Multiple sequence alignment - TraesCS6B01G119100

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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 TraesCS6B01G119100 chr6B 100.000 6860 0 0 1 6860 113842481 113849340 0.000000e+00 12669.0
1 TraesCS6B01G119100 chr6B 94.457 1822 86 13 1791 3605 68722953 68724766 0.000000e+00 2791.0
2 TraesCS6B01G119100 chr6B 88.018 1594 135 14 4876 6451 113783435 113784990 0.000000e+00 1834.0
3 TraesCS6B01G119100 chr6B 87.204 930 117 2 4843 5771 113656666 113657594 0.000000e+00 1057.0
4 TraesCS6B01G119100 chr6B 94.810 578 26 4 1791 2366 457429435 457430010 0.000000e+00 898.0
5 TraesCS6B01G119100 chr6B 94.359 585 19 8 1788 2366 696244759 696245335 0.000000e+00 885.0
6 TraesCS6B01G119100 chr6B 83.974 755 70 19 4117 4832 113782360 113783102 0.000000e+00 676.0
7 TraesCS6B01G119100 chr6B 81.830 798 89 26 3766 4561 114018241 114018984 2.720000e-173 619.0
8 TraesCS6B01G119100 chr6B 92.000 250 20 0 4583 4832 114026232 114026481 1.090000e-92 351.0
9 TraesCS6B01G119100 chr6B 95.614 114 5 0 984 1097 113780957 113781070 4.230000e-42 183.0
10 TraesCS6B01G119100 chr6B 82.727 220 15 2 1488 1684 113781768 113781987 2.540000e-39 174.0
11 TraesCS6B01G119100 chr6B 85.859 99 8 5 6358 6451 114028276 114028373 4.380000e-17 100.0
12 TraesCS6B01G119100 chr6B 93.651 63 4 0 6798 6860 131279566 131279504 2.040000e-15 95.3
13 TraesCS6B01G119100 chr6D 93.610 3302 121 23 3611 6860 45208346 45211609 0.000000e+00 4846.0
14 TraesCS6B01G119100 chr6D 88.123 1625 137 14 4843 6449 45204226 45205812 0.000000e+00 1881.0
15 TraesCS6B01G119100 chr6D 86.437 929 124 2 4843 5770 44506703 44507630 0.000000e+00 1016.0
16 TraesCS6B01G119100 chr6D 87.108 892 115 0 4843 5734 80291174 80292065 0.000000e+00 1011.0
17 TraesCS6B01G119100 chr6D 90.873 756 57 3 5216 5968 45480790 45481536 0.000000e+00 1003.0
18 TraesCS6B01G119100 chr6D 85.991 928 129 1 4843 5770 44736933 44737859 0.000000e+00 992.0
19 TraesCS6B01G119100 chr6D 85.237 928 136 1 4843 5770 44934381 44935307 0.000000e+00 953.0
20 TraesCS6B01G119100 chr6D 84.946 930 128 5 4843 5770 44864049 44864968 0.000000e+00 931.0
21 TraesCS6B01G119100 chr6D 92.079 505 33 3 4329 4832 45479905 45480403 0.000000e+00 704.0
22 TraesCS6B01G119100 chr6D 84.450 746 75 18 4117 4832 45203451 45204185 0.000000e+00 697.0
23 TraesCS6B01G119100 chr6D 94.366 355 20 0 4843 5197 45480444 45480798 4.680000e-151 545.0
24 TraesCS6B01G119100 chr6D 91.429 385 23 3 1169 1545 45206449 45206831 2.840000e-143 520.0
25 TraesCS6B01G119100 chr6D 96.218 238 9 0 1169 1406 45478215 45478452 2.320000e-104 390.0
26 TraesCS6B01G119100 chr6D 82.979 329 41 7 6451 6765 84236634 84236307 4.050000e-72 283.0
27 TraesCS6B01G119100 chr6D 82.934 334 32 11 6451 6759 292083639 292083972 1.880000e-70 278.0
28 TraesCS6B01G119100 chr6D 88.950 181 19 1 5011 5191 80297964 80298143 8.960000e-54 222.0
29 TraesCS6B01G119100 chr6D 94.574 129 7 0 984 1112 45202314 45202442 4.200000e-47 200.0
30 TraesCS6B01G119100 chr6D 97.414 116 3 0 984 1099 45206302 45206417 1.510000e-46 198.0
31 TraesCS6B01G119100 chr6D 83.871 217 12 9 1491 1684 45202831 45203047 1.170000e-42 185.0
32 TraesCS6B01G119100 chr6D 96.226 106 4 0 1578 1683 45206928 45207033 2.540000e-39 174.0
33 TraesCS6B01G119100 chr6D 95.146 103 5 0 991 1093 45478087 45478189 5.510000e-36 163.0
34 TraesCS6B01G119100 chr6D 90.000 100 8 1 992 1089 44502859 44502958 2.010000e-25 128.0
35 TraesCS6B01G119100 chr6D 90.000 100 8 1 992 1089 80288957 80289056 2.010000e-25 128.0
36 TraesCS6B01G119100 chr6D 87.209 86 7 4 6358 6441 45482067 45482150 2.040000e-15 95.3
37 TraesCS6B01G119100 chr6A 93.526 2873 106 20 3611 6451 59785193 59788017 0.000000e+00 4202.0
38 TraesCS6B01G119100 chr6A 88.705 1328 118 17 4843 6153 59709517 59710829 0.000000e+00 1592.0
39 TraesCS6B01G119100 chr6A 86.731 927 123 0 4844 5770 59345310 59346236 0.000000e+00 1031.0
40 TraesCS6B01G119100 chr6A 86.422 928 126 0 4843 5770 59676918 59677845 0.000000e+00 1016.0
41 TraesCS6B01G119100 chr6A 90.370 540 27 3 1169 1683 59783437 59783976 0.000000e+00 686.0
42 TraesCS6B01G119100 chr6A 84.485 709 72 10 4160 4832 59708770 59709476 0.000000e+00 665.0
43 TraesCS6B01G119100 chr6A 90.675 504 39 3 4329 4832 59810035 59810530 0.000000e+00 664.0
44 TraesCS6B01G119100 chr6A 92.177 294 18 3 6161 6451 59710811 59711102 1.780000e-110 411.0
45 TraesCS6B01G119100 chr6A 95.816 239 9 1 1169 1406 59808351 59808589 1.080000e-102 385.0
46 TraesCS6B01G119100 chr6A 96.154 130 5 0 984 1113 59783296 59783425 5.390000e-51 213.0
47 TraesCS6B01G119100 chr6A 95.146 103 5 0 991 1093 59808223 59808325 5.510000e-36 163.0
48 TraesCS6B01G119100 chr6A 91.919 99 8 0 6762 6860 180739310 180739212 9.280000e-29 139.0
49 TraesCS6B01G119100 chr6A 91.000 100 7 1 992 1089 59342798 59342897 4.320000e-27 134.0
50 TraesCS6B01G119100 chr6A 97.101 69 1 1 1712 1780 59784772 59784839 1.560000e-21 115.0
51 TraesCS6B01G119100 chr6A 87.143 70 4 2 1711 1780 59809809 59809873 2.650000e-09 75.0
52 TraesCS6B01G119100 chr6A 94.000 50 2 1 6356 6405 59814590 59814638 2.650000e-09 75.0
53 TraesCS6B01G119100 chr2B 95.390 1822 71 7 1788 3604 172680090 172681903 0.000000e+00 2887.0
54 TraesCS6B01G119100 chr2B 95.225 1822 67 11 1786 3605 626646966 626645163 0.000000e+00 2865.0
55 TraesCS6B01G119100 chr2B 93.382 680 45 0 1 680 542255296 542255975 0.000000e+00 1007.0
56 TraesCS6B01G119100 chr2B 85.123 773 110 4 1 772 579801318 579800550 0.000000e+00 785.0
57 TraesCS6B01G119100 chr2B 86.111 324 31 6 6455 6764 30135756 30135433 3.070000e-88 337.0
58 TraesCS6B01G119100 chr1B 95.298 1829 69 6 1791 3604 62250587 62248761 0.000000e+00 2885.0
59 TraesCS6B01G119100 chr1B 93.510 1849 83 15 1785 3605 395228357 395230196 0.000000e+00 2715.0
60 TraesCS6B01G119100 chr1B 85.852 311 28 8 6451 6747 442951639 442951947 3.990000e-82 316.0
61 TraesCS6B01G119100 chr1B 84.058 276 30 6 6451 6713 568641767 568641493 3.180000e-63 254.0
62 TraesCS6B01G119100 chr7B 96.254 1762 51 12 1791 3544 743400631 743398877 0.000000e+00 2874.0
63 TraesCS6B01G119100 chr7B 95.225 1822 60 11 1791 3605 108557576 108555775 0.000000e+00 2857.0
64 TraesCS6B01G119100 chr7B 93.236 1848 78 22 1785 3604 474281103 474279275 0.000000e+00 2676.0
65 TraesCS6B01G119100 chr7B 89.041 73 4 2 6790 6860 142387321 142387391 3.410000e-13 87.9
66 TraesCS6B01G119100 chr5B 93.141 1837 96 16 1791 3604 590533241 590531412 0.000000e+00 2667.0
67 TraesCS6B01G119100 chr5B 95.157 702 33 1 71 771 466952158 466951457 0.000000e+00 1107.0
68 TraesCS6B01G119100 chr5B 93.274 669 45 0 1 669 555207147 555206479 0.000000e+00 987.0
69 TraesCS6B01G119100 chr5B 84.830 323 35 6 6451 6759 358621075 358621397 5.170000e-81 313.0
70 TraesCS6B01G119100 chr5B 84.868 304 32 6 6457 6746 386533819 386533516 1.870000e-75 294.0
71 TraesCS6B01G119100 chr5B 85.374 294 29 4 6468 6747 332964590 332964883 6.730000e-75 292.0
72 TraesCS6B01G119100 chr5B 90.780 141 13 0 6607 6747 531871994 531871854 9.080000e-44 189.0
73 TraesCS6B01G119100 chr5B 90.780 141 12 1 6607 6747 531907333 531907194 3.270000e-43 187.0
74 TraesCS6B01G119100 chr5B 90.909 99 9 0 6762 6860 249382317 249382415 4.320000e-27 134.0
75 TraesCS6B01G119100 chr5A 92.462 1844 83 16 1791 3604 378278421 378276604 0.000000e+00 2584.0
76 TraesCS6B01G119100 chr5D 94.293 771 44 0 1 771 10498400 10497630 0.000000e+00 1181.0
77 TraesCS6B01G119100 chr5D 86.687 323 28 5 6451 6759 241956370 241956691 1.830000e-90 344.0
78 TraesCS6B01G119100 chr5D 84.802 329 36 8 6451 6765 370715912 370715584 1.110000e-82 318.0
79 TraesCS6B01G119100 chr5D 82.748 313 40 6 6456 6754 332213621 332213933 4.080000e-67 267.0
80 TraesCS6B01G119100 chr4D 93.515 771 44 1 1 771 22554425 22553661 0.000000e+00 1142.0
81 TraesCS6B01G119100 chr4D 85.852 311 28 6 6451 6747 136961750 136961442 3.990000e-82 316.0
82 TraesCS6B01G119100 chr4D 85.209 311 32 6 6451 6747 407117776 407117466 2.400000e-79 307.0
83 TraesCS6B01G119100 chr4D 84.277 318 36 4 6451 6754 12507005 12507322 1.450000e-76 298.0
84 TraesCS6B01G119100 chr4D 85.714 287 27 4 6455 6727 259499087 259498801 2.420000e-74 291.0
85 TraesCS6B01G119100 chr4D 83.974 312 35 2 6451 6747 4929079 4928768 1.130000e-72 285.0
86 TraesCS6B01G119100 chr4D 83.713 307 36 4 6455 6747 468259486 468259792 1.880000e-70 278.0
87 TraesCS6B01G119100 chr4D 82.477 331 42 8 6451 6767 417672731 417672403 6.780000e-70 276.0
88 TraesCS6B01G119100 chr4D 82.965 317 40 4 6451 6753 416853823 416853507 2.440000e-69 274.0
89 TraesCS6B01G119100 chr2A 93.256 771 52 0 1 771 84158023 84157253 0.000000e+00 1136.0
90 TraesCS6B01G119100 chr2A 85.382 301 40 3 6451 6747 376085428 376085728 6.680000e-80 309.0
91 TraesCS6B01G119100 chr4B 92.737 771 54 2 3 772 52414275 52413506 0.000000e+00 1112.0
92 TraesCS6B01G119100 chr4B 86.174 311 28 5 6451 6747 228437472 228437781 8.580000e-84 322.0
93 TraesCS6B01G119100 chr4B 85.852 311 30 4 6451 6747 391557157 391557467 1.110000e-82 318.0
94 TraesCS6B01G119100 chr4B 84.142 309 34 7 6456 6750 657301087 657300780 1.130000e-72 285.0
95 TraesCS6B01G119100 chr4B 81.957 327 43 9 6455 6767 546261884 546261560 5.280000e-66 263.0
96 TraesCS6B01G119100 chr3B 89.766 811 62 11 1795 2593 817067901 817067100 0.000000e+00 1018.0
97 TraesCS6B01G119100 chr3B 95.494 577 18 5 1791 2366 74730313 74729744 0.000000e+00 915.0
98 TraesCS6B01G119100 chr3B 87.789 303 34 2 6451 6753 785735642 785735343 1.090000e-92 351.0
99 TraesCS6B01G119100 chr3B 89.899 99 10 0 6762 6860 462315402 462315304 2.010000e-25 128.0
100 TraesCS6B01G119100 chr3A 83.441 773 123 5 1 772 54442122 54442890 0.000000e+00 713.0
101 TraesCS6B01G119100 chr4A 87.025 316 27 4 6451 6752 440265658 440265343 1.830000e-90 344.0
102 TraesCS6B01G119100 chr2D 86.068 323 30 5 6451 6759 633454565 633454244 3.970000e-87 333.0
103 TraesCS6B01G119100 chr2D 85.531 311 31 3 6451 6747 624849334 624849644 5.170000e-81 313.0
104 TraesCS6B01G119100 chr2D 85.209 311 32 7 6451 6747 138765804 138766114 2.400000e-79 307.0
105 TraesCS6B01G119100 chr2D 85.484 310 28 10 6451 6744 551459954 551460262 2.400000e-79 307.0
106 TraesCS6B01G119100 chr1D 86.495 311 28 8 6451 6747 267803008 267803318 5.130000e-86 329.0
107 TraesCS6B01G119100 chr1D 84.592 331 37 4 6451 6767 342846217 342845887 3.990000e-82 316.0
108 TraesCS6B01G119100 chr1D 85.531 311 31 4 6451 6747 465969149 465969459 5.170000e-81 313.0
109 TraesCS6B01G119100 chr1D 84.906 318 34 5 6451 6754 128471782 128471465 6.680000e-80 309.0
110 TraesCS6B01G119100 chr1D 84.520 323 35 9 6451 6759 408966221 408966542 8.640000e-79 305.0
111 TraesCS6B01G119100 chr1D 83.587 329 34 7 6451 6765 182029848 182029526 2.420000e-74 291.0
112 TraesCS6B01G119100 chr1D 82.315 311 39 14 6451 6746 160532172 160532481 8.830000e-64 255.0
113 TraesCS6B01G119100 chr7A 85.849 318 30 5 6451 6754 61876548 61876232 2.390000e-84 324.0
114 TraesCS6B01G119100 chr1A 84.969 326 38 5 6451 6765 335014144 335013819 3.090000e-83 320.0
115 TraesCS6B01G119100 chr1A 91.919 99 8 0 6762 6860 359872267 359872365 9.280000e-29 139.0
116 TraesCS6B01G119100 chr3D 85.266 319 32 5 6451 6755 76628138 76627821 1.440000e-81 315.0
117 TraesCS6B01G119100 chr3D 83.912 317 37 6 6451 6753 578666562 578666246 2.420000e-74 291.0
118 TraesCS6B01G119100 chr3D 83.601 311 37 6 6451 6747 45031753 45032063 5.240000e-71 279.0
119 TraesCS6B01G119100 chr3D 82.371 329 44 8 6451 6765 170543666 170543338 2.440000e-69 274.0
120 TraesCS6B01G119100 chrUn 84.639 319 35 6 6451 6755 338589856 338589538 8.640000e-79 305.0
121 TraesCS6B01G119100 chrUn 84.516 310 33 6 6451 6746 370969824 370970132 6.730000e-75 292.0
122 TraesCS6B01G119100 chrUn 84.516 310 33 6 6451 6746 458431040 458431348 6.730000e-75 292.0
123 TraesCS6B01G119100 chrUn 84.516 310 33 6 6451 6746 459991782 459992090 6.730000e-75 292.0
124 TraesCS6B01G119100 chrUn 83.923 311 36 4 6451 6747 101611422 101611112 1.130000e-72 285.0
125 TraesCS6B01G119100 chrUn 83.439 314 38 4 6451 6750 309560525 309560212 5.240000e-71 279.0
126 TraesCS6B01G119100 chrUn 83.439 314 38 4 6451 6750 309576597 309576284 5.240000e-71 279.0
127 TraesCS6B01G119100 chrUn 83.280 311 38 4 6451 6747 267049736 267049426 2.440000e-69 274.0
128 TraesCS6B01G119100 chrUn 83.280 311 38 4 6451 6747 282531874 282532184 2.440000e-69 274.0
129 TraesCS6B01G119100 chrUn 82.951 305 44 4 6451 6747 17491796 17492100 1.130000e-67 268.0
130 TraesCS6B01G119100 chrUn 82.951 305 44 4 6451 6747 339822623 339822927 1.130000e-67 268.0
131 TraesCS6B01G119100 chrUn 82.637 311 40 4 6451 6747 95829410 95829100 5.280000e-66 263.0
132 TraesCS6B01G119100 chrUn 82.258 310 39 9 6451 6746 96148793 96149100 3.180000e-63 254.0
133 TraesCS6B01G119100 chrUn 81.877 309 42 5 6451 6745 24022877 24023185 1.480000e-61 248.0
134 TraesCS6B01G119100 chrUn 80.303 330 51 5 6451 6766 47528686 47528357 3.200000e-58 237.0
135 TraesCS6B01G119100 chrUn 79.573 328 43 10 6455 6758 61919653 61919326 5.390000e-51 213.0
136 TraesCS6B01G119100 chrUn 79.268 328 44 10 6452 6755 197801083 197801410 2.510000e-49 207.0
137 TraesCS6B01G119100 chrUn 79.331 329 42 12 6455 6758 206539300 206538973 2.510000e-49 207.0
138 TraesCS6B01G119100 chr7D 83.282 323 40 8 6451 6759 464031990 464032312 1.130000e-72 285.0
139 TraesCS6B01G119100 chr7D 91.919 99 8 0 6762 6860 638567075 638567173 9.280000e-29 139.0


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 TraesCS6B01G119100 chr6B 113842481 113849340 6859 False 12669.000000 12669 100.000000 1 6860 1 chr6B.!!$F3 6859
1 TraesCS6B01G119100 chr6B 68722953 68724766 1813 False 2791.000000 2791 94.457000 1791 3605 1 chr6B.!!$F1 1814
2 TraesCS6B01G119100 chr6B 113656666 113657594 928 False 1057.000000 1057 87.204000 4843 5771 1 chr6B.!!$F2 928
3 TraesCS6B01G119100 chr6B 457429435 457430010 575 False 898.000000 898 94.810000 1791 2366 1 chr6B.!!$F5 575
4 TraesCS6B01G119100 chr6B 696244759 696245335 576 False 885.000000 885 94.359000 1788 2366 1 chr6B.!!$F6 578
5 TraesCS6B01G119100 chr6B 113780957 113784990 4033 False 716.750000 1834 87.583250 984 6451 4 chr6B.!!$F7 5467
6 TraesCS6B01G119100 chr6B 114018241 114018984 743 False 619.000000 619 81.830000 3766 4561 1 chr6B.!!$F4 795
7 TraesCS6B01G119100 chr6B 114026232 114028373 2141 False 225.500000 351 88.929500 4583 6451 2 chr6B.!!$F8 1868
8 TraesCS6B01G119100 chr6D 45202314 45211609 9295 False 1087.625000 4846 91.212125 984 6860 8 chr6D.!!$F7 5876
9 TraesCS6B01G119100 chr6D 44736933 44737859 926 False 992.000000 992 85.991000 4843 5770 1 chr6D.!!$F1 927
10 TraesCS6B01G119100 chr6D 44934381 44935307 926 False 953.000000 953 85.237000 4843 5770 1 chr6D.!!$F3 927
11 TraesCS6B01G119100 chr6D 44864049 44864968 919 False 931.000000 931 84.946000 4843 5770 1 chr6D.!!$F2 927
12 TraesCS6B01G119100 chr6D 44502859 44507630 4771 False 572.000000 1016 88.218500 992 5770 2 chr6D.!!$F6 4778
13 TraesCS6B01G119100 chr6D 80288957 80292065 3108 False 569.500000 1011 88.554000 992 5734 2 chr6D.!!$F9 4742
14 TraesCS6B01G119100 chr6D 45478087 45482150 4063 False 483.383333 1003 92.648500 991 6441 6 chr6D.!!$F8 5450
15 TraesCS6B01G119100 chr6A 59783296 59788017 4721 False 1304.000000 4202 94.287750 984 6451 4 chr6A.!!$F5 5467
16 TraesCS6B01G119100 chr6A 59676918 59677845 927 False 1016.000000 1016 86.422000 4843 5770 1 chr6A.!!$F1 927
17 TraesCS6B01G119100 chr6A 59708770 59711102 2332 False 889.333333 1592 88.455667 4160 6451 3 chr6A.!!$F4 2291
18 TraesCS6B01G119100 chr6A 59342798 59346236 3438 False 582.500000 1031 88.865500 992 5770 2 chr6A.!!$F3 4778
19 TraesCS6B01G119100 chr6A 59808223 59810530 2307 False 321.750000 664 92.195000 991 4832 4 chr6A.!!$F6 3841
20 TraesCS6B01G119100 chr2B 172680090 172681903 1813 False 2887.000000 2887 95.390000 1788 3604 1 chr2B.!!$F1 1816
21 TraesCS6B01G119100 chr2B 626645163 626646966 1803 True 2865.000000 2865 95.225000 1786 3605 1 chr2B.!!$R3 1819
22 TraesCS6B01G119100 chr2B 542255296 542255975 679 False 1007.000000 1007 93.382000 1 680 1 chr2B.!!$F2 679
23 TraesCS6B01G119100 chr2B 579800550 579801318 768 True 785.000000 785 85.123000 1 772 1 chr2B.!!$R2 771
24 TraesCS6B01G119100 chr1B 62248761 62250587 1826 True 2885.000000 2885 95.298000 1791 3604 1 chr1B.!!$R1 1813
25 TraesCS6B01G119100 chr1B 395228357 395230196 1839 False 2715.000000 2715 93.510000 1785 3605 1 chr1B.!!$F1 1820
26 TraesCS6B01G119100 chr7B 743398877 743400631 1754 True 2874.000000 2874 96.254000 1791 3544 1 chr7B.!!$R3 1753
27 TraesCS6B01G119100 chr7B 108555775 108557576 1801 True 2857.000000 2857 95.225000 1791 3605 1 chr7B.!!$R1 1814
28 TraesCS6B01G119100 chr7B 474279275 474281103 1828 True 2676.000000 2676 93.236000 1785 3604 1 chr7B.!!$R2 1819
29 TraesCS6B01G119100 chr5B 590531412 590533241 1829 True 2667.000000 2667 93.141000 1791 3604 1 chr5B.!!$R6 1813
30 TraesCS6B01G119100 chr5B 466951457 466952158 701 True 1107.000000 1107 95.157000 71 771 1 chr5B.!!$R2 700
31 TraesCS6B01G119100 chr5B 555206479 555207147 668 True 987.000000 987 93.274000 1 669 1 chr5B.!!$R5 668
32 TraesCS6B01G119100 chr5A 378276604 378278421 1817 True 2584.000000 2584 92.462000 1791 3604 1 chr5A.!!$R1 1813
33 TraesCS6B01G119100 chr5D 10497630 10498400 770 True 1181.000000 1181 94.293000 1 771 1 chr5D.!!$R1 770
34 TraesCS6B01G119100 chr4D 22553661 22554425 764 True 1142.000000 1142 93.515000 1 771 1 chr4D.!!$R2 770
35 TraesCS6B01G119100 chr2A 84157253 84158023 770 True 1136.000000 1136 93.256000 1 771 1 chr2A.!!$R1 770
36 TraesCS6B01G119100 chr4B 52413506 52414275 769 True 1112.000000 1112 92.737000 3 772 1 chr4B.!!$R1 769
37 TraesCS6B01G119100 chr3B 817067100 817067901 801 True 1018.000000 1018 89.766000 1795 2593 1 chr3B.!!$R4 798
38 TraesCS6B01G119100 chr3B 74729744 74730313 569 True 915.000000 915 95.494000 1791 2366 1 chr3B.!!$R1 575
39 TraesCS6B01G119100 chr3A 54442122 54442890 768 False 713.000000 713 83.441000 1 772 1 chr3A.!!$F1 771

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
921 923 0.247695 GCGCATACAAAAGACCTCGC 60.248 55.0 0.30 0.00 34.61 5.03 F
1706 5993 0.177604 ATACTGCACAGAGCTCCAGC 59.822 55.0 10.93 12.71 45.94 4.85 F
2258 8764 0.246635 GCTGACGCTCCTTCACCTTA 59.753 55.0 0.00 0.00 0.00 2.69 F
3315 10054 0.040058 ATCAATGGCAAGGCTGACCA 59.960 50.0 10.84 10.84 39.06 4.02 F
3608 10352 0.323725 GGCTGGAGATGCCCTTTTGA 60.324 55.0 0.00 0.00 44.32 2.69 F
3789 10537 0.390866 CGGCTCTCACAATGCTGTCT 60.391 55.0 0.00 0.00 31.64 3.41 F
4770 11569 0.763652 ATGGGATACAGGCAGCTGAG 59.236 55.0 20.43 8.88 39.74 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 8749 0.831307 GGGATAAGGTGAAGGAGCGT 59.169 55.000 0.00 0.00 0.00 5.07 R
3286 10025 0.617935 TGCCATTGATTCCTCACGGA 59.382 50.000 0.00 0.00 37.60 4.69 R
3789 10537 0.620556 GGGCTGATCCAAGACCAAGA 59.379 55.000 0.00 0.00 45.75 3.02 R
4581 11373 1.885887 GGTTGCACCAGAACAGCATAA 59.114 47.619 0.00 0.00 38.42 1.90 R
5366 12488 1.482182 CATGACTCGATTCCCACTCCA 59.518 52.381 0.00 0.00 0.00 3.86 R
5534 12658 1.531264 CCGTAACGTCAGATCTGTCCG 60.531 57.143 25.33 25.33 34.23 4.79 R
6125 13447 0.249120 TGGGTACTGCAATCGACTGG 59.751 55.000 0.00 0.00 0.00 4.00 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
81 82 5.219343 TGCAGAATCGATCAATATCCACT 57.781 39.130 0.00 0.00 0.00 4.00
211 212 0.764890 CCCCTTGTGTCACTCCTCAA 59.235 55.000 4.27 0.00 0.00 3.02
242 243 1.545841 GGTTCAAAACCCTAGCCCAG 58.454 55.000 0.00 0.00 46.12 4.45
480 481 6.741992 TCGTCTGAATATGCAACAAATTCT 57.258 33.333 12.67 0.00 32.12 2.40
772 774 2.344025 CTCCTAGTTTTTCGGGGAACG 58.656 52.381 0.00 0.00 46.11 3.95
773 775 0.800631 CCTAGTTTTTCGGGGAACGC 59.199 55.000 0.00 0.00 43.86 4.84
774 776 0.800631 CTAGTTTTTCGGGGAACGCC 59.199 55.000 0.00 0.00 43.86 5.68
775 777 0.950071 TAGTTTTTCGGGGAACGCCG 60.950 55.000 21.17 21.17 43.86 6.46
776 778 3.662153 TTTTTCGGGGAACGCCGC 61.662 61.111 22.12 4.26 43.86 6.53
777 779 4.931633 TTTTCGGGGAACGCCGCA 62.932 61.111 22.12 11.48 46.90 5.69
778 780 4.931633 TTTCGGGGAACGCCGCAA 62.932 61.111 22.12 16.39 46.90 4.85
783 785 3.723348 GGGAACGCCGCAACACTC 61.723 66.667 0.00 0.00 33.83 3.51
785 787 3.335534 GAACGCCGCAACACTCGT 61.336 61.111 0.00 0.00 36.67 4.18
786 788 3.277742 GAACGCCGCAACACTCGTC 62.278 63.158 0.00 0.00 33.72 4.20
788 790 4.059459 CGCCGCAACACTCGTCAC 62.059 66.667 0.00 0.00 0.00 3.67
789 791 2.964925 GCCGCAACACTCGTCACA 60.965 61.111 0.00 0.00 0.00 3.58
790 792 2.317609 GCCGCAACACTCGTCACAT 61.318 57.895 0.00 0.00 0.00 3.21
793 795 1.070821 CGCAACACTCGTCACATGAT 58.929 50.000 0.00 0.00 0.00 2.45
794 796 1.460743 CGCAACACTCGTCACATGATT 59.539 47.619 0.00 0.00 0.00 2.57
795 797 2.472886 CGCAACACTCGTCACATGATTC 60.473 50.000 0.00 0.00 0.00 2.52
796 798 2.738846 GCAACACTCGTCACATGATTCT 59.261 45.455 0.00 0.00 0.00 2.40
797 799 3.187227 GCAACACTCGTCACATGATTCTT 59.813 43.478 0.00 0.00 0.00 2.52
798 800 4.705492 CAACACTCGTCACATGATTCTTG 58.295 43.478 0.00 0.00 0.00 3.02
799 801 2.738846 ACACTCGTCACATGATTCTTGC 59.261 45.455 0.00 0.00 0.00 4.01
801 803 1.325640 CTCGTCACATGATTCTTGCGG 59.674 52.381 0.00 0.00 0.00 5.69
802 804 0.374758 CGTCACATGATTCTTGCGGG 59.625 55.000 0.00 0.00 0.00 6.13
803 805 1.737838 GTCACATGATTCTTGCGGGA 58.262 50.000 0.00 0.00 0.00 5.14
804 806 2.292267 GTCACATGATTCTTGCGGGAT 58.708 47.619 0.00 0.00 0.00 3.85
805 807 2.289002 GTCACATGATTCTTGCGGGATC 59.711 50.000 0.00 0.00 0.00 3.36
806 808 1.605710 CACATGATTCTTGCGGGATCC 59.394 52.381 1.92 1.92 0.00 3.36
808 810 1.878088 CATGATTCTTGCGGGATCCTG 59.122 52.381 16.98 16.98 0.00 3.86
809 811 1.203237 TGATTCTTGCGGGATCCTGA 58.797 50.000 25.54 6.69 0.00 3.86
811 813 2.173356 TGATTCTTGCGGGATCCTGAAT 59.827 45.455 25.54 14.35 0.00 2.57
815 817 3.038280 TCTTGCGGGATCCTGAATTAGA 58.962 45.455 25.54 11.80 0.00 2.10
816 818 2.910688 TGCGGGATCCTGAATTAGAC 57.089 50.000 25.54 4.95 0.00 2.59
817 819 1.416401 TGCGGGATCCTGAATTAGACC 59.584 52.381 25.54 4.18 0.00 3.85
818 820 1.605712 GCGGGATCCTGAATTAGACCG 60.606 57.143 25.54 9.94 42.68 4.79
820 822 2.102588 CGGGATCCTGAATTAGACCGTT 59.897 50.000 16.28 0.00 35.67 4.44
821 823 3.467803 GGGATCCTGAATTAGACCGTTG 58.532 50.000 12.58 0.00 0.00 4.10
824 826 5.011738 GGGATCCTGAATTAGACCGTTGATA 59.988 44.000 12.58 0.00 0.00 2.15
825 827 6.295916 GGGATCCTGAATTAGACCGTTGATAT 60.296 42.308 12.58 0.00 0.00 1.63
826 828 7.162082 GGATCCTGAATTAGACCGTTGATATT 58.838 38.462 3.84 0.00 0.00 1.28
827 829 7.332182 GGATCCTGAATTAGACCGTTGATATTC 59.668 40.741 3.84 0.00 0.00 1.75
828 830 7.361457 TCCTGAATTAGACCGTTGATATTCT 57.639 36.000 0.00 0.00 0.00 2.40
829 831 7.210174 TCCTGAATTAGACCGTTGATATTCTG 58.790 38.462 0.00 0.00 0.00 3.02
831 833 7.495934 CCTGAATTAGACCGTTGATATTCTGTT 59.504 37.037 0.00 0.00 0.00 3.16
832 834 8.196802 TGAATTAGACCGTTGATATTCTGTTG 57.803 34.615 0.00 0.00 0.00 3.33
835 837 8.594881 ATTAGACCGTTGATATTCTGTTGATC 57.405 34.615 0.00 0.00 0.00 2.92
838 840 6.323996 AGACCGTTGATATTCTGTTGATCCTA 59.676 38.462 0.00 0.00 0.00 2.94
839 841 6.884832 ACCGTTGATATTCTGTTGATCCTAA 58.115 36.000 0.00 0.00 0.00 2.69
841 843 7.827236 ACCGTTGATATTCTGTTGATCCTAAAA 59.173 33.333 0.00 0.00 0.00 1.52
842 844 8.338259 CCGTTGATATTCTGTTGATCCTAAAAG 58.662 37.037 0.00 0.00 0.00 2.27
843 845 9.098355 CGTTGATATTCTGTTGATCCTAAAAGA 57.902 33.333 0.00 0.00 0.00 2.52
852 854 9.817809 TCTGTTGATCCTAAAAGATACATGTAC 57.182 33.333 7.96 2.64 0.00 2.90
853 855 9.823647 CTGTTGATCCTAAAAGATACATGTACT 57.176 33.333 7.96 5.01 0.00 2.73
854 856 9.817809 TGTTGATCCTAAAAGATACATGTACTC 57.182 33.333 7.96 7.37 0.00 2.59
855 857 9.262358 GTTGATCCTAAAAGATACATGTACTCC 57.738 37.037 7.96 0.73 0.00 3.85
856 858 7.963532 TGATCCTAAAAGATACATGTACTCCC 58.036 38.462 7.96 0.00 0.00 4.30
857 859 6.742559 TCCTAAAAGATACATGTACTCCCC 57.257 41.667 7.96 0.00 0.00 4.81
858 860 5.605488 TCCTAAAAGATACATGTACTCCCCC 59.395 44.000 7.96 0.00 0.00 5.40
861 863 7.291651 CCTAAAAGATACATGTACTCCCCCTTA 59.708 40.741 7.96 0.13 0.00 2.69
862 864 6.749036 AAAGATACATGTACTCCCCCTTAG 57.251 41.667 7.96 0.00 0.00 2.18
863 865 5.681494 AGATACATGTACTCCCCCTTAGA 57.319 43.478 7.96 0.00 0.00 2.10
867 869 8.410623 AGATACATGTACTCCCCCTTAGATTAT 58.589 37.037 7.96 0.00 0.00 1.28
868 870 8.990693 ATACATGTACTCCCCCTTAGATTATT 57.009 34.615 7.96 0.00 0.00 1.40
869 871 7.707467 ACATGTACTCCCCCTTAGATTATTT 57.293 36.000 0.00 0.00 0.00 1.40
871 873 8.566109 ACATGTACTCCCCCTTAGATTATTTTT 58.434 33.333 0.00 0.00 0.00 1.94
893 895 8.864069 TTTTTAACATCAACACAAACGATCAT 57.136 26.923 0.00 0.00 0.00 2.45
894 896 9.952188 TTTTTAACATCAACACAAACGATCATA 57.048 25.926 0.00 0.00 0.00 2.15
903 905 8.856247 TCAACACAAACGATCATATATATACGC 58.144 33.333 12.68 0.00 0.00 4.42
904 906 7.432543 ACACAAACGATCATATATATACGCG 57.567 36.000 3.53 3.53 0.00 6.01
905 907 6.020916 ACACAAACGATCATATATATACGCGC 60.021 38.462 5.73 0.00 0.00 6.86
906 908 6.020995 CACAAACGATCATATATATACGCGCA 60.021 38.462 5.73 0.00 0.00 6.09
908 910 7.858879 ACAAACGATCATATATATACGCGCATA 59.141 33.333 5.73 2.88 0.00 3.14
910 912 6.894828 ACGATCATATATATACGCGCATACA 58.105 36.000 5.73 0.00 0.00 2.29
911 913 7.357303 ACGATCATATATATACGCGCATACAA 58.643 34.615 5.73 0.00 0.00 2.41
912 914 7.858879 ACGATCATATATATACGCGCATACAAA 59.141 33.333 5.73 0.00 0.00 2.83
913 915 8.687301 CGATCATATATATACGCGCATACAAAA 58.313 33.333 5.73 0.00 0.00 2.44
914 916 9.995379 GATCATATATATACGCGCATACAAAAG 57.005 33.333 5.73 0.00 0.00 2.27
916 918 9.016623 TCATATATATACGCGCATACAAAAGAC 57.983 33.333 5.73 0.00 0.00 3.01
917 919 4.985044 ATATACGCGCATACAAAAGACC 57.015 40.909 5.73 0.00 0.00 3.85
918 920 2.373540 TACGCGCATACAAAAGACCT 57.626 45.000 5.73 0.00 0.00 3.85
919 921 1.076332 ACGCGCATACAAAAGACCTC 58.924 50.000 5.73 0.00 0.00 3.85
921 923 0.247695 GCGCATACAAAAGACCTCGC 60.248 55.000 0.30 0.00 34.61 5.03
923 925 1.665679 CGCATACAAAAGACCTCGCAT 59.334 47.619 0.00 0.00 0.00 4.73
924 926 2.537529 CGCATACAAAAGACCTCGCATG 60.538 50.000 0.00 0.00 0.00 4.06
926 928 3.126858 GCATACAAAAGACCTCGCATGAA 59.873 43.478 0.00 0.00 0.00 2.57
928 930 5.677091 GCATACAAAAGACCTCGCATGAAAT 60.677 40.000 0.00 0.00 0.00 2.17
929 931 4.425577 ACAAAAGACCTCGCATGAAATC 57.574 40.909 0.00 0.00 0.00 2.17
930 932 3.120199 ACAAAAGACCTCGCATGAAATCG 60.120 43.478 0.00 0.00 0.00 3.34
931 933 2.386661 AAGACCTCGCATGAAATCGT 57.613 45.000 0.00 0.00 0.00 3.73
932 934 2.386661 AGACCTCGCATGAAATCGTT 57.613 45.000 0.00 0.00 0.00 3.85
933 935 2.699954 AGACCTCGCATGAAATCGTTT 58.300 42.857 0.00 0.00 0.00 3.60
934 936 3.074412 AGACCTCGCATGAAATCGTTTT 58.926 40.909 0.00 0.00 0.00 2.43
935 937 3.502211 AGACCTCGCATGAAATCGTTTTT 59.498 39.130 0.00 0.00 0.00 1.94
936 938 3.821841 ACCTCGCATGAAATCGTTTTTC 58.178 40.909 0.00 6.64 0.00 2.29
937 939 3.502211 ACCTCGCATGAAATCGTTTTTCT 59.498 39.130 0.00 0.30 0.00 2.52
938 940 4.023193 ACCTCGCATGAAATCGTTTTTCTT 60.023 37.500 0.00 5.94 0.00 2.52
939 941 4.917415 CCTCGCATGAAATCGTTTTTCTTT 59.083 37.500 0.00 1.71 0.00 2.52
940 942 5.402270 CCTCGCATGAAATCGTTTTTCTTTT 59.598 36.000 0.00 0.00 0.00 2.27
958 960 1.938625 TTTTCTTGTTGCAGCCAAGC 58.061 45.000 18.45 0.00 39.30 4.01
961 963 3.230522 CTTGTTGCAGCCAAGCCCC 62.231 63.158 13.27 0.00 33.55 5.80
981 983 3.007506 CCCCCAATAAACCTCAACAAACC 59.992 47.826 0.00 0.00 0.00 3.27
982 984 3.007506 CCCCAATAAACCTCAACAAACCC 59.992 47.826 0.00 0.00 0.00 4.11
983 985 3.007506 CCCAATAAACCTCAACAAACCCC 59.992 47.826 0.00 0.00 0.00 4.95
984 986 3.643792 CCAATAAACCTCAACAAACCCCA 59.356 43.478 0.00 0.00 0.00 4.96
987 989 0.759060 AACCTCAACAAACCCCAGCC 60.759 55.000 0.00 0.00 0.00 4.85
1113 4440 3.461773 CAGACGGCCGTCCCTGAT 61.462 66.667 45.66 29.56 45.59 2.90
1119 4446 4.570663 GCCGTCCCTGATCGTCGG 62.571 72.222 0.00 0.00 43.37 4.79
1120 4447 4.570663 CCGTCCCTGATCGTCGGC 62.571 72.222 0.00 0.00 35.01 5.54
1126 4453 3.514417 CTGATCGTCGGCAGGAGA 58.486 61.111 7.79 0.00 0.00 3.71
1127 4454 1.809869 CTGATCGTCGGCAGGAGAA 59.190 57.895 7.79 0.00 0.00 2.87
1128 4455 0.387202 CTGATCGTCGGCAGGAGAAT 59.613 55.000 7.79 0.00 0.00 2.40
1129 4456 0.385751 TGATCGTCGGCAGGAGAATC 59.614 55.000 0.00 0.00 0.00 2.52
1130 4457 0.671251 GATCGTCGGCAGGAGAATCT 59.329 55.000 0.00 0.00 33.73 2.40
1131 4458 0.671251 ATCGTCGGCAGGAGAATCTC 59.329 55.000 0.71 0.71 33.73 2.75
1132 4459 1.298713 CGTCGGCAGGAGAATCTCG 60.299 63.158 3.96 0.00 33.73 4.04
1133 4460 1.715862 CGTCGGCAGGAGAATCTCGA 61.716 60.000 3.96 0.00 33.73 4.04
1134 4461 0.671251 GTCGGCAGGAGAATCTCGAT 59.329 55.000 3.96 0.00 33.73 3.59
1135 4462 0.670706 TCGGCAGGAGAATCTCGATG 59.329 55.000 3.96 6.93 33.73 3.84
1136 4463 0.943359 CGGCAGGAGAATCTCGATGC 60.943 60.000 22.87 22.87 40.63 3.91
1137 4464 0.392336 GGCAGGAGAATCTCGATGCT 59.608 55.000 26.90 9.26 40.92 3.79
1138 4465 1.500108 GCAGGAGAATCTCGATGCTG 58.500 55.000 23.36 16.66 39.30 4.41
1139 4466 1.202510 GCAGGAGAATCTCGATGCTGT 60.203 52.381 23.36 0.00 39.30 4.40
1140 4467 2.035193 GCAGGAGAATCTCGATGCTGTA 59.965 50.000 23.36 0.00 39.30 2.74
1141 4468 3.637432 CAGGAGAATCTCGATGCTGTAC 58.363 50.000 3.96 0.00 33.73 2.90
1142 4469 3.067320 CAGGAGAATCTCGATGCTGTACA 59.933 47.826 3.96 0.00 33.73 2.90
1143 4470 3.317711 AGGAGAATCTCGATGCTGTACAG 59.682 47.826 18.93 18.93 33.73 2.74
1144 4471 3.551863 GGAGAATCTCGATGCTGTACAGG 60.552 52.174 23.95 7.71 33.73 4.00
1145 4472 3.291584 AGAATCTCGATGCTGTACAGGA 58.708 45.455 23.95 22.09 0.00 3.86
1146 4473 3.317711 AGAATCTCGATGCTGTACAGGAG 59.682 47.826 23.95 19.69 35.26 3.69
1147 4474 2.420058 TCTCGATGCTGTACAGGAGA 57.580 50.000 23.95 21.43 38.67 3.71
1148 4475 2.723273 TCTCGATGCTGTACAGGAGAA 58.277 47.619 23.95 9.98 38.28 2.87
1149 4476 3.291584 TCTCGATGCTGTACAGGAGAAT 58.708 45.455 23.95 6.85 38.28 2.40
1150 4477 3.316588 TCTCGATGCTGTACAGGAGAATC 59.683 47.826 23.95 14.57 38.28 2.52
1151 4478 3.291584 TCGATGCTGTACAGGAGAATCT 58.708 45.455 23.95 6.06 33.73 2.40
1152 4479 3.316588 TCGATGCTGTACAGGAGAATCTC 59.683 47.826 23.95 13.88 33.73 2.75
1153 4480 3.637432 GATGCTGTACAGGAGAATCTCG 58.363 50.000 23.95 0.00 33.73 4.04
1154 4481 2.723273 TGCTGTACAGGAGAATCTCGA 58.277 47.619 23.95 0.00 33.73 4.04
1155 4482 3.291584 TGCTGTACAGGAGAATCTCGAT 58.708 45.455 23.95 0.00 33.73 3.59
1156 4483 4.461198 TGCTGTACAGGAGAATCTCGATA 58.539 43.478 23.95 0.00 33.73 2.92
1157 4484 4.276183 TGCTGTACAGGAGAATCTCGATAC 59.724 45.833 23.95 7.12 33.73 2.24
1158 4485 4.276183 GCTGTACAGGAGAATCTCGATACA 59.724 45.833 23.95 14.78 33.73 2.29
1159 4486 5.561919 GCTGTACAGGAGAATCTCGATACAG 60.562 48.000 26.15 26.15 40.17 2.74
1160 4487 4.822350 TGTACAGGAGAATCTCGATACAGG 59.178 45.833 12.76 0.00 33.73 4.00
1161 4488 4.171878 ACAGGAGAATCTCGATACAGGA 57.828 45.455 3.96 0.00 33.73 3.86
1162 4489 4.141287 ACAGGAGAATCTCGATACAGGAG 58.859 47.826 3.96 0.00 33.73 3.69
1163 4490 4.141367 ACAGGAGAATCTCGATACAGGAGA 60.141 45.833 3.96 0.00 44.08 3.71
1164 4491 4.824537 CAGGAGAATCTCGATACAGGAGAA 59.175 45.833 3.96 0.00 43.26 2.87
1165 4492 5.476599 CAGGAGAATCTCGATACAGGAGAAT 59.523 44.000 3.96 0.00 43.26 2.40
1166 4493 5.710099 AGGAGAATCTCGATACAGGAGAATC 59.290 44.000 3.96 0.00 43.26 2.52
1167 4494 5.391523 GGAGAATCTCGATACAGGAGAATCG 60.392 48.000 3.96 0.00 42.55 3.34
1207 4534 2.811431 CGCTCTACAGGAGAATCTCGAT 59.189 50.000 3.96 0.00 44.45 3.59
1208 4535 3.997681 CGCTCTACAGGAGAATCTCGATA 59.002 47.826 3.96 0.00 44.45 2.92
1435 4772 7.435192 CGCCTTCATATATATTGCTGTTCGATA 59.565 37.037 0.00 0.00 0.00 2.92
1461 4806 6.015504 CACATTTGACATACTAGCGTGTTTC 58.984 40.000 2.53 0.00 0.00 2.78
1489 4846 1.712018 GCAGCGGGTTCGGGATAAAC 61.712 60.000 0.00 0.00 36.79 2.01
1508 4918 3.557228 ACCTCCATTCTGCATTCTCTC 57.443 47.619 0.00 0.00 0.00 3.20
1510 4920 3.134442 ACCTCCATTCTGCATTCTCTCTC 59.866 47.826 0.00 0.00 0.00 3.20
1580 5061 7.379797 GCAAACTGAATGTTCCTTTTAAGACTC 59.620 37.037 0.00 0.00 38.03 3.36
1684 5971 4.944619 TCAGAGGTCAGCATTATAGGTG 57.055 45.455 0.00 0.00 38.31 4.00
1686 5973 2.370189 AGAGGTCAGCATTATAGGTGCC 59.630 50.000 8.16 0.00 43.50 5.01
1688 5975 2.713167 AGGTCAGCATTATAGGTGCCAT 59.287 45.455 8.16 0.00 43.50 4.40
1689 5976 3.909995 AGGTCAGCATTATAGGTGCCATA 59.090 43.478 8.16 0.00 43.50 2.74
1690 5977 4.003648 GGTCAGCATTATAGGTGCCATAC 58.996 47.826 8.16 5.22 43.50 2.39
1691 5978 4.263068 GGTCAGCATTATAGGTGCCATACT 60.263 45.833 8.16 0.00 43.50 2.12
1692 5979 4.692625 GTCAGCATTATAGGTGCCATACTG 59.307 45.833 8.16 0.00 43.50 2.74
1693 5980 3.438087 CAGCATTATAGGTGCCATACTGC 59.562 47.826 8.16 11.31 43.50 4.40
1694 5981 3.072915 AGCATTATAGGTGCCATACTGCA 59.927 43.478 16.68 0.00 43.50 4.41
1700 5987 4.623814 TGCCATACTGCACAGAGC 57.376 55.556 4.31 2.67 45.96 4.09
1704 5991 0.538584 CCATACTGCACAGAGCTCCA 59.461 55.000 10.93 0.00 45.94 3.86
1705 5992 1.472904 CCATACTGCACAGAGCTCCAG 60.473 57.143 10.93 12.86 45.94 3.86
1706 5993 0.177604 ATACTGCACAGAGCTCCAGC 59.822 55.000 10.93 12.71 45.94 4.85
1737 7503 1.821136 CTGAAGGGCAATTGGAGAACC 59.179 52.381 7.72 0.00 0.00 3.62
1779 7545 2.814280 GTTCTCCACGAACTCCAGAA 57.186 50.000 0.00 0.00 46.74 3.02
1780 7546 2.678324 GTTCTCCACGAACTCCAGAAG 58.322 52.381 0.00 0.00 46.74 2.85
1781 7547 1.257743 TCTCCACGAACTCCAGAAGG 58.742 55.000 0.00 0.00 0.00 3.46
1782 7548 0.247736 CTCCACGAACTCCAGAAGGG 59.752 60.000 0.00 0.00 34.83 3.95
1783 7549 1.192146 TCCACGAACTCCAGAAGGGG 61.192 60.000 0.00 0.00 43.03 4.79
2180 8673 1.138883 GTCGCTGTCGCATAGGACA 59.861 57.895 0.00 0.00 44.25 4.02
2258 8764 0.246635 GCTGACGCTCCTTCACCTTA 59.753 55.000 0.00 0.00 0.00 2.69
3315 10054 0.040058 ATCAATGGCAAGGCTGACCA 59.960 50.000 10.84 10.84 39.06 4.02
3606 10350 4.772678 GGCTGGAGATGCCCTTTT 57.227 55.556 0.00 0.00 44.32 2.27
3607 10351 2.196319 GGCTGGAGATGCCCTTTTG 58.804 57.895 0.00 0.00 44.32 2.44
3608 10352 0.323725 GGCTGGAGATGCCCTTTTGA 60.324 55.000 0.00 0.00 44.32 2.69
3609 10353 1.687368 GGCTGGAGATGCCCTTTTGAT 60.687 52.381 0.00 0.00 44.32 2.57
3612 10356 1.358787 TGGAGATGCCCTTTTGATGGT 59.641 47.619 0.00 0.00 34.97 3.55
3615 10359 3.217626 GAGATGCCCTTTTGATGGTAGG 58.782 50.000 0.00 0.00 0.00 3.18
3675 10419 1.908299 CAAGTGGCCTTGGGTTCCC 60.908 63.158 3.32 0.12 43.62 3.97
3789 10537 0.390866 CGGCTCTCACAATGCTGTCT 60.391 55.000 0.00 0.00 31.64 3.41
3868 10617 2.572290 GGGGACTGTAATCCATTTCCG 58.428 52.381 0.00 0.00 40.96 4.30
4045 10794 8.561738 TCAATTAGAAACTCAGTTATGAACCC 57.438 34.615 0.00 0.00 34.23 4.11
4283 11055 5.954296 ACAGTCTGAGATTTGAACAATGG 57.046 39.130 6.91 0.00 0.00 3.16
4500 11277 7.230747 TCACAATAGGAAATGAAGGTTCAAGA 58.769 34.615 0.00 0.00 41.13 3.02
4664 11463 7.466746 AATATCCAGCTGTGTTGTTTTGTAT 57.533 32.000 13.81 0.00 0.00 2.29
4721 11520 2.846206 AGTTGATACCTGGGCATCAAGA 59.154 45.455 20.05 4.31 40.77 3.02
4770 11569 0.763652 ATGGGATACAGGCAGCTGAG 59.236 55.000 20.43 8.88 39.74 3.35
4832 11637 7.533426 ACTTATTCATCTTTGCTTAACTGCTG 58.467 34.615 0.00 0.00 0.00 4.41
4834 11639 8.560355 TTATTCATCTTTGCTTAACTGCTGTA 57.440 30.769 0.00 0.00 0.00 2.74
4835 11640 5.862924 TCATCTTTGCTTAACTGCTGTAC 57.137 39.130 0.00 0.00 0.00 2.90
4836 11641 5.304778 TCATCTTTGCTTAACTGCTGTACA 58.695 37.500 0.00 0.00 0.00 2.90
4838 11643 5.418310 TCTTTGCTTAACTGCTGTACAAC 57.582 39.130 0.00 0.00 0.00 3.32
4840 11645 5.355630 TCTTTGCTTAACTGCTGTACAACAA 59.644 36.000 0.00 0.00 0.00 2.83
4841 11646 4.545823 TGCTTAACTGCTGTACAACAAC 57.454 40.909 0.00 0.00 0.00 3.32
4849 11684 2.872245 TGCTGTACAACAACTGAGAAGC 59.128 45.455 0.00 0.00 0.00 3.86
4952 12046 2.149973 ATCCCCTCCACATTTGAAGC 57.850 50.000 0.00 0.00 0.00 3.86
5213 12335 3.114606 TGTCCTGGCATTTCCTCATCTA 58.885 45.455 0.00 0.00 35.26 1.98
5301 12423 5.499139 TCAAGAAATGCTCGAACAAAAGT 57.501 34.783 0.00 0.00 0.00 2.66
5310 12432 7.667043 ATGCTCGAACAAAAGTTATCTTGTA 57.333 32.000 0.00 0.00 34.71 2.41
5327 12449 5.308014 TCTTGTAATGCTTGAAGCTCTGAA 58.692 37.500 18.94 0.00 42.97 3.02
5366 12488 4.581824 TGAGTCTTTGCAGCAAATCTTTCT 59.418 37.500 20.90 13.64 32.70 2.52
5387 12509 1.202580 GGAGTGGGAATCGAGTCATGG 60.203 57.143 15.56 0.00 0.00 3.66
5501 12623 2.224843 TGTCTCAGGGTCATTGCAATGT 60.225 45.455 32.67 15.61 37.65 2.71
5502 12624 3.008923 TGTCTCAGGGTCATTGCAATGTA 59.991 43.478 32.67 19.77 37.65 2.29
5534 12658 8.068380 GGTTTACATATTTGCCGAGTTCTATTC 58.932 37.037 0.00 0.00 0.00 1.75
5547 12671 5.508200 AGTTCTATTCGGACAGATCTGAC 57.492 43.478 29.27 22.20 40.10 3.51
5553 12677 1.395954 TCGGACAGATCTGACGTTACG 59.604 52.381 29.27 18.37 35.16 3.18
5917 13044 5.241728 AGGCCACTGTAGAATTTTTCTTCAC 59.758 40.000 5.01 0.00 41.14 3.18
5918 13045 5.461526 GCCACTGTAGAATTTTTCTTCACC 58.538 41.667 0.00 0.00 41.14 4.02
6003 13183 6.623549 CGGATTTCTGTACATGAATTGCAAGT 60.624 38.462 4.94 0.59 32.44 3.16
6044 13237 2.100989 GACCCCCTGACTACTGTGTAG 58.899 57.143 3.49 3.49 0.00 2.74
6046 13239 2.651334 ACCCCCTGACTACTGTGTAGTA 59.349 50.000 9.95 0.00 38.36 1.82
6072 13265 6.970043 CCATCTATCTAAGCTGCTAATACGAC 59.030 42.308 0.90 0.00 0.00 4.34
6139 13461 1.512926 GACAACCAGTCGATTGCAGT 58.487 50.000 1.73 0.35 37.53 4.40
6140 13462 2.683968 GACAACCAGTCGATTGCAGTA 58.316 47.619 1.73 0.00 37.53 2.74
6141 13463 2.412089 GACAACCAGTCGATTGCAGTAC 59.588 50.000 1.73 0.00 37.53 2.73
6143 13465 0.249398 ACCAGTCGATTGCAGTACCC 59.751 55.000 1.73 0.00 0.00 3.69
6144 13466 0.249120 CCAGTCGATTGCAGTACCCA 59.751 55.000 1.73 0.00 0.00 4.51
6145 13467 1.645034 CAGTCGATTGCAGTACCCAG 58.355 55.000 0.00 0.00 0.00 4.45
6147 13469 0.249398 GTCGATTGCAGTACCCAGGT 59.751 55.000 0.00 0.00 0.00 4.00
6148 13470 1.479323 GTCGATTGCAGTACCCAGGTA 59.521 52.381 0.00 0.00 0.00 3.08
6149 13471 2.102588 GTCGATTGCAGTACCCAGGTAT 59.897 50.000 0.00 0.00 32.82 2.73
6150 13472 2.769663 TCGATTGCAGTACCCAGGTATT 59.230 45.455 0.00 0.00 32.82 1.89
6151 13473 3.131396 CGATTGCAGTACCCAGGTATTC 58.869 50.000 0.00 0.00 32.82 1.75
6152 13474 3.181465 CGATTGCAGTACCCAGGTATTCT 60.181 47.826 0.00 0.00 32.82 2.40
6154 13476 4.650972 TTGCAGTACCCAGGTATTCTTT 57.349 40.909 0.00 0.00 32.82 2.52
6156 13478 3.585289 TGCAGTACCCAGGTATTCTTTGA 59.415 43.478 0.00 0.00 32.82 2.69
6157 13479 4.192317 GCAGTACCCAGGTATTCTTTGAG 58.808 47.826 0.00 0.00 32.82 3.02
6158 13480 4.770795 CAGTACCCAGGTATTCTTTGAGG 58.229 47.826 0.00 0.00 32.82 3.86
6159 13481 3.780850 AGTACCCAGGTATTCTTTGAGGG 59.219 47.826 0.00 0.00 40.66 4.30
6209 13531 0.948623 TGTTGCCGACCATTCGTGAG 60.949 55.000 0.00 0.00 44.28 3.51
6420 13938 9.790389 CTTAGATAATATAATCACGAGGTGGTC 57.210 37.037 0.00 0.00 33.87 4.02
6459 13977 0.181114 GTATCAGCACCTCATGGGCA 59.819 55.000 0.00 0.00 39.10 5.36
6515 14033 2.183555 GTTGGCGGCGTAGTAGCT 59.816 61.111 9.37 0.00 37.29 3.32
6525 14043 1.221021 GTAGTAGCTGGGGTGTGGC 59.779 63.158 0.00 0.00 0.00 5.01
6570 14088 4.097892 GCCGGGATGAAAACATGTTCTATT 59.902 41.667 12.39 2.26 0.00 1.73
6582 14100 2.963432 TGTTCTATTTTCGGACGGACC 58.037 47.619 0.00 0.00 0.00 4.46
6620 14152 0.107993 TCCCTTCGCTGCTCTCATTG 60.108 55.000 0.00 0.00 0.00 2.82
6624 14156 2.437180 CGCTGCTCTCATTGCCCA 60.437 61.111 0.00 0.00 0.00 5.36
6636 14168 1.094785 ATTGCCCATCGTGTTGCTAC 58.905 50.000 0.00 0.00 0.00 3.58
6647 14179 2.152016 GTGTTGCTACAGGGGAAACTC 58.848 52.381 0.00 0.00 34.24 3.01
6688 14220 4.849329 GGCGCTCCGGTGTCGTAG 62.849 72.222 7.64 2.32 33.95 3.51
6724 14256 1.455849 CCTTGGAGCCCACAGTTCA 59.544 57.895 0.00 0.00 30.78 3.18
6733 14265 2.011548 GCCCACAGTTCATCGTATGCA 61.012 52.381 0.00 0.00 0.00 3.96
6747 14279 3.382865 TCGTATGCAGCTTCATCTCTTCT 59.617 43.478 0.88 0.00 0.00 2.85
6750 14282 1.821136 TGCAGCTTCATCTCTTCTCGA 59.179 47.619 0.00 0.00 0.00 4.04
6759 14291 2.949451 TCTCTTCTCGATGGCTTGTC 57.051 50.000 0.00 0.00 0.00 3.18
6774 14306 2.421424 GCTTGTCCATGGCTTTGACTAG 59.579 50.000 6.96 7.22 35.75 2.57
6775 14307 3.869912 GCTTGTCCATGGCTTTGACTAGA 60.870 47.826 6.96 0.00 34.99 2.43
6817 14349 6.970613 GGGCATTTTTATAAGGACACTTAACG 59.029 38.462 0.00 0.00 42.14 3.18
6818 14350 6.970613 GGCATTTTTATAAGGACACTTAACGG 59.029 38.462 0.00 0.00 42.14 4.44
6823 14355 2.457366 AAGGACACTTAACGGCAGAG 57.543 50.000 0.00 0.00 34.49 3.35
6826 14358 0.391263 GACACTTAACGGCAGAGGGG 60.391 60.000 0.00 0.00 0.00 4.79
6833 14365 1.250840 AACGGCAGAGGGGCAAATTC 61.251 55.000 0.00 0.00 43.60 2.17
6837 14369 1.997928 GCAGAGGGGCAAATTCGAGC 61.998 60.000 0.00 0.00 0.00 5.03
6844 14376 1.553308 GGCAAATTCGAGCATGCTTC 58.447 50.000 23.61 13.83 38.79 3.86
6853 14385 2.866156 TCGAGCATGCTTCGAAATTAGG 59.134 45.455 28.09 9.21 32.68 2.69
6855 14387 2.291741 GAGCATGCTTCGAAATTAGGGG 59.708 50.000 23.61 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 2.046892 GAGGAAGCCTCTGCGCAA 60.047 61.111 13.05 1.37 46.41 4.85
242 243 5.125100 TGCAATTTGACAAACTCAGGATC 57.875 39.130 1.94 0.00 0.00 3.36
772 774 2.317609 ATGTGACGAGTGTTGCGGC 61.318 57.895 0.00 0.00 37.28 6.53
773 775 0.943835 TCATGTGACGAGTGTTGCGG 60.944 55.000 0.00 0.00 0.00 5.69
774 776 1.070821 ATCATGTGACGAGTGTTGCG 58.929 50.000 0.00 0.00 0.00 4.85
775 777 2.738846 AGAATCATGTGACGAGTGTTGC 59.261 45.455 0.00 0.00 0.00 4.17
776 778 4.705492 CAAGAATCATGTGACGAGTGTTG 58.295 43.478 0.00 0.00 0.00 3.33
777 779 3.187227 GCAAGAATCATGTGACGAGTGTT 59.813 43.478 0.00 0.00 0.00 3.32
778 780 2.738846 GCAAGAATCATGTGACGAGTGT 59.261 45.455 0.00 0.00 0.00 3.55
779 781 2.222663 CGCAAGAATCATGTGACGAGTG 60.223 50.000 0.00 0.00 43.02 3.51
780 782 1.995484 CGCAAGAATCATGTGACGAGT 59.005 47.619 0.00 0.00 43.02 4.18
782 784 1.358877 CCGCAAGAATCATGTGACGA 58.641 50.000 0.17 0.00 43.02 4.20
783 785 0.374758 CCCGCAAGAATCATGTGACG 59.625 55.000 0.17 0.00 43.02 4.35
785 787 2.564771 GATCCCGCAAGAATCATGTGA 58.435 47.619 0.17 0.00 43.02 3.58
786 788 1.605710 GGATCCCGCAAGAATCATGTG 59.394 52.381 0.00 0.00 43.02 3.21
788 790 1.878088 CAGGATCCCGCAAGAATCATG 59.122 52.381 8.55 0.00 43.02 3.07
789 791 1.770658 TCAGGATCCCGCAAGAATCAT 59.229 47.619 8.55 0.00 43.02 2.45
790 792 1.203237 TCAGGATCCCGCAAGAATCA 58.797 50.000 8.55 0.00 43.02 2.57
793 795 2.806945 AATTCAGGATCCCGCAAGAA 57.193 45.000 8.55 5.93 43.02 2.52
794 796 3.038280 TCTAATTCAGGATCCCGCAAGA 58.962 45.455 8.55 1.57 43.02 3.02
795 797 3.134458 GTCTAATTCAGGATCCCGCAAG 58.866 50.000 8.55 0.00 0.00 4.01
796 798 2.158813 GGTCTAATTCAGGATCCCGCAA 60.159 50.000 8.55 0.00 0.00 4.85
797 799 1.416401 GGTCTAATTCAGGATCCCGCA 59.584 52.381 8.55 0.00 0.00 5.69
798 800 1.605712 CGGTCTAATTCAGGATCCCGC 60.606 57.143 8.55 0.00 0.00 6.13
799 801 1.687123 ACGGTCTAATTCAGGATCCCG 59.313 52.381 8.55 0.00 0.00 5.14
801 803 4.402056 TCAACGGTCTAATTCAGGATCC 57.598 45.455 2.48 2.48 0.00 3.36
802 804 8.091449 AGAATATCAACGGTCTAATTCAGGATC 58.909 37.037 0.00 0.00 0.00 3.36
803 805 7.875041 CAGAATATCAACGGTCTAATTCAGGAT 59.125 37.037 0.00 0.00 0.00 3.24
804 806 7.147724 ACAGAATATCAACGGTCTAATTCAGGA 60.148 37.037 0.00 0.00 0.00 3.86
805 807 6.986817 ACAGAATATCAACGGTCTAATTCAGG 59.013 38.462 0.00 0.00 0.00 3.86
806 808 8.331022 CAACAGAATATCAACGGTCTAATTCAG 58.669 37.037 0.00 0.00 0.00 3.02
808 810 8.420374 TCAACAGAATATCAACGGTCTAATTC 57.580 34.615 0.00 0.00 0.00 2.17
809 811 8.964476 ATCAACAGAATATCAACGGTCTAATT 57.036 30.769 0.00 0.00 0.00 1.40
811 813 6.984474 GGATCAACAGAATATCAACGGTCTAA 59.016 38.462 0.00 0.00 0.00 2.10
815 817 5.359194 AGGATCAACAGAATATCAACGGT 57.641 39.130 0.00 0.00 0.00 4.83
816 818 7.786178 TTTAGGATCAACAGAATATCAACGG 57.214 36.000 0.00 0.00 0.00 4.44
817 819 9.098355 TCTTTTAGGATCAACAGAATATCAACG 57.902 33.333 0.00 0.00 0.00 4.10
824 826 9.911788 ACATGTATCTTTTAGGATCAACAGAAT 57.088 29.630 0.00 0.00 0.00 2.40
826 828 9.817809 GTACATGTATCTTTTAGGATCAACAGA 57.182 33.333 9.18 0.00 0.00 3.41
827 829 9.823647 AGTACATGTATCTTTTAGGATCAACAG 57.176 33.333 9.18 0.00 0.00 3.16
828 830 9.817809 GAGTACATGTATCTTTTAGGATCAACA 57.182 33.333 9.18 0.00 0.00 3.33
829 831 9.262358 GGAGTACATGTATCTTTTAGGATCAAC 57.738 37.037 9.18 0.00 0.00 3.18
831 833 7.016268 GGGGAGTACATGTATCTTTTAGGATCA 59.984 40.741 9.18 0.00 0.00 2.92
832 834 7.387643 GGGGAGTACATGTATCTTTTAGGATC 58.612 42.308 9.18 0.00 0.00 3.36
835 837 5.607171 AGGGGGAGTACATGTATCTTTTAGG 59.393 44.000 9.18 0.00 0.00 2.69
838 840 6.906901 TCTAAGGGGGAGTACATGTATCTTTT 59.093 38.462 9.18 1.37 0.00 2.27
839 841 6.449956 TCTAAGGGGGAGTACATGTATCTTT 58.550 40.000 9.18 3.09 0.00 2.52
841 843 5.681494 TCTAAGGGGGAGTACATGTATCT 57.319 43.478 9.18 8.14 0.00 1.98
842 844 6.936968 AATCTAAGGGGGAGTACATGTATC 57.063 41.667 9.18 7.65 0.00 2.24
843 845 8.990693 AATAATCTAAGGGGGAGTACATGTAT 57.009 34.615 9.18 0.00 0.00 2.29
845 847 7.707467 AAATAATCTAAGGGGGAGTACATGT 57.293 36.000 2.69 2.69 0.00 3.21
846 848 8.996651 AAAAATAATCTAAGGGGGAGTACATG 57.003 34.615 0.00 0.00 0.00 3.21
868 870 8.864069 ATGATCGTTTGTGTTGATGTTAAAAA 57.136 26.923 0.00 0.00 0.00 1.94
877 879 8.856247 GCGTATATATATGATCGTTTGTGTTGA 58.144 33.333 14.94 0.00 0.00 3.18
878 880 7.834591 CGCGTATATATATGATCGTTTGTGTTG 59.165 37.037 14.94 0.00 0.00 3.33
879 881 7.462331 GCGCGTATATATATGATCGTTTGTGTT 60.462 37.037 14.94 0.00 0.00 3.32
880 882 6.020916 GCGCGTATATATATGATCGTTTGTGT 60.021 38.462 14.94 0.00 0.00 3.72
881 883 6.020995 TGCGCGTATATATATGATCGTTTGTG 60.021 38.462 14.94 0.00 0.00 3.33
883 885 6.490877 TGCGCGTATATATATGATCGTTTG 57.509 37.500 14.94 2.16 0.00 2.93
885 887 7.357303 TGTATGCGCGTATATATATGATCGTT 58.643 34.615 19.79 5.81 0.00 3.85
886 888 6.894828 TGTATGCGCGTATATATATGATCGT 58.105 36.000 19.79 9.08 0.00 3.73
888 890 9.995379 CTTTTGTATGCGCGTATATATATGATC 57.005 33.333 19.79 5.34 0.00 2.92
889 891 9.744468 TCTTTTGTATGCGCGTATATATATGAT 57.256 29.630 19.79 3.68 0.00 2.45
890 892 9.016623 GTCTTTTGTATGCGCGTATATATATGA 57.983 33.333 19.79 15.38 0.00 2.15
891 893 8.266682 GGTCTTTTGTATGCGCGTATATATATG 58.733 37.037 19.79 13.60 0.00 1.78
893 895 7.541162 AGGTCTTTTGTATGCGCGTATATATA 58.459 34.615 19.79 9.81 0.00 0.86
894 896 6.395629 AGGTCTTTTGTATGCGCGTATATAT 58.604 36.000 19.79 0.00 0.00 0.86
895 897 5.775686 AGGTCTTTTGTATGCGCGTATATA 58.224 37.500 19.79 14.59 0.00 0.86
897 899 4.046462 GAGGTCTTTTGTATGCGCGTATA 58.954 43.478 13.13 13.13 0.00 1.47
900 902 1.076332 GAGGTCTTTTGTATGCGCGT 58.924 50.000 8.43 7.55 0.00 6.01
901 903 0.025001 CGAGGTCTTTTGTATGCGCG 59.975 55.000 0.00 0.00 0.00 6.86
902 904 0.247695 GCGAGGTCTTTTGTATGCGC 60.248 55.000 0.00 0.00 36.35 6.09
903 905 1.075542 TGCGAGGTCTTTTGTATGCG 58.924 50.000 0.00 0.00 0.00 4.73
904 906 2.677836 TCATGCGAGGTCTTTTGTATGC 59.322 45.455 0.00 0.00 0.00 3.14
905 907 4.944962 TTCATGCGAGGTCTTTTGTATG 57.055 40.909 0.00 0.00 0.00 2.39
906 908 5.220662 CGATTTCATGCGAGGTCTTTTGTAT 60.221 40.000 0.00 0.00 0.00 2.29
908 910 3.120199 CGATTTCATGCGAGGTCTTTTGT 60.120 43.478 0.00 0.00 0.00 2.83
910 912 3.074412 ACGATTTCATGCGAGGTCTTTT 58.926 40.909 0.00 0.00 0.00 2.27
911 913 2.699954 ACGATTTCATGCGAGGTCTTT 58.300 42.857 0.00 0.00 0.00 2.52
912 914 2.386661 ACGATTTCATGCGAGGTCTT 57.613 45.000 0.00 0.00 0.00 3.01
913 915 2.386661 AACGATTTCATGCGAGGTCT 57.613 45.000 0.00 0.00 0.00 3.85
914 916 3.471495 AAAACGATTTCATGCGAGGTC 57.529 42.857 0.00 0.00 0.00 3.85
916 918 4.083581 AGAAAAACGATTTCATGCGAGG 57.916 40.909 16.62 0.00 0.00 4.63
917 919 6.438327 AAAAGAAAAACGATTTCATGCGAG 57.562 33.333 16.62 0.00 0.00 5.03
918 920 6.820470 AAAAAGAAAAACGATTTCATGCGA 57.180 29.167 16.62 0.00 0.00 5.10
938 940 2.278854 GCTTGGCTGCAACAAGAAAAA 58.721 42.857 26.32 0.00 46.27 1.94
939 941 1.473080 GGCTTGGCTGCAACAAGAAAA 60.473 47.619 26.32 0.00 46.27 2.29
940 942 0.104671 GGCTTGGCTGCAACAAGAAA 59.895 50.000 26.32 0.60 46.27 2.52
942 944 2.202395 GGGCTTGGCTGCAACAAGA 61.202 57.895 26.32 0.00 46.27 3.02
943 945 2.341176 GGGCTTGGCTGCAACAAG 59.659 61.111 20.70 20.70 46.15 3.16
961 963 3.007506 GGGGTTTGTTGAGGTTTATTGGG 59.992 47.826 0.00 0.00 0.00 4.12
963 965 4.799255 GCTGGGGTTTGTTGAGGTTTATTG 60.799 45.833 0.00 0.00 0.00 1.90
965 967 2.897326 GCTGGGGTTTGTTGAGGTTTAT 59.103 45.455 0.00 0.00 0.00 1.40
966 968 2.312390 GCTGGGGTTTGTTGAGGTTTA 58.688 47.619 0.00 0.00 0.00 2.01
967 969 1.119684 GCTGGGGTTTGTTGAGGTTT 58.880 50.000 0.00 0.00 0.00 3.27
968 970 0.759060 GGCTGGGGTTTGTTGAGGTT 60.759 55.000 0.00 0.00 0.00 3.50
970 972 1.152567 TGGCTGGGGTTTGTTGAGG 60.153 57.895 0.00 0.00 0.00 3.86
971 973 0.468029 ACTGGCTGGGGTTTGTTGAG 60.468 55.000 0.00 0.00 0.00 3.02
973 975 0.754957 TGACTGGCTGGGGTTTGTTG 60.755 55.000 0.00 0.00 0.00 3.33
974 976 0.468029 CTGACTGGCTGGGGTTTGTT 60.468 55.000 0.00 0.00 0.00 2.83
976 978 2.270986 GCTGACTGGCTGGGGTTTG 61.271 63.158 0.00 0.00 0.00 2.93
977 979 2.116125 GCTGACTGGCTGGGGTTT 59.884 61.111 0.00 0.00 0.00 3.27
978 980 3.971702 GGCTGACTGGCTGGGGTT 61.972 66.667 0.00 0.00 38.32 4.11
981 983 4.729918 GGTGGCTGACTGGCTGGG 62.730 72.222 7.41 0.00 42.34 4.45
982 984 4.729918 GGGTGGCTGACTGGCTGG 62.730 72.222 7.41 0.00 42.34 4.85
983 985 3.278072 ATGGGTGGCTGACTGGCTG 62.278 63.158 7.41 0.00 42.34 4.85
984 986 2.937689 ATGGGTGGCTGACTGGCT 60.938 61.111 7.41 0.00 42.34 4.75
987 989 1.870055 GCAACATGGGTGGCTGACTG 61.870 60.000 0.00 0.00 41.01 3.51
1113 4440 1.715862 CGAGATTCTCCTGCCGACGA 61.716 60.000 8.09 0.00 0.00 4.20
1116 4443 0.670706 CATCGAGATTCTCCTGCCGA 59.329 55.000 8.09 2.73 0.00 5.54
1119 4446 1.202510 ACAGCATCGAGATTCTCCTGC 60.203 52.381 20.39 20.39 36.52 4.85
1120 4447 2.886862 ACAGCATCGAGATTCTCCTG 57.113 50.000 8.09 11.07 0.00 3.86
1123 4450 3.316588 TCCTGTACAGCATCGAGATTCTC 59.683 47.826 17.86 3.43 0.00 2.87
1124 4451 3.291584 TCCTGTACAGCATCGAGATTCT 58.708 45.455 17.86 0.00 0.00 2.40
1125 4452 3.316588 TCTCCTGTACAGCATCGAGATTC 59.683 47.826 17.86 0.00 31.45 2.52
1126 4453 3.291584 TCTCCTGTACAGCATCGAGATT 58.708 45.455 17.86 0.00 31.45 2.40
1127 4454 2.937519 TCTCCTGTACAGCATCGAGAT 58.062 47.619 17.86 0.00 31.45 2.75
1128 4455 2.420058 TCTCCTGTACAGCATCGAGA 57.580 50.000 17.86 18.90 32.97 4.04
1129 4456 3.317711 AGATTCTCCTGTACAGCATCGAG 59.682 47.826 17.86 17.04 0.00 4.04
1130 4457 3.291584 AGATTCTCCTGTACAGCATCGA 58.708 45.455 17.86 8.25 0.00 3.59
1131 4458 3.637432 GAGATTCTCCTGTACAGCATCG 58.363 50.000 17.86 3.92 0.00 3.84
1132 4459 3.316588 TCGAGATTCTCCTGTACAGCATC 59.683 47.826 17.86 14.06 0.00 3.91
1133 4460 3.291584 TCGAGATTCTCCTGTACAGCAT 58.708 45.455 17.86 6.12 0.00 3.79
1134 4461 2.723273 TCGAGATTCTCCTGTACAGCA 58.277 47.619 17.86 0.81 0.00 4.41
1135 4462 4.276183 TGTATCGAGATTCTCCTGTACAGC 59.724 45.833 17.86 2.56 0.00 4.40
1136 4463 5.049060 CCTGTATCGAGATTCTCCTGTACAG 60.049 48.000 24.06 24.06 36.76 2.74
1137 4464 4.822350 CCTGTATCGAGATTCTCCTGTACA 59.178 45.833 8.09 12.17 0.00 2.90
1138 4465 5.064558 TCCTGTATCGAGATTCTCCTGTAC 58.935 45.833 8.09 8.81 0.00 2.90
1139 4466 5.071923 TCTCCTGTATCGAGATTCTCCTGTA 59.928 44.000 8.09 0.00 31.39 2.74
1140 4467 4.141287 CTCCTGTATCGAGATTCTCCTGT 58.859 47.826 8.09 0.00 0.00 4.00
1141 4468 4.393834 TCTCCTGTATCGAGATTCTCCTG 58.606 47.826 8.09 0.00 31.39 3.86
1142 4469 4.715534 TCTCCTGTATCGAGATTCTCCT 57.284 45.455 8.09 0.00 31.39 3.69
1143 4470 5.391523 CGATTCTCCTGTATCGAGATTCTCC 60.392 48.000 8.09 0.00 43.17 3.71
1144 4471 5.180492 ACGATTCTCCTGTATCGAGATTCTC 59.820 44.000 10.97 3.43 43.17 2.87
1145 4472 5.067273 ACGATTCTCCTGTATCGAGATTCT 58.933 41.667 10.97 0.00 43.17 2.40
1146 4473 5.365403 ACGATTCTCCTGTATCGAGATTC 57.635 43.478 10.97 0.00 43.17 2.52
1147 4474 5.299531 TCAACGATTCTCCTGTATCGAGATT 59.700 40.000 10.97 0.00 43.17 2.40
1148 4475 4.822350 TCAACGATTCTCCTGTATCGAGAT 59.178 41.667 10.97 0.00 43.17 2.75
1149 4476 4.196971 TCAACGATTCTCCTGTATCGAGA 58.803 43.478 10.97 6.05 43.17 4.04
1150 4477 4.532276 CTCAACGATTCTCCTGTATCGAG 58.468 47.826 10.97 4.09 43.17 4.04
1151 4478 3.243101 GCTCAACGATTCTCCTGTATCGA 60.243 47.826 10.97 0.00 43.17 3.59
1152 4479 3.046390 GCTCAACGATTCTCCTGTATCG 58.954 50.000 0.00 0.00 45.02 2.92
1153 4480 3.385577 GGCTCAACGATTCTCCTGTATC 58.614 50.000 0.00 0.00 0.00 2.24
1154 4481 2.223829 CGGCTCAACGATTCTCCTGTAT 60.224 50.000 0.00 0.00 35.47 2.29
1155 4482 1.134367 CGGCTCAACGATTCTCCTGTA 59.866 52.381 0.00 0.00 35.47 2.74
1156 4483 0.108615 CGGCTCAACGATTCTCCTGT 60.109 55.000 0.00 0.00 35.47 4.00
1157 4484 0.108615 ACGGCTCAACGATTCTCCTG 60.109 55.000 0.00 0.00 37.61 3.86
1158 4485 0.173708 GACGGCTCAACGATTCTCCT 59.826 55.000 0.00 0.00 37.61 3.69
1159 4486 1.140407 CGACGGCTCAACGATTCTCC 61.140 60.000 0.00 0.00 37.61 3.71
1160 4487 0.456312 ACGACGGCTCAACGATTCTC 60.456 55.000 0.00 0.00 37.61 2.87
1161 4488 0.732880 CACGACGGCTCAACGATTCT 60.733 55.000 0.00 0.00 37.61 2.40
1162 4489 1.683790 CCACGACGGCTCAACGATTC 61.684 60.000 0.00 0.00 37.61 2.52
1163 4490 1.736645 CCACGACGGCTCAACGATT 60.737 57.895 0.00 0.00 37.61 3.34
1164 4491 1.945354 ATCCACGACGGCTCAACGAT 61.945 55.000 0.00 0.00 37.61 3.73
1165 4492 2.537792 GATCCACGACGGCTCAACGA 62.538 60.000 0.00 0.00 37.61 3.85
1166 4493 2.126071 ATCCACGACGGCTCAACG 60.126 61.111 0.00 0.00 40.31 4.10
1167 4494 1.810030 GGATCCACGACGGCTCAAC 60.810 63.158 6.95 0.00 30.92 3.18
1435 4772 3.932710 CACGCTAGTATGTCAAATGTGGT 59.067 43.478 0.00 0.00 0.00 4.16
1471 4816 1.093496 GGTTTATCCCGAACCCGCTG 61.093 60.000 0.00 0.00 40.52 5.18
1489 4846 3.388676 AGAGAGAGAATGCAGAATGGAGG 59.611 47.826 0.00 0.00 42.42 4.30
1510 4920 9.573133 GTGTGACCTTAAATCAAAATTATCCAG 57.427 33.333 0.00 0.00 0.00 3.86
1580 5061 2.816204 TGGTGATTGCCAACACAATG 57.184 45.000 10.73 0.00 40.31 2.82
1684 5971 0.813210 GGAGCTCTGTGCAGTATGGC 60.813 60.000 14.64 0.00 45.94 4.40
1686 5973 1.937278 CTGGAGCTCTGTGCAGTATG 58.063 55.000 14.64 0.00 45.94 2.39
1688 5975 1.593787 GCTGGAGCTCTGTGCAGTA 59.406 57.895 14.64 0.00 45.94 2.74
1689 5976 2.346739 GCTGGAGCTCTGTGCAGT 59.653 61.111 14.64 0.00 45.94 4.40
1699 5986 3.695747 GAGCCCCTGAAGCTGGAGC 62.696 68.421 0.00 0.00 41.75 4.70
1700 5987 1.994507 AGAGCCCCTGAAGCTGGAG 60.995 63.158 0.00 0.00 41.75 3.86
1709 5996 2.220786 ATTGCCCTTCAGAGCCCCTG 62.221 60.000 0.00 0.00 44.27 4.45
1737 7503 6.118170 ACATCCAACTTCTATCATGTCCTTG 58.882 40.000 0.00 0.00 0.00 3.61
1775 7541 2.373707 CCCTCAGAGCCCCCTTCTG 61.374 68.421 0.00 0.00 42.68 3.02
1776 7542 2.041928 CCCTCAGAGCCCCCTTCT 59.958 66.667 0.00 0.00 0.00 2.85
1777 7543 3.803162 GCCCTCAGAGCCCCCTTC 61.803 72.222 0.00 0.00 0.00 3.46
1779 7545 4.444957 ATGCCCTCAGAGCCCCCT 62.445 66.667 0.00 0.00 0.00 4.79
1780 7546 3.883549 GATGCCCTCAGAGCCCCC 61.884 72.222 0.00 0.00 0.00 5.40
1781 7547 2.771762 AGATGCCCTCAGAGCCCC 60.772 66.667 0.00 0.00 0.00 5.80
1782 7548 2.817056 GGAGATGCCCTCAGAGCCC 61.817 68.421 5.71 0.00 43.76 5.19
1783 7549 2.828145 GGAGATGCCCTCAGAGCC 59.172 66.667 5.71 0.00 43.76 4.70
1907 7689 1.378124 TTTTAATACGCGCCTGGGGC 61.378 55.000 24.41 24.41 46.75 5.80
2243 8749 0.831307 GGGATAAGGTGAAGGAGCGT 59.169 55.000 0.00 0.00 0.00 5.07
2354 8860 1.600636 CAAGCCAAAGACGGAGCCA 60.601 57.895 0.00 0.00 0.00 4.75
2980 9659 1.216710 GAGTCCTGGCTCCTGTTCG 59.783 63.158 6.82 0.00 0.00 3.95
3286 10025 0.617935 TGCCATTGATTCCTCACGGA 59.382 50.000 0.00 0.00 37.60 4.69
3497 10240 4.404098 AGCCCGATTTTCGCCGGT 62.404 61.111 1.90 0.00 43.93 5.28
3675 10419 2.186125 GAGGAAAGGGCGGTACCG 59.814 66.667 30.06 30.06 40.62 4.02
3789 10537 0.620556 GGGCTGATCCAAGACCAAGA 59.379 55.000 0.00 0.00 45.75 3.02
3868 10617 9.614792 ACAAATATTCCTAGATTACTGGTGTTC 57.385 33.333 0.00 0.00 0.00 3.18
4045 10794 8.107399 ACAGCATTCATAATTATCAGTCATGG 57.893 34.615 0.00 0.00 0.00 3.66
4218 10977 5.673337 TTTGTACAGCACATGAAAGAGAC 57.327 39.130 0.00 0.00 36.90 3.36
4283 11055 5.523438 TCAATTGTTTTTGTGGTAGACCC 57.477 39.130 5.13 0.00 34.29 4.46
4581 11373 1.885887 GGTTGCACCAGAACAGCATAA 59.114 47.619 0.00 0.00 38.42 1.90
4770 11569 4.140536 CAGGAAGGCTCCAGAAATATTCC 58.859 47.826 5.90 0.00 45.24 3.01
4832 11637 5.294552 ACTTTCAGCTTCTCAGTTGTTGTAC 59.705 40.000 0.00 0.00 33.10 2.90
4834 11639 4.265073 ACTTTCAGCTTCTCAGTTGTTGT 58.735 39.130 0.00 0.00 33.10 3.32
4835 11640 4.333649 TGACTTTCAGCTTCTCAGTTGTTG 59.666 41.667 0.00 0.00 33.10 3.33
4836 11641 4.517285 TGACTTTCAGCTTCTCAGTTGTT 58.483 39.130 0.00 0.00 33.10 2.83
4838 11643 4.083431 CCATGACTTTCAGCTTCTCAGTTG 60.083 45.833 0.00 0.00 32.57 3.16
4840 11645 3.326006 TCCATGACTTTCAGCTTCTCAGT 59.674 43.478 0.00 0.00 0.00 3.41
4841 11646 3.683822 GTCCATGACTTTCAGCTTCTCAG 59.316 47.826 0.00 0.00 0.00 3.35
4849 11684 3.441572 GGAACCATGTCCATGACTTTCAG 59.558 47.826 8.82 0.00 41.20 3.02
4952 12046 5.727791 GCACTTATACCACTTTCTCGCATTG 60.728 44.000 0.00 0.00 0.00 2.82
5151 12245 5.808366 TGACTTCCTCAGCTTTCTTTAGA 57.192 39.130 0.00 0.00 0.00 2.10
5301 12423 7.105588 TCAGAGCTTCAAGCATTACAAGATAA 58.894 34.615 13.10 0.00 45.56 1.75
5310 12432 7.284716 TCAATCATATTCAGAGCTTCAAGCATT 59.715 33.333 13.10 0.00 45.56 3.56
5366 12488 1.482182 CATGACTCGATTCCCACTCCA 59.518 52.381 0.00 0.00 0.00 3.86
5501 12623 4.571580 CGGCAAATATGTAAACCGTCCTTA 59.428 41.667 0.00 0.00 35.99 2.69
5502 12624 3.375922 CGGCAAATATGTAAACCGTCCTT 59.624 43.478 0.00 0.00 35.99 3.36
5534 12658 1.531264 CCGTAACGTCAGATCTGTCCG 60.531 57.143 25.33 25.33 34.23 4.79
5540 12664 2.228914 GCCGCCGTAACGTCAGATC 61.229 63.158 0.00 0.00 0.00 2.75
5547 12671 4.728102 TCCAGTGCCGCCGTAACG 62.728 66.667 0.00 0.00 0.00 3.18
5553 12677 1.817099 CAAGATCTCCAGTGCCGCC 60.817 63.158 0.00 0.00 0.00 6.13
5643 12767 6.365970 ACATCCTTTGACTCTTCATAGTGT 57.634 37.500 0.00 0.00 30.86 3.55
5917 13044 6.145209 CGACAAGTCATAATTCTGCTCTATGG 59.855 42.308 0.72 0.00 0.00 2.74
5918 13045 6.920210 TCGACAAGTCATAATTCTGCTCTATG 59.080 38.462 0.72 0.00 0.00 2.23
6003 13183 6.484977 GGGTCAAATGTAAAATGCCAAAAGAA 59.515 34.615 0.00 0.00 0.00 2.52
6121 13443 2.413837 GTACTGCAATCGACTGGTTGT 58.586 47.619 0.00 0.00 0.00 3.32
6123 13445 1.338769 GGGTACTGCAATCGACTGGTT 60.339 52.381 0.00 0.00 0.00 3.67
6125 13447 0.249120 TGGGTACTGCAATCGACTGG 59.751 55.000 0.00 0.00 0.00 4.00
6126 13448 1.645034 CTGGGTACTGCAATCGACTG 58.355 55.000 0.00 0.00 0.00 3.51
6127 13449 0.537188 CCTGGGTACTGCAATCGACT 59.463 55.000 0.00 0.00 0.00 4.18
6128 13450 0.249398 ACCTGGGTACTGCAATCGAC 59.751 55.000 0.00 0.00 0.00 4.20
6129 13451 1.855295 TACCTGGGTACTGCAATCGA 58.145 50.000 0.00 0.00 0.00 3.59
6130 13452 2.910688 ATACCTGGGTACTGCAATCG 57.089 50.000 1.19 0.00 33.01 3.34
6132 13454 4.862641 AAGAATACCTGGGTACTGCAAT 57.137 40.909 1.19 0.00 33.01 3.56
6133 13455 4.042311 TCAAAGAATACCTGGGTACTGCAA 59.958 41.667 1.19 0.00 33.01 4.08
6134 13456 3.585289 TCAAAGAATACCTGGGTACTGCA 59.415 43.478 1.19 0.00 33.01 4.41
6135 13457 4.192317 CTCAAAGAATACCTGGGTACTGC 58.808 47.826 1.19 0.00 33.01 4.40
6136 13458 4.384208 CCCTCAAAGAATACCTGGGTACTG 60.384 50.000 1.19 0.00 33.01 2.74
6137 13459 3.780850 CCCTCAAAGAATACCTGGGTACT 59.219 47.826 1.19 0.00 33.01 2.73
6139 13461 3.521937 CACCCTCAAAGAATACCTGGGTA 59.478 47.826 1.70 1.70 43.79 3.69
6140 13462 2.308866 CACCCTCAAAGAATACCTGGGT 59.691 50.000 0.00 0.00 46.23 4.51
6141 13463 2.945890 GCACCCTCAAAGAATACCTGGG 60.946 54.545 0.00 0.00 39.06 4.45
6143 13465 3.012518 CTGCACCCTCAAAGAATACCTG 58.987 50.000 0.00 0.00 0.00 4.00
6144 13466 2.644798 ACTGCACCCTCAAAGAATACCT 59.355 45.455 0.00 0.00 0.00 3.08
6145 13467 3.073274 ACTGCACCCTCAAAGAATACC 57.927 47.619 0.00 0.00 0.00 2.73
6147 13469 4.216411 GGTACTGCACCCTCAAAGAATA 57.784 45.455 0.00 0.00 42.07 1.75
6148 13470 3.073274 GGTACTGCACCCTCAAAGAAT 57.927 47.619 0.00 0.00 42.07 2.40
6149 13471 2.561478 GGTACTGCACCCTCAAAGAA 57.439 50.000 0.00 0.00 42.07 2.52
6159 13481 2.766828 AGAGAATACCTGGGTACTGCAC 59.233 50.000 1.19 0.00 33.01 4.57
6420 13938 6.695713 TGATACTTATTCCTGATCGACAAACG 59.304 38.462 0.00 0.00 44.09 3.60
6501 14019 4.587189 CCCAGCTACTACGCCGCC 62.587 72.222 0.00 0.00 0.00 6.13
6506 14024 1.515954 CCACACCCCAGCTACTACG 59.484 63.158 0.00 0.00 0.00 3.51
6509 14027 3.706373 CGCCACACCCCAGCTACT 61.706 66.667 0.00 0.00 0.00 2.57
6525 14043 4.657824 ACTCACCGCCACCGAACG 62.658 66.667 0.00 0.00 36.29 3.95
6620 14152 1.369091 CCTGTAGCAACACGATGGGC 61.369 60.000 0.00 0.00 0.00 5.36
6624 14156 0.981183 TTCCCCTGTAGCAACACGAT 59.019 50.000 0.00 0.00 0.00 3.73
6636 14168 2.419297 CCGAGAATCAGAGTTTCCCCTG 60.419 54.545 0.00 0.00 33.17 4.45
6647 14179 1.372251 CGCCCGATCCGAGAATCAG 60.372 63.158 0.00 0.00 33.17 2.90
6715 14247 1.328680 GCTGCATACGATGAACTGTGG 59.671 52.381 0.00 0.00 0.00 4.17
6724 14256 4.039004 AGAAGAGATGAAGCTGCATACGAT 59.961 41.667 7.34 0.29 0.00 3.73
6733 14265 2.224018 GCCATCGAGAAGAGATGAAGCT 60.224 50.000 7.67 0.00 46.09 3.74
6759 14291 1.066143 ACCGTCTAGTCAAAGCCATGG 60.066 52.381 7.63 7.63 0.00 3.66
6762 14294 2.352030 CGTTACCGTCTAGTCAAAGCCA 60.352 50.000 0.00 0.00 0.00 4.75
6774 14306 0.108945 CCTTCCCTGTCGTTACCGTC 60.109 60.000 0.00 0.00 35.01 4.79
6775 14307 1.538687 CCCTTCCCTGTCGTTACCGT 61.539 60.000 0.00 0.00 35.01 4.83
6784 14316 4.962362 CCTTATAAAAATGCCCTTCCCTGT 59.038 41.667 0.00 0.00 0.00 4.00
6787 14319 4.959839 TGTCCTTATAAAAATGCCCTTCCC 59.040 41.667 0.00 0.00 0.00 3.97
6789 14321 6.775594 AGTGTCCTTATAAAAATGCCCTTC 57.224 37.500 0.00 0.00 0.00 3.46
6817 14349 1.378514 TCGAATTTGCCCCTCTGCC 60.379 57.895 0.00 0.00 0.00 4.85
6818 14350 1.997928 GCTCGAATTTGCCCCTCTGC 61.998 60.000 0.00 0.00 0.00 4.26
6823 14355 1.227060 GCATGCTCGAATTTGCCCC 60.227 57.895 11.37 0.00 0.00 5.80
6826 14358 1.186030 CGAAGCATGCTCGAATTTGC 58.814 50.000 22.93 0.00 35.34 3.68
6833 14365 2.032549 CCCTAATTTCGAAGCATGCTCG 60.033 50.000 22.93 23.89 0.00 5.03
6837 14369 2.023673 TGCCCCTAATTTCGAAGCATG 58.976 47.619 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.