Multiple sequence alignment - TraesCS2B01G127900

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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 TraesCS2B01G127900 chr2B 100.000 3858 0 0 1 3858 95800256 95796399 0.000000e+00 7125
1 TraesCS2B01G127900 chr2B 97.024 672 17 1 1 669 167855576 167854905 0.000000e+00 1127
2 TraesCS2B01G127900 chr2D 91.218 1355 74 16 785 2128 61025087 61023767 0.000000e+00 1801
3 TraesCS2B01G127900 chr2D 89.731 633 27 13 3231 3857 61022341 61021741 0.000000e+00 774
4 TraesCS2B01G127900 chr2D 90.158 569 39 12 2584 3139 61023312 61022748 0.000000e+00 725
5 TraesCS2B01G127900 chr2D 87.688 398 32 11 2190 2581 61023736 61023350 7.600000e-122 448
6 TraesCS2B01G127900 chr2D 93.798 129 7 1 2097 2225 489410067 489410194 3.930000e-45 193
7 TraesCS2B01G127900 chr2D 92.366 131 10 0 2095 2225 95519664 95519534 1.830000e-43 187
8 TraesCS2B01G127900 chr2D 93.182 88 4 1 2958 3045 61022642 61022557 1.130000e-25 128
9 TraesCS2B01G127900 chr2A 89.591 1441 117 16 678 2102 61491439 61490016 0.000000e+00 1799
10 TraesCS2B01G127900 chr2A 86.740 1267 104 25 2584 3835 61489520 61488303 0.000000e+00 1351
11 TraesCS2B01G127900 chr2A 87.568 185 21 2 2216 2400 61490017 61489835 3.020000e-51 213
12 TraesCS2B01G127900 chr2A 81.143 175 13 6 2399 2573 61489721 61489567 5.230000e-24 122
13 TraesCS2B01G127900 chr6B 97.317 671 14 2 1 668 216440783 216440114 0.000000e+00 1136
14 TraesCS2B01G127900 chr5B 97.168 671 16 1 1 668 504298689 504298019 0.000000e+00 1131
15 TraesCS2B01G127900 chr5B 96.731 673 18 2 1 670 554409781 554409110 0.000000e+00 1118
16 TraesCS2B01G127900 chr5B 87.500 208 24 2 3518 3724 497504868 497504662 4.980000e-59 239
17 TraesCS2B01G127900 chr5B 94.958 119 6 0 2100 2218 81460501 81460383 1.830000e-43 187
18 TraesCS2B01G127900 chr7B 97.019 671 17 1 1 668 439495562 439496232 0.000000e+00 1125
19 TraesCS2B01G127900 chr7B 96.880 673 18 1 1 670 40331933 40331261 0.000000e+00 1123
20 TraesCS2B01G127900 chrUn 96.741 675 19 1 1 672 77540243 77539569 0.000000e+00 1122
21 TraesCS2B01G127900 chrUn 96.593 675 20 1 1 672 119147616 119146942 0.000000e+00 1116
22 TraesCS2B01G127900 chr1B 96.726 672 19 1 1 669 562882360 562881689 0.000000e+00 1116
23 TraesCS2B01G127900 chr1B 94.030 134 8 0 2094 2227 613245922 613246055 1.820000e-48 204
24 TraesCS2B01G127900 chr1B 92.537 134 8 2 2086 2217 426475746 426475879 1.410000e-44 191
25 TraesCS2B01G127900 chr4A 77.939 621 97 28 1084 1676 215248574 215247966 6.130000e-93 351
26 TraesCS2B01G127900 chr4A 86.705 173 23 0 3519 3691 3351736 3351564 3.930000e-45 193
27 TraesCS2B01G127900 chr4B 77.492 622 100 26 1084 1676 362146899 362147509 1.720000e-88 337
28 TraesCS2B01G127900 chr4B 87.283 173 22 0 3516 3688 585822368 585822540 8.450000e-47 198
29 TraesCS2B01G127900 chr4B 85.795 176 24 1 3513 3688 585963794 585963968 6.580000e-43 185
30 TraesCS2B01G127900 chr4D 77.492 622 99 29 1084 1676 294349461 294350070 6.180000e-88 335
31 TraesCS2B01G127900 chr4D 93.750 128 7 1 2095 2221 507908129 507908256 1.410000e-44 191
32 TraesCS2B01G127900 chr4D 86.127 173 24 0 3516 3688 467636119 467636291 1.830000e-43 187
33 TraesCS2B01G127900 chr5D 88.038 209 23 2 3517 3724 412960964 412960757 2.980000e-61 246
34 TraesCS2B01G127900 chr5D 90.071 141 13 1 2100 2239 361646405 361646265 8.510000e-42 182
35 TraesCS2B01G127900 chr5A 88.038 209 23 2 3517 3724 525026298 525026091 2.980000e-61 246
36 TraesCS2B01G127900 chr7D 95.868 121 5 0 2097 2217 64732156 64732036 3.040000e-46 196
37 TraesCS2B01G127900 chr3B 93.750 128 8 0 2097 2224 40227233 40227106 3.930000e-45 193
38 TraesCS2B01G127900 chr1A 90.370 135 13 0 1265 1399 92565370 92565504 1.100000e-40 178


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 TraesCS2B01G127900 chr2B 95796399 95800256 3857 True 7125.00 7125 100.0000 1 3858 1 chr2B.!!$R1 3857
1 TraesCS2B01G127900 chr2B 167854905 167855576 671 True 1127.00 1127 97.0240 1 669 1 chr2B.!!$R2 668
2 TraesCS2B01G127900 chr2D 61021741 61025087 3346 True 775.20 1801 90.3954 785 3857 5 chr2D.!!$R2 3072
3 TraesCS2B01G127900 chr2A 61488303 61491439 3136 True 871.25 1799 86.2605 678 3835 4 chr2A.!!$R1 3157
4 TraesCS2B01G127900 chr6B 216440114 216440783 669 True 1136.00 1136 97.3170 1 668 1 chr6B.!!$R1 667
5 TraesCS2B01G127900 chr5B 504298019 504298689 670 True 1131.00 1131 97.1680 1 668 1 chr5B.!!$R3 667
6 TraesCS2B01G127900 chr5B 554409110 554409781 671 True 1118.00 1118 96.7310 1 670 1 chr5B.!!$R4 669
7 TraesCS2B01G127900 chr7B 439495562 439496232 670 False 1125.00 1125 97.0190 1 668 1 chr7B.!!$F1 667
8 TraesCS2B01G127900 chr7B 40331261 40331933 672 True 1123.00 1123 96.8800 1 670 1 chr7B.!!$R1 669
9 TraesCS2B01G127900 chrUn 77539569 77540243 674 True 1122.00 1122 96.7410 1 672 1 chrUn.!!$R1 671
10 TraesCS2B01G127900 chrUn 119146942 119147616 674 True 1116.00 1116 96.5930 1 672 1 chrUn.!!$R2 671
11 TraesCS2B01G127900 chr1B 562881689 562882360 671 True 1116.00 1116 96.7260 1 669 1 chr1B.!!$R1 668
12 TraesCS2B01G127900 chr4A 215247966 215248574 608 True 351.00 351 77.9390 1084 1676 1 chr4A.!!$R2 592
13 TraesCS2B01G127900 chr4B 362146899 362147509 610 False 337.00 337 77.4920 1084 1676 1 chr4B.!!$F1 592
14 TraesCS2B01G127900 chr4D 294349461 294350070 609 False 335.00 335 77.4920 1084 1676 1 chr4D.!!$F1 592

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
883 892 0.468226 GATTCTCCGCCCACACCATA 59.532 55.0 0.00 0.0 0.00 2.74 F
1319 1376 0.389948 AGTTCAACGCCGTGATCCTC 60.390 55.0 0.00 0.0 0.00 3.71 F
2118 2211 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2192 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.0 13.64 0.00 46.06 2.12 R
2581 2792 0.179034 AAGGGAGAAGCCATCATCGC 60.179 55.0 0.00 0.00 38.95 4.58 R
3838 4423 0.456995 GAGGTACGTCAGTCAGCTGC 60.457 60.0 9.47 4.26 42.29 5.25 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
301 305 1.369625 GAAGACCATGGGTTAGCACG 58.630 55.000 18.09 0.00 35.25 5.34
335 339 4.207165 GGACAATGCTTACCATACCATGT 58.793 43.478 0.00 0.00 32.67 3.21
491 495 2.669924 CTCAACACTCACATGACCGATG 59.330 50.000 0.00 0.00 38.15 3.84
509 513 7.282224 TGACCGATGTTTGGATAATTCCTTAAG 59.718 37.037 0.00 0.00 43.07 1.85
579 583 4.280677 CCAAGAAAAGCCTATGGACAAACA 59.719 41.667 0.00 0.00 32.82 2.83
672 676 3.426695 GCACCGGATGTTCTTTCAATCTG 60.427 47.826 9.46 0.00 0.00 2.90
673 677 2.749621 ACCGGATGTTCTTTCAATCTGC 59.250 45.455 9.46 0.00 0.00 4.26
674 678 3.012518 CCGGATGTTCTTTCAATCTGCT 58.987 45.455 0.00 0.00 0.00 4.24
675 679 3.441572 CCGGATGTTCTTTCAATCTGCTT 59.558 43.478 0.00 0.00 0.00 3.91
676 680 4.409570 CGGATGTTCTTTCAATCTGCTTG 58.590 43.478 0.00 0.00 36.09 4.01
683 687 1.603456 TTCAATCTGCTTGTCGCCAA 58.397 45.000 0.00 0.00 38.05 4.52
705 709 6.980397 CCAACACAATAAGCTCTTCACTTTTT 59.020 34.615 0.00 0.00 0.00 1.94
731 737 0.990374 AGGCAATGAGCTCTTCACCT 59.010 50.000 16.19 15.07 44.79 4.00
733 739 2.165998 GGCAATGAGCTCTTCACCTTT 58.834 47.619 16.19 0.00 44.79 3.11
760 766 1.671328 GGGGAATAAGCGCTTCACTTC 59.329 52.381 28.82 24.56 0.00 3.01
762 768 2.096013 GGGAATAAGCGCTTCACTTCAC 59.904 50.000 28.82 23.18 0.00 3.18
764 770 4.181578 GGAATAAGCGCTTCACTTCACTA 58.818 43.478 28.82 5.83 0.00 2.74
765 771 4.033014 GGAATAAGCGCTTCACTTCACTAC 59.967 45.833 28.82 11.06 0.00 2.73
766 772 2.526304 AAGCGCTTCACTTCACTACA 57.474 45.000 18.98 0.00 0.00 2.74
767 773 1.784525 AGCGCTTCACTTCACTACAC 58.215 50.000 2.64 0.00 0.00 2.90
768 774 0.790814 GCGCTTCACTTCACTACACC 59.209 55.000 0.00 0.00 0.00 4.16
769 775 1.429463 CGCTTCACTTCACTACACCC 58.571 55.000 0.00 0.00 0.00 4.61
771 777 2.417719 GCTTCACTTCACTACACCCTG 58.582 52.381 0.00 0.00 0.00 4.45
772 778 2.037251 GCTTCACTTCACTACACCCTGA 59.963 50.000 0.00 0.00 0.00 3.86
773 779 3.494398 GCTTCACTTCACTACACCCTGAA 60.494 47.826 0.00 0.00 0.00 3.02
774 780 4.703897 CTTCACTTCACTACACCCTGAAA 58.296 43.478 0.00 0.00 0.00 2.69
776 782 5.105567 TCACTTCACTACACCCTGAAAAA 57.894 39.130 0.00 0.00 0.00 1.94
799 807 2.109425 AGTGTTCATCCGTTAAGGCC 57.891 50.000 0.00 0.00 40.77 5.19
880 889 2.511600 CGATTCTCCGCCCACACC 60.512 66.667 0.00 0.00 0.00 4.16
881 890 2.668632 GATTCTCCGCCCACACCA 59.331 61.111 0.00 0.00 0.00 4.17
882 891 1.224592 GATTCTCCGCCCACACCAT 59.775 57.895 0.00 0.00 0.00 3.55
883 892 0.468226 GATTCTCCGCCCACACCATA 59.532 55.000 0.00 0.00 0.00 2.74
884 893 1.072331 GATTCTCCGCCCACACCATAT 59.928 52.381 0.00 0.00 0.00 1.78
1015 1024 3.496130 CGCAACCATGGTAATCTCTCATC 59.504 47.826 20.12 0.00 0.00 2.92
1034 1043 2.115911 CCTCTCCCTCCTCGTCGTG 61.116 68.421 0.00 0.00 0.00 4.35
1043 1052 1.444553 CCTCGTCGTGTTCCTCTGC 60.445 63.158 0.00 0.00 0.00 4.26
1319 1376 0.389948 AGTTCAACGCCGTGATCCTC 60.390 55.000 0.00 0.00 0.00 3.71
1325 1382 2.125512 GCCGTGATCCTCAAGCGT 60.126 61.111 0.00 0.00 0.00 5.07
1438 1506 3.926821 TTTTTGTATCTTTGGTCCGGC 57.073 42.857 0.00 0.00 0.00 6.13
1441 1509 0.981183 TGTATCTTTGGTCCGGCTGT 59.019 50.000 0.00 0.00 0.00 4.40
1612 1700 1.153086 GGCCAGGATCGTCAATGCT 60.153 57.895 0.00 0.00 36.29 3.79
1722 1812 6.337853 CAACTGTATTTGCTAGTAGTGCTC 57.662 41.667 0.00 0.00 0.00 4.26
1773 1865 5.812286 AGTACCCAAAGATTTACAACCGAT 58.188 37.500 0.00 0.00 0.00 4.18
1788 1880 2.288666 ACCGATGCACGCAATTCTATT 58.711 42.857 0.00 0.00 41.07 1.73
1795 1888 3.986572 TGCACGCAATTCTATTTGTTTGG 59.013 39.130 0.00 0.00 0.00 3.28
1857 1950 8.297470 ACCAAGTTTATTGTTCATGCTCATAT 57.703 30.769 0.00 0.00 0.00 1.78
1864 1957 8.914328 TTATTGTTCATGCTCATATTGTGTTG 57.086 30.769 0.00 0.00 0.00 3.33
1869 1962 4.885325 TCATGCTCATATTGTGTTGCAGAT 59.115 37.500 8.85 0.00 39.88 2.90
1870 1963 6.056884 TCATGCTCATATTGTGTTGCAGATA 58.943 36.000 8.85 0.00 39.88 1.98
1907 2000 4.172807 AGGTTGTGGTAGGGTATTCAAGA 58.827 43.478 0.00 0.00 0.00 3.02
1966 2059 6.015350 CCTCTTCTCAGGTGTTAAGAGTACAA 60.015 42.308 16.14 0.00 42.12 2.41
1969 2062 7.872993 TCTTCTCAGGTGTTAAGAGTACAAATG 59.127 37.037 0.00 0.00 0.00 2.32
1980 2073 6.391227 AAGAGTACAAATGAACCAAGTTGG 57.609 37.500 20.76 20.76 45.02 3.77
2005 2098 9.227777 GGTACAACTGTCTAAATCTTTATGGTT 57.772 33.333 0.00 0.00 0.00 3.67
2008 2101 9.131791 ACAACTGTCTAAATCTTTATGGTTTGT 57.868 29.630 0.00 0.00 0.00 2.83
2009 2102 9.965824 CAACTGTCTAAATCTTTATGGTTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
2016 2109 9.906660 CTAAATCTTTATGGTTTGTTTACAGCA 57.093 29.630 0.00 0.00 0.00 4.41
2017 2110 8.816640 AAATCTTTATGGTTTGTTTACAGCAG 57.183 30.769 0.00 0.00 0.00 4.24
2035 2128 4.106029 GCAGATTGCACTCATTTCATGT 57.894 40.909 6.84 0.00 44.26 3.21
2047 2140 3.890756 TCATTTCATGTTTGTGCTGGACT 59.109 39.130 0.00 0.00 0.00 3.85
2067 2160 3.068590 ACTGCTGGTGTCAAATTTCCAAG 59.931 43.478 0.00 0.00 0.00 3.61
2112 2205 6.212888 TGTTAAACTAATACTCCCTCCGTC 57.787 41.667 0.00 0.00 0.00 4.79
2114 2207 1.978454 ACTAATACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2115 2208 1.245732 CTAATACTCCCTCCGTCCGG 58.754 60.000 0.00 0.00 0.00 5.14
2116 2209 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2118 2211 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2128 2221 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2129 2222 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2130 2223 2.660189 TCCGGAAATACTTGTCGGAC 57.340 50.000 0.00 0.00 43.84 4.79
2131 2224 1.135315 TCCGGAAATACTTGTCGGACG 60.135 52.381 0.00 0.00 43.84 4.79
2132 2225 1.135315 CCGGAAATACTTGTCGGACGA 60.135 52.381 0.00 0.15 42.94 4.20
2133 2226 2.598589 CGGAAATACTTGTCGGACGAA 58.401 47.619 3.34 0.00 0.00 3.85
2135 2228 3.000078 CGGAAATACTTGTCGGACGAATG 60.000 47.826 3.34 0.00 0.00 2.67
2137 2230 3.880047 AATACTTGTCGGACGAATGGA 57.120 42.857 3.34 0.00 0.00 3.41
2138 2231 4.402056 AATACTTGTCGGACGAATGGAT 57.598 40.909 3.34 0.00 0.00 3.41
2139 2232 2.010145 ACTTGTCGGACGAATGGATG 57.990 50.000 3.34 0.00 0.00 3.51
2140 2233 1.275291 ACTTGTCGGACGAATGGATGT 59.725 47.619 3.34 0.00 0.00 3.06
2142 2235 3.132289 ACTTGTCGGACGAATGGATGTAT 59.868 43.478 3.34 0.00 0.00 2.29
2143 2236 3.364889 TGTCGGACGAATGGATGTATC 57.635 47.619 3.34 0.00 0.00 2.24
2145 2238 3.243401 TGTCGGACGAATGGATGTATCTG 60.243 47.826 3.34 0.00 0.00 2.90
2147 2240 2.296190 CGGACGAATGGATGTATCTGGA 59.704 50.000 0.00 0.00 0.00 3.86
2148 2241 3.056536 CGGACGAATGGATGTATCTGGAT 60.057 47.826 0.00 0.00 0.00 3.41
2149 2242 4.248859 GGACGAATGGATGTATCTGGATG 58.751 47.826 0.00 0.00 0.00 3.51
2152 2245 6.351371 GGACGAATGGATGTATCTGGATGTAT 60.351 42.308 0.00 0.00 0.00 2.29
2153 2246 7.009179 ACGAATGGATGTATCTGGATGTATT 57.991 36.000 0.00 0.00 0.00 1.89
2155 2248 7.939039 ACGAATGGATGTATCTGGATGTATTTT 59.061 33.333 0.00 0.00 0.00 1.82
2190 2283 7.042797 ACATCCATTTTTATCCATTTCTCCG 57.957 36.000 0.00 0.00 0.00 4.63
2191 2284 6.833416 ACATCCATTTTTATCCATTTCTCCGA 59.167 34.615 0.00 0.00 0.00 4.55
2192 2285 6.693315 TCCATTTTTATCCATTTCTCCGAC 57.307 37.500 0.00 0.00 0.00 4.79
2193 2286 6.184068 TCCATTTTTATCCATTTCTCCGACA 58.816 36.000 0.00 0.00 0.00 4.35
2194 2287 6.661377 TCCATTTTTATCCATTTCTCCGACAA 59.339 34.615 0.00 0.00 0.00 3.18
2195 2288 6.974622 CCATTTTTATCCATTTCTCCGACAAG 59.025 38.462 0.00 0.00 0.00 3.16
2196 2289 7.362920 CCATTTTTATCCATTTCTCCGACAAGT 60.363 37.037 0.00 0.00 0.00 3.16
2197 2290 8.673711 CATTTTTATCCATTTCTCCGACAAGTA 58.326 33.333 0.00 0.00 0.00 2.24
2198 2291 8.801882 TTTTTATCCATTTCTCCGACAAGTAT 57.198 30.769 0.00 0.00 0.00 2.12
2199 2292 8.801882 TTTTATCCATTTCTCCGACAAGTATT 57.198 30.769 0.00 0.00 0.00 1.89
2200 2293 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
2201 2294 6.927294 ATCCATTTCTCCGACAAGTATTTC 57.073 37.500 0.00 0.00 0.00 2.17
2202 2295 6.049955 TCCATTTCTCCGACAAGTATTTCT 57.950 37.500 0.00 0.00 0.00 2.52
2203 2296 5.874810 TCCATTTCTCCGACAAGTATTTCTG 59.125 40.000 0.00 0.00 0.00 3.02
2204 2297 5.065218 CCATTTCTCCGACAAGTATTTCTGG 59.935 44.000 0.00 0.00 0.00 3.86
2255 2348 4.214119 ACAGTCAATCTCAACGGTCAAATG 59.786 41.667 0.00 0.00 0.00 2.32
2300 2393 4.692155 GGTAGTAGTTGCGTTGTTGGTTAT 59.308 41.667 0.00 0.00 0.00 1.89
2329 2422 6.144563 GTCTTGTCTGCTTTATTTTCCTTTGC 59.855 38.462 0.00 0.00 0.00 3.68
2340 2433 9.399403 CTTTATTTTCCTTTGCTAAGAGTTGTC 57.601 33.333 9.62 0.00 32.92 3.18
2381 2474 6.741992 TGTCTTGGCATAAAGAGTAATGTG 57.258 37.500 0.00 0.00 36.86 3.21
2387 2480 7.087409 TGGCATAAAGAGTAATGTGAATGTG 57.913 36.000 0.00 0.00 0.00 3.21
2418 2627 9.874215 GATTCATACATGATAATTCAGTGTGTG 57.126 33.333 0.00 0.00 35.87 3.82
2419 2628 9.617523 ATTCATACATGATAATTCAGTGTGTGA 57.382 29.630 0.00 0.00 38.34 3.58
2430 2639 3.544684 TCAGTGTGTGAATGTTCTTGCT 58.455 40.909 0.00 0.00 29.64 3.91
2454 2663 4.252073 CTGTTCCTTCTTGACCTGATCTG 58.748 47.826 0.00 0.00 0.00 2.90
2516 2727 9.856488 CTTTAGACTTTAGTACATGCTACTGAA 57.144 33.333 14.48 12.22 0.00 3.02
2520 2731 8.414778 AGACTTTAGTACATGCTACTGAATACC 58.585 37.037 14.48 7.56 0.00 2.73
2521 2732 7.201145 ACTTTAGTACATGCTACTGAATACCG 58.799 38.462 14.48 6.74 0.00 4.02
2522 2733 6.947644 TTAGTACATGCTACTGAATACCGA 57.052 37.500 14.48 0.00 0.00 4.69
2526 2737 2.134201 TGCTACTGAATACCGATGCG 57.866 50.000 0.00 0.00 0.00 4.73
2547 2758 6.734137 TGCGAGAATTTTTGACATTGTAGTT 58.266 32.000 0.00 0.00 0.00 2.24
2574 2785 7.506114 TGTAGAGGTATTTGCTCCGATTTATT 58.494 34.615 0.00 0.00 0.00 1.40
2575 2786 7.990886 TGTAGAGGTATTTGCTCCGATTTATTT 59.009 33.333 0.00 0.00 0.00 1.40
2581 2792 7.749126 GGTATTTGCTCCGATTTATTTTATCCG 59.251 37.037 0.00 0.00 0.00 4.18
2582 2793 4.742438 TGCTCCGATTTATTTTATCCGC 57.258 40.909 0.00 0.00 0.00 5.54
2591 2838 4.678509 TTATTTTATCCGCGATGATGGC 57.321 40.909 8.23 0.00 0.00 4.40
2595 2842 0.969149 TATCCGCGATGATGGCTTCT 59.031 50.000 8.23 0.00 0.00 2.85
2613 2860 4.520874 GCTTCTCCCTTCCCATAAATTAGC 59.479 45.833 0.00 0.00 0.00 3.09
2638 2886 3.572632 ACCTCAATATGAGCTGCATGT 57.427 42.857 1.02 0.00 42.98 3.21
2642 2890 4.023963 CCTCAATATGAGCTGCATGTCTTG 60.024 45.833 1.02 0.32 42.98 3.02
2643 2891 4.773013 TCAATATGAGCTGCATGTCTTGA 58.227 39.130 1.02 2.81 37.87 3.02
2644 2892 4.814771 TCAATATGAGCTGCATGTCTTGAG 59.185 41.667 1.02 0.00 37.87 3.02
2646 2894 0.675837 TGAGCTGCATGTCTTGAGGC 60.676 55.000 1.02 0.00 0.00 4.70
2647 2895 0.675837 GAGCTGCATGTCTTGAGGCA 60.676 55.000 1.02 0.00 34.66 4.75
2648 2896 0.034380 AGCTGCATGTCTTGAGGCAT 60.034 50.000 1.02 0.00 35.45 4.40
2821 3077 0.375106 GCAGGAAATTCGAGAAGGCG 59.625 55.000 0.00 0.00 0.00 5.52
2845 3101 1.151810 AAGGAGGAACAGCAGGGGA 60.152 57.895 0.00 0.00 0.00 4.81
2854 3110 0.329596 ACAGCAGGGGATTCAAGGTC 59.670 55.000 0.00 0.00 0.00 3.85
2859 3115 2.505819 GCAGGGGATTCAAGGTCTAAGA 59.494 50.000 0.00 0.00 0.00 2.10
2898 3154 5.678483 CGCACTTGTGTCATATTTTGCTATC 59.322 40.000 2.61 0.00 0.00 2.08
2899 3155 6.457392 CGCACTTGTGTCATATTTTGCTATCT 60.457 38.462 2.61 0.00 0.00 1.98
2906 3165 7.120579 TGTGTCATATTTTGCTATCTTCGGTTT 59.879 33.333 0.00 0.00 0.00 3.27
2910 3169 8.708742 TCATATTTTGCTATCTTCGGTTTATCG 58.291 33.333 0.00 0.00 0.00 2.92
2914 3173 5.196341 TGCTATCTTCGGTTTATCGTCAT 57.804 39.130 0.00 0.00 0.00 3.06
2923 3182 5.239351 TCGGTTTATCGTCATCTTTTTGGA 58.761 37.500 0.00 0.00 0.00 3.53
2933 3192 7.561251 TCGTCATCTTTTTGGATACCAGAATA 58.439 34.615 0.00 0.00 33.81 1.75
2934 3193 8.210946 TCGTCATCTTTTTGGATACCAGAATAT 58.789 33.333 0.00 0.00 33.81 1.28
2966 3225 4.122776 AGATGTCAGTGTCTTGTGTCAAC 58.877 43.478 0.00 0.00 0.00 3.18
2989 3248 8.504005 CAACGAGTATTCAGAACCAGTTAATTT 58.496 33.333 0.00 0.00 0.00 1.82
2990 3249 8.029642 ACGAGTATTCAGAACCAGTTAATTTG 57.970 34.615 0.00 0.00 0.00 2.32
2998 3257 8.006298 TCAGAACCAGTTAATTTGTGTTTCAT 57.994 30.769 0.00 0.00 0.00 2.57
2999 3258 8.134895 TCAGAACCAGTTAATTTGTGTTTCATC 58.865 33.333 0.00 0.00 0.00 2.92
3012 3271 6.347270 TGTGTTTCATCATTTTGCAACTTG 57.653 33.333 0.00 0.00 0.00 3.16
3013 3272 6.104665 TGTGTTTCATCATTTTGCAACTTGA 58.895 32.000 11.71 11.71 0.00 3.02
3074 3333 4.810790 AGTATCAGAAGTTGTCTCCGTTG 58.189 43.478 0.00 0.00 32.70 4.10
3078 3337 0.586802 GAAGTTGTCTCCGTTGGCAC 59.413 55.000 0.00 0.00 0.00 5.01
3093 3352 0.666374 GGCACTGTGGTTGGTGTTAC 59.334 55.000 10.21 0.00 36.03 2.50
3139 3398 7.801315 GCGATGTTCTACTTTTCAAATGTAACA 59.199 33.333 6.86 6.86 0.00 2.41
3162 3455 7.039882 ACATTTTCAGTATCCGTTAGACGATT 58.960 34.615 1.51 0.00 46.05 3.34
3307 3880 2.368548 TGCAAGCAGAAGAGACCAGTTA 59.631 45.455 0.00 0.00 0.00 2.24
3330 3903 6.352016 ACTATCTATCACATAGGCACTTGG 57.648 41.667 0.00 0.00 41.75 3.61
3375 3948 4.770362 TCCATCCCGGGCTCGTCA 62.770 66.667 18.49 0.00 34.36 4.35
3378 3951 2.443952 ATCCCGGGCTCGTCATGA 60.444 61.111 18.49 0.00 33.95 3.07
3393 3966 3.333899 ATGATGCGGCAGCTGGTGA 62.334 57.895 19.82 0.00 45.42 4.02
3479 4052 2.735857 GACGTTGTAGCCGCCGTT 60.736 61.111 0.00 0.00 33.03 4.44
3480 4053 3.007070 GACGTTGTAGCCGCCGTTG 62.007 63.158 0.00 0.00 33.03 4.10
3791 4370 4.367023 GGTACGCTCGGGCACACA 62.367 66.667 8.62 0.00 38.60 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 2.583143 GTTAGGTTGTGGGCAAGTTCT 58.417 47.619 0.00 0.00 34.94 3.01
301 305 1.919918 GCATTGTCCATTACGCTTTGC 59.080 47.619 0.00 0.00 0.00 3.68
509 513 3.876300 GTGATGACCACGGTGCTC 58.124 61.111 1.68 0.00 35.86 4.26
579 583 6.719370 TGGTTGCCTTGAGTTATATTTGAAGT 59.281 34.615 0.00 0.00 0.00 3.01
656 660 5.084722 CGACAAGCAGATTGAAAGAACATC 58.915 41.667 5.14 0.00 41.83 3.06
675 679 1.804151 GAGCTTATTGTGTTGGCGACA 59.196 47.619 2.68 2.68 39.83 4.35
676 680 2.076863 AGAGCTTATTGTGTTGGCGAC 58.923 47.619 0.00 0.00 0.00 5.19
705 709 2.880443 AGAGCTCATTGCCTCCAAAAA 58.120 42.857 17.77 0.00 44.23 1.94
706 710 2.592102 AGAGCTCATTGCCTCCAAAA 57.408 45.000 17.77 0.00 44.23 2.44
710 714 1.377536 GTGAAGAGCTCATTGCCTCC 58.622 55.000 17.77 0.00 44.23 4.30
711 715 1.065564 AGGTGAAGAGCTCATTGCCTC 60.066 52.381 17.77 3.02 44.23 4.70
712 716 0.990374 AGGTGAAGAGCTCATTGCCT 59.010 50.000 17.77 14.47 44.23 4.75
713 717 1.831580 AAGGTGAAGAGCTCATTGCC 58.168 50.000 17.77 12.41 44.23 4.52
714 718 3.930634 AAAAGGTGAAGAGCTCATTGC 57.069 42.857 17.77 3.16 43.29 3.56
738 744 2.116238 AGTGAAGCGCTTATTCCCCTA 58.884 47.619 25.11 0.00 0.00 3.53
739 745 0.912486 AGTGAAGCGCTTATTCCCCT 59.088 50.000 25.11 3.98 0.00 4.79
740 746 1.671328 GAAGTGAAGCGCTTATTCCCC 59.329 52.381 25.11 10.14 34.12 4.81
743 749 4.625742 TGTAGTGAAGTGAAGCGCTTATTC 59.374 41.667 25.11 24.73 34.12 1.75
751 757 2.037251 TCAGGGTGTAGTGAAGTGAAGC 59.963 50.000 0.00 0.00 0.00 3.86
773 779 6.734871 GCCTTAACGGATGAACACTTCTTTTT 60.735 38.462 0.00 0.00 33.16 1.94
774 780 5.278315 GCCTTAACGGATGAACACTTCTTTT 60.278 40.000 0.00 0.00 33.16 2.27
776 782 3.751698 GCCTTAACGGATGAACACTTCTT 59.248 43.478 0.00 0.00 33.16 2.52
777 783 3.335579 GCCTTAACGGATGAACACTTCT 58.664 45.455 0.00 0.00 33.16 2.85
781 787 1.092348 GGGCCTTAACGGATGAACAC 58.908 55.000 0.84 0.00 33.16 3.32
782 788 0.693622 TGGGCCTTAACGGATGAACA 59.306 50.000 4.53 0.00 33.16 3.18
783 789 1.379527 CTGGGCCTTAACGGATGAAC 58.620 55.000 4.53 0.00 33.16 3.18
799 807 1.150081 CCCATAGAAGCCTGCCTGG 59.850 63.158 0.00 0.00 39.35 4.45
880 889 8.037758 GGAGTGGAGTCTAAATATGGTGATATG 58.962 40.741 0.00 0.00 0.00 1.78
881 890 7.958583 AGGAGTGGAGTCTAAATATGGTGATAT 59.041 37.037 0.00 0.00 0.00 1.63
882 891 7.306013 AGGAGTGGAGTCTAAATATGGTGATA 58.694 38.462 0.00 0.00 0.00 2.15
883 892 6.146760 AGGAGTGGAGTCTAAATATGGTGAT 58.853 40.000 0.00 0.00 0.00 3.06
884 893 5.529289 AGGAGTGGAGTCTAAATATGGTGA 58.471 41.667 0.00 0.00 0.00 4.02
1015 1024 2.517402 CGACGAGGAGGGAGAGGG 60.517 72.222 0.00 0.00 0.00 4.30
1034 1043 0.458716 GGCGTAGAGTGCAGAGGAAC 60.459 60.000 0.00 0.00 0.00 3.62
1043 1052 1.095600 TGTCAGCTAGGCGTAGAGTG 58.904 55.000 17.40 12.58 0.00 3.51
1145 1154 1.135373 AGCTTGAGGTACACATCGTCG 60.135 52.381 0.00 0.00 0.00 5.12
1603 1691 2.741985 TCGCCACCAGCATTGACG 60.742 61.111 0.00 0.00 44.04 4.35
1700 1790 6.287589 AGAGCACTACTAGCAAATACAGTT 57.712 37.500 0.00 0.00 0.00 3.16
1714 1804 5.300969 TGAAATGCATCAAAGAGCACTAC 57.699 39.130 0.00 0.00 44.49 2.73
1722 1812 9.961265 ACTCATACAATATGAAATGCATCAAAG 57.039 29.630 0.00 0.00 38.44 2.77
1773 1865 3.986572 CCAAACAAATAGAATTGCGTGCA 59.013 39.130 0.00 0.00 33.52 4.57
1788 1880 7.065803 GTCTAGCATGCTTAATAGTCCAAACAA 59.934 37.037 28.02 0.00 0.00 2.83
1795 1888 6.155827 CAGGAGTCTAGCATGCTTAATAGTC 58.844 44.000 28.02 18.71 0.00 2.59
1857 1950 8.075574 CACATAAAAGTCTTATCTGCAACACAA 58.924 33.333 0.00 0.00 0.00 3.33
1864 1957 8.391106 CAACCTACACATAAAAGTCTTATCTGC 58.609 37.037 0.00 0.00 0.00 4.26
1869 1962 7.511268 ACCACAACCTACACATAAAAGTCTTA 58.489 34.615 0.00 0.00 0.00 2.10
1870 1963 6.362248 ACCACAACCTACACATAAAAGTCTT 58.638 36.000 0.00 0.00 0.00 3.01
1938 2031 4.090090 TCTTAACACCTGAGAAGAGGGAG 58.910 47.826 0.00 0.00 37.45 4.30
1947 2040 7.095187 GGTTCATTTGTACTCTTAACACCTGAG 60.095 40.741 0.00 0.00 0.00 3.35
1983 2076 9.965824 AACAAACCATAAAGATTTAGACAGTTG 57.034 29.630 0.00 0.00 0.00 3.16
1998 2091 6.155827 GCAATCTGCTGTAAACAAACCATAA 58.844 36.000 0.00 0.00 40.96 1.90
2005 2098 3.882288 TGAGTGCAATCTGCTGTAAACAA 59.118 39.130 16.05 0.00 45.31 2.83
2007 2100 4.691860 ATGAGTGCAATCTGCTGTAAAC 57.308 40.909 16.05 0.00 45.31 2.01
2008 2101 5.241285 TGAAATGAGTGCAATCTGCTGTAAA 59.759 36.000 16.05 0.00 45.31 2.01
2009 2102 4.761227 TGAAATGAGTGCAATCTGCTGTAA 59.239 37.500 16.05 0.00 45.31 2.41
2026 2119 7.738227 AGCAGTCCAGCACAAACATGAAATG 62.738 44.000 0.00 0.00 43.77 2.32
2027 2120 3.553508 GCAGTCCAGCACAAACATGAAAT 60.554 43.478 0.00 0.00 0.00 2.17
2035 2128 1.102809 CACCAGCAGTCCAGCACAAA 61.103 55.000 0.00 0.00 36.85 2.83
2047 2140 2.224018 GCTTGGAAATTTGACACCAGCA 60.224 45.455 0.00 0.00 33.85 4.41
2086 2179 7.627311 ACGGAGGGAGTATTAGTTTAACAATT 58.373 34.615 0.00 0.00 0.00 2.32
2090 2183 5.595885 GGACGGAGGGAGTATTAGTTTAAC 58.404 45.833 0.00 0.00 0.00 2.01
2099 2192 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
2112 2205 1.135315 TCGTCCGACAAGTATTTCCGG 60.135 52.381 0.00 0.00 41.36 5.14
2114 2207 3.308866 CCATTCGTCCGACAAGTATTTCC 59.691 47.826 0.00 0.00 0.00 3.13
2115 2208 4.178540 TCCATTCGTCCGACAAGTATTTC 58.821 43.478 0.00 0.00 0.00 2.17
2116 2209 4.196626 TCCATTCGTCCGACAAGTATTT 57.803 40.909 0.00 0.00 0.00 1.40
2118 2211 3.132289 ACATCCATTCGTCCGACAAGTAT 59.868 43.478 0.00 0.00 0.00 2.12
2128 2221 4.887748 ACATCCAGATACATCCATTCGTC 58.112 43.478 0.00 0.00 0.00 4.20
2129 2222 4.963318 ACATCCAGATACATCCATTCGT 57.037 40.909 0.00 0.00 0.00 3.85
2130 2223 7.912056 AAATACATCCAGATACATCCATTCG 57.088 36.000 0.00 0.00 0.00 3.34
2164 2257 8.796475 CGGAGAAATGGATAAAAATGGATGTAT 58.204 33.333 0.00 0.00 0.00 2.29
2167 2260 7.141363 GTCGGAGAAATGGATAAAAATGGATG 58.859 38.462 0.00 0.00 39.69 3.51
2168 2261 6.833416 TGTCGGAGAAATGGATAAAAATGGAT 59.167 34.615 0.00 0.00 39.69 3.41
2169 2262 6.184068 TGTCGGAGAAATGGATAAAAATGGA 58.816 36.000 0.00 0.00 39.69 3.41
2170 2263 6.449635 TGTCGGAGAAATGGATAAAAATGG 57.550 37.500 0.00 0.00 39.69 3.16
2171 2264 7.538575 ACTTGTCGGAGAAATGGATAAAAATG 58.461 34.615 0.00 0.00 39.69 2.32
2172 2265 7.703058 ACTTGTCGGAGAAATGGATAAAAAT 57.297 32.000 0.00 0.00 39.69 1.82
2173 2266 8.801882 ATACTTGTCGGAGAAATGGATAAAAA 57.198 30.769 0.00 0.00 39.69 1.94
2174 2267 8.801882 AATACTTGTCGGAGAAATGGATAAAA 57.198 30.769 0.00 0.00 39.69 1.52
2175 2268 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
2176 2269 8.265055 AGAAATACTTGTCGGAGAAATGGATAA 58.735 33.333 0.00 0.00 39.69 1.75
2177 2270 7.710907 CAGAAATACTTGTCGGAGAAATGGATA 59.289 37.037 0.00 0.00 39.69 2.59
2178 2271 6.540189 CAGAAATACTTGTCGGAGAAATGGAT 59.460 38.462 0.00 0.00 39.69 3.41
2179 2272 5.874810 CAGAAATACTTGTCGGAGAAATGGA 59.125 40.000 0.00 0.00 39.69 3.41
2180 2273 5.065218 CCAGAAATACTTGTCGGAGAAATGG 59.935 44.000 0.00 0.00 39.69 3.16
2181 2274 5.874810 TCCAGAAATACTTGTCGGAGAAATG 59.125 40.000 0.00 0.00 39.69 2.32
2182 2275 5.875359 GTCCAGAAATACTTGTCGGAGAAAT 59.125 40.000 0.00 0.00 39.69 2.17
2183 2276 5.235516 GTCCAGAAATACTTGTCGGAGAAA 58.764 41.667 0.00 0.00 39.69 2.52
2184 2277 4.617530 CGTCCAGAAATACTTGTCGGAGAA 60.618 45.833 0.00 0.00 39.69 2.87
2185 2278 3.119602 CGTCCAGAAATACTTGTCGGAGA 60.120 47.826 0.00 0.00 0.00 3.71
2186 2279 3.179830 CGTCCAGAAATACTTGTCGGAG 58.820 50.000 0.00 0.00 0.00 4.63
2187 2280 2.094390 CCGTCCAGAAATACTTGTCGGA 60.094 50.000 0.00 0.00 42.19 4.55
2188 2281 2.094390 TCCGTCCAGAAATACTTGTCGG 60.094 50.000 0.00 0.00 41.47 4.79
2189 2282 3.179830 CTCCGTCCAGAAATACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
2190 2283 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
2191 2284 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2192 2285 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
2193 2286 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
2194 2287 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
2195 2288 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
2196 2289 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
2197 2290 2.544844 TACTCCCTCCGTCCAGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
2198 2291 2.544844 ATACTCCCTCCGTCCAGAAA 57.455 50.000 0.00 0.00 0.00 2.52
2199 2292 3.897657 ATATACTCCCTCCGTCCAGAA 57.102 47.619 0.00 0.00 0.00 3.02
2200 2293 3.897657 AATATACTCCCTCCGTCCAGA 57.102 47.619 0.00 0.00 0.00 3.86
2201 2294 4.957684 AAAATATACTCCCTCCGTCCAG 57.042 45.455 0.00 0.00 0.00 3.86
2233 2326 4.214119 ACATTTGACCGTTGAGATTGACTG 59.786 41.667 0.00 0.00 0.00 3.51
2243 2336 5.568482 CATATGTACCACATTTGACCGTTG 58.432 41.667 4.35 0.00 39.05 4.10
2300 2393 5.473504 GGAAAATAAAGCAGACAAGACCTCA 59.526 40.000 0.00 0.00 0.00 3.86
2340 2433 9.346725 GCCAAGACAAAGATATTCAAGTTTTAG 57.653 33.333 0.00 0.00 0.00 1.85
2355 2448 7.752239 CACATTACTCTTTATGCCAAGACAAAG 59.248 37.037 0.00 0.00 0.00 2.77
2358 2451 6.472016 TCACATTACTCTTTATGCCAAGACA 58.528 36.000 0.00 0.00 0.00 3.41
2359 2452 6.985188 TCACATTACTCTTTATGCCAAGAC 57.015 37.500 0.00 0.00 0.00 3.01
2364 2457 6.968904 CACACATTCACATTACTCTTTATGCC 59.031 38.462 0.00 0.00 0.00 4.40
2418 2627 2.555757 AGGAACAGCAGCAAGAACATTC 59.444 45.455 0.00 0.00 0.00 2.67
2419 2628 2.590821 AGGAACAGCAGCAAGAACATT 58.409 42.857 0.00 0.00 0.00 2.71
2430 2639 1.768275 TCAGGTCAAGAAGGAACAGCA 59.232 47.619 0.00 0.00 0.00 4.41
2516 2727 4.634004 TGTCAAAAATTCTCGCATCGGTAT 59.366 37.500 0.00 0.00 0.00 2.73
2517 2728 3.997681 TGTCAAAAATTCTCGCATCGGTA 59.002 39.130 0.00 0.00 0.00 4.02
2518 2729 2.811431 TGTCAAAAATTCTCGCATCGGT 59.189 40.909 0.00 0.00 0.00 4.69
2519 2730 3.469899 TGTCAAAAATTCTCGCATCGG 57.530 42.857 0.00 0.00 0.00 4.18
2520 2731 4.853196 ACAATGTCAAAAATTCTCGCATCG 59.147 37.500 0.00 0.00 0.00 3.84
2521 2732 7.023575 ACTACAATGTCAAAAATTCTCGCATC 58.976 34.615 0.00 0.00 0.00 3.91
2522 2733 6.913170 ACTACAATGTCAAAAATTCTCGCAT 58.087 32.000 0.00 0.00 0.00 4.73
2547 2758 6.665992 AATCGGAGCAAATACCTCTACATA 57.334 37.500 0.00 0.00 0.00 2.29
2574 2785 2.143122 GAAGCCATCATCGCGGATAAA 58.857 47.619 6.13 0.00 0.00 1.40
2575 2786 1.344438 AGAAGCCATCATCGCGGATAA 59.656 47.619 6.13 0.00 0.00 1.75
2581 2792 0.179034 AAGGGAGAAGCCATCATCGC 60.179 55.000 0.00 0.00 38.95 4.58
2582 2793 1.542108 GGAAGGGAGAAGCCATCATCG 60.542 57.143 0.00 0.00 38.95 3.84
2591 2838 4.757149 CGCTAATTTATGGGAAGGGAGAAG 59.243 45.833 0.00 0.00 0.00 2.85
2595 2842 4.993705 ATCGCTAATTTATGGGAAGGGA 57.006 40.909 0.00 0.00 34.24 4.20
2644 2892 8.425429 GGTTTGTCCATAGCATGAATAAATGCC 61.425 40.741 0.00 0.00 43.78 4.40
2646 2894 7.490840 TGGTTTGTCCATAGCATGAATAAATG 58.509 34.615 0.00 0.00 41.93 2.32
2647 2895 7.658525 TGGTTTGTCCATAGCATGAATAAAT 57.341 32.000 0.00 0.00 41.93 1.40
2821 3077 1.206849 CTGCTGTTCCTCCTTCCTCTC 59.793 57.143 0.00 0.00 0.00 3.20
2845 3101 8.112183 AGAAATTCCACATCTTAGACCTTGAAT 58.888 33.333 0.00 0.00 0.00 2.57
2854 3110 3.242870 GCGCCAGAAATTCCACATCTTAG 60.243 47.826 0.00 0.00 0.00 2.18
2859 3115 0.527565 GTGCGCCAGAAATTCCACAT 59.472 50.000 4.18 0.00 0.00 3.21
2898 3154 6.021596 CCAAAAAGATGACGATAAACCGAAG 58.978 40.000 0.00 0.00 0.00 3.79
2899 3155 5.701750 TCCAAAAAGATGACGATAAACCGAA 59.298 36.000 0.00 0.00 0.00 4.30
2906 3165 7.119709 TCTGGTATCCAAAAAGATGACGATA 57.880 36.000 0.00 0.00 30.80 2.92
2914 3173 7.227910 GCGGTAATATTCTGGTATCCAAAAAGA 59.772 37.037 0.00 0.00 30.80 2.52
2923 3182 8.594550 ACATCTAAAGCGGTAATATTCTGGTAT 58.405 33.333 0.00 0.00 0.00 2.73
2933 3192 5.086104 ACACTGACATCTAAAGCGGTAAT 57.914 39.130 0.00 0.00 0.00 1.89
2934 3193 4.219944 AGACACTGACATCTAAAGCGGTAA 59.780 41.667 0.00 0.00 0.00 2.85
2966 3225 7.957484 CACAAATTAACTGGTTCTGAATACTCG 59.043 37.037 0.00 0.00 0.00 4.18
2989 3248 6.104665 TCAAGTTGCAAAATGATGAAACACA 58.895 32.000 0.00 0.00 40.69 3.72
2990 3249 6.476380 TCTCAAGTTGCAAAATGATGAAACAC 59.524 34.615 13.91 0.00 40.69 3.32
2998 3257 4.206375 TGGTCTCTCAAGTTGCAAAATGA 58.794 39.130 0.00 7.99 0.00 2.57
2999 3258 4.572985 TGGTCTCTCAAGTTGCAAAATG 57.427 40.909 0.00 3.26 0.00 2.32
3074 3333 0.666374 GTAACACCAACCACAGTGCC 59.334 55.000 0.00 0.00 37.51 5.01
3078 3337 0.586319 CAGCGTAACACCAACCACAG 59.414 55.000 0.00 0.00 0.00 3.66
3093 3352 2.447250 CAATAATGAGCACAAGCAGCG 58.553 47.619 0.00 0.00 45.49 5.18
3139 3398 8.488651 AAAATCGTCTAACGGATACTGAAAAT 57.511 30.769 0.00 0.00 42.81 1.82
3150 3443 1.727880 TCGCCAAAAATCGTCTAACGG 59.272 47.619 0.00 0.00 42.81 4.44
3265 3838 7.504924 TGCATGTAATATTGCCTTTACCTAC 57.495 36.000 0.00 0.00 38.08 3.18
3307 3880 5.247110 CCCAAGTGCCTATGTGATAGATAGT 59.753 44.000 0.00 0.00 34.77 2.12
3375 3948 2.827190 CACCAGCTGCCGCATCAT 60.827 61.111 8.66 0.00 39.10 2.45
3426 3999 2.897207 CCGTCCTACATGGCCGAA 59.103 61.111 0.00 0.00 39.97 4.30
3438 4011 1.376037 CTTCTTCCACCAGCCGTCC 60.376 63.158 0.00 0.00 0.00 4.79
3477 4050 0.936297 ACGACTACGACGTTGCCAAC 60.936 55.000 5.50 0.00 41.18 3.77
3478 4051 0.661187 GACGACTACGACGTTGCCAA 60.661 55.000 5.50 0.00 43.97 4.52
3479 4052 1.081906 GACGACTACGACGTTGCCA 60.082 57.895 5.50 0.00 43.97 4.92
3480 4053 3.746250 GACGACTACGACGTTGCC 58.254 61.111 5.50 0.00 43.97 4.52
3790 4369 4.171005 CCAAGTACTTTGCATTGCATCTG 58.829 43.478 12.95 8.16 38.76 2.90
3791 4370 3.367703 GCCAAGTACTTTGCATTGCATCT 60.368 43.478 22.98 3.94 38.76 2.90
3837 4422 0.896019 AGGTACGTCAGTCAGCTGCT 60.896 55.000 9.47 6.85 42.29 4.24
3838 4423 0.456995 GAGGTACGTCAGTCAGCTGC 60.457 60.000 9.47 4.26 42.29 5.25
3839 4424 3.704381 GAGGTACGTCAGTCAGCTG 57.296 57.895 7.63 7.63 43.87 4.24


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

AutoCloner maintained by Alex Coulton.