Multiple sequence alignment - TraesCS7B01G163700

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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 TraesCS7B01G163700 chr7B 100.000 3264 0 0 1 3264 226177861 226181124 0.000000e+00 6028.0
1 TraesCS7B01G163700 chr7D 95.170 1532 59 6 326 1856 249078886 249080403 0.000000e+00 2405.0
2 TraesCS7B01G163700 chr7D 91.131 654 42 2 2609 3262 249081060 249081697 0.000000e+00 872.0
3 TraesCS7B01G163700 chr7D 93.617 423 25 1 2188 2610 249080671 249081091 5.940000e-177 630.0
4 TraesCS7B01G163700 chr7D 92.917 240 16 1 1 240 249078343 249078581 6.700000e-92 348.0
5 TraesCS7B01G163700 chr7D 79.781 366 47 14 2922 3262 499906226 499905863 1.170000e-59 241.0
6 TraesCS7B01G163700 chr7D 96.154 78 3 0 1992 2069 249080598 249080675 9.510000e-26 128.0
7 TraesCS7B01G163700 chr7A 91.858 1658 99 19 293 1926 266588687 266590332 0.000000e+00 2281.0
8 TraesCS7B01G163700 chr7A 90.879 307 28 0 1 307 266588228 266588534 2.340000e-111 412.0
9 TraesCS7B01G163700 chr7A 92.157 51 3 1 1947 1997 18268227 18268178 1.620000e-08 71.3
10 TraesCS7B01G163700 chr4D 84.688 320 48 1 2741 3059 391479798 391480117 5.260000e-83 318.0
11 TraesCS7B01G163700 chr5B 85.113 309 41 5 2741 3046 313937347 313937653 8.790000e-81 311.0
12 TraesCS7B01G163700 chr5B 94.853 136 5 2 2063 2196 711836948 711837083 9.180000e-51 211.0
13 TraesCS7B01G163700 chr5B 90.152 132 13 0 2612 2743 289166951 289166820 4.330000e-39 172.0
14 TraesCS7B01G163700 chr5B 97.778 45 1 0 1952 1996 664727927 664727971 9.710000e-11 78.7
15 TraesCS7B01G163700 chr2A 83.214 280 39 4 2982 3261 644057799 644058070 1.940000e-62 250.0
16 TraesCS7B01G163700 chr2A 86.321 212 29 0 2741 2952 643806067 643806278 7.040000e-57 231.0
17 TraesCS7B01G163700 chr2A 87.681 138 13 2 2610 2743 643805758 643805895 1.210000e-34 158.0
18 TraesCS7B01G163700 chr2A 95.745 47 2 0 1948 1994 694842534 694842488 3.490000e-10 76.8
19 TraesCS7B01G163700 chr4B 96.324 136 3 2 2057 2191 132331189 132331055 4.240000e-54 222.0
20 TraesCS7B01G163700 chr4B 86.624 157 17 4 2046 2198 40784195 40784039 1.560000e-38 171.0
21 TraesCS7B01G163700 chr1A 94.815 135 6 1 2059 2192 562906919 562906785 3.300000e-50 209.0
22 TraesCS7B01G163700 chr3D 78.142 366 53 15 2922 3262 558622956 558622593 1.190000e-49 207.0
23 TraesCS7B01G163700 chr5D 92.908 141 8 2 2061 2200 370109476 370109337 1.540000e-48 204.0
24 TraesCS7B01G163700 chr5D 90.385 52 5 0 1940 1991 325461869 325461920 5.840000e-08 69.4
25 TraesCS7B01G163700 chr5D 100.000 28 0 0 160 187 336649481 336649508 6.000000e-03 52.8
26 TraesCS7B01G163700 chr4A 94.030 134 6 2 2061 2192 589667162 589667295 5.520000e-48 202.0
27 TraesCS7B01G163700 chr6D 92.806 139 8 2 2056 2192 84028357 84028495 1.990000e-47 200.0
28 TraesCS7B01G163700 chr5A 93.431 137 6 3 2059 2192 708307646 708307782 1.990000e-47 200.0
29 TraesCS7B01G163700 chr3A 92.254 142 9 2 2051 2191 161304045 161303905 1.990000e-47 200.0
30 TraesCS7B01G163700 chr3A 93.431 137 6 3 2059 2192 405827977 405828113 1.990000e-47 200.0
31 TraesCS7B01G163700 chr3A 97.727 44 1 0 1953 1996 683351641 683351598 3.490000e-10 76.8
32 TraesCS7B01G163700 chr2D 82.014 139 18 4 2353 2488 588455077 588455211 9.570000e-21 111.0
33 TraesCS7B01G163700 chr2D 97.778 45 1 0 1947 1991 468098303 468098347 9.710000e-11 78.7
34 TraesCS7B01G163700 chr2D 97.674 43 1 0 1948 1990 540546305 540546347 1.260000e-09 75.0
35 TraesCS7B01G163700 chr2D 93.617 47 3 0 1949 1995 7646267 7646221 1.620000e-08 71.3
36 TraesCS7B01G163700 chr3B 97.727 44 1 0 1948 1991 690430086 690430129 3.490000e-10 76.8
37 TraesCS7B01G163700 chr1D 82.222 90 15 1 2477 2566 86431213 86431125 3.490000e-10 76.8
38 TraesCS7B01G163700 chr1B 87.719 57 6 1 2609 2665 445885427 445885372 7.560000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G163700 chr7B 226177861 226181124 3263 False 6028.0 6028 100.0000 1 3264 1 chr7B.!!$F1 3263
1 TraesCS7B01G163700 chr7D 249078343 249081697 3354 False 876.6 2405 93.7978 1 3262 5 chr7D.!!$F1 3261
2 TraesCS7B01G163700 chr7A 266588228 266590332 2104 False 1346.5 2281 91.3685 1 1926 2 chr7A.!!$F1 1925

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
263 265 0.340208 CCTACTGTTCCTCCCCCTCT 59.660 60.000 0.00 0.00 0.00 3.69 F
358 579 0.617935 TGATGGGCAATGACCTTCGA 59.382 50.000 15.20 3.37 37.66 3.71 F
362 583 1.281867 TGGGCAATGACCTTCGATCTT 59.718 47.619 6.71 0.00 0.00 2.40 F
2085 2380 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 1462 0.108585 TCAAGAAGTCGGCAGCCTTT 59.891 50.0 10.54 0.75 0.00 3.11 R
1816 2048 0.178975 ACAAACCAATCGAAGGCCCA 60.179 50.0 0.00 0.00 0.00 5.36 R
2174 2469 0.406750 TGGTACTCCCTCTGTCCGAA 59.593 55.0 0.00 0.00 0.00 4.30 R
3159 3454 0.471591 ATGGCTCTGCTAGGAGGGAG 60.472 60.0 16.46 5.72 34.21 4.30 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
49 50 9.039870 CACAACTCCACAATAGAGATATTCTTC 57.960 37.037 0.00 0.00 37.36 2.87
111 113 5.980698 ATGCATGAAGTTTCGAGAGTATG 57.019 39.130 0.00 0.00 0.00 2.39
125 127 9.784680 TTTCGAGAGTATGATGTAAAACTACTC 57.215 33.333 0.00 0.00 38.92 2.59
128 130 8.121086 CGAGAGTATGATGTAAAACTACTCGAA 58.879 37.037 0.00 0.00 41.88 3.71
192 194 1.751351 CTCTCTTGGTGCCGATCTACA 59.249 52.381 0.00 0.00 0.00 2.74
212 214 1.355720 AGCTACTTTGCCCTCCACATT 59.644 47.619 0.00 0.00 0.00 2.71
227 229 0.949105 ACATTGACACGTCCTTCGCC 60.949 55.000 0.00 0.00 44.19 5.54
228 230 0.948623 CATTGACACGTCCTTCGCCA 60.949 55.000 0.00 0.00 44.19 5.69
246 248 0.901580 CAAATGGTGGGCTGCTTCCT 60.902 55.000 0.00 0.00 0.00 3.36
247 249 0.704076 AAATGGTGGGCTGCTTCCTA 59.296 50.000 0.00 0.00 0.00 2.94
263 265 0.340208 CCTACTGTTCCTCCCCCTCT 59.660 60.000 0.00 0.00 0.00 3.69
271 273 1.920325 CCTCCCCCTCTGCACTTCA 60.920 63.158 0.00 0.00 0.00 3.02
272 274 1.277580 CCTCCCCCTCTGCACTTCAT 61.278 60.000 0.00 0.00 0.00 2.57
275 277 1.839994 TCCCCCTCTGCACTTCATAAG 59.160 52.381 0.00 0.00 0.00 1.73
281 283 3.431486 CCTCTGCACTTCATAAGGGTCTC 60.431 52.174 0.00 0.00 33.31 3.36
287 289 3.386402 CACTTCATAAGGGTCTCTCCTCC 59.614 52.174 0.00 0.00 35.80 4.30
290 292 3.850752 TCATAAGGGTCTCTCCTCCATC 58.149 50.000 0.00 0.00 35.80 3.51
314 481 1.153168 CACCGCCTGGGAACTATGG 60.153 63.158 0.00 0.00 40.75 2.74
334 555 1.812571 GAGACACCAAAACGGATGCAT 59.187 47.619 0.00 0.00 38.63 3.96
358 579 0.617935 TGATGGGCAATGACCTTCGA 59.382 50.000 15.20 3.37 37.66 3.71
362 583 1.281867 TGGGCAATGACCTTCGATCTT 59.718 47.619 6.71 0.00 0.00 2.40
383 604 4.937201 TGCATCTCGTGTAGTCCATAAT 57.063 40.909 0.00 0.00 0.00 1.28
547 768 3.860641 TCATGTACGTGATGCTCATGTT 58.139 40.909 13.87 0.00 43.56 2.71
561 782 2.158559 TCATGTTGCCGCACTTTGTAT 58.841 42.857 0.00 0.00 0.00 2.29
574 795 6.128172 CCGCACTTTGTATTCATTCTTCTCTT 60.128 38.462 0.00 0.00 0.00 2.85
666 887 7.818930 TCAATGAGAAATATTCAAAGTTTGGGC 59.181 33.333 15.47 0.00 0.00 5.36
895 1116 3.416156 AGAAGAGTTTGATTGGGCAGTC 58.584 45.455 0.00 0.00 0.00 3.51
929 1150 1.604278 GAGGCTTTTGCTTTGTCGAGT 59.396 47.619 0.00 0.00 46.54 4.18
1109 1330 2.277057 CGCACTCGCTAATTGCAATTTG 59.723 45.455 28.45 25.87 43.06 2.32
1112 1333 6.226703 GCACTCGCTAATTGCAATTTGCAG 62.227 45.833 38.55 34.36 44.76 4.41
1134 1355 2.400399 CAGCAGCACCAATTTGTTCTG 58.600 47.619 5.17 5.17 0.00 3.02
1171 1392 4.142447 CCTGCAGTCGCTTAAGAACTAGTA 60.142 45.833 13.81 3.47 39.64 1.82
1189 1418 7.450323 ACTAGTAGTAGCTAGGTAGGAGTTT 57.550 40.000 0.00 0.00 41.93 2.66
1233 1462 1.561643 AGGCCAAGACGAAGATCAGA 58.438 50.000 5.01 0.00 0.00 3.27
1658 1890 1.492176 GGAGGCAATGGAGGAAGATCA 59.508 52.381 0.00 0.00 0.00 2.92
1816 2048 0.748729 CCGGAGCTTCTAGACGTCCT 60.749 60.000 13.01 0.00 0.00 3.85
1844 2076 4.461992 TCGATTGGTTTGTTTCTTCGTC 57.538 40.909 0.00 0.00 0.00 4.20
1856 2088 2.051879 TCTTCGTCACTGAGCTTTCG 57.948 50.000 0.00 0.00 0.00 3.46
1857 2089 1.337071 TCTTCGTCACTGAGCTTTCGT 59.663 47.619 0.00 0.00 0.00 3.85
1858 2090 2.551032 TCTTCGTCACTGAGCTTTCGTA 59.449 45.455 0.00 0.00 0.00 3.43
1859 2091 2.327081 TCGTCACTGAGCTTTCGTAC 57.673 50.000 0.00 0.00 0.00 3.67
1875 2135 9.171877 AGCTTTCGTACTACTACTACATAACTT 57.828 33.333 0.00 0.00 0.00 2.66
1927 2187 1.886886 TTCCCCGTTAAAGTCACAGC 58.113 50.000 0.00 0.00 0.00 4.40
1928 2188 0.320073 TCCCCGTTAAAGTCACAGCG 60.320 55.000 0.00 0.00 0.00 5.18
1929 2189 0.601841 CCCCGTTAAAGTCACAGCGT 60.602 55.000 0.00 0.00 0.00 5.07
1932 2192 2.801679 CCCGTTAAAGTCACAGCGTTAA 59.198 45.455 0.00 0.00 0.00 2.01
1933 2193 3.248125 CCCGTTAAAGTCACAGCGTTAAA 59.752 43.478 0.00 0.00 0.00 1.52
1934 2194 4.451557 CCGTTAAAGTCACAGCGTTAAAG 58.548 43.478 0.00 0.00 0.00 1.85
1935 2195 4.025480 CCGTTAAAGTCACAGCGTTAAAGT 60.025 41.667 0.00 0.00 0.00 2.66
1936 2196 5.128468 CGTTAAAGTCACAGCGTTAAAGTC 58.872 41.667 0.00 0.00 0.00 3.01
1937 2197 5.276489 CGTTAAAGTCACAGCGTTAAAGTCA 60.276 40.000 0.00 0.00 0.00 3.41
1938 2198 4.531659 AAAGTCACAGCGTTAAAGTCAC 57.468 40.909 0.00 0.00 0.00 3.67
1939 2199 3.173668 AGTCACAGCGTTAAAGTCACA 57.826 42.857 0.00 0.00 0.00 3.58
1949 2209 6.584942 CAGCGTTAAAGTCACAGTCATACTTA 59.415 38.462 0.00 0.00 33.24 2.24
1961 2221 6.547880 CACAGTCATACTTATGTACTCCCTCT 59.452 42.308 0.00 0.00 35.26 3.69
1962 2222 6.547880 ACAGTCATACTTATGTACTCCCTCTG 59.452 42.308 0.00 0.00 35.26 3.35
1965 2225 6.773685 GTCATACTTATGTACTCCCTCTGTCT 59.226 42.308 0.00 0.00 35.26 3.41
1981 2241 7.724506 TCCCTCTGTCTCATAATATAAGAACGT 59.275 37.037 0.00 0.00 0.00 3.99
1982 2242 8.361139 CCCTCTGTCTCATAATATAAGAACGTT 58.639 37.037 0.00 0.00 0.00 3.99
2046 2341 8.166422 AGTTTCACAACGATCTTCCTTAATTT 57.834 30.769 0.00 0.00 38.03 1.82
2076 2371 4.683832 CTTGTTATCAAGTACTCCCTCCG 58.316 47.826 0.00 0.00 44.09 4.63
2077 2372 3.705051 TGTTATCAAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
2078 2373 3.698040 TGTTATCAAGTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
2079 2374 1.777941 ATCAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2080 2375 0.324091 TCAAGTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
2081 2376 1.379576 AAGTACTCCCTCCGTCCCG 60.380 63.158 0.00 0.00 0.00 5.14
2082 2377 1.856539 AAGTACTCCCTCCGTCCCGA 61.857 60.000 0.00 0.00 0.00 5.14
2083 2378 1.379044 GTACTCCCTCCGTCCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
2084 2379 0.967380 GTACTCCCTCCGTCCCGAAA 60.967 60.000 0.00 0.00 0.00 3.46
2085 2380 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
2086 2381 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
2087 2382 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
2088 2383 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
2089 2384 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
2090 2385 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
2091 2386 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
2092 2387 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
2093 2388 1.894466 TCCGTCCCGAAATACTTGTCA 59.106 47.619 0.00 0.00 0.00 3.58
2094 2389 2.498481 TCCGTCCCGAAATACTTGTCAT 59.502 45.455 0.00 0.00 0.00 3.06
2095 2390 2.864343 CCGTCCCGAAATACTTGTCATC 59.136 50.000 0.00 0.00 0.00 2.92
2096 2391 3.517602 CGTCCCGAAATACTTGTCATCA 58.482 45.455 0.00 0.00 0.00 3.07
2097 2392 3.930229 CGTCCCGAAATACTTGTCATCAA 59.070 43.478 0.00 0.00 0.00 2.57
2098 2393 4.390603 CGTCCCGAAATACTTGTCATCAAA 59.609 41.667 0.00 0.00 32.87 2.69
2099 2394 5.106869 CGTCCCGAAATACTTGTCATCAAAA 60.107 40.000 0.00 0.00 32.87 2.44
2100 2395 6.403200 CGTCCCGAAATACTTGTCATCAAAAT 60.403 38.462 0.00 0.00 32.87 1.82
2101 2396 6.747280 GTCCCGAAATACTTGTCATCAAAATG 59.253 38.462 0.00 0.00 32.87 2.32
2102 2397 6.657117 TCCCGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2103 2398 7.175816 TCCCGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2104 2399 7.975616 CCCGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2153 2448 9.995003 TTTTAGTTTTAGATGCATCCATTTTGT 57.005 25.926 23.06 5.34 0.00 2.83
2154 2449 9.638239 TTTAGTTTTAGATGCATCCATTTTGTC 57.362 29.630 23.06 6.80 0.00 3.18
2155 2450 6.633856 AGTTTTAGATGCATCCATTTTGTCC 58.366 36.000 23.06 3.05 0.00 4.02
2156 2451 6.211184 AGTTTTAGATGCATCCATTTTGTCCA 59.789 34.615 23.06 0.00 0.00 4.02
2157 2452 6.795144 TTTAGATGCATCCATTTTGTCCAT 57.205 33.333 23.06 2.56 0.00 3.41
2158 2453 6.795144 TTAGATGCATCCATTTTGTCCATT 57.205 33.333 23.06 2.35 0.00 3.16
2159 2454 5.687166 AGATGCATCCATTTTGTCCATTT 57.313 34.783 23.06 0.00 0.00 2.32
2160 2455 6.057321 AGATGCATCCATTTTGTCCATTTT 57.943 33.333 23.06 0.00 0.00 1.82
2161 2456 5.878116 AGATGCATCCATTTTGTCCATTTTG 59.122 36.000 23.06 0.00 0.00 2.44
2162 2457 5.224821 TGCATCCATTTTGTCCATTTTGA 57.775 34.783 0.00 0.00 0.00 2.69
2163 2458 5.806818 TGCATCCATTTTGTCCATTTTGAT 58.193 33.333 0.00 0.00 0.00 2.57
2164 2459 5.644206 TGCATCCATTTTGTCCATTTTGATG 59.356 36.000 0.00 0.00 0.00 3.07
2165 2460 5.875910 GCATCCATTTTGTCCATTTTGATGA 59.124 36.000 0.00 0.00 31.12 2.92
2166 2461 6.183360 GCATCCATTTTGTCCATTTTGATGAC 60.183 38.462 0.00 0.00 31.12 3.06
2167 2462 6.416631 TCCATTTTGTCCATTTTGATGACA 57.583 33.333 0.00 0.00 0.00 3.58
2168 2463 6.824553 TCCATTTTGTCCATTTTGATGACAA 58.175 32.000 0.00 0.00 34.47 3.18
2169 2464 6.930164 TCCATTTTGTCCATTTTGATGACAAG 59.070 34.615 0.00 0.00 37.13 3.16
2170 2465 6.707161 CCATTTTGTCCATTTTGATGACAAGT 59.293 34.615 0.00 0.00 37.13 3.16
2171 2466 7.871973 CCATTTTGTCCATTTTGATGACAAGTA 59.128 33.333 0.00 0.00 37.13 2.24
2172 2467 9.426837 CATTTTGTCCATTTTGATGACAAGTAT 57.573 29.630 0.00 0.00 37.13 2.12
2174 2469 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2175 2470 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2176 2471 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2177 2472 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2178 2473 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2179 2474 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2180 2475 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2181 2476 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
2182 2477 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
2183 2478 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
2184 2479 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
2185 2480 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
2186 2481 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2187 2482 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2188 2483 4.184629 CAAGTATTTTCGGACAGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2189 2484 3.442076 AGTATTTTCGGACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
2348 2643 8.238631 ACTAAGATTTGTCTTCTTCGAGAGTAC 58.761 37.037 0.00 0.00 35.19 2.73
2350 2645 7.164230 AGATTTGTCTTCTTCGAGAGTACAT 57.836 36.000 0.00 0.00 0.00 2.29
2357 2652 7.174426 TGTCTTCTTCGAGAGTACATTTAGACA 59.826 37.037 0.00 0.00 35.94 3.41
2358 2653 8.185505 GTCTTCTTCGAGAGTACATTTAGACAT 58.814 37.037 0.00 0.00 0.00 3.06
2362 2657 9.338622 TCTTCGAGAGTACATTTAGACATATCA 57.661 33.333 0.00 0.00 0.00 2.15
2400 2695 5.243507 TGCAGAAATACCAATGCAAGAGAAA 59.756 36.000 0.00 0.00 45.09 2.52
2415 2710 3.251571 AGAGAAATACAACTCGCCGAAC 58.748 45.455 0.00 0.00 38.08 3.95
2434 2729 1.292992 CAGCGAGCATAGCATGAACA 58.707 50.000 0.00 0.00 40.10 3.18
2435 2730 1.871676 CAGCGAGCATAGCATGAACAT 59.128 47.619 0.00 0.00 40.10 2.71
2439 2734 2.097056 CGAGCATAGCATGAACATCACG 60.097 50.000 0.00 0.00 0.00 4.35
2444 2739 1.730501 AGCATGAACATCACGTCCTG 58.269 50.000 0.00 0.00 0.00 3.86
2448 2743 3.595173 CATGAACATCACGTCCTGGTAA 58.405 45.455 0.00 0.00 0.00 2.85
2518 2813 2.696707 TCCTAACAGAGAACAACACCGT 59.303 45.455 0.00 0.00 0.00 4.83
2532 2827 0.863957 CACCGTGTTTCAACCAACGC 60.864 55.000 0.00 0.00 34.78 4.84
2574 2869 2.683933 TCCCCCTGGACTTCGCTC 60.684 66.667 0.00 0.00 35.03 5.03
2578 2873 2.636412 CCCTGGACTTCGCTCGTCA 61.636 63.158 0.00 0.00 33.11 4.35
2579 2874 1.289066 CCTGGACTTCGCTCGTCAA 59.711 57.895 0.00 0.00 33.11 3.18
2580 2875 1.009389 CCTGGACTTCGCTCGTCAAC 61.009 60.000 0.00 0.00 33.11 3.18
2581 2876 1.337817 CTGGACTTCGCTCGTCAACG 61.338 60.000 0.00 0.00 41.45 4.10
2582 2877 2.717809 GGACTTCGCTCGTCAACGC 61.718 63.158 0.00 0.00 39.60 4.84
2583 2878 2.014554 GACTTCGCTCGTCAACGCA 61.015 57.895 0.00 0.00 39.60 5.24
2584 2879 1.344942 GACTTCGCTCGTCAACGCAT 61.345 55.000 0.00 0.00 39.60 4.73
2585 2880 1.341802 CTTCGCTCGTCAACGCATC 59.658 57.895 0.00 0.00 39.60 3.91
2586 2881 1.344226 CTTCGCTCGTCAACGCATCA 61.344 55.000 0.00 0.00 39.60 3.07
2587 2882 0.941936 TTCGCTCGTCAACGCATCAA 60.942 50.000 0.00 0.00 39.60 2.57
2588 2883 0.735978 TCGCTCGTCAACGCATCAAT 60.736 50.000 0.00 0.00 39.60 2.57
2589 2884 0.314578 CGCTCGTCAACGCATCAATC 60.315 55.000 0.00 0.00 39.60 2.67
2590 2885 0.721154 GCTCGTCAACGCATCAATCA 59.279 50.000 0.00 0.00 39.60 2.57
2591 2886 1.527793 GCTCGTCAACGCATCAATCAC 60.528 52.381 0.00 0.00 39.60 3.06
2592 2887 1.061131 CTCGTCAACGCATCAATCACC 59.939 52.381 0.00 0.00 39.60 4.02
2593 2888 0.096976 CGTCAACGCATCAATCACCC 59.903 55.000 0.00 0.00 0.00 4.61
2594 2889 1.453155 GTCAACGCATCAATCACCCT 58.547 50.000 0.00 0.00 0.00 4.34
2595 2890 1.812571 GTCAACGCATCAATCACCCTT 59.187 47.619 0.00 0.00 0.00 3.95
2596 2891 1.811965 TCAACGCATCAATCACCCTTG 59.188 47.619 0.00 0.00 0.00 3.61
2597 2892 1.811965 CAACGCATCAATCACCCTTGA 59.188 47.619 0.00 0.00 39.35 3.02
2598 2893 2.424601 CAACGCATCAATCACCCTTGAT 59.575 45.455 0.00 0.00 44.66 2.57
2604 2899 4.524802 ATCAATCACCCTTGATGCCTAA 57.475 40.909 0.00 0.00 42.00 2.69
2605 2900 3.889815 TCAATCACCCTTGATGCCTAAG 58.110 45.455 0.00 0.00 42.00 2.18
2606 2901 3.523157 TCAATCACCCTTGATGCCTAAGA 59.477 43.478 0.00 0.00 42.00 2.10
2607 2902 3.853355 ATCACCCTTGATGCCTAAGAG 57.147 47.619 0.00 0.00 41.23 2.85
2648 2943 1.977293 GCCTAAGAGGAGGTGGCAGG 61.977 65.000 0.00 0.00 42.79 4.85
2649 2944 0.618968 CCTAAGAGGAGGTGGCAGGT 60.619 60.000 0.00 0.00 37.67 4.00
2650 2945 0.539051 CTAAGAGGAGGTGGCAGGTG 59.461 60.000 0.00 0.00 0.00 4.00
2651 2946 0.116342 TAAGAGGAGGTGGCAGGTGA 59.884 55.000 0.00 0.00 0.00 4.02
2652 2947 0.768221 AAGAGGAGGTGGCAGGTGAA 60.768 55.000 0.00 0.00 0.00 3.18
2653 2948 0.548682 AGAGGAGGTGGCAGGTGAAT 60.549 55.000 0.00 0.00 0.00 2.57
2654 2949 0.393537 GAGGAGGTGGCAGGTGAATG 60.394 60.000 0.00 0.00 0.00 2.67
2655 2950 1.379044 GGAGGTGGCAGGTGAATGG 60.379 63.158 0.00 0.00 0.00 3.16
2656 2951 2.036256 AGGTGGCAGGTGAATGGC 59.964 61.111 0.00 0.00 45.50 4.40
2664 2959 1.915141 CAGGTGAATGGCAGGACTTT 58.085 50.000 0.00 0.00 0.00 2.66
2674 2969 4.919774 TGGCAGGACTTTATTAGAACCA 57.080 40.909 0.00 0.00 0.00 3.67
2698 2993 1.853963 AGACACCGTCTTAGAGGCAT 58.146 50.000 0.00 0.00 40.28 4.40
2714 3009 1.139989 GCATCGTCGATGGGTGTATG 58.860 55.000 30.80 10.13 40.10 2.39
2719 3014 1.337071 CGTCGATGGGTGTATGTAGCT 59.663 52.381 0.00 0.00 0.00 3.32
2774 3069 3.061848 CCGCCGGCCAGACAAATT 61.062 61.111 23.46 0.00 0.00 1.82
2792 3087 7.833183 AGACAAATTCCTAGCAGATTTTCATCT 59.167 33.333 0.00 0.00 40.79 2.90
2813 3108 1.001378 GATTGTTGCACCTCACCACAC 60.001 52.381 0.00 0.00 0.00 3.82
2820 3115 1.145377 ACCTCACCACACCACGAAC 59.855 57.895 0.00 0.00 0.00 3.95
2891 3186 1.226379 CGCCATTGTAGCCGCAAAG 60.226 57.895 0.00 0.00 31.63 2.77
2892 3187 1.517039 GCCATTGTAGCCGCAAAGC 60.517 57.895 0.00 0.00 31.63 3.51
2893 3188 1.139520 CCATTGTAGCCGCAAAGCC 59.860 57.895 0.00 0.00 31.63 4.35
2894 3189 1.226379 CATTGTAGCCGCAAAGCCG 60.226 57.895 0.00 0.00 31.63 5.52
2895 3190 1.376683 ATTGTAGCCGCAAAGCCGA 60.377 52.632 0.00 0.00 31.63 5.54
2900 3195 0.810031 TAGCCGCAAAGCCGAAGATC 60.810 55.000 0.00 0.00 0.00 2.75
2916 3211 3.435105 AGATCGCATGACAGAGAGAAC 57.565 47.619 0.00 0.00 0.00 3.01
2946 3241 0.467384 CCATCACCTCCACCTAGCTG 59.533 60.000 0.00 0.00 0.00 4.24
2972 3267 4.791069 TAGCCACCCCGACCCTCC 62.791 72.222 0.00 0.00 0.00 4.30
3024 3319 2.440247 CCATTCCAAGGGACGGCC 60.440 66.667 0.00 0.00 29.54 6.13
3029 3324 4.659172 CCAAGGGACGGCCTTGCA 62.659 66.667 7.57 0.00 42.11 4.08
3046 3341 2.203294 AACGTCCCCAGCACCAAC 60.203 61.111 0.00 0.00 0.00 3.77
3057 3352 2.819595 CACCAACGGCCCAGATCG 60.820 66.667 0.00 0.00 0.00 3.69
3115 3410 4.148825 ATCGCTCACCCGCTCACC 62.149 66.667 0.00 0.00 0.00 4.02
3127 3422 1.956170 GCTCACCACACAGACCACG 60.956 63.158 0.00 0.00 0.00 4.94
3159 3454 1.634702 CTCGCTGCTCACTAGGAAAC 58.365 55.000 0.00 0.00 0.00 2.78
3180 3475 1.664873 CCTCCTAGCAGAGCCATCG 59.335 63.158 0.00 0.00 32.17 3.84
3185 3480 0.460811 CTAGCAGAGCCATCGCAACA 60.461 55.000 0.00 0.00 37.52 3.33
3226 3521 4.717629 CTCGCGTCGTTGCCTCCA 62.718 66.667 5.77 0.00 0.00 3.86
3227 3522 4.287781 TCGCGTCGTTGCCTCCAA 62.288 61.111 5.77 0.00 0.00 3.53
3229 3524 3.723348 GCGTCGTTGCCTCCAACC 61.723 66.667 0.00 0.00 46.76 3.77
3230 3525 2.030562 CGTCGTTGCCTCCAACCT 59.969 61.111 1.43 0.00 46.76 3.50
3234 3529 3.365265 GTTGCCTCCAACCTGCCG 61.365 66.667 0.00 0.00 44.37 5.69
3236 3531 3.842925 TTGCCTCCAACCTGCCGTC 62.843 63.158 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.517500 TGGAGTTGTGGAGTGCACATATA 59.482 43.478 18.82 0.41 32.12 0.86
49 50 4.778534 AGACCTTGCATTCATGAACAAG 57.221 40.909 22.77 22.77 39.35 3.16
80 82 7.173218 TCTCGAAACTTCATGCATTTCTACTTT 59.827 33.333 0.00 0.00 31.47 2.66
111 113 8.867112 TGTATGGATTCGAGTAGTTTTACATC 57.133 34.615 0.00 0.00 31.96 3.06
125 127 6.182039 AGTGTGTTCATTTGTATGGATTCG 57.818 37.500 0.00 0.00 32.40 3.34
128 130 6.429692 TCGAAAGTGTGTTCATTTGTATGGAT 59.570 34.615 0.00 0.00 32.40 3.41
192 194 0.995024 ATGTGGAGGGCAAAGTAGCT 59.005 50.000 0.00 0.00 34.17 3.32
212 214 0.250124 ATTTGGCGAAGGACGTGTCA 60.250 50.000 0.00 0.00 44.60 3.58
227 229 0.901580 AGGAAGCAGCCCACCATTTG 60.902 55.000 0.00 0.00 0.00 2.32
228 230 0.704076 TAGGAAGCAGCCCACCATTT 59.296 50.000 0.00 0.00 0.00 2.32
241 243 1.205055 GGGGGAGGAACAGTAGGAAG 58.795 60.000 0.00 0.00 0.00 3.46
246 248 0.617820 GCAGAGGGGGAGGAACAGTA 60.618 60.000 0.00 0.00 0.00 2.74
247 249 1.920835 GCAGAGGGGGAGGAACAGT 60.921 63.158 0.00 0.00 0.00 3.55
263 265 2.501723 GGAGAGACCCTTATGAAGTGCA 59.498 50.000 0.00 0.00 0.00 4.57
271 273 3.582164 GTGATGGAGGAGAGACCCTTAT 58.418 50.000 0.00 0.00 40.05 1.73
272 274 2.687014 CGTGATGGAGGAGAGACCCTTA 60.687 54.545 0.00 0.00 40.05 2.69
275 277 2.022240 GCGTGATGGAGGAGAGACCC 62.022 65.000 0.00 0.00 40.05 4.46
281 283 1.142748 GGTGAGCGTGATGGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69
307 309 3.071892 TCCGTTTTGGTGTCTCCATAGTT 59.928 43.478 0.00 0.00 46.60 2.24
314 481 1.234821 TGCATCCGTTTTGGTGTCTC 58.765 50.000 0.00 0.00 39.52 3.36
349 570 2.480244 CGAGATGCAAGATCGAAGGTCA 60.480 50.000 11.78 0.00 38.72 4.02
358 579 2.760650 TGGACTACACGAGATGCAAGAT 59.239 45.455 0.00 0.00 0.00 2.40
362 583 4.937201 ATTATGGACTACACGAGATGCA 57.063 40.909 0.00 0.00 0.00 3.96
383 604 1.030488 CCAGAGGCGGACGTCTTCTA 61.030 60.000 16.46 0.00 38.96 2.10
423 644 2.128771 AACATAGTGGCCAATCGCTT 57.871 45.000 10.05 0.00 37.74 4.68
547 768 3.081061 AGAATGAATACAAAGTGCGGCA 58.919 40.909 0.00 0.00 0.00 5.69
584 805 8.964150 CGAATACGTGAAGATTGTGTATCATTA 58.036 33.333 0.00 0.00 33.70 1.90
657 878 2.100989 TGTGTAAAACCGCCCAAACTT 58.899 42.857 0.00 0.00 0.00 2.66
666 887 4.033817 TCCGTGTACTTTTGTGTAAAACCG 59.966 41.667 0.00 0.00 32.62 4.44
929 1150 4.529716 AAGGTACCAAGAAACTTGGGAA 57.470 40.909 26.94 15.92 43.71 3.97
1109 1330 2.444700 AAATTGGTGCTGCTGGCTGC 62.445 55.000 15.66 15.66 42.39 5.25
1112 1333 0.249996 AACAAATTGGTGCTGCTGGC 60.250 50.000 0.00 0.00 42.22 4.85
1134 1355 1.527034 TGCAGGAATGCAGACAAGAC 58.473 50.000 0.00 0.00 40.23 3.01
1154 1375 6.362210 AGCTACTACTAGTTCTTAAGCGAC 57.638 41.667 0.00 0.00 31.86 5.19
1171 1392 6.254522 TCTTTCAAACTCCTACCTAGCTACT 58.745 40.000 0.00 0.00 0.00 2.57
1189 1418 5.769662 TCATCTTTTTGGCTAGCTTCTTTCA 59.230 36.000 15.72 0.00 0.00 2.69
1233 1462 0.108585 TCAAGAAGTCGGCAGCCTTT 59.891 50.000 10.54 0.75 0.00 3.11
1422 1651 2.125512 GCCATCGTCGACAAGGCT 60.126 61.111 26.47 1.90 42.01 4.58
1461 1690 1.446099 GTCGACTCCATGCTTCGCA 60.446 57.895 8.70 0.00 44.86 5.10
1466 1695 2.711922 GGGACGTCGACTCCATGCT 61.712 63.158 25.48 1.01 0.00 3.79
1496 1725 0.312102 GACCACTTCTTGCAACAGCC 59.688 55.000 0.00 0.00 0.00 4.85
1658 1890 4.427661 GCTCGTCGTCAGGCAGCT 62.428 66.667 0.00 0.00 0.00 4.24
1816 2048 0.178975 ACAAACCAATCGAAGGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
1844 2076 5.548706 AGTAGTAGTACGAAAGCTCAGTG 57.451 43.478 2.04 0.00 33.97 3.66
1875 2135 5.504853 TCTGTCATATGCCATGTTTAACCA 58.495 37.500 0.00 0.00 0.00 3.67
1927 2187 8.462143 ACATAAGTATGACTGTGACTTTAACG 57.538 34.615 5.33 0.00 37.15 3.18
1932 2192 7.147880 GGGAGTACATAAGTATGACTGTGACTT 60.148 40.741 5.33 0.00 37.15 3.01
1933 2193 6.321690 GGGAGTACATAAGTATGACTGTGACT 59.678 42.308 5.33 0.00 37.15 3.41
1934 2194 6.321690 AGGGAGTACATAAGTATGACTGTGAC 59.678 42.308 5.33 0.00 37.15 3.67
1935 2195 6.432581 AGGGAGTACATAAGTATGACTGTGA 58.567 40.000 5.33 0.00 37.15 3.58
1936 2196 6.547880 AGAGGGAGTACATAAGTATGACTGTG 59.452 42.308 5.33 0.00 37.15 3.66
1937 2197 6.547880 CAGAGGGAGTACATAAGTATGACTGT 59.452 42.308 5.33 0.00 37.15 3.55
1938 2198 6.547880 ACAGAGGGAGTACATAAGTATGACTG 59.452 42.308 5.33 0.00 37.15 3.51
1939 2199 6.674573 ACAGAGGGAGTACATAAGTATGACT 58.325 40.000 5.33 4.68 37.15 3.41
1965 2225 9.961266 CGTGTCAAAAACGTTCTTATATTATGA 57.039 29.630 0.00 0.00 36.31 2.15
2008 2303 8.556517 TCGTTGTGAAACTAATATGACGATAG 57.443 34.615 0.00 0.00 38.04 2.08
2060 2355 1.688627 GGGACGGAGGGAGTACTTGAT 60.689 57.143 0.00 0.00 0.00 2.57
2073 2368 8.687116 TTTGATGACAAGTATTTCGGGACGGA 62.687 42.308 0.00 0.00 44.62 4.69
2074 2369 6.592789 TTTGATGACAAGTATTTCGGGACGG 61.593 44.000 0.00 0.00 44.62 4.79
2075 2370 4.390603 TTTGATGACAAGTATTTCGGGACG 59.609 41.667 0.00 0.00 45.38 4.79
2076 2371 5.873179 TTTGATGACAAGTATTTCGGGAC 57.127 39.130 0.00 0.00 37.32 4.46
2077 2372 6.657117 TCATTTTGATGACAAGTATTTCGGGA 59.343 34.615 0.00 0.00 37.32 5.14
2078 2373 6.851609 TCATTTTGATGACAAGTATTTCGGG 58.148 36.000 0.00 0.00 37.32 5.14
2079 2374 8.915871 ATTCATTTTGATGACAAGTATTTCGG 57.084 30.769 0.00 0.00 37.32 4.30
2127 2422 9.995003 ACAAAATGGATGCATCTAAAACTAAAA 57.005 25.926 25.28 0.70 0.00 1.52
2128 2423 9.638239 GACAAAATGGATGCATCTAAAACTAAA 57.362 29.630 25.28 2.12 0.00 1.85
2129 2424 8.250332 GGACAAAATGGATGCATCTAAAACTAA 58.750 33.333 25.28 3.09 0.00 2.24
2130 2425 7.395772 TGGACAAAATGGATGCATCTAAAACTA 59.604 33.333 25.28 5.97 0.00 2.24
2131 2426 6.211184 TGGACAAAATGGATGCATCTAAAACT 59.789 34.615 25.28 2.21 0.00 2.66
2132 2427 6.397272 TGGACAAAATGGATGCATCTAAAAC 58.603 36.000 25.28 9.59 0.00 2.43
2133 2428 6.602410 TGGACAAAATGGATGCATCTAAAA 57.398 33.333 25.28 10.04 0.00 1.52
2134 2429 6.795144 ATGGACAAAATGGATGCATCTAAA 57.205 33.333 25.28 12.43 0.00 1.85
2135 2430 6.795144 AATGGACAAAATGGATGCATCTAA 57.205 33.333 25.28 14.87 0.00 2.10
2136 2431 6.795144 AAATGGACAAAATGGATGCATCTA 57.205 33.333 25.28 20.79 0.00 1.98
2137 2432 5.687166 AAATGGACAAAATGGATGCATCT 57.313 34.783 25.28 4.53 0.00 2.90
2138 2433 5.875910 TCAAAATGGACAAAATGGATGCATC 59.124 36.000 18.81 18.81 0.00 3.91
2139 2434 5.806818 TCAAAATGGACAAAATGGATGCAT 58.193 33.333 0.00 0.00 0.00 3.96
2140 2435 5.224821 TCAAAATGGACAAAATGGATGCA 57.775 34.783 0.00 0.00 0.00 3.96
2141 2436 5.875910 TCATCAAAATGGACAAAATGGATGC 59.124 36.000 0.00 0.00 33.42 3.91
2142 2437 6.874664 TGTCATCAAAATGGACAAAATGGATG 59.125 34.615 0.00 0.00 33.42 3.51
2143 2438 7.006865 TGTCATCAAAATGGACAAAATGGAT 57.993 32.000 0.00 0.00 33.42 3.41
2144 2439 6.416631 TGTCATCAAAATGGACAAAATGGA 57.583 33.333 0.00 0.00 33.42 3.41
2145 2440 6.707161 ACTTGTCATCAAAATGGACAAAATGG 59.293 34.615 7.70 0.11 34.98 3.16
2146 2441 7.718272 ACTTGTCATCAAAATGGACAAAATG 57.282 32.000 7.70 0.41 34.98 2.32
2148 2443 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2149 2444 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2150 2445 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2151 2446 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2152 2447 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2153 2448 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2154 2449 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2155 2450 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
2156 2451 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
2157 2452 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
2158 2453 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
2159 2454 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
2160 2455 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
2161 2456 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
2162 2457 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
2163 2458 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2164 2459 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2165 2460 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2166 2461 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2167 2462 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
2168 2463 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
2169 2464 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
2170 2465 3.703052 GGTACTCCCTCTGTCCGAAAATA 59.297 47.826 0.00 0.00 0.00 1.40
2171 2466 2.500504 GGTACTCCCTCTGTCCGAAAAT 59.499 50.000 0.00 0.00 0.00 1.82
2172 2467 1.897802 GGTACTCCCTCTGTCCGAAAA 59.102 52.381 0.00 0.00 0.00 2.29
2173 2468 1.203087 TGGTACTCCCTCTGTCCGAAA 60.203 52.381 0.00 0.00 0.00 3.46
2174 2469 0.406750 TGGTACTCCCTCTGTCCGAA 59.593 55.000 0.00 0.00 0.00 4.30
2175 2470 0.406750 TTGGTACTCCCTCTGTCCGA 59.593 55.000 0.00 0.00 0.00 4.55
2176 2471 1.486211 ATTGGTACTCCCTCTGTCCG 58.514 55.000 0.00 0.00 0.00 4.79
2177 2472 5.839606 AGTATAATTGGTACTCCCTCTGTCC 59.160 44.000 0.00 0.00 0.00 4.02
2178 2473 6.980416 AGTATAATTGGTACTCCCTCTGTC 57.020 41.667 0.00 0.00 0.00 3.51
2179 2474 7.011382 CCTAGTATAATTGGTACTCCCTCTGT 58.989 42.308 8.18 0.00 34.43 3.41
2180 2475 7.239438 TCCTAGTATAATTGGTACTCCCTCTG 58.761 42.308 8.18 0.00 34.43 3.35
2181 2476 7.417811 TCCTAGTATAATTGGTACTCCCTCT 57.582 40.000 8.18 0.00 34.43 3.69
2182 2477 8.667592 AATCCTAGTATAATTGGTACTCCCTC 57.332 38.462 8.18 0.00 34.43 4.30
2183 2478 9.461734 AAAATCCTAGTATAATTGGTACTCCCT 57.538 33.333 8.18 0.00 34.43 4.20
2310 2605 5.699839 ACAAATCTTAGTTTCCAACATCGC 58.300 37.500 0.00 0.00 0.00 4.58
2315 2610 7.798982 CGAAGAAGACAAATCTTAGTTTCCAAC 59.201 37.037 0.00 0.00 45.60 3.77
2332 2627 7.528307 TGTCTAAATGTACTCTCGAAGAAGAC 58.472 38.462 0.00 0.00 34.09 3.01
2362 2657 9.461312 TGGTATTTCTGCATTCTACAAAGTTAT 57.539 29.630 0.00 0.00 0.00 1.89
2370 2665 6.135290 TGCATTGGTATTTCTGCATTCTAC 57.865 37.500 0.00 0.00 39.54 2.59
2376 2671 4.334552 TCTCTTGCATTGGTATTTCTGCA 58.665 39.130 0.00 0.00 42.48 4.41
2400 2695 2.750815 GCTGTTCGGCGAGTTGTAT 58.249 52.632 10.46 0.00 0.00 2.29
2415 2710 1.292992 TGTTCATGCTATGCTCGCTG 58.707 50.000 0.00 0.00 0.00 5.18
2434 2729 1.344065 TGGTGTTACCAGGACGTGAT 58.656 50.000 0.00 0.00 44.79 3.06
2435 2730 2.823587 TGGTGTTACCAGGACGTGA 58.176 52.632 0.00 0.00 44.79 4.35
2444 2739 0.179001 AGGGTGTGCTTGGTGTTACC 60.179 55.000 0.00 0.00 39.22 2.85
2448 2743 2.515901 GGAGGGTGTGCTTGGTGT 59.484 61.111 0.00 0.00 0.00 4.16
2455 2750 3.936203 TGTGGTCGGAGGGTGTGC 61.936 66.667 0.00 0.00 0.00 4.57
2518 2813 2.482333 CCCGGCGTTGGTTGAAACA 61.482 57.895 6.01 0.00 0.00 2.83
2532 2827 2.359975 GTCTTTGGAGGTGCCCGG 60.360 66.667 0.00 0.00 34.97 5.73
2544 2839 0.701310 AGGGGGAGTTGGTGGTCTTT 60.701 55.000 0.00 0.00 0.00 2.52
2574 2869 0.096976 GGGTGATTGATGCGTTGACG 59.903 55.000 0.00 0.00 43.27 4.35
2578 2873 2.198827 TCAAGGGTGATTGATGCGTT 57.801 45.000 0.00 0.00 34.31 4.84
2579 2874 2.425143 ATCAAGGGTGATTGATGCGT 57.575 45.000 1.35 0.00 45.82 5.24
2584 2879 3.523157 TCTTAGGCATCAAGGGTGATTGA 59.477 43.478 0.00 0.00 42.03 2.57
2585 2880 3.881688 CTCTTAGGCATCAAGGGTGATTG 59.118 47.826 0.00 0.00 42.03 2.67
2586 2881 3.117738 CCTCTTAGGCATCAAGGGTGATT 60.118 47.826 0.00 0.00 42.03 2.57
2587 2882 2.441001 CCTCTTAGGCATCAAGGGTGAT 59.559 50.000 0.00 0.00 45.80 3.06
2588 2883 1.839994 CCTCTTAGGCATCAAGGGTGA 59.160 52.381 0.00 0.00 38.41 4.02
2589 2884 1.839994 TCCTCTTAGGCATCAAGGGTG 59.160 52.381 0.00 0.00 34.61 4.61
2590 2885 1.840635 GTCCTCTTAGGCATCAAGGGT 59.159 52.381 0.00 0.00 34.61 4.34
2591 2886 1.202580 CGTCCTCTTAGGCATCAAGGG 60.203 57.143 0.00 0.00 34.61 3.95
2592 2887 1.808133 GCGTCCTCTTAGGCATCAAGG 60.808 57.143 0.00 0.00 34.61 3.61
2593 2888 1.134699 TGCGTCCTCTTAGGCATCAAG 60.135 52.381 0.00 0.00 35.48 3.02
2594 2889 0.901827 TGCGTCCTCTTAGGCATCAA 59.098 50.000 0.00 0.00 35.48 2.57
2595 2890 0.175760 GTGCGTCCTCTTAGGCATCA 59.824 55.000 0.00 0.00 41.75 3.07
2596 2891 0.530870 GGTGCGTCCTCTTAGGCATC 60.531 60.000 0.00 0.00 41.75 3.91
2597 2892 1.264749 TGGTGCGTCCTCTTAGGCAT 61.265 55.000 0.00 0.00 41.75 4.40
2598 2893 1.476845 TTGGTGCGTCCTCTTAGGCA 61.477 55.000 0.00 0.00 37.88 4.75
2599 2894 0.107654 ATTGGTGCGTCCTCTTAGGC 60.108 55.000 0.00 0.00 34.61 3.93
2600 2895 1.207089 TGATTGGTGCGTCCTCTTAGG 59.793 52.381 0.00 0.00 36.46 2.69
2601 2896 2.271800 GTGATTGGTGCGTCCTCTTAG 58.728 52.381 0.00 0.00 37.07 2.18
2602 2897 1.066430 GGTGATTGGTGCGTCCTCTTA 60.066 52.381 0.00 0.00 37.07 2.10
2603 2898 0.321653 GGTGATTGGTGCGTCCTCTT 60.322 55.000 0.00 0.00 37.07 2.85
2604 2899 1.296715 GGTGATTGGTGCGTCCTCT 59.703 57.895 0.00 0.00 37.07 3.69
2605 2900 1.745489 GGGTGATTGGTGCGTCCTC 60.745 63.158 0.00 0.00 37.07 3.71
2606 2901 1.779061 AAGGGTGATTGGTGCGTCCT 61.779 55.000 0.00 0.00 37.07 3.85
2607 2902 1.303317 AAGGGTGATTGGTGCGTCC 60.303 57.895 0.00 0.00 0.00 4.79
2648 2943 6.183360 GGTTCTAATAAAGTCCTGCCATTCAC 60.183 42.308 0.00 0.00 0.00 3.18
2649 2944 5.885912 GGTTCTAATAAAGTCCTGCCATTCA 59.114 40.000 0.00 0.00 0.00 2.57
2650 2945 5.885912 TGGTTCTAATAAAGTCCTGCCATTC 59.114 40.000 0.00 0.00 0.00 2.67
2651 2946 5.826643 TGGTTCTAATAAAGTCCTGCCATT 58.173 37.500 0.00 0.00 0.00 3.16
2652 2947 5.450818 TGGTTCTAATAAAGTCCTGCCAT 57.549 39.130 0.00 0.00 0.00 4.40
2653 2948 4.919774 TGGTTCTAATAAAGTCCTGCCA 57.080 40.909 0.00 0.00 0.00 4.92
2654 2949 5.497474 TCTTGGTTCTAATAAAGTCCTGCC 58.503 41.667 0.00 0.00 0.00 4.85
2655 2950 7.390718 TCTTTCTTGGTTCTAATAAAGTCCTGC 59.609 37.037 0.00 0.00 30.36 4.85
2656 2951 8.722394 GTCTTTCTTGGTTCTAATAAAGTCCTG 58.278 37.037 0.00 0.00 30.36 3.86
2657 2952 8.437575 TGTCTTTCTTGGTTCTAATAAAGTCCT 58.562 33.333 0.00 0.00 30.36 3.85
2658 2953 8.504815 GTGTCTTTCTTGGTTCTAATAAAGTCC 58.495 37.037 0.00 0.00 30.36 3.85
2664 2959 6.014840 AGACGGTGTCTTTCTTGGTTCTAATA 60.015 38.462 0.00 0.00 40.28 0.98
2691 2986 1.758514 ACCCATCGACGATGCCTCT 60.759 57.895 28.45 9.93 38.59 3.69
2698 2993 1.335810 GCTACATACACCCATCGACGA 59.664 52.381 0.00 0.00 0.00 4.20
2774 3069 6.656902 ACAATCAGATGAAAATCTGCTAGGA 58.343 36.000 10.25 0.00 45.70 2.94
2792 3087 3.817187 TGGTGAGGTGCAACAATCA 57.183 47.368 3.64 0.00 42.37 2.57
2813 3108 1.501741 CTGCCCAATTCGTTCGTGG 59.498 57.895 0.00 0.00 0.00 4.94
2820 3115 1.503542 GACAGTGCTGCCCAATTCG 59.496 57.895 0.00 0.00 0.00 3.34
2867 3162 2.472909 GGCTACAATGGCGAGGTGC 61.473 63.158 0.00 0.00 45.38 5.01
2891 3186 0.528466 TCTGTCATGCGATCTTCGGC 60.528 55.000 0.00 0.00 40.84 5.54
2892 3187 1.066152 TCTCTGTCATGCGATCTTCGG 59.934 52.381 0.00 0.00 40.84 4.30
2893 3188 2.032675 TCTCTCTGTCATGCGATCTTCG 59.967 50.000 0.00 0.00 43.89 3.79
2894 3189 3.706802 TCTCTCTGTCATGCGATCTTC 57.293 47.619 0.00 0.00 0.00 2.87
2895 3190 3.733380 CGTTCTCTCTGTCATGCGATCTT 60.733 47.826 0.00 0.00 0.00 2.40
2900 3195 1.416813 GCCGTTCTCTCTGTCATGCG 61.417 60.000 0.00 0.00 0.00 4.73
3022 3317 3.365265 CTGGGGACGTTGCAAGGC 61.365 66.667 18.61 11.24 0.00 4.35
3024 3319 2.594303 TGCTGGGGACGTTGCAAG 60.594 61.111 0.00 0.00 32.32 4.01
3029 3324 2.203294 GTTGGTGCTGGGGACGTT 60.203 61.111 0.00 0.00 0.00 3.99
3096 3391 4.147449 TGAGCGGGTGAGCGATGG 62.147 66.667 0.00 0.00 43.00 3.51
3115 3410 2.280797 CCACCCGTGGTCTGTGTG 60.281 66.667 5.66 0.00 45.53 3.82
3152 3447 2.585900 TCTGCTAGGAGGGAGTTTCCTA 59.414 50.000 11.76 1.44 43.21 2.94
3159 3454 0.471591 ATGGCTCTGCTAGGAGGGAG 60.472 60.000 16.46 5.72 34.21 4.30
3180 3475 2.279186 GTTTGGTGGCGGTGTTGC 60.279 61.111 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.