Multiple sequence alignment - TraesCS6D01G383700

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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 TraesCS6D01G383700 chr6D 100.000 3600 0 0 1 3600 462532046 462528447 0.000000e+00 6649.0
1 TraesCS6D01G383700 chr6D 94.783 115 5 1 276 389 470655328 470655214 1.030000e-40 178.0
2 TraesCS6D01G383700 chr6D 94.690 113 6 0 31 143 259582589 259582701 3.690000e-40 176.0
3 TraesCS6D01G383700 chr6D 85.311 177 5 4 141 315 470655395 470655238 2.880000e-36 163.0
4 TraesCS6D01G383700 chr6D 94.340 106 5 1 276 380 322574581 322574686 1.030000e-35 161.0
5 TraesCS6D01G383700 chr6D 92.793 111 7 1 31 141 34649271 34649162 3.720000e-35 159.0
6 TraesCS6D01G383700 chr6D 98.876 89 1 0 140 228 201987438 201987350 3.720000e-35 159.0
7 TraesCS6D01G383700 chr6D 98.864 88 1 0 141 228 353652704 353652617 1.340000e-34 158.0
8 TraesCS6D01G383700 chr6D 84.659 176 6 7 142 315 322574515 322574671 4.810000e-34 156.0
9 TraesCS6D01G383700 chr6D 98.851 87 1 0 142 228 335300551 335300465 4.810000e-34 156.0
10 TraesCS6D01G383700 chr6D 98.851 87 1 0 142 228 394929767 394929853 4.810000e-34 156.0
11 TraesCS6D01G383700 chr6D 97.727 88 2 0 141 228 284659556 284659643 6.230000e-33 152.0
12 TraesCS6D01G383700 chr6D 97.727 88 2 0 141 228 381548894 381548981 6.230000e-33 152.0
13 TraesCS6D01G383700 chr6D 98.824 85 1 0 144 228 382340001 382340085 6.230000e-33 152.0
14 TraesCS6D01G383700 chr6D 91.743 109 8 1 33 141 94401768 94401875 2.240000e-32 150.0
15 TraesCS6D01G383700 chr6D 93.750 96 6 0 48 143 274978016 274977921 1.040000e-30 145.0
16 TraesCS6D01G383700 chr6D 86.000 150 2 3 142 291 11192759 11192889 3.750000e-30 143.0
17 TraesCS6D01G383700 chr6D 87.050 139 2 1 141 279 61789308 61789186 3.750000e-30 143.0
18 TraesCS6D01G383700 chr6D 90.826 109 7 3 274 380 110782727 110782834 3.750000e-30 143.0
19 TraesCS6D01G383700 chr6D 92.708 96 7 0 48 143 135718583 135718488 4.850000e-29 139.0
20 TraesCS6D01G383700 chr6D 85.333 150 3 3 142 291 427225075 427225205 1.740000e-28 137.0
21 TraesCS6D01G383700 chr6D 86.232 138 3 1 142 279 104588767 104588646 6.270000e-28 135.0
22 TraesCS6D01G383700 chr6D 88.430 121 2 1 276 384 201987370 201987250 6.270000e-28 135.0
23 TraesCS6D01G383700 chr6D 91.667 96 8 0 48 143 385091272 385091177 2.250000e-27 134.0
24 TraesCS6D01G383700 chr6D 82.840 169 7 7 276 422 382340065 382340233 8.110000e-27 132.0
25 TraesCS6D01G383700 chr6D 81.921 177 11 6 141 315 470111515 470111672 2.920000e-26 130.0
26 TraesCS6D01G383700 chr6D 87.500 120 3 5 276 383 353652637 353652518 1.050000e-25 128.0
27 TraesCS6D01G383700 chr6D 89.320 103 10 1 42 143 362663888 362663786 1.050000e-25 128.0
28 TraesCS6D01G383700 chr6D 86.777 121 4 5 276 384 381548961 381549081 1.360000e-24 124.0
29 TraesCS6D01G383700 chr6D 86.047 129 3 8 274 388 462470494 462470367 1.360000e-24 124.0
30 TraesCS6D01G383700 chr6D 92.857 56 0 3 380 433 133811574 133811627 1.070000e-10 78.7
31 TraesCS6D01G383700 chr6D 100.000 28 0 0 5 32 304697933 304697906 6.000000e-03 52.8
32 TraesCS6D01G383700 chr6D 100.000 28 0 0 733 760 471015148 471015175 6.000000e-03 52.8
33 TraesCS6D01G383700 chr6B 92.674 2457 83 38 380 2777 705157384 705154966 0.000000e+00 3450.0
34 TraesCS6D01G383700 chr6B 85.816 846 89 12 2778 3600 27644363 27643526 0.000000e+00 869.0
35 TraesCS6D01G383700 chr6B 87.141 661 64 12 2951 3599 352213557 352212906 0.000000e+00 730.0
36 TraesCS6D01G383700 chr6B 82.393 443 46 16 2778 3215 707786532 707786947 1.230000e-94 357.0
37 TraesCS6D01G383700 chr6B 92.135 178 14 0 2778 2955 27591659 27591836 5.970000e-63 252.0
38 TraesCS6D01G383700 chr6B 96.154 52 0 1 380 429 341468497 341468446 2.300000e-12 84.2
39 TraesCS6D01G383700 chr6A 93.510 2157 92 14 425 2557 609378468 609376336 0.000000e+00 3164.0
40 TraesCS6D01G383700 chr6A 94.690 113 6 0 31 143 311636086 311636198 3.690000e-40 176.0
41 TraesCS6D01G383700 chr6A 100.000 33 0 0 1 33 243490355 243490323 1.080000e-05 62.1
42 TraesCS6D01G383700 chr6A 100.000 33 0 0 1 33 338593259 338593291 1.080000e-05 62.1
43 TraesCS6D01G383700 chr6A 100.000 33 0 0 1 33 580925563 580925531 1.080000e-05 62.1
44 TraesCS6D01G383700 chr6A 100.000 32 0 0 1 32 155518268 155518299 3.880000e-05 60.2
45 TraesCS6D01G383700 chr6A 100.000 32 0 0 1 32 213641079 213641048 3.880000e-05 60.2
46 TraesCS6D01G383700 chr2D 85.629 835 103 8 2778 3599 276922584 276921754 0.000000e+00 861.0
47 TraesCS6D01G383700 chr2D 82.869 251 23 6 31 279 627332606 627332374 1.310000e-49 207.0
48 TraesCS6D01G383700 chr2D 96.330 109 3 1 276 383 458715911 458715803 1.030000e-40 178.0
49 TraesCS6D01G383700 chr2D 95.455 110 4 1 276 384 373147961 373148070 1.330000e-39 174.0
50 TraesCS6D01G383700 chr2D 85.876 177 4 4 141 315 110750803 110750646 6.180000e-38 169.0
51 TraesCS6D01G383700 chr2D 98.876 89 1 0 140 228 389280413 389280325 3.720000e-35 159.0
52 TraesCS6D01G383700 chr2D 88.636 132 8 4 97 228 180927648 180927772 1.730000e-33 154.0
53 TraesCS6D01G383700 chr2D 92.857 56 0 3 380 433 178921788 178921841 1.070000e-10 78.7
54 TraesCS6D01G383700 chr2D 94.340 53 0 2 379 429 243577871 243577820 1.070000e-10 78.7
55 TraesCS6D01G383700 chr1B 84.360 844 95 25 2778 3599 12599944 12599116 0.000000e+00 793.0
56 TraesCS6D01G383700 chr1B 97.345 113 3 0 31 143 306028633 306028521 3.670000e-45 193.0
57 TraesCS6D01G383700 chr1B 95.575 113 5 0 31 143 471375233 471375345 7.940000e-42 182.0
58 TraesCS6D01G383700 chr1B 95.575 113 5 0 31 143 651401119 651401231 7.940000e-42 182.0
59 TraesCS6D01G383700 chr1B 100.000 33 0 0 1 33 673278673 673278641 1.080000e-05 62.1
60 TraesCS6D01G383700 chr7B 87.917 629 62 7 2981 3599 677418404 677417780 0.000000e+00 728.0
61 TraesCS6D01G383700 chr7B 96.460 113 4 0 31 143 682971162 682971274 1.710000e-43 187.0
62 TraesCS6D01G383700 chr7B 96.429 112 4 0 31 142 497767773 497767884 6.140000e-43 185.0
63 TraesCS6D01G383700 chr7B 95.575 113 5 0 31 143 27546998 27547110 7.940000e-42 182.0
64 TraesCS6D01G383700 chr7B 94.737 114 5 1 276 388 493504944 493505057 3.690000e-40 176.0
65 TraesCS6D01G383700 chr7B 96.262 107 3 1 278 383 328179700 328179806 1.330000e-39 174.0
66 TraesCS6D01G383700 chr7B 95.413 109 3 2 274 381 729255083 729255190 4.780000e-39 172.0
67 TraesCS6D01G383700 chr7B 97.895 95 2 0 134 228 584015604 584015510 8.000000e-37 165.0
68 TraesCS6D01G383700 chr7B 94.059 101 4 2 128 228 583372858 583372760 6.230000e-33 152.0
69 TraesCS6D01G383700 chr7B 95.122 41 1 1 1 41 504952093 504952132 3.000000e-06 63.9
70 TraesCS6D01G383700 chr5B 87.917 629 62 6 2981 3599 551766381 551765757 0.000000e+00 728.0
71 TraesCS6D01G383700 chr5B 86.687 661 67 12 2951 3599 526554619 526555270 0.000000e+00 713.0
72 TraesCS6D01G383700 chr5B 97.345 113 3 0 31 143 650690481 650690369 3.670000e-45 193.0
73 TraesCS6D01G383700 chr5B 96.460 113 4 0 31 143 497321776 497321888 1.710000e-43 187.0
74 TraesCS6D01G383700 chr5B 93.277 119 6 2 276 393 711157132 711157015 1.330000e-39 174.0
75 TraesCS6D01G383700 chr5B 87.121 132 10 6 99 228 32134185 32134059 3.750000e-30 143.0
76 TraesCS6D01G383700 chr5B 94.340 53 0 2 379 429 616807664 616807715 1.070000e-10 78.7
77 TraesCS6D01G383700 chr5B 100.000 29 0 0 733 761 62317369 62317341 2.000000e-03 54.7
78 TraesCS6D01G383700 chr1A 86.970 660 67 10 2951 3599 432877656 432877005 0.000000e+00 725.0
79 TraesCS6D01G383700 chr1A 84.321 287 40 4 2778 3061 585137006 585136722 3.540000e-70 276.0
80 TraesCS6D01G383700 chr1A 96.190 105 3 1 276 379 547856371 547856267 1.720000e-38 171.0
81 TraesCS6D01G383700 chr1A 94.444 108 4 2 274 380 585522454 585522348 8.000000e-37 165.0
82 TraesCS6D01G383700 chr1A 92.241 116 8 1 276 390 204817282 204817167 2.880000e-36 163.0
83 TraesCS6D01G383700 chr1A 86.111 72 4 5 380 446 30543125 30543055 4.990000e-09 73.1
84 TraesCS6D01G383700 chr1A 100.000 33 0 0 1 33 428295601 428295633 1.080000e-05 62.1
85 TraesCS6D01G383700 chr7A 83.155 843 91 28 2781 3598 734274906 734274090 0.000000e+00 723.0
86 TraesCS6D01G383700 chr7A 100.000 33 0 0 1 33 409017497 409017529 1.080000e-05 62.1
87 TraesCS6D01G383700 chr5A 86.687 661 67 12 2951 3599 205830510 205831161 0.000000e+00 713.0
88 TraesCS6D01G383700 chr5A 87.413 143 17 1 1 143 68485791 68485650 2.880000e-36 163.0
89 TraesCS6D01G383700 chr5A 82.286 175 28 3 1970 2143 657555149 657554977 8.050000e-32 148.0
90 TraesCS6D01G383700 chr5A 92.727 55 1 2 381 433 570317607 570317660 3.850000e-10 76.8
91 TraesCS6D01G383700 chr3A 91.351 185 16 0 2778 2962 739912472 739912288 1.660000e-63 254.0
92 TraesCS6D01G383700 chr3A 86.000 100 14 0 2016 2115 615715302 615715203 1.370000e-19 108.0
93 TraesCS6D01G383700 chr3A 94.737 38 2 0 2 39 490959381 490959418 3.880000e-05 60.2
94 TraesCS6D01G383700 chr4A 90.909 187 17 0 2778 2964 641826796 641826610 5.970000e-63 252.0
95 TraesCS6D01G383700 chr3B 85.106 235 30 5 2778 3009 695547895 695547663 6.010000e-58 235.0
96 TraesCS6D01G383700 chr3B 96.460 113 4 0 31 143 722378054 722377942 1.710000e-43 187.0
97 TraesCS6D01G383700 chr3B 85.000 100 15 0 2016 2115 628470771 628470672 6.360000e-18 102.0
98 TraesCS6D01G383700 chr2B 85.281 231 30 4 2780 3009 13503357 13503130 6.010000e-58 235.0
99 TraesCS6D01G383700 chr2B 96.460 113 4 0 31 143 134756391 134756279 1.710000e-43 187.0
100 TraesCS6D01G383700 chr2B 78.161 174 31 5 1778 1948 464466706 464466875 1.770000e-18 104.0
101 TraesCS6D01G383700 chr2B 90.476 63 3 2 369 429 106151563 106151624 2.980000e-11 80.5
102 TraesCS6D01G383700 chr2B 92.857 56 0 3 380 433 235064876 235064929 1.070000e-10 78.7
103 TraesCS6D01G383700 chr7D 86.500 200 23 4 31 228 600713213 600713410 2.180000e-52 217.0
104 TraesCS6D01G383700 chr7D 96.460 113 4 0 31 143 378650239 378650127 1.710000e-43 187.0
105 TraesCS6D01G383700 chr7D 94.340 53 0 2 379 429 408510469 408510418 1.070000e-10 78.7
106 TraesCS6D01G383700 chr4B 95.575 113 5 0 31 143 131562668 131562780 7.940000e-42 182.0
107 TraesCS6D01G383700 chr4B 95.575 113 5 0 31 143 332440253 332440141 7.940000e-42 182.0
108 TraesCS6D01G383700 chr4B 84.659 176 6 5 142 315 598403532 598403376 4.810000e-34 156.0
109 TraesCS6D01G383700 chr4B 96.000 50 1 1 380 429 22107520 22107568 2.980000e-11 80.5
110 TraesCS6D01G383700 chr5D 95.536 112 4 1 277 387 33023442 33023331 1.030000e-40 178.0
111 TraesCS6D01G383700 chr5D 94.643 112 5 1 276 386 381906795 381906684 4.780000e-39 172.0
112 TraesCS6D01G383700 chr5D 85.795 176 4 4 142 315 75415328 75415172 2.220000e-37 167.0
113 TraesCS6D01G383700 chr5D 85.311 177 5 5 141 315 381906862 381906705 2.880000e-36 163.0
114 TraesCS6D01G383700 chr5D 97.849 93 2 0 136 228 89377283 89377375 1.030000e-35 161.0
115 TraesCS6D01G383700 chr5D 81.595 163 27 3 1984 2143 529542631 529542469 8.110000e-27 132.0
116 TraesCS6D01G383700 chr5D 100.000 33 0 0 1 33 77347043 77347011 1.080000e-05 62.1
117 TraesCS6D01G383700 chr3D 94.068 118 5 2 276 392 1258339 1258455 1.030000e-40 178.0
118 TraesCS6D01G383700 chr3D 85.027 187 6 6 132 315 133998258 133998091 1.720000e-38 171.0
119 TraesCS6D01G383700 chr3D 95.370 108 3 2 274 380 240009364 240009470 1.720000e-38 171.0
120 TraesCS6D01G383700 chr3D 94.545 110 5 1 276 384 253591457 253591566 6.180000e-38 169.0
121 TraesCS6D01G383700 chr3D 96.809 94 3 0 135 228 23551314 23551407 1.340000e-34 158.0
122 TraesCS6D01G383700 chr3D 83.439 157 5 4 161 315 518545472 518545609 3.770000e-25 126.0
123 TraesCS6D01G383700 chr3D 84.000 100 16 0 2016 2115 473455875 473455776 2.960000e-16 97.1
124 TraesCS6D01G383700 chr1D 95.495 111 5 0 31 141 29899255 29899365 1.030000e-40 178.0
125 TraesCS6D01G383700 chr1D 96.330 109 3 1 276 383 326157678 326157570 1.030000e-40 178.0
126 TraesCS6D01G383700 chr1D 94.690 113 6 0 31 143 182289849 182289961 3.690000e-40 176.0
127 TraesCS6D01G383700 chr1D 94.690 113 6 0 31 143 220841926 220841814 3.690000e-40 176.0
128 TraesCS6D01G383700 chr1D 94.690 113 6 0 31 143 290037009 290036897 3.690000e-40 176.0
129 TraesCS6D01G383700 chr1D 94.643 112 6 0 31 142 336915424 336915313 1.330000e-39 174.0
130 TraesCS6D01G383700 chr1D 85.795 176 5 4 141 315 18296106 18295950 6.180000e-38 169.0
131 TraesCS6D01G383700 chr1D 94.545 110 5 1 276 384 427001621 427001512 6.180000e-38 169.0
132 TraesCS6D01G383700 chr1D 95.283 106 4 1 276 380 60183555 60183660 2.220000e-37 167.0
133 TraesCS6D01G383700 chr1D 93.694 111 7 0 31 141 436709309 436709419 2.220000e-37 167.0
134 TraesCS6D01G383700 chr1D 85.311 177 5 4 141 315 326157745 326157588 2.880000e-36 163.0
135 TraesCS6D01G383700 chr1D 93.636 110 5 2 276 384 470222787 470222679 2.880000e-36 163.0
136 TraesCS6D01G383700 chr1D 94.340 106 4 2 276 380 320215379 320215483 1.030000e-35 161.0
137 TraesCS6D01G383700 chr1D 94.340 106 5 1 276 380 339049364 339049259 1.030000e-35 161.0
138 TraesCS6D01G383700 chr1D 95.918 98 4 0 131 228 377014064 377014161 3.720000e-35 159.0
139 TraesCS6D01G383700 chr1D 98.864 88 1 0 141 228 176953156 176953069 1.340000e-34 158.0
140 TraesCS6D01G383700 chr1D 98.851 87 1 0 142 228 93501167 93501081 4.810000e-34 156.0
141 TraesCS6D01G383700 chr1D 83.784 185 8 7 133 315 320215304 320215468 4.810000e-34 156.0
142 TraesCS6D01G383700 chr1D 84.483 174 6 4 144 315 60183491 60183645 6.230000e-33 152.0
143 TraesCS6D01G383700 chr1D 83.889 180 8 4 138 315 427001691 427001531 6.230000e-33 152.0
144 TraesCS6D01G383700 chr1D 91.743 109 6 2 276 383 493758007 493757901 8.050000e-32 148.0
145 TraesCS6D01G383700 chr1D 85.350 157 5 4 125 279 203683905 203683765 2.900000e-31 147.0
146 TraesCS6D01G383700 chr1D 83.908 174 7 4 142 313 339049430 339049276 2.900000e-31 147.0
147 TraesCS6D01G383700 chr1D 83.333 174 10 6 142 315 493758073 493757919 3.750000e-30 143.0
148 TraesCS6D01G383700 chr1D 80.645 186 13 12 132 315 5439713 5439549 4.880000e-24 122.0
149 TraesCS6D01G383700 chr1D 100.000 33 0 0 1 33 267863091 267863059 1.080000e-05 62.1
150 TraesCS6D01G383700 chr1D 100.000 28 0 0 5 32 344057732 344057705 6.000000e-03 52.8
151 TraesCS6D01G383700 chr4D 94.690 113 6 0 31 143 63413232 63413120 3.690000e-40 176.0
152 TraesCS6D01G383700 chr4D 94.690 113 6 0 31 143 340060211 340060099 3.690000e-40 176.0
153 TraesCS6D01G383700 chr4D 86.364 176 4 6 141 315 101438407 101438251 1.330000e-39 174.0
154 TraesCS6D01G383700 chr4D 96.226 106 3 1 276 380 118575155 118575260 4.780000e-39 172.0
155 TraesCS6D01G383700 chr4D 85.311 177 5 4 141 315 118575088 118575245 2.880000e-36 163.0
156 TraesCS6D01G383700 chr4D 97.849 93 2 0 136 228 3873049 3872957 1.030000e-35 161.0
157 TraesCS6D01G383700 chr4D 95.050 101 4 1 128 228 81663842 81663743 1.340000e-34 158.0
158 TraesCS6D01G383700 chr4D 97.802 91 2 0 138 228 503922020 503922110 1.340000e-34 158.0
159 TraesCS6D01G383700 chr4D 96.078 51 0 2 380 429 322661340 322661291 8.280000e-12 82.4
160 TraesCS6D01G383700 chr4D 100.000 33 0 0 1 33 91380649 91380617 1.080000e-05 62.1
161 TraesCS6D01G383700 chr4D 100.000 28 0 0 5 32 486727675 486727648 6.000000e-03 52.8
162 TraesCS6D01G383700 chr2A 96.296 108 3 1 280 386 30798512 30798619 3.690000e-40 176.0
163 TraesCS6D01G383700 chr2A 96.296 108 3 1 280 386 30818232 30818339 3.690000e-40 176.0
164 TraesCS6D01G383700 chr2A 76.000 225 34 17 1740 1948 530380702 530380922 8.230000e-17 99.0
165 TraesCS6D01G383700 chrUn 93.805 113 7 0 31 143 203525134 203525022 1.720000e-38 171.0
166 TraesCS6D01G383700 chrUn 93.805 113 7 0 31 143 203528853 203528741 1.720000e-38 171.0
167 TraesCS6D01G383700 chrUn 95.833 96 3 1 140 234 93661598 93661693 1.730000e-33 154.0
168 TraesCS6D01G383700 chrUn 96.591 88 3 0 141 228 254817554 254817641 2.900000e-31 147.0
169 TraesCS6D01G383700 chrUn 96.552 87 3 0 142 228 7598136 7598050 1.040000e-30 145.0
170 TraesCS6D01G383700 chrUn 96.552 87 3 0 142 228 21551016 21550930 1.040000e-30 145.0
171 TraesCS6D01G383700 chrUn 97.619 84 2 0 145 228 24946330 24946413 1.040000e-30 145.0
172 TraesCS6D01G383700 chrUn 96.552 87 3 0 142 228 26772377 26772463 1.040000e-30 145.0
173 TraesCS6D01G383700 chrUn 95.402 87 3 1 142 228 30235395 30235310 1.740000e-28 137.0
174 TraesCS6D01G383700 chrUn 86.232 138 3 1 142 279 269895174 269895053 6.270000e-28 135.0
175 TraesCS6D01G383700 chrUn 94.253 87 5 0 142 228 50612317 50612403 2.250000e-27 134.0
176 TraesCS6D01G383700 chrUn 88.136 118 4 4 273 380 26772440 26772557 8.110000e-27 132.0
177 TraesCS6D01G383700 chrUn 84.667 150 4 5 142 291 255618635 255618765 8.110000e-27 132.0
178 TraesCS6D01G383700 chrUn 84.667 150 4 5 142 291 347384144 347384014 8.110000e-27 132.0
179 TraesCS6D01G383700 chrUn 84.667 150 4 5 142 291 404982680 404982550 8.110000e-27 132.0
180 TraesCS6D01G383700 chrUn 88.034 117 2 1 276 380 260615613 260615729 1.050000e-25 128.0
181 TraesCS6D01G383700 chrUn 87.826 115 2 1 278 380 255618703 255618817 1.360000e-24 124.0
182 TraesCS6D01G383700 chrUn 87.826 115 2 1 278 380 347384076 347383962 1.360000e-24 124.0
183 TraesCS6D01G383700 chrUn 87.826 115 2 1 278 380 404982612 404982498 1.360000e-24 124.0
184 TraesCS6D01G383700 chrUn 86.364 110 15 0 34 143 244164664 244164555 1.760000e-23 121.0
185 TraesCS6D01G383700 chrUn 86.364 110 15 0 34 143 244177299 244177190 1.760000e-23 121.0
186 TraesCS6D01G383700 chrUn 93.750 80 5 0 143 222 289331054 289330975 1.760000e-23 121.0
187 TraesCS6D01G383700 chrUn 86.364 110 15 0 34 143 316237083 316237192 1.760000e-23 121.0
188 TraesCS6D01G383700 chrUn 86.325 117 4 1 276 380 30235330 30235214 2.270000e-22 117.0
189 TraesCS6D01G383700 chrUn 83.942 137 6 1 143 279 260615548 260615668 2.270000e-22 117.0
190 TraesCS6D01G383700 chrUn 85.714 119 4 6 274 380 21550951 21550834 2.940000e-21 113.0
191 TraesCS6D01G383700 chrUn 98.333 60 1 0 325 384 93661718 93661777 4.920000e-19 106.0
192 TraesCS6D01G383700 chrUn 85.849 106 3 2 287 380 103940087 103940192 6.360000e-18 102.0
193 TraesCS6D01G383700 chrUn 97.959 49 1 0 231 279 24946400 24946448 6.400000e-13 86.1
194 TraesCS6D01G383700 chrUn 97.959 49 1 0 231 279 30235323 30235275 6.400000e-13 86.1
195 TraesCS6D01G383700 chrUn 93.333 60 1 2 232 291 254817629 254817685 6.400000e-13 86.1
196 TraesCS6D01G383700 chrUn 95.918 49 0 1 231 279 26772450 26772496 1.070000e-10 78.7
197 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 2363665 2363615 3.850000e-10 76.8
198 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 16162058 16162108 3.850000e-10 76.8
199 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 20108275 20108225 3.850000e-10 76.8
200 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 21018797 21018847 3.850000e-10 76.8
201 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 21858139 21858089 3.850000e-10 76.8
202 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 31581634 31581684 3.850000e-10 76.8
203 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 40943720 40943770 3.850000e-10 76.8
204 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 69153924 69153874 3.850000e-10 76.8
205 TraesCS6D01G383700 chrUn 94.231 52 0 2 380 429 102977205 102977155 3.850000e-10 76.8


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 TraesCS6D01G383700 chr6D 462528447 462532046 3599 True 6649 6649 100.000 1 3600 1 chr6D.!!$R11 3599
1 TraesCS6D01G383700 chr6B 705154966 705157384 2418 True 3450 3450 92.674 380 2777 1 chr6B.!!$R4 2397
2 TraesCS6D01G383700 chr6B 27643526 27644363 837 True 869 869 85.816 2778 3600 1 chr6B.!!$R1 822
3 TraesCS6D01G383700 chr6B 352212906 352213557 651 True 730 730 87.141 2951 3599 1 chr6B.!!$R3 648
4 TraesCS6D01G383700 chr6A 609376336 609378468 2132 True 3164 3164 93.510 425 2557 1 chr6A.!!$R4 2132
5 TraesCS6D01G383700 chr2D 276921754 276922584 830 True 861 861 85.629 2778 3599 1 chr2D.!!$R3 821
6 TraesCS6D01G383700 chr1B 12599116 12599944 828 True 793 793 84.360 2778 3599 1 chr1B.!!$R1 821
7 TraesCS6D01G383700 chr7B 677417780 677418404 624 True 728 728 87.917 2981 3599 1 chr7B.!!$R3 618
8 TraesCS6D01G383700 chr5B 551765757 551766381 624 True 728 728 87.917 2981 3599 1 chr5B.!!$R3 618
9 TraesCS6D01G383700 chr5B 526554619 526555270 651 False 713 713 86.687 2951 3599 1 chr5B.!!$F2 648
10 TraesCS6D01G383700 chr1A 432877005 432877656 651 True 725 725 86.970 2951 3599 1 chr1A.!!$R3 648
11 TraesCS6D01G383700 chr7A 734274090 734274906 816 True 723 723 83.155 2781 3598 1 chr7A.!!$R1 817
12 TraesCS6D01G383700 chr5A 205830510 205831161 651 False 713 713 86.687 2951 3599 1 chr5A.!!$F1 648

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
274 275 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.0 0.0 0.0 34.77 3.62 F
1301 1341 0.106894 CCGGTCTGCTTATTCCCCTC 59.893 60.0 0.0 0.0 0.00 4.30 F
1309 1349 0.468648 CTTATTCCCCTCCGTCACCC 59.531 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1898 0.108329 GGTGGTCGGAGTACATGTGG 60.108 60.000 9.11 0.00 0.0 4.17 R
2189 2243 1.153745 CTTCCCCTCGACGAGCTTG 60.154 63.158 19.55 9.43 0.0 4.01 R
2979 3092 1.375523 CTCTTAACCAAGCCGCCGT 60.376 57.895 0.00 0.00 0.0 5.68 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
24 25 5.772393 TGAGCCTTATAAACTGGAAAGGA 57.228 39.130 4.19 0.00 40.85 3.36
25 26 5.745227 TGAGCCTTATAAACTGGAAAGGAG 58.255 41.667 4.19 0.00 40.85 3.69
26 27 5.117406 AGCCTTATAAACTGGAAAGGAGG 57.883 43.478 4.19 0.00 40.85 4.30
27 28 4.079730 AGCCTTATAAACTGGAAAGGAGGG 60.080 45.833 4.19 0.00 40.85 4.30
28 29 4.079958 GCCTTATAAACTGGAAAGGAGGGA 60.080 45.833 4.19 0.00 40.85 4.20
29 30 5.685728 CCTTATAAACTGGAAAGGAGGGAG 58.314 45.833 0.00 0.00 40.85 4.30
30 31 5.191921 CCTTATAAACTGGAAAGGAGGGAGT 59.808 44.000 0.00 0.00 40.85 3.85
31 32 6.386050 CCTTATAAACTGGAAAGGAGGGAGTA 59.614 42.308 0.00 0.00 40.85 2.59
32 33 7.072581 CCTTATAAACTGGAAAGGAGGGAGTAT 59.927 40.741 0.00 0.00 40.85 2.12
33 34 4.576330 AAACTGGAAAGGAGGGAGTATG 57.424 45.455 0.00 0.00 0.00 2.39
34 35 3.207044 ACTGGAAAGGAGGGAGTATGT 57.793 47.619 0.00 0.00 0.00 2.29
35 36 3.532102 ACTGGAAAGGAGGGAGTATGTT 58.468 45.455 0.00 0.00 0.00 2.71
36 37 4.695606 ACTGGAAAGGAGGGAGTATGTTA 58.304 43.478 0.00 0.00 0.00 2.41
37 38 4.470304 ACTGGAAAGGAGGGAGTATGTTAC 59.530 45.833 0.00 0.00 0.00 2.50
38 39 4.695606 TGGAAAGGAGGGAGTATGTTACT 58.304 43.478 0.00 0.00 42.86 2.24
39 40 4.469945 TGGAAAGGAGGGAGTATGTTACTG 59.530 45.833 0.00 0.00 39.59 2.74
40 41 4.470304 GGAAAGGAGGGAGTATGTTACTGT 59.530 45.833 0.00 0.00 39.59 3.55
41 42 5.659971 GGAAAGGAGGGAGTATGTTACTGTA 59.340 44.000 0.00 0.00 39.59 2.74
42 43 6.155737 GGAAAGGAGGGAGTATGTTACTGTAA 59.844 42.308 0.00 0.00 39.59 2.41
43 44 6.541934 AAGGAGGGAGTATGTTACTGTAAC 57.458 41.667 20.87 20.87 39.59 2.50
56 57 6.770542 TGTTACTGTAACATAACACATCCCA 58.229 36.000 25.14 2.58 43.23 4.37
57 58 7.225011 TGTTACTGTAACATAACACATCCCAA 58.775 34.615 25.14 2.12 43.23 4.12
58 59 7.389330 TGTTACTGTAACATAACACATCCCAAG 59.611 37.037 25.14 0.00 43.23 3.61
59 60 6.121776 ACTGTAACATAACACATCCCAAGA 57.878 37.500 0.00 0.00 0.00 3.02
60 61 6.721318 ACTGTAACATAACACATCCCAAGAT 58.279 36.000 0.00 0.00 0.00 2.40
61 62 7.857456 ACTGTAACATAACACATCCCAAGATA 58.143 34.615 0.00 0.00 0.00 1.98
62 63 8.325787 ACTGTAACATAACACATCCCAAGATAA 58.674 33.333 0.00 0.00 0.00 1.75
63 64 9.173021 CTGTAACATAACACATCCCAAGATAAA 57.827 33.333 0.00 0.00 0.00 1.40
64 65 9.521841 TGTAACATAACACATCCCAAGATAAAA 57.478 29.630 0.00 0.00 0.00 1.52
67 68 8.821686 ACATAACACATCCCAAGATAAAATGA 57.178 30.769 0.00 0.00 0.00 2.57
68 69 8.906867 ACATAACACATCCCAAGATAAAATGAG 58.093 33.333 0.00 0.00 0.00 2.90
69 70 8.906867 CATAACACATCCCAAGATAAAATGAGT 58.093 33.333 0.00 0.00 0.00 3.41
70 71 7.396540 AACACATCCCAAGATAAAATGAGTC 57.603 36.000 0.00 0.00 0.00 3.36
71 72 6.725364 ACACATCCCAAGATAAAATGAGTCT 58.275 36.000 0.00 0.00 0.00 3.24
72 73 7.861629 ACACATCCCAAGATAAAATGAGTCTA 58.138 34.615 0.00 0.00 0.00 2.59
73 74 8.497745 ACACATCCCAAGATAAAATGAGTCTAT 58.502 33.333 0.00 0.00 0.00 1.98
98 99 9.976511 ATATCTCAATTAATGAAGGTTTGCATG 57.023 29.630 0.00 0.00 37.67 4.06
99 100 7.230849 TCTCAATTAATGAAGGTTTGCATGT 57.769 32.000 0.00 0.00 37.67 3.21
100 101 7.669427 TCTCAATTAATGAAGGTTTGCATGTT 58.331 30.769 0.00 0.00 37.67 2.71
101 102 8.801299 TCTCAATTAATGAAGGTTTGCATGTTA 58.199 29.630 0.00 0.00 37.67 2.41
102 103 8.755696 TCAATTAATGAAGGTTTGCATGTTAC 57.244 30.769 0.00 0.00 34.30 2.50
103 104 7.816995 TCAATTAATGAAGGTTTGCATGTTACC 59.183 33.333 0.00 0.00 34.30 2.85
104 105 6.656632 TTAATGAAGGTTTGCATGTTACCA 57.343 33.333 13.20 0.00 34.32 3.25
105 106 5.743636 AATGAAGGTTTGCATGTTACCAT 57.256 34.783 13.20 3.88 34.32 3.55
106 107 4.782019 TGAAGGTTTGCATGTTACCATC 57.218 40.909 13.20 11.40 34.32 3.51
107 108 3.509575 TGAAGGTTTGCATGTTACCATCC 59.490 43.478 13.20 1.97 34.32 3.51
108 109 3.168035 AGGTTTGCATGTTACCATCCA 57.832 42.857 13.20 0.00 34.32 3.41
109 110 3.711863 AGGTTTGCATGTTACCATCCAT 58.288 40.909 13.20 0.00 34.32 3.41
110 111 4.865905 AGGTTTGCATGTTACCATCCATA 58.134 39.130 13.20 0.00 34.32 2.74
111 112 5.457686 AGGTTTGCATGTTACCATCCATAT 58.542 37.500 13.20 0.00 34.32 1.78
112 113 5.302568 AGGTTTGCATGTTACCATCCATATG 59.697 40.000 13.20 0.00 34.32 1.78
113 114 5.068987 GGTTTGCATGTTACCATCCATATGT 59.931 40.000 1.24 0.00 32.12 2.29
114 115 6.406849 GGTTTGCATGTTACCATCCATATGTT 60.407 38.462 1.24 0.00 32.12 2.71
115 116 7.201866 GGTTTGCATGTTACCATCCATATGTTA 60.202 37.037 1.24 0.00 32.12 2.41
116 117 6.875948 TGCATGTTACCATCCATATGTTAC 57.124 37.500 1.24 0.00 0.00 2.50
117 118 6.600388 TGCATGTTACCATCCATATGTTACT 58.400 36.000 1.24 0.00 0.00 2.24
118 119 7.740805 TGCATGTTACCATCCATATGTTACTA 58.259 34.615 1.24 0.00 0.00 1.82
119 120 8.382405 TGCATGTTACCATCCATATGTTACTAT 58.618 33.333 1.24 0.00 0.00 2.12
120 121 8.883731 GCATGTTACCATCCATATGTTACTATC 58.116 37.037 1.24 0.00 0.00 2.08
121 122 9.383519 CATGTTACCATCCATATGTTACTATCC 57.616 37.037 1.24 0.00 0.00 2.59
122 123 8.499288 TGTTACCATCCATATGTTACTATCCA 57.501 34.615 1.24 0.00 0.00 3.41
123 124 8.372459 TGTTACCATCCATATGTTACTATCCAC 58.628 37.037 1.24 0.00 0.00 4.02
124 125 8.594550 GTTACCATCCATATGTTACTATCCACT 58.405 37.037 1.24 0.00 0.00 4.00
125 126 9.831682 TTACCATCCATATGTTACTATCCACTA 57.168 33.333 1.24 0.00 0.00 2.74
126 127 8.917414 ACCATCCATATGTTACTATCCACTAT 57.083 34.615 1.24 0.00 0.00 2.12
127 128 8.762645 ACCATCCATATGTTACTATCCACTATG 58.237 37.037 1.24 0.00 0.00 2.23
128 129 8.981659 CCATCCATATGTTACTATCCACTATGA 58.018 37.037 1.24 0.00 0.00 2.15
131 132 9.035890 TCCATATGTTACTATCCACTATGAAGG 57.964 37.037 1.24 0.00 0.00 3.46
132 133 8.816894 CCATATGTTACTATCCACTATGAAGGT 58.183 37.037 1.24 0.00 0.00 3.50
137 138 9.925545 TGTTACTATCCACTATGAAGGTAGTAA 57.074 33.333 0.00 0.00 34.88 2.24
139 140 9.925545 TTACTATCCACTATGAAGGTAGTAACA 57.074 33.333 0.00 0.00 33.78 2.41
143 144 7.834881 TCCACTATGAAGGTAGTAACATAGG 57.165 40.000 0.81 0.00 43.39 2.57
144 145 6.781014 TCCACTATGAAGGTAGTAACATAGGG 59.219 42.308 0.81 0.00 43.39 3.53
145 146 6.994221 CACTATGAAGGTAGTAACATAGGGG 58.006 44.000 0.81 0.00 43.39 4.79
146 147 6.014499 CACTATGAAGGTAGTAACATAGGGGG 60.014 46.154 0.81 0.00 43.39 5.40
147 148 4.357313 TGAAGGTAGTAACATAGGGGGT 57.643 45.455 0.00 0.00 0.00 4.95
148 149 4.035112 TGAAGGTAGTAACATAGGGGGTG 58.965 47.826 0.00 0.00 0.00 4.61
149 150 3.790022 AGGTAGTAACATAGGGGGTGT 57.210 47.619 0.00 0.00 0.00 4.16
150 151 4.084466 AGGTAGTAACATAGGGGGTGTT 57.916 45.455 0.00 0.00 42.12 3.32
151 152 4.441757 AGGTAGTAACATAGGGGGTGTTT 58.558 43.478 0.00 0.00 40.13 2.83
152 153 4.226620 AGGTAGTAACATAGGGGGTGTTTG 59.773 45.833 0.00 0.00 40.13 2.93
153 154 3.732048 AGTAACATAGGGGGTGTTTGG 57.268 47.619 0.00 0.00 40.13 3.28
154 155 2.990998 AGTAACATAGGGGGTGTTTGGT 59.009 45.455 0.00 0.00 40.13 3.67
155 156 3.399983 AGTAACATAGGGGGTGTTTGGTT 59.600 43.478 0.00 0.00 40.13 3.67
156 157 2.597578 ACATAGGGGGTGTTTGGTTC 57.402 50.000 0.00 0.00 0.00 3.62
157 158 1.783979 ACATAGGGGGTGTTTGGTTCA 59.216 47.619 0.00 0.00 0.00 3.18
158 159 2.225017 ACATAGGGGGTGTTTGGTTCAG 60.225 50.000 0.00 0.00 0.00 3.02
159 160 1.822425 TAGGGGGTGTTTGGTTCAGA 58.178 50.000 0.00 0.00 0.00 3.27
160 161 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
161 162 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
162 163 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
163 164 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
164 165 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
165 166 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
166 167 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
167 168 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
168 169 4.065789 GTGTTTGGTTCAGAAGTCCTAGG 58.934 47.826 0.82 0.82 0.00 3.02
169 170 3.971305 TGTTTGGTTCAGAAGTCCTAGGA 59.029 43.478 7.62 7.62 0.00 2.94
170 171 4.202326 TGTTTGGTTCAGAAGTCCTAGGAC 60.202 45.833 31.29 31.29 44.86 3.85
235 236 9.590828 AGTAGAGTCTTTTCCTAGTAAAGTCTT 57.409 33.333 0.00 7.80 33.31 3.01
245 246 9.993454 TTTCCTAGTAAAGTCTTTTTCTAGTCC 57.007 33.333 21.94 1.32 40.16 3.85
246 247 8.131847 TCCTAGTAAAGTCTTTTTCTAGTCCC 57.868 38.462 21.94 0.62 40.16 4.46
247 248 7.954620 TCCTAGTAAAGTCTTTTTCTAGTCCCT 59.045 37.037 21.94 5.63 40.16 4.20
248 249 8.035984 CCTAGTAAAGTCTTTTTCTAGTCCCTG 58.964 40.741 21.94 11.73 40.16 4.45
249 250 7.376335 AGTAAAGTCTTTTTCTAGTCCCTGT 57.624 36.000 2.51 0.00 0.00 4.00
250 251 8.488308 AGTAAAGTCTTTTTCTAGTCCCTGTA 57.512 34.615 2.51 0.00 0.00 2.74
251 252 8.586744 AGTAAAGTCTTTTTCTAGTCCCTGTAG 58.413 37.037 2.51 0.00 0.00 2.74
252 253 7.613551 AAAGTCTTTTTCTAGTCCCTGTAGA 57.386 36.000 0.00 0.00 0.00 2.59
253 254 7.613551 AAGTCTTTTTCTAGTCCCTGTAGAA 57.386 36.000 0.00 0.00 35.21 2.10
254 255 7.613551 AGTCTTTTTCTAGTCCCTGTAGAAA 57.386 36.000 1.96 1.96 42.24 2.52
260 261 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
261 262 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
262 263 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
263 264 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
264 265 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
265 266 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
266 267 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
267 268 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
268 269 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
269 270 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
270 271 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
271 272 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
272 273 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
273 274 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
274 275 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
275 276 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
276 277 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
277 278 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
278 279 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
279 280 0.981943 CCTCCCGTTTGGTTCCTAGT 59.018 55.000 0.00 0.00 34.77 2.57
280 281 2.181975 CCTCCCGTTTGGTTCCTAGTA 58.818 52.381 0.00 0.00 34.77 1.82
281 282 2.167900 CCTCCCGTTTGGTTCCTAGTAG 59.832 54.545 0.00 0.00 34.77 2.57
282 283 3.094572 CTCCCGTTTGGTTCCTAGTAGA 58.905 50.000 0.00 0.00 34.77 2.59
283 284 3.094572 TCCCGTTTGGTTCCTAGTAGAG 58.905 50.000 0.00 0.00 34.77 2.43
284 285 2.830321 CCCGTTTGGTTCCTAGTAGAGT 59.170 50.000 0.00 0.00 0.00 3.24
285 286 3.119209 CCCGTTTGGTTCCTAGTAGAGTC 60.119 52.174 0.00 0.00 0.00 3.36
286 287 3.762823 CCGTTTGGTTCCTAGTAGAGTCT 59.237 47.826 0.00 0.00 0.00 3.24
287 288 4.220163 CCGTTTGGTTCCTAGTAGAGTCTT 59.780 45.833 0.00 0.00 0.00 3.01
288 289 5.279356 CCGTTTGGTTCCTAGTAGAGTCTTT 60.279 44.000 0.00 0.00 0.00 2.52
289 290 6.221659 CGTTTGGTTCCTAGTAGAGTCTTTT 58.778 40.000 0.00 0.00 0.00 2.27
290 291 6.704937 CGTTTGGTTCCTAGTAGAGTCTTTTT 59.295 38.462 0.00 0.00 0.00 1.94
291 292 7.095732 CGTTTGGTTCCTAGTAGAGTCTTTTTC 60.096 40.741 0.00 0.00 0.00 2.29
292 293 7.613551 TTGGTTCCTAGTAGAGTCTTTTTCT 57.386 36.000 0.00 0.00 0.00 2.52
293 294 8.716674 TTGGTTCCTAGTAGAGTCTTTTTCTA 57.283 34.615 0.00 0.00 0.00 2.10
294 295 8.350852 TGGTTCCTAGTAGAGTCTTTTTCTAG 57.649 38.462 0.00 6.24 0.00 2.43
295 296 7.949006 TGGTTCCTAGTAGAGTCTTTTTCTAGT 59.051 37.037 0.00 0.00 35.53 2.57
296 297 8.461222 GGTTCCTAGTAGAGTCTTTTTCTAGTC 58.539 40.741 0.00 0.93 33.84 2.59
297 298 8.461222 GTTCCTAGTAGAGTCTTTTTCTAGTCC 58.539 40.741 0.00 0.00 33.84 3.85
298 299 7.118060 TCCTAGTAGAGTCTTTTTCTAGTCCC 58.882 42.308 0.00 0.00 33.84 4.46
299 300 7.036717 TCCTAGTAGAGTCTTTTTCTAGTCCCT 60.037 40.741 0.00 0.00 33.84 4.20
300 301 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
301 302 6.316513 AGTAGAGTCTTTTTCTAGTCCCTGT 58.683 40.000 0.00 0.00 0.00 4.00
302 303 7.468496 AGTAGAGTCTTTTTCTAGTCCCTGTA 58.532 38.462 0.00 0.00 0.00 2.74
303 304 7.949006 AGTAGAGTCTTTTTCTAGTCCCTGTAA 59.051 37.037 0.00 0.00 0.00 2.41
304 305 7.613551 AGAGTCTTTTTCTAGTCCCTGTAAA 57.386 36.000 0.00 0.00 0.00 2.01
305 306 8.030913 AGAGTCTTTTTCTAGTCCCTGTAAAA 57.969 34.615 0.00 0.00 0.00 1.52
306 307 8.491958 AGAGTCTTTTTCTAGTCCCTGTAAAAA 58.508 33.333 0.00 0.00 0.00 1.94
324 325 2.447408 AAAAGTCCCTTCCGTTTGGT 57.553 45.000 0.00 0.00 36.30 3.67
325 326 2.447408 AAAGTCCCTTCCGTTTGGTT 57.553 45.000 0.00 0.00 36.30 3.67
326 327 2.447408 AAGTCCCTTCCGTTTGGTTT 57.553 45.000 0.00 0.00 36.30 3.27
327 328 2.447408 AGTCCCTTCCGTTTGGTTTT 57.553 45.000 0.00 0.00 36.30 2.43
328 329 3.581265 AGTCCCTTCCGTTTGGTTTTA 57.419 42.857 0.00 0.00 36.30 1.52
329 330 3.483421 AGTCCCTTCCGTTTGGTTTTAG 58.517 45.455 0.00 0.00 36.30 1.85
330 331 2.555325 GTCCCTTCCGTTTGGTTTTAGG 59.445 50.000 0.00 0.00 36.30 2.69
331 332 1.890489 CCCTTCCGTTTGGTTTTAGGG 59.110 52.381 0.00 0.00 35.81 3.53
332 333 2.489437 CCCTTCCGTTTGGTTTTAGGGA 60.489 50.000 0.00 0.00 40.28 4.20
333 334 2.555325 CCTTCCGTTTGGTTTTAGGGAC 59.445 50.000 0.00 0.00 36.30 4.46
334 335 3.483421 CTTCCGTTTGGTTTTAGGGACT 58.517 45.455 0.00 0.00 38.62 3.85
335 336 3.581265 TCCGTTTGGTTTTAGGGACTT 57.419 42.857 0.00 0.00 36.72 3.01
336 337 3.900971 TCCGTTTGGTTTTAGGGACTTT 58.099 40.909 0.00 0.00 36.72 2.66
337 338 4.279982 TCCGTTTGGTTTTAGGGACTTTT 58.720 39.130 0.00 0.00 36.72 2.27
338 339 4.710865 TCCGTTTGGTTTTAGGGACTTTTT 59.289 37.500 0.00 0.00 36.72 1.94
339 340 5.045215 CCGTTTGGTTTTAGGGACTTTTTC 58.955 41.667 0.00 0.00 41.75 2.29
340 341 5.163488 CCGTTTGGTTTTAGGGACTTTTTCT 60.163 40.000 0.00 0.00 41.75 2.52
341 342 6.039605 CCGTTTGGTTTTAGGGACTTTTTCTA 59.960 38.462 0.00 0.00 41.75 2.10
342 343 7.136772 CGTTTGGTTTTAGGGACTTTTTCTAG 58.863 38.462 0.00 0.00 41.75 2.43
343 344 7.201758 CGTTTGGTTTTAGGGACTTTTTCTAGT 60.202 37.037 0.00 0.00 41.75 2.57
344 345 7.812690 TTGGTTTTAGGGACTTTTTCTAGTC 57.187 36.000 0.00 0.00 43.05 2.59
345 346 7.145474 TGGTTTTAGGGACTTTTTCTAGTCT 57.855 36.000 0.00 0.00 43.26 3.24
346 347 7.222161 TGGTTTTAGGGACTTTTTCTAGTCTC 58.778 38.462 0.00 0.00 44.42 3.36
350 351 4.209307 GGGACTTTTTCTAGTCTCTGGG 57.791 50.000 0.00 0.00 41.50 4.45
351 352 3.838903 GGGACTTTTTCTAGTCTCTGGGA 59.161 47.826 0.00 0.00 41.50 4.37
352 353 4.322877 GGGACTTTTTCTAGTCTCTGGGAC 60.323 50.000 0.00 0.00 41.50 4.46
373 374 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
374 375 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
375 376 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
376 377 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
377 378 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
378 379 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
396 397 5.837438 ACACCCCCATAGACTAGTAACATAC 59.163 44.000 0.00 0.00 0.00 2.39
397 398 5.836898 CACCCCCATAGACTAGTAACATACA 59.163 44.000 0.00 0.00 0.00 2.29
399 400 6.497259 ACCCCCATAGACTAGTAACATACATG 59.503 42.308 0.00 0.00 0.00 3.21
444 456 3.997021 ACTTATGCAGTTCACTTTCGAGG 59.003 43.478 0.00 0.00 27.32 4.63
455 467 4.065088 TCACTTTCGAGGGAAATCAAGTG 58.935 43.478 13.59 13.59 41.12 3.16
463 475 4.512944 CGAGGGAAATCAAGTGGTATGATG 59.487 45.833 0.00 0.00 37.58 3.07
538 550 7.568738 TGGAAGAATTCTATCCTCTACCAATGA 59.431 37.037 24.65 8.73 46.56 2.57
571 588 1.508632 GTCGCCTAGAAACACTGCAA 58.491 50.000 0.00 0.00 0.00 4.08
573 590 0.163788 CGCCTAGAAACACTGCAACG 59.836 55.000 0.00 0.00 0.00 4.10
642 659 0.923358 TTAATTCCATGGCGAGGGGT 59.077 50.000 6.96 0.00 0.00 4.95
726 745 1.478510 TCTTCCACTCTTCGCTGGATC 59.521 52.381 0.00 0.00 36.42 3.36
732 751 0.371645 CTCTTCGCTGGATCGTTTGC 59.628 55.000 0.00 0.00 0.00 3.68
733 752 1.019278 TCTTCGCTGGATCGTTTGCC 61.019 55.000 0.00 0.00 0.00 4.52
734 753 1.298157 CTTCGCTGGATCGTTTGCCA 61.298 55.000 0.00 0.00 0.00 4.92
737 756 4.722193 CTGGATCGTTTGCCAGGT 57.278 55.556 0.00 0.00 46.24 4.00
740 759 1.002624 GGATCGTTTGCCAGGTCCA 60.003 57.895 0.00 0.00 0.00 4.02
923 942 4.821589 CCGCGCCCTTGTCCTCTC 62.822 72.222 0.00 0.00 0.00 3.20
934 953 3.069729 CCTTGTCCTCTCCTATAAACCGG 59.930 52.174 0.00 0.00 0.00 5.28
935 954 3.393426 TGTCCTCTCCTATAAACCGGT 57.607 47.619 0.00 0.00 0.00 5.28
936 955 3.716431 TGTCCTCTCCTATAAACCGGTT 58.284 45.455 15.86 15.86 0.00 4.44
983 1003 0.317479 GGAGTTGTGGACGTAGCTGT 59.683 55.000 0.00 0.00 0.00 4.40
1191 1211 2.998480 TCGCCCACCTCCGCTAAA 60.998 61.111 0.00 0.00 0.00 1.85
1278 1308 0.889306 CTTCCCTTCTTCTCGACGGT 59.111 55.000 0.00 0.00 29.24 4.83
1301 1341 0.106894 CCGGTCTGCTTATTCCCCTC 59.893 60.000 0.00 0.00 0.00 4.30
1309 1349 0.468648 CTTATTCCCCTCCGTCACCC 59.531 60.000 0.00 0.00 0.00 4.61
1310 1350 1.332144 TTATTCCCCTCCGTCACCCG 61.332 60.000 0.00 0.00 0.00 5.28
1679 1733 2.183046 GAGCACCAGAGCCTCGTC 59.817 66.667 0.00 0.00 34.23 4.20
1844 1898 2.181021 CACGCCGTCACCTACCTC 59.819 66.667 0.00 0.00 0.00 3.85
2477 2537 1.295792 GCGATTTCTGCCCGATGTAA 58.704 50.000 0.00 0.00 0.00 2.41
2498 2558 8.964476 TGTAATTTTGTTTTGATTTGGCCTTA 57.036 26.923 3.32 0.00 0.00 2.69
2576 2640 6.071165 AGCTTTAAAGACTTGATCAAATGGGG 60.071 38.462 19.48 0.00 0.00 4.96
2601 2665 2.571212 TGACCATGAAACAAGCGACTT 58.429 42.857 0.00 0.00 0.00 3.01
2616 2680 7.307839 CAAGCGACTTGTAATTAAACACTTG 57.692 36.000 10.30 0.00 36.79 3.16
2666 2732 5.232414 GCATTAGAGAATACCGTGTGACTTC 59.768 44.000 0.00 0.00 0.00 3.01
2684 2750 7.547019 TGTGACTTCTCATGATACTTTTGCTAG 59.453 37.037 0.00 0.00 0.00 3.42
2754 2823 0.721718 ACGCTTTGCTATCGCTCAAC 59.278 50.000 0.00 0.00 36.97 3.18
2755 2824 0.721154 CGCTTTGCTATCGCTCAACA 59.279 50.000 0.00 0.00 36.97 3.33
2803 2872 1.045911 GGAGAAGTCGGAGAGGCCAT 61.046 60.000 5.01 0.00 36.95 4.40
2901 2970 0.974010 TGGCCGAGGAAGATAACGGT 60.974 55.000 0.00 0.00 45.91 4.83
2939 3008 0.723981 GTGCTGGATGAAGACGAAGC 59.276 55.000 0.00 0.00 0.00 3.86
2946 3015 0.687354 ATGAAGACGAAGCAGGTGGT 59.313 50.000 0.00 0.00 0.00 4.16
2979 3092 3.760035 GCGGCCGAAGAGGAGTGA 61.760 66.667 33.48 0.00 45.00 3.41
2988 3101 4.070552 GAGGAGTGACGGCGGCTT 62.071 66.667 16.45 1.03 0.00 4.35
3105 3219 3.702555 GCGGCGCATACCACGATC 61.703 66.667 29.21 0.00 0.00 3.69
3106 3220 3.394874 CGGCGCATACCACGATCG 61.395 66.667 14.88 14.88 0.00 3.69
3107 3221 2.027024 GGCGCATACCACGATCGA 59.973 61.111 24.34 0.00 0.00 3.59
3138 3253 3.399181 GGGGACTGCGATGGACCA 61.399 66.667 0.00 0.00 0.00 4.02
3142 3257 2.994995 ACTGCGATGGACCACGGA 60.995 61.111 15.24 12.43 0.00 4.69
3343 3458 1.433471 CATGCCACGCTCTCTACGA 59.567 57.895 0.00 0.00 0.00 3.43
3500 3623 1.192146 CCGGGAGAAGAACCACAGGA 61.192 60.000 0.00 0.00 0.00 3.86
3588 3712 3.306641 GCTGAACTCAGGACAGTCTTCAT 60.307 47.826 8.74 0.00 43.94 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.731467 TCCTTTCCAGTTTATAAGGCTCAAT 58.269 36.000 0.00 0.00 37.62 2.57
1 2 6.134535 TCCTTTCCAGTTTATAAGGCTCAA 57.865 37.500 0.00 0.00 37.62 3.02
2 3 5.339200 CCTCCTTTCCAGTTTATAAGGCTCA 60.339 44.000 0.00 0.00 37.62 4.26
3 4 5.126779 CCTCCTTTCCAGTTTATAAGGCTC 58.873 45.833 0.00 0.00 37.62 4.70
4 5 4.079730 CCCTCCTTTCCAGTTTATAAGGCT 60.080 45.833 0.00 0.00 37.62 4.58
5 6 4.079958 TCCCTCCTTTCCAGTTTATAAGGC 60.080 45.833 0.00 0.00 37.62 4.35
6 7 5.191921 ACTCCCTCCTTTCCAGTTTATAAGG 59.808 44.000 0.00 0.00 38.78 2.69
7 8 6.314899 ACTCCCTCCTTTCCAGTTTATAAG 57.685 41.667 0.00 0.00 0.00 1.73
8 9 7.404980 ACATACTCCCTCCTTTCCAGTTTATAA 59.595 37.037 0.00 0.00 0.00 0.98
9 10 6.906901 ACATACTCCCTCCTTTCCAGTTTATA 59.093 38.462 0.00 0.00 0.00 0.98
10 11 5.731678 ACATACTCCCTCCTTTCCAGTTTAT 59.268 40.000 0.00 0.00 0.00 1.40
11 12 5.098663 ACATACTCCCTCCTTTCCAGTTTA 58.901 41.667 0.00 0.00 0.00 2.01
12 13 3.916989 ACATACTCCCTCCTTTCCAGTTT 59.083 43.478 0.00 0.00 0.00 2.66
13 14 3.532102 ACATACTCCCTCCTTTCCAGTT 58.468 45.455 0.00 0.00 0.00 3.16
14 15 3.207044 ACATACTCCCTCCTTTCCAGT 57.793 47.619 0.00 0.00 0.00 4.00
15 16 4.717280 AGTAACATACTCCCTCCTTTCCAG 59.283 45.833 0.00 0.00 32.47 3.86
16 17 4.469945 CAGTAACATACTCCCTCCTTTCCA 59.530 45.833 0.00 0.00 36.76 3.53
17 18 4.470304 ACAGTAACATACTCCCTCCTTTCC 59.530 45.833 0.00 0.00 36.76 3.13
18 19 5.678955 ACAGTAACATACTCCCTCCTTTC 57.321 43.478 0.00 0.00 36.76 2.62
19 20 6.499350 TGTTACAGTAACATACTCCCTCCTTT 59.501 38.462 20.32 0.00 43.23 3.11
20 21 6.021030 TGTTACAGTAACATACTCCCTCCTT 58.979 40.000 20.32 0.00 43.23 3.36
21 22 5.586877 TGTTACAGTAACATACTCCCTCCT 58.413 41.667 20.32 0.00 43.23 3.69
22 23 5.927281 TGTTACAGTAACATACTCCCTCC 57.073 43.478 20.32 0.00 43.23 4.30
33 34 7.604927 TCTTGGGATGTGTTATGTTACAGTAAC 59.395 37.037 15.58 15.58 39.11 2.50
34 35 7.681679 TCTTGGGATGTGTTATGTTACAGTAA 58.318 34.615 0.00 0.00 0.00 2.24
35 36 7.247456 TCTTGGGATGTGTTATGTTACAGTA 57.753 36.000 0.00 0.00 0.00 2.74
36 37 6.121776 TCTTGGGATGTGTTATGTTACAGT 57.878 37.500 0.00 0.00 0.00 3.55
37 38 8.731275 TTATCTTGGGATGTGTTATGTTACAG 57.269 34.615 0.00 0.00 33.71 2.74
38 39 9.521841 TTTTATCTTGGGATGTGTTATGTTACA 57.478 29.630 0.00 0.00 33.71 2.41
41 42 9.253832 TCATTTTATCTTGGGATGTGTTATGTT 57.746 29.630 0.00 0.00 33.71 2.71
42 43 8.821686 TCATTTTATCTTGGGATGTGTTATGT 57.178 30.769 0.00 0.00 33.71 2.29
43 44 8.906867 ACTCATTTTATCTTGGGATGTGTTATG 58.093 33.333 0.00 0.00 33.71 1.90
44 45 9.125026 GACTCATTTTATCTTGGGATGTGTTAT 57.875 33.333 0.00 0.00 33.71 1.89
45 46 8.328758 AGACTCATTTTATCTTGGGATGTGTTA 58.671 33.333 0.00 0.00 33.71 2.41
46 47 7.177878 AGACTCATTTTATCTTGGGATGTGTT 58.822 34.615 0.00 0.00 33.71 3.32
47 48 6.725364 AGACTCATTTTATCTTGGGATGTGT 58.275 36.000 0.00 0.00 33.71 3.72
48 49 8.915057 ATAGACTCATTTTATCTTGGGATGTG 57.085 34.615 0.00 0.00 33.71 3.21
72 73 9.976511 CATGCAAACCTTCATTAATTGAGATAT 57.023 29.630 0.00 0.00 35.27 1.63
73 74 8.970020 ACATGCAAACCTTCATTAATTGAGATA 58.030 29.630 0.00 0.00 35.27 1.98
74 75 7.844009 ACATGCAAACCTTCATTAATTGAGAT 58.156 30.769 0.00 0.00 35.27 2.75
75 76 7.230849 ACATGCAAACCTTCATTAATTGAGA 57.769 32.000 0.00 0.00 35.27 3.27
76 77 7.894376 AACATGCAAACCTTCATTAATTGAG 57.106 32.000 0.00 0.00 35.27 3.02
77 78 7.816995 GGTAACATGCAAACCTTCATTAATTGA 59.183 33.333 0.00 0.00 0.00 2.57
78 79 7.601886 TGGTAACATGCAAACCTTCATTAATTG 59.398 33.333 11.67 0.00 46.17 2.32
79 80 7.675062 TGGTAACATGCAAACCTTCATTAATT 58.325 30.769 11.67 0.00 46.17 1.40
80 81 7.238486 TGGTAACATGCAAACCTTCATTAAT 57.762 32.000 11.67 0.00 46.17 1.40
81 82 6.656632 TGGTAACATGCAAACCTTCATTAA 57.343 33.333 11.67 0.00 46.17 1.40
98 99 8.594550 AGTGGATAGTAACATATGGATGGTAAC 58.405 37.037 7.80 0.00 36.99 2.50
99 100 8.736097 AGTGGATAGTAACATATGGATGGTAA 57.264 34.615 7.80 0.00 36.99 2.85
101 102 8.762645 CATAGTGGATAGTAACATATGGATGGT 58.237 37.037 7.80 0.00 37.39 3.55
102 103 8.981659 TCATAGTGGATAGTAACATATGGATGG 58.018 37.037 7.80 0.00 37.39 3.51
105 106 9.035890 CCTTCATAGTGGATAGTAACATATGGA 57.964 37.037 7.80 0.00 0.00 3.41
106 107 8.816894 ACCTTCATAGTGGATAGTAACATATGG 58.183 37.037 7.80 0.00 0.00 2.74
111 112 9.925545 TTACTACCTTCATAGTGGATAGTAACA 57.074 33.333 0.00 0.00 36.09 2.41
113 114 9.925545 TGTTACTACCTTCATAGTGGATAGTAA 57.074 33.333 0.00 0.00 36.09 2.24
117 118 9.529823 CCTATGTTACTACCTTCATAGTGGATA 57.470 37.037 0.00 0.00 38.47 2.59
118 119 7.455008 CCCTATGTTACTACCTTCATAGTGGAT 59.545 40.741 0.00 0.00 38.47 3.41
119 120 6.781014 CCCTATGTTACTACCTTCATAGTGGA 59.219 42.308 0.00 0.00 38.47 4.02
120 121 6.014499 CCCCTATGTTACTACCTTCATAGTGG 60.014 46.154 0.00 0.00 38.47 4.00
121 122 6.014499 CCCCCTATGTTACTACCTTCATAGTG 60.014 46.154 0.00 0.00 38.47 2.74
122 123 6.082707 CCCCCTATGTTACTACCTTCATAGT 58.917 44.000 0.00 0.00 38.47 2.12
123 124 6.014499 CACCCCCTATGTTACTACCTTCATAG 60.014 46.154 0.00 0.00 39.29 2.23
124 125 5.842328 CACCCCCTATGTTACTACCTTCATA 59.158 44.000 0.00 0.00 0.00 2.15
125 126 4.658901 CACCCCCTATGTTACTACCTTCAT 59.341 45.833 0.00 0.00 0.00 2.57
126 127 4.035112 CACCCCCTATGTTACTACCTTCA 58.965 47.826 0.00 0.00 0.00 3.02
127 128 4.035814 ACACCCCCTATGTTACTACCTTC 58.964 47.826 0.00 0.00 0.00 3.46
128 129 4.084466 ACACCCCCTATGTTACTACCTT 57.916 45.455 0.00 0.00 0.00 3.50
129 130 3.790022 ACACCCCCTATGTTACTACCT 57.210 47.619 0.00 0.00 0.00 3.08
130 131 4.520179 CAAACACCCCCTATGTTACTACC 58.480 47.826 0.00 0.00 39.36 3.18
131 132 4.019051 ACCAAACACCCCCTATGTTACTAC 60.019 45.833 0.00 0.00 39.36 2.73
132 133 4.177546 ACCAAACACCCCCTATGTTACTA 58.822 43.478 0.00 0.00 39.36 1.82
133 134 2.990998 ACCAAACACCCCCTATGTTACT 59.009 45.455 0.00 0.00 39.36 2.24
134 135 3.444792 ACCAAACACCCCCTATGTTAC 57.555 47.619 0.00 0.00 39.36 2.50
135 136 3.398292 TGAACCAAACACCCCCTATGTTA 59.602 43.478 0.00 0.00 39.36 2.41
136 137 2.178106 TGAACCAAACACCCCCTATGTT 59.822 45.455 0.00 0.00 42.07 2.71
137 138 1.783979 TGAACCAAACACCCCCTATGT 59.216 47.619 0.00 0.00 0.00 2.29
138 139 2.041081 TCTGAACCAAACACCCCCTATG 59.959 50.000 0.00 0.00 0.00 2.23
139 140 2.354328 TCTGAACCAAACACCCCCTAT 58.646 47.619 0.00 0.00 0.00 2.57
140 141 1.822425 TCTGAACCAAACACCCCCTA 58.178 50.000 0.00 0.00 0.00 3.53
141 142 0.930726 TTCTGAACCAAACACCCCCT 59.069 50.000 0.00 0.00 0.00 4.79
142 143 1.328279 CTTCTGAACCAAACACCCCC 58.672 55.000 0.00 0.00 0.00 5.40
143 144 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
144 145 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
145 146 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
146 147 4.065789 CCTAGGACTTCTGAACCAAACAC 58.934 47.826 1.05 0.00 0.00 3.32
147 148 3.971305 TCCTAGGACTTCTGAACCAAACA 59.029 43.478 7.62 0.00 0.00 2.83
148 149 4.316645 GTCCTAGGACTTCTGAACCAAAC 58.683 47.826 31.12 3.26 41.57 2.93
149 150 4.618920 GTCCTAGGACTTCTGAACCAAA 57.381 45.455 31.12 0.00 41.57 3.28
209 210 9.590828 AAGACTTTACTAGGAAAAGACTCTACT 57.409 33.333 20.52 7.29 37.77 2.57
219 220 9.993454 GGACTAGAAAAAGACTTTACTAGGAAA 57.007 33.333 27.11 0.00 35.77 3.13
220 221 8.591940 GGGACTAGAAAAAGACTTTACTAGGAA 58.408 37.037 27.11 0.00 35.77 3.36
221 222 7.954620 AGGGACTAGAAAAAGACTTTACTAGGA 59.045 37.037 27.11 9.48 36.02 2.94
222 223 8.035984 CAGGGACTAGAAAAAGACTTTACTAGG 58.964 40.741 27.11 17.67 36.02 3.02
223 224 8.586744 ACAGGGACTAGAAAAAGACTTTACTAG 58.413 37.037 24.68 24.68 36.02 2.57
224 225 8.488308 ACAGGGACTAGAAAAAGACTTTACTA 57.512 34.615 0.00 7.54 36.02 1.82
225 226 7.376335 ACAGGGACTAGAAAAAGACTTTACT 57.624 36.000 0.00 6.80 36.02 2.24
226 227 8.583296 TCTACAGGGACTAGAAAAAGACTTTAC 58.417 37.037 0.00 0.00 36.02 2.01
227 228 8.716674 TCTACAGGGACTAGAAAAAGACTTTA 57.283 34.615 0.00 0.00 36.02 1.85
228 229 7.613551 TCTACAGGGACTAGAAAAAGACTTT 57.386 36.000 0.00 0.00 36.02 2.66
229 230 7.613551 TTCTACAGGGACTAGAAAAAGACTT 57.386 36.000 0.00 0.00 36.02 3.01
230 231 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
231 232 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
235 236 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
236 237 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
237 238 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
238 239 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
239 240 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
240 241 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
241 242 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
242 243 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
243 244 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
244 245 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
245 246 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
246 247 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
247 248 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
248 249 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
249 250 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
250 251 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
251 252 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
252 253 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
253 254 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
254 255 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
255 256 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
257 258 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
258 259 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
259 260 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
260 261 0.981943 ACTAGGAACCAAACGGGAGG 59.018 55.000 0.00 0.00 41.15 4.30
261 262 3.094572 TCTACTAGGAACCAAACGGGAG 58.905 50.000 0.00 0.00 41.15 4.30
262 263 3.094572 CTCTACTAGGAACCAAACGGGA 58.905 50.000 0.00 0.00 41.15 5.14
263 264 2.830321 ACTCTACTAGGAACCAAACGGG 59.170 50.000 0.00 0.00 44.81 5.28
264 265 3.762823 AGACTCTACTAGGAACCAAACGG 59.237 47.826 0.00 0.00 0.00 4.44
265 266 5.388408 AAGACTCTACTAGGAACCAAACG 57.612 43.478 0.00 0.00 0.00 3.60
266 267 7.932491 AGAAAAAGACTCTACTAGGAACCAAAC 59.068 37.037 0.00 0.00 0.00 2.93
267 268 8.030913 AGAAAAAGACTCTACTAGGAACCAAA 57.969 34.615 0.00 0.00 0.00 3.28
268 269 7.613551 AGAAAAAGACTCTACTAGGAACCAA 57.386 36.000 0.00 0.00 0.00 3.67
269 270 7.949006 ACTAGAAAAAGACTCTACTAGGAACCA 59.051 37.037 0.00 0.00 33.83 3.67
270 271 8.352137 ACTAGAAAAAGACTCTACTAGGAACC 57.648 38.462 0.00 0.00 33.83 3.62
271 272 8.461222 GGACTAGAAAAAGACTCTACTAGGAAC 58.539 40.741 0.00 0.00 33.83 3.62
272 273 7.614974 GGGACTAGAAAAAGACTCTACTAGGAA 59.385 40.741 0.00 0.00 33.83 3.36
273 274 7.036717 AGGGACTAGAAAAAGACTCTACTAGGA 60.037 40.741 0.00 0.00 36.02 2.94
274 275 7.067737 CAGGGACTAGAAAAAGACTCTACTAGG 59.932 44.444 0.00 0.00 36.02 3.02
275 276 7.612633 ACAGGGACTAGAAAAAGACTCTACTAG 59.387 40.741 0.00 0.00 36.02 2.57
276 277 7.468496 ACAGGGACTAGAAAAAGACTCTACTA 58.532 38.462 0.00 0.00 36.02 1.82
277 278 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
278 279 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
279 280 8.716674 TTTACAGGGACTAGAAAAAGACTCTA 57.283 34.615 0.00 0.00 36.02 2.43
280 281 7.613551 TTTACAGGGACTAGAAAAAGACTCT 57.386 36.000 0.00 0.00 36.02 3.24
281 282 8.672823 TTTTTACAGGGACTAGAAAAAGACTC 57.327 34.615 0.00 0.00 36.74 3.36
308 309 6.815252 CCCTAAAACCAAACGGAAGGGACT 62.815 50.000 0.00 0.00 44.18 3.85
309 310 2.555325 CCTAAAACCAAACGGAAGGGAC 59.445 50.000 0.00 0.00 0.00 4.46
310 311 2.489437 CCCTAAAACCAAACGGAAGGGA 60.489 50.000 0.00 0.00 44.18 4.20
311 312 1.890489 CCCTAAAACCAAACGGAAGGG 59.110 52.381 0.00 0.00 36.51 3.95
312 313 2.555325 GTCCCTAAAACCAAACGGAAGG 59.445 50.000 0.00 0.00 0.00 3.46
313 314 3.483421 AGTCCCTAAAACCAAACGGAAG 58.517 45.455 0.00 0.00 0.00 3.46
314 315 3.581265 AGTCCCTAAAACCAAACGGAA 57.419 42.857 0.00 0.00 0.00 4.30
315 316 3.581265 AAGTCCCTAAAACCAAACGGA 57.419 42.857 0.00 0.00 0.00 4.69
316 317 4.659111 AAAAGTCCCTAAAACCAAACGG 57.341 40.909 0.00 0.00 0.00 4.44
317 318 5.898174 AGAAAAAGTCCCTAAAACCAAACG 58.102 37.500 0.00 0.00 0.00 3.60
318 319 8.004087 ACTAGAAAAAGTCCCTAAAACCAAAC 57.996 34.615 0.00 0.00 0.00 2.93
319 320 8.057011 AGACTAGAAAAAGTCCCTAAAACCAAA 58.943 33.333 0.00 0.00 45.86 3.28
320 321 7.580007 AGACTAGAAAAAGTCCCTAAAACCAA 58.420 34.615 0.00 0.00 45.86 3.67
321 322 7.072076 AGAGACTAGAAAAAGTCCCTAAAACCA 59.928 37.037 0.00 0.00 45.86 3.67
322 323 7.388224 CAGAGACTAGAAAAAGTCCCTAAAACC 59.612 40.741 0.00 0.00 45.86 3.27
323 324 7.388224 CCAGAGACTAGAAAAAGTCCCTAAAAC 59.612 40.741 0.00 0.00 45.86 2.43
324 325 7.450903 CCAGAGACTAGAAAAAGTCCCTAAAA 58.549 38.462 0.00 0.00 45.86 1.52
325 326 6.013639 CCCAGAGACTAGAAAAAGTCCCTAAA 60.014 42.308 0.00 0.00 45.86 1.85
326 327 5.484290 CCCAGAGACTAGAAAAAGTCCCTAA 59.516 44.000 0.00 0.00 45.86 2.69
327 328 5.024118 CCCAGAGACTAGAAAAAGTCCCTA 58.976 45.833 0.00 0.00 45.86 3.53
328 329 3.841255 CCCAGAGACTAGAAAAAGTCCCT 59.159 47.826 0.00 0.00 45.86 4.20
329 330 3.838903 TCCCAGAGACTAGAAAAAGTCCC 59.161 47.826 0.00 0.00 45.86 4.46
330 331 4.823157 GTCCCAGAGACTAGAAAAAGTCC 58.177 47.826 0.00 0.00 45.86 3.85
350 351 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
351 352 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
352 353 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
353 354 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
354 355 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
355 356 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
356 357 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
357 358 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
358 359 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
359 360 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
360 361 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
361 362 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
362 363 0.178935 ATGGGGGTGTTTGGTTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
363 364 2.041081 TCTATGGGGGTGTTTGGTTCAG 59.959 50.000 0.00 0.00 0.00 3.02
364 365 2.066592 TCTATGGGGGTGTTTGGTTCA 58.933 47.619 0.00 0.00 0.00 3.18
365 366 2.041216 AGTCTATGGGGGTGTTTGGTTC 59.959 50.000 0.00 0.00 0.00 3.62
366 367 2.070573 AGTCTATGGGGGTGTTTGGTT 58.929 47.619 0.00 0.00 0.00 3.67
367 368 1.755200 AGTCTATGGGGGTGTTTGGT 58.245 50.000 0.00 0.00 0.00 3.67
368 369 2.844348 ACTAGTCTATGGGGGTGTTTGG 59.156 50.000 0.00 0.00 0.00 3.28
369 370 5.046159 TGTTACTAGTCTATGGGGGTGTTTG 60.046 44.000 0.00 0.00 0.00 2.93
370 371 5.095809 TGTTACTAGTCTATGGGGGTGTTT 58.904 41.667 0.00 0.00 0.00 2.83
371 372 4.691238 TGTTACTAGTCTATGGGGGTGTT 58.309 43.478 0.00 0.00 0.00 3.32
372 373 4.341863 TGTTACTAGTCTATGGGGGTGT 57.658 45.455 0.00 0.00 0.00 4.16
373 374 5.836898 TGTATGTTACTAGTCTATGGGGGTG 59.163 44.000 0.00 0.00 0.00 4.61
374 375 6.034442 TGTATGTTACTAGTCTATGGGGGT 57.966 41.667 0.00 0.00 0.00 4.95
375 376 6.497259 ACATGTATGTTACTAGTCTATGGGGG 59.503 42.308 0.00 0.00 37.90 5.40
376 377 7.540474 ACATGTATGTTACTAGTCTATGGGG 57.460 40.000 0.00 0.00 37.90 4.96
396 397 7.341256 TGGGGAGTAACTTAGACTAGTAACATG 59.659 40.741 0.00 0.00 0.00 3.21
397 398 7.341512 GTGGGGAGTAACTTAGACTAGTAACAT 59.658 40.741 0.00 0.00 0.00 2.71
399 400 6.889177 AGTGGGGAGTAACTTAGACTAGTAAC 59.111 42.308 0.00 0.00 0.00 2.50
401 402 6.649041 AGTGGGGAGTAACTTAGACTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
402 403 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
403 404 7.470286 GCATAAGTGGGGAGTAACTTAGACTAG 60.470 44.444 0.00 0.00 41.02 2.57
404 405 6.323225 GCATAAGTGGGGAGTAACTTAGACTA 59.677 42.308 0.00 0.00 41.02 2.59
405 406 5.128991 GCATAAGTGGGGAGTAACTTAGACT 59.871 44.000 0.00 0.00 41.02 3.24
406 407 5.105064 TGCATAAGTGGGGAGTAACTTAGAC 60.105 44.000 0.00 0.00 41.02 2.59
407 408 5.027460 TGCATAAGTGGGGAGTAACTTAGA 58.973 41.667 0.00 0.00 41.02 2.10
410 411 3.587506 ACTGCATAAGTGGGGAGTAACTT 59.412 43.478 0.00 0.00 37.88 2.66
412 413 3.629142 ACTGCATAAGTGGGGAGTAAC 57.371 47.619 0.00 0.00 37.88 2.50
413 414 3.585289 TGAACTGCATAAGTGGGGAGTAA 59.415 43.478 0.00 0.00 39.81 2.24
415 416 1.985159 TGAACTGCATAAGTGGGGAGT 59.015 47.619 0.00 0.00 39.81 3.85
416 417 2.026822 AGTGAACTGCATAAGTGGGGAG 60.027 50.000 0.00 0.00 39.81 4.30
417 418 1.985159 AGTGAACTGCATAAGTGGGGA 59.015 47.619 0.00 0.00 39.81 4.81
418 419 2.496899 AGTGAACTGCATAAGTGGGG 57.503 50.000 0.00 0.00 39.81 4.96
419 420 3.120199 CGAAAGTGAACTGCATAAGTGGG 60.120 47.826 0.00 0.00 39.81 4.61
444 456 7.814264 AGAATCATCATACCACTTGATTTCC 57.186 36.000 0.00 0.00 38.55 3.13
472 484 4.125703 CCAGATCAGCTACAAGGATTCAC 58.874 47.826 0.00 0.00 0.00 3.18
508 520 3.643792 AGAGGATAGAATTCTTCCACCCG 59.356 47.826 25.56 0.00 31.65 5.28
531 543 6.680378 GCGACCTTTTATAAATGCTCATTGGT 60.680 38.462 0.00 0.00 0.00 3.67
538 550 5.925509 TCTAGGCGACCTTTTATAAATGCT 58.074 37.500 3.71 0.00 34.61 3.79
571 588 2.660064 GGGACCCAGATGCAGTCGT 61.660 63.158 5.33 0.00 0.00 4.34
573 590 1.899437 TTCGGGACCCAGATGCAGTC 61.899 60.000 12.15 0.00 0.00 3.51
581 598 1.003718 GGAACACTTCGGGACCCAG 60.004 63.158 12.15 3.55 0.00 4.45
614 631 1.202132 CCATGGAATTAACGTGTGCCG 60.202 52.381 5.56 0.00 44.03 5.69
726 745 1.966451 GACCTGGACCTGGCAAACG 60.966 63.158 17.00 0.00 0.00 3.60
733 752 2.294078 GGACCTGGACCTGGACCTG 61.294 68.421 25.06 14.74 35.33 4.00
734 753 2.122954 GGACCTGGACCTGGACCT 59.877 66.667 25.06 5.34 35.33 3.85
735 754 2.203938 TGGACCTGGACCTGGACC 60.204 66.667 25.42 25.42 37.66 4.46
736 755 2.294078 CCTGGACCTGGACCTGGAC 61.294 68.421 28.41 16.79 45.37 4.02
737 756 2.122729 CCTGGACCTGGACCTGGA 59.877 66.667 28.41 4.64 45.37 3.86
740 759 2.122954 GGACCTGGACCTGGACCT 59.877 66.667 25.06 5.34 35.33 3.85
923 942 3.549070 CGAAGTCGAAACCGGTTTATAGG 59.451 47.826 31.70 20.10 43.02 2.57
983 1003 2.459969 ATGTCCCACACACAGGCCA 61.460 57.895 5.01 0.00 38.04 5.36
1083 1103 2.508887 GAGAGCTGCTGCGACCAG 60.509 66.667 7.01 0.00 45.42 4.00
1176 1196 0.322187 TCTTTTTAGCGGAGGTGGGC 60.322 55.000 0.00 0.00 40.22 5.36
1188 1208 4.398319 CCTGCTTGGACCTCTTCTTTTTA 58.602 43.478 0.00 0.00 38.35 1.52
1191 1211 1.546548 GCCTGCTTGGACCTCTTCTTT 60.547 52.381 0.00 0.00 38.35 2.52
1278 1308 1.143183 GAATAAGCAGACCGGCCGA 59.857 57.895 30.73 3.37 0.00 5.54
1309 1349 2.223971 ACAGTAAGACCAACACAGTCCG 60.224 50.000 0.00 0.00 34.67 4.79
1310 1350 3.470645 ACAGTAAGACCAACACAGTCC 57.529 47.619 0.00 0.00 34.67 3.85
1844 1898 0.108329 GGTGGTCGGAGTACATGTGG 60.108 60.000 9.11 0.00 0.00 4.17
2189 2243 1.153745 CTTCCCCTCGACGAGCTTG 60.154 63.158 19.55 9.43 0.00 4.01
2411 2465 4.452733 CTGGCCCGGTCGGAGAAC 62.453 72.222 11.39 0.00 43.60 3.01
2447 2501 4.344865 AAATCGCCGGTGGTGCCT 62.345 61.111 16.49 0.00 32.51 4.75
2470 2530 7.014702 GGCCAAATCAAAACAAAATTACATCG 58.985 34.615 0.00 0.00 0.00 3.84
2477 2537 8.922931 AGAATAAGGCCAAATCAAAACAAAAT 57.077 26.923 5.01 0.00 0.00 1.82
2550 2610 7.122650 CCCCATTTGATCAAGTCTTTAAAGCTA 59.877 37.037 10.51 0.00 0.00 3.32
2551 2611 6.071165 CCCCATTTGATCAAGTCTTTAAAGCT 60.071 38.462 10.51 8.15 0.00 3.74
2576 2640 2.409378 CGCTTGTTTCATGGTCAATTGC 59.591 45.455 0.00 0.00 0.00 3.56
2684 2750 7.383102 TCAACCTTGCAAGATAGATTTCTTC 57.617 36.000 28.05 0.00 33.69 2.87
2754 2823 5.309323 ACCATTATGTCACGAAATTGGTG 57.691 39.130 1.54 1.54 36.74 4.17
2755 2824 4.398044 GGACCATTATGTCACGAAATTGGT 59.602 41.667 0.00 0.00 36.97 3.67
2803 2872 1.440708 GTCGTCGAGTCCTTCTCTGA 58.559 55.000 0.00 0.00 40.75 3.27
2885 2954 1.533338 CGTCACCGTTATCTTCCTCGG 60.533 57.143 0.00 0.00 46.98 4.63
2968 3081 2.182030 CCGCCGTCACTCCTCTTC 59.818 66.667 0.00 0.00 0.00 2.87
2974 3087 2.775032 TAACCAAGCCGCCGTCACTC 62.775 60.000 0.00 0.00 0.00 3.51
2979 3092 1.375523 CTCTTAACCAAGCCGCCGT 60.376 57.895 0.00 0.00 0.00 5.68
3217 3332 4.003788 CCCACGGTCCTTGCGACT 62.004 66.667 0.00 0.00 41.64 4.18
3241 3356 4.530857 CCCCTTCGGGCTGTAGCG 62.531 72.222 0.00 0.00 44.50 4.26
3326 3441 1.433879 GTCGTAGAGAGCGTGGCAT 59.566 57.895 0.00 0.00 36.95 4.40
3545 3668 2.269529 GCCCCTCTACCGATCGAGG 61.270 68.421 18.66 15.01 45.10 4.63
3575 3698 1.566298 GGCCCCATGAAGACTGTCCT 61.566 60.000 3.76 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.