTGCTGGGGAATCCGACGG 62.740 68.421 7.84 7.84 38.76 4.79
520 526 2.202932 CTGCTGGGGAATCCGACG 60.203 66.667 0.00 0.00 38.76 5.12
521 527 2.190578 CCTGCTGGGGAATCCGAC 59.809 66.667 0.71 0.00 38.76 4.79
523 529 4.883354 GGCCTGCTGGGGAATCCG 62.883 72.222 12.06 0.00 38.76 4.18
524 530 3.728292 CTGGCCTGCTGGGGAATCC 62.728 68.421 12.06 4.10 35.12 3.01
525 531 2.123982 CTGGCCTGCTGGGGAATC 60.124 66.667 12.06 0.00 35.12 2.52
526 532 4.453892 GCTGGCCTGCTGGGGAAT 62.454 66.667 25.99 0.00 35.12 3.01
531 537 4.960866 TGTGTGCTGGCCTGCTGG 62.961 66.667 31.50 5.03 0.00 4.85
532 538 3.362797 CTGTGTGCTGGCCTGCTG 61.363 66.667 31.50 14.64 0.00 4.41
550 646 3.965539 CTGCAGCGGGTGGAAGGAG 62.966 68.421 9.49 0.00 0.00 3.69
551 647 4.020617 CTGCAGCGGGTGGAAGGA 62.021 66.667 9.49 0.00 0.00 3.36
580 676 0.551396 GAGGGTTTCGGATGGGGAAT 59.449 55.000 0.00 0.00 0.00 3.01
852 976 0.696143 TGGTGGTGGGGAAGAAGTGA 60.696 55.000 0.00 0.00 0.00 3.41
1171 1769 4.261489 GCCATCTTCTTCAATCGCATCAAT 60.261 41.667 0.00 0.00 0.00 2.57
1177 1775 0.305922 CCGCCATCTTCTTCAATCGC 59.694 55.000 0.00 0.00 0.00 4.58
1196 1797 0.986992 GCATGCGCTCACAAAACATC 59.013 50.000 9.73 0.00 34.30 3.06
1403 2019 8.783660 AGATACCAGGTCATACTTGAGAATTA 57.216 34.615 0.00 0.00 30.85 1.40
1785 2413 6.560003 TGTGGATGGTAGAAACTCATGTAT 57.440 37.500 0.00 0.00 0.00 2.29
1930 7596 2.256391 TGCTCGGGCACATTTCAAG 58.744 52.632 5.44 0.00 44.28 3.02
1953 7620 7.923344 AGTTGTAATTACATAGCTAGCACTCAG 59.077 37.037 18.69 4.35 35.89 3.35
2031 7699 9.950680 CAAGTGTAAATTTGTCAGTGTAATTCT 57.049 29.630 0.00 0.00 0.00 2.40
2135 7806 6.760770 CCTTGTAGCCTTGAATTTGTTTTTGA 59.239 34.615 0.00 0.00 0.00 2.69
2142 7813 3.193479 GGACCCTTGTAGCCTTGAATTTG 59.807 47.826 0.00 0.00 0.00 2.32
2148 7829 0.108138 CGAGGACCCTTGTAGCCTTG 60.108 60.000 0.00 0.00 0.00 3.61
2164 7845 7.234384 CACAAAACCAACTACTAAATAGCGAG 58.766 38.462 0.00 0.00 33.73 5.03
2192 8052 2.798283 CAGCATGAAAAACAAGCACCAG 59.202 45.455 0.00 0.00 44.34 4.00
2328 8196 3.403038 AGTTCATGGCTACTGACAACAC 58.597 45.455 0.00 0.00 33.27 3.32
2618 9120 0.170561 GAGCATCTGCAACAGCCTTG 59.829 55.000 4.79 0.00 45.16 3.61
2878 11038 1.352083 TAGCCCTGTGAGCTGAAGTT 58.648 50.000 0.00 0.00 41.71 2.66
2902 11065 1.610554 GCCTGAGCAACATTGGGCAT 61.611 55.000 0.00 0.00 37.33 4.40
2967 11130 1.270550 CGCCATTTCTTGCTCCAAAGT 59.729 47.619 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.