Multiple sequence alignment - TraesCS1B01G286000

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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 TraesCS1B01G286000 chr1B 100.000 4953 0 0 1 4953 497469705 497474657 0.000000e+00 9147.0
1 TraesCS1B01G286000 chr1B 78.180 857 152 26 2165 3002 497780326 497781166 9.510000e-142 514.0
2 TraesCS1B01G286000 chr1B 80.971 515 64 13 3626 4135 497781450 497781935 1.300000e-100 377.0
3 TraesCS1B01G286000 chr1B 82.697 393 57 6 1495 1882 497799764 497800150 6.140000e-89 339.0
4 TraesCS1B01G286000 chr1B 89.130 230 25 0 1663 1892 497779645 497779874 2.260000e-73 287.0
5 TraesCS1B01G286000 chr1B 80.412 388 64 12 2170 2551 497820570 497820951 8.110000e-73 285.0
6 TraesCS1B01G286000 chr1B 91.045 67 6 0 1697 1763 67503003 67502937 1.900000e-14 91.6
7 TraesCS1B01G286000 chr1B 90.741 54 4 1 2113 2166 618697571 618697623 2.470000e-08 71.3
8 TraesCS1B01G286000 chr1B 91.667 48 4 0 1845 1892 497780053 497780100 3.200000e-07 67.6
9 TraesCS1B01G286000 chr1A 90.385 2985 200 36 64 3002 472078841 472081784 0.000000e+00 3842.0
10 TraesCS1B01G286000 chr1A 91.301 1207 67 17 3082 4266 472081781 472082971 0.000000e+00 1613.0
11 TraesCS1B01G286000 chr1A 85.897 702 72 10 4268 4943 472083880 472084580 0.000000e+00 723.0
12 TraesCS1B01G286000 chr1A 78.271 856 149 27 2165 3002 472141892 472142728 2.640000e-142 516.0
13 TraesCS1B01G286000 chr1A 80.000 520 65 21 3624 4135 472143012 472143500 1.020000e-91 348.0
14 TraesCS1B01G286000 chr1A 81.527 406 55 12 1488 1892 472141269 472141655 2.880000e-82 316.0
15 TraesCS1B01G286000 chr1A 81.510 384 53 11 1516 1894 472164972 472165342 2.900000e-77 300.0
16 TraesCS1B01G286000 chr1A 79.948 384 60 16 2172 2549 472167535 472167907 2.940000e-67 267.0
17 TraesCS1B01G286000 chr1A 77.019 322 63 9 2386 2705 526909134 526909446 1.830000e-39 174.0
18 TraesCS1B01G286000 chr1A 91.111 90 8 0 1040 1129 472164566 472164655 6.730000e-24 122.0
19 TraesCS1B01G286000 chr1A 87.640 89 10 1 3165 3252 461681041 461680953 8.770000e-18 102.0
20 TraesCS1B01G286000 chr1A 91.837 49 3 1 2119 2166 498671258 498671210 3.200000e-07 67.6
21 TraesCS1B01G286000 chr1A 73.939 165 34 4 4299 4455 305605262 305605099 1.930000e-04 58.4
22 TraesCS1B01G286000 chr1D 89.425 1201 67 27 771 1947 372834634 372835798 0.000000e+00 1459.0
23 TraesCS1B01G286000 chr1D 89.187 1156 65 22 3082 4221 372836944 372838055 0.000000e+00 1387.0
24 TraesCS1B01G286000 chr1D 92.071 845 44 11 2170 3002 372836114 372836947 0.000000e+00 1168.0
25 TraesCS1B01G286000 chr1D 85.695 741 85 9 4222 4952 372857041 372857770 0.000000e+00 761.0
26 TraesCS1B01G286000 chr1D 82.970 734 93 16 34 757 372833880 372834591 6.990000e-178 634.0
27 TraesCS1B01G286000 chr1D 77.868 863 148 29 2165 3002 372861276 372862120 3.440000e-136 496.0
28 TraesCS1B01G286000 chr1D 81.431 517 62 13 3624 4135 372862400 372862887 4.650000e-105 392.0
29 TraesCS1B01G286000 chr1D 83.377 385 48 10 1520 1894 372875061 372875439 4.750000e-90 342.0
30 TraesCS1B01G286000 chr1D 81.535 417 58 13 1488 1892 372860610 372861019 4.780000e-85 326.0
31 TraesCS1B01G286000 chr1D 89.677 155 14 2 3468 3622 7349862 7349710 3.910000e-46 196.0
32 TraesCS1B01G286000 chr1D 87.975 158 16 3 3467 3622 468265425 468265269 3.050000e-42 183.0
33 TraesCS1B01G286000 chr1D 82.390 159 19 6 1040 1190 372874667 372874824 4.020000e-26 130.0
34 TraesCS1B01G286000 chr1D 89.535 86 7 2 3168 3253 372837111 372837028 1.890000e-19 108.0
35 TraesCS1B01G286000 chr1D 85.437 103 10 4 3153 3253 313214580 313214481 8.770000e-18 102.0
36 TraesCS1B01G286000 chr1D 97.778 45 1 0 2122 2166 64895541 64895585 1.480000e-10 78.7
37 TraesCS1B01G286000 chr1D 75.758 165 31 4 4299 4455 240983469 240983306 1.910000e-09 75.0
38 TraesCS1B01G286000 chr1D 95.556 45 2 0 1902 1946 279100789 279100745 6.880000e-09 73.1
39 TraesCS1B01G286000 chr1D 92.000 50 4 0 1900 1949 164421706 164421657 2.470000e-08 71.3
40 TraesCS1B01G286000 chr1D 90.741 54 2 2 1901 1952 249030405 249030353 8.900000e-08 69.4
41 TraesCS1B01G286000 chr1D 91.837 49 3 1 2119 2166 403524379 403524331 3.200000e-07 67.6
42 TraesCS1B01G286000 chr1D 95.122 41 2 0 2121 2161 101291259 101291219 1.150000e-06 65.8
43 TraesCS1B01G286000 chr1D 93.023 43 3 0 2120 2162 319565716 319565758 4.140000e-06 63.9
44 TraesCS1B01G286000 chr4B 90.066 151 13 2 3472 3622 483581985 483582133 1.410000e-45 195.0
45 TraesCS1B01G286000 chr4B 100.000 42 0 0 2121 2162 23667321 23667362 1.480000e-10 78.7
46 TraesCS1B01G286000 chr4B 89.062 64 5 1 1907 1970 166760900 166760961 1.480000e-10 78.7
47 TraesCS1B01G286000 chr4B 94.000 50 3 0 1894 1943 31873210 31873161 5.320000e-10 76.8
48 TraesCS1B01G286000 chr3D 88.608 158 15 3 3466 3622 516202490 516202335 6.550000e-44 189.0
49 TraesCS1B01G286000 chr3D 93.103 87 5 1 3001 3086 47483256 47483342 5.210000e-25 126.0
50 TraesCS1B01G286000 chr3D 88.235 68 6 1 1903 1970 61675399 61675464 4.110000e-11 80.5
51 TraesCS1B01G286000 chr3D 92.593 54 3 1 2114 2166 131489159 131489212 5.320000e-10 76.8
52 TraesCS1B01G286000 chr3D 95.652 46 2 0 1903 1948 520715242 520715287 1.910000e-09 75.0
53 TraesCS1B01G286000 chr3D 71.067 356 88 11 4485 4826 39434957 39435311 6.880000e-09 73.1
54 TraesCS1B01G286000 chr3D 92.157 51 3 1 2113 2162 429043497 429043547 2.470000e-08 71.3
55 TraesCS1B01G286000 chr5B 86.982 169 19 3 3455 3622 299602395 299602229 2.350000e-43 187.0
56 TraesCS1B01G286000 chr5B 96.512 86 3 0 3000 3085 429030693 429030608 5.170000e-30 143.0
57 TraesCS1B01G286000 chr5B 97.778 45 1 0 2122 2166 391148494 391148450 1.480000e-10 78.7
58 TraesCS1B01G286000 chr5A 85.549 173 20 4 3451 3622 354544060 354544228 5.100000e-40 176.0
59 TraesCS1B01G286000 chr5A 92.079 101 5 3 2999 3098 526577359 526577261 6.690000e-29 139.0
60 TraesCS1B01G286000 chr3A 85.465 172 21 4 3470 3638 509865411 509865241 5.100000e-40 176.0
61 TraesCS1B01G286000 chr3A 91.667 60 3 2 1890 1948 515889367 515889309 1.140000e-11 82.4
62 TraesCS1B01G286000 chrUn 96.512 86 3 0 3000 3085 224653394 224653309 5.170000e-30 143.0
63 TraesCS1B01G286000 chrUn 95.402 87 4 0 2999 3085 94846970 94847056 6.690000e-29 139.0
64 TraesCS1B01G286000 chrUn 83.810 105 11 5 3163 3264 100208279 100208380 1.470000e-15 95.3
65 TraesCS1B01G286000 chrUn 92.593 54 2 2 1901 1952 50304285 50304232 5.320000e-10 76.8
66 TraesCS1B01G286000 chrUn 95.349 43 2 0 1903 1945 2656057 2656099 8.900000e-08 69.4
67 TraesCS1B01G286000 chrUn 88.235 51 6 0 1885 1935 462835157 462835107 1.490000e-05 62.1
68 TraesCS1B01G286000 chrUn 94.737 38 2 0 2124 2161 101887522 101887485 5.350000e-05 60.2
69 TraesCS1B01G286000 chrUn 97.059 34 1 0 1914 1947 332381678 332381645 1.930000e-04 58.4
70 TraesCS1B01G286000 chrUn 100.000 28 0 0 2119 2146 293280893 293280920 9.000000e-03 52.8
71 TraesCS1B01G286000 chr3B 92.079 101 6 2 3001 3100 3660855 3660756 1.860000e-29 141.0
72 TraesCS1B01G286000 chr3B 87.156 109 12 2 2985 3092 132527283 132527390 6.730000e-24 122.0
73 TraesCS1B01G286000 chr3B 89.691 97 7 3 3001 3097 572266710 572266803 2.420000e-23 121.0
74 TraesCS1B01G286000 chr3B 88.235 68 6 2 1904 1969 70300280 70300347 4.110000e-11 80.5
75 TraesCS1B01G286000 chr3B 100.000 41 0 0 2122 2162 746342194 746342154 5.320000e-10 76.8
76 TraesCS1B01G286000 chr3B 85.484 62 5 3 4767 4826 417490415 417490356 1.490000e-05 62.1
77 TraesCS1B01G286000 chr2D 93.617 94 6 0 2992 3085 422331546 422331639 1.860000e-29 141.0
78 TraesCS1B01G286000 chr2D 92.453 53 2 2 1903 1953 554308419 554308367 1.910000e-09 75.0
79 TraesCS1B01G286000 chr2D 88.710 62 5 1 1909 1968 565157057 565156996 1.910000e-09 75.0
80 TraesCS1B01G286000 chr2D 95.556 45 2 0 2113 2157 67236159 67236203 6.880000e-09 73.1
81 TraesCS1B01G286000 chr2D 92.000 50 2 2 2113 2160 644147798 644147749 8.900000e-08 69.4
82 TraesCS1B01G286000 chr6B 94.505 91 4 1 3001 3091 366432025 366431936 6.690000e-29 139.0
83 TraesCS1B01G286000 chr6B 93.478 92 6 0 2999 3090 85789655 85789746 2.400000e-28 137.0
84 TraesCS1B01G286000 chr6B 90.361 83 8 0 3168 3250 705317530 705317448 5.240000e-20 110.0
85 TraesCS1B01G286000 chr6B 88.406 69 6 1 1903 1969 120677309 120677377 1.140000e-11 82.4
86 TraesCS1B01G286000 chr2B 90.385 104 8 2 3000 3101 798196762 798196659 8.650000e-28 135.0
87 TraesCS1B01G286000 chr2B 92.000 75 6 0 3185 3259 620274925 620274851 6.780000e-19 106.0
88 TraesCS1B01G286000 chr2B 89.552 67 3 1 1902 1968 136176059 136176121 1.140000e-11 82.4
89 TraesCS1B01G286000 chr7D 90.000 100 8 2 3001 3099 32381745 32381647 1.450000e-25 128.0
90 TraesCS1B01G286000 chr7D 90.625 96 6 3 3001 3096 181911918 181912010 1.870000e-24 124.0
91 TraesCS1B01G286000 chr7D 90.164 61 5 1 1908 1968 22657757 22657816 1.480000e-10 78.7
92 TraesCS1B01G286000 chr5D 89.691 97 7 3 3001 3096 56467606 56467700 2.420000e-23 121.0
93 TraesCS1B01G286000 chr5D 97.778 45 1 0 1903 1947 458811248 458811292 1.480000e-10 78.7
94 TraesCS1B01G286000 chr5D 97.619 42 1 0 1903 1944 191259025 191259066 6.880000e-09 73.1
95 TraesCS1B01G286000 chr5D 97.619 42 1 0 2121 2162 428572974 428573015 6.880000e-09 73.1
96 TraesCS1B01G286000 chr5D 97.561 41 1 0 2122 2162 11299522 11299562 2.470000e-08 71.3
97 TraesCS1B01G286000 chr5D 95.238 42 2 0 2121 2162 530069378 530069337 3.200000e-07 67.6
98 TraesCS1B01G286000 chr6D 92.593 81 6 0 3164 3244 305735284 305735364 3.130000e-22 117.0
99 TraesCS1B01G286000 chr6D 100.000 40 0 0 1908 1947 93644405 93644444 1.910000e-09 75.0
100 TraesCS1B01G286000 chr6D 93.333 45 3 0 1903 1947 302639638 302639682 3.200000e-07 67.6
101 TraesCS1B01G286000 chr6D 95.122 41 0 1 1914 1952 93644474 93644434 4.140000e-06 63.9
102 TraesCS1B01G286000 chr6D 94.872 39 2 0 2115 2153 441969830 441969792 1.490000e-05 62.1
103 TraesCS1B01G286000 chr6D 100.000 28 0 0 2121 2148 338806258 338806231 9.000000e-03 52.8
104 TraesCS1B01G286000 chr2A 89.552 67 3 1 1902 1968 84959113 84959175 1.140000e-11 82.4
105 TraesCS1B01G286000 chr2A 89.552 67 3 1 1902 1968 84974334 84974396 1.140000e-11 82.4
106 TraesCS1B01G286000 chr2A 96.078 51 1 1 2112 2162 587741674 587741625 1.140000e-11 82.4
107 TraesCS1B01G286000 chr2A 100.000 41 0 0 2122 2162 551818014 551817974 5.320000e-10 76.8
108 TraesCS1B01G286000 chr6A 92.727 55 4 0 1903 1957 614006880 614006826 4.110000e-11 80.5
109 TraesCS1B01G286000 chr6A 92.453 53 3 1 2115 2166 604890758 604890706 1.910000e-09 75.0
110 TraesCS1B01G286000 chr6A 93.750 48 3 0 2119 2166 34179546 34179593 6.880000e-09 73.1
111 TraesCS1B01G286000 chr4D 97.826 46 1 0 1902 1947 402560207 402560162 4.110000e-11 80.5
112 TraesCS1B01G286000 chr4D 100.000 42 0 0 2121 2162 13062717 13062758 1.480000e-10 78.7
113 TraesCS1B01G286000 chr4D 94.231 52 1 2 1903 1952 139045058 139045007 1.480000e-10 78.7
114 TraesCS1B01G286000 chr4D 97.619 42 1 0 2121 2162 48537862 48537903 6.880000e-09 73.1
115 TraesCS1B01G286000 chr4D 93.333 45 3 0 1903 1947 36591523 36591567 3.200000e-07 67.6
116 TraesCS1B01G286000 chr4D 90.196 51 4 1 2113 2162 483432466 483432416 1.150000e-06 65.8
117 TraesCS1B01G286000 chr4D 93.023 43 3 0 2120 2162 261053150 261053108 4.140000e-06 63.9
118 TraesCS1B01G286000 chr4D 100.000 29 0 0 2121 2149 260735373 260735401 2.000000e-03 54.7
119 TraesCS1B01G286000 chr4A 91.379 58 3 2 1897 1952 246711251 246711308 1.480000e-10 78.7


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 TraesCS1B01G286000 chr1B 497469705 497474657 4952 False 9147.000000 9147 100.000000 1 4953 1 chr1B.!!$F1 4952
1 TraesCS1B01G286000 chr1B 497779645 497781935 2290 False 311.400000 514 84.987000 1663 4135 4 chr1B.!!$F5 2472
2 TraesCS1B01G286000 chr1A 472078841 472084580 5739 False 2059.333333 3842 89.194333 64 4943 3 chr1A.!!$F2 4879
3 TraesCS1B01G286000 chr1A 472141269 472143500 2231 False 393.333333 516 79.932667 1488 4135 3 chr1A.!!$F3 2647
4 TraesCS1B01G286000 chr1A 472164566 472167907 3341 False 229.666667 300 84.189667 1040 2549 3 chr1A.!!$F4 1509
5 TraesCS1B01G286000 chr1D 372833880 372838055 4175 False 1162.000000 1459 88.413250 34 4221 4 chr1D.!!$F3 4187
6 TraesCS1B01G286000 chr1D 372857041 372862887 5846 False 493.750000 761 81.632250 1488 4952 4 chr1D.!!$F4 3464
7 TraesCS1B01G286000 chr1D 372874667 372875439 772 False 236.000000 342 82.883500 1040 1894 2 chr1D.!!$F5 854

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
41 42 0.250467 GCACCACCACAGATCACACT 60.250 55.0 0.00 0.0 0.0 3.55 F
206 207 0.600557 CTGACACGACTGGAGAGCTT 59.399 55.0 0.00 0.0 0.0 3.74 F
559 565 1.317613 AAATTGTTCACCTGCGCTCA 58.682 45.0 9.73 0.0 0.0 4.26 F
1034 1089 1.731720 ATCAAGAAGAAGGCTGCGAC 58.268 50.0 0.00 0.0 0.0 5.19 F
2363 6862 0.963355 TTAGCAATGTTGGGGCGGTC 60.963 55.0 0.00 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1364 1.672030 TGGTGCATCAACTCCTGCG 60.672 57.895 0.00 0.00 41.32 5.18 R
1374 1437 2.349438 GCTTTTGTCGTCGATGCAAGAA 60.349 45.455 0.00 9.76 0.00 2.52 R
2323 6822 0.749818 TGCAAAGCAAACTGTCCCGA 60.750 50.000 0.00 0.00 34.76 5.14 R
2701 7212 0.586802 GTTGGGTCAAGAGCGAACAC 59.413 55.000 18.07 0.00 43.68 3.32 R
3967 8537 0.107831 TGGAGCTGGCTTTGTACGTT 59.892 50.000 0.00 0.00 0.00 3.99 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
28 29 3.737172 GCACGACCATGGCACCAC 61.737 66.667 13.04 0.00 0.00 4.16
29 30 3.055719 CACGACCATGGCACCACC 61.056 66.667 13.04 0.00 39.84 4.61
37 38 3.573673 TGGCACCACCACAGATCA 58.426 55.556 0.00 0.00 46.36 2.92
40 41 1.237285 GGCACCACCACAGATCACAC 61.237 60.000 0.00 0.00 38.86 3.82
41 42 0.250467 GCACCACCACAGATCACACT 60.250 55.000 0.00 0.00 0.00 3.55
42 43 1.516161 CACCACCACAGATCACACTG 58.484 55.000 0.00 0.00 42.78 3.66
44 45 0.957395 CCACCACAGATCACACTGCC 60.957 60.000 0.00 0.00 41.06 4.85
45 46 1.004560 ACCACAGATCACACTGCCG 60.005 57.895 0.00 0.00 41.06 5.69
74 75 2.524640 TAGCACCACGTCCCACCA 60.525 61.111 0.00 0.00 0.00 4.17
90 91 3.283684 CAGCAAACACGGCCGGAA 61.284 61.111 31.76 0.00 0.00 4.30
125 126 1.331399 GGAGGACCACCACTAGCTCC 61.331 65.000 2.58 0.00 38.94 4.70
157 158 1.815421 CCGGTTCCCAATCTCTGCG 60.815 63.158 0.00 0.00 0.00 5.18
206 207 0.600557 CTGACACGACTGGAGAGCTT 59.399 55.000 0.00 0.00 0.00 3.74
211 212 2.344203 CGACTGGAGAGCTTCCCGT 61.344 63.158 10.29 10.29 46.19 5.28
243 246 1.586154 CCACGTGAGAATGCAACCCC 61.586 60.000 19.30 0.00 0.00 4.95
271 274 2.983879 ATCGGTGAGGGGGCTTTGG 61.984 63.158 0.00 0.00 0.00 3.28
346 349 3.403057 GCGTTTGCGACTGCTCGA 61.403 61.111 0.00 0.00 43.06 4.04
347 350 2.765785 CGTTTGCGACTGCTCGAG 59.234 61.111 8.45 8.45 43.06 4.04
485 489 5.634859 GCACCTGGATGAACAGTAAAATTTG 59.365 40.000 0.00 0.00 36.75 2.32
559 565 1.317613 AAATTGTTCACCTGCGCTCA 58.682 45.000 9.73 0.00 0.00 4.26
766 809 4.767255 AGCTCGAGCCCGCCAAAG 62.767 66.667 32.94 0.00 43.38 2.77
804 850 7.659390 GTCCTGATTTGGTAATCTTGGAGATAG 59.341 40.741 10.87 0.00 40.83 2.08
942 997 2.034221 GTGCTCCGGCTTTTCCCT 59.966 61.111 0.00 0.00 39.59 4.20
970 1025 9.991388 CAGTAAGCGTATATATAAACTCTCCTC 57.009 37.037 0.00 0.00 0.00 3.71
1028 1083 3.134458 CCACGGATATCAAGAAGAAGGC 58.866 50.000 4.83 0.00 0.00 4.35
1034 1089 1.731720 ATCAAGAAGAAGGCTGCGAC 58.268 50.000 0.00 0.00 0.00 5.19
1151 1210 3.873952 CAGCCTAATCTGTAGCTTCCAAC 59.126 47.826 0.00 0.00 31.93 3.77
1180 1243 9.717942 ATCATTTCATACAGCTCTTACTAATCC 57.282 33.333 0.00 0.00 0.00 3.01
1365 1428 6.449830 ACCTCCTGTTGACCTTAGTTTATT 57.550 37.500 0.00 0.00 0.00 1.40
1374 1437 9.802039 TGTTGACCTTAGTTTATTTACCAATCT 57.198 29.630 0.00 0.00 0.00 2.40
1391 1454 2.432206 TCTTCTTGCATCGACGACAA 57.568 45.000 0.00 0.00 0.00 3.18
1553 3688 3.516700 ACCTTGGTATTGGTACTTAGCGT 59.483 43.478 0.00 0.00 34.36 5.07
1630 3781 7.275888 ACTTCAGTGAGATGCAAAATAAACA 57.724 32.000 0.00 0.00 0.00 2.83
1631 3782 7.141363 ACTTCAGTGAGATGCAAAATAAACAC 58.859 34.615 0.00 0.00 0.00 3.32
1632 3783 5.688823 TCAGTGAGATGCAAAATAAACACG 58.311 37.500 0.00 0.00 33.18 4.49
1650 3812 3.006967 ACACGTTATCTTTGCTCCTGACT 59.993 43.478 0.00 0.00 0.00 3.41
1876 4070 4.525487 TGCTCCTTTCAGATGCAAAATCTT 59.475 37.500 0.00 0.00 0.00 2.40
1905 4099 5.221561 TGAGCAAGGTAAGTAAGCAACTACA 60.222 40.000 0.00 0.00 37.50 2.74
2053 6211 7.005709 ACAAACCTAGGATATATAGGCACAC 57.994 40.000 17.98 0.00 43.15 3.82
2066 6224 2.508526 AGGCACACCATGAAGTTCTTC 58.491 47.619 4.17 5.70 39.06 2.87
2323 6822 1.645919 AGGGGATGCCCTTGTTATTGT 59.354 47.619 21.18 0.00 44.66 2.71
2359 6858 1.655484 GCATTTAGCAATGTTGGGGC 58.345 50.000 0.00 0.00 41.84 5.80
2363 6862 0.963355 TTAGCAATGTTGGGGCGGTC 60.963 55.000 0.00 0.00 0.00 4.79
2370 6869 3.164977 TTGGGGCGGTCAGTGACA 61.165 61.111 24.20 0.00 33.68 3.58
2494 6998 3.773117 GTGGAACTTGTTGCGATGG 57.227 52.632 0.95 0.00 0.00 3.51
2567 7074 8.755941 CCACAGTTCACTATTAATTACAGATCG 58.244 37.037 0.00 0.00 0.00 3.69
2571 7078 9.962783 AGTTCACTATTAATTACAGATCGGTAC 57.037 33.333 5.11 0.00 0.00 3.34
2701 7212 5.049405 ACACTTTTCTGGAGCAAAATACTCG 60.049 40.000 0.00 0.00 34.87 4.18
2706 7217 3.994392 TCTGGAGCAAAATACTCGTGTTC 59.006 43.478 0.00 0.00 34.87 3.18
2717 7228 1.006571 TCGTGTTCGCTCTTGACCC 60.007 57.895 0.00 0.00 36.96 4.46
2718 7229 1.300620 CGTGTTCGCTCTTGACCCA 60.301 57.895 0.00 0.00 0.00 4.51
2781 7292 1.620822 ATTGCCTGGTCTCCAACAAC 58.379 50.000 0.00 0.00 34.14 3.32
3002 7534 6.371825 AGGCAGAAATTAAGCTACACAAGTAC 59.628 38.462 0.00 0.00 0.00 2.73
3003 7535 6.371825 GGCAGAAATTAAGCTACACAAGTACT 59.628 38.462 0.00 0.00 0.00 2.73
3005 7537 7.413109 GCAGAAATTAAGCTACACAAGTACTCC 60.413 40.741 0.00 0.00 0.00 3.85
3006 7538 7.064728 CAGAAATTAAGCTACACAAGTACTCCC 59.935 40.741 0.00 0.00 0.00 4.30
3007 7539 6.622427 AATTAAGCTACACAAGTACTCCCT 57.378 37.500 0.00 0.00 0.00 4.20
3008 7540 5.656213 TTAAGCTACACAAGTACTCCCTC 57.344 43.478 0.00 0.00 0.00 4.30
3009 7541 2.458620 AGCTACACAAGTACTCCCTCC 58.541 52.381 0.00 0.00 0.00 4.30
3010 7542 1.134560 GCTACACAAGTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
3012 7544 1.254954 ACACAAGTACTCCCTCCGTC 58.745 55.000 0.00 0.00 0.00 4.79
3013 7545 0.531200 CACAAGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
3014 7546 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
3015 7547 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
3016 7548 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3017 7549 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3018 7550 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3019 7551 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3020 7552 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3021 7553 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3022 7554 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3023 7555 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3024 7556 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3025 7557 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3026 7558 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3028 7560 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3029 7561 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3030 7562 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3031 7563 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3032 7564 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3033 7565 6.245724 CGTCCCATAATGTAAGACGTTTTTC 58.754 40.000 0.00 0.00 43.89 2.29
3034 7566 6.245724 GTCCCATAATGTAAGACGTTTTTCG 58.754 40.000 0.00 0.00 46.00 3.46
3035 7567 6.091169 GTCCCATAATGTAAGACGTTTTTCGA 59.909 38.462 0.00 0.00 42.86 3.71
3036 7568 6.091169 TCCCATAATGTAAGACGTTTTTCGAC 59.909 38.462 0.00 0.00 42.86 4.20
3038 7570 2.909076 TGTAAGACGTTTTTCGACGC 57.091 45.000 0.00 0.00 46.47 5.19
3039 7571 2.462889 TGTAAGACGTTTTTCGACGCT 58.537 42.857 0.00 0.00 46.47 5.07
3040 7572 3.626977 TGTAAGACGTTTTTCGACGCTA 58.373 40.909 0.00 0.00 46.47 4.26
3041 7573 3.665409 TGTAAGACGTTTTTCGACGCTAG 59.335 43.478 0.00 0.00 46.47 3.42
3042 7574 2.412421 AGACGTTTTTCGACGCTAGT 57.588 45.000 0.00 0.00 46.47 2.57
3043 7575 2.049228 AGACGTTTTTCGACGCTAGTG 58.951 47.619 0.59 0.59 46.47 2.74
3044 7576 1.783140 GACGTTTTTCGACGCTAGTGT 59.217 47.619 9.11 9.11 46.47 3.55
3045 7577 2.973224 GACGTTTTTCGACGCTAGTGTA 59.027 45.455 9.36 0.00 46.47 2.90
3046 7578 2.975851 ACGTTTTTCGACGCTAGTGTAG 59.024 45.455 9.36 9.72 46.47 2.74
3047 7579 2.975851 CGTTTTTCGACGCTAGTGTAGT 59.024 45.455 9.36 0.00 42.86 2.73
3048 7580 3.181556 CGTTTTTCGACGCTAGTGTAGTG 60.182 47.826 9.36 2.74 42.86 2.74
3088 7620 2.940514 TGGGACAGAGGGAGTATGAA 57.059 50.000 0.00 0.00 0.00 2.57
3089 7621 3.199442 TGGGACAGAGGGAGTATGAAA 57.801 47.619 0.00 0.00 0.00 2.69
3090 7622 2.838202 TGGGACAGAGGGAGTATGAAAC 59.162 50.000 0.00 0.00 0.00 2.78
3091 7623 2.838202 GGGACAGAGGGAGTATGAAACA 59.162 50.000 0.00 0.00 0.00 2.83
3092 7624 3.263425 GGGACAGAGGGAGTATGAAACAA 59.737 47.826 0.00 0.00 0.00 2.83
3093 7625 4.254492 GGACAGAGGGAGTATGAAACAAC 58.746 47.826 0.00 0.00 0.00 3.32
3094 7626 4.020128 GGACAGAGGGAGTATGAAACAACT 60.020 45.833 0.00 0.00 0.00 3.16
3122 7654 3.056107 TGGTCCGAACAAGGAGTTATGAG 60.056 47.826 0.00 0.00 41.51 2.90
3172 7704 6.147985 GCAAGCTACTTGGCTAATATTACTCC 59.852 42.308 9.23 0.00 42.24 3.85
3177 7709 4.597940 ACTTGGCTAATATTACTCCCTCCC 59.402 45.833 0.00 0.00 0.00 4.30
3180 7712 5.232347 TGGCTAATATTACTCCCTCCCTTT 58.768 41.667 0.00 0.00 0.00 3.11
3233 7765 9.458374 AAATTTGAACTAAAACCACGATACTTG 57.542 29.630 0.00 0.00 0.00 3.16
3238 7770 7.911205 TGAACTAAAACCACGATACTTGTTTTG 59.089 33.333 8.90 3.34 40.16 2.44
3239 7771 6.731164 ACTAAAACCACGATACTTGTTTTGG 58.269 36.000 8.90 8.45 41.80 3.28
3278 7810 8.103305 ACTTCATTAGGAACTATCAGCAAGAAA 58.897 33.333 0.00 0.00 42.38 2.52
3281 7813 4.917906 AGGAACTATCAGCAAGAAAGGT 57.082 40.909 0.00 0.00 36.02 3.50
3292 7824 6.405538 TCAGCAAGAAAGGTTGTTTCATTTT 58.594 32.000 0.68 0.00 0.00 1.82
3493 8039 8.522542 AATATATACTCCCTCCGTTCACTATC 57.477 38.462 0.00 0.00 0.00 2.08
3508 8054 9.698309 CCGTTCACTATCATAAGATGTTCTAAT 57.302 33.333 0.00 0.00 35.67 1.73
3622 8169 7.979444 AACGTCTTATTTTTCTGAATGGAGA 57.021 32.000 0.00 0.00 0.00 3.71
3671 8233 3.786635 CAGATCAACTGGCTGTACTACC 58.213 50.000 0.00 0.00 42.39 3.18
3729 8291 7.648510 CGTCTACTCACTGAAGTAAGTTCTTTT 59.351 37.037 0.00 0.00 35.99 2.27
3783 8351 5.120674 TCAGTCATTGCAGAAATCTAACACG 59.879 40.000 0.00 0.00 0.00 4.49
3936 8505 4.142182 CCAAGAAAACAAGCAACTGGAAGA 60.142 41.667 0.00 0.00 37.43 2.87
3963 8533 3.200825 CACATCTGTTAGGGGGTCTCAAT 59.799 47.826 0.00 0.00 0.00 2.57
3964 8534 3.456277 ACATCTGTTAGGGGGTCTCAATC 59.544 47.826 0.00 0.00 0.00 2.67
3965 8535 3.491766 TCTGTTAGGGGGTCTCAATCT 57.508 47.619 0.00 0.00 0.00 2.40
3966 8536 3.375699 TCTGTTAGGGGGTCTCAATCTC 58.624 50.000 0.00 0.00 0.00 2.75
3967 8537 3.107601 CTGTTAGGGGGTCTCAATCTCA 58.892 50.000 0.00 0.00 0.00 3.27
3968 8538 3.519510 CTGTTAGGGGGTCTCAATCTCAA 59.480 47.826 0.00 0.00 0.00 3.02
4177 8754 9.914834 AAATACAGCCATAGTTACCAAAATAGA 57.085 29.630 0.00 0.00 0.00 1.98
4216 8793 7.442656 ACTACACACCATAATGAAGCCTATAC 58.557 38.462 0.00 0.00 0.00 1.47
4221 8798 8.097038 CACACCATAATGAAGCCTATACTGTAT 58.903 37.037 5.53 5.53 0.00 2.29
4222 8799 9.321532 ACACCATAATGAAGCCTATACTGTATA 57.678 33.333 7.28 7.28 0.00 1.47
4225 8802 8.204836 CCATAATGAAGCCTATACTGTATACCC 58.795 40.741 3.44 0.00 0.00 3.69
4226 8803 6.622427 AATGAAGCCTATACTGTATACCCC 57.378 41.667 3.44 0.00 0.00 4.95
4227 8804 4.422984 TGAAGCCTATACTGTATACCCCC 58.577 47.826 3.44 0.00 0.00 5.40
4228 8805 4.109106 TGAAGCCTATACTGTATACCCCCT 59.891 45.833 3.44 0.00 0.00 4.79
4229 8806 4.334208 AGCCTATACTGTATACCCCCTC 57.666 50.000 3.44 0.00 0.00 4.30
4238 8815 2.021441 TGTATACCCCCTCTGTTCCCAT 60.021 50.000 0.00 0.00 0.00 4.00
4245 8822 3.048600 CCCCTCTGTTCCCATCAGAATA 58.951 50.000 0.00 0.00 40.68 1.75
4266 8843 9.582431 AGAATAATCAATTTTCATGCAAGTCAG 57.418 29.630 0.00 0.00 0.00 3.51
4274 9758 6.822667 TTTTCATGCAAGTCAGACATATGT 57.177 33.333 8.43 8.43 0.00 2.29
4283 9767 8.664798 TGCAAGTCAGACATATGTATGTTTAAC 58.335 33.333 25.42 17.64 46.20 2.01
4287 9771 9.905713 AGTCAGACATATGTATGTTTAACCAAT 57.094 29.630 25.42 5.49 46.20 3.16
4460 9953 9.840427 AATAATACACATTATATTTTGGAGCGC 57.160 29.630 0.00 0.00 36.51 5.92
4501 9994 6.371548 GGAGTTTCTTTTTGCCAGAAAACTTT 59.628 34.615 0.00 0.00 40.99 2.66
4502 9995 7.364522 AGTTTCTTTTTGCCAGAAAACTTTC 57.635 32.000 0.00 0.00 40.99 2.62
4523 10016 9.113838 ACTTTCGATCTTTTCATTATAGCATGT 57.886 29.630 0.00 0.00 0.00 3.21
4528 10021 8.008279 CGATCTTTTCATTATAGCATGTCAGTG 58.992 37.037 0.00 0.00 0.00 3.66
4531 10024 9.665719 TCTTTTCATTATAGCATGTCAGTGTAA 57.334 29.630 0.00 0.00 0.00 2.41
4572 10065 9.547753 ACAATAATTACATCCATGTCTGTAGAC 57.452 33.333 5.09 5.09 44.97 2.59
4575 10068 3.895232 ACATCCATGTCTGTAGACCAC 57.105 47.619 9.37 0.00 44.15 4.16
4576 10069 2.166459 ACATCCATGTCTGTAGACCACG 59.834 50.000 9.37 0.00 44.15 4.94
4580 10073 2.479730 CCATGTCTGTAGACCACGTAGC 60.480 54.545 9.37 0.00 44.15 3.58
4602 10095 3.717707 GACGAATATAAGCACTGGAGCA 58.282 45.455 0.00 0.00 36.85 4.26
4607 10100 0.329261 ATAAGCACTGGAGCAAGCCA 59.671 50.000 0.00 0.00 36.85 4.75
4621 10114 2.671619 GCCAAAGGCGTGCTACCA 60.672 61.111 0.00 0.00 39.62 3.25
4628 10121 0.761187 AGGCGTGCTACCATCATCAT 59.239 50.000 0.00 0.00 0.00 2.45
4666 10175 2.496111 CGGGCCAAACTTGTTGTAGTA 58.504 47.619 4.39 0.00 0.00 1.82
4667 10176 2.224784 CGGGCCAAACTTGTTGTAGTAC 59.775 50.000 4.39 0.00 0.00 2.73
4669 10178 3.004002 GGGCCAAACTTGTTGTAGTACAC 59.996 47.826 4.39 0.00 0.00 2.90
4674 10183 5.583061 CCAAACTTGTTGTAGTACACAGTCA 59.417 40.000 1.43 0.00 38.72 3.41
4679 10188 5.601583 TGTTGTAGTACACAGTCAGGAAA 57.398 39.130 1.43 0.00 38.72 3.13
4681 10190 6.588204 TGTTGTAGTACACAGTCAGGAAATT 58.412 36.000 1.43 0.00 38.72 1.82
4684 10193 6.220930 TGTAGTACACAGTCAGGAAATTGTC 58.779 40.000 0.00 0.00 31.89 3.18
4692 10201 3.997021 AGTCAGGAAATTGTCGTGCTAAG 59.003 43.478 0.00 0.00 41.11 2.18
4693 10202 3.994392 GTCAGGAAATTGTCGTGCTAAGA 59.006 43.478 0.00 0.00 41.11 2.10
4704 10214 0.977395 GTGCTAAGACCCACAGGACT 59.023 55.000 0.00 0.00 40.10 3.85
4711 10221 0.905357 GACCCACAGGACTAGCACAT 59.095 55.000 0.00 0.00 36.73 3.21
4712 10222 0.615331 ACCCACAGGACTAGCACATG 59.385 55.000 0.00 0.00 36.73 3.21
4719 10229 3.324846 ACAGGACTAGCACATGAGAACAA 59.675 43.478 0.00 0.00 0.00 2.83
4731 10241 4.154737 ACATGAGAACAACAACCATCATCG 59.845 41.667 0.00 0.00 0.00 3.84
4765 10275 7.588497 AGTATAAATTGAAAGAATCCAGCCC 57.412 36.000 0.00 0.00 0.00 5.19
4766 10276 7.125391 AGTATAAATTGAAAGAATCCAGCCCA 58.875 34.615 0.00 0.00 0.00 5.36
4769 10279 6.475596 AAATTGAAAGAATCCAGCCCATAG 57.524 37.500 0.00 0.00 0.00 2.23
4795 10305 2.036733 ACGAACGAAGACTGGATCCAAA 59.963 45.455 17.00 0.00 0.00 3.28
4796 10306 2.412089 CGAACGAAGACTGGATCCAAAC 59.588 50.000 17.00 12.41 0.00 2.93
4822 10332 0.037605 ACCGAAGACCAACACCGATC 60.038 55.000 0.00 0.00 0.00 3.69
4825 10335 1.667756 CGAAGACCAACACCGATCGAA 60.668 52.381 18.66 0.00 0.00 3.71
4848 10358 0.914644 AGAGCCTAGCAGCCATCAAA 59.085 50.000 0.00 0.00 0.00 2.69
4874 10384 6.825721 GGGATATGGACAATGACTATGAATCC 59.174 42.308 3.56 3.56 0.00 3.01
4878 10388 6.566079 TGGACAATGACTATGAATCCTCTT 57.434 37.500 0.00 0.00 0.00 2.85
4885 10395 6.161855 TGACTATGAATCCTCTTTGCGTAT 57.838 37.500 0.00 0.00 0.00 3.06
4934 10444 4.763793 CCCATATCCTTCACAATGATGACC 59.236 45.833 0.00 0.00 0.00 4.02
4943 10453 3.932710 TCACAATGATGACCGAAGCTTAC 59.067 43.478 0.00 0.00 0.00 2.34
4944 10454 3.063997 CACAATGATGACCGAAGCTTACC 59.936 47.826 0.00 0.00 0.00 2.85
4945 10455 2.225068 ATGATGACCGAAGCTTACCG 57.775 50.000 0.00 0.00 0.00 4.02
4946 10456 0.459585 TGATGACCGAAGCTTACCGC 60.460 55.000 0.00 0.00 39.57 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.737172 GTGGTGCCATGGTCGTGC 61.737 66.667 14.67 0.00 0.00 5.34
12 13 3.055719 GGTGGTGCCATGGTCGTG 61.056 66.667 14.67 0.00 37.17 4.35
13 14 3.565214 TGGTGGTGCCATGGTCGT 61.565 61.111 14.67 0.00 43.61 4.34
20 21 1.073025 GTGATCTGTGGTGGTGCCA 59.927 57.895 0.00 0.00 46.95 4.92
21 22 1.073025 TGTGATCTGTGGTGGTGCC 59.927 57.895 0.00 0.00 37.90 5.01
22 23 0.250467 AGTGTGATCTGTGGTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
23 24 1.516161 CAGTGTGATCTGTGGTGGTG 58.484 55.000 0.00 0.00 0.00 4.17
25 26 0.957395 GGCAGTGTGATCTGTGGTGG 60.957 60.000 0.00 0.00 37.70 4.61
26 27 1.293963 CGGCAGTGTGATCTGTGGTG 61.294 60.000 0.00 0.00 37.70 4.17
27 28 1.004560 CGGCAGTGTGATCTGTGGT 60.005 57.895 0.00 0.00 37.70 4.16
28 29 2.393768 GCGGCAGTGTGATCTGTGG 61.394 63.158 0.00 0.00 37.70 4.17
29 30 2.733671 CGCGGCAGTGTGATCTGTG 61.734 63.158 0.00 0.00 37.70 3.66
30 31 2.433145 CGCGGCAGTGTGATCTGT 60.433 61.111 0.00 0.00 37.70 3.41
31 32 3.857854 GCGCGGCAGTGTGATCTG 61.858 66.667 8.83 0.00 38.35 2.90
32 33 3.997064 GAGCGCGGCAGTGTGATCT 62.997 63.158 8.83 0.00 32.32 2.75
33 34 3.558411 GAGCGCGGCAGTGTGATC 61.558 66.667 8.83 0.00 0.00 2.92
54 55 3.702048 TGGGACGTGGTGCTAGGC 61.702 66.667 0.00 0.00 0.00 3.93
74 75 3.284449 GTTCCGGCCGTGTTTGCT 61.284 61.111 26.12 0.00 0.00 3.91
206 207 2.745037 CGGTTTCTTCCCACGGGA 59.255 61.111 0.00 0.00 43.52 5.14
211 212 2.281208 CGTGGCGGTTTCTTCCCA 60.281 61.111 0.00 0.00 0.00 4.37
253 256 2.677228 CAAAGCCCCCTCACCGAT 59.323 61.111 0.00 0.00 0.00 4.18
286 289 1.025113 CGTCTCCTCCGCTACAGTCA 61.025 60.000 0.00 0.00 0.00 3.41
331 334 2.472049 GCTCGAGCAGTCGCAAAC 59.528 61.111 31.91 0.00 46.39 2.93
349 352 3.710722 CTTGGGGGCAGCTCGAGT 61.711 66.667 15.13 0.00 0.00 4.18
350 353 3.382803 CTCTTGGGGGCAGCTCGAG 62.383 68.421 8.45 8.45 0.00 4.04
357 360 3.706373 GTCGCTCTCTTGGGGGCA 61.706 66.667 0.00 0.00 0.00 5.36
716 724 4.502259 CCCGGTGAAATCCAAAAACAATGA 60.502 41.667 0.00 0.00 0.00 2.57
766 809 5.067805 ACCAAATCAGGACAGTGTTTCTTTC 59.932 40.000 0.00 0.00 0.00 2.62
804 850 2.094894 CGTGTGACCATCTCATTGAAGC 59.905 50.000 0.00 0.00 0.00 3.86
970 1025 0.697079 AGCCTCATATGGGGATGCAG 59.303 55.000 26.65 1.95 0.00 4.41
1180 1243 7.701501 GGGTAATTCTTAGTAACTGAGAACGAG 59.298 40.741 0.00 0.00 38.55 4.18
1294 1357 3.259064 GCATCAACTCCTGCGTAAGTTA 58.741 45.455 0.00 0.00 34.05 2.24
1295 1358 2.076863 GCATCAACTCCTGCGTAAGTT 58.923 47.619 0.00 0.00 41.68 2.66
1301 1364 1.672030 TGGTGCATCAACTCCTGCG 60.672 57.895 0.00 0.00 41.32 5.18
1365 1428 3.616821 CGTCGATGCAAGAAGATTGGTAA 59.383 43.478 0.00 0.00 0.00 2.85
1374 1437 2.349438 GCTTTTGTCGTCGATGCAAGAA 60.349 45.455 0.00 9.76 0.00 2.52
1628 3779 3.006967 AGTCAGGAGCAAAGATAACGTGT 59.993 43.478 0.00 0.00 0.00 4.49
1629 3780 3.589988 AGTCAGGAGCAAAGATAACGTG 58.410 45.455 0.00 0.00 0.00 4.49
1630 3781 3.963428 AGTCAGGAGCAAAGATAACGT 57.037 42.857 0.00 0.00 0.00 3.99
1631 3782 5.592054 TCATAGTCAGGAGCAAAGATAACG 58.408 41.667 0.00 0.00 0.00 3.18
1876 4070 4.222810 TGCTTACTTACCTTGCTCATCTGA 59.777 41.667 0.00 0.00 0.00 3.27
1905 4099 3.265995 ACAAGAATTATGGAACGGAGGGT 59.734 43.478 0.00 0.00 0.00 4.34
1970 6127 6.618287 TCTTCATTGGTGTTGTAAGTCTTG 57.382 37.500 0.00 0.00 0.00 3.02
2177 6675 9.527157 TGGGTTCATGAATTAGTCTTTGATTTA 57.473 29.630 12.12 0.00 0.00 1.40
2186 6684 5.343249 GCATGTTGGGTTCATGAATTAGTC 58.657 41.667 12.12 0.00 43.47 2.59
2323 6822 0.749818 TGCAAAGCAAACTGTCCCGA 60.750 50.000 0.00 0.00 34.76 5.14
2359 6858 7.921214 AGAATATGTATAGTTTGTCACTGACCG 59.079 37.037 6.72 0.00 35.97 4.79
2363 6862 8.654230 AGCAGAATATGTATAGTTTGTCACTG 57.346 34.615 0.00 0.00 35.97 3.66
2416 6920 7.801716 TCAAGAAAATTGCTGTACTTACTGT 57.198 32.000 0.00 0.00 0.00 3.55
2426 6930 6.334989 TCCTGCATATTCAAGAAAATTGCTG 58.665 36.000 12.79 12.05 0.00 4.41
2435 6939 6.653020 ACACAGTATTCCTGCATATTCAAGA 58.347 36.000 0.00 0.00 45.68 3.02
2494 6998 5.008613 TGACAAGCAACTGAAATAGTCCAAC 59.991 40.000 0.00 0.00 39.18 3.77
2567 7074 8.723942 AATAGATCATGTCAGTTTTCTGTACC 57.276 34.615 0.00 0.00 46.98 3.34
2701 7212 0.586802 GTTGGGTCAAGAGCGAACAC 59.413 55.000 18.07 0.00 43.68 3.32
2706 7217 1.403679 TGTTTTGTTGGGTCAAGAGCG 59.596 47.619 0.00 0.00 0.00 5.03
2740 7251 4.623932 TGCTTCTAGGCTCTTTCTTTCA 57.376 40.909 0.00 0.00 0.00 2.69
2781 7292 4.501071 ACCAAAACTATAGTGTGCTACCG 58.499 43.478 6.06 0.00 0.00 4.02
2850 7376 5.482006 AGGGCAAAATATTCAAAGCAGAAC 58.518 37.500 0.00 0.00 0.00 3.01
3002 7534 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3003 7535 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3005 7537 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3006 7538 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3007 7539 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3010 7542 6.091169 TCGAAAAACGTCTTACATTATGGGAC 59.909 38.462 0.00 1.75 43.13 4.46
3012 7544 6.245724 GTCGAAAAACGTCTTACATTATGGG 58.754 40.000 0.00 0.00 43.13 4.00
3013 7545 5.949787 CGTCGAAAAACGTCTTACATTATGG 59.050 40.000 0.00 0.00 43.13 2.74
3014 7546 5.443763 GCGTCGAAAAACGTCTTACATTATG 59.556 40.000 0.00 0.00 44.38 1.90
3015 7547 5.346822 AGCGTCGAAAAACGTCTTACATTAT 59.653 36.000 0.00 0.00 44.38 1.28
3016 7548 4.681025 AGCGTCGAAAAACGTCTTACATTA 59.319 37.500 0.00 0.00 44.38 1.90
3017 7549 3.492011 AGCGTCGAAAAACGTCTTACATT 59.508 39.130 0.00 0.00 44.38 2.71
3018 7550 3.054878 AGCGTCGAAAAACGTCTTACAT 58.945 40.909 0.00 0.00 44.38 2.29
3019 7551 2.462889 AGCGTCGAAAAACGTCTTACA 58.537 42.857 0.00 0.00 44.38 2.41
3020 7552 3.665871 ACTAGCGTCGAAAAACGTCTTAC 59.334 43.478 0.00 0.00 44.38 2.34
3021 7553 3.665409 CACTAGCGTCGAAAAACGTCTTA 59.335 43.478 0.00 0.00 44.38 2.10
3022 7554 2.470257 CACTAGCGTCGAAAAACGTCTT 59.530 45.455 0.00 0.00 44.38 3.01
3023 7555 2.049228 CACTAGCGTCGAAAAACGTCT 58.951 47.619 0.00 0.00 44.38 4.18
3024 7556 1.783140 ACACTAGCGTCGAAAAACGTC 59.217 47.619 0.00 0.00 44.38 4.34
3025 7557 1.843992 ACACTAGCGTCGAAAAACGT 58.156 45.000 0.00 0.00 44.38 3.99
3026 7558 2.975851 ACTACACTAGCGTCGAAAAACG 59.024 45.455 0.00 0.00 45.31 3.60
3027 7559 3.732721 ACACTACACTAGCGTCGAAAAAC 59.267 43.478 0.00 0.00 0.00 2.43
3028 7560 3.968649 ACACTACACTAGCGTCGAAAAA 58.031 40.909 0.00 0.00 0.00 1.94
3029 7561 3.003585 TGACACTACACTAGCGTCGAAAA 59.996 43.478 0.00 0.00 39.95 2.29
3030 7562 2.549329 TGACACTACACTAGCGTCGAAA 59.451 45.455 0.00 0.00 39.95 3.46
3031 7563 2.145536 TGACACTACACTAGCGTCGAA 58.854 47.619 0.00 0.00 39.95 3.71
3032 7564 1.799544 TGACACTACACTAGCGTCGA 58.200 50.000 0.00 0.00 39.95 4.20
3033 7565 2.606717 TTGACACTACACTAGCGTCG 57.393 50.000 0.00 0.00 39.95 5.12
3052 7584 8.795842 TCTGTCCCATAATGTAATACGTTTTT 57.204 30.769 2.96 0.00 0.00 1.94
3053 7585 7.497909 CCTCTGTCCCATAATGTAATACGTTTT 59.502 37.037 2.96 0.00 0.00 2.43
3054 7586 6.990349 CCTCTGTCCCATAATGTAATACGTTT 59.010 38.462 2.96 0.00 0.00 3.60
3055 7587 6.463897 CCCTCTGTCCCATAATGTAATACGTT 60.464 42.308 0.00 3.19 0.00 3.99
3056 7588 5.011738 CCCTCTGTCCCATAATGTAATACGT 59.988 44.000 0.00 0.00 0.00 3.57
3057 7589 5.245301 TCCCTCTGTCCCATAATGTAATACG 59.755 44.000 0.00 0.00 0.00 3.06
3058 7590 6.270231 ACTCCCTCTGTCCCATAATGTAATAC 59.730 42.308 0.00 0.00 0.00 1.89
3059 7591 6.390504 ACTCCCTCTGTCCCATAATGTAATA 58.609 40.000 0.00 0.00 0.00 0.98
3060 7592 5.227593 ACTCCCTCTGTCCCATAATGTAAT 58.772 41.667 0.00 0.00 0.00 1.89
3061 7593 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
3062 7594 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
3063 7595 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
3064 7596 4.840680 TCATACTCCCTCTGTCCCATAATG 59.159 45.833 0.00 0.00 0.00 1.90
3065 7597 5.093236 TCATACTCCCTCTGTCCCATAAT 57.907 43.478 0.00 0.00 0.00 1.28
3066 7598 4.552883 TCATACTCCCTCTGTCCCATAA 57.447 45.455 0.00 0.00 0.00 1.90
3067 7599 4.552883 TTCATACTCCCTCTGTCCCATA 57.447 45.455 0.00 0.00 0.00 2.74
3068 7600 3.421394 TTCATACTCCCTCTGTCCCAT 57.579 47.619 0.00 0.00 0.00 4.00
3069 7601 2.838202 GTTTCATACTCCCTCTGTCCCA 59.162 50.000 0.00 0.00 0.00 4.37
3070 7602 2.838202 TGTTTCATACTCCCTCTGTCCC 59.162 50.000 0.00 0.00 0.00 4.46
3071 7603 4.020128 AGTTGTTTCATACTCCCTCTGTCC 60.020 45.833 0.00 0.00 0.00 4.02
3072 7604 5.153950 AGTTGTTTCATACTCCCTCTGTC 57.846 43.478 0.00 0.00 0.00 3.51
3073 7605 6.681729 TTAGTTGTTTCATACTCCCTCTGT 57.318 37.500 0.00 0.00 0.00 3.41
3074 7606 7.979444 TTTTAGTTGTTTCATACTCCCTCTG 57.021 36.000 0.00 0.00 0.00 3.35
3075 7607 9.014297 CAATTTTAGTTGTTTCATACTCCCTCT 57.986 33.333 0.00 0.00 0.00 3.69
3076 7608 8.244113 CCAATTTTAGTTGTTTCATACTCCCTC 58.756 37.037 0.00 0.00 0.00 4.30
3077 7609 7.728532 ACCAATTTTAGTTGTTTCATACTCCCT 59.271 33.333 0.00 0.00 0.00 4.20
3078 7610 7.892609 ACCAATTTTAGTTGTTTCATACTCCC 58.107 34.615 0.00 0.00 0.00 4.30
3079 7611 8.027189 GGACCAATTTTAGTTGTTTCATACTCC 58.973 37.037 0.00 0.00 0.00 3.85
3080 7612 7.749126 CGGACCAATTTTAGTTGTTTCATACTC 59.251 37.037 0.00 0.00 0.00 2.59
3081 7613 7.446013 TCGGACCAATTTTAGTTGTTTCATACT 59.554 33.333 0.00 0.00 0.00 2.12
3082 7614 7.586747 TCGGACCAATTTTAGTTGTTTCATAC 58.413 34.615 0.00 0.00 0.00 2.39
3083 7615 7.747155 TCGGACCAATTTTAGTTGTTTCATA 57.253 32.000 0.00 0.00 0.00 2.15
3084 7616 6.642707 TCGGACCAATTTTAGTTGTTTCAT 57.357 33.333 0.00 0.00 0.00 2.57
3085 7617 6.127703 TGTTCGGACCAATTTTAGTTGTTTCA 60.128 34.615 0.00 0.00 0.00 2.69
3086 7618 6.267070 TGTTCGGACCAATTTTAGTTGTTTC 58.733 36.000 0.00 0.00 0.00 2.78
3087 7619 6.210287 TGTTCGGACCAATTTTAGTTGTTT 57.790 33.333 0.00 0.00 0.00 2.83
3088 7620 5.838531 TGTTCGGACCAATTTTAGTTGTT 57.161 34.783 0.00 0.00 0.00 2.83
3089 7621 5.221165 CCTTGTTCGGACCAATTTTAGTTGT 60.221 40.000 0.00 0.00 0.00 3.32
3090 7622 5.009210 TCCTTGTTCGGACCAATTTTAGTTG 59.991 40.000 0.00 0.00 0.00 3.16
3091 7623 5.134661 TCCTTGTTCGGACCAATTTTAGTT 58.865 37.500 0.00 0.00 0.00 2.24
3092 7624 4.721132 TCCTTGTTCGGACCAATTTTAGT 58.279 39.130 0.00 0.00 0.00 2.24
3093 7625 4.760204 ACTCCTTGTTCGGACCAATTTTAG 59.240 41.667 0.00 0.00 0.00 1.85
3094 7626 4.721132 ACTCCTTGTTCGGACCAATTTTA 58.279 39.130 0.00 0.00 0.00 1.52
3145 7677 7.283329 AGTAATATTAGCCAAGTAGCTTGCTT 58.717 34.615 0.00 0.00 41.41 3.91
3146 7678 6.831976 AGTAATATTAGCCAAGTAGCTTGCT 58.168 36.000 0.00 0.00 41.41 3.91
3147 7679 6.147985 GGAGTAATATTAGCCAAGTAGCTTGC 59.852 42.308 0.00 0.54 41.41 4.01
3148 7680 6.651225 GGGAGTAATATTAGCCAAGTAGCTTG 59.349 42.308 13.53 2.16 41.41 4.01
3160 7692 9.868160 ATTTTGAAAGGGAGGGAGTAATATTAG 57.132 33.333 0.00 0.00 0.00 1.73
3172 7704 6.350445 CCATGACACTTATTTTGAAAGGGAGG 60.350 42.308 0.00 0.00 31.57 4.30
3213 7745 7.377662 CCAAAACAAGTATCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 40.38 3.01
3228 7760 2.438763 TCCCTCCGTTCCAAAACAAGTA 59.561 45.455 0.00 0.00 34.93 2.24
3233 7765 2.038164 AGTACTCCCTCCGTTCCAAAAC 59.962 50.000 0.00 0.00 0.00 2.43
3238 7770 1.553706 TGAAGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3239 7771 3.889520 AATGAAGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
3298 7830 6.110707 GGGCTAAACTACTATTGCACTGTAA 58.889 40.000 0.00 0.00 0.00 2.41
3530 8076 7.388290 ACAAACACACTAAAATGCGTTTATG 57.612 32.000 3.90 6.51 33.63 1.90
3534 8080 5.287513 GTGAACAAACACACTAAAATGCGTT 59.712 36.000 0.00 0.00 40.11 4.84
3608 8155 9.060347 GTCAGCATATATTCTCCATTCAGAAAA 57.940 33.333 0.00 0.00 35.99 2.29
3612 8159 7.822822 TCATGTCAGCATATATTCTCCATTCAG 59.177 37.037 0.00 0.00 33.30 3.02
3622 8169 9.070179 TGCAACTAAATCATGTCAGCATATATT 57.930 29.630 0.00 0.00 33.30 1.28
3671 8233 2.012673 GGCCACAACTGAGAATGCTAG 58.987 52.381 0.00 0.00 0.00 3.42
3729 8291 0.526211 CATGGGTCTCGAACGTCTCA 59.474 55.000 0.00 0.00 0.00 3.27
3783 8351 7.645340 CACTTCATACATTACAAGCAATTAGGC 59.355 37.037 0.00 0.00 0.00 3.93
3833 8402 0.535797 GCCGCTTCTGTACCCTTAGT 59.464 55.000 0.00 0.00 0.00 2.24
3882 8451 6.803154 AATTAGAACCACTTGTTGAGCTAC 57.197 37.500 0.00 0.00 37.29 3.58
3936 8505 1.561542 CCCCCTAACAGATGTGAGCTT 59.438 52.381 0.00 0.00 0.00 3.74
3963 8533 1.070134 AGCTGGCTTTGTACGTTGAGA 59.930 47.619 0.00 0.00 0.00 3.27
3964 8534 1.461127 GAGCTGGCTTTGTACGTTGAG 59.539 52.381 0.00 0.00 0.00 3.02
3965 8535 1.508632 GAGCTGGCTTTGTACGTTGA 58.491 50.000 0.00 0.00 0.00 3.18
3966 8536 0.517316 GGAGCTGGCTTTGTACGTTG 59.483 55.000 0.00 0.00 0.00 4.10
3967 8537 0.107831 TGGAGCTGGCTTTGTACGTT 59.892 50.000 0.00 0.00 0.00 3.99
3968 8538 0.324943 ATGGAGCTGGCTTTGTACGT 59.675 50.000 0.00 0.00 0.00 3.57
4157 8734 6.364701 TGCATCTATTTTGGTAACTATGGCT 58.635 36.000 0.00 0.00 37.61 4.75
4177 8754 2.903784 TGTGTAGTTGTAGGTCCTGCAT 59.096 45.455 10.80 0.00 0.00 3.96
4216 8793 2.047830 GGGAACAGAGGGGGTATACAG 58.952 57.143 5.01 0.00 0.00 2.74
4238 8815 9.577110 GACTTGCATGAAAATTGATTATTCTGA 57.423 29.630 6.60 0.00 0.00 3.27
4245 8822 6.751157 TGTCTGACTTGCATGAAAATTGATT 58.249 32.000 9.51 0.00 0.00 2.57
4262 8839 9.935682 CATTGGTTAAACATACATATGTCTGAC 57.064 33.333 23.63 13.04 45.55 3.51
4299 9783 7.709269 TTAGTATTGCGGACACTGATATTTC 57.291 36.000 1.12 0.00 0.00 2.17
4302 9786 9.772973 TTTATTTAGTATTGCGGACACTGATAT 57.227 29.630 1.12 0.00 0.00 1.63
4440 9933 3.625764 ACGCGCTCCAAAATATAATGTGT 59.374 39.130 5.73 0.00 0.00 3.72
4455 9948 4.092383 TCCTTTTTAAATACTCACGCGCTC 59.908 41.667 5.73 0.00 0.00 5.03
4457 9950 4.142966 ACTCCTTTTTAAATACTCACGCGC 60.143 41.667 5.73 0.00 0.00 6.86
4460 9953 9.946165 AAAGAAACTCCTTTTTAAATACTCACG 57.054 29.630 0.00 0.00 32.89 4.35
4501 9994 7.928167 ACTGACATGCTATAATGAAAAGATCGA 59.072 33.333 0.00 0.00 0.00 3.59
4502 9995 8.008279 CACTGACATGCTATAATGAAAAGATCG 58.992 37.037 0.00 0.00 0.00 3.69
4550 10043 7.497595 GTGGTCTACAGACATGGATGTAATTA 58.502 38.462 11.31 0.00 46.47 1.40
4566 10059 1.789751 CGTCGCTACGTGGTCTACA 59.210 57.895 2.05 0.00 44.21 2.74
4567 10060 4.659002 CGTCGCTACGTGGTCTAC 57.341 61.111 2.05 0.00 44.21 2.59
4576 10069 3.669122 CCAGTGCTTATATTCGTCGCTAC 59.331 47.826 0.00 0.00 0.00 3.58
4580 10073 2.726760 GCTCCAGTGCTTATATTCGTCG 59.273 50.000 0.00 0.00 0.00 5.12
4585 10078 3.217626 GGCTTGCTCCAGTGCTTATATT 58.782 45.455 0.00 0.00 0.00 1.28
4586 10079 2.173356 TGGCTTGCTCCAGTGCTTATAT 59.827 45.455 0.00 0.00 0.00 0.86
4592 10085 1.288127 CTTTGGCTTGCTCCAGTGC 59.712 57.895 0.00 0.00 37.44 4.40
4607 10100 1.065491 TGATGATGGTAGCACGCCTTT 60.065 47.619 0.00 0.00 0.00 3.11
4614 10107 2.373169 GGAAGGGATGATGATGGTAGCA 59.627 50.000 0.00 0.00 0.00 3.49
4615 10108 2.641815 AGGAAGGGATGATGATGGTAGC 59.358 50.000 0.00 0.00 0.00 3.58
4617 10110 3.648067 GTGAGGAAGGGATGATGATGGTA 59.352 47.826 0.00 0.00 0.00 3.25
4618 10111 2.441001 GTGAGGAAGGGATGATGATGGT 59.559 50.000 0.00 0.00 0.00 3.55
4621 10114 2.709934 CCAGTGAGGAAGGGATGATGAT 59.290 50.000 0.00 0.00 41.22 2.45
4666 10175 2.872245 CACGACAATTTCCTGACTGTGT 59.128 45.455 0.00 0.00 0.00 3.72
4667 10176 2.349817 GCACGACAATTTCCTGACTGTG 60.350 50.000 0.00 0.00 0.00 3.66
4669 10178 2.146342 AGCACGACAATTTCCTGACTG 58.854 47.619 0.00 0.00 0.00 3.51
4674 10183 3.335579 GGTCTTAGCACGACAATTTCCT 58.664 45.455 0.00 0.00 33.11 3.36
4679 10188 1.346395 TGTGGGTCTTAGCACGACAAT 59.654 47.619 0.00 0.00 33.11 2.71
4681 10190 0.317160 CTGTGGGTCTTAGCACGACA 59.683 55.000 0.00 0.00 33.11 4.35
4684 10193 0.389948 GTCCTGTGGGTCTTAGCACG 60.390 60.000 0.00 0.00 0.00 5.34
4692 10201 0.905357 ATGTGCTAGTCCTGTGGGTC 59.095 55.000 0.00 0.00 0.00 4.46
4693 10202 0.615331 CATGTGCTAGTCCTGTGGGT 59.385 55.000 0.00 0.00 0.00 4.51
4704 10214 3.814625 TGGTTGTTGTTCTCATGTGCTA 58.185 40.909 0.00 0.00 0.00 3.49
4711 10221 4.001618 TCGATGATGGTTGTTGTTCTCA 57.998 40.909 0.00 0.00 0.00 3.27
4712 10222 4.631377 TCATCGATGATGGTTGTTGTTCTC 59.369 41.667 23.99 0.00 40.15 2.87
4719 10229 6.173339 ACTTAACTTCATCGATGATGGTTGT 58.827 36.000 33.34 27.48 40.15 3.32
4750 10260 3.523157 TGTCTATGGGCTGGATTCTTTCA 59.477 43.478 0.00 0.00 0.00 2.69
4762 10272 0.108992 TCGTTCGTGTGTCTATGGGC 60.109 55.000 0.00 0.00 0.00 5.36
4765 10275 3.604198 CAGTCTTCGTTCGTGTGTCTATG 59.396 47.826 0.00 0.00 0.00 2.23
4766 10276 3.366070 CCAGTCTTCGTTCGTGTGTCTAT 60.366 47.826 0.00 0.00 0.00 1.98
4769 10279 1.129326 CCAGTCTTCGTTCGTGTGTC 58.871 55.000 0.00 0.00 0.00 3.67
4802 10312 0.395312 ATCGGTGTTGGTCTTCGGTT 59.605 50.000 0.00 0.00 0.00 4.44
4825 10335 2.291153 TGATGGCTGCTAGGCTCTTTTT 60.291 45.455 0.00 0.00 41.96 1.94
4840 10350 3.228188 TGTCCATATCCCTTTGATGGC 57.772 47.619 0.00 0.00 40.06 4.40
4848 10358 7.311549 GGATTCATAGTCATTGTCCATATCCCT 60.312 40.741 0.00 0.00 0.00 4.20
4874 10384 7.763172 ATCTTCTCTGTTTATACGCAAAGAG 57.237 36.000 0.00 0.00 31.74 2.85
4878 10388 9.594478 TTATGAATCTTCTCTGTTTATACGCAA 57.406 29.630 0.00 0.00 0.00 4.85
4885 10395 9.102757 GCTGTCATTATGAATCTTCTCTGTTTA 57.897 33.333 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.