Multiple sequence alignment - TraesCS3D01G526200

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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 TraesCS3D01G526200 chr3D 100.000 3109 0 0 1 3109 605033295 605036403 0.000000e+00 5742.0
1 TraesCS3D01G526200 chr3D 79.289 956 164 24 1120 2068 604968318 604967390 3.380000e-179 638.0
2 TraesCS3D01G526200 chr3D 90.341 176 17 0 1099 1274 605027070 605026895 6.710000e-57 231.0
3 TraesCS3D01G526200 chr3D 75.056 445 63 28 2712 3109 419562626 419563069 2.480000e-36 163.0
4 TraesCS3D01G526200 chr3D 83.041 171 24 5 2943 3109 11319055 11318886 1.930000e-32 150.0
5 TraesCS3D01G526200 chr3B 95.005 2082 89 9 1032 3107 812798821 812800893 0.000000e+00 3254.0
6 TraesCS3D01G526200 chr3B 90.703 839 44 12 177 986 812797973 812798806 0.000000e+00 1086.0
7 TraesCS3D01G526200 chr3B 79.762 756 128 18 1350 2095 812726791 812726051 2.750000e-145 525.0
8 TraesCS3D01G526200 chr3B 76.901 710 158 5 1385 2091 812682478 812681772 6.250000e-107 398.0
9 TraesCS3D01G526200 chr3B 91.954 174 14 0 1100 1273 813902306 813902479 8.610000e-61 244.0
10 TraesCS3D01G526200 chr3B 87.222 180 22 1 1099 1277 812727067 812726888 1.460000e-48 204.0
11 TraesCS3D01G526200 chr3B 79.538 303 40 12 2829 3109 132574002 132574304 2.450000e-46 196.0
12 TraesCS3D01G526200 chr3B 85.556 90 6 2 34 119 812790963 812791049 1.540000e-13 87.9
13 TraesCS3D01G526200 chrUn 81.447 760 134 7 1354 2110 46203765 46204520 1.580000e-172 616.0
14 TraesCS3D01G526200 chrUn 80.721 721 130 6 1350 2066 46200224 46200939 1.260000e-153 553.0
15 TraesCS3D01G526200 chrUn 88.636 176 20 0 1100 1275 46203560 46203735 6.750000e-52 215.0
16 TraesCS3D01G526200 chr3A 80.028 726 134 8 1385 2109 737181150 737181865 7.640000e-146 527.0
17 TraesCS3D01G526200 chr3A 88.889 180 20 0 1094 1273 737180905 737181084 4.040000e-54 222.0
18 TraesCS3D01G526200 chr3A 88.439 173 11 6 1120 1285 735976319 735976149 1.890000e-47 200.0
19 TraesCS3D01G526200 chr4D 79.017 753 138 13 1363 2110 484929908 484929171 5.990000e-137 497.0
20 TraesCS3D01G526200 chr4D 90.536 317 25 4 2368 2684 205755381 205755070 6.200000e-112 414.0
21 TraesCS3D01G526200 chr4D 89.968 309 27 3 2377 2684 441122638 441122943 2.250000e-106 396.0
22 TraesCS3D01G526200 chr5A 77.929 734 144 15 1385 2110 666073510 666072787 2.850000e-120 442.0
23 TraesCS3D01G526200 chr7B 91.961 311 20 4 2377 2684 374490509 374490201 6.160000e-117 431.0
24 TraesCS3D01G526200 chr7B 75.874 286 52 12 2835 3108 559677963 559677683 2.520000e-26 130.0
25 TraesCS3D01G526200 chr1A 91.026 312 24 3 2374 2684 472152342 472152650 4.800000e-113 418.0
26 TraesCS3D01G526200 chr2A 90.385 312 28 1 2373 2684 27603489 27603798 2.890000e-110 409.0
27 TraesCS3D01G526200 chr2A 90.354 311 24 5 2377 2685 434863482 434863788 1.340000e-108 403.0
28 TraesCS3D01G526200 chr2A 75.547 274 56 9 2843 3109 398459044 398458775 1.170000e-24 124.0
29 TraesCS3D01G526200 chr2A 75.547 274 56 9 2843 3109 398856529 398856798 1.170000e-24 124.0
30 TraesCS3D01G526200 chr4B 90.385 312 26 3 2373 2683 232497779 232498087 1.040000e-109 407.0
31 TraesCS3D01G526200 chr4B 84.865 185 26 2 1098 1281 618252113 618251930 5.290000e-43 185.0
32 TraesCS3D01G526200 chr4B 79.688 256 31 16 2711 2947 559842696 559842949 6.900000e-37 165.0
33 TraesCS3D01G526200 chr7D 90.000 310 27 4 2374 2683 517003755 517004060 6.250000e-107 398.0
34 TraesCS3D01G526200 chr2B 79.452 292 43 15 2832 3109 373064065 373064353 1.140000e-44 191.0
35 TraesCS3D01G526200 chr2B 80.357 280 28 18 2854 3109 768565741 768566017 1.470000e-43 187.0
36 TraesCS3D01G526200 chr2B 78.767 292 45 17 2832 3109 373090499 373090787 2.460000e-41 180.0
37 TraesCS3D01G526200 chr2B 76.042 288 42 16 2843 3108 373091289 373091571 1.170000e-24 124.0
38 TraesCS3D01G526200 chr6D 79.252 294 44 12 2832 3109 338736091 338735799 4.090000e-44 189.0
39 TraesCS3D01G526200 chr2D 77.551 294 43 20 2832 3109 304226295 304226581 4.150000e-34 156.0
40 TraesCS3D01G526200 chr7A 93.750 48 3 0 2712 2759 634449519 634449472 4.300000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G526200 chr3D 605033295 605036403 3108 False 5742.000000 5742 100.000000 1 3109 1 chr3D.!!$F2 3108
1 TraesCS3D01G526200 chr3D 604967390 604968318 928 True 638.000000 638 79.289000 1120 2068 1 chr3D.!!$R2 948
2 TraesCS3D01G526200 chr3B 812797973 812800893 2920 False 2170.000000 3254 92.854000 177 3107 2 chr3B.!!$F4 2930
3 TraesCS3D01G526200 chr3B 812681772 812682478 706 True 398.000000 398 76.901000 1385 2091 1 chr3B.!!$R1 706
4 TraesCS3D01G526200 chr3B 812726051 812727067 1016 True 364.500000 525 83.492000 1099 2095 2 chr3B.!!$R2 996
5 TraesCS3D01G526200 chrUn 46200224 46204520 4296 False 461.333333 616 83.601333 1100 2110 3 chrUn.!!$F1 1010
6 TraesCS3D01G526200 chr3A 737180905 737181865 960 False 374.500000 527 84.458500 1094 2109 2 chr3A.!!$F1 1015
7 TraesCS3D01G526200 chr4D 484929171 484929908 737 True 497.000000 497 79.017000 1363 2110 1 chr4D.!!$R2 747
8 TraesCS3D01G526200 chr5A 666072787 666073510 723 True 442.000000 442 77.929000 1385 2110 1 chr5A.!!$R1 725

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
124 125 0.104855 TACTGATGCATGACTCCCGC 59.895 55.0 2.46 0.0 0.0 6.13 F
989 1018 0.320073 TTCAAGTAGGGACAACGCCG 60.320 55.0 0.00 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 3995 0.400213 TTTCAATGGGTGCTCCGTCT 59.600 50.0 0.0 0.0 38.76 4.18 R
2738 5065 0.248866 CCAAACAACACCAACGGCTC 60.249 55.0 0.0 0.0 0.00 4.70 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.721425 TCGGTTGTTTTCCAGGAACT 57.279 45.000 0.00 0.00 43.88 3.01
32 33 1.640917 AGGAACTGAAGGAACCGCTA 58.359 50.000 0.00 0.00 37.18 4.26
33 34 1.975680 AGGAACTGAAGGAACCGCTAA 59.024 47.619 0.00 0.00 37.18 3.09
34 35 2.572104 AGGAACTGAAGGAACCGCTAAT 59.428 45.455 0.00 0.00 37.18 1.73
35 36 2.678336 GGAACTGAAGGAACCGCTAATG 59.322 50.000 0.00 0.00 0.00 1.90
36 37 3.596214 GAACTGAAGGAACCGCTAATGA 58.404 45.455 0.00 0.00 0.00 2.57
37 38 3.695830 ACTGAAGGAACCGCTAATGAA 57.304 42.857 0.00 0.00 0.00 2.57
38 39 4.222124 ACTGAAGGAACCGCTAATGAAT 57.778 40.909 0.00 0.00 0.00 2.57
39 40 3.941483 ACTGAAGGAACCGCTAATGAATG 59.059 43.478 0.00 0.00 0.00 2.67
40 41 4.191544 CTGAAGGAACCGCTAATGAATGA 58.808 43.478 0.00 0.00 0.00 2.57
41 42 4.584874 TGAAGGAACCGCTAATGAATGAA 58.415 39.130 0.00 0.00 0.00 2.57
42 43 5.007034 TGAAGGAACCGCTAATGAATGAAA 58.993 37.500 0.00 0.00 0.00 2.69
44 45 6.152661 TGAAGGAACCGCTAATGAATGAAAAT 59.847 34.615 0.00 0.00 0.00 1.82
45 46 6.136541 AGGAACCGCTAATGAATGAAAATC 57.863 37.500 0.00 0.00 0.00 2.17
46 47 5.652014 AGGAACCGCTAATGAATGAAAATCA 59.348 36.000 0.00 0.00 0.00 2.57
48 49 5.895636 ACCGCTAATGAATGAAAATCACA 57.104 34.783 0.00 0.00 0.00 3.58
49 50 5.640732 ACCGCTAATGAATGAAAATCACAC 58.359 37.500 0.00 0.00 0.00 3.82
51 52 5.163622 CCGCTAATGAATGAAAATCACACCT 60.164 40.000 0.00 0.00 0.00 4.00
52 53 6.038161 CCGCTAATGAATGAAAATCACACCTA 59.962 38.462 0.00 0.00 0.00 3.08
53 54 7.415095 CCGCTAATGAATGAAAATCACACCTAA 60.415 37.037 0.00 0.00 0.00 2.69
54 55 7.967854 CGCTAATGAATGAAAATCACACCTAAA 59.032 33.333 0.00 0.00 0.00 1.85
55 56 9.076596 GCTAATGAATGAAAATCACACCTAAAC 57.923 33.333 0.00 0.00 0.00 2.01
58 59 8.816640 ATGAATGAAAATCACACCTAAACAAC 57.183 30.769 0.00 0.00 0.00 3.32
59 60 6.915300 TGAATGAAAATCACACCTAAACAACG 59.085 34.615 0.00 0.00 0.00 4.10
60 61 6.627395 ATGAAAATCACACCTAAACAACGA 57.373 33.333 0.00 0.00 0.00 3.85
61 62 6.438259 TGAAAATCACACCTAAACAACGAA 57.562 33.333 0.00 0.00 0.00 3.85
63 64 5.821516 AAATCACACCTAAACAACGAACA 57.178 34.783 0.00 0.00 0.00 3.18
64 65 5.821516 AATCACACCTAAACAACGAACAA 57.178 34.783 0.00 0.00 0.00 2.83
65 66 4.868450 TCACACCTAAACAACGAACAAG 57.132 40.909 0.00 0.00 0.00 3.16
66 67 4.255301 TCACACCTAAACAACGAACAAGT 58.745 39.130 0.00 0.00 0.00 3.16
67 68 5.417811 TCACACCTAAACAACGAACAAGTA 58.582 37.500 0.00 0.00 0.00 2.24
68 69 5.291614 TCACACCTAAACAACGAACAAGTAC 59.708 40.000 0.00 0.00 0.00 2.73
69 70 5.292589 CACACCTAAACAACGAACAAGTACT 59.707 40.000 0.00 0.00 0.00 2.73
71 72 7.010367 CACACCTAAACAACGAACAAGTACTAA 59.990 37.037 0.00 0.00 0.00 2.24
73 74 7.010367 CACCTAAACAACGAACAAGTACTAACA 59.990 37.037 0.00 0.00 0.00 2.41
74 75 7.223387 ACCTAAACAACGAACAAGTACTAACAG 59.777 37.037 0.00 0.00 0.00 3.16
75 76 7.436080 CCTAAACAACGAACAAGTACTAACAGA 59.564 37.037 0.00 0.00 0.00 3.41
76 77 7.599630 AAACAACGAACAAGTACTAACAGAA 57.400 32.000 0.00 0.00 0.00 3.02
77 78 6.823678 ACAACGAACAAGTACTAACAGAAG 57.176 37.500 0.00 0.00 0.00 2.85
78 79 6.567050 ACAACGAACAAGTACTAACAGAAGA 58.433 36.000 0.00 0.00 0.00 2.87
79 80 7.037438 ACAACGAACAAGTACTAACAGAAGAA 58.963 34.615 0.00 0.00 0.00 2.52
81 82 6.803642 ACGAACAAGTACTAACAGAAGAACT 58.196 36.000 0.00 0.00 0.00 3.01
96 97 6.770746 AGAAGAACTGATATTTGCATGCTT 57.229 33.333 20.33 6.43 0.00 3.91
97 98 6.793349 AGAAGAACTGATATTTGCATGCTTC 58.207 36.000 20.33 10.58 0.00 3.86
99 100 5.198965 AGAACTGATATTTGCATGCTTCCT 58.801 37.500 20.33 3.62 0.00 3.36
101 102 6.485984 AGAACTGATATTTGCATGCTTCCTAG 59.514 38.462 20.33 10.67 0.00 3.02
103 104 6.830912 ACTGATATTTGCATGCTTCCTAGTA 58.169 36.000 20.33 2.95 0.00 1.82
104 105 7.456725 ACTGATATTTGCATGCTTCCTAGTAT 58.543 34.615 20.33 7.49 0.00 2.12
109 110 6.925610 TTTGCATGCTTCCTAGTATTACTG 57.074 37.500 20.33 0.00 0.00 2.74
110 111 5.869649 TGCATGCTTCCTAGTATTACTGA 57.130 39.130 20.33 0.00 0.00 3.41
111 112 6.425210 TGCATGCTTCCTAGTATTACTGAT 57.575 37.500 20.33 0.00 0.00 2.90
112 113 6.226052 TGCATGCTTCCTAGTATTACTGATG 58.774 40.000 20.33 0.77 0.00 3.07
113 114 5.121454 GCATGCTTCCTAGTATTACTGATGC 59.879 44.000 11.37 9.87 0.00 3.91
114 115 5.869649 TGCTTCCTAGTATTACTGATGCA 57.130 39.130 15.16 15.16 32.66 3.96
115 116 6.425210 TGCTTCCTAGTATTACTGATGCAT 57.575 37.500 15.16 0.00 31.25 3.96
116 117 6.226052 TGCTTCCTAGTATTACTGATGCATG 58.774 40.000 2.46 0.00 31.25 4.06
118 119 6.367422 GCTTCCTAGTATTACTGATGCATGAC 59.633 42.308 2.46 0.00 28.40 3.06
119 120 7.603180 TTCCTAGTATTACTGATGCATGACT 57.397 36.000 2.46 0.00 0.00 3.41
120 121 7.220741 TCCTAGTATTACTGATGCATGACTC 57.779 40.000 2.46 0.00 0.00 3.36
121 122 6.209589 TCCTAGTATTACTGATGCATGACTCC 59.790 42.308 2.46 0.00 0.00 3.85
122 123 5.220710 AGTATTACTGATGCATGACTCCC 57.779 43.478 2.46 0.00 0.00 4.30
124 125 0.104855 TACTGATGCATGACTCCCGC 59.895 55.000 2.46 0.00 0.00 6.13
125 126 1.153309 CTGATGCATGACTCCCGCA 60.153 57.895 2.46 0.00 40.50 5.69
126 127 0.745486 CTGATGCATGACTCCCGCAA 60.745 55.000 2.46 0.00 39.48 4.85
128 129 0.810648 GATGCATGACTCCCGCAAAA 59.189 50.000 2.46 0.00 39.48 2.44
129 130 1.202114 GATGCATGACTCCCGCAAAAA 59.798 47.619 2.46 0.00 39.48 1.94
163 164 5.922053 TGATGGATGACAACAGATAGGAAG 58.078 41.667 0.00 0.00 0.00 3.46
164 165 5.426509 TGATGGATGACAACAGATAGGAAGT 59.573 40.000 0.00 0.00 0.00 3.01
166 167 7.290948 TGATGGATGACAACAGATAGGAAGTAT 59.709 37.037 0.00 0.00 0.00 2.12
167 168 6.820335 TGGATGACAACAGATAGGAAGTATG 58.180 40.000 0.00 0.00 0.00 2.39
168 169 5.698545 GGATGACAACAGATAGGAAGTATGC 59.301 44.000 0.00 0.00 0.00 3.14
169 170 5.675684 TGACAACAGATAGGAAGTATGCA 57.324 39.130 0.00 0.00 0.00 3.96
170 171 5.419542 TGACAACAGATAGGAAGTATGCAC 58.580 41.667 0.00 0.00 0.00 4.57
171 172 5.046663 TGACAACAGATAGGAAGTATGCACA 60.047 40.000 0.00 0.00 0.00 4.57
172 173 5.178797 ACAACAGATAGGAAGTATGCACAC 58.821 41.667 0.00 0.00 0.00 3.82
174 175 3.134804 ACAGATAGGAAGTATGCACACCC 59.865 47.826 0.00 0.00 0.00 4.61
176 177 3.389329 AGATAGGAAGTATGCACACCCTG 59.611 47.826 3.43 0.00 32.87 4.45
178 179 1.985159 AGGAAGTATGCACACCCTGAA 59.015 47.619 0.00 0.00 30.45 3.02
179 180 2.026822 AGGAAGTATGCACACCCTGAAG 60.027 50.000 0.00 0.00 30.45 3.02
180 181 2.290323 GGAAGTATGCACACCCTGAAGT 60.290 50.000 0.00 0.00 0.00 3.01
182 183 1.977854 AGTATGCACACCCTGAAGTGA 59.022 47.619 0.00 0.00 40.34 3.41
183 184 2.573462 AGTATGCACACCCTGAAGTGAT 59.427 45.455 0.00 0.00 40.34 3.06
187 188 4.835284 TGCACACCCTGAAGTGATATTA 57.165 40.909 0.00 0.00 40.34 0.98
188 189 4.769688 TGCACACCCTGAAGTGATATTAG 58.230 43.478 0.00 0.00 40.34 1.73
191 192 3.181465 ACACCCTGAAGTGATATTAGCCG 60.181 47.826 0.00 0.00 40.34 5.52
200 201 5.537300 AGTGATATTAGCCGTGAAGTGAT 57.463 39.130 0.00 0.00 0.00 3.06
201 202 5.292765 AGTGATATTAGCCGTGAAGTGATG 58.707 41.667 0.00 0.00 0.00 3.07
203 204 5.523916 GTGATATTAGCCGTGAAGTGATGTT 59.476 40.000 0.00 0.00 0.00 2.71
204 205 5.523552 TGATATTAGCCGTGAAGTGATGTTG 59.476 40.000 0.00 0.00 0.00 3.33
205 206 3.394674 TTAGCCGTGAAGTGATGTTGA 57.605 42.857 0.00 0.00 0.00 3.18
209 210 4.323417 AGCCGTGAAGTGATGTTGATAAA 58.677 39.130 0.00 0.00 0.00 1.40
210 211 4.393062 AGCCGTGAAGTGATGTTGATAAAG 59.607 41.667 0.00 0.00 0.00 1.85
213 214 6.668323 CCGTGAAGTGATGTTGATAAAGTTT 58.332 36.000 0.00 0.00 0.00 2.66
222 223 5.365403 TGTTGATAAAGTTTTACCCTGCG 57.635 39.130 0.00 0.00 0.00 5.18
235 236 0.807667 CCCTGCGTGGAAGAGAATCG 60.808 60.000 0.00 0.00 38.12 3.34
239 240 1.272781 GCGTGGAAGAGAATCGACTG 58.727 55.000 0.00 0.00 42.67 3.51
242 243 3.686128 CGTGGAAGAGAATCGACTGTAG 58.314 50.000 0.00 0.00 42.67 2.74
246 247 5.585445 GTGGAAGAGAATCGACTGTAGACTA 59.415 44.000 0.00 0.00 42.67 2.59
317 323 4.828387 AGGTAGAGTCGGATTAGGACAATC 59.172 45.833 0.00 0.00 36.87 2.67
333 339 7.630242 AGGACAATCAAAAGGTATACACATG 57.370 36.000 5.01 0.00 0.00 3.21
342 349 3.886123 AGGTATACACATGCACCTTTCC 58.114 45.455 5.01 0.00 38.23 3.13
461 468 4.695455 GCCTGCAAGTGATTACTAAACAGA 59.305 41.667 13.03 0.00 35.69 3.41
557 564 1.388093 CAGATGCGTGTCTCTGTTTCG 59.612 52.381 0.00 0.00 35.28 3.46
561 568 1.300620 CGTGTCTCTGTTTCGGCCA 60.301 57.895 2.24 0.00 0.00 5.36
573 580 4.785453 CGGCCAAGCTGACTCCCC 62.785 72.222 2.24 0.00 37.02 4.81
620 633 4.260784 GCAAAGATAATTGATTCCGTCGCT 60.261 41.667 0.00 0.00 31.84 4.93
638 651 5.171476 GTCGCTCATACATATGCCTAACAT 58.829 41.667 1.58 0.00 43.18 2.71
639 652 6.330278 GTCGCTCATACATATGCCTAACATA 58.670 40.000 1.58 0.00 45.25 2.29
692 708 4.371624 ACCATGTGAAAGAGAATCACCA 57.628 40.909 4.40 0.00 45.19 4.17
693 709 4.927049 ACCATGTGAAAGAGAATCACCAT 58.073 39.130 4.40 0.00 45.19 3.55
701 717 7.041167 TGTGAAAGAGAATCACCATGTTTAGTG 60.041 37.037 4.40 0.00 45.19 2.74
723 739 5.406477 GTGATCAATTCTTGTTTGGGAAAGC 59.594 40.000 0.00 0.00 0.00 3.51
738 754 2.814336 GGAAAGCAGGAACAGTAGTTGG 59.186 50.000 0.00 0.00 38.30 3.77
784 800 9.911788 AGAGTGTAATTATGATGATCAAAAGGT 57.088 29.630 0.00 0.00 0.00 3.50
813 829 1.047801 GCCAAACCCACAATCCAAGT 58.952 50.000 0.00 0.00 0.00 3.16
823 839 5.600484 ACCCACAATCCAAGTCATAAACAAA 59.400 36.000 0.00 0.00 0.00 2.83
827 843 7.329226 CCACAATCCAAGTCATAAACAAATCAC 59.671 37.037 0.00 0.00 0.00 3.06
982 1011 3.005578 ACTTCGTCACTTCAAGTAGGGAC 59.994 47.826 0.00 0.00 43.62 4.46
984 1013 2.960384 TCGTCACTTCAAGTAGGGACAA 59.040 45.455 9.31 0.00 46.67 3.18
985 1014 3.057734 CGTCACTTCAAGTAGGGACAAC 58.942 50.000 9.31 0.00 46.67 3.32
987 1016 1.798813 CACTTCAAGTAGGGACAACGC 59.201 52.381 0.00 0.00 0.00 4.84
988 1017 1.270678 ACTTCAAGTAGGGACAACGCC 60.271 52.381 0.00 0.00 0.00 5.68
989 1018 0.320073 TTCAAGTAGGGACAACGCCG 60.320 55.000 0.00 0.00 0.00 6.46
990 1019 1.005394 CAAGTAGGGACAACGCCGT 60.005 57.895 0.00 0.00 0.00 5.68
991 1020 1.005394 AAGTAGGGACAACGCCGTG 60.005 57.895 0.00 0.00 0.00 4.94
992 1021 3.116531 GTAGGGACAACGCCGTGC 61.117 66.667 0.00 0.00 0.00 5.34
1000 1029 2.515057 AACGCCGTGCCAACAAGA 60.515 55.556 0.00 0.00 0.00 3.02
1002 1031 2.128853 AACGCCGTGCCAACAAGATG 62.129 55.000 0.00 0.00 0.00 2.90
1003 1032 2.568090 GCCGTGCCAACAAGATGG 59.432 61.111 0.00 0.00 43.70 3.51
1009 1038 3.451894 CCAACAAGATGGCCCGGC 61.452 66.667 0.00 0.00 32.78 6.13
1010 1039 2.676121 CAACAAGATGGCCCGGCA 60.676 61.111 12.58 0.00 0.00 5.69
1011 1040 2.117206 AACAAGATGGCCCGGCAA 59.883 55.556 12.58 0.00 0.00 4.52
1012 1041 2.275380 AACAAGATGGCCCGGCAAC 61.275 57.895 12.58 0.00 0.00 4.17
1013 1042 2.361610 CAAGATGGCCCGGCAACT 60.362 61.111 12.58 1.60 0.00 3.16
1014 1043 2.044946 AAGATGGCCCGGCAACTC 60.045 61.111 12.58 4.40 0.00 3.01
1015 1044 3.976701 AAGATGGCCCGGCAACTCG 62.977 63.158 12.58 0.00 0.00 4.18
1026 1055 3.349006 CAACTCGCGGCAGTGCTT 61.349 61.111 16.11 0.00 0.00 3.91
1027 1056 3.349006 AACTCGCGGCAGTGCTTG 61.349 61.111 16.11 9.28 0.00 4.01
1336 3591 7.948357 TCACACATACTAGTTATGTCCATACC 58.052 38.462 0.00 0.00 46.84 2.73
1697 4022 0.457035 CACCCATTGAAATCCCTGCG 59.543 55.000 0.00 0.00 0.00 5.18
1711 4036 2.904866 TGCGAACCTTGGTGCCAC 60.905 61.111 0.00 0.00 0.00 5.01
1825 4150 1.474077 GGCTAAAGTTGTGCCCATCAG 59.526 52.381 7.87 0.00 40.71 2.90
1919 4244 6.458342 GGTTCAAGTTCAACAACCTTACTGAG 60.458 42.308 1.75 0.00 36.19 3.35
2110 4435 4.870991 GGTTACTGCTCAGGCTAACTAAAG 59.129 45.833 1.66 0.00 39.59 1.85
2143 4468 2.031919 GCCACCATCCGTGTGTGA 59.968 61.111 0.00 0.00 41.26 3.58
2174 4499 9.619316 CATAAATAAATTTGTTCTCACGGACAA 57.381 29.630 0.00 0.00 0.00 3.18
2190 4515 7.802738 TCACGGACAAAAGTAGTTGATAATTG 58.197 34.615 0.00 0.00 32.59 2.32
2191 4516 7.442969 TCACGGACAAAAGTAGTTGATAATTGT 59.557 33.333 0.00 0.00 32.68 2.71
2192 4517 8.073768 CACGGACAAAAGTAGTTGATAATTGTT 58.926 33.333 0.18 0.00 30.37 2.83
2233 4558 6.605471 TGTTACTGTCCAAGATATCACTGT 57.395 37.500 5.32 7.02 0.00 3.55
2235 4560 6.210584 TGTTACTGTCCAAGATATCACTGTGA 59.789 38.462 13.60 13.60 0.00 3.58
2236 4561 5.336150 ACTGTCCAAGATATCACTGTGAG 57.664 43.478 16.46 1.25 0.00 3.51
2237 4562 4.118410 CTGTCCAAGATATCACTGTGAGC 58.882 47.826 16.46 8.11 0.00 4.26
2238 4563 3.771479 TGTCCAAGATATCACTGTGAGCT 59.229 43.478 16.46 10.17 0.00 4.09
2240 4565 4.569966 GTCCAAGATATCACTGTGAGCTTG 59.430 45.833 26.77 26.77 35.56 4.01
2241 4566 3.311871 CCAAGATATCACTGTGAGCTTGC 59.688 47.826 27.55 13.93 35.01 4.01
2244 4569 4.440880 AGATATCACTGTGAGCTTGCTTC 58.559 43.478 16.46 5.27 0.00 3.86
2249 4574 3.937079 TCACTGTGAGCTTGCTTCATATG 59.063 43.478 6.36 0.00 0.00 1.78
2263 4588 9.447040 CTTGCTTCATATGTGTAAATCAATGAG 57.553 33.333 1.90 0.00 0.00 2.90
2386 4713 9.683870 ATTCTACTTATATACTTACTCCCTCCG 57.316 37.037 0.00 0.00 0.00 4.63
2397 4724 0.604578 CTCCCTCCGTACGGTGAAAA 59.395 55.000 32.15 17.81 36.47 2.29
2403 4730 3.552684 CCTCCGTACGGTGAAAAGTGTAA 60.553 47.826 32.15 10.42 36.47 2.41
2404 4731 4.050553 CTCCGTACGGTGAAAAGTGTAAA 58.949 43.478 32.16 8.68 36.47 2.01
2405 4732 4.437239 TCCGTACGGTGAAAAGTGTAAAA 58.563 39.130 32.16 6.33 36.47 1.52
2411 4738 5.404096 ACGGTGAAAAGTGTAAAAGTTTGG 58.596 37.500 0.00 0.00 31.54 3.28
2424 4751 9.005180 GTGTAAAAGTTTGGCTTTAAAATTTGC 57.995 29.630 0.00 0.00 45.91 3.68
2447 4774 6.765989 TGCCCACAAAATAGTGTACATCTATC 59.234 38.462 14.40 0.00 37.82 2.08
2451 4778 9.046296 CCACAAAATAGTGTACATCTATCTTCC 57.954 37.037 14.40 0.00 37.82 3.46
2463 4790 5.533903 ACATCTATCTTCCCAATGCACATTC 59.466 40.000 0.00 0.00 0.00 2.67
2466 4793 4.730949 ATCTTCCCAATGCACATTCAAG 57.269 40.909 0.00 0.00 0.00 3.02
2521 4848 7.116948 CGGTAATCAAGACCAATAGCATTCTAG 59.883 40.741 0.00 0.00 36.72 2.43
2536 4863 7.372260 AGCATTCTAGACATGGTCTCTTTAT 57.628 36.000 1.55 0.00 42.40 1.40
2581 4908 6.524545 TTGGGGGTAGGATAATTAAAGAGG 57.475 41.667 0.00 0.00 0.00 3.69
2592 4919 8.016054 AGGATAATTAAAGAGGAGAGAGATGGT 58.984 37.037 0.00 0.00 0.00 3.55
2600 4927 0.463474 GAGAGAGATGGTGGCTTGCC 60.463 60.000 4.43 4.43 0.00 4.52
2602 4929 2.440980 GAGATGGTGGCTTGCCCC 60.441 66.667 9.35 10.21 0.00 5.80
2606 4933 1.152052 ATGGTGGCTTGCCCCTTTT 60.152 52.632 9.35 0.00 0.00 2.27
2672 4999 7.356089 TCTATATGTACACTTTTCACCGGAT 57.644 36.000 9.46 0.00 0.00 4.18
2738 5065 2.427410 GTTGGACGCGCTTTGCTG 60.427 61.111 5.73 0.00 43.27 4.41
2739 5066 2.590291 TTGGACGCGCTTTGCTGA 60.590 55.556 5.73 0.00 43.27 4.26
2757 5084 0.248866 GAGCCGTTGGTGTTGTTTGG 60.249 55.000 0.00 0.00 0.00 3.28
2802 5129 7.766278 TCTCTCTTCTCAAAATATAAGGTGTGC 59.234 37.037 0.00 0.00 0.00 4.57
2805 5132 8.718102 TCTTCTCAAAATATAAGGTGTGCTAC 57.282 34.615 0.00 0.00 0.00 3.58
2922 5251 8.739039 TGTAGTATTGTGGATCTGGAATTTTTG 58.261 33.333 0.00 0.00 0.00 2.44
2928 5257 4.019174 TGGATCTGGAATTTTTGGCTCTC 58.981 43.478 0.00 0.00 0.00 3.20
3011 5342 5.067023 GGATTTGATTTGATGAGTGGAGGAC 59.933 44.000 0.00 0.00 0.00 3.85
3074 5405 1.004277 GGTGGGCCTTTCATAGTGTGA 59.996 52.381 4.53 0.00 34.25 3.58
3107 5438 9.726438 GTTATCTGCTAATCAACCCATACTTAT 57.274 33.333 0.00 0.00 0.00 1.73
3108 5439 9.725019 TTATCTGCTAATCAACCCATACTTATG 57.275 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.092861 TCAGTTCCTGGAAAACAACCGA 60.093 45.455 11.40 0.00 31.51 4.69
6 7 3.318275 GGTTCCTTCAGTTCCTGGAAAAC 59.682 47.826 11.40 9.72 39.85 2.43
7 8 3.562182 GGTTCCTTCAGTTCCTGGAAAA 58.438 45.455 11.40 1.15 39.85 2.29
9 10 1.071699 CGGTTCCTTCAGTTCCTGGAA 59.928 52.381 4.68 4.68 36.37 3.53
10 11 0.685097 CGGTTCCTTCAGTTCCTGGA 59.315 55.000 0.00 0.00 31.51 3.86
11 12 0.955919 GCGGTTCCTTCAGTTCCTGG 60.956 60.000 0.00 0.00 31.51 4.45
12 13 0.035458 AGCGGTTCCTTCAGTTCCTG 59.965 55.000 0.00 0.00 0.00 3.86
13 14 1.640917 TAGCGGTTCCTTCAGTTCCT 58.359 50.000 0.00 0.00 0.00 3.36
14 15 2.467566 TTAGCGGTTCCTTCAGTTCC 57.532 50.000 0.00 0.00 0.00 3.62
15 16 3.596214 TCATTAGCGGTTCCTTCAGTTC 58.404 45.455 0.00 0.00 0.00 3.01
16 17 3.695830 TCATTAGCGGTTCCTTCAGTT 57.304 42.857 0.00 0.00 0.00 3.16
17 18 3.695830 TTCATTAGCGGTTCCTTCAGT 57.304 42.857 0.00 0.00 0.00 3.41
18 19 4.191544 TCATTCATTAGCGGTTCCTTCAG 58.808 43.478 0.00 0.00 0.00 3.02
19 20 4.214986 TCATTCATTAGCGGTTCCTTCA 57.785 40.909 0.00 0.00 0.00 3.02
20 21 5.560966 TTTCATTCATTAGCGGTTCCTTC 57.439 39.130 0.00 0.00 0.00 3.46
21 22 5.975693 TTTTCATTCATTAGCGGTTCCTT 57.024 34.783 0.00 0.00 0.00 3.36
23 24 5.743872 GTGATTTTCATTCATTAGCGGTTCC 59.256 40.000 0.00 0.00 0.00 3.62
24 25 6.251376 GTGTGATTTTCATTCATTAGCGGTTC 59.749 38.462 0.00 0.00 0.00 3.62
25 26 6.092748 GTGTGATTTTCATTCATTAGCGGTT 58.907 36.000 0.00 0.00 0.00 4.44
26 27 5.393027 GGTGTGATTTTCATTCATTAGCGGT 60.393 40.000 0.00 0.00 0.00 5.68
27 28 5.036737 GGTGTGATTTTCATTCATTAGCGG 58.963 41.667 0.00 0.00 0.00 5.52
28 29 5.883661 AGGTGTGATTTTCATTCATTAGCG 58.116 37.500 0.00 0.00 0.00 4.26
29 30 9.076596 GTTTAGGTGTGATTTTCATTCATTAGC 57.923 33.333 0.00 0.00 0.00 3.09
32 33 9.260002 GTTGTTTAGGTGTGATTTTCATTCATT 57.740 29.630 0.00 0.00 0.00 2.57
33 34 7.594758 CGTTGTTTAGGTGTGATTTTCATTCAT 59.405 33.333 0.00 0.00 0.00 2.57
34 35 6.915300 CGTTGTTTAGGTGTGATTTTCATTCA 59.085 34.615 0.00 0.00 0.00 2.57
35 36 7.136119 TCGTTGTTTAGGTGTGATTTTCATTC 58.864 34.615 0.00 0.00 0.00 2.67
36 37 7.033530 TCGTTGTTTAGGTGTGATTTTCATT 57.966 32.000 0.00 0.00 0.00 2.57
37 38 6.627395 TCGTTGTTTAGGTGTGATTTTCAT 57.373 33.333 0.00 0.00 0.00 2.57
38 39 6.127980 TGTTCGTTGTTTAGGTGTGATTTTCA 60.128 34.615 0.00 0.00 0.00 2.69
39 40 6.259638 TGTTCGTTGTTTAGGTGTGATTTTC 58.740 36.000 0.00 0.00 0.00 2.29
40 41 6.197364 TGTTCGTTGTTTAGGTGTGATTTT 57.803 33.333 0.00 0.00 0.00 1.82
41 42 5.821516 TGTTCGTTGTTTAGGTGTGATTT 57.178 34.783 0.00 0.00 0.00 2.17
42 43 5.355910 ACTTGTTCGTTGTTTAGGTGTGATT 59.644 36.000 0.00 0.00 0.00 2.57
44 45 4.255301 ACTTGTTCGTTGTTTAGGTGTGA 58.745 39.130 0.00 0.00 0.00 3.58
45 46 4.609691 ACTTGTTCGTTGTTTAGGTGTG 57.390 40.909 0.00 0.00 0.00 3.82
46 47 5.422145 AGTACTTGTTCGTTGTTTAGGTGT 58.578 37.500 0.00 0.00 0.00 4.16
48 49 7.041107 TGTTAGTACTTGTTCGTTGTTTAGGT 58.959 34.615 0.00 0.00 0.00 3.08
49 50 7.436080 TCTGTTAGTACTTGTTCGTTGTTTAGG 59.564 37.037 0.00 0.00 0.00 2.69
51 52 8.700722 TTCTGTTAGTACTTGTTCGTTGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
52 53 7.546667 TCTTCTGTTAGTACTTGTTCGTTGTTT 59.453 33.333 0.00 0.00 0.00 2.83
53 54 7.037438 TCTTCTGTTAGTACTTGTTCGTTGTT 58.963 34.615 0.00 0.00 0.00 2.83
54 55 6.567050 TCTTCTGTTAGTACTTGTTCGTTGT 58.433 36.000 0.00 0.00 0.00 3.32
55 56 7.222224 AGTTCTTCTGTTAGTACTTGTTCGTTG 59.778 37.037 0.00 0.00 0.00 4.10
56 57 7.222224 CAGTTCTTCTGTTAGTACTTGTTCGTT 59.778 37.037 0.00 0.00 39.17 3.85
57 58 6.696148 CAGTTCTTCTGTTAGTACTTGTTCGT 59.304 38.462 0.00 0.00 39.17 3.85
58 59 6.916387 TCAGTTCTTCTGTTAGTACTTGTTCG 59.084 38.462 0.00 0.00 43.97 3.95
59 60 8.819643 ATCAGTTCTTCTGTTAGTACTTGTTC 57.180 34.615 0.00 0.00 43.97 3.18
64 65 9.372369 GCAAATATCAGTTCTTCTGTTAGTACT 57.628 33.333 0.00 0.00 43.97 2.73
65 66 9.151471 TGCAAATATCAGTTCTTCTGTTAGTAC 57.849 33.333 0.00 0.00 43.97 2.73
66 67 9.890629 ATGCAAATATCAGTTCTTCTGTTAGTA 57.109 29.630 0.00 0.00 43.97 1.82
67 68 8.671921 CATGCAAATATCAGTTCTTCTGTTAGT 58.328 33.333 0.00 0.00 43.97 2.24
68 69 7.642978 GCATGCAAATATCAGTTCTTCTGTTAG 59.357 37.037 14.21 0.00 43.97 2.34
69 70 7.337689 AGCATGCAAATATCAGTTCTTCTGTTA 59.662 33.333 21.98 0.00 43.97 2.41
71 72 5.651139 AGCATGCAAATATCAGTTCTTCTGT 59.349 36.000 21.98 0.00 43.97 3.41
73 74 6.183360 GGAAGCATGCAAATATCAGTTCTTCT 60.183 38.462 21.98 0.00 0.00 2.85
74 75 5.975939 GGAAGCATGCAAATATCAGTTCTTC 59.024 40.000 21.98 9.51 0.00 2.87
75 76 5.655532 AGGAAGCATGCAAATATCAGTTCTT 59.344 36.000 21.98 4.93 0.00 2.52
76 77 5.198965 AGGAAGCATGCAAATATCAGTTCT 58.801 37.500 21.98 0.27 0.00 3.01
77 78 5.511234 AGGAAGCATGCAAATATCAGTTC 57.489 39.130 21.98 10.97 0.00 3.01
78 79 6.125029 ACTAGGAAGCATGCAAATATCAGTT 58.875 36.000 21.98 1.00 0.00 3.16
79 80 5.688807 ACTAGGAAGCATGCAAATATCAGT 58.311 37.500 21.98 10.61 0.00 3.41
81 82 9.219603 GTAATACTAGGAAGCATGCAAATATCA 57.780 33.333 21.98 0.00 0.00 2.15
82 83 9.442047 AGTAATACTAGGAAGCATGCAAATATC 57.558 33.333 21.98 9.43 0.00 1.63
83 84 9.224267 CAGTAATACTAGGAAGCATGCAAATAT 57.776 33.333 21.98 4.04 0.00 1.28
84 85 8.428852 TCAGTAATACTAGGAAGCATGCAAATA 58.571 33.333 21.98 6.13 0.00 1.40
85 86 7.282585 TCAGTAATACTAGGAAGCATGCAAAT 58.717 34.615 21.98 5.29 0.00 2.32
86 87 6.649155 TCAGTAATACTAGGAAGCATGCAAA 58.351 36.000 21.98 0.00 0.00 3.68
87 88 6.233905 TCAGTAATACTAGGAAGCATGCAA 57.766 37.500 21.98 0.00 0.00 4.08
88 89 5.869649 TCAGTAATACTAGGAAGCATGCA 57.130 39.130 21.98 0.00 0.00 3.96
89 90 5.121454 GCATCAGTAATACTAGGAAGCATGC 59.879 44.000 10.51 10.51 0.00 4.06
90 91 6.226052 TGCATCAGTAATACTAGGAAGCATG 58.774 40.000 6.58 0.00 25.71 4.06
92 93 5.869649 TGCATCAGTAATACTAGGAAGCA 57.130 39.130 6.58 6.58 27.38 3.91
94 95 7.665690 AGTCATGCATCAGTAATACTAGGAAG 58.334 38.462 0.00 0.00 0.00 3.46
95 96 7.255977 GGAGTCATGCATCAGTAATACTAGGAA 60.256 40.741 0.00 0.00 0.00 3.36
96 97 6.209589 GGAGTCATGCATCAGTAATACTAGGA 59.790 42.308 0.00 0.00 0.00 2.94
97 98 6.393990 GGAGTCATGCATCAGTAATACTAGG 58.606 44.000 0.00 0.00 0.00 3.02
99 100 5.048013 CGGGAGTCATGCATCAGTAATACTA 60.048 44.000 0.00 0.00 0.00 1.82
101 102 3.990469 CGGGAGTCATGCATCAGTAATAC 59.010 47.826 0.00 0.00 0.00 1.89
103 104 2.808202 GCGGGAGTCATGCATCAGTAAT 60.808 50.000 0.00 0.00 0.00 1.89
104 105 1.473257 GCGGGAGTCATGCATCAGTAA 60.473 52.381 0.00 0.00 0.00 2.24
109 110 0.810648 TTTTGCGGGAGTCATGCATC 59.189 50.000 9.06 0.00 38.60 3.91
110 111 1.255882 TTTTTGCGGGAGTCATGCAT 58.744 45.000 9.06 0.00 38.60 3.96
111 112 2.725811 TTTTTGCGGGAGTCATGCA 58.274 47.368 4.57 4.57 36.72 3.96
132 133 6.064060 TCTGTTGTCATCCATCAGACTTTTT 58.936 36.000 0.00 0.00 42.33 1.94
133 134 5.624159 TCTGTTGTCATCCATCAGACTTTT 58.376 37.500 0.00 0.00 42.33 2.27
134 135 5.233083 TCTGTTGTCATCCATCAGACTTT 57.767 39.130 0.00 0.00 42.33 2.66
135 136 4.897509 TCTGTTGTCATCCATCAGACTT 57.102 40.909 0.00 0.00 42.33 3.01
139 140 5.541953 TCCTATCTGTTGTCATCCATCAG 57.458 43.478 0.00 0.00 40.69 2.90
140 141 5.426509 ACTTCCTATCTGTTGTCATCCATCA 59.573 40.000 0.00 0.00 0.00 3.07
141 142 5.923204 ACTTCCTATCTGTTGTCATCCATC 58.077 41.667 0.00 0.00 0.00 3.51
142 143 5.965033 ACTTCCTATCTGTTGTCATCCAT 57.035 39.130 0.00 0.00 0.00 3.41
143 144 6.686378 GCATACTTCCTATCTGTTGTCATCCA 60.686 42.308 0.00 0.00 0.00 3.41
144 145 5.698545 GCATACTTCCTATCTGTTGTCATCC 59.301 44.000 0.00 0.00 0.00 3.51
145 146 6.201806 GTGCATACTTCCTATCTGTTGTCATC 59.798 42.308 0.00 0.00 0.00 2.92
146 147 6.051717 GTGCATACTTCCTATCTGTTGTCAT 58.948 40.000 0.00 0.00 0.00 3.06
147 148 5.046663 TGTGCATACTTCCTATCTGTTGTCA 60.047 40.000 0.00 0.00 0.00 3.58
148 149 5.292101 GTGTGCATACTTCCTATCTGTTGTC 59.708 44.000 6.31 0.00 0.00 3.18
149 150 5.178797 GTGTGCATACTTCCTATCTGTTGT 58.821 41.667 6.31 0.00 0.00 3.32
150 151 4.572389 GGTGTGCATACTTCCTATCTGTTG 59.428 45.833 13.64 0.00 0.00 3.33
151 152 4.384208 GGGTGTGCATACTTCCTATCTGTT 60.384 45.833 13.64 0.00 0.00 3.16
152 153 3.134804 GGGTGTGCATACTTCCTATCTGT 59.865 47.826 13.64 0.00 0.00 3.41
153 154 3.389329 AGGGTGTGCATACTTCCTATCTG 59.611 47.826 13.64 0.00 31.51 2.90
155 156 3.388024 TCAGGGTGTGCATACTTCCTATC 59.612 47.826 13.64 0.00 31.86 2.08
156 157 3.384168 TCAGGGTGTGCATACTTCCTAT 58.616 45.455 13.64 0.00 31.86 2.57
158 159 1.656587 TCAGGGTGTGCATACTTCCT 58.343 50.000 13.64 9.37 32.76 3.36
159 160 2.290323 ACTTCAGGGTGTGCATACTTCC 60.290 50.000 13.64 7.14 0.00 3.46
160 161 2.744202 CACTTCAGGGTGTGCATACTTC 59.256 50.000 13.64 6.48 33.04 3.01
161 162 2.371841 TCACTTCAGGGTGTGCATACTT 59.628 45.455 13.64 0.00 38.28 2.24
163 164 2.472695 TCACTTCAGGGTGTGCATAC 57.527 50.000 4.79 4.79 38.28 2.39
164 165 5.372343 AATATCACTTCAGGGTGTGCATA 57.628 39.130 0.00 0.00 38.28 3.14
166 167 3.719268 AATATCACTTCAGGGTGTGCA 57.281 42.857 0.00 0.00 38.28 4.57
167 168 3.561725 GCTAATATCACTTCAGGGTGTGC 59.438 47.826 0.00 0.00 38.28 4.57
168 169 4.130118 GGCTAATATCACTTCAGGGTGTG 58.870 47.826 0.00 0.00 38.28 3.82
169 170 3.181465 CGGCTAATATCACTTCAGGGTGT 60.181 47.826 0.00 0.00 38.28 4.16
170 171 3.181465 ACGGCTAATATCACTTCAGGGTG 60.181 47.826 0.00 0.00 38.44 4.61
171 172 3.039011 ACGGCTAATATCACTTCAGGGT 58.961 45.455 0.00 0.00 0.00 4.34
172 173 3.069586 TCACGGCTAATATCACTTCAGGG 59.930 47.826 0.00 0.00 0.00 4.45
174 175 5.233050 CACTTCACGGCTAATATCACTTCAG 59.767 44.000 0.00 0.00 0.00 3.02
176 177 5.348986 TCACTTCACGGCTAATATCACTTC 58.651 41.667 0.00 0.00 0.00 3.01
178 179 5.163405 ACATCACTTCACGGCTAATATCACT 60.163 40.000 0.00 0.00 0.00 3.41
179 180 5.050490 ACATCACTTCACGGCTAATATCAC 58.950 41.667 0.00 0.00 0.00 3.06
180 181 5.276461 ACATCACTTCACGGCTAATATCA 57.724 39.130 0.00 0.00 0.00 2.15
182 183 5.670485 TCAACATCACTTCACGGCTAATAT 58.330 37.500 0.00 0.00 0.00 1.28
183 184 5.079689 TCAACATCACTTCACGGCTAATA 57.920 39.130 0.00 0.00 0.00 0.98
187 188 2.479566 ATCAACATCACTTCACGGCT 57.520 45.000 0.00 0.00 0.00 5.52
188 189 4.154195 ACTTTATCAACATCACTTCACGGC 59.846 41.667 0.00 0.00 0.00 5.68
191 192 9.394477 GGTAAAACTTTATCAACATCACTTCAC 57.606 33.333 0.00 0.00 0.00 3.18
200 201 4.822896 ACGCAGGGTAAAACTTTATCAACA 59.177 37.500 0.00 0.00 0.00 3.33
201 202 5.151389 CACGCAGGGTAAAACTTTATCAAC 58.849 41.667 0.00 0.00 0.00 3.18
203 204 3.754323 CCACGCAGGGTAAAACTTTATCA 59.246 43.478 0.00 0.00 0.00 2.15
204 205 4.004982 TCCACGCAGGGTAAAACTTTATC 58.995 43.478 0.00 0.00 38.24 1.75
205 206 4.023726 TCCACGCAGGGTAAAACTTTAT 57.976 40.909 0.00 0.00 38.24 1.40
209 210 1.418637 TCTTCCACGCAGGGTAAAACT 59.581 47.619 0.00 0.00 38.24 2.66
210 211 1.804748 CTCTTCCACGCAGGGTAAAAC 59.195 52.381 0.00 0.00 38.24 2.43
213 214 1.344065 TTCTCTTCCACGCAGGGTAA 58.656 50.000 0.00 0.00 38.24 2.85
222 223 4.396790 AGTCTACAGTCGATTCTCTTCCAC 59.603 45.833 0.00 0.00 0.00 4.02
242 243 8.080083 TCCTTCGTTGTTAAACAAGAATAGTC 57.920 34.615 0.00 0.00 39.00 2.59
246 247 7.936584 TGATTCCTTCGTTGTTAAACAAGAAT 58.063 30.769 0.00 0.00 39.00 2.40
333 339 0.034896 TCAGAGTTCGGGAAAGGTGC 59.965 55.000 0.00 0.00 0.00 5.01
342 349 2.234908 AGGACTTGGATTCAGAGTTCGG 59.765 50.000 0.00 0.00 0.00 4.30
557 564 4.785453 CGGGGAGTCAGCTTGGCC 62.785 72.222 0.00 0.00 0.00 5.36
659 675 7.015292 TCTCTTTCACATGGTACTAGACAACTT 59.985 37.037 0.00 0.00 0.00 2.66
723 739 2.270352 TTGGCCAACTACTGTTCCTG 57.730 50.000 16.05 0.00 33.52 3.86
738 754 3.443681 TCTTGTAATTAGCTGGCTTTGGC 59.556 43.478 0.00 0.00 37.82 4.52
784 800 2.243810 GTGGGTTTGGCAAAGGTATCA 58.756 47.619 13.94 4.90 0.00 2.15
790 806 1.415659 TGGATTGTGGGTTTGGCAAAG 59.584 47.619 13.94 0.00 0.00 2.77
813 829 7.396907 ACTGGATTCATGGTGATTTGTTTATGA 59.603 33.333 0.00 0.00 0.00 2.15
823 839 4.164796 TGAGCTTACTGGATTCATGGTGAT 59.835 41.667 0.00 0.00 0.00 3.06
827 843 4.125703 GTCTGAGCTTACTGGATTCATGG 58.874 47.826 0.00 0.00 0.00 3.66
982 1011 2.128853 ATCTTGTTGGCACGGCGTTG 62.129 55.000 11.19 7.52 0.00 4.10
984 1013 2.281484 ATCTTGTTGGCACGGCGT 60.281 55.556 6.77 6.77 0.00 5.68
985 1014 2.176546 CATCTTGTTGGCACGGCG 59.823 61.111 4.80 4.80 0.00 6.46
992 1021 3.451894 GCCGGGCCATCTTGTTGG 61.452 66.667 8.12 0.00 39.94 3.77
993 1022 2.274645 TTGCCGGGCCATCTTGTTG 61.275 57.895 17.97 0.00 0.00 3.33
994 1023 2.117206 TTGCCGGGCCATCTTGTT 59.883 55.556 17.97 0.00 0.00 2.83
995 1024 2.676471 GTTGCCGGGCCATCTTGT 60.676 61.111 17.97 0.00 0.00 3.16
1009 1038 3.349006 AAGCACTGCCGCGAGTTG 61.349 61.111 8.23 0.00 36.85 3.16
1010 1039 3.349006 CAAGCACTGCCGCGAGTT 61.349 61.111 8.23 0.00 36.85 3.01
1023 1052 2.488820 GCTAGCAAGGCAGCAAGC 59.511 61.111 10.63 0.00 44.65 4.01
1091 1120 3.976701 TTCTTAGGCAGCGCAGGGC 62.977 63.158 11.47 14.35 44.05 5.19
1095 1124 1.079127 GGAGTTCTTAGGCAGCGCA 60.079 57.895 11.47 0.00 0.00 6.09
1104 1133 3.199946 GGTGGATCATGTGGGAGTTCTTA 59.800 47.826 0.00 0.00 0.00 2.10
1324 3579 8.479689 TCGACTTCTTAATTGGTATGGACATAA 58.520 33.333 0.00 0.00 0.00 1.90
1336 3591 9.994432 AATTTAAGCATCTCGACTTCTTAATTG 57.006 29.630 0.00 0.00 31.73 2.32
1670 3995 0.400213 TTTCAATGGGTGCTCCGTCT 59.600 50.000 0.00 0.00 38.76 4.18
1697 4022 1.535204 CCCATGTGGCACCAAGGTTC 61.535 60.000 16.26 0.00 0.00 3.62
1711 4036 2.544685 GAACGATGTCAGACTCCCATG 58.455 52.381 1.31 0.00 0.00 3.66
1790 4115 4.745125 ACTTTAGCCATGATATCGAACACG 59.255 41.667 0.00 0.00 0.00 4.49
1919 4244 3.365291 TAGCACGCCGTGGACATCC 62.365 63.158 20.07 0.36 33.64 3.51
2110 4435 1.290009 GGCCACATTGAAGCCACAC 59.710 57.895 14.23 0.00 46.34 3.82
2164 4489 7.596749 ATTATCAACTACTTTTGTCCGTGAG 57.403 36.000 0.00 0.00 0.00 3.51
2233 4558 6.598850 TGATTTACACATATGAAGCAAGCTCA 59.401 34.615 10.38 3.75 0.00 4.26
2235 4560 7.395190 TTGATTTACACATATGAAGCAAGCT 57.605 32.000 10.38 0.00 0.00 3.74
2236 4561 7.916977 TCATTGATTTACACATATGAAGCAAGC 59.083 33.333 10.38 0.70 31.94 4.01
2237 4562 9.447040 CTCATTGATTTACACATATGAAGCAAG 57.553 33.333 10.38 3.61 31.94 4.01
2238 4563 9.176460 TCTCATTGATTTACACATATGAAGCAA 57.824 29.630 10.38 8.73 32.80 3.91
2240 4565 9.661187 CTTCTCATTGATTTACACATATGAAGC 57.339 33.333 10.38 0.00 0.00 3.86
2293 4619 7.992692 CGAGTTCAAATTTCTTTTTGTTCATCG 59.007 33.333 0.00 0.00 37.73 3.84
2361 4688 8.664079 ACGGAGGGAGTAAGTATATAAGTAGAA 58.336 37.037 0.00 0.00 0.00 2.10
2367 4694 6.173339 CCGTACGGAGGGAGTAAGTATATAA 58.827 44.000 30.64 0.00 37.50 0.98
2377 4704 0.540365 TTTCACCGTACGGAGGGAGT 60.540 55.000 39.52 14.50 38.96 3.85
2386 4713 6.469915 CCAAACTTTTACACTTTTCACCGTAC 59.530 38.462 0.00 0.00 0.00 3.67
2411 4738 7.802720 CACTATTTTGTGGGCAAATTTTAAAGC 59.197 33.333 0.00 0.00 43.26 3.51
2424 4751 8.964476 AAGATAGATGTACACTATTTTGTGGG 57.036 34.615 14.92 0.00 41.84 4.61
2440 4767 5.533528 TGAATGTGCATTGGGAAGATAGATG 59.466 40.000 1.77 0.00 0.00 2.90
2447 4774 3.947910 ACTTGAATGTGCATTGGGAAG 57.052 42.857 1.77 4.76 0.00 3.46
2478 4805 5.661056 TTACCGTGTGATGAGAGAGAAAT 57.339 39.130 0.00 0.00 0.00 2.17
2479 4806 5.185056 TGATTACCGTGTGATGAGAGAGAAA 59.815 40.000 0.00 0.00 0.00 2.52
2488 4815 3.595173 TGGTCTTGATTACCGTGTGATG 58.405 45.455 0.00 0.00 40.08 3.07
2521 4848 8.125448 GCATGTAGAAAATAAAGAGACCATGTC 58.875 37.037 0.00 0.00 0.00 3.06
2536 4863 6.150976 CCAATGACCTAAGTGCATGTAGAAAA 59.849 38.462 7.92 0.00 0.00 2.29
2540 4867 3.879295 CCCAATGACCTAAGTGCATGTAG 59.121 47.826 0.00 0.00 0.00 2.74
2581 4908 0.463474 GGCAAGCCACCATCTCTCTC 60.463 60.000 6.14 0.00 35.81 3.20
2592 4919 0.686224 CATTGAAAAGGGGCAAGCCA 59.314 50.000 13.87 0.00 37.98 4.75
2672 4999 4.417437 GAGTTAGGCATATACTCCCTCCA 58.583 47.826 8.57 0.00 33.77 3.86
2704 5031 5.334879 CGTCCAACCCTTCTAGTTTTCATTG 60.335 44.000 0.00 0.00 0.00 2.82
2715 5042 2.676163 AAAGCGCGTCCAACCCTTCT 62.676 55.000 8.43 0.00 0.00 2.85
2738 5065 0.248866 CCAAACAACACCAACGGCTC 60.249 55.000 0.00 0.00 0.00 4.70
2739 5066 0.968393 ACCAAACAACACCAACGGCT 60.968 50.000 0.00 0.00 0.00 5.52
2860 5187 6.888088 AGTTCATTTCATGATGAGTCCAATGA 59.112 34.615 13.43 13.43 39.39 2.57
2897 5224 8.190784 CCAAAAATTCCAGATCCACAATACTAC 58.809 37.037 0.00 0.00 0.00 2.73
2922 5251 8.784043 TCTTTAACTTTTATCAAGTTGAGAGCC 58.216 33.333 11.91 0.00 40.38 4.70
2964 5295 3.014623 CCCTCGGTTCCAAAATAAGGTC 58.985 50.000 0.00 0.00 0.00 3.85
3011 5342 6.869421 AAAAAGAAAACACACTTCATCGTG 57.131 33.333 0.00 0.00 40.67 4.35
3033 5364 9.137459 CCCACCATAACACCACATTATAAATAA 57.863 33.333 0.00 0.00 0.00 1.40
3045 5376 0.485099 AAAGGCCCACCATAACACCA 59.515 50.000 0.00 0.00 39.06 4.17
3074 5405 5.527582 GGTTGATTAGCAGATAACACCGAAT 59.472 40.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.