Multiple sequence alignment - TraesCS7D01G430700

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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 TraesCS7D01G430700 chr7D 100.000 5545 0 0 1 5545 550100074 550094530 0.000000e+00 10240.0
1 TraesCS7D01G430700 chr7D 97.222 36 1 0 540 575 154090284 154090249 1.670000e-05 62.1
2 TraesCS7D01G430700 chr7D 97.222 36 1 0 540 575 619662117 619662152 1.670000e-05 62.1
3 TraesCS7D01G430700 chr7D 94.444 36 2 0 540 575 164496261 164496296 7.760000e-04 56.5
4 TraesCS7D01G430700 chr7A 94.995 2038 69 15 780 2801 635497386 635495366 0.000000e+00 3168.0
5 TraesCS7D01G430700 chr7A 92.077 934 40 15 4053 4970 635494157 635493242 0.000000e+00 1284.0
6 TraesCS7D01G430700 chr7A 94.557 790 37 3 3272 4058 635494973 635494187 0.000000e+00 1216.0
7 TraesCS7D01G430700 chr7A 95.739 399 17 0 2753 3151 635495365 635494967 1.300000e-180 643.0
8 TraesCS7D01G430700 chr7A 94.581 203 8 2 209 408 635497908 635497706 1.500000e-80 311.0
9 TraesCS7D01G430700 chr7A 85.549 173 19 4 1 170 635498819 635498650 5.710000e-40 176.0
10 TraesCS7D01G430700 chr7A 100.000 36 0 0 540 575 158655394 158655429 3.580000e-07 67.6
11 TraesCS7D01G430700 chr7A 91.489 47 4 0 4906 4952 506300183 506300137 1.290000e-06 65.8
12 TraesCS7D01G430700 chr7B 89.168 1994 102 71 1 1933 594415913 594413973 0.000000e+00 2381.0
13 TraesCS7D01G430700 chr7B 87.756 1903 133 48 3690 5545 594221321 594219472 0.000000e+00 2132.0
14 TraesCS7D01G430700 chr7B 95.797 928 39 0 2019 2946 594413930 594413003 0.000000e+00 1498.0
15 TraesCS7D01G430700 chr7B 92.787 818 32 16 4053 4854 594411793 594410987 0.000000e+00 1158.0
16 TraesCS7D01G430700 chr7B 93.642 346 22 0 2497 2842 594259046 594258701 8.230000e-143 518.0
17 TraesCS7D01G430700 chr7B 91.667 240 13 4 3824 4057 594412062 594411824 5.360000e-85 326.0
18 TraesCS7D01G430700 chr7B 93.443 183 11 1 3276 3457 594412826 594412644 2.550000e-68 270.0
19 TraesCS7D01G430700 chr7B 91.667 180 10 3 3456 3635 594412235 594412061 1.540000e-60 244.0
20 TraesCS7D01G430700 chr7B 80.180 333 32 21 4545 4870 594367718 594367413 9.350000e-53 219.0
21 TraesCS7D01G430700 chr7B 92.857 126 9 0 3001 3126 594413002 594412877 3.410000e-42 183.0
22 TraesCS7D01G430700 chr7B 92.079 101 8 0 2841 2941 594258586 594258486 5.790000e-30 143.0
23 TraesCS7D01G430700 chr7B 85.938 64 2 5 513 575 715547276 715547333 1.670000e-05 62.1
24 TraesCS7D01G430700 chr6A 97.000 100 3 0 3150 3249 592800064 592799965 9.550000e-38 169.0
25 TraesCS7D01G430700 chr5D 97.222 36 1 0 4905 4940 373764512 373764477 1.670000e-05 62.1
26 TraesCS7D01G430700 chr1D 94.872 39 2 0 540 578 142656850 142656888 1.670000e-05 62.1
27 TraesCS7D01G430700 chr4B 94.872 39 0 2 4906 4942 517166859 517166821 6.000000e-05 60.2
28 TraesCS7D01G430700 chr4A 97.143 35 1 0 4906 4940 45680627 45680661 6.000000e-05 60.2
29 TraesCS7D01G430700 chr4A 97.059 34 1 0 4907 4940 605425356 605425389 2.160000e-04 58.4
30 TraesCS7D01G430700 chr1B 94.737 38 2 0 4903 4940 380884217 380884254 6.000000e-05 60.2
31 TraesCS7D01G430700 chr5B 88.889 45 5 0 4903 4947 538714250 538714294 7.760000e-04 56.5


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 TraesCS7D01G430700 chr7D 550094530 550100074 5544 True 10240.000000 10240 100.000000 1 5545 1 chr7D.!!$R2 5544
1 TraesCS7D01G430700 chr7A 635493242 635498819 5577 True 1133.000000 3168 92.916333 1 4970 6 chr7A.!!$R2 4969
2 TraesCS7D01G430700 chr7B 594219472 594221321 1849 True 2132.000000 2132 87.756000 3690 5545 1 chr7B.!!$R1 1855
3 TraesCS7D01G430700 chr7B 594410987 594415913 4926 True 865.714286 2381 92.483714 1 4854 7 chr7B.!!$R4 4853
4 TraesCS7D01G430700 chr7B 594258486 594259046 560 True 330.500000 518 92.860500 2497 2941 2 chr7B.!!$R3 444

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
351 1104 0.109226 GAGTCGTAAGCAAGTCGCCT 60.109 55.0 0.00 0.0 44.04 5.52 F
777 1634 0.473117 TTCCTCTCCCCGTCCAAGTT 60.473 55.0 0.00 0.0 0.00 2.66 F
1949 2832 0.530744 TGCGCACACTTCCCTACTAG 59.469 55.0 5.66 0.0 0.00 2.57 F
3170 4242 0.181114 CACCAGGCCAAGCTAGCATA 59.819 55.0 18.83 0.0 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 3129 0.959372 CTGAAGAGTTGCAGGCAGGG 60.959 60.0 0.0 0.0 0.00 4.45 R
2393 3276 0.747283 CTGCCTCCTTCCACAGCATC 60.747 60.0 0.0 0.0 32.11 3.91 R
3198 4270 0.037046 GCCTGAAAAATGCCTGGTGG 60.037 55.0 0.0 0.0 0.00 4.61 R
5132 6720 0.596082 CCCAAAGTACAAAGCCCGTG 59.404 55.0 0.0 0.0 0.00 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.446413 CCCGGACGGTTTCCCTCG 62.446 72.222 0.73 0.00 42.27 4.63
86 94 2.352805 GAGGGTGGAAGGGCACAG 59.647 66.667 0.00 0.00 0.00 3.66
93 101 2.671070 GAAGGGCACAGCTAGGCA 59.329 61.111 12.89 0.00 0.00 4.75
95 103 1.903877 GAAGGGCACAGCTAGGCAGA 61.904 60.000 12.89 0.00 0.00 4.26
159 169 9.512588 AAAAGAATATTGTTCTGTCTCATGTCT 57.487 29.630 0.00 0.00 0.00 3.41
160 170 8.715191 AAGAATATTGTTCTGTCTCATGTCTC 57.285 34.615 0.00 0.00 0.00 3.36
161 171 8.076910 AGAATATTGTTCTGTCTCATGTCTCT 57.923 34.615 0.00 0.00 0.00 3.10
162 172 8.196771 AGAATATTGTTCTGTCTCATGTCTCTC 58.803 37.037 0.00 0.00 0.00 3.20
163 173 4.527509 TTGTTCTGTCTCATGTCTCTCC 57.472 45.455 0.00 0.00 0.00 3.71
164 174 3.500343 TGTTCTGTCTCATGTCTCTCCA 58.500 45.455 0.00 0.00 0.00 3.86
165 175 4.092279 TGTTCTGTCTCATGTCTCTCCAT 58.908 43.478 0.00 0.00 0.00 3.41
166 176 4.081807 TGTTCTGTCTCATGTCTCTCCATG 60.082 45.833 0.00 0.00 42.89 3.66
167 177 2.429971 TCTGTCTCATGTCTCTCCATGC 59.570 50.000 0.00 0.00 41.60 4.06
168 178 1.483827 TGTCTCATGTCTCTCCATGCC 59.516 52.381 0.00 0.00 41.60 4.40
169 179 0.749049 TCTCATGTCTCTCCATGCCG 59.251 55.000 0.00 0.00 41.60 5.69
170 180 0.879400 CTCATGTCTCTCCATGCCGC 60.879 60.000 0.00 0.00 41.60 6.53
171 181 1.890979 CATGTCTCTCCATGCCGCC 60.891 63.158 0.00 0.00 36.15 6.13
172 182 3.451556 ATGTCTCTCCATGCCGCCG 62.452 63.158 0.00 0.00 0.00 6.46
173 183 4.148825 GTCTCTCCATGCCGCCGT 62.149 66.667 0.00 0.00 0.00 5.68
205 224 0.535780 TCTTGCCACTGCCACTCAAG 60.536 55.000 0.00 0.00 36.42 3.02
242 970 5.891551 GCAATAAGAAATTCTAGGTGGGGAA 59.108 40.000 0.00 0.00 0.00 3.97
264 1013 6.311690 GGAACTTCGACCAAACAAATGAAAAA 59.688 34.615 0.00 0.00 0.00 1.94
298 1047 1.084289 GGCGAGTCTGCCGTATTTTT 58.916 50.000 9.67 0.00 46.75 1.94
351 1104 0.109226 GAGTCGTAAGCAAGTCGCCT 60.109 55.000 0.00 0.00 44.04 5.52
425 1178 2.204034 TCACAGACCAGGAGCCCA 59.796 61.111 0.00 0.00 0.00 5.36
481 1249 5.408909 TCAATCATTGTAAACGTTCGGCTAA 59.591 36.000 0.00 0.00 0.00 3.09
485 1253 6.670233 TCATTGTAAACGTTCGGCTAAAAAT 58.330 32.000 0.00 0.00 0.00 1.82
486 1254 7.804712 TCATTGTAAACGTTCGGCTAAAAATA 58.195 30.769 0.00 0.00 0.00 1.40
489 1257 9.925268 ATTGTAAACGTTCGGCTAAAAATATAG 57.075 29.630 0.00 0.00 0.00 1.31
491 1259 9.579768 TGTAAACGTTCGGCTAAAAATATAGTA 57.420 29.630 0.00 0.00 0.00 1.82
526 1364 6.863126 CCACTAAAAAGAAAACATAGTGCCAG 59.137 38.462 5.87 0.00 41.19 4.85
530 1368 9.696917 CTAAAAAGAAAACATAGTGCCAGAATT 57.303 29.630 0.00 0.00 0.00 2.17
580 1418 3.443045 GTCCCATGCGGTGCCAAG 61.443 66.667 0.00 0.00 0.00 3.61
593 1436 7.283625 TGCGGTGCCAAGAAATATATAAAAT 57.716 32.000 0.00 0.00 0.00 1.82
594 1437 7.367285 TGCGGTGCCAAGAAATATATAAAATC 58.633 34.615 0.00 0.00 0.00 2.17
595 1438 7.013750 TGCGGTGCCAAGAAATATATAAAATCA 59.986 33.333 0.00 0.00 0.00 2.57
624 1475 9.607285 AAGCAAATAAAATGTAACTCGTACAAG 57.393 29.630 0.00 0.00 45.81 3.16
626 1477 9.601971 GCAAATAAAATGTAACTCGTACAAGAA 57.398 29.630 0.00 0.00 45.81 2.52
775 1632 1.901085 CTTCCTCTCCCCGTCCAAG 59.099 63.158 0.00 0.00 0.00 3.61
776 1633 0.905337 CTTCCTCTCCCCGTCCAAGT 60.905 60.000 0.00 0.00 0.00 3.16
777 1634 0.473117 TTCCTCTCCCCGTCCAAGTT 60.473 55.000 0.00 0.00 0.00 2.66
778 1635 0.473117 TCCTCTCCCCGTCCAAGTTT 60.473 55.000 0.00 0.00 0.00 2.66
856 1717 1.152387 ACCAAACCCATCCCATCCCA 61.152 55.000 0.00 0.00 0.00 4.37
866 1729 2.038438 CCATCCCATCCCCTCCCA 60.038 66.667 0.00 0.00 0.00 4.37
997 1868 2.910479 TATCGCCGCGGACCATCT 60.910 61.111 33.48 8.87 0.00 2.90
1014 1885 3.392595 CTACCCACCGACGAGCGAC 62.393 68.421 0.00 0.00 44.57 5.19
1031 1905 3.341043 CTGCGGCCGATTGATCCG 61.341 66.667 33.48 1.62 45.46 4.18
1306 2186 1.153469 CTTCCGCTTCTCCAGGCTC 60.153 63.158 0.00 0.00 0.00 4.70
1405 2285 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1411 2291 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1948 2831 1.191535 ATGCGCACACTTCCCTACTA 58.808 50.000 14.90 0.00 0.00 1.82
1949 2832 0.530744 TGCGCACACTTCCCTACTAG 59.469 55.000 5.66 0.00 0.00 2.57
1950 2833 0.531200 GCGCACACTTCCCTACTAGT 59.469 55.000 0.30 0.00 0.00 2.57
1953 2836 2.416972 CGCACACTTCCCTACTAGTTCC 60.417 54.545 0.00 0.00 0.00 3.62
1954 2837 2.832733 GCACACTTCCCTACTAGTTCCT 59.167 50.000 0.00 0.00 0.00 3.36
1955 2838 4.021916 GCACACTTCCCTACTAGTTCCTA 58.978 47.826 0.00 0.00 0.00 2.94
1964 2847 8.572884 TTCCCTACTAGTTCCTACTACTCATA 57.427 38.462 0.00 0.00 35.78 2.15
1997 2880 1.825474 GCCTGCCTGTAACAGAGAGTA 59.175 52.381 0.00 0.00 37.32 2.59
2003 2886 5.269991 TGCCTGTAACAGAGAGTATAAGGT 58.730 41.667 0.00 0.00 32.44 3.50
2005 2888 5.360144 GCCTGTAACAGAGAGTATAAGGTGA 59.640 44.000 0.00 0.00 32.44 4.02
2006 2889 6.680872 GCCTGTAACAGAGAGTATAAGGTGAC 60.681 46.154 0.00 0.00 32.44 3.67
2246 3129 2.993853 CCTCTTCCAGTCCAGGGC 59.006 66.667 0.00 0.00 0.00 5.19
2264 3147 1.073722 CCCTGCCTGCAACTCTTCA 59.926 57.895 0.00 0.00 0.00 3.02
2390 3273 2.508526 GCTGGGTTTGTGATGAACTCT 58.491 47.619 0.00 0.00 0.00 3.24
2393 3276 4.256920 CTGGGTTTGTGATGAACTCTAGG 58.743 47.826 0.00 0.00 0.00 3.02
2474 3357 2.371510 GGAGAATGGGGAGGAGATTGAG 59.628 54.545 0.00 0.00 0.00 3.02
2546 3429 2.234908 CTGTGGGAAGAAGGTCCTACTG 59.765 54.545 8.87 5.06 46.52 2.74
2585 3468 3.423154 CGGGCCGACAGCAAGTTC 61.423 66.667 24.41 0.00 46.50 3.01
2650 3533 7.856145 TGTGTTGCTGGTCATTTTAATTTTT 57.144 28.000 0.00 0.00 0.00 1.94
2692 3575 7.727181 AGTATTGTGATGTTCTATAGGACACC 58.273 38.462 16.34 7.36 0.00 4.16
2743 3626 5.300411 TCATGCAACCACAGATCATAGAT 57.700 39.130 0.00 0.00 0.00 1.98
2801 3730 2.706190 AGTTACAAGCCCAGTCTCACTT 59.294 45.455 0.00 0.00 0.00 3.16
2818 3747 3.949113 TCACTTTTTGAAGGGTACACCAC 59.051 43.478 0.00 0.00 43.89 4.16
2823 3752 2.536761 TGAAGGGTACACCACGAAAG 57.463 50.000 0.00 0.00 43.89 2.62
2932 3977 0.615331 CACAGCCACCATGTACCTCT 59.385 55.000 0.00 0.00 0.00 3.69
2978 4023 4.323562 CCCCGTTTAGTCTCTGGAGAATTT 60.324 45.833 5.90 0.00 39.48 1.82
3009 4054 4.990910 AGAGGTGGGCTGGTGGCT 62.991 66.667 0.00 0.00 41.46 4.75
3108 4153 4.826733 AGTGATGTGCTTGGTTGTTGAATA 59.173 37.500 0.00 0.00 0.00 1.75
3149 4221 2.160721 ATCGTGGACACCCAGATAGT 57.839 50.000 0.00 0.00 44.55 2.12
3150 4222 1.933021 TCGTGGACACCCAGATAGTT 58.067 50.000 0.00 0.00 44.55 2.24
3151 4223 1.822990 TCGTGGACACCCAGATAGTTC 59.177 52.381 0.00 0.00 44.55 3.01
3152 4224 1.548719 CGTGGACACCCAGATAGTTCA 59.451 52.381 0.00 0.00 44.55 3.18
3153 4225 2.674177 CGTGGACACCCAGATAGTTCAC 60.674 54.545 0.00 0.00 44.55 3.18
3154 4226 1.906574 TGGACACCCAGATAGTTCACC 59.093 52.381 0.00 0.00 37.58 4.02
3155 4227 1.906574 GGACACCCAGATAGTTCACCA 59.093 52.381 0.00 0.00 0.00 4.17
3156 4228 2.093447 GGACACCCAGATAGTTCACCAG 60.093 54.545 0.00 0.00 0.00 4.00
3157 4229 1.909302 ACACCCAGATAGTTCACCAGG 59.091 52.381 0.00 0.00 0.00 4.45
3158 4230 0.912486 ACCCAGATAGTTCACCAGGC 59.088 55.000 0.00 0.00 0.00 4.85
3159 4231 0.181350 CCCAGATAGTTCACCAGGCC 59.819 60.000 0.00 0.00 0.00 5.19
3160 4232 0.911769 CCAGATAGTTCACCAGGCCA 59.088 55.000 5.01 0.00 0.00 5.36
3161 4233 1.281867 CCAGATAGTTCACCAGGCCAA 59.718 52.381 5.01 0.00 0.00 4.52
3162 4234 2.636830 CAGATAGTTCACCAGGCCAAG 58.363 52.381 5.01 0.00 0.00 3.61
3163 4235 1.065126 AGATAGTTCACCAGGCCAAGC 60.065 52.381 5.01 0.00 0.00 4.01
3164 4236 0.995024 ATAGTTCACCAGGCCAAGCT 59.005 50.000 5.01 0.00 0.00 3.74
3165 4237 1.651737 TAGTTCACCAGGCCAAGCTA 58.348 50.000 5.01 0.00 0.00 3.32
3166 4238 0.326264 AGTTCACCAGGCCAAGCTAG 59.674 55.000 5.01 0.00 0.00 3.42
3167 4239 1.002134 TTCACCAGGCCAAGCTAGC 60.002 57.895 6.62 6.62 0.00 3.42
3168 4240 1.778017 TTCACCAGGCCAAGCTAGCA 61.778 55.000 18.83 0.00 0.00 3.49
3169 4241 1.077212 CACCAGGCCAAGCTAGCAT 60.077 57.895 18.83 0.65 0.00 3.79
3170 4242 0.181114 CACCAGGCCAAGCTAGCATA 59.819 55.000 18.83 0.00 0.00 3.14
3171 4243 1.143813 ACCAGGCCAAGCTAGCATAT 58.856 50.000 18.83 0.00 0.00 1.78
3172 4244 1.202855 ACCAGGCCAAGCTAGCATATG 60.203 52.381 18.83 12.44 0.00 1.78
3173 4245 1.202855 CCAGGCCAAGCTAGCATATGT 60.203 52.381 18.83 0.00 0.00 2.29
3174 4246 2.579873 CAGGCCAAGCTAGCATATGTT 58.420 47.619 18.83 0.08 0.00 2.71
3175 4247 2.954318 CAGGCCAAGCTAGCATATGTTT 59.046 45.455 18.83 0.00 0.00 2.83
3176 4248 3.382546 CAGGCCAAGCTAGCATATGTTTT 59.617 43.478 18.83 0.00 0.00 2.43
3177 4249 4.026052 AGGCCAAGCTAGCATATGTTTTT 58.974 39.130 18.83 0.00 0.00 1.94
3178 4250 4.098501 AGGCCAAGCTAGCATATGTTTTTC 59.901 41.667 18.83 0.00 0.00 2.29
3179 4251 4.363138 GCCAAGCTAGCATATGTTTTTCC 58.637 43.478 18.83 0.00 0.00 3.13
3180 4252 4.142182 GCCAAGCTAGCATATGTTTTTCCA 60.142 41.667 18.83 0.00 0.00 3.53
3181 4253 5.585390 CCAAGCTAGCATATGTTTTTCCAG 58.415 41.667 18.83 0.00 0.00 3.86
3182 4254 5.450965 CCAAGCTAGCATATGTTTTTCCAGG 60.451 44.000 18.83 0.00 0.00 4.45
3183 4255 5.116084 AGCTAGCATATGTTTTTCCAGGA 57.884 39.130 18.83 0.00 0.00 3.86
3184 4256 4.884164 AGCTAGCATATGTTTTTCCAGGAC 59.116 41.667 18.83 0.00 0.00 3.85
3185 4257 4.036852 GCTAGCATATGTTTTTCCAGGACC 59.963 45.833 10.63 0.00 0.00 4.46
3186 4258 4.322057 AGCATATGTTTTTCCAGGACCT 57.678 40.909 4.29 0.00 0.00 3.85
3187 4259 4.273318 AGCATATGTTTTTCCAGGACCTC 58.727 43.478 4.29 0.00 0.00 3.85
3188 4260 4.016444 GCATATGTTTTTCCAGGACCTCA 58.984 43.478 4.29 0.00 0.00 3.86
3189 4261 4.462483 GCATATGTTTTTCCAGGACCTCAA 59.538 41.667 4.29 0.00 0.00 3.02
3190 4262 5.622233 GCATATGTTTTTCCAGGACCTCAAC 60.622 44.000 4.29 0.00 0.00 3.18
3191 4263 2.661718 TGTTTTTCCAGGACCTCAACC 58.338 47.619 0.00 0.00 0.00 3.77
3192 4264 2.024846 TGTTTTTCCAGGACCTCAACCA 60.025 45.455 0.00 0.00 0.00 3.67
3193 4265 3.028130 GTTTTTCCAGGACCTCAACCAA 58.972 45.455 0.00 0.00 0.00 3.67
3194 4266 3.390175 TTTTCCAGGACCTCAACCAAA 57.610 42.857 0.00 0.00 0.00 3.28
3195 4267 2.358322 TTCCAGGACCTCAACCAAAC 57.642 50.000 0.00 0.00 0.00 2.93
3196 4268 1.217916 TCCAGGACCTCAACCAAACA 58.782 50.000 0.00 0.00 0.00 2.83
3197 4269 1.142870 TCCAGGACCTCAACCAAACAG 59.857 52.381 0.00 0.00 0.00 3.16
3198 4270 0.954452 CAGGACCTCAACCAAACAGC 59.046 55.000 0.00 0.00 0.00 4.40
3199 4271 0.178990 AGGACCTCAACCAAACAGCC 60.179 55.000 0.00 0.00 0.00 4.85
3200 4272 0.467290 GGACCTCAACCAAACAGCCA 60.467 55.000 0.00 0.00 0.00 4.75
3201 4273 0.668535 GACCTCAACCAAACAGCCAC 59.331 55.000 0.00 0.00 0.00 5.01
3202 4274 0.755327 ACCTCAACCAAACAGCCACC 60.755 55.000 0.00 0.00 0.00 4.61
3203 4275 0.754957 CCTCAACCAAACAGCCACCA 60.755 55.000 0.00 0.00 0.00 4.17
3204 4276 0.670162 CTCAACCAAACAGCCACCAG 59.330 55.000 0.00 0.00 0.00 4.00
3205 4277 0.754957 TCAACCAAACAGCCACCAGG 60.755 55.000 0.00 0.00 38.23 4.45
3217 4289 0.037046 CCACCAGGCATTTTTCAGGC 60.037 55.000 0.00 0.00 0.00 4.85
3218 4290 0.680618 CACCAGGCATTTTTCAGGCA 59.319 50.000 0.00 0.00 0.00 4.75
3219 4291 1.276989 CACCAGGCATTTTTCAGGCAT 59.723 47.619 0.00 0.00 0.00 4.40
3220 4292 1.276989 ACCAGGCATTTTTCAGGCATG 59.723 47.619 0.00 0.00 38.89 4.06
3221 4293 1.365699 CAGGCATTTTTCAGGCATGC 58.634 50.000 9.90 9.90 42.26 4.06
3222 4294 1.066430 CAGGCATTTTTCAGGCATGCT 60.066 47.619 18.92 0.11 42.55 3.79
3223 4295 1.206371 AGGCATTTTTCAGGCATGCTC 59.794 47.619 18.92 7.89 42.55 4.26
3224 4296 1.648504 GCATTTTTCAGGCATGCTCC 58.351 50.000 18.92 1.03 40.23 4.70
3225 4297 1.066716 GCATTTTTCAGGCATGCTCCA 60.067 47.619 18.92 0.00 40.23 3.86
3226 4298 2.888594 CATTTTTCAGGCATGCTCCAG 58.111 47.619 18.92 5.30 0.00 3.86
3227 4299 1.259609 TTTTTCAGGCATGCTCCAGG 58.740 50.000 18.92 3.07 0.00 4.45
3228 4300 1.252904 TTTTCAGGCATGCTCCAGGC 61.253 55.000 18.92 0.00 40.63 4.85
3237 4309 4.537433 GCTCCAGGCCAGGCGTAG 62.537 72.222 9.89 2.91 34.27 3.51
3250 4322 4.647654 CGTAGCACAACGTGGAGT 57.352 55.556 0.00 0.00 38.07 3.85
3251 4323 2.895039 CGTAGCACAACGTGGAGTT 58.105 52.632 0.00 0.00 45.45 3.01
3259 4331 3.074594 AACGTGGAGTTGTGGACAC 57.925 52.632 0.00 0.00 42.39 3.67
3260 4332 0.463116 AACGTGGAGTTGTGGACACC 60.463 55.000 0.00 0.00 42.39 4.16
3261 4333 1.145156 CGTGGAGTTGTGGACACCA 59.855 57.895 0.00 0.00 45.24 4.17
3273 4345 2.629002 GACACCATCCAAACACGCT 58.371 52.632 0.00 0.00 0.00 5.07
3274 4346 1.803334 GACACCATCCAAACACGCTA 58.197 50.000 0.00 0.00 0.00 4.26
3458 4941 3.181480 CCTCTAGCCTGTCTTGTCTAAGC 60.181 52.174 0.00 0.00 33.82 3.09
3470 4953 3.678056 TGTCTAAGCGTTCCATTCTGT 57.322 42.857 0.00 0.00 0.00 3.41
3511 4994 8.625651 TGTGTTGTGCTTGTAATACAGTTAAAT 58.374 29.630 0.00 0.00 0.00 1.40
3527 5010 8.801882 ACAGTTAAATTAATCTTTGGGATCGA 57.198 30.769 0.00 0.00 32.76 3.59
3561 5044 4.402474 GGCCTATGATAGTTTTGCTTGGTT 59.598 41.667 0.00 0.00 0.00 3.67
3562 5045 5.105351 GGCCTATGATAGTTTTGCTTGGTTT 60.105 40.000 0.00 0.00 0.00 3.27
3563 5046 6.398095 GCCTATGATAGTTTTGCTTGGTTTT 58.602 36.000 0.00 0.00 0.00 2.43
3620 5103 7.581213 TGATTCTGGTTTACACTTTGACATT 57.419 32.000 0.00 0.00 0.00 2.71
3646 5129 8.830580 TCATTTACAATCTGCTAAAGTGCTATC 58.169 33.333 0.00 0.00 0.00 2.08
3675 5158 5.452078 TCTGTATTTCCAAACAAAGGCTG 57.548 39.130 0.00 0.00 0.00 4.85
3707 5192 2.545952 CGGAATGTCCCTGTTATCGAGG 60.546 54.545 0.00 0.00 31.13 4.63
3998 5491 6.472686 AGTGTTTAAATTTTGCACCCTACA 57.527 33.333 0.00 0.00 0.00 2.74
4038 5531 7.151308 AGCATCGTCAAATTGAATGGTTTAAA 58.849 30.769 6.55 0.00 25.08 1.52
4089 5617 4.657436 TGGTTTCCAAAACCATGTGTAC 57.343 40.909 17.96 0.00 44.74 2.90
4090 5618 3.385111 TGGTTTCCAAAACCATGTGTACC 59.615 43.478 17.96 0.00 44.74 3.34
4148 5686 4.574599 AAAACTCTGGATTTCACTGCAC 57.425 40.909 0.00 0.00 0.00 4.57
4159 5697 6.371548 TGGATTTCACTGCACTCAAATAGTAC 59.628 38.462 0.00 0.00 35.76 2.73
4175 5713 9.371136 TCAAATAGTACAAGATTCTGCTAACTG 57.629 33.333 0.00 0.00 0.00 3.16
4217 5755 7.483059 CAGATTTGTTCGCTTAGATTTTTCCTC 59.517 37.037 0.00 0.00 0.00 3.71
4271 5814 8.603304 TCTTCTTCTTTAGGCTGTAATAACCTT 58.397 33.333 0.00 0.00 34.92 3.50
4274 5817 7.985752 TCTTCTTTAGGCTGTAATAACCTTAGC 59.014 37.037 0.00 0.00 34.92 3.09
4432 5981 0.034756 TAGACGCCAAGCAAGAGCAA 59.965 50.000 0.00 0.00 45.49 3.91
4495 6044 2.317609 CCGAAGCACCACCACGAAG 61.318 63.158 0.00 0.00 0.00 3.79
4777 6332 3.498397 TCTCAAGAAAATGGCGTCTGAAC 59.502 43.478 0.00 0.00 0.00 3.18
4786 6342 1.278985 TGGCGTCTGAACTTGGATGAT 59.721 47.619 0.00 0.00 0.00 2.45
4811 6367 2.838736 ACGCATGTCAACTCTGAAGTT 58.161 42.857 0.00 0.00 46.80 2.66
4935 6492 9.647797 TCTAAACGCTCTCATATTTCTTTACAA 57.352 29.630 0.00 0.00 0.00 2.41
4941 6498 7.494625 CGCTCTCATATTTCTTTACAAAGGGTA 59.505 37.037 2.04 0.00 36.67 3.69
4965 6522 0.889306 AGTTACTGCCTCCGTCTCAC 59.111 55.000 0.00 0.00 0.00 3.51
4970 6527 0.036952 CTGCCTCCGTCTCACAATGT 60.037 55.000 0.00 0.00 0.00 2.71
4971 6528 1.204704 CTGCCTCCGTCTCACAATGTA 59.795 52.381 0.00 0.00 0.00 2.29
4972 6529 1.621317 TGCCTCCGTCTCACAATGTAA 59.379 47.619 0.00 0.00 0.00 2.41
4973 6530 2.271800 GCCTCCGTCTCACAATGTAAG 58.728 52.381 0.00 0.00 0.00 2.34
4974 6531 2.094182 GCCTCCGTCTCACAATGTAAGA 60.094 50.000 0.00 0.00 0.00 2.10
4975 6532 3.512680 CCTCCGTCTCACAATGTAAGAC 58.487 50.000 6.61 6.61 36.82 3.01
4982 6539 6.526566 GTCTCACAATGTAAGACGTTTTCT 57.473 37.500 0.29 0.00 35.32 2.52
4983 6540 6.355638 GTCTCACAATGTAAGACGTTTTCTG 58.644 40.000 0.29 0.00 33.46 3.02
4984 6541 5.465390 TCTCACAATGTAAGACGTTTTCTGG 59.535 40.000 0.00 0.00 33.46 3.86
4985 6542 4.513692 TCACAATGTAAGACGTTTTCTGGG 59.486 41.667 0.00 0.00 33.46 4.45
4986 6543 3.818773 ACAATGTAAGACGTTTTCTGGGG 59.181 43.478 0.00 0.00 33.46 4.96
4987 6544 4.069304 CAATGTAAGACGTTTTCTGGGGA 58.931 43.478 0.00 0.00 33.46 4.81
4988 6545 3.116079 TGTAAGACGTTTTCTGGGGAC 57.884 47.619 0.00 0.00 33.46 4.46
4989 6546 2.435069 TGTAAGACGTTTTCTGGGGACA 59.565 45.455 0.00 0.00 33.46 4.02
4990 6547 2.951229 AAGACGTTTTCTGGGGACAT 57.049 45.000 0.00 0.00 41.51 3.06
4991 6548 2.951229 AGACGTTTTCTGGGGACATT 57.049 45.000 0.00 0.00 41.51 2.71
4992 6549 4.360951 AAGACGTTTTCTGGGGACATTA 57.639 40.909 0.00 0.00 41.51 1.90
4993 6550 4.569719 AGACGTTTTCTGGGGACATTAT 57.430 40.909 0.00 0.00 41.51 1.28
4994 6551 4.261801 AGACGTTTTCTGGGGACATTATG 58.738 43.478 0.00 0.00 41.51 1.90
5019 6607 0.111446 TTTTCTGGGCGGACATTGGA 59.889 50.000 0.00 0.00 0.00 3.53
5038 6626 0.818938 AAAAACCGTTGGCGTCCTTT 59.181 45.000 0.00 0.00 36.15 3.11
5084 6672 2.011947 TCGCCTCTGATTGCTTTGATG 58.988 47.619 0.00 0.00 0.00 3.07
5102 6690 1.712056 TGTGCCTACTGTACACCTGT 58.288 50.000 0.00 0.00 34.39 4.00
5125 6713 1.446792 CACAAGCCAGATCGCGACT 60.447 57.895 12.93 8.32 0.00 4.18
5160 6748 3.935818 TTGTACTTTGGGTCACTTGGA 57.064 42.857 0.00 0.00 0.00 3.53
5195 6783 4.176851 GAGCTCCGTCCGTCCGTC 62.177 72.222 0.87 0.00 0.00 4.79
5207 6795 0.457853 CGTCCGTCCGTGTGAATGAT 60.458 55.000 0.00 0.00 0.00 2.45
5214 6802 0.729116 CCGTGTGAATGATGTGAGCC 59.271 55.000 0.00 0.00 0.00 4.70
5240 6828 3.566210 CAGGTCCCCCGTGTGGTT 61.566 66.667 0.00 0.00 35.12 3.67
5241 6829 3.246880 AGGTCCCCCGTGTGGTTC 61.247 66.667 0.00 0.00 35.12 3.62
5252 6840 1.227615 TGTGGTTCGGTTCGGTTCC 60.228 57.895 0.00 0.00 0.00 3.62
5254 6842 2.359107 GGTTCGGTTCGGTTCCCC 60.359 66.667 0.00 0.00 0.00 4.81
5273 6861 2.494530 GGGCGAGCGAGAGATCCTT 61.495 63.158 0.00 0.00 45.36 3.36
5283 6871 1.221840 GAGATCCTTCCGCCAGCAA 59.778 57.895 0.00 0.00 0.00 3.91
5322 6910 2.088674 GACTGCGTGGAGTGGTCAGT 62.089 60.000 0.00 0.00 40.31 3.41
5329 6917 0.402887 TGGAGTGGTCAGTCGGTAGA 59.597 55.000 0.36 0.00 0.00 2.59
5349 6937 0.463295 AGCCGAGAACATGGATGCAG 60.463 55.000 0.00 0.00 0.00 4.41
5431 7019 4.404654 GTGCAAAAGCCGAGGCCG 62.405 66.667 10.95 0.00 43.17 6.13
5440 7028 2.657237 CCGAGGCCGAGAACAAGT 59.343 61.111 0.00 0.00 38.22 3.16
5455 7043 2.229792 ACAAGTGACGGTGCATTTCAT 58.770 42.857 0.00 0.00 0.00 2.57
5456 7044 2.622942 ACAAGTGACGGTGCATTTCATT 59.377 40.909 0.00 0.00 0.00 2.57
5457 7045 3.068024 ACAAGTGACGGTGCATTTCATTT 59.932 39.130 0.00 0.00 0.00 2.32
5458 7046 3.559238 AGTGACGGTGCATTTCATTTC 57.441 42.857 0.00 0.00 0.00 2.17
5460 7048 3.317711 AGTGACGGTGCATTTCATTTCAA 59.682 39.130 0.00 0.00 0.00 2.69
5461 7049 3.425193 GTGACGGTGCATTTCATTTCAAC 59.575 43.478 0.00 0.00 0.00 3.18
5462 7050 3.067320 TGACGGTGCATTTCATTTCAACA 59.933 39.130 0.00 0.00 0.00 3.33
5463 7051 3.641648 ACGGTGCATTTCATTTCAACAG 58.358 40.909 0.00 0.00 0.00 3.16
5464 7052 3.317711 ACGGTGCATTTCATTTCAACAGA 59.682 39.130 0.00 0.00 0.00 3.41
5465 7053 4.022068 ACGGTGCATTTCATTTCAACAGAT 60.022 37.500 0.00 0.00 0.00 2.90
5477 7065 3.870723 TCAACAGATAAACGTGCACAC 57.129 42.857 18.64 0.62 0.00 3.82
5492 7080 1.601903 GCACACACATTGTTCTTCCGA 59.398 47.619 0.00 0.00 35.67 4.55
5514 7102 7.389884 TCCGAACTATGTACACAGATAGATACC 59.610 40.741 8.45 0.00 33.31 2.73
5528 7116 2.240279 AGATACCGCTATGACTGACCC 58.760 52.381 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.763448 AGAGGTGTGCTAAGATGAGGAC 59.237 50.000 0.00 0.00 38.21 3.85
86 94 2.893637 TGACTTCGAATTCTGCCTAGC 58.106 47.619 15.49 0.00 0.00 3.42
93 101 8.571336 ACAATCATTCTTTTGACTTCGAATTCT 58.429 29.630 15.49 0.00 0.00 2.40
95 103 7.809806 GGACAATCATTCTTTTGACTTCGAATT 59.190 33.333 0.00 0.00 0.00 2.17
157 167 4.147449 CACGGCGGCATGGAGAGA 62.147 66.667 13.24 0.00 0.00 3.10
168 178 4.794439 TCGACATGGAGCACGGCG 62.794 66.667 4.80 4.80 0.00 6.46
169 179 2.202932 ATCGACATGGAGCACGGC 60.203 61.111 0.00 0.00 0.00 5.68
170 180 0.179100 AAGATCGACATGGAGCACGG 60.179 55.000 0.00 0.00 0.00 4.94
171 181 0.926155 CAAGATCGACATGGAGCACG 59.074 55.000 0.00 0.00 0.00 5.34
172 182 0.654683 GCAAGATCGACATGGAGCAC 59.345 55.000 0.00 0.00 0.00 4.40
173 183 0.462581 GGCAAGATCGACATGGAGCA 60.463 55.000 0.00 0.00 0.00 4.26
242 970 5.290885 GCTTTTTCATTTGTTTGGTCGAAGT 59.709 36.000 0.00 0.00 0.00 3.01
491 1259 9.005777 TGTTTTCTTTTTAGTGGCGTCTAATAT 57.994 29.630 0.00 0.00 31.28 1.28
494 1262 6.680874 TGTTTTCTTTTTAGTGGCGTCTAA 57.319 33.333 0.00 0.00 0.00 2.10
495 1263 6.870971 ATGTTTTCTTTTTAGTGGCGTCTA 57.129 33.333 0.00 0.00 0.00 2.59
497 1265 6.577427 CACTATGTTTTCTTTTTAGTGGCGTC 59.423 38.462 0.00 0.00 37.29 5.19
502 1270 7.648142 TCTGGCACTATGTTTTCTTTTTAGTG 58.352 34.615 0.00 0.00 41.58 2.74
537 1375 7.028926 TGTGGTTAGCAAACTTAAAATTCGA 57.971 32.000 0.00 0.00 35.81 3.71
539 1377 8.587952 ACATGTGGTTAGCAAACTTAAAATTC 57.412 30.769 0.00 0.00 35.81 2.17
609 1452 7.390996 TCTCTCTCTTTCTTGTACGAGTTACAT 59.609 37.037 10.00 0.00 40.53 2.29
613 1456 6.636562 TTCTCTCTCTTTCTTGTACGAGTT 57.363 37.500 10.00 0.00 0.00 3.01
660 1517 3.288092 GTCCTTGTCTTTTCCACCTTGT 58.712 45.455 0.00 0.00 0.00 3.16
661 1518 2.290641 CGTCCTTGTCTTTTCCACCTTG 59.709 50.000 0.00 0.00 0.00 3.61
662 1519 2.572290 CGTCCTTGTCTTTTCCACCTT 58.428 47.619 0.00 0.00 0.00 3.50
700 1557 1.595929 GGGTCGTCAGCGTTTCCAA 60.596 57.895 0.00 0.00 39.49 3.53
762 1619 1.133363 TTGAAACTTGGACGGGGAGA 58.867 50.000 0.00 0.00 0.00 3.71
775 1632 1.962822 GTCGGGTCGGGGTTGAAAC 60.963 63.158 0.00 0.00 0.00 2.78
776 1633 2.426887 GTCGGGTCGGGGTTGAAA 59.573 61.111 0.00 0.00 0.00 2.69
777 1634 3.993584 CGTCGGGTCGGGGTTGAA 61.994 66.667 0.00 0.00 0.00 2.69
856 1717 1.221909 GGAAAAGGGTGGGAGGGGAT 61.222 60.000 0.00 0.00 0.00 3.85
866 1729 0.185175 GGTCAGGTGTGGAAAAGGGT 59.815 55.000 0.00 0.00 0.00 4.34
997 1868 3.434319 GTCGCTCGTCGGTGGGTA 61.434 66.667 0.00 0.00 39.05 3.69
1014 1885 3.341043 CGGATCAATCGGCCGCAG 61.341 66.667 23.51 12.86 38.46 5.18
1052 1926 2.367512 ATCTGGTGGGCTCCCTCC 60.368 66.667 17.07 17.07 46.78 4.30
1222 2102 2.285743 AAGGTGGAGGAGGAGGCC 60.286 66.667 0.00 0.00 0.00 5.19
1306 2186 2.168313 GGAGAAGAGCAGGAAGAAGAGG 59.832 54.545 0.00 0.00 0.00 3.69
1405 2285 2.590575 GTGGTGGTCGTGGTGGTG 60.591 66.667 0.00 0.00 0.00 4.17
1411 2291 2.184167 GTTGGTGGTGGTGGTCGTG 61.184 63.158 0.00 0.00 0.00 4.35
1948 2831 5.390087 TCTGGCTATGAGTAGTAGGAACT 57.610 43.478 0.00 0.00 46.37 3.01
1949 2832 6.127842 GCTATCTGGCTATGAGTAGTAGGAAC 60.128 46.154 0.00 0.00 0.00 3.62
1950 2833 5.946972 GCTATCTGGCTATGAGTAGTAGGAA 59.053 44.000 0.00 0.00 0.00 3.36
1953 2836 5.828299 GGCTATCTGGCTATGAGTAGTAG 57.172 47.826 0.00 0.00 38.32 2.57
2003 2886 9.685276 AAACCAATCATCATCAGTAATAAGTCA 57.315 29.630 0.00 0.00 0.00 3.41
2246 3129 0.959372 CTGAAGAGTTGCAGGCAGGG 60.959 60.000 0.00 0.00 0.00 4.45
2264 3147 1.382146 CCATCCAGCCAAATGCCCT 60.382 57.895 0.00 0.00 42.71 5.19
2390 3273 1.500474 CCTCCTTCCACAGCATCCTA 58.500 55.000 0.00 0.00 0.00 2.94
2393 3276 0.747283 CTGCCTCCTTCCACAGCATC 60.747 60.000 0.00 0.00 32.11 3.91
2474 3357 7.171337 GCATCATTCAAGAGAGTAAGAGGATTC 59.829 40.741 0.00 0.00 0.00 2.52
2546 3429 1.507141 CTTCAACACGGAGCCACCAC 61.507 60.000 0.00 0.00 38.90 4.16
2650 3533 9.996554 TCACAATACTTTCTGATAAGAAACAGA 57.003 29.630 0.61 0.00 40.66 3.41
2673 3556 5.593010 GTGAGGTGTCCTATAGAACATCAC 58.407 45.833 21.25 21.25 44.05 3.06
2692 3575 8.410141 TGTTTAAAGTATTGGACAAAAGGTGAG 58.590 33.333 0.00 0.00 0.00 3.51
2743 3626 3.520721 GGCCTAACTAACAGGAAGGGTTA 59.479 47.826 0.00 0.00 34.91 2.85
2801 3730 3.278668 TTCGTGGTGTACCCTTCAAAA 57.721 42.857 0.00 0.00 34.29 2.44
2818 3747 1.737838 TGGCTTAGGTCATGCTTTCG 58.262 50.000 0.00 0.00 0.00 3.46
2823 3752 5.343249 CAAAATAGTTGGCTTAGGTCATGC 58.657 41.667 0.00 0.00 0.00 4.06
2924 3969 1.922881 TGCCCATGCCAGAGGTACA 60.923 57.895 0.00 0.00 36.33 2.90
2932 3977 0.106569 CCTGATAAGTGCCCATGCCA 60.107 55.000 0.00 0.00 36.33 4.92
3009 4054 2.314852 TCCCTCCTACATTCCTGAGACA 59.685 50.000 0.00 0.00 0.00 3.41
3108 4153 9.436957 ACGATACAGTGACAATTCTTAAAATCT 57.563 29.630 0.00 0.00 0.00 2.40
3149 4221 1.002134 GCTAGCTTGGCCTGGTGAA 60.002 57.895 7.70 0.00 0.00 3.18
3150 4222 1.565390 ATGCTAGCTTGGCCTGGTGA 61.565 55.000 17.23 0.00 0.00 4.02
3151 4223 0.181114 TATGCTAGCTTGGCCTGGTG 59.819 55.000 17.23 0.00 0.00 4.17
3152 4224 1.143813 ATATGCTAGCTTGGCCTGGT 58.856 50.000 17.23 5.19 0.00 4.00
3153 4225 1.202855 ACATATGCTAGCTTGGCCTGG 60.203 52.381 17.23 0.00 0.00 4.45
3154 4226 2.267174 ACATATGCTAGCTTGGCCTG 57.733 50.000 17.23 9.00 0.00 4.85
3155 4227 3.303351 AAACATATGCTAGCTTGGCCT 57.697 42.857 17.23 0.00 0.00 5.19
3156 4228 4.363138 GAAAAACATATGCTAGCTTGGCC 58.637 43.478 17.23 0.00 0.00 5.36
3157 4229 4.142182 TGGAAAAACATATGCTAGCTTGGC 60.142 41.667 17.23 0.00 0.00 4.52
3158 4230 5.450965 CCTGGAAAAACATATGCTAGCTTGG 60.451 44.000 17.23 9.14 0.00 3.61
3159 4231 5.357878 TCCTGGAAAAACATATGCTAGCTTG 59.642 40.000 17.23 13.04 0.00 4.01
3160 4232 5.358160 GTCCTGGAAAAACATATGCTAGCTT 59.642 40.000 17.23 12.56 0.00 3.74
3161 4233 4.884164 GTCCTGGAAAAACATATGCTAGCT 59.116 41.667 17.23 4.07 0.00 3.32
3162 4234 4.036852 GGTCCTGGAAAAACATATGCTAGC 59.963 45.833 8.10 8.10 0.00 3.42
3163 4235 5.440610 AGGTCCTGGAAAAACATATGCTAG 58.559 41.667 1.58 0.00 0.00 3.42
3164 4236 5.045213 TGAGGTCCTGGAAAAACATATGCTA 60.045 40.000 1.58 0.00 0.00 3.49
3165 4237 4.263905 TGAGGTCCTGGAAAAACATATGCT 60.264 41.667 1.58 0.00 0.00 3.79
3166 4238 4.016444 TGAGGTCCTGGAAAAACATATGC 58.984 43.478 1.58 0.00 0.00 3.14
3167 4239 5.105756 GGTTGAGGTCCTGGAAAAACATATG 60.106 44.000 0.00 0.00 0.00 1.78
3168 4240 5.016831 GGTTGAGGTCCTGGAAAAACATAT 58.983 41.667 0.00 0.00 0.00 1.78
3169 4241 4.141135 TGGTTGAGGTCCTGGAAAAACATA 60.141 41.667 0.00 0.00 0.00 2.29
3170 4242 3.230976 GGTTGAGGTCCTGGAAAAACAT 58.769 45.455 0.00 0.00 0.00 2.71
3171 4243 2.024846 TGGTTGAGGTCCTGGAAAAACA 60.025 45.455 0.00 0.00 0.00 2.83
3172 4244 2.661718 TGGTTGAGGTCCTGGAAAAAC 58.338 47.619 0.00 0.89 0.00 2.43
3173 4245 3.390175 TTGGTTGAGGTCCTGGAAAAA 57.610 42.857 0.00 0.00 0.00 1.94
3174 4246 3.028130 GTTTGGTTGAGGTCCTGGAAAA 58.972 45.455 0.00 0.00 0.00 2.29
3175 4247 2.024846 TGTTTGGTTGAGGTCCTGGAAA 60.025 45.455 0.00 0.00 0.00 3.13
3176 4248 1.566703 TGTTTGGTTGAGGTCCTGGAA 59.433 47.619 0.00 0.00 0.00 3.53
3177 4249 1.142870 CTGTTTGGTTGAGGTCCTGGA 59.857 52.381 0.00 0.00 0.00 3.86
3178 4250 1.609208 CTGTTTGGTTGAGGTCCTGG 58.391 55.000 0.00 0.00 0.00 4.45
3179 4251 0.954452 GCTGTTTGGTTGAGGTCCTG 59.046 55.000 0.00 0.00 0.00 3.86
3180 4252 0.178990 GGCTGTTTGGTTGAGGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
3181 4253 0.467290 TGGCTGTTTGGTTGAGGTCC 60.467 55.000 0.00 0.00 0.00 4.46
3182 4254 0.668535 GTGGCTGTTTGGTTGAGGTC 59.331 55.000 0.00 0.00 0.00 3.85
3183 4255 0.755327 GGTGGCTGTTTGGTTGAGGT 60.755 55.000 0.00 0.00 0.00 3.85
3184 4256 0.754957 TGGTGGCTGTTTGGTTGAGG 60.755 55.000 0.00 0.00 0.00 3.86
3185 4257 0.670162 CTGGTGGCTGTTTGGTTGAG 59.330 55.000 0.00 0.00 0.00 3.02
3186 4258 0.754957 CCTGGTGGCTGTTTGGTTGA 60.755 55.000 0.00 0.00 0.00 3.18
3187 4259 1.741525 CCTGGTGGCTGTTTGGTTG 59.258 57.895 0.00 0.00 0.00 3.77
3188 4260 4.275781 CCTGGTGGCTGTTTGGTT 57.724 55.556 0.00 0.00 0.00 3.67
3198 4270 0.037046 GCCTGAAAAATGCCTGGTGG 60.037 55.000 0.00 0.00 0.00 4.61
3199 4271 0.680618 TGCCTGAAAAATGCCTGGTG 59.319 50.000 0.00 0.00 0.00 4.17
3200 4272 1.276989 CATGCCTGAAAAATGCCTGGT 59.723 47.619 0.00 0.00 0.00 4.00
3201 4273 2.010043 GCATGCCTGAAAAATGCCTGG 61.010 52.381 6.36 0.00 40.65 4.45
3202 4274 1.066430 AGCATGCCTGAAAAATGCCTG 60.066 47.619 15.66 0.00 46.28 4.85
3203 4275 1.206371 GAGCATGCCTGAAAAATGCCT 59.794 47.619 15.66 0.00 46.28 4.75
3204 4276 1.648504 GAGCATGCCTGAAAAATGCC 58.351 50.000 15.66 0.00 46.28 4.40
3205 4277 1.066716 TGGAGCATGCCTGAAAAATGC 60.067 47.619 15.66 0.00 45.62 3.56
3206 4278 2.418197 CCTGGAGCATGCCTGAAAAATG 60.418 50.000 15.66 0.00 0.00 2.32
3207 4279 1.829222 CCTGGAGCATGCCTGAAAAAT 59.171 47.619 15.66 0.00 0.00 1.82
3208 4280 1.259609 CCTGGAGCATGCCTGAAAAA 58.740 50.000 15.66 0.00 0.00 1.94
3209 4281 1.252904 GCCTGGAGCATGCCTGAAAA 61.253 55.000 15.66 0.00 42.97 2.29
3210 4282 1.679977 GCCTGGAGCATGCCTGAAA 60.680 57.895 15.66 0.00 42.97 2.69
3211 4283 2.044650 GCCTGGAGCATGCCTGAA 60.045 61.111 15.66 0.00 42.97 3.02
3212 4284 4.119363 GGCCTGGAGCATGCCTGA 62.119 66.667 15.66 0.00 46.50 3.86
3213 4285 4.435970 TGGCCTGGAGCATGCCTG 62.436 66.667 15.66 3.92 43.78 4.85
3214 4286 4.124943 CTGGCCTGGAGCATGCCT 62.125 66.667 15.66 1.01 43.78 4.75
3220 4292 4.537433 CTACGCCTGGCCTGGAGC 62.537 72.222 31.43 15.96 42.60 4.70
3221 4293 4.537433 GCTACGCCTGGCCTGGAG 62.537 72.222 31.43 29.22 0.00 3.86
3224 4296 3.899981 TTGTGCTACGCCTGGCCTG 62.900 63.158 14.12 2.54 0.00 4.85
3225 4297 3.636231 TTGTGCTACGCCTGGCCT 61.636 61.111 14.12 3.97 0.00 5.19
3226 4298 3.431725 GTTGTGCTACGCCTGGCC 61.432 66.667 14.12 0.00 0.00 5.36
3227 4299 3.788766 CGTTGTGCTACGCCTGGC 61.789 66.667 9.11 9.11 34.45 4.85
3228 4300 2.357034 ACGTTGTGCTACGCCTGG 60.357 61.111 6.13 0.00 45.06 4.45
3229 4301 2.667318 CCACGTTGTGCTACGCCTG 61.667 63.158 6.13 0.00 45.06 4.85
3230 4302 2.357034 CCACGTTGTGCTACGCCT 60.357 61.111 6.13 0.00 45.06 5.52
3231 4303 2.356553 TCCACGTTGTGCTACGCC 60.357 61.111 6.13 0.00 45.06 5.68
3232 4304 1.219522 AACTCCACGTTGTGCTACGC 61.220 55.000 6.13 0.00 45.06 4.42
3233 4305 0.506932 CAACTCCACGTTGTGCTACG 59.493 55.000 4.80 4.80 46.23 3.51
3241 4313 0.463116 GGTGTCCACAACTCCACGTT 60.463 55.000 0.00 0.00 40.58 3.99
3242 4314 1.145377 GGTGTCCACAACTCCACGT 59.855 57.895 0.00 0.00 40.58 4.49
3243 4315 1.145156 TGGTGTCCACAACTCCACG 59.855 57.895 0.00 0.00 44.58 4.94
3246 4318 3.249687 GGATGGTGTCCACAACTCC 57.750 57.895 0.00 0.00 46.96 3.85
3255 4327 1.803334 TAGCGTGTTTGGATGGTGTC 58.197 50.000 0.00 0.00 0.00 3.67
3256 4328 2.489938 ATAGCGTGTTTGGATGGTGT 57.510 45.000 0.00 0.00 0.00 4.16
3257 4329 4.955925 TTAATAGCGTGTTTGGATGGTG 57.044 40.909 0.00 0.00 0.00 4.17
3258 4330 4.578928 GGATTAATAGCGTGTTTGGATGGT 59.421 41.667 0.00 0.00 0.00 3.55
3259 4331 4.821805 AGGATTAATAGCGTGTTTGGATGG 59.178 41.667 0.00 0.00 0.00 3.51
3260 4332 5.751680 CAGGATTAATAGCGTGTTTGGATG 58.248 41.667 0.00 0.00 0.00 3.51
3261 4333 4.275936 GCAGGATTAATAGCGTGTTTGGAT 59.724 41.667 0.00 0.00 0.00 3.41
3262 4334 3.625764 GCAGGATTAATAGCGTGTTTGGA 59.374 43.478 0.00 0.00 0.00 3.53
3263 4335 3.627577 AGCAGGATTAATAGCGTGTTTGG 59.372 43.478 0.00 0.00 0.00 3.28
3264 4336 4.094887 ACAGCAGGATTAATAGCGTGTTTG 59.905 41.667 0.00 0.00 0.00 2.93
3265 4337 4.261801 ACAGCAGGATTAATAGCGTGTTT 58.738 39.130 0.00 0.00 0.00 2.83
3266 4338 3.873910 ACAGCAGGATTAATAGCGTGTT 58.126 40.909 0.00 0.00 0.00 3.32
3267 4339 3.543680 ACAGCAGGATTAATAGCGTGT 57.456 42.857 0.00 0.00 0.00 4.49
3268 4340 5.615544 GCAATACAGCAGGATTAATAGCGTG 60.616 44.000 0.00 0.00 0.00 5.34
3269 4341 4.452455 GCAATACAGCAGGATTAATAGCGT 59.548 41.667 0.00 0.08 0.00 5.07
3270 4342 4.142816 GGCAATACAGCAGGATTAATAGCG 60.143 45.833 0.00 0.00 35.83 4.26
3271 4343 4.156739 GGGCAATACAGCAGGATTAATAGC 59.843 45.833 0.00 0.00 35.83 2.97
3272 4344 5.316167 TGGGCAATACAGCAGGATTAATAG 58.684 41.667 0.00 0.00 35.83 1.73
3273 4345 5.316167 CTGGGCAATACAGCAGGATTAATA 58.684 41.667 0.00 0.00 35.83 0.98
3274 4346 4.147321 CTGGGCAATACAGCAGGATTAAT 58.853 43.478 0.00 0.00 35.83 1.40
3330 4402 6.545666 TCAGCCCAACATAACCATACTAAATG 59.454 38.462 0.00 0.00 0.00 2.32
3458 4941 6.743575 AAAATCCTAGAACAGAATGGAACG 57.256 37.500 0.00 0.00 43.62 3.95
3504 4987 9.331282 CTCTCGATCCCAAAGATTAATTTAACT 57.669 33.333 0.00 0.00 34.42 2.24
3511 4994 3.717707 CGCTCTCGATCCCAAAGATTAA 58.282 45.455 0.00 0.00 34.42 1.40
3525 5008 1.064803 CATAGGCCTATAGCGCTCTCG 59.935 57.143 25.00 5.78 45.17 4.04
3527 5010 2.516227 TCATAGGCCTATAGCGCTCT 57.484 50.000 25.00 6.94 45.17 4.09
3562 5045 8.680039 TCCGAAACTAGTATGAAAAGGAAAAA 57.320 30.769 0.00 0.00 0.00 1.94
3563 5046 8.680039 TTCCGAAACTAGTATGAAAAGGAAAA 57.320 30.769 0.00 0.00 31.97 2.29
3620 5103 8.737168 ATAGCACTTTAGCAGATTGTAAATGA 57.263 30.769 0.00 0.00 36.85 2.57
3646 5129 7.095523 CCTTTGTTTGGAAATACAGAATGCAAG 60.096 37.037 0.00 0.00 42.53 4.01
3675 5158 1.393883 GGACATTCCGCGAAGAGAAAC 59.606 52.381 8.23 0.00 0.00 2.78
3707 5192 9.786105 GAGAGTCAAAACTATAGTAGTACAACC 57.214 37.037 5.65 0.00 38.26 3.77
3890 5383 5.123502 CAGTGGAAGAGGTCAATCTCAAATG 59.876 44.000 0.00 0.00 36.30 2.32
3979 5472 7.500992 TGACAATGTAGGGTGCAAAATTTAAA 58.499 30.769 0.00 0.00 0.00 1.52
3998 5491 6.106003 TGACGATGCTAAACTACATGACAAT 58.894 36.000 0.00 0.00 0.00 2.71
4038 5531 4.812626 ACACGAGGAAATGTTCTTAAACGT 59.187 37.500 0.00 0.00 38.28 3.99
4087 5615 3.564571 CCTCAAGTCTCTCAGAAGGGGTA 60.565 52.174 0.00 0.00 0.00 3.69
4089 5617 1.830477 CCTCAAGTCTCTCAGAAGGGG 59.170 57.143 0.00 0.00 0.00 4.79
4090 5618 2.813907 TCCTCAAGTCTCTCAGAAGGG 58.186 52.381 0.00 0.00 0.00 3.95
4148 5686 9.593134 AGTTAGCAGAATCTTGTACTATTTGAG 57.407 33.333 0.00 0.00 0.00 3.02
4159 5697 6.817641 AGAGTTGATCAGTTAGCAGAATCTTG 59.182 38.462 0.00 0.00 0.00 3.02
4201 5739 5.293079 CAGAAGAGGAGGAAAAATCTAAGCG 59.707 44.000 0.00 0.00 0.00 4.68
4217 5755 5.363101 TGAGCATGCTTAATACAGAAGAGG 58.637 41.667 23.61 0.00 0.00 3.69
4271 5814 8.632679 CAGCCTAAAAATGGATAATTTCAGCTA 58.367 33.333 0.00 0.00 37.51 3.32
4342 5885 1.535226 GCGGGAACAACAACTTCCAAC 60.535 52.381 0.00 0.00 39.29 3.77
4777 6332 5.473039 TGACATGCGTATAGATCATCCAAG 58.527 41.667 0.00 0.00 0.00 3.61
4786 6342 5.125578 ACTTCAGAGTTGACATGCGTATAGA 59.874 40.000 0.00 0.00 31.71 1.98
4811 6367 7.195839 TGAAAACATTCATCACACGATACAA 57.804 32.000 0.00 0.00 0.00 2.41
4935 6492 5.245526 CGGAGGCAGTAACTAATATACCCTT 59.754 44.000 0.00 0.00 0.00 3.95
4941 6498 5.009811 GTGAGACGGAGGCAGTAACTAATAT 59.990 44.000 0.00 0.00 0.00 1.28
4965 6522 4.069304 TCCCCAGAAAACGTCTTACATTG 58.931 43.478 0.00 0.00 32.70 2.82
4970 6527 4.360951 AATGTCCCCAGAAAACGTCTTA 57.639 40.909 0.00 0.00 32.70 2.10
4971 6528 2.951229 ATGTCCCCAGAAAACGTCTT 57.049 45.000 0.00 0.00 32.70 3.01
4972 6529 2.951229 AATGTCCCCAGAAAACGTCT 57.049 45.000 0.00 0.00 36.88 4.18
4973 6530 4.258543 TCATAATGTCCCCAGAAAACGTC 58.741 43.478 0.00 0.00 0.00 4.34
4974 6531 4.019681 TCTCATAATGTCCCCAGAAAACGT 60.020 41.667 0.00 0.00 0.00 3.99
4975 6532 4.332819 GTCTCATAATGTCCCCAGAAAACG 59.667 45.833 0.00 0.00 0.00 3.60
4976 6533 4.332819 CGTCTCATAATGTCCCCAGAAAAC 59.667 45.833 0.00 0.00 0.00 2.43
4977 6534 4.019681 ACGTCTCATAATGTCCCCAGAAAA 60.020 41.667 0.00 0.00 0.00 2.29
4978 6535 3.517901 ACGTCTCATAATGTCCCCAGAAA 59.482 43.478 0.00 0.00 0.00 2.52
4979 6536 3.104512 ACGTCTCATAATGTCCCCAGAA 58.895 45.455 0.00 0.00 0.00 3.02
4980 6537 2.747177 ACGTCTCATAATGTCCCCAGA 58.253 47.619 0.00 0.00 0.00 3.86
4981 6538 3.543680 AACGTCTCATAATGTCCCCAG 57.456 47.619 0.00 0.00 0.00 4.45
4982 6539 3.992943 AAACGTCTCATAATGTCCCCA 57.007 42.857 0.00 0.00 0.00 4.96
4983 6540 4.332819 CAGAAAACGTCTCATAATGTCCCC 59.667 45.833 0.00 0.00 32.70 4.81
4984 6541 4.332819 CCAGAAAACGTCTCATAATGTCCC 59.667 45.833 0.00 0.00 32.70 4.46
4985 6542 4.332819 CCCAGAAAACGTCTCATAATGTCC 59.667 45.833 0.00 0.00 32.70 4.02
4986 6543 4.201822 GCCCAGAAAACGTCTCATAATGTC 60.202 45.833 0.00 0.00 32.70 3.06
4987 6544 3.689649 GCCCAGAAAACGTCTCATAATGT 59.310 43.478 0.00 0.00 32.70 2.71
4988 6545 3.242413 CGCCCAGAAAACGTCTCATAATG 60.242 47.826 0.00 0.00 32.70 1.90
4989 6546 2.936498 CGCCCAGAAAACGTCTCATAAT 59.064 45.455 0.00 0.00 32.70 1.28
4990 6547 2.343101 CGCCCAGAAAACGTCTCATAA 58.657 47.619 0.00 0.00 32.70 1.90
4991 6548 1.404986 CCGCCCAGAAAACGTCTCATA 60.405 52.381 0.00 0.00 32.70 2.15
4992 6549 0.673644 CCGCCCAGAAAACGTCTCAT 60.674 55.000 0.00 0.00 32.70 2.90
4993 6550 1.301401 CCGCCCAGAAAACGTCTCA 60.301 57.895 0.00 0.00 32.70 3.27
4994 6551 1.005394 TCCGCCCAGAAAACGTCTC 60.005 57.895 0.00 0.00 32.70 3.36
5019 6607 0.818938 AAAGGACGCCAACGGTTTTT 59.181 45.000 0.00 0.00 46.04 1.94
5084 6672 1.893801 AGACAGGTGTACAGTAGGCAC 59.106 52.381 0.00 0.00 0.00 5.01
5102 6690 1.900351 CGATCTGGCTTGTGGGAGA 59.100 57.895 0.00 0.00 0.00 3.71
5132 6720 0.596082 CCCAAAGTACAAAGCCCGTG 59.404 55.000 0.00 0.00 0.00 4.94
5141 6729 2.486548 GCTCCAAGTGACCCAAAGTACA 60.487 50.000 0.00 0.00 0.00 2.90
5160 6748 1.079127 CCTCGTGGAAATGGTCGCT 60.079 57.895 0.00 0.00 34.57 4.93
5194 6782 1.675714 GGCTCACATCATTCACACGGA 60.676 52.381 0.00 0.00 0.00 4.69
5195 6783 0.729116 GGCTCACATCATTCACACGG 59.271 55.000 0.00 0.00 0.00 4.94
5196 6784 0.371301 CGGCTCACATCATTCACACG 59.629 55.000 0.00 0.00 0.00 4.49
5197 6785 1.129251 CACGGCTCACATCATTCACAC 59.871 52.381 0.00 0.00 0.00 3.82
5198 6786 1.270785 ACACGGCTCACATCATTCACA 60.271 47.619 0.00 0.00 0.00 3.58
5234 6822 1.227615 GGAACCGAACCGAACCACA 60.228 57.895 0.00 0.00 0.00 4.17
5254 6842 4.335584 GGATCTCTCGCTCGCCCG 62.336 72.222 0.00 0.00 0.00 6.13
5258 6846 1.281353 CGGAAGGATCTCTCGCTCG 59.719 63.158 0.00 0.00 0.00 5.03
5263 6851 1.068921 GCTGGCGGAAGGATCTCTC 59.931 63.158 0.00 0.00 0.00 3.20
5264 6852 1.267574 TTGCTGGCGGAAGGATCTCT 61.268 55.000 0.00 0.00 0.00 3.10
5273 6861 2.852495 GATCGGAAGTTGCTGGCGGA 62.852 60.000 0.00 0.00 0.00 5.54
5283 6871 3.252215 GTCTCTCATCATCGATCGGAAGT 59.748 47.826 16.41 0.00 0.00 3.01
5329 6917 0.035152 TGCATCCATGTTCTCGGCTT 60.035 50.000 0.00 0.00 0.00 4.35
5334 6922 2.941720 GAGGAACTGCATCCATGTTCTC 59.058 50.000 9.02 4.85 41.55 2.87
5424 7012 1.009389 GTCACTTGTTCTCGGCCTCG 61.009 60.000 0.00 0.00 37.82 4.63
5426 7014 1.006102 CGTCACTTGTTCTCGGCCT 60.006 57.895 0.00 0.00 0.00 5.19
5431 7019 1.512926 ATGCACCGTCACTTGTTCTC 58.487 50.000 0.00 0.00 0.00 2.87
5440 7028 3.067320 TGTTGAAATGAAATGCACCGTCA 59.933 39.130 0.00 0.00 0.00 4.35
5455 7043 4.095036 TGTGTGCACGTTTATCTGTTGAAA 59.905 37.500 13.13 0.00 0.00 2.69
5456 7044 3.623510 TGTGTGCACGTTTATCTGTTGAA 59.376 39.130 13.13 0.00 0.00 2.69
5457 7045 3.001838 GTGTGTGCACGTTTATCTGTTGA 59.998 43.478 13.13 0.00 35.75 3.18
5458 7046 3.288242 GTGTGTGCACGTTTATCTGTTG 58.712 45.455 13.13 0.00 35.75 3.33
5492 7080 6.715718 AGCGGTATCTATCTGTGTACATAGTT 59.284 38.462 17.92 12.85 0.00 2.24
5495 7083 8.044908 TCATAGCGGTATCTATCTGTGTACATA 58.955 37.037 3.66 0.00 0.00 2.29
5496 7084 6.884836 TCATAGCGGTATCTATCTGTGTACAT 59.115 38.462 3.66 0.00 0.00 2.29
5497 7085 6.148976 GTCATAGCGGTATCTATCTGTGTACA 59.851 42.308 3.66 0.00 0.00 2.90
5498 7086 6.372103 AGTCATAGCGGTATCTATCTGTGTAC 59.628 42.308 3.66 0.00 0.00 2.90
5514 7102 0.537188 AACCTGGGTCAGTCATAGCG 59.463 55.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.