Multiple sequence alignment - TraesCS4A01G129500

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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 TraesCS4A01G129500 chr4A 100.000 2705 0 0 1 2705 169249534 169246830 0.000000e+00 4996.0
1 TraesCS4A01G129500 chr4A 91.043 2657 191 11 94 2703 169211397 169208741 0.000000e+00 3544.0
2 TraesCS4A01G129500 chr4A 79.930 1141 147 62 93 1198 324911183 324910090 0.000000e+00 763.0
3 TraesCS4A01G129500 chr4A 80.613 1011 128 49 93 1075 324903128 324902158 0.000000e+00 719.0
4 TraesCS4A01G129500 chr4A 81.596 902 115 34 94 973 549333983 549334855 0.000000e+00 699.0
5 TraesCS4A01G129500 chr4A 91.496 341 25 4 2364 2703 240020687 240020350 1.470000e-127 466.0
6 TraesCS4A01G129500 chr4A 88.095 252 24 6 2458 2705 428502549 428502300 7.320000e-76 294.0
7 TraesCS4A01G129500 chr4A 87.568 185 22 1 1446 1630 516497090 516496907 2.110000e-51 213.0
8 TraesCS4A01G129500 chr4A 85.279 197 26 3 1623 1817 126920810 126921005 1.640000e-47 200.0
9 TraesCS4A01G129500 chr4A 92.553 94 6 1 1 93 362700085 362699992 1.690000e-27 134.0
10 TraesCS4A01G129500 chr4A 86.905 84 8 1 1232 1312 303362001 303362084 1.030000e-14 91.6
11 TraesCS4A01G129500 chr4A 88.889 63 7 0 1275 1337 212630780 212630842 8.030000e-11 78.7
12 TraesCS4A01G129500 chr7A 82.691 1167 143 26 94 1229 299015131 299013993 0.000000e+00 981.0
13 TraesCS4A01G129500 chr7A 82.158 1149 145 31 112 1229 299023081 299021962 0.000000e+00 931.0
14 TraesCS4A01G129500 chr7A 84.978 892 96 24 94 974 259186165 259187029 0.000000e+00 870.0
15 TraesCS4A01G129500 chr7A 84.545 880 99 19 94 970 591936430 591935585 0.000000e+00 837.0
16 TraesCS4A01G129500 chr7A 90.909 319 21 6 2379 2696 515482735 515482424 3.220000e-114 422.0
17 TraesCS4A01G129500 chr7A 93.403 288 13 5 2379 2666 515490944 515490663 3.220000e-114 422.0
18 TraesCS4A01G129500 chr7A 86.792 106 9 3 1210 1312 444379499 444379396 2.200000e-21 113.0
19 TraesCS4A01G129500 chr6D 82.741 1153 144 38 94 1229 168911633 168910519 0.000000e+00 976.0
20 TraesCS4A01G129500 chr6D 88.830 761 74 8 94 845 136188630 136187872 0.000000e+00 924.0
21 TraesCS4A01G129500 chr6D 78.986 276 40 18 2390 2658 243808417 243808153 3.580000e-39 172.0
22 TraesCS4A01G129500 chr6D 95.349 86 4 0 1 86 145231448 145231363 1.310000e-28 137.0
23 TraesCS4A01G129500 chr3A 82.333 1166 152 26 94 1227 683318978 683320121 0.000000e+00 963.0
24 TraesCS4A01G129500 chr3A 81.458 1084 147 24 176 1227 683301018 683302079 0.000000e+00 839.0
25 TraesCS4A01G129500 chr3A 89.855 276 22 6 2432 2705 307287269 307286998 1.540000e-92 350.0
26 TraesCS4A01G129500 chr3A 89.493 276 23 6 2432 2705 307381284 307381013 7.170000e-91 344.0
27 TraesCS4A01G129500 chr3A 87.634 186 22 1 1447 1632 287532086 287531902 5.870000e-52 215.0
28 TraesCS4A01G129500 chr3A 84.694 98 11 2 1218 1312 496004186 496004090 7.970000e-16 95.3
29 TraesCS4A01G129500 chr1A 82.040 1186 144 42 94 1242 115484712 115485865 0.000000e+00 946.0
30 TraesCS4A01G129500 chr1A 86.230 886 90 22 98 975 180002741 180001880 0.000000e+00 931.0
31 TraesCS4A01G129500 chr1A 88.947 760 77 5 94 848 246007181 246006424 0.000000e+00 931.0
32 TraesCS4A01G129500 chr1A 93.538 325 16 4 2379 2703 355427880 355427561 1.880000e-131 479.0
33 TraesCS4A01G129500 chr1A 91.815 281 18 4 2423 2703 355417684 355417409 1.170000e-103 387.0
34 TraesCS4A01G129500 chr1A 89.892 277 21 6 2432 2705 279688088 279687816 1.540000e-92 350.0
35 TraesCS4A01G129500 chr1A 89.139 267 18 9 2351 2611 147099719 147099980 3.360000e-84 322.0
36 TraesCS4A01G129500 chr1A 86.429 280 28 7 2432 2705 43956026 43955751 5.660000e-77 298.0
37 TraesCS4A01G129500 chr1A 85.714 273 24 11 2351 2611 147092366 147092635 9.540000e-70 274.0
38 TraesCS4A01G129500 chr1A 80.539 334 49 13 2379 2703 203716683 203717009 2.690000e-60 243.0
39 TraesCS4A01G129500 chr1A 84.141 227 30 6 2481 2705 224509722 224509944 5.870000e-52 215.0
40 TraesCS4A01G129500 chr1A 87.568 185 22 1 1446 1630 315781426 315781609 2.110000e-51 213.0
41 TraesCS4A01G129500 chr1A 84.071 226 31 5 2482 2705 377234524 377234746 2.110000e-51 213.0
42 TraesCS4A01G129500 chr1A 87.027 185 23 1 1446 1630 315773526 315773709 9.820000e-50 207.0
43 TraesCS4A01G129500 chr1A 79.153 307 51 12 2403 2705 426335800 426336097 1.640000e-47 200.0
44 TraesCS4A01G129500 chr1A 78.797 316 49 16 2401 2705 27340647 27340339 2.120000e-46 196.0
45 TraesCS4A01G129500 chr1A 76.522 345 49 25 2373 2697 428005338 428005006 2.790000e-35 159.0
46 TraesCS4A01G129500 chr1A 75.806 310 61 14 2373 2676 226478022 226478323 7.810000e-31 145.0
47 TraesCS4A01G129500 chr1A 92.473 93 6 1 2 93 136720855 136720763 6.080000e-27 132.0
48 TraesCS4A01G129500 chr1A 91.579 95 7 1 1 94 260415302 260415208 2.190000e-26 130.0
49 TraesCS4A01G129500 chr1A 89.899 99 9 1 1 98 209109509 209109411 2.830000e-25 126.0
50 TraesCS4A01G129500 chr1A 89.855 69 5 2 2353 2420 274661897 274661830 1.330000e-13 87.9
51 TraesCS4A01G129500 chr1A 87.179 78 7 1 1238 1312 163211463 163211386 4.800000e-13 86.1
52 TraesCS4A01G129500 chr4D 89.093 761 71 8 94 845 365914505 365915262 0.000000e+00 935.0
53 TraesCS4A01G129500 chr4D 89.065 759 71 8 94 843 365905363 365906118 0.000000e+00 931.0
54 TraesCS4A01G129500 chr4D 88.699 761 74 8 94 845 154050511 154051268 0.000000e+00 918.0
55 TraesCS4A01G129500 chr4D 86.667 150 19 1 1630 1779 145388689 145388837 5.990000e-37 165.0
56 TraesCS4A01G129500 chr4D 94.186 86 5 0 1 86 350243111 350243196 6.080000e-27 132.0
57 TraesCS4A01G129500 chr4D 95.062 81 4 0 1 81 139226749 139226669 7.860000e-26 128.0
58 TraesCS4A01G129500 chr4D 95.062 81 4 0 1 81 223201777 223201857 7.860000e-26 128.0
59 TraesCS4A01G129500 chr4D 95.062 81 4 0 1 81 458868440 458868520 7.860000e-26 128.0
60 TraesCS4A01G129500 chr4D 95.000 80 4 0 2 81 210530719 210530640 2.830000e-25 126.0
61 TraesCS4A01G129500 chr4D 93.827 81 5 0 1 81 121644576 121644496 3.660000e-24 122.0
62 TraesCS4A01G129500 chr4D 93.827 81 5 0 1 81 130901031 130900951 3.660000e-24 122.0
63 TraesCS4A01G129500 chr4D 93.827 81 5 0 1 81 214452921 214453001 3.660000e-24 122.0
64 TraesCS4A01G129500 chr4D 93.827 81 5 0 1 81 220739418 220739338 3.660000e-24 122.0
65 TraesCS4A01G129500 chr4D 90.426 94 8 1 1 93 252986668 252986761 3.660000e-24 122.0
66 TraesCS4A01G129500 chr4D 90.426 94 7 2 1 93 321632672 321632764 3.660000e-24 122.0
67 TraesCS4A01G129500 chr4D 90.426 94 7 2 2 94 432556582 432556674 3.660000e-24 122.0
68 TraesCS4A01G129500 chr4D 90.217 92 8 1 3 93 216040468 216040559 4.730000e-23 119.0
69 TraesCS4A01G129500 chr4D 91.176 68 6 0 1501 1568 180970203 180970136 2.870000e-15 93.5
70 TraesCS4A01G129500 chr3D 88.962 761 73 7 94 845 410327827 410327069 0.000000e+00 929.0
71 TraesCS4A01G129500 chr3D 88.613 764 75 9 94 848 283086430 283085670 0.000000e+00 918.0
72 TraesCS4A01G129500 chr3D 87.333 150 18 1 1630 1779 420481431 420481579 1.290000e-38 171.0
73 TraesCS4A01G129500 chr3D 92.553 94 6 1 1 93 228435091 228434998 1.690000e-27 134.0
74 TraesCS4A01G129500 chr2D 88.411 768 77 9 94 854 469208107 469207345 0.000000e+00 915.0
75 TraesCS4A01G129500 chr2D 92.708 96 6 1 1 95 134556236 134556141 1.310000e-28 137.0
76 TraesCS4A01G129500 chr2D 91.837 98 7 1 1 97 255244782 255244685 4.700000e-28 135.0
77 TraesCS4A01G129500 chr5B 80.940 1170 149 50 94 1229 192568789 192569918 0.000000e+00 857.0
78 TraesCS4A01G129500 chr5B 80.251 319 42 19 2399 2705 469788455 469788764 1.260000e-53 220.0
79 TraesCS4A01G129500 chr5B 89.362 141 14 1 1489 1629 384158968 384159107 2.770000e-40 176.0
80 TraesCS4A01G129500 chr2A 84.424 886 107 18 94 974 244959997 244959138 0.000000e+00 843.0
81 TraesCS4A01G129500 chr2A 80.034 1177 161 46 94 1235 190050082 190048945 0.000000e+00 804.0
82 TraesCS4A01G129500 chr2A 87.027 185 23 1 1446 1630 374958513 374958330 9.820000e-50 207.0
83 TraesCS4A01G129500 chr2A 87.578 161 19 1 1737 1897 161922887 161923046 4.600000e-43 185.0
84 TraesCS4A01G129500 chr5A 81.517 936 110 28 329 1229 576366894 576365987 0.000000e+00 712.0
85 TraesCS4A01G129500 chr5A 89.381 226 21 3 2481 2705 373891890 373891667 5.700000e-72 281.0
86 TraesCS4A01G129500 chr5A 90.674 193 17 1 1895 2086 215816689 215816497 3.460000e-64 255.0
87 TraesCS4A01G129500 chr5A 88.770 187 20 1 1446 1632 299166396 299166581 7.530000e-56 228.0
88 TraesCS4A01G129500 chr5A 84.783 184 27 1 1446 1629 502454646 502454828 1.650000e-42 183.0
89 TraesCS4A01G129500 chr5A 92.632 95 6 1 1 94 260047162 260047256 4.700000e-28 135.0
90 TraesCS4A01G129500 chr5A 90.278 72 5 2 2350 2420 442364475 442364545 2.870000e-15 93.5
91 TraesCS4A01G129500 chr5A 90.278 72 5 2 2350 2420 442372578 442372648 2.870000e-15 93.5
92 TraesCS4A01G129500 chr1B 80.317 315 51 10 2395 2705 357153283 357152976 7.530000e-56 228.0
93 TraesCS4A01G129500 chr1B 80.198 303 47 13 2410 2705 288787253 288786957 5.870000e-52 215.0
94 TraesCS4A01G129500 chr1B 80.479 292 46 10 2418 2704 106107444 106107729 2.110000e-51 213.0
95 TraesCS4A01G129500 chr1B 79.365 315 54 10 2395 2705 357145015 357144708 7.590000e-51 211.0
96 TraesCS4A01G129500 chr6A 81.272 283 39 12 2429 2705 441783279 441783553 1.630000e-52 217.0
97 TraesCS4A01G129500 chr6A 87.970 133 11 3 1501 1632 492924730 492924858 4.660000e-33 152.0
98 TraesCS4A01G129500 chr6A 96.512 86 2 1 1 86 491663126 491663042 1.010000e-29 141.0
99 TraesCS4A01G129500 chr6A 96.386 83 3 0 1 83 186308839 186308921 1.310000e-28 137.0
100 TraesCS4A01G129500 chr6A 92.553 94 6 1 1 93 101274548 101274455 1.690000e-27 134.0
101 TraesCS4A01G129500 chr6A 96.053 76 3 0 1557 1632 346194361 346194436 1.020000e-24 124.0
102 TraesCS4A01G129500 chr6A 94.286 70 4 0 1563 1632 371819638 371819569 1.020000e-19 108.0
103 TraesCS4A01G129500 chr6A 85.567 97 11 1 1219 1312 404812670 404812766 6.160000e-17 99.0
104 TraesCS4A01G129500 chr6A 91.304 69 4 2 2353 2420 241933425 241933358 2.870000e-15 93.5
105 TraesCS4A01G129500 chr6A 94.828 58 3 0 2354 2411 438490968 438490911 1.030000e-14 91.6
106 TraesCS4A01G129500 chr4B 86.631 187 22 3 1446 1632 345645806 345645623 1.270000e-48 204.0
107 TraesCS4A01G129500 chr4B 85.714 182 25 1 1446 1627 345642461 345642281 9.890000e-45 191.0
108 TraesCS4A01G129500 chr7B 90.780 141 12 1 1492 1632 502038924 502038785 1.280000e-43 187.0
109 TraesCS4A01G129500 chr7B 85.606 132 17 2 1657 1786 604690199 604690068 1.310000e-28 137.0
110 TraesCS4A01G129500 chr7D 88.667 150 16 1 1630 1779 258632958 258633106 5.950000e-42 182.0
111 TraesCS4A01G129500 chr7D 88.000 150 17 1 1630 1779 160902967 160903115 2.770000e-40 176.0
112 TraesCS4A01G129500 chr7D 87.333 150 18 1 1630 1779 347859616 347859468 1.290000e-38 171.0
113 TraesCS4A01G129500 chr7D 87.333 150 18 1 1630 1779 357305609 357305757 1.290000e-38 171.0
114 TraesCS4A01G129500 chr6B 88.652 141 15 1 1489 1629 214681164 214681303 1.290000e-38 171.0
115 TraesCS4A01G129500 chr6B 89.216 102 11 0 1 102 640714116 640714217 7.860000e-26 128.0
116 TraesCS4A01G129500 chr6B 89.552 67 6 1 2020 2086 212224831 212224766 1.730000e-12 84.2
117 TraesCS4A01G129500 chrUn 78.889 270 42 13 2438 2701 119017006 119016746 4.630000e-38 169.0
118 TraesCS4A01G129500 chrUn 92.500 80 6 0 2 81 25144348 25144427 6.120000e-22 115.0
119 TraesCS4A01G129500 chrUn 92.500 80 6 0 2 81 25147132 25147211 6.120000e-22 115.0
120 TraesCS4A01G129500 chrUn 92.500 80 6 0 2 81 25377952 25377873 6.120000e-22 115.0
121 TraesCS4A01G129500 chrUn 87.629 97 10 2 1 96 344588726 344588821 7.920000e-21 111.0
122 TraesCS4A01G129500 chrUn 88.608 79 9 0 1 79 25942866 25942788 2.220000e-16 97.1
123 TraesCS4A01G129500 chrUn 88.608 79 9 0 1 79 266045543 266045621 2.220000e-16 97.1
124 TraesCS4A01G129500 chrUn 87.654 81 9 1 1 81 177306001 177305922 2.870000e-15 93.5
125 TraesCS4A01G129500 chrUn 83.721 86 14 0 1 86 136145094 136145179 6.210000e-12 82.4
126 TraesCS4A01G129500 chrUn 81.915 94 16 1 2 94 285250480 285250573 8.030000e-11 78.7
127 TraesCS4A01G129500 chr5D 86.667 150 19 1 1630 1779 26447004 26447152 5.990000e-37 165.0
128 TraesCS4A01G129500 chr5D 91.667 96 7 1 1 95 224413844 224413749 6.080000e-27 132.0
129 TraesCS4A01G129500 chr3B 84.848 165 22 3 1923 2086 459536978 459536816 2.150000e-36 163.0
130 TraesCS4A01G129500 chr3B 92.537 67 4 1 2020 2086 297173574 297173639 7.970000e-16 95.3
131 TraesCS4A01G129500 chr3B 91.045 67 5 1 2020 2086 297181240 297181305 3.710000e-14 89.8
132 TraesCS4A01G129500 chr3B 92.982 57 4 0 2024 2080 474209861 474209805 1.730000e-12 84.2
133 TraesCS4A01G129500 chr1D 83.333 162 20 7 2500 2658 64293371 64293528 2.810000e-30 143.0
134 TraesCS4A01G129500 chr1D 97.531 81 2 0 1 81 148927470 148927390 3.630000e-29 139.0
135 TraesCS4A01G129500 chr1D 94.186 86 5 0 1 86 255200667 255200582 6.080000e-27 132.0
136 TraesCS4A01G129500 chr1D 88.785 107 10 2 1 105 255193132 255193026 2.190000e-26 130.0
137 TraesCS4A01G129500 chr1D 91.489 94 7 1 1 93 308008191 308008098 7.860000e-26 128.0
138 TraesCS4A01G129500 chr1D 91.489 94 7 1 1 93 308015433 308015340 7.860000e-26 128.0
139 TraesCS4A01G129500 chr1D 92.222 90 6 1 5 93 305666514 305666425 2.830000e-25 126.0
140 TraesCS4A01G129500 chr1D 87.273 110 10 4 3 111 260073234 260073128 3.660000e-24 122.0


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 TraesCS4A01G129500 chr4A 169246830 169249534 2704 True 4996 4996 100.000 1 2705 1 chr4A.!!$R2 2704
1 TraesCS4A01G129500 chr4A 169208741 169211397 2656 True 3544 3544 91.043 94 2703 1 chr4A.!!$R1 2609
2 TraesCS4A01G129500 chr4A 324910090 324911183 1093 True 763 763 79.930 93 1198 1 chr4A.!!$R5 1105
3 TraesCS4A01G129500 chr4A 324902158 324903128 970 True 719 719 80.613 93 1075 1 chr4A.!!$R4 982
4 TraesCS4A01G129500 chr4A 549333983 549334855 872 False 699 699 81.596 94 973 1 chr4A.!!$F4 879
5 TraesCS4A01G129500 chr7A 299013993 299015131 1138 True 981 981 82.691 94 1229 1 chr7A.!!$R1 1135
6 TraesCS4A01G129500 chr7A 299021962 299023081 1119 True 931 931 82.158 112 1229 1 chr7A.!!$R2 1117
7 TraesCS4A01G129500 chr7A 259186165 259187029 864 False 870 870 84.978 94 974 1 chr7A.!!$F1 880
8 TraesCS4A01G129500 chr7A 591935585 591936430 845 True 837 837 84.545 94 970 1 chr7A.!!$R6 876
9 TraesCS4A01G129500 chr6D 168910519 168911633 1114 True 976 976 82.741 94 1229 1 chr6D.!!$R3 1135
10 TraesCS4A01G129500 chr6D 136187872 136188630 758 True 924 924 88.830 94 845 1 chr6D.!!$R1 751
11 TraesCS4A01G129500 chr3A 683318978 683320121 1143 False 963 963 82.333 94 1227 1 chr3A.!!$F2 1133
12 TraesCS4A01G129500 chr3A 683301018 683302079 1061 False 839 839 81.458 176 1227 1 chr3A.!!$F1 1051
13 TraesCS4A01G129500 chr1A 115484712 115485865 1153 False 946 946 82.040 94 1242 1 chr1A.!!$F1 1148
14 TraesCS4A01G129500 chr1A 180001880 180002741 861 True 931 931 86.230 98 975 1 chr1A.!!$R5 877
15 TraesCS4A01G129500 chr1A 246006424 246007181 757 True 931 931 88.947 94 848 1 chr1A.!!$R7 754
16 TraesCS4A01G129500 chr4D 365914505 365915262 757 False 935 935 89.093 94 845 1 chr4D.!!$F10 751
17 TraesCS4A01G129500 chr4D 365905363 365906118 755 False 931 931 89.065 94 843 1 chr4D.!!$F9 749
18 TraesCS4A01G129500 chr4D 154050511 154051268 757 False 918 918 88.699 94 845 1 chr4D.!!$F2 751
19 TraesCS4A01G129500 chr3D 410327069 410327827 758 True 929 929 88.962 94 845 1 chr3D.!!$R3 751
20 TraesCS4A01G129500 chr3D 283085670 283086430 760 True 918 918 88.613 94 848 1 chr3D.!!$R2 754
21 TraesCS4A01G129500 chr2D 469207345 469208107 762 True 915 915 88.411 94 854 1 chr2D.!!$R3 760
22 TraesCS4A01G129500 chr5B 192568789 192569918 1129 False 857 857 80.940 94 1229 1 chr5B.!!$F1 1135
23 TraesCS4A01G129500 chr2A 244959138 244959997 859 True 843 843 84.424 94 974 1 chr2A.!!$R2 880
24 TraesCS4A01G129500 chr2A 190048945 190050082 1137 True 804 804 80.034 94 1235 1 chr2A.!!$R1 1141
25 TraesCS4A01G129500 chr5A 576365987 576366894 907 True 712 712 81.517 329 1229 1 chr5A.!!$R3 900

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
357 393 0.318762 GATCTCGAGGGTATGGCCAC 59.681 60.0 8.16 0.0 39.65 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2413 0.041833 CTCTCCCTCACCTTCTCCCA 59.958 60.0 0.0 0.0 0.0 4.37 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
18 19 3.173540 TTGATGAAGATGGGCCGTG 57.826 52.632 1.02 0.00 0.00 4.94
19 20 1.031571 TTGATGAAGATGGGCCGTGC 61.032 55.000 1.02 0.00 0.00 5.34
20 21 1.451927 GATGAAGATGGGCCGTGCA 60.452 57.895 1.02 0.00 0.00 4.57
21 22 1.442526 GATGAAGATGGGCCGTGCAG 61.443 60.000 1.02 0.00 0.00 4.41
22 23 2.825836 GAAGATGGGCCGTGCAGG 60.826 66.667 1.02 0.00 44.97 4.85
43 44 4.166011 GCTAGCAAAGCCACGCCG 62.166 66.667 10.63 0.00 46.25 6.46
44 45 2.742372 CTAGCAAAGCCACGCCGT 60.742 61.111 0.00 0.00 0.00 5.68
45 46 3.027170 CTAGCAAAGCCACGCCGTG 62.027 63.158 10.95 10.95 0.00 4.94
65 66 2.433446 CCACAGGCAGGCAAGTCT 59.567 61.111 0.00 0.00 0.00 3.24
66 67 1.679311 CCACAGGCAGGCAAGTCTA 59.321 57.895 0.00 0.00 0.00 2.59
67 68 0.392193 CCACAGGCAGGCAAGTCTAG 60.392 60.000 0.00 0.00 0.00 2.43
68 69 0.392193 CACAGGCAGGCAAGTCTAGG 60.392 60.000 0.00 0.00 0.00 3.02
69 70 1.222936 CAGGCAGGCAAGTCTAGGG 59.777 63.158 0.00 0.00 0.00 3.53
70 71 1.081092 AGGCAGGCAAGTCTAGGGA 59.919 57.895 0.00 0.00 0.00 4.20
71 72 1.222113 GGCAGGCAAGTCTAGGGAC 59.778 63.158 0.00 0.00 42.41 4.46
72 73 1.222113 GCAGGCAAGTCTAGGGACC 59.778 63.158 0.00 0.00 43.05 4.46
73 74 1.908483 CAGGCAAGTCTAGGGACCC 59.092 63.158 0.59 0.59 43.05 4.46
74 75 1.307084 AGGCAAGTCTAGGGACCCC 60.307 63.158 7.00 1.17 43.05 4.95
75 76 2.376165 GGCAAGTCTAGGGACCCCC 61.376 68.421 7.00 0.00 45.90 5.40
84 85 3.824815 GGGACCCCCGTTCCTAAA 58.175 61.111 0.00 0.00 34.32 1.85
85 86 2.077579 GGGACCCCCGTTCCTAAAA 58.922 57.895 0.00 0.00 34.32 1.52
86 87 0.405198 GGGACCCCCGTTCCTAAAAA 59.595 55.000 0.00 0.00 34.32 1.94
87 88 1.538047 GGACCCCCGTTCCTAAAAAC 58.462 55.000 0.00 0.00 0.00 2.43
88 89 1.538047 GACCCCCGTTCCTAAAAACC 58.462 55.000 0.00 0.00 0.00 3.27
89 90 0.852155 ACCCCCGTTCCTAAAAACCA 59.148 50.000 0.00 0.00 0.00 3.67
90 91 1.217436 ACCCCCGTTCCTAAAAACCAA 59.783 47.619 0.00 0.00 0.00 3.67
91 92 1.614903 CCCCCGTTCCTAAAAACCAAC 59.385 52.381 0.00 0.00 0.00 3.77
92 93 2.308690 CCCCGTTCCTAAAAACCAACA 58.691 47.619 0.00 0.00 0.00 3.33
296 319 0.682852 ACAAGTGGTAGGTAGCGCAA 59.317 50.000 11.47 0.00 36.72 4.85
341 375 8.940768 ACTAGCAAGAAAAGATAGAAGTGATC 57.059 34.615 0.00 0.00 0.00 2.92
354 390 1.333177 AGTGATCTCGAGGGTATGGC 58.667 55.000 13.56 0.00 0.00 4.40
357 393 0.318762 GATCTCGAGGGTATGGCCAC 59.681 60.000 8.16 0.00 39.65 5.01
395 431 3.243907 ACAAGGAAGAAGAACGAGTCCAG 60.244 47.826 0.00 0.00 0.00 3.86
397 433 1.619332 GGAAGAAGAACGAGTCCAGGT 59.381 52.381 0.00 0.00 0.00 4.00
418 454 4.863131 GGTAGAAGACAAACGGACATAGTG 59.137 45.833 0.00 0.00 0.00 2.74
480 522 3.305629 CGAGAGAAGCAAATCGGAAAGAG 59.694 47.826 0.00 0.00 0.00 2.85
562 611 3.851838 GCATGTCCGGTTTAAATATGGCG 60.852 47.826 0.00 0.00 0.00 5.69
598 649 7.539366 GCACAAACAAAACTACAAGTTAAGTGA 59.461 33.333 0.00 0.00 37.47 3.41
644 697 2.761559 TCGACGAAACACCACATTCAT 58.238 42.857 0.00 0.00 0.00 2.57
713 770 3.508845 AAACATGGCAGTAGGTGAAGT 57.491 42.857 0.00 0.00 0.00 3.01
714 771 2.479566 ACATGGCAGTAGGTGAAGTG 57.520 50.000 0.00 0.00 0.00 3.16
1054 1164 1.687612 CAAGATGGTGGGGTGCTCT 59.312 57.895 0.00 0.00 0.00 4.09
1110 1237 3.040147 ACGAGTGACAATTCGGACATT 57.960 42.857 13.28 0.00 39.65 2.71
1133 1260 2.670905 TGCAAACATACGGTTCATCTCG 59.329 45.455 0.00 0.00 39.29 4.04
1146 1273 5.588240 GGTTCATCTCGTACATCACACATA 58.412 41.667 0.00 0.00 0.00 2.29
1147 1274 6.216569 GGTTCATCTCGTACATCACACATAT 58.783 40.000 0.00 0.00 0.00 1.78
1242 1374 2.602878 GAAGTAGGCGTTCATGTTCGA 58.397 47.619 14.11 0.00 0.00 3.71
1259 1391 1.131126 TCGAAAAGCGGTAGAGGTACG 59.869 52.381 0.00 0.00 41.33 3.67
1267 1399 1.679944 CGGTAGAGGTACGGGTCTTCA 60.680 57.143 0.00 0.00 0.00 3.02
1273 1405 1.764134 AGGTACGGGTCTTCAACAACA 59.236 47.619 0.00 0.00 0.00 3.33
1279 1411 2.544277 CGGGTCTTCAACAACAGTCGTA 60.544 50.000 0.00 0.00 0.00 3.43
1280 1412 2.798847 GGGTCTTCAACAACAGTCGTAC 59.201 50.000 0.00 0.00 0.00 3.67
1281 1413 3.450578 GGTCTTCAACAACAGTCGTACA 58.549 45.455 0.00 0.00 0.00 2.90
1282 1414 4.056050 GGTCTTCAACAACAGTCGTACAT 58.944 43.478 0.00 0.00 0.00 2.29
1283 1415 4.084537 GGTCTTCAACAACAGTCGTACATG 60.085 45.833 0.00 0.00 0.00 3.21
1284 1416 3.493129 TCTTCAACAACAGTCGTACATGC 59.507 43.478 0.00 0.00 0.00 4.06
1285 1417 3.106242 TCAACAACAGTCGTACATGCT 57.894 42.857 0.00 0.00 0.00 3.79
1286 1418 3.462982 TCAACAACAGTCGTACATGCTT 58.537 40.909 0.00 0.00 0.00 3.91
1313 1448 1.338337 CATCGGTAGAGGTTCTCGCAT 59.662 52.381 0.00 0.00 35.36 4.73
1316 1451 0.175760 GGTAGAGGTTCTCGCATGCA 59.824 55.000 19.57 4.02 35.36 3.96
1318 1453 1.134965 GTAGAGGTTCTCGCATGCACT 60.135 52.381 19.57 5.15 35.36 4.40
1320 1455 1.135915 AGAGGTTCTCGCATGCACTAG 59.864 52.381 19.57 11.69 35.36 2.57
1321 1456 0.176680 AGGTTCTCGCATGCACTAGG 59.823 55.000 19.57 0.14 0.00 3.02
1335 1470 0.179936 ACTAGGGTCGTCGGTAGAGG 59.820 60.000 0.00 0.00 0.00 3.69
1340 1475 0.731994 GGTCGTCGGTAGAGGTTCTC 59.268 60.000 0.00 0.00 34.19 2.87
1342 1477 0.036952 TCGTCGGTAGAGGTTCTCGT 60.037 55.000 0.00 0.00 35.36 4.18
1370 1505 4.464951 TCGAAGATGGTAGTGGTACATGTT 59.535 41.667 2.30 0.00 44.52 2.71
1378 1513 5.998981 TGGTAGTGGTACATGTTTTTGTAGG 59.001 40.000 2.30 0.00 44.52 3.18
1379 1514 5.106436 GGTAGTGGTACATGTTTTTGTAGGC 60.106 44.000 2.30 0.00 44.52 3.93
1388 1523 2.540931 TGTTTTTGTAGGCGTTCGAGTC 59.459 45.455 0.00 0.00 0.00 3.36
1400 1535 4.138366 CGTTCGAGTCATCGTTAACGGC 62.138 54.545 26.51 14.54 46.67 5.68
1401 1536 3.024423 CGAGTCATCGTTAACGGCA 57.976 52.632 26.51 9.99 44.09 5.69
1413 1548 2.812011 GTTAACGGCACTTGGTGAATCT 59.188 45.455 1.57 0.00 35.23 2.40
1415 1550 0.396435 ACGGCACTTGGTGAATCTCA 59.604 50.000 1.57 0.00 35.23 3.27
1418 1553 2.350772 CGGCACTTGGTGAATCTCAAAC 60.351 50.000 1.57 0.00 35.23 2.93
1419 1554 2.029918 GGCACTTGGTGAATCTCAAACC 60.030 50.000 1.57 0.00 35.23 3.27
1474 1609 0.040157 TTTCCGTGTGGTACTCGTCG 60.040 55.000 0.00 0.00 33.75 5.12
1477 1612 1.511464 CGTGTGGTACTCGTCGAGC 60.511 63.158 22.00 6.74 32.04 5.03
1480 1615 0.039798 TGTGGTACTCGTCGAGCAAC 60.040 55.000 22.00 18.69 32.04 4.17
1484 1619 1.068748 GGTACTCGTCGAGCAACAGAA 60.069 52.381 22.00 0.00 32.04 3.02
1490 1625 2.128035 CGTCGAGCAACAGAAGAAGTT 58.872 47.619 0.00 0.00 0.00 2.66
1502 1637 3.187227 CAGAAGAAGTTGTGGTTCGATGG 59.813 47.826 0.00 0.00 0.00 3.51
1555 1690 1.882989 GCCGTCAGAGAGGAAGCAGT 61.883 60.000 0.00 0.00 0.00 4.40
1647 1784 2.032223 CTGCTGGTGCTGCTCACT 59.968 61.111 0.00 0.00 44.98 3.41
1660 1797 2.018544 CTCACTAGCGAGAGGACGG 58.981 63.158 1.23 0.00 34.79 4.79
1683 1820 3.760035 GAGGAGCAAGACGGCGGA 61.760 66.667 13.24 0.00 39.27 5.54
1749 1886 4.135153 CGGACTGGTGGCTCTCCG 62.135 72.222 2.07 2.07 39.78 4.63
1761 1898 3.302347 CTCTCCGGCGAACTTGGCT 62.302 63.158 9.30 0.00 0.00 4.75
1767 1904 2.629656 GGCGAACTTGGCTGCATGT 61.630 57.895 0.50 0.00 0.00 3.21
1771 1908 1.156736 GAACTTGGCTGCATGTACGT 58.843 50.000 0.50 0.00 0.00 3.57
1781 1918 1.413767 GCATGTACGTGCGAGGTCTG 61.414 60.000 23.44 0.00 35.10 3.51
1807 1944 1.966451 GGGTGCGTGAGGGAAACAG 60.966 63.158 0.00 0.00 0.00 3.16
1881 2018 0.033228 GAGCATCTCAGGATCGGGTG 59.967 60.000 0.00 0.00 0.00 4.61
1889 2026 0.470833 CAGGATCGGGTGAGGAGGAT 60.471 60.000 0.00 0.00 0.00 3.24
1897 2034 2.285368 TGAGGAGGATGGCGGGTT 60.285 61.111 0.00 0.00 0.00 4.11
1910 2047 2.281484 GGGTTGCAGACGGCTTGA 60.281 61.111 0.00 0.00 45.15 3.02
1927 2064 1.139095 GAGGAGGCGTCGTACTTGG 59.861 63.158 0.98 0.00 0.00 3.61
1959 2096 2.432456 TACGAGCAAGGCACTGCG 60.432 61.111 6.01 0.00 40.86 5.18
2009 2146 1.379146 GGTGAAGACCCCAGGGAAC 59.621 63.158 7.25 0.00 36.03 3.62
2010 2147 1.423794 GGTGAAGACCCCAGGGAACA 61.424 60.000 7.25 1.04 36.03 3.18
2011 2148 0.036875 GTGAAGACCCCAGGGAACAG 59.963 60.000 7.25 0.00 38.96 3.16
2038 2176 2.740714 GCAACGACGATGGTGCTCC 61.741 63.158 13.12 0.00 0.00 4.70
2060 2198 3.465403 CTCCTGGTGCTCCTCCGG 61.465 72.222 6.34 0.00 34.23 5.14
2224 2362 2.202756 GACATGGCGACGGGAGAC 60.203 66.667 0.00 0.00 0.00 3.36
2226 2364 2.202797 CATGGCGACGGGAGACAG 60.203 66.667 0.00 0.00 0.00 3.51
2239 2377 0.965439 GAGACAGATGAGGGGATCGG 59.035 60.000 0.00 0.00 0.00 4.18
2244 2382 1.906824 GATGAGGGGATCGGGCGTA 60.907 63.158 0.00 0.00 0.00 4.42
2258 2396 2.941013 CGTACGCGTGCGGTACTC 60.941 66.667 36.71 9.90 44.69 2.59
2268 2406 3.687102 CGGTACTCGTGGGTGGCA 61.687 66.667 0.00 0.00 0.00 4.92
2270 2408 2.280552 GGTACTCGTGGGTGGCAGA 61.281 63.158 0.00 0.00 0.00 4.26
2271 2409 1.669440 GTACTCGTGGGTGGCAGAA 59.331 57.895 0.00 0.00 0.00 3.02
2275 2413 2.047274 CGTGGGTGGCAGAACGAT 60.047 61.111 10.11 0.00 38.27 3.73
2358 2496 1.786441 AGAGGCTGTAGAGCTAGGGAT 59.214 52.381 12.15 0.00 45.44 3.85
2366 2504 3.465966 TGTAGAGCTAGGGATTAGGTGGA 59.534 47.826 0.00 0.00 40.11 4.02
2429 2577 4.469657 GGCTCTCTCTCTCTTATCTCCAA 58.530 47.826 0.00 0.00 0.00 3.53
2435 2583 9.130661 CTCTCTCTCTCTTATCTCCAAATAACA 57.869 37.037 0.00 0.00 0.00 2.41
2475 2623 4.858519 AGGAGAAGAAAAGGAAGGGGTTAT 59.141 41.667 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.031571 GCACGGCCCATCTTCATCAA 61.032 55.000 0.00 0.00 0.00 2.57
1 2 1.451927 GCACGGCCCATCTTCATCA 60.452 57.895 0.00 0.00 0.00 3.07
2 3 1.442526 CTGCACGGCCCATCTTCATC 61.443 60.000 0.00 0.00 0.00 2.92
3 4 1.452651 CTGCACGGCCCATCTTCAT 60.453 57.895 0.00 0.00 0.00 2.57
5 6 2.825836 CCTGCACGGCCCATCTTC 60.826 66.667 0.00 0.00 0.00 2.87
27 28 2.742372 ACGGCGTGGCTTTGCTAG 60.742 61.111 13.76 0.00 0.00 3.42
28 29 3.047280 CACGGCGTGGCTTTGCTA 61.047 61.111 31.19 0.00 0.00 3.49
48 49 0.392193 CTAGACTTGCCTGCCTGTGG 60.392 60.000 0.00 0.00 0.00 4.17
49 50 0.392193 CCTAGACTTGCCTGCCTGTG 60.392 60.000 0.00 0.00 0.00 3.66
50 51 1.557269 CCCTAGACTTGCCTGCCTGT 61.557 60.000 0.00 0.00 0.00 4.00
51 52 1.222936 CCCTAGACTTGCCTGCCTG 59.777 63.158 0.00 0.00 0.00 4.85
52 53 1.081092 TCCCTAGACTTGCCTGCCT 59.919 57.895 0.00 0.00 0.00 4.75
53 54 1.222113 GTCCCTAGACTTGCCTGCC 59.778 63.158 0.00 0.00 40.10 4.85
54 55 1.222113 GGTCCCTAGACTTGCCTGC 59.778 63.158 0.00 0.00 43.05 4.85
55 56 1.627297 GGGGTCCCTAGACTTGCCTG 61.627 65.000 8.15 0.00 43.05 4.85
56 57 1.307084 GGGGTCCCTAGACTTGCCT 60.307 63.158 8.15 0.00 43.05 4.75
57 58 2.376165 GGGGGTCCCTAGACTTGCC 61.376 68.421 8.15 0.00 43.05 4.52
58 59 2.732619 CGGGGGTCCCTAGACTTGC 61.733 68.421 8.15 0.00 42.67 4.01
59 60 0.908180 AACGGGGGTCCCTAGACTTG 60.908 60.000 8.15 0.00 42.67 3.16
60 61 0.616964 GAACGGGGGTCCCTAGACTT 60.617 60.000 8.15 0.00 42.67 3.01
61 62 1.001376 GAACGGGGGTCCCTAGACT 59.999 63.158 8.15 0.00 42.67 3.24
62 63 2.062777 GGAACGGGGGTCCCTAGAC 61.063 68.421 8.15 2.93 42.67 2.59
63 64 0.925720 TAGGAACGGGGGTCCCTAGA 60.926 60.000 8.15 0.00 42.67 2.43
64 65 0.031817 TTAGGAACGGGGGTCCCTAG 60.032 60.000 8.15 4.70 42.67 3.02
65 66 0.417035 TTTAGGAACGGGGGTCCCTA 59.583 55.000 8.15 0.00 42.67 3.53
66 67 0.476219 TTTTAGGAACGGGGGTCCCT 60.476 55.000 8.15 0.00 42.67 4.20
67 68 0.405198 TTTTTAGGAACGGGGGTCCC 59.595 55.000 0.00 0.00 41.09 4.46
68 69 1.538047 GTTTTTAGGAACGGGGGTCC 58.462 55.000 0.00 0.00 35.17 4.46
69 70 1.202915 TGGTTTTTAGGAACGGGGGTC 60.203 52.381 0.00 0.00 0.00 4.46
70 71 0.852155 TGGTTTTTAGGAACGGGGGT 59.148 50.000 0.00 0.00 0.00 4.95
71 72 1.614903 GTTGGTTTTTAGGAACGGGGG 59.385 52.381 0.00 0.00 0.00 5.40
72 73 2.308690 TGTTGGTTTTTAGGAACGGGG 58.691 47.619 0.00 0.00 0.00 5.73
73 74 4.388378 TTTGTTGGTTTTTAGGAACGGG 57.612 40.909 0.00 0.00 0.00 5.28
74 75 8.421673 TTTAATTTGTTGGTTTTTAGGAACGG 57.578 30.769 0.00 0.00 0.00 4.44
144 152 3.119531 TGCAGGTGAAGTTGAAGTTTGTG 60.120 43.478 0.00 0.00 0.00 3.33
296 319 3.057033 AGTTGTTCGTTCTACCGCTATGT 60.057 43.478 0.00 0.00 0.00 2.29
341 375 1.338136 AAGGTGGCCATACCCTCGAG 61.338 60.000 9.72 5.13 41.83 4.04
354 390 1.380380 GGAATCCCAGGCAAGGTGG 60.380 63.158 0.00 0.00 34.52 4.61
357 393 0.251742 TTGTGGAATCCCAGGCAAGG 60.252 55.000 0.00 0.00 44.55 3.61
395 431 4.863131 CACTATGTCCGTTTGTCTTCTACC 59.137 45.833 0.00 0.00 0.00 3.18
397 433 4.768448 TCCACTATGTCCGTTTGTCTTCTA 59.232 41.667 0.00 0.00 0.00 2.10
418 454 2.289444 TGGAGTTGTGAGGATTCGTTCC 60.289 50.000 0.00 0.00 45.85 3.62
480 522 2.223923 TGTGTTTACCATGTTGCTTGCC 60.224 45.455 0.00 0.00 0.00 4.52
562 611 1.719600 TTGTTTGTGCACTTTGCCAC 58.280 45.000 19.41 6.10 44.23 5.01
598 649 4.346734 CAACTCGTTGCATATTGAGCTT 57.653 40.909 0.00 0.00 33.45 3.74
644 697 7.981142 ACCTAACTGGGAGTGAACTAAATAAA 58.019 34.615 0.00 0.00 41.11 1.40
998 1101 2.618709 CCTATCTTTTTCACCGGCATCC 59.381 50.000 0.00 0.00 0.00 3.51
1110 1237 3.407698 AGATGAACCGTATGTTTGCACA 58.592 40.909 0.00 0.00 37.29 4.57
1133 1260 8.347729 TGTGAACGAATATATGTGTGATGTAC 57.652 34.615 0.00 0.00 0.00 2.90
1146 1273 4.278669 AGACTATCGCCTGTGAACGAATAT 59.721 41.667 0.00 0.00 42.31 1.28
1147 1274 3.630769 AGACTATCGCCTGTGAACGAATA 59.369 43.478 0.00 0.00 42.31 1.75
1242 1374 0.533951 CCCGTACCTCTACCGCTTTT 59.466 55.000 0.00 0.00 0.00 2.27
1259 1391 1.949465 ACGACTGTTGTTGAAGACCC 58.051 50.000 0.00 0.00 0.00 4.46
1267 1399 2.475111 CGAAGCATGTACGACTGTTGTT 59.525 45.455 5.91 0.00 0.00 2.83
1273 1405 1.132643 GACCTCGAAGCATGTACGACT 59.867 52.381 0.00 0.00 32.72 4.18
1313 1448 1.002257 TACCGACGACCCTAGTGCA 60.002 57.895 0.00 0.00 0.00 4.57
1316 1451 0.179936 CCTCTACCGACGACCCTAGT 59.820 60.000 0.00 0.00 0.00 2.57
1318 1453 0.620556 AACCTCTACCGACGACCCTA 59.379 55.000 0.00 0.00 0.00 3.53
1320 1455 0.679321 AGAACCTCTACCGACGACCC 60.679 60.000 0.00 0.00 0.00 4.46
1321 1456 0.731994 GAGAACCTCTACCGACGACC 59.268 60.000 0.00 0.00 0.00 4.79
1340 1475 3.172050 CACTACCATCTTCGAGTTCACG 58.828 50.000 0.00 0.00 0.00 4.35
1342 1477 3.162666 ACCACTACCATCTTCGAGTTCA 58.837 45.455 0.00 0.00 0.00 3.18
1348 1483 4.386867 ACATGTACCACTACCATCTTCG 57.613 45.455 0.00 0.00 0.00 3.79
1350 1485 6.775629 ACAAAAACATGTACCACTACCATCTT 59.224 34.615 0.00 0.00 0.00 2.40
1351 1486 6.303839 ACAAAAACATGTACCACTACCATCT 58.696 36.000 0.00 0.00 0.00 2.90
1352 1487 6.569179 ACAAAAACATGTACCACTACCATC 57.431 37.500 0.00 0.00 0.00 3.51
1354 1489 5.998981 CCTACAAAAACATGTACCACTACCA 59.001 40.000 0.00 0.00 34.75 3.25
1370 1505 2.512485 TGACTCGAACGCCTACAAAA 57.488 45.000 0.00 0.00 0.00 2.44
1378 1513 4.138366 CCGTTAACGATGACTCGAACGC 62.138 54.545 28.79 0.00 45.80 4.84
1388 1523 1.136085 CACCAAGTGCCGTTAACGATG 60.136 52.381 28.79 14.22 43.02 3.84
1393 1528 3.071479 GAGATTCACCAAGTGCCGTTAA 58.929 45.455 0.00 0.00 32.98 2.01
1396 1531 0.396435 TGAGATTCACCAAGTGCCGT 59.604 50.000 0.00 0.00 32.98 5.68
1398 1533 2.029918 GGTTTGAGATTCACCAAGTGCC 60.030 50.000 0.00 0.00 32.98 5.01
1400 1535 2.226437 CCGGTTTGAGATTCACCAAGTG 59.774 50.000 0.00 0.00 34.45 3.16
1401 1536 2.158667 ACCGGTTTGAGATTCACCAAGT 60.159 45.455 0.00 0.00 0.00 3.16
1413 1548 1.595929 GACGCCAAGACCGGTTTGA 60.596 57.895 22.92 0.00 0.00 2.69
1415 1550 1.301479 GAGACGCCAAGACCGGTTT 60.301 57.895 9.42 0.00 0.00 3.27
1418 1553 1.519455 GATGAGACGCCAAGACCGG 60.519 63.158 0.00 0.00 0.00 5.28
1419 1554 1.874019 CGATGAGACGCCAAGACCG 60.874 63.158 0.00 0.00 0.00 4.79
1474 1609 2.945668 ACCACAACTTCTTCTGTTGCTC 59.054 45.455 6.53 0.00 46.03 4.26
1480 1615 3.187227 CCATCGAACCACAACTTCTTCTG 59.813 47.826 0.00 0.00 0.00 3.02
1484 1619 2.368875 AGACCATCGAACCACAACTTCT 59.631 45.455 0.00 0.00 0.00 2.85
1490 1625 0.605319 GCCAAGACCATCGAACCACA 60.605 55.000 0.00 0.00 0.00 4.17
1502 1637 2.644992 CACCTTTGCGGCCAAGAC 59.355 61.111 14.75 0.00 35.61 3.01
1542 1677 2.977178 CGCCACTGCTTCCTCTCT 59.023 61.111 0.00 0.00 34.43 3.10
1560 1695 4.559063 CTGCCATGGCCCTCCTCG 62.559 72.222 33.44 9.34 41.09 4.63
1647 1784 2.895865 CTCGCCGTCCTCTCGCTA 60.896 66.667 0.00 0.00 0.00 4.26
1660 1797 2.185608 GTCTTGCTCCTCCCTCGC 59.814 66.667 0.00 0.00 0.00 5.03
1683 1820 1.265454 ATCCCCGAGCTCCGAGTTTT 61.265 55.000 8.47 0.00 41.76 2.43
1722 1859 3.710722 CCAGTCCGCTGCTTCCCT 61.711 66.667 0.00 0.00 41.26 4.20
1749 1886 1.305219 TACATGCAGCCAAGTTCGCC 61.305 55.000 0.00 0.00 0.00 5.54
1761 1898 1.445410 GACCTCGCACGTACATGCA 60.445 57.895 15.00 0.47 46.47 3.96
1767 1904 3.035576 CTCGCAGACCTCGCACGTA 62.036 63.158 0.00 0.00 0.00 3.57
1771 1908 4.121669 GAGCTCGCAGACCTCGCA 62.122 66.667 0.00 0.00 28.95 5.10
1786 1923 3.234630 TTTCCCTCACGCACCCGAG 62.235 63.158 0.00 0.00 38.29 4.63
1796 1933 1.073722 CTGCTGGCTGTTTCCCTCA 59.926 57.895 0.00 0.00 0.00 3.86
1807 1944 4.154347 CTCCTCGACCCTGCTGGC 62.154 72.222 3.63 0.00 37.83 4.85
1848 1985 2.049618 GCTCTCCATCGCTAGCCG 60.050 66.667 9.66 4.62 38.61 5.52
1870 2007 0.470833 ATCCTCCTCACCCGATCCTG 60.471 60.000 0.00 0.00 0.00 3.86
1874 2011 2.143419 GCCATCCTCCTCACCCGAT 61.143 63.158 0.00 0.00 0.00 4.18
1877 2014 3.866582 CCGCCATCCTCCTCACCC 61.867 72.222 0.00 0.00 0.00 4.61
1881 2018 2.190578 CAACCCGCCATCCTCCTC 59.809 66.667 0.00 0.00 0.00 3.71
1897 2034 2.659016 CTCCTCAAGCCGTCTGCA 59.341 61.111 0.00 0.00 44.83 4.41
1910 2047 1.605738 ACCAAGTACGACGCCTCCT 60.606 57.895 0.00 0.00 0.00 3.69
1927 2064 2.416260 GTACCCCGCGAGATCCAC 59.584 66.667 8.23 0.00 0.00 4.02
1954 2091 2.261671 CAGGCTCGTTACCGCAGT 59.738 61.111 0.00 0.00 0.00 4.40
1959 2096 1.067582 CCGATCCAGGCTCGTTACC 59.932 63.158 11.70 0.00 34.36 2.85
1961 2098 1.107538 CCTCCGATCCAGGCTCGTTA 61.108 60.000 11.70 0.00 34.36 3.18
1991 2128 1.379146 GTTCCCTGGGGTCTTCACC 59.621 63.158 14.00 0.00 42.90 4.02
2009 2146 3.636231 TCGTTGCCCCACTCCCTG 61.636 66.667 0.00 0.00 0.00 4.45
2010 2147 3.637273 GTCGTTGCCCCACTCCCT 61.637 66.667 0.00 0.00 0.00 4.20
2014 2151 2.047274 CATCGTCGTTGCCCCACT 60.047 61.111 0.00 0.00 0.00 4.00
2015 2152 3.124921 CCATCGTCGTTGCCCCAC 61.125 66.667 0.00 0.00 0.00 4.61
2016 2153 3.632080 ACCATCGTCGTTGCCCCA 61.632 61.111 0.00 0.00 0.00 4.96
2038 2176 2.046507 GGAGCACCAGGAGCAGTG 60.047 66.667 11.90 0.00 37.05 3.66
2042 2180 4.154347 CGGAGGAGCACCAGGAGC 62.154 72.222 2.07 0.00 38.94 4.70
2112 2250 2.284921 CACCCCCTCCTCTGCTCA 60.285 66.667 0.00 0.00 0.00 4.26
2174 2312 3.737172 CGGTTGCTTCTTGGCCCG 61.737 66.667 0.00 0.00 32.70 6.13
2208 2346 2.994995 TGTCTCCCGTCGCCATGT 60.995 61.111 0.00 0.00 0.00 3.21
2224 2362 2.746359 GCCCGATCCCCTCATCTG 59.254 66.667 0.00 0.00 0.00 2.90
2226 2364 1.906824 TACGCCCGATCCCCTCATC 60.907 63.158 0.00 0.00 0.00 2.92
2258 2396 2.047274 ATCGTTCTGCCACCCACG 60.047 61.111 0.00 0.00 0.00 4.94
2268 2406 1.827969 CTCACCTTCTCCCATCGTTCT 59.172 52.381 0.00 0.00 0.00 3.01
2270 2408 0.905357 CCTCACCTTCTCCCATCGTT 59.095 55.000 0.00 0.00 0.00 3.85
2271 2409 0.978146 CCCTCACCTTCTCCCATCGT 60.978 60.000 0.00 0.00 0.00 3.73
2275 2413 0.041833 CTCTCCCTCACCTTCTCCCA 59.958 60.000 0.00 0.00 0.00 4.37
2358 2496 2.808761 TAGCAGGCCGGTCCACCTAA 62.809 60.000 15.92 0.00 37.29 2.69
2399 2537 2.365370 AGAGAGAGCCCAGCCAGG 60.365 66.667 0.00 0.00 37.03 4.45
2475 2623 1.281867 CCTCATGCCAAACTCTACCCA 59.718 52.381 0.00 0.00 0.00 4.51
2605 2753 5.160386 ACCTTCCTTTTACCAAGTCCTAGA 58.840 41.667 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.