Multiple sequence alignment - TraesCS2B01G614600

Loading Multiple Alignment...

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 TraesCS2B01G614600 chr2B 100.000 2291 0 0 1 2291 793231211 793228921 0.000000e+00 4231
1 TraesCS2B01G614600 chr2B 83.544 869 137 6 1 867 731599178 731600042 0.000000e+00 808
2 TraesCS2B01G614600 chr2B 84.549 466 62 8 978 1434 250728992 250728528 9.650000e-124 453
3 TraesCS2B01G614600 chr2A 92.786 1206 80 6 865 2065 768982657 768983860 0.000000e+00 1738
4 TraesCS2B01G614600 chr2A 88.825 698 64 11 865 1551 768729413 768730107 0.000000e+00 845
5 TraesCS2B01G614600 chr2A 82.199 573 81 15 978 1540 209384897 209384336 7.410000e-130 473
6 TraesCS2B01G614600 chr2A 87.162 148 17 2 1567 1713 768730267 768730413 1.410000e-37 167
7 TraesCS2B01G614600 chr2D 90.539 1205 82 11 865 2065 643853854 643855030 0.000000e+00 1565
8 TraesCS2B01G614600 chr2D 82.206 562 75 15 978 1527 194752322 194751774 5.770000e-126 460
9 TraesCS2B01G614600 chr4A 90.553 868 81 1 1 867 702720212 702719345 0.000000e+00 1147
10 TraesCS2B01G614600 chr4A 90.104 869 85 1 1 868 701263866 701264734 0.000000e+00 1127
11 TraesCS2B01G614600 chr7D 86.406 868 117 1 1 867 42961289 42962156 0.000000e+00 948
12 TraesCS2B01G614600 chr7D 81.650 703 123 5 167 866 29301160 29300461 1.530000e-161 579
13 TraesCS2B01G614600 chr3D 83.409 880 134 6 1 871 559777479 559778355 0.000000e+00 806
14 TraesCS2B01G614600 chr6D 82.848 892 141 6 1 882 15780405 15781294 0.000000e+00 789
15 TraesCS2B01G614600 chr3B 82.778 871 142 6 1 866 555242204 555243071 0.000000e+00 771
16 TraesCS2B01G614600 chr3B 95.671 231 10 0 2061 2291 269118545 269118315 2.780000e-99 372
17 TraesCS2B01G614600 chr1D 81.712 853 155 1 16 867 254620210 254621062 0.000000e+00 710
18 TraesCS2B01G614600 chr5D 79.745 864 159 14 16 870 563438033 563437177 1.500000e-171 612
19 TraesCS2B01G614600 chr5D 79.601 853 166 7 16 864 41839014 41838166 2.520000e-169 604
20 TraesCS2B01G614600 chr6B 97.345 226 6 0 2066 2291 190677161 190676936 3.570000e-103 385
21 TraesCS2B01G614600 chr6B 96.476 227 8 0 2065 2291 555625425 555625651 2.150000e-100 375
22 TraesCS2B01G614600 chr4B 97.345 226 6 0 2066 2291 74449285 74449060 3.570000e-103 385
23 TraesCS2B01G614600 chr4B 96.460 226 8 0 2066 2291 50487139 50486914 7.730000e-100 374
24 TraesCS2B01G614600 chr4B 96.460 226 8 0 2066 2291 237182678 237182453 7.730000e-100 374
25 TraesCS2B01G614600 chr7B 95.417 240 9 2 2052 2290 395784494 395784732 4.620000e-102 381
26 TraesCS2B01G614600 chr7B 96.903 226 7 0 2066 2291 63849001 63849226 1.660000e-101 379
27 TraesCS2B01G614600 chr7B 96.460 226 8 0 2066 2291 701359690 701359915 7.730000e-100 374


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 TraesCS2B01G614600 chr2B 793228921 793231211 2290 True 4231 4231 100.0000 1 2291 1 chr2B.!!$R2 2290
1 TraesCS2B01G614600 chr2B 731599178 731600042 864 False 808 808 83.5440 1 867 1 chr2B.!!$F1 866
2 TraesCS2B01G614600 chr2A 768982657 768983860 1203 False 1738 1738 92.7860 865 2065 1 chr2A.!!$F1 1200
3 TraesCS2B01G614600 chr2A 768729413 768730413 1000 False 506 845 87.9935 865 1713 2 chr2A.!!$F2 848
4 TraesCS2B01G614600 chr2A 209384336 209384897 561 True 473 473 82.1990 978 1540 1 chr2A.!!$R1 562
5 TraesCS2B01G614600 chr2D 643853854 643855030 1176 False 1565 1565 90.5390 865 2065 1 chr2D.!!$F1 1200
6 TraesCS2B01G614600 chr2D 194751774 194752322 548 True 460 460 82.2060 978 1527 1 chr2D.!!$R1 549
7 TraesCS2B01G614600 chr4A 702719345 702720212 867 True 1147 1147 90.5530 1 867 1 chr4A.!!$R1 866
8 TraesCS2B01G614600 chr4A 701263866 701264734 868 False 1127 1127 90.1040 1 868 1 chr4A.!!$F1 867
9 TraesCS2B01G614600 chr7D 42961289 42962156 867 False 948 948 86.4060 1 867 1 chr7D.!!$F1 866
10 TraesCS2B01G614600 chr7D 29300461 29301160 699 True 579 579 81.6500 167 866 1 chr7D.!!$R1 699
11 TraesCS2B01G614600 chr3D 559777479 559778355 876 False 806 806 83.4090 1 871 1 chr3D.!!$F1 870
12 TraesCS2B01G614600 chr6D 15780405 15781294 889 False 789 789 82.8480 1 882 1 chr6D.!!$F1 881
13 TraesCS2B01G614600 chr3B 555242204 555243071 867 False 771 771 82.7780 1 866 1 chr3B.!!$F1 865
14 TraesCS2B01G614600 chr1D 254620210 254621062 852 False 710 710 81.7120 16 867 1 chr1D.!!$F1 851
15 TraesCS2B01G614600 chr5D 563437177 563438033 856 True 612 612 79.7450 16 870 1 chr5D.!!$R2 854
16 TraesCS2B01G614600 chr5D 41838166 41839014 848 True 604 604 79.6010 16 864 1 chr5D.!!$R1 848

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
266 269 0.325933 TGTGGTGCTCCTGAAGATGG 59.674 55.0 6.34 0.0 34.23 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1996 0.030369 CCTACAGGTACGCCGACATC 59.97 60.0 0.0 0.0 40.5 3.06 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
38 39 0.530744 CAGCCAGACACGGTAAGCTA 59.469 55.000 0.00 0.00 0.00 3.32
39 40 1.067142 CAGCCAGACACGGTAAGCTAA 60.067 52.381 0.00 0.00 0.00 3.09
86 87 9.052759 GTTCACGGTTAAATCCTTATATCACAT 57.947 33.333 0.00 0.00 0.00 3.21
147 150 1.729484 GAAAGCGCGGTTGCCTTTC 60.729 57.895 25.77 20.28 43.96 2.62
156 159 3.501950 GCGGTTGCCTTTCAAGATAAAG 58.498 45.455 0.00 0.00 34.91 1.85
186 189 3.119531 TCTGGCAAATGTTCCGCAATAAG 60.120 43.478 0.00 0.00 0.00 1.73
266 269 0.325933 TGTGGTGCTCCTGAAGATGG 59.674 55.000 6.34 0.00 34.23 3.51
267 270 0.326264 GTGGTGCTCCTGAAGATGGT 59.674 55.000 6.34 0.00 34.23 3.55
268 271 0.325933 TGGTGCTCCTGAAGATGGTG 59.674 55.000 6.34 0.00 34.23 4.17
271 274 2.356535 GGTGCTCCTGAAGATGGTGATT 60.357 50.000 0.00 0.00 0.00 2.57
273 276 4.125703 GTGCTCCTGAAGATGGTGATTAG 58.874 47.826 0.00 0.00 0.00 1.73
279 282 5.104776 TCCTGAAGATGGTGATTAGGTCTTG 60.105 44.000 0.00 0.00 29.89 3.02
292 295 0.893727 GGTCTTGTTTCGGTGCCCAT 60.894 55.000 0.00 0.00 0.00 4.00
322 325 3.403057 CGTGGAGCGTGGTTCGTG 61.403 66.667 0.00 0.00 42.13 4.35
393 396 5.905331 TCAGTTATTAGATGTGATCCAGGGT 59.095 40.000 0.00 0.00 0.00 4.34
440 443 2.452491 AGGGGCACTCCTTTGGGT 60.452 61.111 0.00 0.00 32.13 4.51
441 444 2.283173 GGGGCACTCCTTTGGGTG 60.283 66.667 0.00 0.00 36.62 4.61
446 449 1.477923 GGCACTCCTTTGGGTGTTGTA 60.478 52.381 0.00 0.00 37.24 2.41
465 468 9.533253 GTGTTGTAGTTAACTAGGAACAAACTA 57.467 33.333 26.83 14.49 35.49 2.24
518 521 6.365839 CGGCTAATGTTATCTACAAATGCAG 58.634 40.000 0.00 0.00 40.89 4.41
563 566 3.797353 GGGGAGGCGCAAGGATGA 61.797 66.667 10.83 0.00 38.28 2.92
583 586 1.273759 TGAGATGCTCAAGACTGCCT 58.726 50.000 0.00 0.00 37.57 4.75
601 604 4.088634 TGCCTAAGACCTTTTGATGCAAT 58.911 39.130 0.00 0.00 0.00 3.56
609 612 5.009610 AGACCTTTTGATGCAATTGTACGTT 59.990 36.000 7.40 0.00 0.00 3.99
657 660 4.620589 TTAGGACGTGGTGTATTTTGGA 57.379 40.909 0.00 0.00 0.00 3.53
692 695 1.375523 CGCTCTGTACGGGCCTTTT 60.376 57.895 0.84 0.00 0.00 2.27
741 751 2.607771 GCCCTTCGTCGTAACTGTAACA 60.608 50.000 0.00 0.00 0.00 2.41
924 944 9.548631 ACCTGATAATAGCTACACCTGTATATT 57.451 33.333 0.00 0.00 0.00 1.28
973 993 5.486526 ACATTTGTTGCCTTTGTCTTTCAA 58.513 33.333 0.00 0.00 0.00 2.69
1025 1045 1.527370 GCCTTAGACGCCCCTCAAT 59.473 57.895 0.00 0.00 0.00 2.57
1075 1095 0.753479 TCCCTTAGGAGCTCTGCGAG 60.753 60.000 14.64 6.80 37.19 5.03
1157 1177 1.523154 GCAAACCGCCCATTGTCTCA 61.523 55.000 0.00 0.00 32.94 3.27
1169 1189 4.387598 CCATTGTCTCATCATCTTCCTCC 58.612 47.826 0.00 0.00 0.00 4.30
1189 1209 1.597742 GAAGAAGCCACAGTTGAGCA 58.402 50.000 0.00 0.00 0.00 4.26
1200 1220 1.979469 CAGTTGAGCACTACGTTCTCG 59.021 52.381 0.00 0.00 36.99 4.04
1222 1242 1.137282 TCTCGCACCGTATATTTGGCA 59.863 47.619 0.00 0.00 0.00 4.92
1234 1254 1.829523 ATTTGGCATTGCGCTGGGTT 61.830 50.000 9.73 0.00 41.91 4.11
1248 1268 2.224719 GCTGGGTTCTGCCATCATATCT 60.225 50.000 0.00 0.00 39.65 1.98
1249 1269 3.409570 CTGGGTTCTGCCATCATATCTG 58.590 50.000 0.00 0.00 39.65 2.90
1302 1331 2.103094 TGGTGTCTGAGTGAAACAGAGG 59.897 50.000 0.00 0.00 43.58 3.69
1310 1339 0.606673 GTGAAACAGAGGTGAGGGGC 60.607 60.000 0.00 0.00 36.32 5.80
1322 1351 1.675641 GAGGGGCGACATTGCTGTT 60.676 57.895 0.00 0.00 35.14 3.16
1333 1363 2.036217 ACATTGCTGTTGGTGTTCCATG 59.964 45.455 0.00 0.00 43.91 3.66
1361 1391 2.553602 CACAATGCAACTCTAGGTGCAA 59.446 45.455 25.15 10.20 36.29 4.08
1481 1513 6.154877 TCGGGTATTTGTTGTTATGAGGTCTA 59.845 38.462 0.00 0.00 0.00 2.59
1633 1810 7.645058 TTTGGCCTCCTAATTCTCTTAATTG 57.355 36.000 3.32 0.00 0.00 2.32
1723 1900 9.187996 TCTTTGTTAATCATGAATGAATAGGCA 57.812 29.630 0.00 0.00 40.69 4.75
1760 1937 3.490348 ACCACAAGCTAAGTTGATGCTT 58.510 40.909 6.73 6.73 46.38 3.91
1780 1957 4.688021 CTTAATTCCTCTCTTCTCCACGG 58.312 47.826 0.00 0.00 0.00 4.94
1807 1984 3.444034 TCATCCTCTACCTTTCAGTGTCG 59.556 47.826 0.00 0.00 0.00 4.35
1831 2008 2.654404 GGAGCGATGTCGGCGTAC 60.654 66.667 6.85 4.58 40.23 3.67
1880 2057 5.340803 CATGGCATCAGATTCAAAACTCAG 58.659 41.667 0.00 0.00 0.00 3.35
1889 2066 5.762218 CAGATTCAAAACTCAGGAAGTCAGT 59.238 40.000 0.00 0.00 37.17 3.41
1890 2067 5.762218 AGATTCAAAACTCAGGAAGTCAGTG 59.238 40.000 0.00 0.00 37.17 3.66
1902 2079 1.610363 AGTCAGTGTCTTCTCGAGCA 58.390 50.000 7.81 0.00 0.00 4.26
1903 2080 2.166829 AGTCAGTGTCTTCTCGAGCAT 58.833 47.619 7.81 0.00 0.00 3.79
1908 2085 2.036475 AGTGTCTTCTCGAGCATGTGTT 59.964 45.455 7.81 0.00 0.00 3.32
1915 2092 1.002134 CGAGCATGTGTTCCCCCTT 60.002 57.895 0.00 0.00 0.00 3.95
1938 2115 1.067821 GGCCATGTCTACTCCTCTTCG 59.932 57.143 0.00 0.00 0.00 3.79
1948 2126 3.713826 ACTCCTCTTCGGCCAAAATTA 57.286 42.857 2.24 0.00 0.00 1.40
1958 2137 5.309323 TCGGCCAAAATTAGATCTTGTTG 57.691 39.130 2.24 0.00 0.00 3.33
2047 2226 2.509651 TTTACGACGGTGGGCCAGT 61.510 57.895 6.40 0.90 34.09 4.00
2065 2244 4.621274 GCCAGTGTTCCACAATTGCATAAT 60.621 41.667 5.05 0.00 35.35 1.28
2066 2245 4.865925 CCAGTGTTCCACAATTGCATAATG 59.134 41.667 5.05 0.00 36.74 1.90
2067 2246 5.472148 CAGTGTTCCACAATTGCATAATGT 58.528 37.500 5.05 0.00 36.74 2.71
2068 2247 6.350027 CCAGTGTTCCACAATTGCATAATGTA 60.350 38.462 5.05 0.00 36.74 2.29
2069 2248 7.089538 CAGTGTTCCACAATTGCATAATGTAA 58.910 34.615 5.05 0.00 36.74 2.41
2070 2249 7.274033 CAGTGTTCCACAATTGCATAATGTAAG 59.726 37.037 5.05 0.00 36.74 2.34
2071 2250 7.039784 AGTGTTCCACAATTGCATAATGTAAGT 60.040 33.333 5.05 0.00 36.74 2.24
2072 2251 7.062138 GTGTTCCACAATTGCATAATGTAAGTG 59.938 37.037 5.05 0.00 42.23 3.16
2073 2252 5.649557 TCCACAATTGCATAATGTAAGTGC 58.350 37.500 5.05 0.00 40.69 4.40
2074 2253 5.184671 TCCACAATTGCATAATGTAAGTGCA 59.815 36.000 5.05 0.00 40.69 4.57
2075 2254 6.044046 CCACAATTGCATAATGTAAGTGCAT 58.956 36.000 5.05 0.00 46.90 3.96
2076 2255 6.199531 CCACAATTGCATAATGTAAGTGCATC 59.800 38.462 5.05 0.00 46.90 3.91
2077 2256 6.976349 CACAATTGCATAATGTAAGTGCATCT 59.024 34.615 5.05 0.00 46.90 2.90
2078 2257 8.130469 CACAATTGCATAATGTAAGTGCATCTA 58.870 33.333 5.05 0.00 46.90 1.98
2079 2258 8.347771 ACAATTGCATAATGTAAGTGCATCTAG 58.652 33.333 5.05 0.00 46.90 2.43
2080 2259 8.347771 CAATTGCATAATGTAAGTGCATCTAGT 58.652 33.333 0.00 0.00 46.90 2.57
2081 2260 6.849588 TGCATAATGTAAGTGCATCTAGTG 57.150 37.500 0.00 0.00 43.30 2.74
2092 2271 1.794714 CATCTAGTGCCACCCCTAGT 58.205 55.000 0.00 0.00 33.81 2.57
2093 2272 2.119495 CATCTAGTGCCACCCCTAGTT 58.881 52.381 0.00 0.00 33.81 2.24
2094 2273 1.568504 TCTAGTGCCACCCCTAGTTG 58.431 55.000 0.00 0.00 33.81 3.16
2095 2274 0.541863 CTAGTGCCACCCCTAGTTGG 59.458 60.000 0.00 0.00 0.00 3.77
2096 2275 0.178885 TAGTGCCACCCCTAGTTGGT 60.179 55.000 0.00 0.53 36.21 3.67
2097 2276 1.065997 AGTGCCACCCCTAGTTGGTT 61.066 55.000 0.00 0.00 32.46 3.67
2098 2277 0.178973 GTGCCACCCCTAGTTGGTTT 60.179 55.000 0.00 0.00 32.46 3.27
2099 2278 0.558712 TGCCACCCCTAGTTGGTTTT 59.441 50.000 0.00 0.00 32.46 2.43
2100 2279 0.966179 GCCACCCCTAGTTGGTTTTG 59.034 55.000 0.00 0.00 32.46 2.44
2101 2280 1.627864 CCACCCCTAGTTGGTTTTGG 58.372 55.000 0.00 0.00 32.46 3.28
2102 2281 1.146152 CCACCCCTAGTTGGTTTTGGA 59.854 52.381 0.00 0.00 32.46 3.53
2103 2282 2.425102 CCACCCCTAGTTGGTTTTGGAA 60.425 50.000 0.00 0.00 32.46 3.53
2104 2283 3.506398 CACCCCTAGTTGGTTTTGGAAT 58.494 45.455 0.00 0.00 32.46 3.01
2105 2284 3.258123 CACCCCTAGTTGGTTTTGGAATG 59.742 47.826 0.00 0.00 32.46 2.67
2106 2285 3.116900 ACCCCTAGTTGGTTTTGGAATGT 60.117 43.478 0.00 0.00 29.75 2.71
2107 2286 3.901222 CCCCTAGTTGGTTTTGGAATGTT 59.099 43.478 0.00 0.00 0.00 2.71
2108 2287 4.262420 CCCCTAGTTGGTTTTGGAATGTTG 60.262 45.833 0.00 0.00 0.00 3.33
2109 2288 4.586841 CCCTAGTTGGTTTTGGAATGTTGA 59.413 41.667 0.00 0.00 0.00 3.18
2110 2289 5.508994 CCCTAGTTGGTTTTGGAATGTTGAC 60.509 44.000 0.00 0.00 0.00 3.18
2111 2290 4.040445 AGTTGGTTTTGGAATGTTGACG 57.960 40.909 0.00 0.00 0.00 4.35
2112 2291 3.697045 AGTTGGTTTTGGAATGTTGACGA 59.303 39.130 0.00 0.00 0.00 4.20
2113 2292 3.701532 TGGTTTTGGAATGTTGACGAC 57.298 42.857 0.00 0.00 0.00 4.34
2114 2293 3.017442 TGGTTTTGGAATGTTGACGACA 58.983 40.909 0.00 0.00 43.71 4.35
2115 2294 3.444034 TGGTTTTGGAATGTTGACGACAA 59.556 39.130 0.00 0.00 42.62 3.18
2116 2295 4.082190 TGGTTTTGGAATGTTGACGACAAA 60.082 37.500 0.97 0.00 42.62 2.83
2117 2296 4.266739 GGTTTTGGAATGTTGACGACAAAC 59.733 41.667 0.97 0.00 42.62 2.93
2118 2297 3.701532 TTGGAATGTTGACGACAAACC 57.298 42.857 0.97 7.09 42.62 3.27
2119 2298 2.925724 TGGAATGTTGACGACAAACCT 58.074 42.857 17.08 0.00 42.62 3.50
2120 2299 2.616376 TGGAATGTTGACGACAAACCTG 59.384 45.455 17.08 0.00 42.62 4.00
2121 2300 2.031157 GGAATGTTGACGACAAACCTGG 60.031 50.000 0.97 0.00 42.62 4.45
2122 2301 2.341846 ATGTTGACGACAAACCTGGT 57.658 45.000 0.97 0.00 42.62 4.00
2123 2302 2.116827 TGTTGACGACAAACCTGGTT 57.883 45.000 6.18 6.18 37.77 3.67
2124 2303 1.740585 TGTTGACGACAAACCTGGTTG 59.259 47.619 13.79 9.84 37.77 3.77
2125 2304 2.011222 GTTGACGACAAACCTGGTTGA 58.989 47.619 13.79 0.00 37.77 3.18
2126 2305 1.948104 TGACGACAAACCTGGTTGAG 58.052 50.000 13.79 11.47 32.59 3.02
2137 2316 2.991250 CCTGGTTGAGGGACTAATGTG 58.009 52.381 0.00 0.00 41.55 3.21
2138 2317 2.305927 CCTGGTTGAGGGACTAATGTGT 59.694 50.000 0.00 0.00 41.55 3.72
2139 2318 3.244911 CCTGGTTGAGGGACTAATGTGTT 60.245 47.826 0.00 0.00 41.55 3.32
2140 2319 4.398319 CTGGTTGAGGGACTAATGTGTTT 58.602 43.478 0.00 0.00 41.55 2.83
2141 2320 4.141287 TGGTTGAGGGACTAATGTGTTTG 58.859 43.478 0.00 0.00 41.55 2.93
2142 2321 4.142038 GGTTGAGGGACTAATGTGTTTGT 58.858 43.478 0.00 0.00 41.55 2.83
2143 2322 4.023193 GGTTGAGGGACTAATGTGTTTGTG 60.023 45.833 0.00 0.00 41.55 3.33
2144 2323 4.698201 TGAGGGACTAATGTGTTTGTGA 57.302 40.909 0.00 0.00 41.55 3.58
2145 2324 4.641396 TGAGGGACTAATGTGTTTGTGAG 58.359 43.478 0.00 0.00 41.55 3.51
2146 2325 4.346709 TGAGGGACTAATGTGTTTGTGAGA 59.653 41.667 0.00 0.00 41.55 3.27
2147 2326 5.163248 TGAGGGACTAATGTGTTTGTGAGAA 60.163 40.000 0.00 0.00 41.55 2.87
2148 2327 5.880901 AGGGACTAATGTGTTTGTGAGAAT 58.119 37.500 0.00 0.00 36.02 2.40
2149 2328 6.306987 AGGGACTAATGTGTTTGTGAGAATT 58.693 36.000 0.00 0.00 36.02 2.17
2150 2329 7.458397 AGGGACTAATGTGTTTGTGAGAATTA 58.542 34.615 0.00 0.00 36.02 1.40
2151 2330 7.390718 AGGGACTAATGTGTTTGTGAGAATTAC 59.609 37.037 0.00 0.00 36.02 1.89
2152 2331 7.174253 GGGACTAATGTGTTTGTGAGAATTACA 59.826 37.037 0.00 0.00 0.00 2.41
2153 2332 8.230486 GGACTAATGTGTTTGTGAGAATTACAG 58.770 37.037 0.00 0.00 0.00 2.74
2154 2333 8.099364 ACTAATGTGTTTGTGAGAATTACAGG 57.901 34.615 0.00 0.00 0.00 4.00
2155 2334 7.936847 ACTAATGTGTTTGTGAGAATTACAGGA 59.063 33.333 0.00 0.00 0.00 3.86
2156 2335 7.765695 AATGTGTTTGTGAGAATTACAGGAT 57.234 32.000 0.00 0.00 0.00 3.24
2157 2336 8.862325 AATGTGTTTGTGAGAATTACAGGATA 57.138 30.769 0.00 0.00 0.00 2.59
2158 2337 8.862325 ATGTGTTTGTGAGAATTACAGGATAA 57.138 30.769 0.00 0.00 0.00 1.75
2159 2338 8.094798 TGTGTTTGTGAGAATTACAGGATAAC 57.905 34.615 0.00 0.00 0.00 1.89
2160 2339 7.717436 TGTGTTTGTGAGAATTACAGGATAACA 59.283 33.333 0.00 0.00 0.00 2.41
2161 2340 8.015658 GTGTTTGTGAGAATTACAGGATAACAC 58.984 37.037 8.44 8.44 38.13 3.32
2162 2341 7.717436 TGTTTGTGAGAATTACAGGATAACACA 59.283 33.333 0.00 0.00 34.69 3.72
2163 2342 7.905604 TTGTGAGAATTACAGGATAACACAG 57.094 36.000 0.00 0.00 37.13 3.66
2164 2343 6.406370 TGTGAGAATTACAGGATAACACAGG 58.594 40.000 0.00 0.00 33.10 4.00
2165 2344 6.013725 TGTGAGAATTACAGGATAACACAGGT 60.014 38.462 0.00 0.00 33.10 4.00
2166 2345 7.179516 TGTGAGAATTACAGGATAACACAGGTA 59.820 37.037 0.00 0.00 33.10 3.08
2167 2346 7.707035 GTGAGAATTACAGGATAACACAGGTAG 59.293 40.741 0.00 0.00 0.00 3.18
2168 2347 7.399191 TGAGAATTACAGGATAACACAGGTAGT 59.601 37.037 0.00 0.00 0.00 2.73
2169 2348 8.834004 AGAATTACAGGATAACACAGGTAGTA 57.166 34.615 0.00 0.00 0.00 1.82
2170 2349 8.915036 AGAATTACAGGATAACACAGGTAGTAG 58.085 37.037 0.00 0.00 0.00 2.57
2171 2350 8.605325 AATTACAGGATAACACAGGTAGTAGT 57.395 34.615 0.00 0.00 0.00 2.73
2172 2351 7.636150 TTACAGGATAACACAGGTAGTAGTC 57.364 40.000 0.00 0.00 0.00 2.59
2173 2352 4.954826 ACAGGATAACACAGGTAGTAGTCC 59.045 45.833 0.00 0.00 0.00 3.85
2174 2353 5.202004 CAGGATAACACAGGTAGTAGTCCT 58.798 45.833 0.00 0.00 34.95 3.85
2175 2354 6.069206 ACAGGATAACACAGGTAGTAGTCCTA 60.069 42.308 0.00 0.00 33.70 2.94
2176 2355 7.005296 CAGGATAACACAGGTAGTAGTCCTAT 58.995 42.308 0.00 0.00 33.70 2.57
2177 2356 8.162085 CAGGATAACACAGGTAGTAGTCCTATA 58.838 40.741 0.00 0.00 33.70 1.31
2178 2357 8.902881 AGGATAACACAGGTAGTAGTCCTATAT 58.097 37.037 0.00 0.00 33.70 0.86
2179 2358 9.531158 GGATAACACAGGTAGTAGTCCTATATT 57.469 37.037 0.00 0.00 33.54 1.28
2183 2362 9.435570 AACACAGGTAGTAGTCCTATATTGATT 57.564 33.333 0.00 0.00 33.54 2.57
2184 2363 9.080097 ACACAGGTAGTAGTCCTATATTGATTC 57.920 37.037 0.00 0.00 33.54 2.52
2185 2364 8.237949 CACAGGTAGTAGTCCTATATTGATTCG 58.762 40.741 0.00 0.00 33.54 3.34
2186 2365 7.393796 ACAGGTAGTAGTCCTATATTGATTCGG 59.606 40.741 0.00 0.00 33.54 4.30
2187 2366 7.393796 CAGGTAGTAGTCCTATATTGATTCGGT 59.606 40.741 0.00 0.00 33.54 4.69
2188 2367 7.949006 AGGTAGTAGTCCTATATTGATTCGGTT 59.051 37.037 0.00 0.00 33.04 4.44
2189 2368 8.583296 GGTAGTAGTCCTATATTGATTCGGTTT 58.417 37.037 0.00 0.00 0.00 3.27
2192 2371 8.583296 AGTAGTCCTATATTGATTCGGTTTACC 58.417 37.037 0.00 0.00 0.00 2.85
2193 2372 7.613551 AGTCCTATATTGATTCGGTTTACCT 57.386 36.000 0.00 0.00 0.00 3.08
2194 2373 8.716674 AGTCCTATATTGATTCGGTTTACCTA 57.283 34.615 0.00 0.00 0.00 3.08
2195 2374 8.583296 AGTCCTATATTGATTCGGTTTACCTAC 58.417 37.037 0.00 0.00 0.00 3.18
2196 2375 7.816513 GTCCTATATTGATTCGGTTTACCTACC 59.183 40.741 0.00 0.00 34.72 3.18
2197 2376 7.510001 TCCTATATTGATTCGGTTTACCTACCA 59.490 37.037 0.00 0.00 38.12 3.25
2198 2377 7.817962 CCTATATTGATTCGGTTTACCTACCAG 59.182 40.741 0.00 0.00 38.12 4.00
2199 2378 5.687166 ATTGATTCGGTTTACCTACCAGA 57.313 39.130 0.00 0.00 38.12 3.86
2200 2379 4.730949 TGATTCGGTTTACCTACCAGAG 57.269 45.455 0.00 0.00 38.12 3.35
2201 2380 4.346730 TGATTCGGTTTACCTACCAGAGA 58.653 43.478 0.00 0.00 38.12 3.10
2202 2381 4.960469 TGATTCGGTTTACCTACCAGAGAT 59.040 41.667 0.00 0.00 38.12 2.75
2203 2382 4.730949 TTCGGTTTACCTACCAGAGATG 57.269 45.455 0.00 0.00 38.12 2.90
2204 2383 3.972133 TCGGTTTACCTACCAGAGATGA 58.028 45.455 0.00 0.00 38.12 2.92
2205 2384 3.698040 TCGGTTTACCTACCAGAGATGAC 59.302 47.826 0.00 0.00 38.12 3.06
2206 2385 3.181478 CGGTTTACCTACCAGAGATGACC 60.181 52.174 0.00 0.00 38.12 4.02
2207 2386 3.134262 GGTTTACCTACCAGAGATGACCC 59.866 52.174 0.00 0.00 38.12 4.46
2208 2387 2.769602 TACCTACCAGAGATGACCCC 57.230 55.000 0.00 0.00 0.00 4.95
2209 2388 1.019650 ACCTACCAGAGATGACCCCT 58.980 55.000 0.00 0.00 0.00 4.79
2210 2389 2.224077 ACCTACCAGAGATGACCCCTA 58.776 52.381 0.00 0.00 0.00 3.53
2211 2390 2.590611 ACCTACCAGAGATGACCCCTAA 59.409 50.000 0.00 0.00 0.00 2.69
2212 2391 3.013648 ACCTACCAGAGATGACCCCTAAA 59.986 47.826 0.00 0.00 0.00 1.85
2213 2392 4.037927 CCTACCAGAGATGACCCCTAAAA 58.962 47.826 0.00 0.00 0.00 1.52
2214 2393 4.473559 CCTACCAGAGATGACCCCTAAAAA 59.526 45.833 0.00 0.00 0.00 1.94
2215 2394 5.132816 CCTACCAGAGATGACCCCTAAAAAT 59.867 44.000 0.00 0.00 0.00 1.82
2216 2395 4.860022 ACCAGAGATGACCCCTAAAAATG 58.140 43.478 0.00 0.00 0.00 2.32
2217 2396 4.292306 ACCAGAGATGACCCCTAAAAATGT 59.708 41.667 0.00 0.00 0.00 2.71
2218 2397 4.641989 CCAGAGATGACCCCTAAAAATGTG 59.358 45.833 0.00 0.00 0.00 3.21
2219 2398 5.256474 CAGAGATGACCCCTAAAAATGTGT 58.744 41.667 0.00 0.00 0.00 3.72
2220 2399 5.124457 CAGAGATGACCCCTAAAAATGTGTG 59.876 44.000 0.00 0.00 0.00 3.82
2221 2400 5.014123 AGAGATGACCCCTAAAAATGTGTGA 59.986 40.000 0.00 0.00 0.00 3.58
2222 2401 5.640147 AGATGACCCCTAAAAATGTGTGAA 58.360 37.500 0.00 0.00 0.00 3.18
2223 2402 5.711976 AGATGACCCCTAAAAATGTGTGAAG 59.288 40.000 0.00 0.00 0.00 3.02
2224 2403 5.055265 TGACCCCTAAAAATGTGTGAAGA 57.945 39.130 0.00 0.00 0.00 2.87
2225 2404 4.825085 TGACCCCTAAAAATGTGTGAAGAC 59.175 41.667 0.00 0.00 0.00 3.01
2226 2405 4.798882 ACCCCTAAAAATGTGTGAAGACA 58.201 39.130 0.00 0.00 0.00 3.41
2227 2406 5.393866 ACCCCTAAAAATGTGTGAAGACAT 58.606 37.500 0.00 0.00 38.23 3.06
2228 2407 5.838521 ACCCCTAAAAATGTGTGAAGACATT 59.161 36.000 0.26 0.26 46.35 2.71
2229 2408 6.158598 CCCCTAAAAATGTGTGAAGACATTG 58.841 40.000 6.59 0.00 44.15 2.82
2230 2409 6.015519 CCCCTAAAAATGTGTGAAGACATTGA 60.016 38.462 6.59 0.00 44.15 2.57
2231 2410 7.432869 CCCTAAAAATGTGTGAAGACATTGAA 58.567 34.615 6.59 0.00 44.15 2.69
2232 2411 7.596248 CCCTAAAAATGTGTGAAGACATTGAAG 59.404 37.037 6.59 5.21 44.15 3.02
2233 2412 8.352201 CCTAAAAATGTGTGAAGACATTGAAGA 58.648 33.333 6.59 0.00 44.15 2.87
2234 2413 7.992180 AAAAATGTGTGAAGACATTGAAGAC 57.008 32.000 6.59 0.00 44.15 3.01
2235 2414 6.698008 AAATGTGTGAAGACATTGAAGACA 57.302 33.333 6.59 0.00 44.15 3.41
2236 2415 6.698008 AATGTGTGAAGACATTGAAGACAA 57.302 33.333 5.13 0.00 43.45 3.18
2237 2416 6.889301 ATGTGTGAAGACATTGAAGACAAT 57.111 33.333 0.00 0.00 46.10 2.71
2248 2427 4.383850 TTGAAGACAATGGTGGTTTGTG 57.616 40.909 0.00 0.00 37.43 3.33
2249 2428 3.625853 TGAAGACAATGGTGGTTTGTGA 58.374 40.909 0.00 0.00 37.43 3.58
2250 2429 4.019858 TGAAGACAATGGTGGTTTGTGAA 58.980 39.130 0.00 0.00 37.43 3.18
2251 2430 4.097741 TGAAGACAATGGTGGTTTGTGAAG 59.902 41.667 0.00 0.00 37.43 3.02
2252 2431 3.897239 AGACAATGGTGGTTTGTGAAGA 58.103 40.909 0.00 0.00 37.43 2.87
2253 2432 3.632145 AGACAATGGTGGTTTGTGAAGAC 59.368 43.478 0.00 0.00 37.43 3.01
2254 2433 3.360867 ACAATGGTGGTTTGTGAAGACA 58.639 40.909 0.00 0.00 36.02 3.41
2255 2434 3.960102 ACAATGGTGGTTTGTGAAGACAT 59.040 39.130 0.00 0.00 36.02 3.06
2256 2435 4.405358 ACAATGGTGGTTTGTGAAGACATT 59.595 37.500 0.00 0.00 36.02 2.71
2257 2436 4.853924 ATGGTGGTTTGTGAAGACATTC 57.146 40.909 0.00 0.00 35.87 2.67
2258 2437 3.625853 TGGTGGTTTGTGAAGACATTCA 58.374 40.909 0.00 0.00 43.20 2.57
2272 2451 8.260270 TGAAGACATTCACATTGAAGACTATG 57.740 34.615 0.00 0.00 40.05 2.23
2273 2452 8.096414 TGAAGACATTCACATTGAAGACTATGA 58.904 33.333 0.00 0.00 40.05 2.15
2274 2453 7.840342 AGACATTCACATTGAAGACTATGAC 57.160 36.000 0.00 0.00 40.05 3.06
2275 2454 7.389232 AGACATTCACATTGAAGACTATGACA 58.611 34.615 0.00 0.00 40.05 3.58
2276 2455 7.548427 AGACATTCACATTGAAGACTATGACAG 59.452 37.037 0.00 0.00 40.05 3.51
2277 2456 6.093219 ACATTCACATTGAAGACTATGACAGC 59.907 38.462 0.00 0.00 40.05 4.40
2278 2457 5.151297 TCACATTGAAGACTATGACAGCA 57.849 39.130 0.00 0.00 34.41 4.41
2279 2458 5.173664 TCACATTGAAGACTATGACAGCAG 58.826 41.667 0.00 0.00 34.41 4.24
2280 2459 5.047092 TCACATTGAAGACTATGACAGCAGA 60.047 40.000 0.00 0.00 34.41 4.26
2281 2460 5.640783 CACATTGAAGACTATGACAGCAGAA 59.359 40.000 0.00 0.00 34.41 3.02
2282 2461 5.873712 ACATTGAAGACTATGACAGCAGAAG 59.126 40.000 0.00 0.00 34.41 2.85
2283 2462 5.728637 TTGAAGACTATGACAGCAGAAGA 57.271 39.130 0.00 0.00 0.00 2.87
2284 2463 5.065704 TGAAGACTATGACAGCAGAAGAC 57.934 43.478 0.00 0.00 0.00 3.01
2285 2464 4.524328 TGAAGACTATGACAGCAGAAGACA 59.476 41.667 0.00 0.00 0.00 3.41
2286 2465 5.186603 TGAAGACTATGACAGCAGAAGACAT 59.813 40.000 0.00 0.00 0.00 3.06
2287 2466 5.261209 AGACTATGACAGCAGAAGACATC 57.739 43.478 0.00 0.00 0.00 3.06
2288 2467 4.039151 ACTATGACAGCAGAAGACATCG 57.961 45.455 0.00 0.00 0.00 3.84
2289 2468 1.649664 ATGACAGCAGAAGACATCGC 58.350 50.000 0.00 0.00 0.00 4.58
2290 2469 0.733909 TGACAGCAGAAGACATCGCG 60.734 55.000 0.00 0.00 34.29 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.227823 CGTGTCTGGCTGGTCCAAA 60.228 57.895 0.00 0.00 46.01 3.28
14 15 3.625897 CCGTGTCTGGCTGGTCCA 61.626 66.667 0.00 0.00 44.18 4.02
107 108 0.670162 CAGCCCTTTGACCACAAGTG 59.330 55.000 0.00 0.00 37.32 3.16
147 150 5.371526 TGCCAGAGGAATAGCTTTATCTTG 58.628 41.667 0.00 0.00 0.00 3.02
156 159 3.067320 GGAACATTTGCCAGAGGAATAGC 59.933 47.826 0.00 0.00 0.00 2.97
186 189 2.610859 TTCAGGGAGGTGGGGAGC 60.611 66.667 0.00 0.00 0.00 4.70
266 269 3.120304 GCACCGAAACAAGACCTAATCAC 60.120 47.826 0.00 0.00 0.00 3.06
267 270 3.071479 GCACCGAAACAAGACCTAATCA 58.929 45.455 0.00 0.00 0.00 2.57
268 271 2.418976 GGCACCGAAACAAGACCTAATC 59.581 50.000 0.00 0.00 0.00 1.75
271 274 0.035739 GGGCACCGAAACAAGACCTA 59.964 55.000 0.00 0.00 40.86 3.08
273 276 3.351450 GGGCACCGAAACAAGACC 58.649 61.111 0.00 0.00 40.86 3.85
292 295 0.669318 CTCCACGCAAACCTCGCTAA 60.669 55.000 0.00 0.00 0.00 3.09
349 352 0.464036 ATTAGTTCGGCCGCAGATCA 59.536 50.000 23.51 0.00 0.00 2.92
393 396 6.539173 ACTCCACATAACACATTTAACAGGA 58.461 36.000 0.00 0.00 0.00 3.86
446 449 7.601508 CGATGGTTAGTTTGTTCCTAGTTAACT 59.398 37.037 13.68 13.68 33.89 2.24
518 521 0.737219 CCACTGCTGCAAGAATAGGC 59.263 55.000 3.02 0.00 34.07 3.93
563 566 1.838715 AGGCAGTCTTGAGCATCTCAT 59.161 47.619 0.00 0.00 40.39 2.90
583 586 6.205853 ACGTACAATTGCATCAAAAGGTCTTA 59.794 34.615 5.05 0.00 0.00 2.10
601 604 1.822990 CTCCCTAGCCAGAACGTACAA 59.177 52.381 0.00 0.00 0.00 2.41
692 695 1.272490 CCACGAGCAGTCTTACAAGGA 59.728 52.381 0.00 0.00 0.00 3.36
741 751 1.525535 GCCCTCGCAAGCATGATCT 60.526 57.895 0.00 0.00 34.03 2.75
840 859 0.033504 AGAACGAAGACGCCACATGT 59.966 50.000 0.00 0.00 43.96 3.21
898 918 9.548631 AATATACAGGTGTAGCTATTATCAGGT 57.451 33.333 0.00 0.00 33.52 4.00
924 944 5.190925 ACCAGGCACCATTAGTAGTTAATCA 59.809 40.000 0.00 0.00 29.37 2.57
934 954 4.462483 ACAAATGTAACCAGGCACCATTAG 59.538 41.667 0.00 0.00 0.00 1.73
940 960 2.403259 GCAACAAATGTAACCAGGCAC 58.597 47.619 0.00 0.00 0.00 5.01
1075 1095 2.045524 TCCAGATGGAGGCATCTTCTC 58.954 52.381 0.00 0.00 39.69 2.87
1096 1116 2.756760 GACTTGTGTGTAGGGATCGGTA 59.243 50.000 0.00 0.00 0.00 4.02
1169 1189 0.514691 GCTCAACTGTGGCTTCTTCG 59.485 55.000 0.00 0.00 0.00 3.79
1189 1209 1.062294 GTGCGAGATCGAGAACGTAGT 59.938 52.381 6.39 0.00 43.61 2.73
1200 1220 2.412089 GCCAAATATACGGTGCGAGATC 59.588 50.000 0.00 0.00 0.00 2.75
1222 1242 3.064324 GGCAGAACCCAGCGCAAT 61.064 61.111 11.47 0.00 0.00 3.56
1234 1254 4.229639 AGAGGAACAGATATGATGGCAGA 58.770 43.478 0.00 0.00 0.00 4.26
1248 1268 3.135712 TGAACTTGGTAGCAAGAGGAACA 59.864 43.478 34.80 22.81 36.16 3.18
1249 1269 3.740115 TGAACTTGGTAGCAAGAGGAAC 58.260 45.455 34.80 21.06 36.16 3.62
1302 1331 2.045926 AGCAATGTCGCCCCTCAC 60.046 61.111 0.00 0.00 0.00 3.51
1310 1339 1.334960 GGAACACCAACAGCAATGTCG 60.335 52.381 0.00 0.00 0.00 4.35
1333 1363 0.319813 GAGTTGCATTGTGCCCAACC 60.320 55.000 0.00 0.00 44.23 3.77
1361 1391 3.685550 GCCTGGTAAGATGTTATGGCAGT 60.686 47.826 14.73 0.00 34.60 4.40
1457 1489 5.183228 AGACCTCATAACAACAAATACCCG 58.817 41.667 0.00 0.00 0.00 5.28
1462 1494 9.520515 AGATTTGTAGACCTCATAACAACAAAT 57.479 29.630 9.54 9.54 44.39 2.32
1504 1536 5.358922 CAAGGAAAACATTCAAGCCAAAGA 58.641 37.500 0.00 0.00 0.00 2.52
1633 1810 4.210331 ACTCAAATATGGATCTGCAACCC 58.790 43.478 0.00 0.00 0.00 4.11
1700 1877 8.291191 TGTGCCTATTCATTCATGATTAACAA 57.709 30.769 0.00 0.00 36.56 2.83
1742 1919 6.660949 AGGAATTAAGCATCAACTTAGCTTGT 59.339 34.615 8.96 0.00 46.98 3.16
1760 1937 3.700038 GACCGTGGAGAAGAGAGGAATTA 59.300 47.826 0.00 0.00 0.00 1.40
1780 1957 5.814705 CACTGAAAGGTAGAGGATGATTGAC 59.185 44.000 0.00 0.00 39.30 3.18
1807 1984 2.512515 GACATCGCTCCCAGGCAC 60.513 66.667 0.00 0.00 0.00 5.01
1819 1996 0.030369 CCTACAGGTACGCCGACATC 59.970 60.000 0.00 0.00 40.50 3.06
1831 2008 2.096248 GAGTCTCCAGTGACCTACAGG 58.904 57.143 0.00 0.00 37.66 4.00
1880 2057 2.669950 GCTCGAGAAGACACTGACTTCC 60.670 54.545 18.75 8.04 43.01 3.46
1889 2066 2.610479 GGAACACATGCTCGAGAAGACA 60.610 50.000 18.75 4.56 0.00 3.41
1890 2067 1.996191 GGAACACATGCTCGAGAAGAC 59.004 52.381 18.75 0.00 0.00 3.01
1915 2092 0.691078 GAGGAGTAGACATGGCCCCA 60.691 60.000 0.00 0.00 0.00 4.96
1938 2115 6.071616 TGGTACAACAAGATCTAATTTTGGCC 60.072 38.462 0.00 0.00 31.92 5.36
1981 2160 6.475727 GGTGGCTTTTCTTTCTTAAGTTTGTC 59.524 38.462 1.63 0.00 32.98 3.18
2014 2193 5.505159 CCGTCGTAAACATATAGACAGAGCA 60.505 44.000 0.00 0.00 32.57 4.26
2015 2194 4.910456 CCGTCGTAAACATATAGACAGAGC 59.090 45.833 0.00 0.00 32.57 4.09
2016 2195 5.907945 CACCGTCGTAAACATATAGACAGAG 59.092 44.000 0.00 0.00 32.57 3.35
2017 2196 5.220912 CCACCGTCGTAAACATATAGACAGA 60.221 44.000 0.00 0.00 32.57 3.41
2047 2226 8.264250 GCACTTACATTATGCAATTGTGGAACA 61.264 37.037 7.40 0.00 41.79 3.18
2073 2252 1.794714 ACTAGGGGTGGCACTAGATG 58.205 55.000 18.45 8.10 39.16 2.90
2074 2253 2.119495 CAACTAGGGGTGGCACTAGAT 58.881 52.381 18.45 3.55 39.16 1.98
2075 2254 1.568504 CAACTAGGGGTGGCACTAGA 58.431 55.000 18.45 0.00 39.16 2.43
2076 2255 0.541863 CCAACTAGGGGTGGCACTAG 59.458 60.000 18.45 13.59 41.83 2.57
2077 2256 0.178885 ACCAACTAGGGGTGGCACTA 60.179 55.000 18.45 0.98 43.89 2.74
2078 2257 1.065997 AACCAACTAGGGGTGGCACT 61.066 55.000 18.45 0.00 43.89 4.40
2079 2258 0.178973 AAACCAACTAGGGGTGGCAC 60.179 55.000 9.70 9.70 43.89 5.01
2080 2259 0.558712 AAAACCAACTAGGGGTGGCA 59.441 50.000 8.90 0.00 43.89 4.92
2081 2260 0.966179 CAAAACCAACTAGGGGTGGC 59.034 55.000 8.90 0.00 43.89 5.01
2082 2261 1.146152 TCCAAAACCAACTAGGGGTGG 59.854 52.381 8.90 8.22 43.89 4.61
2083 2262 2.668144 TCCAAAACCAACTAGGGGTG 57.332 50.000 8.90 0.00 43.89 4.61
2084 2263 3.116900 ACATTCCAAAACCAACTAGGGGT 60.117 43.478 2.70 2.70 43.89 4.95
2085 2264 3.506398 ACATTCCAAAACCAACTAGGGG 58.494 45.455 0.00 0.00 43.89 4.79
2086 2265 4.586841 TCAACATTCCAAAACCAACTAGGG 59.413 41.667 0.00 0.00 43.89 3.53
2087 2266 5.528870 GTCAACATTCCAAAACCAACTAGG 58.471 41.667 0.00 0.00 45.67 3.02
2088 2267 5.008217 TCGTCAACATTCCAAAACCAACTAG 59.992 40.000 0.00 0.00 0.00 2.57
2089 2268 4.882427 TCGTCAACATTCCAAAACCAACTA 59.118 37.500 0.00 0.00 0.00 2.24
2090 2269 3.697045 TCGTCAACATTCCAAAACCAACT 59.303 39.130 0.00 0.00 0.00 3.16
2091 2270 3.794564 GTCGTCAACATTCCAAAACCAAC 59.205 43.478 0.00 0.00 0.00 3.77
2092 2271 3.444034 TGTCGTCAACATTCCAAAACCAA 59.556 39.130 0.00 0.00 31.20 3.67
2093 2272 3.017442 TGTCGTCAACATTCCAAAACCA 58.983 40.909 0.00 0.00 31.20 3.67
2094 2273 3.701532 TGTCGTCAACATTCCAAAACC 57.298 42.857 0.00 0.00 31.20 3.27
2095 2274 4.266739 GGTTTGTCGTCAACATTCCAAAAC 59.733 41.667 0.00 0.00 37.82 2.43
2096 2275 4.158764 AGGTTTGTCGTCAACATTCCAAAA 59.841 37.500 0.00 0.00 37.82 2.44
2097 2276 3.697045 AGGTTTGTCGTCAACATTCCAAA 59.303 39.130 0.00 0.00 37.82 3.28
2098 2277 3.066064 CAGGTTTGTCGTCAACATTCCAA 59.934 43.478 0.00 0.00 37.82 3.53
2099 2278 2.616376 CAGGTTTGTCGTCAACATTCCA 59.384 45.455 0.00 0.00 37.82 3.53
2100 2279 2.031157 CCAGGTTTGTCGTCAACATTCC 60.031 50.000 0.00 0.00 37.82 3.01
2101 2280 2.616842 ACCAGGTTTGTCGTCAACATTC 59.383 45.455 0.00 0.00 37.82 2.67
2102 2281 2.650322 ACCAGGTTTGTCGTCAACATT 58.350 42.857 0.00 0.00 37.82 2.71
2103 2282 2.341846 ACCAGGTTTGTCGTCAACAT 57.658 45.000 0.00 0.00 37.82 2.71
2104 2283 1.740585 CAACCAGGTTTGTCGTCAACA 59.259 47.619 0.44 0.00 35.59 3.33
2105 2284 2.011222 TCAACCAGGTTTGTCGTCAAC 58.989 47.619 0.44 0.00 32.93 3.18
2106 2285 2.285083 CTCAACCAGGTTTGTCGTCAA 58.715 47.619 0.44 0.00 0.00 3.18
2107 2286 1.474320 CCTCAACCAGGTTTGTCGTCA 60.474 52.381 0.44 0.00 37.53 4.35
2108 2287 1.226746 CCTCAACCAGGTTTGTCGTC 58.773 55.000 0.44 0.00 37.53 4.20
2109 2288 0.179029 CCCTCAACCAGGTTTGTCGT 60.179 55.000 0.44 0.00 41.51 4.34
2110 2289 0.107831 TCCCTCAACCAGGTTTGTCG 59.892 55.000 0.44 0.00 41.51 4.35
2111 2290 1.143073 AGTCCCTCAACCAGGTTTGTC 59.857 52.381 0.44 0.00 41.51 3.18
2112 2291 1.222567 AGTCCCTCAACCAGGTTTGT 58.777 50.000 0.44 0.00 41.51 2.83
2113 2292 3.502123 TTAGTCCCTCAACCAGGTTTG 57.498 47.619 0.44 0.00 41.51 2.93
2114 2293 3.397955 ACATTAGTCCCTCAACCAGGTTT 59.602 43.478 0.44 0.00 41.51 3.27
2115 2294 2.986728 ACATTAGTCCCTCAACCAGGTT 59.013 45.455 0.00 0.00 41.51 3.50
2116 2295 2.305927 CACATTAGTCCCTCAACCAGGT 59.694 50.000 0.00 0.00 41.51 4.00
2117 2296 2.305927 ACACATTAGTCCCTCAACCAGG 59.694 50.000 0.00 0.00 43.01 4.45
2118 2297 3.703001 ACACATTAGTCCCTCAACCAG 57.297 47.619 0.00 0.00 0.00 4.00
2119 2298 4.141287 CAAACACATTAGTCCCTCAACCA 58.859 43.478 0.00 0.00 0.00 3.67
2120 2299 4.023193 CACAAACACATTAGTCCCTCAACC 60.023 45.833 0.00 0.00 0.00 3.77
2121 2300 4.819630 TCACAAACACATTAGTCCCTCAAC 59.180 41.667 0.00 0.00 0.00 3.18
2122 2301 5.042463 TCACAAACACATTAGTCCCTCAA 57.958 39.130 0.00 0.00 0.00 3.02
2123 2302 4.346709 TCTCACAAACACATTAGTCCCTCA 59.653 41.667 0.00 0.00 0.00 3.86
2124 2303 4.894784 TCTCACAAACACATTAGTCCCTC 58.105 43.478 0.00 0.00 0.00 4.30
2125 2304 4.974645 TCTCACAAACACATTAGTCCCT 57.025 40.909 0.00 0.00 0.00 4.20
2126 2305 6.575162 AATTCTCACAAACACATTAGTCCC 57.425 37.500 0.00 0.00 0.00 4.46
2127 2306 8.094798 TGTAATTCTCACAAACACATTAGTCC 57.905 34.615 0.00 0.00 0.00 3.85
2128 2307 8.230486 CCTGTAATTCTCACAAACACATTAGTC 58.770 37.037 0.00 0.00 0.00 2.59
2129 2308 7.936847 TCCTGTAATTCTCACAAACACATTAGT 59.063 33.333 0.00 0.00 0.00 2.24
2130 2309 8.322906 TCCTGTAATTCTCACAAACACATTAG 57.677 34.615 0.00 0.00 0.00 1.73
2131 2310 8.862325 ATCCTGTAATTCTCACAAACACATTA 57.138 30.769 0.00 0.00 0.00 1.90
2132 2311 7.765695 ATCCTGTAATTCTCACAAACACATT 57.234 32.000 0.00 0.00 0.00 2.71
2133 2312 8.730680 GTTATCCTGTAATTCTCACAAACACAT 58.269 33.333 0.00 0.00 0.00 3.21
2134 2313 7.717436 TGTTATCCTGTAATTCTCACAAACACA 59.283 33.333 0.00 0.00 0.00 3.72
2135 2314 8.015658 GTGTTATCCTGTAATTCTCACAAACAC 58.984 37.037 8.44 8.44 37.04 3.32
2136 2315 7.717436 TGTGTTATCCTGTAATTCTCACAAACA 59.283 33.333 0.00 0.00 31.85 2.83
2137 2316 8.094798 TGTGTTATCCTGTAATTCTCACAAAC 57.905 34.615 0.00 0.00 31.85 2.93
2138 2317 7.390440 CCTGTGTTATCCTGTAATTCTCACAAA 59.610 37.037 0.00 0.00 33.91 2.83
2139 2318 6.878923 CCTGTGTTATCCTGTAATTCTCACAA 59.121 38.462 0.00 0.00 33.91 3.33
2140 2319 6.013725 ACCTGTGTTATCCTGTAATTCTCACA 60.014 38.462 0.00 0.00 33.38 3.58
2141 2320 6.407202 ACCTGTGTTATCCTGTAATTCTCAC 58.593 40.000 0.00 0.00 0.00 3.51
2142 2321 6.620877 ACCTGTGTTATCCTGTAATTCTCA 57.379 37.500 0.00 0.00 0.00 3.27
2143 2322 7.783042 ACTACCTGTGTTATCCTGTAATTCTC 58.217 38.462 0.00 0.00 0.00 2.87
2144 2323 7.735326 ACTACCTGTGTTATCCTGTAATTCT 57.265 36.000 0.00 0.00 0.00 2.40
2145 2324 8.693625 ACTACTACCTGTGTTATCCTGTAATTC 58.306 37.037 0.00 0.00 0.00 2.17
2146 2325 8.605325 ACTACTACCTGTGTTATCCTGTAATT 57.395 34.615 0.00 0.00 0.00 1.40
2147 2326 7.287235 GGACTACTACCTGTGTTATCCTGTAAT 59.713 40.741 0.00 0.00 0.00 1.89
2148 2327 6.604795 GGACTACTACCTGTGTTATCCTGTAA 59.395 42.308 0.00 0.00 0.00 2.41
2149 2328 6.069206 AGGACTACTACCTGTGTTATCCTGTA 60.069 42.308 0.00 0.00 36.30 2.74
2150 2329 4.954826 GGACTACTACCTGTGTTATCCTGT 59.045 45.833 0.00 0.00 0.00 4.00
2151 2330 5.202004 AGGACTACTACCTGTGTTATCCTG 58.798 45.833 0.00 0.00 36.30 3.86
2152 2331 5.469210 AGGACTACTACCTGTGTTATCCT 57.531 43.478 0.00 0.00 36.30 3.24
2153 2332 9.531158 AATATAGGACTACTACCTGTGTTATCC 57.469 37.037 0.00 0.00 38.31 2.59
2157 2336 9.435570 AATCAATATAGGACTACTACCTGTGTT 57.564 33.333 0.00 0.00 38.31 3.32
2158 2337 9.080097 GAATCAATATAGGACTACTACCTGTGT 57.920 37.037 0.00 0.00 38.31 3.72
2159 2338 8.237949 CGAATCAATATAGGACTACTACCTGTG 58.762 40.741 0.00 0.00 38.31 3.66
2160 2339 7.393796 CCGAATCAATATAGGACTACTACCTGT 59.606 40.741 0.00 0.00 38.31 4.00
2161 2340 7.393796 ACCGAATCAATATAGGACTACTACCTG 59.606 40.741 0.00 0.00 38.31 4.00
2162 2341 7.468496 ACCGAATCAATATAGGACTACTACCT 58.532 38.462 0.00 0.00 41.05 3.08
2163 2342 7.700022 ACCGAATCAATATAGGACTACTACC 57.300 40.000 0.00 0.00 33.70 3.18
2166 2345 8.583296 GGTAAACCGAATCAATATAGGACTACT 58.417 37.037 0.00 0.00 0.00 2.57
2167 2346 8.583296 AGGTAAACCGAATCAATATAGGACTAC 58.417 37.037 0.00 0.00 42.08 2.73
2168 2347 8.716674 AGGTAAACCGAATCAATATAGGACTA 57.283 34.615 0.00 0.00 42.08 2.59
2169 2348 7.613551 AGGTAAACCGAATCAATATAGGACT 57.386 36.000 0.00 0.00 42.08 3.85
2170 2349 7.816513 GGTAGGTAAACCGAATCAATATAGGAC 59.183 40.741 0.00 0.00 42.08 3.85
2171 2350 7.510001 TGGTAGGTAAACCGAATCAATATAGGA 59.490 37.037 0.00 0.00 42.91 2.94
2172 2351 7.673180 TGGTAGGTAAACCGAATCAATATAGG 58.327 38.462 0.00 0.00 42.91 2.57
2173 2352 8.582437 TCTGGTAGGTAAACCGAATCAATATAG 58.418 37.037 0.00 0.00 42.91 1.31
2174 2353 8.481492 TCTGGTAGGTAAACCGAATCAATATA 57.519 34.615 0.00 0.00 42.91 0.86
2175 2354 7.289317 TCTCTGGTAGGTAAACCGAATCAATAT 59.711 37.037 0.00 0.00 42.91 1.28
2176 2355 6.608405 TCTCTGGTAGGTAAACCGAATCAATA 59.392 38.462 0.00 0.00 42.91 1.90
2177 2356 5.424252 TCTCTGGTAGGTAAACCGAATCAAT 59.576 40.000 0.00 0.00 42.91 2.57
2178 2357 4.773674 TCTCTGGTAGGTAAACCGAATCAA 59.226 41.667 0.00 0.00 42.91 2.57
2179 2358 4.346730 TCTCTGGTAGGTAAACCGAATCA 58.653 43.478 0.00 0.00 42.91 2.57
2180 2359 4.996788 TCTCTGGTAGGTAAACCGAATC 57.003 45.455 0.00 0.00 42.91 2.52
2181 2360 4.960469 TCATCTCTGGTAGGTAAACCGAAT 59.040 41.667 0.00 0.00 42.91 3.34
2182 2361 4.159135 GTCATCTCTGGTAGGTAAACCGAA 59.841 45.833 0.00 0.00 42.91 4.30
2183 2362 3.698040 GTCATCTCTGGTAGGTAAACCGA 59.302 47.826 0.00 0.00 42.91 4.69
2184 2363 3.181478 GGTCATCTCTGGTAGGTAAACCG 60.181 52.174 0.00 0.00 42.91 4.44
2185 2364 3.134262 GGGTCATCTCTGGTAGGTAAACC 59.866 52.174 0.00 0.00 40.19 3.27
2186 2365 3.134262 GGGGTCATCTCTGGTAGGTAAAC 59.866 52.174 0.00 0.00 0.00 2.01
2187 2366 3.013648 AGGGGTCATCTCTGGTAGGTAAA 59.986 47.826 0.00 0.00 0.00 2.01
2188 2367 2.590611 AGGGGTCATCTCTGGTAGGTAA 59.409 50.000 0.00 0.00 0.00 2.85
2189 2368 2.224077 AGGGGTCATCTCTGGTAGGTA 58.776 52.381 0.00 0.00 0.00 3.08
2190 2369 1.019650 AGGGGTCATCTCTGGTAGGT 58.980 55.000 0.00 0.00 0.00 3.08
2191 2370 3.330126 TTAGGGGTCATCTCTGGTAGG 57.670 52.381 0.00 0.00 0.00 3.18
2192 2371 5.693769 TTTTTAGGGGTCATCTCTGGTAG 57.306 43.478 0.00 0.00 0.00 3.18
2193 2372 5.491078 ACATTTTTAGGGGTCATCTCTGGTA 59.509 40.000 0.00 0.00 0.00 3.25
2194 2373 4.292306 ACATTTTTAGGGGTCATCTCTGGT 59.708 41.667 0.00 0.00 0.00 4.00
2195 2374 4.641989 CACATTTTTAGGGGTCATCTCTGG 59.358 45.833 0.00 0.00 0.00 3.86
2196 2375 5.124457 CACACATTTTTAGGGGTCATCTCTG 59.876 44.000 0.00 0.00 0.00 3.35
2197 2376 5.014123 TCACACATTTTTAGGGGTCATCTCT 59.986 40.000 0.00 0.00 0.00 3.10
2198 2377 5.253330 TCACACATTTTTAGGGGTCATCTC 58.747 41.667 0.00 0.00 0.00 2.75
2199 2378 5.255397 TCACACATTTTTAGGGGTCATCT 57.745 39.130 0.00 0.00 0.00 2.90
2200 2379 5.710099 TCTTCACACATTTTTAGGGGTCATC 59.290 40.000 0.00 0.00 0.00 2.92
2201 2380 5.476945 GTCTTCACACATTTTTAGGGGTCAT 59.523 40.000 0.00 0.00 0.00 3.06
2202 2381 4.825085 GTCTTCACACATTTTTAGGGGTCA 59.175 41.667 0.00 0.00 0.00 4.02
2203 2382 4.825085 TGTCTTCACACATTTTTAGGGGTC 59.175 41.667 0.00 0.00 0.00 4.46
2204 2383 4.798882 TGTCTTCACACATTTTTAGGGGT 58.201 39.130 0.00 0.00 0.00 4.95
2205 2384 5.982890 ATGTCTTCACACATTTTTAGGGG 57.017 39.130 0.00 0.00 32.81 4.79
2206 2385 6.980593 TCAATGTCTTCACACATTTTTAGGG 58.019 36.000 0.00 0.00 43.17 3.53
2207 2386 8.352201 TCTTCAATGTCTTCACACATTTTTAGG 58.648 33.333 0.00 0.00 43.17 2.69
2208 2387 9.173939 GTCTTCAATGTCTTCACACATTTTTAG 57.826 33.333 0.00 0.00 43.17 1.85
2209 2388 8.681806 TGTCTTCAATGTCTTCACACATTTTTA 58.318 29.630 0.00 0.00 43.17 1.52
2210 2389 7.546358 TGTCTTCAATGTCTTCACACATTTTT 58.454 30.769 0.00 0.00 43.17 1.94
2211 2390 7.099266 TGTCTTCAATGTCTTCACACATTTT 57.901 32.000 0.00 0.00 43.17 1.82
2212 2391 6.698008 TGTCTTCAATGTCTTCACACATTT 57.302 33.333 0.00 0.00 43.17 2.32
2213 2392 6.698008 TTGTCTTCAATGTCTTCACACATT 57.302 33.333 0.00 0.00 46.00 2.71
2214 2393 6.889301 ATTGTCTTCAATGTCTTCACACAT 57.111 33.333 0.00 0.00 41.95 3.21
2226 2405 4.648762 TCACAAACCACCATTGTCTTCAAT 59.351 37.500 0.00 0.00 44.02 2.57
2227 2406 4.019858 TCACAAACCACCATTGTCTTCAA 58.980 39.130 0.00 0.00 38.90 2.69
2228 2407 3.625853 TCACAAACCACCATTGTCTTCA 58.374 40.909 0.00 0.00 38.90 3.02
2229 2408 4.338118 TCTTCACAAACCACCATTGTCTTC 59.662 41.667 0.00 0.00 38.90 2.87
2230 2409 4.097892 GTCTTCACAAACCACCATTGTCTT 59.902 41.667 0.00 0.00 38.90 3.01
2231 2410 3.632145 GTCTTCACAAACCACCATTGTCT 59.368 43.478 0.00 0.00 38.90 3.41
2232 2411 3.380004 TGTCTTCACAAACCACCATTGTC 59.620 43.478 0.00 0.00 38.90 3.18
2233 2412 3.360867 TGTCTTCACAAACCACCATTGT 58.639 40.909 0.00 0.00 41.50 2.71
2234 2413 4.589216 ATGTCTTCACAAACCACCATTG 57.411 40.909 0.00 0.00 35.64 2.82
2235 2414 4.648762 TGAATGTCTTCACAAACCACCATT 59.351 37.500 0.00 0.00 36.46 3.16
2236 2415 4.214310 TGAATGTCTTCACAAACCACCAT 58.786 39.130 0.00 0.00 36.46 3.55
2237 2416 3.625853 TGAATGTCTTCACAAACCACCA 58.374 40.909 0.00 0.00 36.46 4.17
2247 2426 8.096414 TCATAGTCTTCAATGTGAATGTCTTCA 58.904 33.333 0.00 0.00 39.07 3.02
2248 2427 8.386606 GTCATAGTCTTCAATGTGAATGTCTTC 58.613 37.037 0.00 0.00 35.59 2.87
2249 2428 7.879677 TGTCATAGTCTTCAATGTGAATGTCTT 59.120 33.333 0.00 0.00 35.59 3.01
2250 2429 7.389232 TGTCATAGTCTTCAATGTGAATGTCT 58.611 34.615 0.00 0.00 35.59 3.41
2251 2430 7.601073 TGTCATAGTCTTCAATGTGAATGTC 57.399 36.000 0.00 0.00 35.59 3.06
2252 2431 6.093219 GCTGTCATAGTCTTCAATGTGAATGT 59.907 38.462 0.00 0.00 35.59 2.71
2253 2432 6.093082 TGCTGTCATAGTCTTCAATGTGAATG 59.907 38.462 0.00 0.00 35.59 2.67
2254 2433 6.175471 TGCTGTCATAGTCTTCAATGTGAAT 58.825 36.000 0.00 0.00 35.59 2.57
2255 2434 5.550290 TGCTGTCATAGTCTTCAATGTGAA 58.450 37.500 0.00 0.00 34.79 3.18
2256 2435 5.047092 TCTGCTGTCATAGTCTTCAATGTGA 60.047 40.000 0.00 0.00 0.00 3.58
2257 2436 5.173664 TCTGCTGTCATAGTCTTCAATGTG 58.826 41.667 0.00 0.00 0.00 3.21
2258 2437 5.411831 TCTGCTGTCATAGTCTTCAATGT 57.588 39.130 0.00 0.00 0.00 2.71
2259 2438 6.035866 GTCTTCTGCTGTCATAGTCTTCAATG 59.964 42.308 0.00 0.00 0.00 2.82
2260 2439 6.105333 GTCTTCTGCTGTCATAGTCTTCAAT 58.895 40.000 0.00 0.00 0.00 2.57
2261 2440 5.011023 TGTCTTCTGCTGTCATAGTCTTCAA 59.989 40.000 0.00 0.00 0.00 2.69
2262 2441 4.524328 TGTCTTCTGCTGTCATAGTCTTCA 59.476 41.667 0.00 0.00 0.00 3.02
2263 2442 5.065704 TGTCTTCTGCTGTCATAGTCTTC 57.934 43.478 0.00 0.00 0.00 2.87
2264 2443 5.659463 GATGTCTTCTGCTGTCATAGTCTT 58.341 41.667 0.00 0.00 0.00 3.01
2265 2444 4.202000 CGATGTCTTCTGCTGTCATAGTCT 60.202 45.833 0.00 0.00 0.00 3.24
2266 2445 4.041049 CGATGTCTTCTGCTGTCATAGTC 58.959 47.826 0.00 0.00 0.00 2.59
2267 2446 3.736433 GCGATGTCTTCTGCTGTCATAGT 60.736 47.826 0.00 0.00 0.00 2.12
2268 2447 2.793790 GCGATGTCTTCTGCTGTCATAG 59.206 50.000 0.00 0.00 0.00 2.23
2269 2448 2.796032 CGCGATGTCTTCTGCTGTCATA 60.796 50.000 0.00 0.00 0.00 2.15
2270 2449 1.649664 GCGATGTCTTCTGCTGTCAT 58.350 50.000 0.00 0.00 0.00 3.06
2271 2450 0.733909 CGCGATGTCTTCTGCTGTCA 60.734 55.000 0.00 0.00 0.00 3.58
2272 2451 1.994467 CGCGATGTCTTCTGCTGTC 59.006 57.895 0.00 0.00 0.00 3.51
2273 2452 4.175599 CGCGATGTCTTCTGCTGT 57.824 55.556 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.