Multiple sequence alignment - TraesCS2A01G246700

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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 TraesCS2A01G246700 chr2A 100.000 7398 0 0 1 7398 361379397 361386794 0.000000e+00 13662.0
1 TraesCS2A01G246700 chr2A 95.724 2549 100 5 2723 5270 65246876 65244336 0.000000e+00 4095.0
2 TraesCS2A01G246700 chr2A 92.196 1166 40 13 5255 6408 65244259 65243133 0.000000e+00 1602.0
3 TraesCS2A01G246700 chr2A 86.433 1253 87 37 990 2221 65295195 65294005 0.000000e+00 1295.0
4 TraesCS2A01G246700 chr2A 92.120 368 25 3 2305 2670 65294002 65293637 3.960000e-142 516.0
5 TraesCS2A01G246700 chr2A 95.775 142 3 1 7044 7182 196518009 196518150 7.470000e-55 226.0
6 TraesCS2A01G246700 chr2A 95.714 140 4 1 7044 7181 384675708 384675847 2.690000e-54 224.0
7 TraesCS2A01G246700 chr2A 93.960 149 4 3 7044 7188 63805753 63805900 3.470000e-53 220.0
8 TraesCS2A01G246700 chr2A 96.970 66 2 0 2665 2730 65271139 65271074 2.180000e-20 111.0
9 TraesCS2A01G246700 chr2B 96.817 5750 114 24 1039 6759 354880391 354874682 0.000000e+00 9540.0
10 TraesCS2A01G246700 chr2B 88.696 345 32 3 6702 7046 354874445 354874108 1.490000e-111 414.0
11 TraesCS2A01G246700 chr2B 94.495 218 12 0 7181 7398 354874105 354873888 3.310000e-88 337.0
12 TraesCS2A01G246700 chr2B 88.889 72 7 1 7181 7252 357892918 357892988 3.680000e-13 87.9
13 TraesCS2A01G246700 chr2D 97.552 5229 104 10 990 6209 294472727 294477940 0.000000e+00 8925.0
14 TraesCS2A01G246700 chr2D 94.230 4281 185 29 2305 6556 63626370 63622123 0.000000e+00 6481.0
15 TraesCS2A01G246700 chr2D 95.088 570 22 3 1657 2221 63626941 63626373 0.000000e+00 893.0
16 TraesCS2A01G246700 chr2D 93.833 600 16 7 990 1586 63627523 63626942 0.000000e+00 883.0
17 TraesCS2A01G246700 chr2D 93.864 440 21 3 6608 7043 294478617 294479054 0.000000e+00 658.0
18 TraesCS2A01G246700 chr2D 94.620 316 6 7 6253 6561 294477939 294478250 5.190000e-131 479.0
19 TraesCS2A01G246700 chr2D 95.413 218 10 0 7181 7398 294479061 294479278 1.530000e-91 348.0
20 TraesCS2A01G246700 chr2D 97.778 90 2 0 2218 2307 643235819 643235908 9.940000e-34 156.0
21 TraesCS2A01G246700 chr2D 91.429 105 7 2 2215 2319 534925458 534925560 7.740000e-30 143.0
22 TraesCS2A01G246700 chr2D 89.474 95 10 0 6949 7043 404295928 404296022 3.630000e-23 121.0
23 TraesCS2A01G246700 chr2D 90.141 71 7 0 7182 7252 404296029 404296099 7.900000e-15 93.5
24 TraesCS2A01G246700 chr2D 88.732 71 7 1 7183 7253 344358799 344358730 1.320000e-12 86.1
25 TraesCS2A01G246700 chr2D 86.076 79 5 3 6598 6672 63622052 63621976 6.150000e-11 80.5
26 TraesCS2A01G246700 chr1A 94.427 969 51 3 1 966 570045229 570046197 0.000000e+00 1487.0
27 TraesCS2A01G246700 chr1A 95.714 140 3 1 7044 7180 330766007 330765868 9.660000e-54 222.0
28 TraesCS2A01G246700 chr1A 93.878 147 8 1 7044 7189 397087585 397087439 3.470000e-53 220.0
29 TraesCS2A01G246700 chr1A 94.928 138 7 0 7044 7181 495129027 495129164 4.490000e-52 217.0
30 TraesCS2A01G246700 chr1A 94.326 141 6 1 7044 7182 420572892 420573032 1.620000e-51 215.0
31 TraesCS2A01G246700 chr5A 94.324 969 51 4 1 966 616364008 616364975 0.000000e+00 1482.0
32 TraesCS2A01G246700 chr5A 94.130 971 54 3 1 968 610753749 610752779 0.000000e+00 1474.0
33 TraesCS2A01G246700 chr5A 94.021 970 54 4 1 966 211619570 211620539 0.000000e+00 1467.0
34 TraesCS2A01G246700 chr5A 95.775 142 3 1 7044 7182 390235266 390235125 7.470000e-55 226.0
35 TraesCS2A01G246700 chr5A 95.105 143 6 1 7044 7185 693639118 693638976 2.690000e-54 224.0
36 TraesCS2A01G246700 chr5A 92.053 151 8 2 7044 7190 10831225 10831075 7.520000e-50 209.0
37 TraesCS2A01G246700 chr5A 91.398 93 8 0 6951 7043 125992917 125992825 2.170000e-25 128.0
38 TraesCS2A01G246700 chrUn 94.014 969 55 3 1 966 1715771 1716739 0.000000e+00 1465.0
39 TraesCS2A01G246700 chrUn 93.602 969 58 4 1 966 363162999 363162032 0.000000e+00 1443.0
40 TraesCS2A01G246700 chrUn 94.366 142 5 1 7044 7182 71546737 71546596 1.620000e-51 215.0
41 TraesCS2A01G246700 chrUn 94.366 142 5 1 7044 7182 268022317 268022176 1.620000e-51 215.0
42 TraesCS2A01G246700 chr3A 94.014 969 54 4 1 966 698713259 698712292 0.000000e+00 1465.0
43 TraesCS2A01G246700 chr3A 94.014 969 55 3 1 966 713897029 713896061 0.000000e+00 1465.0
44 TraesCS2A01G246700 chr3A 93.588 967 60 2 1 965 666226308 666225342 0.000000e+00 1441.0
45 TraesCS2A01G246700 chr3A 96.350 137 5 0 7044 7180 732662744 732662608 7.470000e-55 226.0
46 TraesCS2A01G246700 chr3A 92.157 153 8 4 7044 7192 740079696 740079544 5.810000e-51 213.0
47 TraesCS2A01G246700 chr4A 97.163 141 4 0 7044 7184 466937476 466937336 9.590000e-59 239.0
48 TraesCS2A01G246700 chr7A 93.960 149 7 2 7044 7190 162776160 162776308 2.690000e-54 224.0
49 TraesCS2A01G246700 chr7A 94.366 142 8 0 7044 7185 572183311 572183170 1.250000e-52 219.0
50 TraesCS2A01G246700 chr6D 94.964 139 5 2 7044 7180 44360381 44360243 4.490000e-52 217.0
51 TraesCS2A01G246700 chr6D 93.617 141 6 2 7044 7181 372784277 372784417 2.710000e-49 207.0
52 TraesCS2A01G246700 chr6D 93.571 140 6 1 7044 7180 82959089 82958950 9.730000e-49 206.0
53 TraesCS2A01G246700 chr6D 92.806 139 6 4 7044 7178 451017801 451017663 1.630000e-46 198.0
54 TraesCS2A01G246700 chr6D 91.608 143 8 3 7044 7182 209921589 209921447 2.110000e-45 195.0
55 TraesCS2A01G246700 chr6D 90.000 150 11 4 7044 7189 28399405 28399256 2.720000e-44 191.0
56 TraesCS2A01G246700 chr6D 91.367 139 8 1 7044 7182 68917751 68917617 3.520000e-43 187.0
57 TraesCS2A01G246700 chr6D 89.726 146 14 1 7044 7188 303526960 303526815 1.270000e-42 185.0
58 TraesCS2A01G246700 chr6D 90.780 141 9 4 7044 7180 412014478 412014338 1.270000e-42 185.0
59 TraesCS2A01G246700 chr6D 95.699 93 3 1 2220 2312 114156703 114156794 1.660000e-31 148.0
60 TraesCS2A01G246700 chr6D 94.792 96 3 2 2218 2312 296699582 296699488 1.660000e-31 148.0
61 TraesCS2A01G246700 chr6D 94.681 94 5 0 2214 2307 427344948 427344855 5.980000e-31 147.0
62 TraesCS2A01G246700 chr6D 97.647 85 1 1 2223 2307 1551883 1551800 2.150000e-30 145.0
63 TraesCS2A01G246700 chr6D 96.552 87 3 0 2221 2307 28032527 28032441 2.150000e-30 145.0
64 TraesCS2A01G246700 chr6D 96.512 86 3 0 2222 2307 9406777 9406692 7.740000e-30 143.0
65 TraesCS2A01G246700 chr6D 96.512 86 3 0 2222 2307 199210413 199210328 7.740000e-30 143.0
66 TraesCS2A01G246700 chr6D 95.714 70 3 0 7183 7252 418280769 418280838 6.070000e-21 113.0
67 TraesCS2A01G246700 chr6D 88.889 72 7 1 7183 7254 445457536 445457606 3.680000e-13 87.9
68 TraesCS2A01G246700 chr6D 88.571 70 7 1 7183 7252 445421516 445421584 4.760000e-12 84.2
69 TraesCS2A01G246700 chr6D 90.909 44 2 2 7184 7227 439927187 439927146 2.880000e-04 58.4
70 TraesCS2A01G246700 chr6D 88.636 44 3 2 7184 7227 166891045 166891004 1.300000e-02 52.8
71 TraesCS2A01G246700 chr6A 94.964 139 6 1 7044 7182 147454375 147454512 4.490000e-52 217.0
72 TraesCS2A01G246700 chr6A 87.500 72 8 1 7181 7252 203000361 203000431 1.710000e-11 82.4
73 TraesCS2A01G246700 chr5D 94.964 139 6 1 7044 7181 66765069 66765207 4.490000e-52 217.0
74 TraesCS2A01G246700 chr5D 96.703 91 3 0 2221 2311 310705352 310705262 1.290000e-32 152.0
75 TraesCS2A01G246700 chr5D 91.071 112 6 2 2218 2328 334012303 334012195 1.660000e-31 148.0
76 TraesCS2A01G246700 chr5D 87.143 70 8 1 7183 7252 197125994 197126062 2.210000e-10 78.7
77 TraesCS2A01G246700 chr5D 87.143 70 8 1 7183 7252 231847498 231847566 2.210000e-10 78.7
78 TraesCS2A01G246700 chr5D 85.714 70 9 1 7183 7252 231892249 231892317 1.030000e-08 73.1
79 TraesCS2A01G246700 chr1D 92.617 149 7 4 7044 7188 314506235 314506383 2.090000e-50 211.0
80 TraesCS2A01G246700 chr1D 92.568 148 8 3 7044 7188 468861595 468861448 7.520000e-50 209.0
81 TraesCS2A01G246700 chr1D 93.571 140 6 3 7044 7180 493673684 493673823 9.730000e-49 206.0
82 TraesCS2A01G246700 chr1D 98.864 88 1 0 2220 2307 318382791 318382878 2.760000e-34 158.0
83 TraesCS2A01G246700 chr1D 93.878 98 4 2 2222 2319 411756911 411757006 5.980000e-31 147.0
84 TraesCS2A01G246700 chr1D 92.000 50 3 1 7181 7230 18754900 18754948 1.330000e-07 69.4
85 TraesCS2A01G246700 chr4D 93.617 141 6 1 7044 7181 93704747 93704607 2.710000e-49 207.0
86 TraesCS2A01G246700 chr4D 92.199 141 8 3 7044 7181 62231360 62231220 5.860000e-46 196.0
87 TraesCS2A01G246700 chr4D 89.677 155 11 4 7044 7194 326477195 326477348 7.570000e-45 193.0
88 TraesCS2A01G246700 chr4D 97.727 88 2 0 2221 2308 324227847 324227760 1.290000e-32 152.0
89 TraesCS2A01G246700 chr4D 96.667 90 3 0 2218 2307 64347356 64347445 4.620000e-32 150.0
90 TraesCS2A01G246700 chr4D 97.701 87 2 0 2221 2307 469582270 469582356 4.620000e-32 150.0
91 TraesCS2A01G246700 chr4D 96.629 89 3 0 2222 2310 252173789 252173701 1.660000e-31 148.0
92 TraesCS2A01G246700 chr4D 95.652 92 4 0 2220 2311 423945401 423945310 1.660000e-31 148.0
93 TraesCS2A01G246700 chr4D 91.579 95 8 0 6949 7043 481346110 481346204 1.670000e-26 132.0
94 TraesCS2A01G246700 chr4D 90.426 94 7 2 6951 7043 431747874 431747782 1.010000e-23 122.0
95 TraesCS2A01G246700 chr4D 92.683 82 6 0 6951 7032 65187386 65187305 1.300000e-22 119.0
96 TraesCS2A01G246700 chr4D 89.247 93 10 0 6951 7043 431735789 431735697 4.690000e-22 117.0
97 TraesCS2A01G246700 chr4D 86.957 92 12 0 6952 7043 431676241 431676150 3.650000e-18 104.0
98 TraesCS2A01G246700 chr4D 86.022 93 13 0 6951 7043 481339655 481339747 4.720000e-17 100.0
99 TraesCS2A01G246700 chr4D 90.411 73 7 0 7180 7252 431747777 431747705 6.110000e-16 97.1
100 TraesCS2A01G246700 chr4D 87.500 80 9 1 7181 7259 65187288 65187209 2.840000e-14 91.6
101 TraesCS2A01G246700 chr4D 91.228 57 5 0 6987 7043 431557046 431556990 2.210000e-10 78.7
102 TraesCS2A01G246700 chr4D 91.111 45 2 2 7183 7227 464515094 464515052 8.020000e-05 60.2
103 TraesCS2A01G246700 chr4D 90.909 44 2 2 7184 7227 351849752 351849711 2.880000e-04 58.4
104 TraesCS2A01G246700 chr4D 90.909 44 2 2 7184 7227 351922517 351922476 2.880000e-04 58.4
105 TraesCS2A01G246700 chr4D 90.909 44 2 2 7184 7227 372501916 372501875 2.880000e-04 58.4
106 TraesCS2A01G246700 chr7B 98.889 90 1 0 2218 2307 639796288 639796199 2.140000e-35 161.0
107 TraesCS2A01G246700 chr7B 93.269 104 6 1 2217 2320 428966933 428966831 1.290000e-32 152.0
108 TraesCS2A01G246700 chr5B 97.872 94 0 2 2219 2312 264876389 264876298 2.140000e-35 161.0
109 TraesCS2A01G246700 chr5B 95.833 96 4 0 2215 2310 62940415 62940320 9.940000e-34 156.0
110 TraesCS2A01G246700 chr5B 88.172 93 11 0 6951 7043 134047591 134047683 2.180000e-20 111.0
111 TraesCS2A01G246700 chr5B 88.172 93 11 0 6951 7043 583577220 583577128 2.180000e-20 111.0
112 TraesCS2A01G246700 chr5B 88.889 72 8 0 7181 7252 134047689 134047760 1.020000e-13 89.8
113 TraesCS2A01G246700 chr4B 97.826 92 2 0 2222 2313 447451709 447451800 7.680000e-35 159.0
114 TraesCS2A01G246700 chr7D 98.876 89 0 1 2219 2307 498229835 498229922 2.760000e-34 158.0
115 TraesCS2A01G246700 chr7D 98.851 87 1 0 2221 2307 167548506 167548420 9.940000e-34 156.0
116 TraesCS2A01G246700 chr3B 96.809 94 3 0 2214 2307 200860776 200860683 2.760000e-34 158.0
117 TraesCS2A01G246700 chr3D 95.699 93 4 0 2218 2310 302930476 302930384 4.620000e-32 150.0
118 TraesCS2A01G246700 chr3D 88.172 93 10 1 6951 7043 478692166 478692075 7.850000e-20 110.0
119 TraesCS2A01G246700 chr3D 87.500 96 9 3 6951 7044 478661305 478661211 2.820000e-19 108.0
120 TraesCS2A01G246700 chr3D 87.143 70 9 0 7183 7252 496301084 496301015 6.150000e-11 80.5


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 TraesCS2A01G246700 chr2A 361379397 361386794 7397 False 13662.000000 13662 100.00000 1 7398 1 chr2A.!!$F3 7397
1 TraesCS2A01G246700 chr2A 65243133 65246876 3743 True 2848.500000 4095 93.96000 2723 6408 2 chr2A.!!$R2 3685
2 TraesCS2A01G246700 chr2A 65293637 65295195 1558 True 905.500000 1295 89.27650 990 2670 2 chr2A.!!$R3 1680
3 TraesCS2A01G246700 chr2B 354873888 354880391 6503 True 3430.333333 9540 93.33600 1039 7398 3 chr2B.!!$R1 6359
4 TraesCS2A01G246700 chr2D 294472727 294479278 6551 False 2602.500000 8925 95.36225 990 7398 4 chr2D.!!$F3 6408
5 TraesCS2A01G246700 chr2D 63621976 63627523 5547 True 2084.375000 6481 92.30675 990 6672 4 chr2D.!!$R2 5682
6 TraesCS2A01G246700 chr1A 570045229 570046197 968 False 1487.000000 1487 94.42700 1 966 1 chr1A.!!$F3 965
7 TraesCS2A01G246700 chr5A 616364008 616364975 967 False 1482.000000 1482 94.32400 1 966 1 chr5A.!!$F2 965
8 TraesCS2A01G246700 chr5A 610752779 610753749 970 True 1474.000000 1474 94.13000 1 968 1 chr5A.!!$R4 967
9 TraesCS2A01G246700 chr5A 211619570 211620539 969 False 1467.000000 1467 94.02100 1 966 1 chr5A.!!$F1 965
10 TraesCS2A01G246700 chrUn 1715771 1716739 968 False 1465.000000 1465 94.01400 1 966 1 chrUn.!!$F1 965
11 TraesCS2A01G246700 chrUn 363162032 363162999 967 True 1443.000000 1443 93.60200 1 966 1 chrUn.!!$R3 965
12 TraesCS2A01G246700 chr3A 698712292 698713259 967 True 1465.000000 1465 94.01400 1 966 1 chr3A.!!$R2 965
13 TraesCS2A01G246700 chr3A 713896061 713897029 968 True 1465.000000 1465 94.01400 1 966 1 chr3A.!!$R3 965
14 TraesCS2A01G246700 chr3A 666225342 666226308 966 True 1441.000000 1441 93.58800 1 965 1 chr3A.!!$R1 964

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
253 254 0.246635 ATGAAGTACTGCGGCTTCGT 59.753 50.000 0.00 5.43 42.77 3.85 F
1136 1142 0.103026 TCGATCGATTCTGGCTGTGG 59.897 55.000 15.15 0.00 0.00 4.17 F
1137 1143 0.103026 CGATCGATTCTGGCTGTGGA 59.897 55.000 10.26 0.00 0.00 4.02 F
1139 1145 0.467384 ATCGATTCTGGCTGTGGAGG 59.533 55.000 0.00 0.00 0.00 4.30 F
1141 1147 0.467384 CGATTCTGGCTGTGGAGGAT 59.533 55.000 0.00 0.00 0.00 3.24 F
1490 1517 1.028330 GTAAACCGGTTAGGGCTGGC 61.028 60.000 22.60 1.18 46.96 4.85 F
3197 3254 1.135460 GCATTGAAGCTCTCTGCAACC 60.135 52.381 0.00 0.00 40.53 3.77 F
3780 3837 1.939980 AGGAACTACCCTTTCTCGCT 58.060 50.000 0.00 0.00 36.02 4.93 F
4060 4117 2.465813 CTCTGAAGAGATGGGGTCACT 58.534 52.381 0.74 0.00 44.74 3.41 F
5934 6105 1.066908 CGCAACCATGACCACAAGTTT 59.933 47.619 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1139 1145 0.103026 GCGCCCAAATCCTCCAAATC 59.897 55.000 0.00 0.0 0.00 2.17 R
2957 3014 0.523072 CACCAGGAGATTGTTTGGCG 59.477 55.000 0.00 0.0 33.98 5.69 R
3197 3254 3.130164 AGACAAGGACATGAGATGAGTCG 59.870 47.826 0.00 0.0 33.18 4.18 R
3275 3332 2.936202 ACTGTCAGCACAACCAATTCT 58.064 42.857 0.00 0.0 29.82 2.40 R
3276 3333 3.715628 AACTGTCAGCACAACCAATTC 57.284 42.857 0.00 0.0 29.82 2.17 R
3315 3372 3.316308 GGATGCTTTGTCAACTGTTCTGT 59.684 43.478 0.00 0.0 0.00 3.41 R
4060 4117 2.887783 TGATTTCCTGCGGTTGCTTTTA 59.112 40.909 0.00 0.0 43.34 1.52 R
5881 6052 1.164041 CCAGCGTCTTGTTCCCGTTT 61.164 55.000 0.00 0.0 0.00 3.60 R
6160 6331 0.033504 GCCCAAACTCAGTGAGACGA 59.966 55.000 26.86 0.0 33.32 4.20 R
7224 8057 0.040499 AGGAGGAGAGGGACTGTGTC 59.960 60.000 0.00 0.0 41.55 3.67 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
167 168 3.820590 CAAGCCACGTGGTTGTCA 58.179 55.556 33.92 0.00 45.31 3.58
179 180 1.372499 GTTGTCAGCGGCGTACTGA 60.372 57.895 12.27 12.27 41.78 3.41
196 197 1.081277 GAGGGAGGGAGAGTTGGGT 59.919 63.158 0.00 0.00 0.00 4.51
253 254 0.246635 ATGAAGTACTGCGGCTTCGT 59.753 50.000 0.00 5.43 42.77 3.85
731 735 4.338710 CGAGGCCGTTGGGGGAAA 62.339 66.667 0.00 0.00 35.78 3.13
753 757 2.027024 GGTGTCGTGTCGCTGACA 59.973 61.111 7.20 7.20 42.49 3.58
882 887 2.953466 CGGTGAAAATCGGACTCCTA 57.047 50.000 0.00 0.00 0.00 2.94
893 898 1.518792 GACTCCTAAAGGCGCGACC 60.519 63.158 9.25 10.36 39.61 4.79
943 948 1.280457 ATCGACTGGAAAGGCCTTCT 58.720 50.000 20.79 9.27 37.63 2.85
956 962 4.467084 CTTCTTGGGCCGCGGCTA 62.467 66.667 45.23 32.62 41.60 3.93
971 977 1.393603 GGCTAGAGATGCCCAAAACC 58.606 55.000 0.00 0.00 44.32 3.27
972 978 1.393603 GCTAGAGATGCCCAAAACCC 58.606 55.000 0.00 0.00 0.00 4.11
973 979 2.024306 GCTAGAGATGCCCAAAACCCC 61.024 57.143 0.00 0.00 0.00 4.95
974 980 1.284785 CTAGAGATGCCCAAAACCCCA 59.715 52.381 0.00 0.00 0.00 4.96
975 981 0.251787 AGAGATGCCCAAAACCCCAC 60.252 55.000 0.00 0.00 0.00 4.61
976 982 1.229177 AGATGCCCAAAACCCCACC 60.229 57.895 0.00 0.00 0.00 4.61
977 983 2.603171 ATGCCCAAAACCCCACCG 60.603 61.111 0.00 0.00 0.00 4.94
978 984 4.924187 TGCCCAAAACCCCACCGG 62.924 66.667 0.00 0.00 37.81 5.28
979 985 4.607025 GCCCAAAACCCCACCGGA 62.607 66.667 9.46 0.00 34.64 5.14
980 986 2.599281 CCCAAAACCCCACCGGAC 60.599 66.667 9.46 0.00 34.64 4.79
981 987 2.981350 CCAAAACCCCACCGGACG 60.981 66.667 9.46 0.00 34.64 4.79
982 988 2.981350 CAAAACCCCACCGGACGG 60.981 66.667 9.46 9.56 42.03 4.79
983 989 3.169956 AAAACCCCACCGGACGGA 61.170 61.111 18.80 0.00 38.96 4.69
984 990 2.754962 AAAACCCCACCGGACGGAA 61.755 57.895 18.80 0.00 38.96 4.30
985 991 2.685804 AAAACCCCACCGGACGGAAG 62.686 60.000 18.80 9.19 38.96 3.46
1086 1092 4.506255 CCATTCCCACCCCTCGGC 62.506 72.222 0.00 0.00 0.00 5.54
1130 1136 3.192212 TCTCATCCATCGATCGATTCTGG 59.808 47.826 27.45 25.58 31.62 3.86
1134 1140 1.269988 CCATCGATCGATTCTGGCTGT 60.270 52.381 27.45 1.70 31.62 4.40
1135 1141 1.791204 CATCGATCGATTCTGGCTGTG 59.209 52.381 27.45 11.27 31.62 3.66
1136 1142 0.103026 TCGATCGATTCTGGCTGTGG 59.897 55.000 15.15 0.00 0.00 4.17
1137 1143 0.103026 CGATCGATTCTGGCTGTGGA 59.897 55.000 10.26 0.00 0.00 4.02
1138 1144 1.863267 GATCGATTCTGGCTGTGGAG 58.137 55.000 0.00 0.00 0.00 3.86
1139 1145 0.467384 ATCGATTCTGGCTGTGGAGG 59.533 55.000 0.00 0.00 0.00 4.30
1140 1146 0.614697 TCGATTCTGGCTGTGGAGGA 60.615 55.000 0.00 0.00 0.00 3.71
1141 1147 0.467384 CGATTCTGGCTGTGGAGGAT 59.533 55.000 0.00 0.00 0.00 3.24
1142 1148 1.134280 CGATTCTGGCTGTGGAGGATT 60.134 52.381 0.00 0.00 0.00 3.01
1490 1517 1.028330 GTAAACCGGTTAGGGCTGGC 61.028 60.000 22.60 1.18 46.96 4.85
1633 1664 1.961394 TCTGTAGTGTATGATCCGGGC 59.039 52.381 0.00 0.00 0.00 6.13
1894 1940 8.585471 ACAATTCTCATAAACAATGATCAGGT 57.415 30.769 0.09 0.00 43.70 4.00
1946 1992 2.901249 TCCTTTGTGCGATAGGTTAGC 58.099 47.619 0.00 0.00 0.00 3.09
2001 2049 8.892723 GTTCCATGATGTACAATGTTCTTCATA 58.107 33.333 16.64 4.86 35.48 2.15
2015 2063 8.723942 ATGTTCTTCATACTATGGACAAGTTC 57.276 34.615 0.00 0.00 34.67 3.01
2313 2363 1.700955 TACGGAGGGAGTAGATTGGC 58.299 55.000 0.00 0.00 0.00 4.52
2320 2370 4.385754 GGAGGGAGTAGATTGGCATTTTCT 60.386 45.833 0.00 0.00 0.00 2.52
2612 2667 4.449068 GTCCGAGCACATGTTTCTATATGG 59.551 45.833 0.00 0.00 0.00 2.74
2613 2668 4.100963 TCCGAGCACATGTTTCTATATGGT 59.899 41.667 0.00 0.00 0.00 3.55
2614 2669 4.816385 CCGAGCACATGTTTCTATATGGTT 59.184 41.667 0.00 0.00 0.00 3.67
2714 2771 6.358178 TGTCTACGATATCCTTCTGAGTTCT 58.642 40.000 0.00 0.00 0.00 3.01
2885 2942 3.411446 TGCTTGTGATGTTAAGGTCCAG 58.589 45.455 0.00 0.00 0.00 3.86
2957 3014 6.650807 TGGTTCTTTCGATGATCTATAATGCC 59.349 38.462 0.00 0.00 0.00 4.40
3197 3254 1.135460 GCATTGAAGCTCTCTGCAACC 60.135 52.381 0.00 0.00 40.53 3.77
3245 3302 4.461081 AGGTCAGTACAGAGTCAGTGATTC 59.539 45.833 7.53 7.53 0.00 2.52
3275 3332 8.019656 AGTCTTGACTTCTTAACCTTTACAGA 57.980 34.615 0.00 0.00 0.00 3.41
3276 3333 8.145122 AGTCTTGACTTCTTAACCTTTACAGAG 58.855 37.037 0.00 0.00 0.00 3.35
3302 3359 4.013728 TGGTTGTGCTGACAGTTTAAAGT 58.986 39.130 3.99 0.00 32.26 2.66
3337 3394 3.316308 ACAGAACAGTTGACAAAGCATCC 59.684 43.478 0.00 0.00 0.00 3.51
3460 3517 8.148351 TGTGTAATAAATAAGCGAGCTTCCTAT 58.852 33.333 14.09 6.94 37.47 2.57
3780 3837 1.939980 AGGAACTACCCTTTCTCGCT 58.060 50.000 0.00 0.00 36.02 4.93
4060 4117 2.465813 CTCTGAAGAGATGGGGTCACT 58.534 52.381 0.74 0.00 44.74 3.41
4574 4632 5.078411 TGAAGGACAGCAGAAAGAGATAC 57.922 43.478 0.00 0.00 0.00 2.24
4589 4647 7.340999 AGAAAGAGATACCTCCTAGAAGTCAAC 59.659 40.741 0.00 0.00 40.30 3.18
4891 4952 3.896888 TGGAGTTCTCCGTAAAGGTGTTA 59.103 43.478 13.27 0.00 41.99 2.41
5465 5625 7.930217 TCCTTTTGAACTGTTTGTATCTTCTG 58.070 34.615 0.00 0.00 0.00 3.02
5556 5726 6.599244 TGTTAGTTCCTGATGTGGATTTGATC 59.401 38.462 0.00 0.00 35.83 2.92
5632 5802 4.992951 ACATACCTGAAGGACGTTTGTAAC 59.007 41.667 2.62 0.00 38.94 2.50
5881 6052 2.362077 GCTTTGCCAAACAAGGAAGAGA 59.638 45.455 0.00 0.00 40.06 3.10
5883 6054 4.680440 GCTTTGCCAAACAAGGAAGAGAAA 60.680 41.667 0.00 0.00 40.06 2.52
5885 6056 2.357637 TGCCAAACAAGGAAGAGAAACG 59.642 45.455 0.00 0.00 0.00 3.60
5901 6072 2.742372 CGGGAACAAGACGCTGGG 60.742 66.667 0.00 0.00 0.00 4.45
5902 6073 2.430367 GGGAACAAGACGCTGGGT 59.570 61.111 0.00 0.00 0.00 4.51
5934 6105 1.066908 CGCAACCATGACCACAAGTTT 59.933 47.619 0.00 0.00 0.00 2.66
5960 6131 2.583441 CGAGGTCCCAGTTCCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
6160 6331 4.384208 GGGAATGGCCTAACGCATCTATAT 60.384 45.833 3.32 0.00 40.31 0.86
6190 6361 2.169769 TGAGTTTGGGCGGAGGTAATAG 59.830 50.000 0.00 0.00 0.00 1.73
6205 6376 4.202441 GGTAATAGTACCTGACTCACCGA 58.798 47.826 12.14 0.00 45.72 4.69
6213 6387 1.410365 CCTGACTCACCGACCTCCTAT 60.410 57.143 0.00 0.00 0.00 2.57
6214 6388 1.950909 CTGACTCACCGACCTCCTATC 59.049 57.143 0.00 0.00 0.00 2.08
6215 6389 1.320507 GACTCACCGACCTCCTATCC 58.679 60.000 0.00 0.00 0.00 2.59
6216 6390 0.465824 ACTCACCGACCTCCTATCCG 60.466 60.000 0.00 0.00 0.00 4.18
6217 6391 0.179026 CTCACCGACCTCCTATCCGA 60.179 60.000 0.00 0.00 0.00 4.55
6218 6392 0.179026 TCACCGACCTCCTATCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
6219 6393 0.179026 CACCGACCTCCTATCCGAGA 60.179 60.000 0.00 0.00 30.97 4.04
6220 6394 0.772384 ACCGACCTCCTATCCGAGAT 59.228 55.000 0.00 0.00 30.97 2.75
6221 6395 1.169577 CCGACCTCCTATCCGAGATG 58.830 60.000 0.00 0.00 30.97 2.90
6222 6396 1.271434 CCGACCTCCTATCCGAGATGA 60.271 57.143 0.00 0.00 30.97 2.92
6223 6397 2.619332 CCGACCTCCTATCCGAGATGAT 60.619 54.545 0.00 0.00 30.97 2.45
6224 6398 2.421775 CGACCTCCTATCCGAGATGATG 59.578 54.545 0.00 0.00 30.97 3.07
6225 6399 3.691575 GACCTCCTATCCGAGATGATGA 58.308 50.000 0.00 0.00 30.97 2.92
6226 6400 3.694072 GACCTCCTATCCGAGATGATGAG 59.306 52.174 0.00 0.00 30.97 2.90
6227 6401 3.332187 ACCTCCTATCCGAGATGATGAGA 59.668 47.826 0.00 0.00 30.97 3.27
6228 6402 3.694072 CCTCCTATCCGAGATGATGAGAC 59.306 52.174 0.00 0.00 30.97 3.36
6229 6403 4.567537 CCTCCTATCCGAGATGATGAGACT 60.568 50.000 0.00 0.00 30.97 3.24
6230 6404 5.338789 CCTCCTATCCGAGATGATGAGACTA 60.339 48.000 0.00 0.00 30.97 2.59
6231 6405 6.320434 TCCTATCCGAGATGATGAGACTAT 57.680 41.667 0.00 0.00 0.00 2.12
6409 6590 5.428253 TCTGTACTGGGCAAAATGACTATC 58.572 41.667 0.00 0.00 0.00 2.08
6412 6593 3.624777 ACTGGGCAAAATGACTATCTGG 58.375 45.455 0.00 0.00 0.00 3.86
6421 6602 7.436376 GGCAAAATGACTATCTGGCTATTTTTC 59.564 37.037 0.00 0.00 28.85 2.29
6424 6608 5.023533 TGACTATCTGGCTATTTTTCGCT 57.976 39.130 0.00 0.00 0.00 4.93
6425 6609 5.428253 TGACTATCTGGCTATTTTTCGCTT 58.572 37.500 0.00 0.00 0.00 4.68
6426 6610 5.880332 TGACTATCTGGCTATTTTTCGCTTT 59.120 36.000 0.00 0.00 0.00 3.51
6556 6760 2.521224 AGGATCGTAGGTCCCGCC 60.521 66.667 0.00 0.00 36.36 6.13
6734 7567 1.965930 TCATCGCAACAGCACCACC 60.966 57.895 0.00 0.00 0.00 4.61
6830 7663 5.801380 AGGGCGATACGGATATGTAAATTT 58.199 37.500 0.00 0.00 0.00 1.82
6850 7683 5.462034 TTTGCCATTTTGAAAAAGTGTCG 57.538 34.783 0.00 0.00 0.00 4.35
6852 7685 4.109050 TGCCATTTTGAAAAAGTGTCGAC 58.891 39.130 9.11 9.11 0.00 4.20
6941 7774 7.208080 ACGTATATAGGTCTTCTCGCAAAAAT 58.792 34.615 2.21 0.00 0.00 1.82
6949 7782 8.506168 AGGTCTTCTCGCAAAAATAATAATCA 57.494 30.769 0.00 0.00 0.00 2.57
6995 7828 1.824230 GCACCTGTCATGTCTCTCTCT 59.176 52.381 0.00 0.00 0.00 3.10
7043 7876 1.140252 ACAAGACACTAAACGCACCCT 59.860 47.619 0.00 0.00 0.00 4.34
7046 7879 2.522185 AGACACTAAACGCACCCTCTA 58.478 47.619 0.00 0.00 0.00 2.43
7047 7880 2.895404 AGACACTAAACGCACCCTCTAA 59.105 45.455 0.00 0.00 0.00 2.10
7048 7881 3.056749 AGACACTAAACGCACCCTCTAAG 60.057 47.826 0.00 0.00 0.00 2.18
7049 7882 2.631545 ACACTAAACGCACCCTCTAAGT 59.368 45.455 0.00 0.00 0.00 2.24
7050 7883 2.993899 CACTAAACGCACCCTCTAAGTG 59.006 50.000 0.00 0.00 38.30 3.16
7051 7884 2.895404 ACTAAACGCACCCTCTAAGTGA 59.105 45.455 0.00 0.00 37.42 3.41
7052 7885 2.457366 AAACGCACCCTCTAAGTGAG 57.543 50.000 0.00 0.00 42.30 3.51
7053 7886 3.053146 ACGCACCCTCTAAGTGAGT 57.947 52.632 0.00 0.00 42.41 3.41
7054 7887 0.603569 ACGCACCCTCTAAGTGAGTG 59.396 55.000 0.00 0.00 44.93 3.51
7055 7888 0.888619 CGCACCCTCTAAGTGAGTGA 59.111 55.000 0.00 0.00 41.11 3.41
7056 7889 1.272490 CGCACCCTCTAAGTGAGTGAA 59.728 52.381 0.00 0.00 41.11 3.18
7057 7890 2.093973 CGCACCCTCTAAGTGAGTGAAT 60.094 50.000 0.00 0.00 41.11 2.57
7058 7891 3.526534 GCACCCTCTAAGTGAGTGAATC 58.473 50.000 0.00 0.00 41.11 2.52
7059 7892 3.055819 GCACCCTCTAAGTGAGTGAATCA 60.056 47.826 0.00 0.00 41.11 2.57
7060 7893 4.563580 GCACCCTCTAAGTGAGTGAATCAA 60.564 45.833 0.00 0.00 40.43 2.57
7061 7894 5.174395 CACCCTCTAAGTGAGTGAATCAAG 58.826 45.833 0.00 0.00 40.43 3.02
7062 7895 4.187694 CCCTCTAAGTGAGTGAATCAAGC 58.812 47.826 0.00 0.00 40.43 4.01
7063 7896 4.323028 CCCTCTAAGTGAGTGAATCAAGCA 60.323 45.833 0.00 0.00 40.43 3.91
7064 7897 5.426504 CCTCTAAGTGAGTGAATCAAGCAT 58.573 41.667 0.00 0.00 40.43 3.79
7065 7898 6.407412 CCCTCTAAGTGAGTGAATCAAGCATA 60.407 42.308 0.00 0.00 40.43 3.14
7066 7899 7.044181 CCTCTAAGTGAGTGAATCAAGCATAA 58.956 38.462 0.00 0.00 40.43 1.90
7067 7900 7.550551 CCTCTAAGTGAGTGAATCAAGCATAAA 59.449 37.037 0.00 0.00 40.43 1.40
7068 7901 8.484641 TCTAAGTGAGTGAATCAAGCATAAAG 57.515 34.615 0.00 0.00 40.43 1.85
7069 7902 8.314021 TCTAAGTGAGTGAATCAAGCATAAAGA 58.686 33.333 0.00 0.00 40.43 2.52
7070 7903 6.981762 AGTGAGTGAATCAAGCATAAAGAG 57.018 37.500 0.00 0.00 40.43 2.85
7071 7904 6.705302 AGTGAGTGAATCAAGCATAAAGAGA 58.295 36.000 0.00 0.00 40.43 3.10
7072 7905 7.164122 AGTGAGTGAATCAAGCATAAAGAGAA 58.836 34.615 0.00 0.00 40.43 2.87
7073 7906 7.663081 AGTGAGTGAATCAAGCATAAAGAGAAA 59.337 33.333 0.00 0.00 40.43 2.52
7074 7907 8.292448 GTGAGTGAATCAAGCATAAAGAGAAAA 58.708 33.333 0.00 0.00 40.43 2.29
7075 7908 8.849168 TGAGTGAATCAAGCATAAAGAGAAAAA 58.151 29.630 0.00 0.00 34.02 1.94
7076 7909 9.339492 GAGTGAATCAAGCATAAAGAGAAAAAG 57.661 33.333 0.00 0.00 0.00 2.27
7077 7910 9.071276 AGTGAATCAAGCATAAAGAGAAAAAGA 57.929 29.630 0.00 0.00 0.00 2.52
7078 7911 9.683069 GTGAATCAAGCATAAAGAGAAAAAGAA 57.317 29.630 0.00 0.00 0.00 2.52
7107 7940 8.777865 AAAAGAAGATATTCACACGAATCTCA 57.222 30.769 2.42 0.00 41.09 3.27
7108 7941 8.777865 AAAGAAGATATTCACACGAATCTCAA 57.222 30.769 2.42 0.00 41.09 3.02
7109 7942 8.954950 AAGAAGATATTCACACGAATCTCAAT 57.045 30.769 2.42 0.00 41.09 2.57
7110 7943 8.362860 AGAAGATATTCACACGAATCTCAATG 57.637 34.615 2.42 0.00 41.09 2.82
7111 7944 7.984050 AGAAGATATTCACACGAATCTCAATGT 59.016 33.333 2.42 0.00 41.09 2.71
7112 7945 9.249457 GAAGATATTCACACGAATCTCAATGTA 57.751 33.333 0.00 0.00 41.09 2.29
7113 7946 9.599866 AAGATATTCACACGAATCTCAATGTAA 57.400 29.630 0.00 0.00 41.09 2.41
7114 7947 9.599866 AGATATTCACACGAATCTCAATGTAAA 57.400 29.630 0.00 0.00 41.09 2.01
7118 7951 7.665561 TCACACGAATCTCAATGTAAAATCA 57.334 32.000 0.00 0.00 0.00 2.57
7119 7952 8.093659 TCACACGAATCTCAATGTAAAATCAA 57.906 30.769 0.00 0.00 0.00 2.57
7120 7953 8.729756 TCACACGAATCTCAATGTAAAATCAAT 58.270 29.630 0.00 0.00 0.00 2.57
7121 7954 8.791605 CACACGAATCTCAATGTAAAATCAATG 58.208 33.333 0.00 0.00 0.00 2.82
7122 7955 8.729756 ACACGAATCTCAATGTAAAATCAATGA 58.270 29.630 0.00 0.00 0.00 2.57
7123 7956 9.003112 CACGAATCTCAATGTAAAATCAATGAC 57.997 33.333 0.00 0.00 0.00 3.06
7124 7957 8.729756 ACGAATCTCAATGTAAAATCAATGACA 58.270 29.630 0.00 0.00 0.00 3.58
7125 7958 9.726232 CGAATCTCAATGTAAAATCAATGACAT 57.274 29.630 0.00 0.00 34.00 3.06
7140 7973 7.719778 TCAATGACATATGACTTAGATGTGC 57.280 36.000 10.38 0.00 41.09 4.57
7141 7974 7.274447 TCAATGACATATGACTTAGATGTGCA 58.726 34.615 10.38 0.00 41.09 4.57
7142 7975 7.769970 TCAATGACATATGACTTAGATGTGCAA 59.230 33.333 10.38 0.00 41.09 4.08
7143 7976 8.565416 CAATGACATATGACTTAGATGTGCAAT 58.435 33.333 10.38 0.00 41.09 3.56
7144 7977 9.783081 AATGACATATGACTTAGATGTGCAATA 57.217 29.630 10.38 0.00 41.09 1.90
7145 7978 8.593492 TGACATATGACTTAGATGTGCAATAC 57.407 34.615 10.38 0.00 41.09 1.89
7146 7979 8.424133 TGACATATGACTTAGATGTGCAATACT 58.576 33.333 10.38 0.00 41.09 2.12
7147 7980 9.265901 GACATATGACTTAGATGTGCAATACTT 57.734 33.333 10.38 0.00 41.09 2.24
7151 7984 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
7152 7985 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
7153 7986 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
7179 8012 8.665175 CATCTAGATGTGCTTTAACAAAACTG 57.335 34.615 22.42 0.00 34.23 3.16
7224 8057 6.309436 CACGATCAATGGAAATTATCGATGG 58.691 40.000 8.54 0.00 41.38 3.51
7230 8063 6.260714 TCAATGGAAATTATCGATGGACACAG 59.739 38.462 8.54 0.00 0.00 3.66
7259 8092 7.982354 CCTCTCCTCCTAACTTACAAAACATAG 59.018 40.741 0.00 0.00 0.00 2.23
7293 8126 8.582437 AGTTGAATTCAGAATGTCAATTGTCAT 58.418 29.630 11.72 11.72 37.40 3.06
7325 8158 1.140312 GTGGATTCCATGGCTCCCTA 58.860 55.000 23.18 9.06 35.28 3.53
7355 8188 6.605471 TCAGCAAATCAGTAGAACCTCTAA 57.395 37.500 0.00 0.00 29.58 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 3.141488 CTCCCTCAGTACGCCGCT 61.141 66.667 0.00 0.00 0.00 5.52
179 180 1.229658 CACCCAACTCTCCCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
235 236 0.388134 GACGAAGCCGCAGTACTTCA 60.388 55.000 0.00 0.00 41.95 3.02
463 465 0.104725 CCAGCCCCTCCCTCTATCTT 60.105 60.000 0.00 0.00 0.00 2.40
776 780 1.448922 CGGGGCGAACTGTTTTGGAA 61.449 55.000 0.00 0.00 0.00 3.53
777 781 1.894756 CGGGGCGAACTGTTTTGGA 60.895 57.895 0.00 0.00 0.00 3.53
928 933 0.113190 CCCAAGAAGGCCTTTCCAGT 59.887 55.000 21.54 0.00 36.40 4.00
956 962 0.251787 GTGGGGTTTTGGGCATCTCT 60.252 55.000 0.00 0.00 0.00 3.10
968 974 3.633116 CTTCCGTCCGGTGGGGTT 61.633 66.667 14.22 0.00 37.00 4.11
1086 1092 2.345341 GCGGAAAAGAATGAATTTGCGG 59.655 45.455 12.66 0.00 46.20 5.69
1130 1136 0.620556 TCCTCCAAATCCTCCACAGC 59.379 55.000 0.00 0.00 0.00 4.40
1134 1140 2.024080 CCCAAATCCTCCAAATCCTCCA 60.024 50.000 0.00 0.00 0.00 3.86
1135 1141 2.670939 CCCAAATCCTCCAAATCCTCC 58.329 52.381 0.00 0.00 0.00 4.30
1136 1142 2.034878 GCCCAAATCCTCCAAATCCTC 58.965 52.381 0.00 0.00 0.00 3.71
1137 1143 1.686115 CGCCCAAATCCTCCAAATCCT 60.686 52.381 0.00 0.00 0.00 3.24
1138 1144 0.746659 CGCCCAAATCCTCCAAATCC 59.253 55.000 0.00 0.00 0.00 3.01
1139 1145 0.103026 GCGCCCAAATCCTCCAAATC 59.897 55.000 0.00 0.00 0.00 2.17
1140 1146 1.666209 CGCGCCCAAATCCTCCAAAT 61.666 55.000 0.00 0.00 0.00 2.32
1141 1147 2.339556 CGCGCCCAAATCCTCCAAA 61.340 57.895 0.00 0.00 0.00 3.28
1142 1148 2.749839 CGCGCCCAAATCCTCCAA 60.750 61.111 0.00 0.00 0.00 3.53
1612 1639 2.288273 GCCCGGATCATACACTACAGAC 60.288 54.545 0.73 0.00 0.00 3.51
1946 1992 7.819415 TGTTATACATGCCAAATAGCTAGCTAG 59.181 37.037 27.42 16.84 31.45 3.42
2001 2049 6.620877 TGGTTATCAGAACTTGTCCATAGT 57.379 37.500 0.00 0.00 0.00 2.12
2297 2347 3.584733 AAATGCCAATCTACTCCCTCC 57.415 47.619 0.00 0.00 0.00 4.30
2313 2363 2.906691 TGGGCAACACCAAGAAAATG 57.093 45.000 0.00 0.00 42.05 2.32
2320 2370 1.047002 CCTGAAATGGGCAACACCAA 58.953 50.000 0.00 0.00 45.13 3.67
2496 2550 4.611310 TCTATCAGTCTGTCGTTTACGG 57.389 45.455 2.09 0.00 40.29 4.02
2732 2789 6.998802 AGCATAGAAGTATAGCCTTGTTAGG 58.001 40.000 0.00 0.00 45.02 2.69
2831 2888 7.339466 GCTGAAATAGGTATCTTTCCAAGGAAA 59.661 37.037 13.26 13.26 41.22 3.13
2957 3014 0.523072 CACCAGGAGATTGTTTGGCG 59.477 55.000 0.00 0.00 33.98 5.69
3197 3254 3.130164 AGACAAGGACATGAGATGAGTCG 59.870 47.826 0.00 0.00 33.18 4.18
3275 3332 2.936202 ACTGTCAGCACAACCAATTCT 58.064 42.857 0.00 0.00 29.82 2.40
3276 3333 3.715628 AACTGTCAGCACAACCAATTC 57.284 42.857 0.00 0.00 29.82 2.17
3315 3372 3.316308 GGATGCTTTGTCAACTGTTCTGT 59.684 43.478 0.00 0.00 0.00 3.41
3337 3394 6.418101 TGGGAAATAAAACCTCATCTCAGAG 58.582 40.000 0.00 0.00 35.39 3.35
3460 3517 7.398618 TCTCCATAAATTGTTTGGCCAGAAATA 59.601 33.333 5.11 0.00 0.00 1.40
4060 4117 2.887783 TGATTTCCTGCGGTTGCTTTTA 59.112 40.909 0.00 0.00 43.34 1.52
4540 4598 3.686726 GCTGTCCTTCATAAACAGGTGAG 59.313 47.826 4.14 0.00 40.57 3.51
4574 4632 5.413309 ACTCATTGTTGACTTCTAGGAGG 57.587 43.478 2.30 0.00 0.00 4.30
4589 4647 6.094603 CCCCTATCTCAAACTCAAACTCATTG 59.905 42.308 0.00 0.00 40.58 2.82
4891 4952 9.930693 CTATCTTCTAAAGGTTCAGTTACTTGT 57.069 33.333 0.00 0.00 0.00 3.16
5489 5655 8.296713 TCAATTCTAGAACAAAACCAAGCATAC 58.703 33.333 7.48 0.00 0.00 2.39
5556 5726 5.972382 GCGTTCACTCCTACAGTAATTCTAG 59.028 44.000 0.00 0.00 32.21 2.43
5632 5802 5.827797 ACATTTTATGTAGCATGGGTACTGG 59.172 40.000 7.07 0.00 42.78 4.00
5779 5950 5.586243 CCGGACAGAATGAACTCAATACAAT 59.414 40.000 0.00 0.00 39.69 2.71
5881 6052 1.164041 CCAGCGTCTTGTTCCCGTTT 61.164 55.000 0.00 0.00 0.00 3.60
5883 6054 2.030562 CCAGCGTCTTGTTCCCGT 59.969 61.111 0.00 0.00 0.00 5.28
5885 6056 1.671379 GACCCAGCGTCTTGTTCCC 60.671 63.158 0.00 0.00 38.57 3.97
6160 6331 0.033504 GCCCAAACTCAGTGAGACGA 59.966 55.000 26.86 0.00 33.32 4.20
6190 6361 0.810016 GAGGTCGGTGAGTCAGGTAC 59.190 60.000 0.00 0.00 0.00 3.34
6205 6376 3.332187 TCTCATCATCTCGGATAGGAGGT 59.668 47.826 0.00 0.00 34.74 3.85
6213 6387 3.008049 TCGGATAGTCTCATCATCTCGGA 59.992 47.826 0.00 0.00 0.00 4.55
6214 6388 3.339141 TCGGATAGTCTCATCATCTCGG 58.661 50.000 0.00 0.00 0.00 4.63
6215 6389 4.249661 TCTCGGATAGTCTCATCATCTCG 58.750 47.826 0.00 0.00 0.00 4.04
6216 6390 5.879777 TCATCTCGGATAGTCTCATCATCTC 59.120 44.000 0.00 0.00 0.00 2.75
6217 6391 5.814481 TCATCTCGGATAGTCTCATCATCT 58.186 41.667 0.00 0.00 0.00 2.90
6218 6392 6.318396 TCATCATCTCGGATAGTCTCATCATC 59.682 42.308 0.00 0.00 0.00 2.92
6219 6393 6.186234 TCATCATCTCGGATAGTCTCATCAT 58.814 40.000 0.00 0.00 0.00 2.45
6220 6394 5.564550 TCATCATCTCGGATAGTCTCATCA 58.435 41.667 0.00 0.00 0.00 3.07
6221 6395 5.879777 TCTCATCATCTCGGATAGTCTCATC 59.120 44.000 0.00 0.00 0.00 2.92
6222 6396 5.647658 GTCTCATCATCTCGGATAGTCTCAT 59.352 44.000 0.00 0.00 0.00 2.90
6223 6397 5.000591 GTCTCATCATCTCGGATAGTCTCA 58.999 45.833 0.00 0.00 0.00 3.27
6224 6398 5.122239 CAGTCTCATCATCTCGGATAGTCTC 59.878 48.000 0.00 0.00 0.00 3.36
6225 6399 5.003160 CAGTCTCATCATCTCGGATAGTCT 58.997 45.833 0.00 0.00 0.00 3.24
6226 6400 4.379394 GCAGTCTCATCATCTCGGATAGTC 60.379 50.000 0.00 0.00 0.00 2.59
6227 6401 3.505680 GCAGTCTCATCATCTCGGATAGT 59.494 47.826 0.00 0.00 0.00 2.12
6228 6402 3.758023 AGCAGTCTCATCATCTCGGATAG 59.242 47.826 0.00 0.00 0.00 2.08
6229 6403 3.760738 AGCAGTCTCATCATCTCGGATA 58.239 45.455 0.00 0.00 0.00 2.59
6230 6404 2.596346 AGCAGTCTCATCATCTCGGAT 58.404 47.619 0.00 0.00 0.00 4.18
6231 6405 2.064434 AGCAGTCTCATCATCTCGGA 57.936 50.000 0.00 0.00 0.00 4.55
6409 6590 3.578688 AGCAAAAGCGAAAAATAGCCAG 58.421 40.909 0.00 0.00 0.00 4.85
6412 6593 4.608470 GCAAAAGCAAAAGCGAAAAATAGC 59.392 37.500 0.00 0.00 0.00 2.97
6421 6602 2.732500 TCATCATGCAAAAGCAAAAGCG 59.267 40.909 0.00 0.00 0.00 4.68
6424 6608 6.762187 TCTTTCTTCATCATGCAAAAGCAAAA 59.238 30.769 0.00 0.00 0.00 2.44
6425 6609 6.282167 TCTTTCTTCATCATGCAAAAGCAAA 58.718 32.000 0.00 0.00 0.00 3.68
6426 6610 5.845103 TCTTTCTTCATCATGCAAAAGCAA 58.155 33.333 0.00 0.00 0.00 3.91
6577 6800 0.108138 GCGACATAACAGCTGGAGGT 60.108 55.000 19.93 13.27 0.00 3.85
6804 7637 7.828508 ATTTACATATCCGTATCGCCCTATA 57.171 36.000 0.00 0.00 0.00 1.31
6830 7663 4.109050 GTCGACACTTTTTCAAAATGGCA 58.891 39.130 11.55 0.00 0.00 4.92
6850 7683 6.875926 AATAGTAAAACGTATCACCGTGTC 57.124 37.500 0.00 0.00 41.65 3.67
6966 7799 3.689347 ACATGACAGGTGCAATGTACAT 58.311 40.909 1.41 1.41 0.00 2.29
6995 7828 6.464222 CCAAGATACAACAAGTTACAGAGGA 58.536 40.000 0.00 0.00 0.00 3.71
7043 7876 8.314021 TCTTTATGCTTGATTCACTCACTTAGA 58.686 33.333 0.00 0.00 32.17 2.10
7046 7879 7.164122 TCTCTTTATGCTTGATTCACTCACTT 58.836 34.615 0.00 0.00 32.17 3.16
7047 7880 6.705302 TCTCTTTATGCTTGATTCACTCACT 58.295 36.000 0.00 0.00 32.17 3.41
7048 7881 6.974932 TCTCTTTATGCTTGATTCACTCAC 57.025 37.500 0.00 0.00 32.17 3.51
7049 7882 7.984422 TTTCTCTTTATGCTTGATTCACTCA 57.016 32.000 0.00 0.00 0.00 3.41
7050 7883 9.339492 CTTTTTCTCTTTATGCTTGATTCACTC 57.661 33.333 0.00 0.00 0.00 3.51
7051 7884 9.071276 TCTTTTTCTCTTTATGCTTGATTCACT 57.929 29.630 0.00 0.00 0.00 3.41
7052 7885 9.683069 TTCTTTTTCTCTTTATGCTTGATTCAC 57.317 29.630 0.00 0.00 0.00 3.18
7093 7926 8.093659 TGATTTTACATTGAGATTCGTGTGAA 57.906 30.769 0.00 0.00 38.76 3.18
7094 7927 7.665561 TGATTTTACATTGAGATTCGTGTGA 57.334 32.000 0.00 0.00 0.00 3.58
7095 7928 8.791605 CATTGATTTTACATTGAGATTCGTGTG 58.208 33.333 0.00 0.00 0.00 3.82
7096 7929 8.729756 TCATTGATTTTACATTGAGATTCGTGT 58.270 29.630 0.00 0.00 0.00 4.49
7097 7930 9.003112 GTCATTGATTTTACATTGAGATTCGTG 57.997 33.333 0.00 0.00 33.09 4.35
7098 7931 8.729756 TGTCATTGATTTTACATTGAGATTCGT 58.270 29.630 0.00 0.00 33.09 3.85
7099 7932 9.726232 ATGTCATTGATTTTACATTGAGATTCG 57.274 29.630 0.00 0.00 33.57 3.34
7114 7947 8.781196 GCACATCTAAGTCATATGTCATTGATT 58.219 33.333 1.90 0.00 31.60 2.57
7115 7948 7.935210 TGCACATCTAAGTCATATGTCATTGAT 59.065 33.333 1.90 0.00 31.60 2.57
7116 7949 7.274447 TGCACATCTAAGTCATATGTCATTGA 58.726 34.615 1.90 0.00 31.60 2.57
7117 7950 7.486802 TGCACATCTAAGTCATATGTCATTG 57.513 36.000 1.90 0.00 31.60 2.82
7118 7951 8.687292 ATTGCACATCTAAGTCATATGTCATT 57.313 30.769 1.90 0.00 31.60 2.57
7119 7952 9.212641 GTATTGCACATCTAAGTCATATGTCAT 57.787 33.333 1.90 0.00 31.60 3.06
7120 7953 8.424133 AGTATTGCACATCTAAGTCATATGTCA 58.576 33.333 1.90 0.00 31.60 3.58
7121 7954 8.824159 AGTATTGCACATCTAAGTCATATGTC 57.176 34.615 1.90 0.00 31.60 3.06
7125 7958 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
7126 7959 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
7127 7960 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
7128 7961 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
7129 7962 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
7130 7963 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
7138 7971 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
7139 7972 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
7154 7987 8.506437 TCAGTTTTGTTAAAGCACATCTAGATG 58.494 33.333 27.63 27.63 44.15 2.90
7155 7988 8.621532 TCAGTTTTGTTAAAGCACATCTAGAT 57.378 30.769 0.00 0.00 0.00 1.98
7156 7989 8.621532 ATCAGTTTTGTTAAAGCACATCTAGA 57.378 30.769 0.00 0.00 0.00 2.43
7157 7990 8.725148 AGATCAGTTTTGTTAAAGCACATCTAG 58.275 33.333 0.00 0.00 0.00 2.43
7158 7991 8.621532 AGATCAGTTTTGTTAAAGCACATCTA 57.378 30.769 0.00 0.00 0.00 1.98
7159 7992 7.516198 AGATCAGTTTTGTTAAAGCACATCT 57.484 32.000 0.00 0.00 0.00 2.90
7171 8004 9.935241 CTAGGCACATATATAGATCAGTTTTGT 57.065 33.333 0.00 0.00 0.00 2.83
7172 8005 9.935241 ACTAGGCACATATATAGATCAGTTTTG 57.065 33.333 0.00 0.00 0.00 2.44
7173 8006 9.935241 CACTAGGCACATATATAGATCAGTTTT 57.065 33.333 0.00 0.00 0.00 2.43
7174 8007 8.037758 GCACTAGGCACATATATAGATCAGTTT 58.962 37.037 0.00 0.00 43.97 2.66
7175 8008 7.551585 GCACTAGGCACATATATAGATCAGTT 58.448 38.462 0.00 0.00 43.97 3.16
7176 8009 7.106439 GCACTAGGCACATATATAGATCAGT 57.894 40.000 0.00 0.00 43.97 3.41
7224 8057 0.040499 AGGAGGAGAGGGACTGTGTC 59.960 60.000 0.00 0.00 41.55 3.67
7230 8063 3.978610 TGTAAGTTAGGAGGAGAGGGAC 58.021 50.000 0.00 0.00 0.00 4.46
7259 8092 9.809096 TGACATTCTGAATTCAACTCTATACTC 57.191 33.333 9.88 0.00 0.00 2.59
7293 8126 3.006940 GGAATCCACGCATGTACAAAGA 58.993 45.455 0.00 0.00 0.00 2.52
7325 8158 3.840666 TCTACTGATTTGCTGAAGGAGGT 59.159 43.478 0.00 0.00 0.00 3.85
7355 8188 7.661437 TGATCATGTTGCTTTGAGTAGTTACTT 59.339 33.333 0.00 0.00 36.50 2.24


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

AutoCloner maintained by Alex Coulton.