Multiple sequence alignment - TraesCS3B01G384800

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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 TraesCS3B01G384800 chr3B 100.000 5242 0 0 1 5242 605018449 605013208 0.000000e+00 9681.0
1 TraesCS3B01G384800 chr3B 80.769 286 38 14 1087 1365 145362453 145362728 1.910000e-49 207.0
2 TraesCS3B01G384800 chr3B 82.787 122 17 4 2072 2190 322159051 322159171 7.180000e-19 106.0
3 TraesCS3B01G384800 chr3D 88.603 2062 120 59 50 2068 457407424 457405435 0.000000e+00 2399.0
4 TraesCS3B01G384800 chr3D 94.572 1216 54 5 2186 3389 457405407 457404192 0.000000e+00 1869.0
5 TraesCS3B01G384800 chr3D 92.997 1228 64 16 3381 4599 457404160 457402946 0.000000e+00 1772.0
6 TraesCS3B01G384800 chr3D 92.571 673 35 8 4583 5242 457402928 457402258 0.000000e+00 952.0
7 TraesCS3B01G384800 chr3D 80.645 279 39 12 1093 1365 94721511 94721242 8.900000e-48 202.0
8 TraesCS3B01G384800 chr3A 94.404 1376 66 7 2198 3568 600318852 600317483 0.000000e+00 2104.0
9 TraesCS3B01G384800 chr3A 86.209 1501 85 62 1 1405 600320982 600319508 0.000000e+00 1513.0
10 TraesCS3B01G384800 chr3A 90.415 772 45 6 4488 5242 600316532 600315773 0.000000e+00 989.0
11 TraesCS3B01G384800 chr3A 86.860 898 87 17 3597 4489 600317484 600316613 0.000000e+00 976.0
12 TraesCS3B01G384800 chr3A 84.882 635 55 15 1479 2091 600319473 600318858 2.090000e-168 603.0
13 TraesCS3B01G384800 chr3A 80.702 285 40 12 1087 1365 549265047 549265322 1.910000e-49 207.0
14 TraesCS3B01G384800 chr5B 92.157 102 5 2 2082 2181 680856471 680856571 1.970000e-29 141.0
15 TraesCS3B01G384800 chr5B 89.091 55 6 0 1479 1533 421861205 421861151 9.420000e-08 69.4
16 TraesCS3B01G384800 chr4A 90.196 102 8 1 2080 2179 631960151 631960050 1.180000e-26 132.0
17 TraesCS3B01G384800 chr4B 89.691 97 8 1 2084 2178 654204980 654204884 7.130000e-24 122.0
18 TraesCS3B01G384800 chr4B 88.462 104 7 4 2086 2185 654204884 654204986 2.560000e-23 121.0
19 TraesCS3B01G384800 chr1B 88.889 99 6 2 2082 2178 463548759 463548664 3.320000e-22 117.0
20 TraesCS3B01G384800 chr6D 88.660 97 8 2 2082 2175 62122923 62122827 1.190000e-21 115.0
21 TraesCS3B01G384800 chr1A 87.379 103 10 2 2081 2180 508966137 508966239 1.190000e-21 115.0
22 TraesCS3B01G384800 chr7B 82.645 121 16 4 2075 2192 398421254 398421372 9.290000e-18 102.0
23 TraesCS3B01G384800 chr5D 89.091 55 6 0 1479 1533 357080041 357079987 9.420000e-08 69.4


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 TraesCS3B01G384800 chr3B 605013208 605018449 5241 True 9681 9681 100.00000 1 5242 1 chr3B.!!$R1 5241
1 TraesCS3B01G384800 chr3D 457402258 457407424 5166 True 1748 2399 92.18575 50 5242 4 chr3D.!!$R2 5192
2 TraesCS3B01G384800 chr3A 600315773 600320982 5209 True 1237 2104 88.55400 1 5242 5 chr3A.!!$R1 5241

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
909 1000 0.663568 GCAAGTGCAAGCAAGCTCAG 60.664 55.0 0.00 0.0 41.59 3.35 F
1374 1468 0.250553 CCTGGAACAAGGGTGCGTAA 60.251 55.0 0.00 0.0 38.70 3.18 F
1584 1683 0.320697 AGACGCCAAGACAGGTAACC 59.679 55.0 0.00 0.0 37.17 2.85 F
2734 2866 0.096628 GAGCAATGCAGTTCAGCTCG 59.903 55.0 8.35 0.0 41.75 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2294 0.470341 GCTTGTACTCCCTCCATCCC 59.530 60.0 0.0 0.0 0.00 3.85 R
2269 2399 0.839946 GGCCATGACTCCACCAGTAT 59.160 55.0 0.0 0.0 34.41 2.12 R
3420 3603 0.762418 AATCCGCCCAATACGATCCA 59.238 50.0 0.0 0.0 0.00 3.41 R
4630 4936 0.721718 GTCAACTCGCTGGGAATTCG 59.278 55.0 0.0 0.0 0.00 3.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.790437 CACTCCAGCGGGCCTCAT 61.790 66.667 0.84 0.00 0.00 2.90
83 93 0.831711 TAGCCAGCACAGGTCACTCA 60.832 55.000 0.00 0.00 0.00 3.41
240 268 2.975799 CACCACCCCACGTTTCCG 60.976 66.667 0.00 0.00 40.83 4.30
295 328 2.933834 CTTCCTCCCACCCCCGTT 60.934 66.667 0.00 0.00 0.00 4.44
408 441 1.227380 CCAGCCGATCTGTAGCACC 60.227 63.158 0.00 0.00 41.25 5.01
412 445 2.655364 CGATCTGTAGCACCCGCG 60.655 66.667 0.00 0.00 45.49 6.46
419 452 2.108157 TAGCACCCGCGCCTAATG 59.892 61.111 0.00 0.00 45.49 1.90
436 469 5.482908 CCTAATGTAGTCTTGCAAGTCAGT 58.517 41.667 25.19 19.23 0.00 3.41
437 470 5.349817 CCTAATGTAGTCTTGCAAGTCAGTG 59.650 44.000 25.19 13.02 0.00 3.66
506 553 3.390521 CCGCCACCCTGAGCTGTA 61.391 66.667 0.00 0.00 0.00 2.74
637 688 0.809241 GCTGGTCAGAGCGAATGAGG 60.809 60.000 1.65 0.00 0.00 3.86
694 751 7.134815 CCATTATTTCTTTAGTGCTTCCATCG 58.865 38.462 0.00 0.00 0.00 3.84
802 862 2.229690 AATCCATGCAAGCAACCCGC 62.230 55.000 0.00 0.00 42.91 6.13
803 863 4.440127 CCATGCAAGCAACCCGCC 62.440 66.667 0.00 0.00 44.04 6.13
833 910 4.337145 CCCGAGTATCTTATAGCTCCTGT 58.663 47.826 0.00 0.00 0.00 4.00
841 929 1.043816 TATAGCTCCTGTCAGCAGCC 58.956 55.000 12.33 0.00 42.40 4.85
860 948 2.981909 CAGCAGTGGTGGTGGCAG 60.982 66.667 14.66 0.00 46.56 4.85
909 1000 0.663568 GCAAGTGCAAGCAAGCTCAG 60.664 55.000 0.00 0.00 41.59 3.35
910 1001 0.663568 CAAGTGCAAGCAAGCTCAGC 60.664 55.000 11.16 11.16 34.99 4.26
911 1002 0.822532 AAGTGCAAGCAAGCTCAGCT 60.823 50.000 16.72 7.74 45.97 4.24
912 1003 1.209640 GTGCAAGCAAGCTCAGCTC 59.790 57.895 13.32 11.43 42.53 4.09
914 1005 1.970114 GCAAGCAAGCTCAGCTCCA 60.970 57.895 13.32 0.00 42.53 3.86
970 1064 2.046507 GCCACAGTCCAGCTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
974 1068 1.922369 ACAGTCCAGCTCCAGCCAT 60.922 57.895 0.00 0.00 43.38 4.40
987 1081 2.274760 GCCATTGGAGCCTGCTCT 59.725 61.111 17.90 0.00 42.38 4.09
989 1083 1.302285 CCATTGGAGCCTGCTCTGT 59.698 57.895 17.90 2.92 42.38 3.41
991 1085 0.747283 CATTGGAGCCTGCTCTGTCC 60.747 60.000 17.90 3.84 42.38 4.02
992 1086 2.249413 ATTGGAGCCTGCTCTGTCCG 62.249 60.000 17.90 0.00 42.38 4.79
1060 1154 1.154338 GCAGCGTCAGTGTCATTGC 60.154 57.895 0.00 0.00 0.00 3.56
1063 1157 2.317609 GCGTCAGTGTCATTGCCGT 61.318 57.895 0.80 0.00 0.00 5.68
1064 1158 1.781555 CGTCAGTGTCATTGCCGTC 59.218 57.895 0.00 0.00 0.00 4.79
1065 1159 1.626654 CGTCAGTGTCATTGCCGTCC 61.627 60.000 0.00 0.00 0.00 4.79
1169 1263 1.735559 GCTACGTCACGGTCAACCC 60.736 63.158 0.35 0.00 0.00 4.11
1203 1297 0.524392 CGCTCTTCTACTGGCTCGTG 60.524 60.000 0.00 0.00 0.00 4.35
1343 1437 1.303888 ACGGGAAGACGCTCTACCA 60.304 57.895 0.00 0.00 37.37 3.25
1374 1468 0.250553 CCTGGAACAAGGGTGCGTAA 60.251 55.000 0.00 0.00 38.70 3.18
1375 1469 1.613255 CCTGGAACAAGGGTGCGTAAT 60.613 52.381 0.00 0.00 38.70 1.89
1377 1471 1.349688 TGGAACAAGGGTGCGTAATCT 59.650 47.619 0.00 0.00 31.92 2.40
1378 1472 2.224670 TGGAACAAGGGTGCGTAATCTT 60.225 45.455 0.00 0.00 31.92 2.40
1379 1473 2.418976 GGAACAAGGGTGCGTAATCTTC 59.581 50.000 0.00 0.00 0.00 2.87
1380 1474 3.335579 GAACAAGGGTGCGTAATCTTCT 58.664 45.455 0.00 0.00 0.00 2.85
1415 1509 4.853268 GCTTGAGCTCCAATTATTAGCAC 58.147 43.478 12.15 0.00 38.75 4.40
1584 1683 0.320697 AGACGCCAAGACAGGTAACC 59.679 55.000 0.00 0.00 37.17 2.85
1639 1738 3.040147 TCCGGTGACACTGATTCTTTC 57.960 47.619 16.28 0.00 0.00 2.62
1640 1739 1.726791 CCGGTGACACTGATTCTTTCG 59.273 52.381 16.28 2.24 0.00 3.46
1643 1742 2.996621 GGTGACACTGATTCTTTCGGAG 59.003 50.000 5.39 0.00 34.56 4.63
1729 1831 1.268079 GCTTTTCTGGTGAACTGGCTC 59.732 52.381 0.00 0.00 31.02 4.70
1791 1893 2.961741 CTGGAGAGAGCTATGCAGGTAA 59.038 50.000 5.83 0.00 36.75 2.85
1793 1895 3.323115 TGGAGAGAGCTATGCAGGTAATG 59.677 47.826 0.00 0.00 30.99 1.90
1799 1901 6.951198 AGAGAGCTATGCAGGTAATGTACTAT 59.049 38.462 0.00 0.00 30.99 2.12
1803 1905 8.383318 AGCTATGCAGGTAATGTACTATTTTG 57.617 34.615 0.00 0.00 0.00 2.44
1804 1906 7.993183 AGCTATGCAGGTAATGTACTATTTTGT 59.007 33.333 0.00 0.00 0.00 2.83
1805 1907 9.268268 GCTATGCAGGTAATGTACTATTTTGTA 57.732 33.333 0.00 0.00 0.00 2.41
1808 1910 8.500753 TGCAGGTAATGTACTATTTTGTAAGG 57.499 34.615 0.00 0.00 0.00 2.69
1809 1911 7.066525 TGCAGGTAATGTACTATTTTGTAAGGC 59.933 37.037 0.00 0.00 0.00 4.35
1810 1912 7.468220 GCAGGTAATGTACTATTTTGTAAGGCC 60.468 40.741 0.00 0.00 0.00 5.19
1811 1913 7.773690 CAGGTAATGTACTATTTTGTAAGGCCT 59.226 37.037 0.00 0.00 0.00 5.19
1812 1914 7.773690 AGGTAATGTACTATTTTGTAAGGCCTG 59.226 37.037 5.69 0.00 0.00 4.85
1836 1938 4.095410 TGTAATGCAGGAATTTCGCAAG 57.905 40.909 7.23 0.00 39.48 4.01
1873 1975 3.903090 TGGTTCAATTCTGGCAGGAATTT 59.097 39.130 15.73 0.00 42.02 1.82
1949 2074 8.877864 TTAATGGAAGACTGGTTATTTCACAT 57.122 30.769 0.00 0.00 0.00 3.21
1957 2082 5.783111 ACTGGTTATTTCACATTTTCAGGC 58.217 37.500 0.00 0.00 0.00 4.85
1975 2100 1.144913 GGCCATTATGTTCCCCAGCTA 59.855 52.381 0.00 0.00 0.00 3.32
2009 2134 3.626028 ACGAAAAGAACAATGGCACTC 57.374 42.857 0.00 0.00 0.00 3.51
2039 2164 6.210584 TCCAACAATTAACCTCAAAGGATTCC 59.789 38.462 0.00 0.00 37.67 3.01
2091 2221 7.947782 TGGACTATTTTCCAATATACTCCCT 57.052 36.000 0.00 0.00 43.04 4.20
2094 2224 7.005709 ACTATTTTCCAATATACTCCCTCCG 57.994 40.000 0.00 0.00 0.00 4.63
2095 2225 5.906772 ATTTTCCAATATACTCCCTCCGT 57.093 39.130 0.00 0.00 0.00 4.69
2096 2226 4.950205 TTTCCAATATACTCCCTCCGTC 57.050 45.455 0.00 0.00 0.00 4.79
2097 2227 2.885616 TCCAATATACTCCCTCCGTCC 58.114 52.381 0.00 0.00 0.00 4.79
2098 2228 1.900486 CCAATATACTCCCTCCGTCCC 59.100 57.143 0.00 0.00 0.00 4.46
2099 2229 2.605257 CAATATACTCCCTCCGTCCCA 58.395 52.381 0.00 0.00 0.00 4.37
2100 2230 2.969950 CAATATACTCCCTCCGTCCCAA 59.030 50.000 0.00 0.00 0.00 4.12
2101 2231 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2102 2232 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2103 2233 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2104 2234 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2105 2235 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2106 2236 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2107 2237 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2108 2238 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2109 2239 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2110 2240 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2111 2241 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2112 2242 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2113 2243 4.721132 TCCGTCCCAAAATAAGTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
2114 2244 4.517453 TCCGTCCCAAAATAAGTGTCTTTG 59.483 41.667 0.00 0.00 0.00 2.77
2115 2245 4.517453 CCGTCCCAAAATAAGTGTCTTTGA 59.483 41.667 0.00 0.00 32.87 2.69
2116 2246 5.183140 CCGTCCCAAAATAAGTGTCTTTGAT 59.817 40.000 0.00 0.00 32.87 2.57
2117 2247 6.294508 CCGTCCCAAAATAAGTGTCTTTGATT 60.295 38.462 0.00 0.00 32.87 2.57
2118 2248 7.145323 CGTCCCAAAATAAGTGTCTTTGATTT 58.855 34.615 0.00 0.00 32.87 2.17
2119 2249 8.293867 CGTCCCAAAATAAGTGTCTTTGATTTA 58.706 33.333 0.00 0.00 32.87 1.40
2120 2250 9.626045 GTCCCAAAATAAGTGTCTTTGATTTAG 57.374 33.333 0.00 0.00 32.87 1.85
2121 2251 9.362151 TCCCAAAATAAGTGTCTTTGATTTAGT 57.638 29.630 0.00 0.00 32.87 2.24
2173 2303 7.838079 TCAAACATATATTTTGGGATGGAGG 57.162 36.000 14.77 0.00 35.12 4.30
2174 2304 6.782000 TCAAACATATATTTTGGGATGGAGGG 59.218 38.462 14.77 0.00 35.12 4.30
2175 2305 6.544327 AACATATATTTTGGGATGGAGGGA 57.456 37.500 0.00 0.00 0.00 4.20
2176 2306 6.144845 ACATATATTTTGGGATGGAGGGAG 57.855 41.667 0.00 0.00 0.00 4.30
2177 2307 5.616986 ACATATATTTTGGGATGGAGGGAGT 59.383 40.000 0.00 0.00 0.00 3.85
2178 2308 6.797540 ACATATATTTTGGGATGGAGGGAGTA 59.202 38.462 0.00 0.00 0.00 2.59
2179 2309 3.953542 ATTTTGGGATGGAGGGAGTAC 57.046 47.619 0.00 0.00 0.00 2.73
2180 2310 2.352561 TTTGGGATGGAGGGAGTACA 57.647 50.000 0.00 0.00 0.00 2.90
2181 2311 2.352561 TTGGGATGGAGGGAGTACAA 57.647 50.000 0.00 0.00 0.00 2.41
2182 2312 1.879575 TGGGATGGAGGGAGTACAAG 58.120 55.000 0.00 0.00 0.00 3.16
2183 2313 0.470341 GGGATGGAGGGAGTACAAGC 59.530 60.000 0.00 0.00 0.00 4.01
2184 2314 1.501582 GGATGGAGGGAGTACAAGCT 58.498 55.000 0.00 0.00 0.00 3.74
2193 2323 3.515901 AGGGAGTACAAGCTAGTTTCTGG 59.484 47.826 0.00 0.00 0.00 3.86
2196 2326 5.172205 GGAGTACAAGCTAGTTTCTGGAAG 58.828 45.833 0.00 0.00 0.00 3.46
2209 2339 7.735326 AGTTTCTGGAAGCTTACTATTCCTA 57.265 36.000 10.74 0.00 44.46 2.94
2236 2366 1.751544 GGTGGGGAATGCGGTTACC 60.752 63.158 0.00 0.00 40.45 2.85
2269 2399 6.209192 ACAATGACTATCTTGGCACATTTGAA 59.791 34.615 0.00 0.00 39.30 2.69
2341 2471 6.039605 TGAAGAAGACATGCTTGTTTGATTCA 59.960 34.615 6.70 11.50 39.89 2.57
2407 2537 2.427506 AGTTCCGAAGAAGGCAACATC 58.572 47.619 0.00 0.00 41.41 3.06
2425 2555 3.573110 ACATCGACCCTTATAGCCTGTAC 59.427 47.826 0.00 0.00 0.00 2.90
2470 2600 0.610232 CTCTCAAACTTGGCCTGGGG 60.610 60.000 3.32 0.00 0.00 4.96
2496 2626 4.083484 ACGCTATGTAAGTGTTTTGCTTCC 60.083 41.667 0.00 0.00 46.97 3.46
2497 2627 4.403453 GCTATGTAAGTGTTTTGCTTCCG 58.597 43.478 0.00 0.00 0.00 4.30
2500 2630 4.281525 TGTAAGTGTTTTGCTTCCGAAC 57.718 40.909 0.00 0.00 0.00 3.95
2549 2680 8.718734 ACTCGTTAAAATTCCAGTTCTTACATC 58.281 33.333 0.00 0.00 0.00 3.06
2559 2691 8.918202 TTCCAGTTCTTACATCAAAAGTACAT 57.082 30.769 0.00 0.00 29.51 2.29
2734 2866 0.096628 GAGCAATGCAGTTCAGCTCG 59.903 55.000 8.35 0.00 41.75 5.03
2749 2882 0.458716 GCTCGGTGTAGTTCTCTGCC 60.459 60.000 0.00 0.00 0.00 4.85
2794 2927 8.243289 CAATAAATGGAAACCAAATGTCTGAC 57.757 34.615 0.00 0.00 36.95 3.51
2830 2963 5.650266 ACGGGTGCAATGAATAAATTGTCTA 59.350 36.000 0.00 0.00 39.33 2.59
2867 3003 0.503117 GCGATTACGTTCGATCAGGC 59.497 55.000 13.55 2.98 41.62 4.85
2869 3005 1.836383 GATTACGTTCGATCAGGCGT 58.164 50.000 0.00 9.70 40.76 5.68
2989 3131 8.258708 AGTGGTACCAAGTATTTTAGATCAGAC 58.741 37.037 18.31 0.00 0.00 3.51
3004 3146 8.667076 TTAGATCAGACATACATGAATGTTGG 57.333 34.615 0.00 0.00 40.17 3.77
3335 3477 6.227298 TGGAAAACTTGCAGGTTTAAATCA 57.773 33.333 25.06 17.25 34.81 2.57
3420 3603 8.236585 TGGCTATTTATTGCAGTGATATTGTT 57.763 30.769 0.00 0.00 0.00 2.83
3565 3748 6.427853 CAGATTTCTTATATTCCGCATGACCA 59.572 38.462 0.00 0.00 0.00 4.02
3588 3772 4.069304 AGCCATTTACGAGTTTGCTTGTA 58.931 39.130 0.00 0.00 39.85 2.41
3646 3830 6.706270 TGAAGTCCATCTTGTTTCTGAGTTAC 59.294 38.462 0.00 0.00 36.40 2.50
3658 3842 6.590292 TGTTTCTGAGTTACGGAATCATCTTC 59.410 38.462 0.00 0.00 42.52 2.87
3680 3864 7.717436 TCTTCATGTGTTTGGTATTGACTAACA 59.283 33.333 0.00 0.00 31.87 2.41
3692 3876 8.755028 TGGTATTGACTAACAGCAGTATCTAAA 58.245 33.333 0.00 0.00 0.00 1.85
3730 3916 7.905604 TCGATATTGGCTTGTCTATAAATGG 57.094 36.000 0.00 0.00 0.00 3.16
3764 3950 6.069323 TCCAAACATTTAGACTATTGCCCCTA 60.069 38.462 0.00 0.00 0.00 3.53
3804 3990 7.175641 GGAATAGAACTCCATATTCCCACATTG 59.824 40.741 11.32 0.00 46.29 2.82
3822 4008 6.707161 CCACATTGTGAAATGATTTCTGGTTT 59.293 34.615 18.33 0.00 40.32 3.27
3832 4018 4.706035 TGATTTCTGGTTTGCTGCAAAAT 58.294 34.783 27.49 16.77 35.03 1.82
3891 4077 6.267496 AGTGACCATGCATTTTACCTTTAC 57.733 37.500 0.00 0.00 0.00 2.01
3932 4118 0.938713 TTGTTCCTGTAACCGCAACG 59.061 50.000 0.00 0.00 37.27 4.10
3965 4151 0.670546 GCGCTCTCAAGCTACCAACA 60.671 55.000 0.00 0.00 46.91 3.33
4010 4196 1.378514 CCATGGGAAGGTGGGTTCG 60.379 63.158 2.85 0.00 0.00 3.95
4012 4198 3.282374 ATGGGAAGGTGGGTTCGCC 62.282 63.158 0.00 0.00 43.69 5.54
4023 4209 3.119743 GGTGGGTTCGCCAAAATAGTTAC 60.120 47.826 0.00 0.00 42.90 2.50
4032 4218 7.355332 TCGCCAAAATAGTTACTCACTAAAC 57.645 36.000 0.00 0.00 41.56 2.01
4049 4235 6.423905 TCACTAAACTGAGAAAATTCTGTCCG 59.576 38.462 0.00 0.00 37.73 4.79
4077 4263 6.869315 TGAACCGTTTCAATCTTACATCAA 57.131 33.333 0.00 0.00 38.87 2.57
4079 4265 7.881142 TGAACCGTTTCAATCTTACATCAAAT 58.119 30.769 0.00 0.00 38.87 2.32
4080 4266 7.807433 TGAACCGTTTCAATCTTACATCAAATG 59.193 33.333 0.00 0.00 38.87 2.32
4082 4268 6.071952 ACCGTTTCAATCTTACATCAAATGCT 60.072 34.615 0.00 0.00 0.00 3.79
4084 4270 7.329226 CCGTTTCAATCTTACATCAAATGCTTT 59.671 33.333 0.00 0.00 0.00 3.51
4085 4271 9.340695 CGTTTCAATCTTACATCAAATGCTTTA 57.659 29.630 0.00 0.00 0.00 1.85
4145 4331 0.109412 GACTAACCCTCGTCACCGTG 60.109 60.000 0.00 0.00 35.01 4.94
4232 4418 1.003839 GAAGGACACACCGATGCCA 60.004 57.895 0.00 0.00 44.74 4.92
4294 4482 8.173130 ACTACGAAAATCATATTCACCGTTTTC 58.827 33.333 0.00 0.00 34.14 2.29
4295 4483 6.904498 ACGAAAATCATATTCACCGTTTTCA 58.096 32.000 0.00 0.00 36.09 2.69
4296 4484 6.799925 ACGAAAATCATATTCACCGTTTTCAC 59.200 34.615 0.00 0.00 36.09 3.18
4297 4485 6.799441 CGAAAATCATATTCACCGTTTTCACA 59.201 34.615 0.00 0.00 36.09 3.58
4298 4486 7.484641 CGAAAATCATATTCACCGTTTTCACAT 59.515 33.333 0.00 0.00 36.09 3.21
4300 4488 8.687824 AAATCATATTCACCGTTTTCACATTC 57.312 30.769 0.00 0.00 0.00 2.67
4471 4659 8.105829 AGAAGTACAATTTCCAGATTCACTCAT 58.894 33.333 0.00 0.00 0.00 2.90
4476 4664 4.771590 TTTCCAGATTCACTCATTGCAC 57.228 40.909 0.00 0.00 0.00 4.57
4483 4671 4.458295 AGATTCACTCATTGCACAGAAAGG 59.542 41.667 0.00 0.00 0.00 3.11
4491 4679 5.698832 TCATTGCACAGAAAGGAAATAACG 58.301 37.500 0.00 0.00 0.00 3.18
4538 4809 7.411486 TTGGAACAGAAAAATGGTGTTTCTA 57.589 32.000 0.00 0.00 42.15 2.10
4539 4810 7.038154 TGGAACAGAAAAATGGTGTTTCTAG 57.962 36.000 0.00 0.00 42.15 2.43
4540 4811 6.605594 TGGAACAGAAAAATGGTGTTTCTAGT 59.394 34.615 0.00 0.00 42.15 2.57
4542 4813 6.635030 ACAGAAAAATGGTGTTTCTAGTCC 57.365 37.500 0.00 0.00 42.15 3.85
4543 4814 5.535030 ACAGAAAAATGGTGTTTCTAGTCCC 59.465 40.000 0.00 0.00 42.15 4.46
4544 4815 5.534654 CAGAAAAATGGTGTTTCTAGTCCCA 59.465 40.000 0.00 0.00 42.15 4.37
4546 4817 6.782494 AGAAAAATGGTGTTTCTAGTCCCATT 59.218 34.615 0.00 0.00 45.39 3.16
4547 4818 5.982890 AAATGGTGTTTCTAGTCCCATTG 57.017 39.130 3.20 0.00 43.30 2.82
4586 4892 1.453155 GGTACTGGTTGCATGGACTG 58.547 55.000 0.00 0.00 0.00 3.51
4630 4936 4.220602 ACCTTAATGTTGTGCTCCAATTCC 59.779 41.667 0.00 0.00 35.02 3.01
4667 4973 6.701340 AGTTGACTGCATACAAGAACTGATA 58.299 36.000 6.05 0.00 0.00 2.15
4668 4974 7.334090 AGTTGACTGCATACAAGAACTGATAT 58.666 34.615 6.05 0.00 0.00 1.63
4670 4976 8.454106 GTTGACTGCATACAAGAACTGATATTT 58.546 33.333 6.05 0.00 0.00 1.40
4840 5151 7.066766 ACAGAAAGCTAGAATTAAGCCATTGAG 59.933 37.037 8.31 3.49 41.02 3.02
4879 5190 2.512692 ATTGCAACCATGGCTCACTA 57.487 45.000 13.04 0.00 0.00 2.74
4939 5250 2.057922 ACACATCAAACTCTGGGGTCT 58.942 47.619 0.00 0.00 0.00 3.85
4948 5259 1.352083 CTCTGGGGTCTGTCTTCCAA 58.648 55.000 0.00 0.00 0.00 3.53
5008 5330 8.859090 GTCATATCATATCATAGAGAGAAGGGG 58.141 40.741 0.00 0.00 0.00 4.79
5020 5342 2.612115 AAGGGGTCAGCAGGAGGG 60.612 66.667 0.00 0.00 0.00 4.30
5059 5381 4.957684 AGCGCGCCGATCCTGATG 62.958 66.667 30.33 0.00 0.00 3.07
5077 5399 3.300013 AGGTAGTTCCTGCGCCTC 58.700 61.111 4.18 0.00 46.19 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.758251 CACGGGACATGGCGAGCA 62.758 66.667 0.00 0.00 0.00 4.26
46 47 2.868044 GCTAGCTATGGTTCCCGACATG 60.868 54.545 7.70 0.00 0.00 3.21
109 119 4.436998 GCGTCCCGTCCTGTGGAG 62.437 72.222 0.00 0.00 29.39 3.86
159 186 2.325509 AAATAATAATTCGCGGCGCC 57.674 45.000 27.87 19.07 0.00 6.53
210 237 1.248785 GGTGGTGGCGAGAGTAGACA 61.249 60.000 0.00 0.00 0.00 3.41
267 295 0.105778 GGGAGGAAGAAGATGAGGCG 59.894 60.000 0.00 0.00 0.00 5.52
295 328 0.179032 AGCGTGGGTGTGTGAATGAA 60.179 50.000 0.00 0.00 0.00 2.57
408 441 1.209128 CAAGACTACATTAGGCGCGG 58.791 55.000 8.83 0.00 39.39 6.46
412 445 4.253685 TGACTTGCAAGACTACATTAGGC 58.746 43.478 32.50 3.22 0.00 3.93
419 452 3.060602 GGTCACTGACTTGCAAGACTAC 58.939 50.000 32.50 19.98 34.08 2.73
637 688 1.866063 GCCGATCTCGTCACATTCCTC 60.866 57.143 0.00 0.00 37.74 3.71
803 863 3.925090 GATACTCGGGGGTGCCGG 61.925 72.222 0.00 0.00 0.00 6.13
805 865 1.349067 ATAAGATACTCGGGGGTGCC 58.651 55.000 0.00 0.00 0.00 5.01
806 866 2.094130 GCTATAAGATACTCGGGGGTGC 60.094 54.545 0.00 0.00 0.00 5.01
808 868 3.563915 GGAGCTATAAGATACTCGGGGGT 60.564 52.174 0.00 0.00 0.00 4.95
809 869 3.025262 GGAGCTATAAGATACTCGGGGG 58.975 54.545 0.00 0.00 0.00 5.40
813 885 5.391523 GCTGACAGGAGCTATAAGATACTCG 60.392 48.000 4.26 0.00 35.95 4.18
868 956 1.203313 GTACGCAAACACTCGTGCC 59.797 57.895 0.00 0.00 39.46 5.01
910 1001 3.672295 GAAGAGGCGGGCAGTGGAG 62.672 68.421 3.78 0.00 0.00 3.86
911 1002 3.706373 GAAGAGGCGGGCAGTGGA 61.706 66.667 3.78 0.00 0.00 4.02
912 1003 4.785453 GGAAGAGGCGGGCAGTGG 62.785 72.222 3.78 0.00 0.00 4.00
914 1005 4.021925 GTGGAAGAGGCGGGCAGT 62.022 66.667 3.78 0.00 0.00 4.40
917 1011 4.475135 GGAGTGGAAGAGGCGGGC 62.475 72.222 0.00 0.00 0.00 6.13
970 1064 2.119655 CAGAGCAGGCTCCAATGGC 61.120 63.158 17.16 0.00 43.70 4.40
974 1068 2.947532 CGGACAGAGCAGGCTCCAA 61.948 63.158 17.16 0.00 43.70 3.53
1042 1136 1.154338 GCAATGACACTGACGCTGC 60.154 57.895 0.00 0.00 0.00 5.25
1043 1137 1.499056 GGCAATGACACTGACGCTG 59.501 57.895 0.00 0.00 0.00 5.18
1044 1138 2.029288 CGGCAATGACACTGACGCT 61.029 57.895 0.00 0.00 38.71 5.07
1050 1144 2.742372 GCGGACGGCAATGACACT 60.742 61.111 0.00 0.00 42.87 3.55
1133 1227 1.935327 GCCCGAGTACTGCGAGAAGT 61.935 60.000 0.00 0.00 0.00 3.01
1343 1437 4.342092 CCTTGTTCCAGGAATTCTTGTTGT 59.658 41.667 15.60 0.00 35.71 3.32
1374 1468 6.767456 TCAAGCTGAAGAAGAAGAAGAAGAT 58.233 36.000 0.00 0.00 0.00 2.40
1375 1469 6.166984 TCAAGCTGAAGAAGAAGAAGAAGA 57.833 37.500 0.00 0.00 0.00 2.87
1377 1471 4.754114 GCTCAAGCTGAAGAAGAAGAAGAA 59.246 41.667 0.00 0.00 38.21 2.52
1378 1472 4.314121 GCTCAAGCTGAAGAAGAAGAAGA 58.686 43.478 0.00 0.00 38.21 2.87
1379 1473 4.666928 GCTCAAGCTGAAGAAGAAGAAG 57.333 45.455 0.00 0.00 38.21 2.85
1404 1498 2.287547 CCAATGCGGCGTGCTAATAATT 60.288 45.455 9.37 0.00 46.63 1.40
1415 1509 2.102749 CATTGGACCAATGCGGCG 59.897 61.111 29.54 10.23 43.38 6.46
1639 1738 2.351738 GGAAGTTGGCATCAAAACTCCG 60.352 50.000 0.00 0.00 35.60 4.63
1640 1739 2.893489 AGGAAGTTGGCATCAAAACTCC 59.107 45.455 0.00 0.00 35.60 3.85
1643 1742 3.552890 GGACAGGAAGTTGGCATCAAAAC 60.553 47.826 0.00 0.00 34.28 2.43
1729 1831 3.193691 ACTTGTACTGTGGGAATCTCTCG 59.806 47.826 0.00 0.00 0.00 4.04
1791 1893 7.450323 ACAAACAGGCCTTACAAAATAGTACAT 59.550 33.333 0.00 0.00 0.00 2.29
1793 1895 7.210718 ACAAACAGGCCTTACAAAATAGTAC 57.789 36.000 0.00 0.00 0.00 2.73
1799 1901 5.163405 TGCATTACAAACAGGCCTTACAAAA 60.163 36.000 0.00 0.00 0.00 2.44
1803 1905 3.119495 CCTGCATTACAAACAGGCCTTAC 60.119 47.826 0.00 0.00 44.16 2.34
1804 1906 3.088532 CCTGCATTACAAACAGGCCTTA 58.911 45.455 0.00 0.00 44.16 2.69
1805 1907 1.895131 CCTGCATTACAAACAGGCCTT 59.105 47.619 0.00 0.00 44.16 4.35
1806 1908 1.549203 CCTGCATTACAAACAGGCCT 58.451 50.000 0.00 0.00 44.16 5.19
1810 1912 4.324402 GCGAAATTCCTGCATTACAAACAG 59.676 41.667 0.00 0.00 0.00 3.16
1811 1913 4.233789 GCGAAATTCCTGCATTACAAACA 58.766 39.130 0.00 0.00 0.00 2.83
1812 1914 4.233789 TGCGAAATTCCTGCATTACAAAC 58.766 39.130 0.00 0.00 32.86 2.93
1829 1931 4.909696 TTTCCTGTTGAATTCTTGCGAA 57.090 36.364 7.05 0.00 31.67 4.70
1836 1938 7.874528 AGAATTGAACCATTTCCTGTTGAATTC 59.125 33.333 14.98 14.98 46.34 2.17
1838 1940 7.156673 CAGAATTGAACCATTTCCTGTTGAAT 58.843 34.615 0.00 0.00 31.08 2.57
1841 1943 5.232463 CCAGAATTGAACCATTTCCTGTTG 58.768 41.667 0.00 0.00 0.00 3.33
1842 1944 4.262592 GCCAGAATTGAACCATTTCCTGTT 60.263 41.667 0.00 0.00 0.00 3.16
1876 1978 8.192743 TCAAATTTGGAAGATGAGATTTTCCA 57.807 30.769 17.90 4.81 46.33 3.53
1877 1979 9.662947 ATTCAAATTTGGAAGATGAGATTTTCC 57.337 29.630 17.90 0.00 40.59 3.13
1883 1985 8.737175 CAGAGAATTCAAATTTGGAAGATGAGA 58.263 33.333 17.90 0.00 0.00 3.27
1913 2027 9.981460 ACCAGTCTTCCATTAAATAAAGAATCT 57.019 29.630 0.00 0.00 30.10 2.40
1922 2036 9.308000 TGTGAAATAACCAGTCTTCCATTAAAT 57.692 29.630 0.00 0.00 0.00 1.40
1926 2040 7.781324 AATGTGAAATAACCAGTCTTCCATT 57.219 32.000 0.00 0.00 0.00 3.16
1938 2052 8.819974 CATAATGGCCTGAAAATGTGAAATAAC 58.180 33.333 3.32 0.00 0.00 1.89
1941 2066 6.949715 ACATAATGGCCTGAAAATGTGAAAT 58.050 32.000 3.32 0.00 0.00 2.17
1945 2070 5.111293 GGAACATAATGGCCTGAAAATGTG 58.889 41.667 3.32 0.00 0.00 3.21
1947 2072 4.443315 GGGGAACATAATGGCCTGAAAATG 60.443 45.833 3.32 3.49 0.00 2.32
1949 2074 3.103742 GGGGAACATAATGGCCTGAAAA 58.896 45.455 3.32 0.00 0.00 2.29
1957 2082 2.508526 GCTAGCTGGGGAACATAATGG 58.491 52.381 7.70 0.00 0.00 3.16
1975 2100 5.023533 TCTTTTCGTATATGAGCTTGGCT 57.976 39.130 0.00 0.00 43.88 4.75
1989 2114 2.948979 TGAGTGCCATTGTTCTTTTCGT 59.051 40.909 0.00 0.00 0.00 3.85
2009 2134 7.039784 TCCTTTGAGGTTAATTGTTGGATTCTG 60.040 37.037 0.00 0.00 36.53 3.02
2068 2197 7.395617 GGAGGGAGTATATTGGAAAATAGTCC 58.604 42.308 7.42 7.42 43.28 3.85
2069 2198 7.097834 CGGAGGGAGTATATTGGAAAATAGTC 58.902 42.308 0.00 0.00 0.00 2.59
2070 2199 6.557633 ACGGAGGGAGTATATTGGAAAATAGT 59.442 38.462 0.00 0.00 0.00 2.12
2072 2201 6.013984 GGACGGAGGGAGTATATTGGAAAATA 60.014 42.308 0.00 0.00 0.00 1.40
2074 2203 4.102054 GGACGGAGGGAGTATATTGGAAAA 59.898 45.833 0.00 0.00 0.00 2.29
2075 2204 3.644738 GGACGGAGGGAGTATATTGGAAA 59.355 47.826 0.00 0.00 0.00 3.13
2091 2221 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
2094 2224 9.626045 CTAAATCAAAGACACTTATTTTGGGAC 57.374 33.333 0.00 0.00 33.70 4.46
2095 2225 9.362151 ACTAAATCAAAGACACTTATTTTGGGA 57.638 29.630 0.00 0.00 33.70 4.37
2147 2277 8.873144 CCTCCATCCCAAAATATATGTTTGATT 58.127 33.333 15.85 0.00 38.05 2.57
2148 2278 7.455638 CCCTCCATCCCAAAATATATGTTTGAT 59.544 37.037 15.85 6.72 38.05 2.57
2149 2279 6.782000 CCCTCCATCCCAAAATATATGTTTGA 59.218 38.462 15.85 5.13 38.05 2.69
2150 2280 6.782000 TCCCTCCATCCCAAAATATATGTTTG 59.218 38.462 0.00 2.98 36.03 2.93
2151 2281 6.932753 TCCCTCCATCCCAAAATATATGTTT 58.067 36.000 0.00 0.00 0.00 2.83
2152 2282 6.104691 ACTCCCTCCATCCCAAAATATATGTT 59.895 38.462 0.00 0.00 0.00 2.71
2153 2283 5.616986 ACTCCCTCCATCCCAAAATATATGT 59.383 40.000 0.00 0.00 0.00 2.29
2154 2284 6.144845 ACTCCCTCCATCCCAAAATATATG 57.855 41.667 0.00 0.00 0.00 1.78
2155 2285 6.797540 TGTACTCCCTCCATCCCAAAATATAT 59.202 38.462 0.00 0.00 0.00 0.86
2156 2286 6.154645 TGTACTCCCTCCATCCCAAAATATA 58.845 40.000 0.00 0.00 0.00 0.86
2157 2287 4.981647 TGTACTCCCTCCATCCCAAAATAT 59.018 41.667 0.00 0.00 0.00 1.28
2158 2288 4.376223 TGTACTCCCTCCATCCCAAAATA 58.624 43.478 0.00 0.00 0.00 1.40
2159 2289 3.197983 TGTACTCCCTCCATCCCAAAAT 58.802 45.455 0.00 0.00 0.00 1.82
2160 2290 2.638325 TGTACTCCCTCCATCCCAAAA 58.362 47.619 0.00 0.00 0.00 2.44
2161 2291 2.352561 TGTACTCCCTCCATCCCAAA 57.647 50.000 0.00 0.00 0.00 3.28
2162 2292 2.196595 CTTGTACTCCCTCCATCCCAA 58.803 52.381 0.00 0.00 0.00 4.12
2163 2293 1.879575 CTTGTACTCCCTCCATCCCA 58.120 55.000 0.00 0.00 0.00 4.37
2164 2294 0.470341 GCTTGTACTCCCTCCATCCC 59.530 60.000 0.00 0.00 0.00 3.85
2165 2295 1.501582 AGCTTGTACTCCCTCCATCC 58.498 55.000 0.00 0.00 0.00 3.51
2166 2296 3.301274 ACTAGCTTGTACTCCCTCCATC 58.699 50.000 0.00 0.00 0.00 3.51
2167 2297 3.406512 ACTAGCTTGTACTCCCTCCAT 57.593 47.619 0.00 0.00 0.00 3.41
2168 2298 2.921834 ACTAGCTTGTACTCCCTCCA 57.078 50.000 0.00 0.00 0.00 3.86
2169 2299 3.770388 AGAAACTAGCTTGTACTCCCTCC 59.230 47.826 0.00 0.00 0.00 4.30
2170 2300 4.382147 CCAGAAACTAGCTTGTACTCCCTC 60.382 50.000 0.00 0.00 0.00 4.30
2171 2301 3.515901 CCAGAAACTAGCTTGTACTCCCT 59.484 47.826 0.00 0.00 0.00 4.20
2172 2302 3.514309 TCCAGAAACTAGCTTGTACTCCC 59.486 47.826 0.00 0.00 0.00 4.30
2173 2303 4.803098 TCCAGAAACTAGCTTGTACTCC 57.197 45.455 0.00 0.00 0.00 3.85
2174 2304 4.627900 GCTTCCAGAAACTAGCTTGTACTC 59.372 45.833 0.00 1.94 0.00 2.59
2175 2305 4.284746 AGCTTCCAGAAACTAGCTTGTACT 59.715 41.667 0.00 1.90 40.91 2.73
2176 2306 4.570930 AGCTTCCAGAAACTAGCTTGTAC 58.429 43.478 0.00 0.00 40.91 2.90
2177 2307 4.891992 AGCTTCCAGAAACTAGCTTGTA 57.108 40.909 0.00 0.00 40.91 2.41
2178 2308 3.778954 AGCTTCCAGAAACTAGCTTGT 57.221 42.857 0.00 0.00 40.91 3.16
2181 2311 6.800072 ATAGTAAGCTTCCAGAAACTAGCT 57.200 37.500 0.00 0.00 45.35 3.32
2182 2312 6.480651 GGAATAGTAAGCTTCCAGAAACTAGC 59.519 42.308 0.00 1.11 40.57 3.42
2183 2313 7.787028 AGGAATAGTAAGCTTCCAGAAACTAG 58.213 38.462 0.00 0.00 42.83 2.57
2184 2314 7.735326 AGGAATAGTAAGCTTCCAGAAACTA 57.265 36.000 0.00 4.46 42.83 2.24
2209 2339 3.055458 CCGCATTCCCCACCTTAATTTTT 60.055 43.478 0.00 0.00 0.00 1.94
2236 2366 4.970611 CCAAGATAGTCATTGTAGTCGTCG 59.029 45.833 0.00 0.00 0.00 5.12
2269 2399 0.839946 GGCCATGACTCCACCAGTAT 59.160 55.000 0.00 0.00 34.41 2.12
2341 2471 1.083706 AGGGGAAGGGTGCTCTGAT 59.916 57.895 0.00 0.00 0.00 2.90
2407 2537 2.691526 TGTGTACAGGCTATAAGGGTCG 59.308 50.000 0.00 0.00 0.00 4.79
2425 2555 1.133790 GAGCTATTGCAGGGCTTTGTG 59.866 52.381 10.57 0.00 42.74 3.33
2470 2600 3.425758 GCAAAACACTTACATAGCGTCCC 60.426 47.826 0.00 0.00 0.00 4.46
2496 2626 9.340695 TGCAAAATGATCAGTTATAAAAGTTCG 57.659 29.630 9.10 0.00 0.00 3.95
2549 2680 5.964958 ATCCACACTCCAATGTACTTTTG 57.035 39.130 0.00 0.00 0.00 2.44
2559 2691 3.519107 TGCTCATAGAATCCACACTCCAA 59.481 43.478 0.00 0.00 0.00 3.53
2646 2778 2.673368 CAATTCAGTTCGTCTACCCTGC 59.327 50.000 0.00 0.00 0.00 4.85
2692 2824 4.261197 CCTTATTCAGTCTAAAATGGCGGC 60.261 45.833 0.00 0.00 0.00 6.53
2734 2866 1.623811 TCCTTGGCAGAGAACTACACC 59.376 52.381 0.00 0.00 0.00 4.16
2749 2882 2.041081 TGGACCAATTGTACCCTCCTTG 59.959 50.000 4.43 0.00 0.00 3.61
2794 2927 1.944024 TGCACCCGTTACTTCAGTTTG 59.056 47.619 0.00 0.00 0.00 2.93
2830 2963 9.445786 CGTAATCGCCAAAATATAAGTTTCAAT 57.554 29.630 0.00 0.00 0.00 2.57
2892 3028 4.793216 GCACTCTGTACAACACACAAAAAG 59.207 41.667 0.00 0.00 32.33 2.27
2893 3029 4.216472 TGCACTCTGTACAACACACAAAAA 59.784 37.500 0.00 0.00 32.33 1.94
2989 3131 5.230516 CGTTTCATGCCAACATTCATGTATG 59.769 40.000 10.48 10.48 40.80 2.39
3004 3146 6.926280 TTGAATAAACATCACGTTTCATGC 57.074 33.333 0.00 0.00 44.78 4.06
3341 3483 8.974060 ACAGAACTTTAAGGTGTATTTTCAGA 57.026 30.769 0.00 0.00 0.00 3.27
3397 3580 8.352201 TCCAACAATATCACTGCAATAAATAGC 58.648 33.333 0.00 0.00 0.00 2.97
3420 3603 0.762418 AATCCGCCCAATACGATCCA 59.238 50.000 0.00 0.00 0.00 3.41
3565 3748 3.317993 ACAAGCAAACTCGTAAATGGCTT 59.682 39.130 0.00 0.00 40.41 4.35
3618 3802 3.190118 CAGAAACAAGATGGACTTCAGGC 59.810 47.826 0.00 0.00 36.61 4.85
3646 3830 4.156556 ACCAAACACATGAAGATGATTCCG 59.843 41.667 0.00 0.00 33.36 4.30
3658 3842 6.086222 GCTGTTAGTCAATACCAAACACATG 58.914 40.000 0.00 0.00 31.94 3.21
3692 3876 8.079211 AGCCAATATCGATATAATGTGGTACT 57.921 34.615 24.69 16.20 0.00 2.73
3713 3897 6.753913 AGATCTCCATTTATAGACAAGCCA 57.246 37.500 0.00 0.00 0.00 4.75
3764 3950 6.794534 AGTTCTATTCCTGTTCATTCCCTTT 58.205 36.000 0.00 0.00 0.00 3.11
3772 3958 7.420214 GGGAATATGGAGTTCTATTCCTGTTCA 60.420 40.741 16.69 0.00 46.71 3.18
3797 3983 5.786311 ACCAGAAATCATTTCACAATGTGG 58.214 37.500 13.95 11.62 42.10 4.17
3804 3990 4.151157 GCAGCAAACCAGAAATCATTTCAC 59.849 41.667 12.74 0.00 42.10 3.18
3822 4008 7.921786 AATACAACTAGACTATTTTGCAGCA 57.078 32.000 0.00 0.00 0.00 4.41
3891 4077 0.882042 GCATCTGTATCCCCACTGCG 60.882 60.000 0.00 0.00 0.00 5.18
3932 4118 4.975788 TGAGAGCGCTTATCGAATATCTC 58.024 43.478 13.26 10.24 41.67 2.75
4010 4196 8.319143 TCAGTTTAGTGAGTAACTATTTTGGC 57.681 34.615 0.00 0.00 41.10 4.52
4023 4209 7.359598 CGGACAGAATTTTCTCAGTTTAGTGAG 60.360 40.741 8.04 8.04 44.71 3.51
4049 4235 7.129109 TGTAAGATTGAAACGGTTCATTCTC 57.871 36.000 30.44 22.33 46.43 2.87
4054 4240 6.869315 TTGATGTAAGATTGAAACGGTTCA 57.131 33.333 12.93 12.93 42.12 3.18
4057 4243 6.071952 AGCATTTGATGTAAGATTGAAACGGT 60.072 34.615 0.00 0.00 0.00 4.83
4059 4245 7.801547 AAGCATTTGATGTAAGATTGAAACG 57.198 32.000 0.00 0.00 0.00 3.60
4070 4256 9.920133 TGCAAAATAGTTAAAGCATTTGATGTA 57.080 25.926 0.00 0.00 39.63 2.29
4072 4258 8.385111 CCTGCAAAATAGTTAAAGCATTTGATG 58.615 33.333 0.00 0.00 39.63 3.07
4073 4259 8.096414 ACCTGCAAAATAGTTAAAGCATTTGAT 58.904 29.630 0.00 0.00 39.63 2.57
4077 4263 6.650390 CCAACCTGCAAAATAGTTAAAGCATT 59.350 34.615 0.00 0.00 0.00 3.56
4079 4265 5.303078 TCCAACCTGCAAAATAGTTAAAGCA 59.697 36.000 0.00 0.00 0.00 3.91
4080 4266 5.778862 TCCAACCTGCAAAATAGTTAAAGC 58.221 37.500 0.00 0.00 0.00 3.51
4082 4268 5.836358 ACCTCCAACCTGCAAAATAGTTAAA 59.164 36.000 0.00 0.00 0.00 1.52
4084 4270 4.993028 ACCTCCAACCTGCAAAATAGTTA 58.007 39.130 0.00 0.00 0.00 2.24
4085 4271 3.844640 ACCTCCAACCTGCAAAATAGTT 58.155 40.909 0.00 0.00 0.00 2.24
4086 4272 3.525800 ACCTCCAACCTGCAAAATAGT 57.474 42.857 0.00 0.00 0.00 2.12
4087 4273 3.056607 CCAACCTCCAACCTGCAAAATAG 60.057 47.826 0.00 0.00 0.00 1.73
4088 4274 2.896685 CCAACCTCCAACCTGCAAAATA 59.103 45.455 0.00 0.00 0.00 1.40
4089 4275 1.693606 CCAACCTCCAACCTGCAAAAT 59.306 47.619 0.00 0.00 0.00 1.82
4145 4331 4.746309 TCATGCCCTGCACCTGCC 62.746 66.667 0.00 0.00 43.04 4.85
4232 4418 3.754965 TGCTTCAAGTGGCTATTGAGTT 58.245 40.909 5.37 0.00 37.91 3.01
4374 4562 5.520748 ACAAATGTCAGTTTCCCCTATCT 57.479 39.130 0.00 0.00 0.00 1.98
4375 4563 6.415573 AGTACAAATGTCAGTTTCCCCTATC 58.584 40.000 0.00 0.00 0.00 2.08
4452 4640 5.575606 GTGCAATGAGTGAATCTGGAAATTG 59.424 40.000 0.00 0.00 0.00 2.32
4465 4653 4.572985 TTTCCTTTCTGTGCAATGAGTG 57.427 40.909 0.00 0.00 0.00 3.51
4471 4659 3.254657 CCCGTTATTTCCTTTCTGTGCAA 59.745 43.478 0.00 0.00 0.00 4.08
4476 4664 4.718940 AATGCCCGTTATTTCCTTTCTG 57.281 40.909 0.00 0.00 0.00 3.02
4483 4671 5.405269 GGATATGCAAAATGCCCGTTATTTC 59.595 40.000 0.00 0.00 44.23 2.17
4491 4679 6.453926 AAAAATTGGATATGCAAAATGCCC 57.546 33.333 14.00 0.00 44.23 5.36
4513 4784 6.706295 AGAAACACCATTTTTCTGTTCCAAA 58.294 32.000 0.00 0.00 40.93 3.28
4519 4790 5.535030 GGGACTAGAAACACCATTTTTCTGT 59.465 40.000 0.00 4.36 42.15 3.41
4538 4809 4.598036 ATCAGTTGGATTCAATGGGACT 57.402 40.909 0.00 0.00 35.10 3.85
4539 4810 6.378280 AGTTAATCAGTTGGATTCAATGGGAC 59.622 38.462 0.00 0.00 42.62 4.46
4540 4811 6.377996 CAGTTAATCAGTTGGATTCAATGGGA 59.622 38.462 0.00 0.00 42.62 4.37
4542 4813 6.406177 CCCAGTTAATCAGTTGGATTCAATGG 60.406 42.308 9.53 9.53 46.99 3.16
4543 4814 6.406177 CCCCAGTTAATCAGTTGGATTCAATG 60.406 42.308 0.00 0.00 42.62 2.82
4544 4815 5.658190 CCCCAGTTAATCAGTTGGATTCAAT 59.342 40.000 0.00 0.00 42.62 2.57
4546 4817 4.044065 ACCCCAGTTAATCAGTTGGATTCA 59.956 41.667 0.00 0.00 42.62 2.57
4547 4818 4.600062 ACCCCAGTTAATCAGTTGGATTC 58.400 43.478 0.00 0.00 42.62 2.52
4586 4892 1.376553 GCAGTCAAGGCTCCAGGTC 60.377 63.158 0.00 0.00 0.00 3.85
4630 4936 0.721718 GTCAACTCGCTGGGAATTCG 59.278 55.000 0.00 0.00 0.00 3.34
4691 5002 7.201758 GGCTGACAAGATAAATTCATGTGATGA 60.202 37.037 0.00 0.00 36.45 2.92
4840 5151 6.036470 GCAATTTTGAGCCACCTAGTATTTC 58.964 40.000 0.00 0.00 0.00 2.17
4879 5190 8.161425 ACTATAGTTTTTGTGTCCTGGTAATGT 58.839 33.333 0.00 0.00 0.00 2.71
4939 5250 6.775142 TGTTCCTTTGTTCATATTGGAAGACA 59.225 34.615 0.00 0.00 34.73 3.41
4948 5259 8.149647 TGCTGAATTTTGTTCCTTTGTTCATAT 58.850 29.630 0.00 0.00 0.00 1.78
5008 5330 2.801631 CGATCCCCCTCCTGCTGAC 61.802 68.421 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.