Multiple sequence alignment - TraesCS3B01G261300

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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 TraesCS3B01G261300 chr3B 100.000 2465 0 0 1 2465 419280272 419282736 0.000000e+00 4553.0
1 TraesCS3B01G261300 chr3A 87.307 2072 184 38 18 2046 433426522 433428557 0.000000e+00 2296.0
2 TraesCS3B01G261300 chr3A 79.866 298 38 9 2175 2461 433429202 433429488 5.380000e-47 198.0
3 TraesCS3B01G261300 chr3A 77.545 334 42 20 229 537 710836299 710835974 1.170000e-38 171.0
4 TraesCS3B01G261300 chr3A 81.308 107 15 4 231 332 727915532 727915638 5.650000e-12 82.4
5 TraesCS3B01G261300 chr3D 90.115 1649 110 34 46 1673 301772849 301771233 0.000000e+00 2093.0
6 TraesCS3B01G261300 chr3D 80.366 382 61 8 1675 2046 497760045 497759668 6.710000e-71 278.0
7 TraesCS3B01G261300 chr3D 74.699 332 53 20 229 536 433563263 433563587 4.310000e-23 119.0
8 TraesCS3B01G261300 chr2D 85.942 313 32 7 2151 2459 73215898 73215594 8.500000e-85 324.0
9 TraesCS3B01G261300 chr2D 80.000 380 64 6 1675 2046 380062668 380063043 1.120000e-68 270.0
10 TraesCS3B01G261300 chr2D 78.947 323 40 14 244 539 484477909 484477588 6.960000e-46 195.0
11 TraesCS3B01G261300 chr2D 77.636 313 59 7 2151 2459 7731058 7730753 1.950000e-41 180.0
12 TraesCS3B01G261300 chr6A 84.566 311 36 9 2151 2457 480315383 480315081 5.150000e-77 298.0
13 TraesCS3B01G261300 chr4B 80.475 379 61 5 1676 2046 24052244 24052617 6.710000e-71 278.0
14 TraesCS3B01G261300 chr5B 88.546 227 26 0 1120 1346 36602520 36602294 2.410000e-70 276.0
15 TraesCS3B01G261300 chr5B 83.843 229 34 3 1120 1346 37046654 37046881 5.340000e-52 215.0
16 TraesCS3B01G261300 chr5B 84.286 210 31 2 1138 1346 36891386 36891594 1.160000e-48 204.0
17 TraesCS3B01G261300 chr5B 77.830 212 44 2 2251 2459 670248926 670248715 7.160000e-26 128.0
18 TraesCS3B01G261300 chrUn 80.488 369 63 4 1687 2046 111150659 111150291 8.680000e-70 274.0
19 TraesCS3B01G261300 chrUn 76.923 182 38 3 2272 2450 263448264 263448084 1.560000e-17 100.0
20 TraesCS3B01G261300 chrUn 76.923 182 38 3 2272 2450 268147506 268147326 1.560000e-17 100.0
21 TraesCS3B01G261300 chrUn 94.286 35 2 0 509 543 38014694 38014660 1.000000e-03 54.7
22 TraesCS3B01G261300 chr7A 80.435 368 61 5 1687 2046 39240996 39241360 1.120000e-68 270.0
23 TraesCS3B01G261300 chr7A 76.655 287 42 13 229 492 112169623 112169907 4.280000e-28 135.0
24 TraesCS3B01G261300 chr5A 87.773 229 24 3 1120 1346 30634376 30634602 5.230000e-67 265.0
25 TraesCS3B01G261300 chr5A 79.310 348 65 2 1698 2038 290729967 290730314 1.140000e-58 237.0
26 TraesCS3B01G261300 chr5A 79.331 329 38 20 230 536 656051543 656051223 1.160000e-48 204.0
27 TraesCS3B01G261300 chr5A 86.339 183 24 1 355 537 415411152 415410971 5.380000e-47 198.0
28 TraesCS3B01G261300 chr5A 83.333 210 33 2 1138 1346 30659923 30660131 2.500000e-45 193.0
29 TraesCS3B01G261300 chr5A 76.506 332 52 16 231 537 295878146 295878476 9.130000e-35 158.0
30 TraesCS3B01G261300 chr5A 80.800 125 12 8 414 536 310043364 310043478 1.210000e-13 87.9
31 TraesCS3B01G261300 chr1A 79.781 366 66 4 1687 2044 403133617 403133252 2.430000e-65 259.0
32 TraesCS3B01G261300 chr1A 79.620 368 67 3 1687 2046 554013663 554014030 8.750000e-65 257.0
33 TraesCS3B01G261300 chr7B 78.590 383 68 8 1673 2046 595711089 595711466 8.810000e-60 241.0
34 TraesCS3B01G261300 chr5D 84.286 210 31 2 1138 1346 42086921 42087129 1.160000e-48 204.0
35 TraesCS3B01G261300 chr5D 84.286 210 31 2 1138 1346 42205818 42206026 1.160000e-48 204.0
36 TraesCS3B01G261300 chr5D 78.866 194 25 9 356 546 72877730 72877910 1.550000e-22 117.0
37 TraesCS3B01G261300 chr7D 77.812 329 49 14 231 541 616253442 616253764 5.420000e-42 182.0
38 TraesCS3B01G261300 chr7D 85.366 123 17 1 416 537 582057993 582058115 2.570000e-25 126.0
39 TraesCS3B01G261300 chr6D 75.362 345 53 18 224 537 460563739 460563396 1.190000e-28 137.0
40 TraesCS3B01G261300 chr4A 74.815 270 39 14 228 469 665145022 665144754 7.260000e-16 95.3


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 TraesCS3B01G261300 chr3B 419280272 419282736 2464 False 4553 4553 100.0000 1 2465 1 chr3B.!!$F1 2464
1 TraesCS3B01G261300 chr3A 433426522 433429488 2966 False 1247 2296 83.5865 18 2461 2 chr3A.!!$F2 2443
2 TraesCS3B01G261300 chr3D 301771233 301772849 1616 True 2093 2093 90.1150 46 1673 1 chr3D.!!$R1 1627

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
773 794 0.027586 GCGCAATTACGTGTCCCATC 59.972 55.0 0.3 0.0 34.88 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2054 0.036294 AAACTTAGAGCGTCCCTGCC 60.036 55.0 0.0 0.0 34.65 4.85 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
96 97 6.806739 CAGACTGTAGAACAATCATTGTACGA 59.193 38.462 2.67 0.00 44.59 3.43
204 207 3.629398 AGAATGACATTTTGGATCTCGGC 59.371 43.478 1.39 0.00 0.00 5.54
271 274 3.895232 AGGATGTGAGGTGTATGTGTC 57.105 47.619 0.00 0.00 0.00 3.67
273 276 3.196469 AGGATGTGAGGTGTATGTGTCTG 59.804 47.826 0.00 0.00 0.00 3.51
274 277 3.525537 GATGTGAGGTGTATGTGTCTGG 58.474 50.000 0.00 0.00 0.00 3.86
304 307 6.094742 TCAGAATAAAATACAATGAAGCGGCA 59.905 34.615 1.45 0.00 0.00 5.69
312 315 1.745087 CAATGAAGCGGCAACCTGTAT 59.255 47.619 1.45 0.00 0.00 2.29
341 358 7.502120 AGACAAATTCATGGTAGTATCATGC 57.498 36.000 17.21 3.22 41.11 4.06
342 359 7.056006 AGACAAATTCATGGTAGTATCATGCA 58.944 34.615 17.21 8.28 41.11 3.96
345 362 8.698210 ACAAATTCATGGTAGTATCATGCATTT 58.302 29.630 21.28 21.28 43.64 2.32
355 372 7.229506 GGTAGTATCATGCATTTAAAAGCCTCT 59.770 37.037 12.50 5.15 0.00 3.69
356 373 7.651027 AGTATCATGCATTTAAAAGCCTCTT 57.349 32.000 12.50 0.00 0.00 2.85
387 406 5.872617 CACAACCCTCATCTCAACGTATTTA 59.127 40.000 0.00 0.00 0.00 1.40
431 450 8.896744 ACTTATGTATTATGCCATCATGTATGC 58.103 33.333 0.00 0.00 33.92 3.14
433 452 4.635324 TGTATTATGCCATCATGTATGCCG 59.365 41.667 0.00 0.00 33.92 5.69
505 524 2.636768 GCATTTTGCGTTTAGAGGCT 57.363 45.000 0.00 0.00 37.54 4.58
507 526 3.317150 GCATTTTGCGTTTAGAGGCTTT 58.683 40.909 0.00 0.00 37.54 3.51
552 571 7.237920 AGCAATTTCAGTTTCAAATGTCAAC 57.762 32.000 0.00 0.00 0.00 3.18
593 612 0.389817 TCTGACGGCATGTGCACTAC 60.390 55.000 19.41 7.09 44.36 2.73
694 714 5.592282 TGTCAATTCACAAACTGGAGCTAAA 59.408 36.000 0.00 0.00 0.00 1.85
699 719 8.490355 CAATTCACAAACTGGAGCTAAATTTTC 58.510 33.333 0.00 0.00 0.00 2.29
711 731 8.908903 TGGAGCTAAATTTTCTTTCACAAACTA 58.091 29.630 0.00 0.00 0.00 2.24
726 746 3.119316 ACAAACTAGTGCTGAGGAGATCG 60.119 47.826 11.26 0.00 0.00 3.69
771 792 2.384309 CGCGCAATTACGTGTCCCA 61.384 57.895 8.75 0.00 38.69 4.37
772 793 1.701545 CGCGCAATTACGTGTCCCAT 61.702 55.000 8.75 0.00 38.69 4.00
773 794 0.027586 GCGCAATTACGTGTCCCATC 59.972 55.000 0.30 0.00 34.88 3.51
774 795 1.364721 CGCAATTACGTGTCCCATCA 58.635 50.000 0.00 0.00 0.00 3.07
844 866 2.013400 ACAATTGAACACACGTGAGCA 58.987 42.857 25.01 11.15 0.00 4.26
886 908 1.078848 ATCCAGCAAGCGGAGTCAC 60.079 57.895 10.40 0.00 35.56 3.67
1017 1039 1.075542 TCACAACGATTAGCAAGCGG 58.924 50.000 10.38 0.00 45.98 5.52
1018 1040 1.075542 CACAACGATTAGCAAGCGGA 58.924 50.000 10.38 0.00 45.98 5.54
1019 1041 1.061131 CACAACGATTAGCAAGCGGAG 59.939 52.381 10.38 5.61 45.98 4.63
1020 1042 1.337823 ACAACGATTAGCAAGCGGAGT 60.338 47.619 10.38 6.10 45.98 3.85
1021 1043 2.094390 ACAACGATTAGCAAGCGGAGTA 60.094 45.455 10.38 0.00 45.98 2.59
1022 1044 2.493713 ACGATTAGCAAGCGGAGTAG 57.506 50.000 10.38 0.00 45.98 2.57
1023 1045 1.132588 CGATTAGCAAGCGGAGTAGC 58.867 55.000 0.00 0.00 36.51 3.58
1047 1073 2.545526 ACCATCAATTTCTAGCGCATCG 59.454 45.455 11.47 0.00 0.00 3.84
1068 1094 3.871006 CGATCCATCCATCAAACTTCGAA 59.129 43.478 0.00 0.00 0.00 3.71
1069 1095 4.260375 CGATCCATCCATCAAACTTCGAAC 60.260 45.833 0.00 0.00 0.00 3.95
1070 1096 4.014569 TCCATCCATCAAACTTCGAACA 57.985 40.909 0.00 0.00 0.00 3.18
1091 1117 4.190001 CACAAGCATTCTATCTGACAGCT 58.810 43.478 0.00 0.00 36.85 4.24
1157 1183 2.280797 GTGCAGTGCGGGACAAGA 60.281 61.111 11.20 0.00 0.00 3.02
1429 1455 3.801698 CTGTGTCATGTAATCTGGGAGG 58.198 50.000 0.00 0.00 0.00 4.30
1468 1494 3.120477 TCAGCGTGTGTTTAATAAAGCGG 60.120 43.478 0.00 0.00 0.00 5.52
1483 1509 1.947146 GCGGGGTTTTTGTTGTCGC 60.947 57.895 0.00 0.00 35.12 5.19
1517 1543 2.202703 CGCCGTGGCTGTACCTAC 60.203 66.667 9.55 0.00 40.22 3.18
1535 1561 5.100259 ACCTACTATTTGTTCGTCGATGTG 58.900 41.667 4.21 0.00 0.00 3.21
1579 1605 1.480954 CCCCGAGTGCTGTGTAATAGT 59.519 52.381 0.00 0.00 0.00 2.12
1624 1650 8.788806 TCTTTTCGGAAAATGCTCTTTATGTAA 58.211 29.630 15.64 0.00 0.00 2.41
1648 1674 3.739830 GCTCCCTCCGATCTTCTCTTTTC 60.740 52.174 0.00 0.00 0.00 2.29
1660 1686 7.806960 CGATCTTCTCTTTTCTGAAAAATGCTT 59.193 33.333 15.67 0.04 34.00 3.91
1734 1772 9.405587 CAACTTAAAATGTCCGTACAATCATTT 57.594 29.630 11.00 11.00 39.58 2.32
1745 1783 9.698617 GTCCGTACAATCATTTATTACAAACTC 57.301 33.333 0.00 0.00 0.00 3.01
1746 1784 8.885722 TCCGTACAATCATTTATTACAAACTCC 58.114 33.333 0.00 0.00 0.00 3.85
1748 1786 7.372396 CGTACAATCATTTATTACAAACTCCGC 59.628 37.037 0.00 0.00 0.00 5.54
1752 1790 5.004448 TCATTTATTACAAACTCCGCCACA 58.996 37.500 0.00 0.00 0.00 4.17
1755 1793 1.588674 TTACAAACTCCGCCACACAG 58.411 50.000 0.00 0.00 0.00 3.66
1757 1795 2.113139 AAACTCCGCCACACAGGG 59.887 61.111 0.00 0.00 38.09 4.45
1781 1819 6.128822 GGCGGAACAGAATGAAAAAGAAAATC 60.129 38.462 0.00 0.00 39.69 2.17
1821 1862 3.371965 ACTAAACTTATCTCGGGAGCCA 58.628 45.455 0.00 0.00 0.00 4.75
1823 1864 0.831307 AACTTATCTCGGGAGCCACC 59.169 55.000 0.00 0.00 38.08 4.61
1853 1897 5.045872 GCCCTGTTGATCTTTGAAATATGC 58.954 41.667 0.00 0.00 0.00 3.14
1876 1920 5.867716 GCAAATTCAACAGCATCTTTGAGAT 59.132 36.000 0.00 0.00 34.74 2.75
1883 1927 8.791327 TCAACAGCATCTTTGAGATATTTACA 57.209 30.769 0.00 0.00 32.12 2.41
1886 1930 8.565896 ACAGCATCTTTGAGATATTTACAACA 57.434 30.769 0.00 0.00 32.12 3.33
1887 1931 9.182214 ACAGCATCTTTGAGATATTTACAACAT 57.818 29.630 0.00 0.00 32.12 2.71
1910 1954 6.152638 TCCTCCTTTAAATCAACAAGGGAT 57.847 37.500 0.00 0.00 38.13 3.85
1914 1958 6.310941 TCCTTTAAATCAACAAGGGATGACA 58.689 36.000 0.00 0.00 38.13 3.58
1918 1962 7.537596 TTAAATCAACAAGGGATGACATGTT 57.462 32.000 0.00 0.00 36.49 2.71
1927 1971 6.664816 ACAAGGGATGACATGTTCATACAATT 59.335 34.615 17.11 10.95 46.61 2.32
1937 1981 7.092716 ACATGTTCATACAATTTCTTCCAAGC 58.907 34.615 0.00 0.00 37.91 4.01
1941 1985 6.647334 TCATACAATTTCTTCCAAGCACAA 57.353 33.333 0.00 0.00 0.00 3.33
1945 1989 4.060205 CAATTTCTTCCAAGCACAAAGGG 58.940 43.478 0.00 0.00 0.00 3.95
1946 1990 1.039856 TTCTTCCAAGCACAAAGGGC 58.960 50.000 0.00 0.00 0.00 5.19
1947 1991 0.106268 TCTTCCAAGCACAAAGGGCA 60.106 50.000 0.00 0.00 0.00 5.36
1951 1995 0.530431 CCAAGCACAAAGGGCACAAC 60.530 55.000 0.00 0.00 0.00 3.32
1957 2001 2.192861 CAAAGGGCACAACGGAGCA 61.193 57.895 0.00 0.00 31.64 4.26
1962 2006 1.523154 GGGCACAACGGAGCAATCAA 61.523 55.000 0.00 0.00 31.64 2.57
1966 2010 3.059166 GCACAACGGAGCAATCAATTTT 58.941 40.909 0.00 0.00 0.00 1.82
1967 2011 3.494251 GCACAACGGAGCAATCAATTTTT 59.506 39.130 0.00 0.00 0.00 1.94
1968 2012 4.683781 GCACAACGGAGCAATCAATTTTTA 59.316 37.500 0.00 0.00 0.00 1.52
1969 2013 5.176590 GCACAACGGAGCAATCAATTTTTAA 59.823 36.000 0.00 0.00 0.00 1.52
1970 2014 6.292596 GCACAACGGAGCAATCAATTTTTAAA 60.293 34.615 0.00 0.00 0.00 1.52
1971 2015 7.625553 CACAACGGAGCAATCAATTTTTAAAA 58.374 30.769 0.00 0.00 0.00 1.52
1972 2016 8.281893 CACAACGGAGCAATCAATTTTTAAAAT 58.718 29.630 0.55 0.00 0.00 1.82
1973 2017 9.482627 ACAACGGAGCAATCAATTTTTAAAATA 57.517 25.926 3.17 0.00 0.00 1.40
1976 2020 9.482627 ACGGAGCAATCAATTTTTAAAATAACA 57.517 25.926 3.17 0.00 0.00 2.41
1977 2021 9.956797 CGGAGCAATCAATTTTTAAAATAACAG 57.043 29.630 3.17 0.00 0.00 3.16
1994 2038 9.871238 AAAATAACAGATACGTCTAGTGTCATT 57.129 29.630 0.00 0.00 42.57 2.57
1995 2039 9.871238 AAATAACAGATACGTCTAGTGTCATTT 57.129 29.630 0.00 0.00 42.57 2.32
1996 2040 9.517609 AATAACAGATACGTCTAGTGTCATTTC 57.482 33.333 0.00 0.00 42.57 2.17
1997 2041 6.510879 ACAGATACGTCTAGTGTCATTTCA 57.489 37.500 0.00 0.00 42.57 2.69
1998 2042 6.920817 ACAGATACGTCTAGTGTCATTTCAA 58.079 36.000 0.00 0.00 42.57 2.69
1999 2043 7.548097 ACAGATACGTCTAGTGTCATTTCAAT 58.452 34.615 0.00 0.00 42.57 2.57
2000 2044 8.683615 ACAGATACGTCTAGTGTCATTTCAATA 58.316 33.333 0.00 0.00 42.57 1.90
2001 2045 9.684448 CAGATACGTCTAGTGTCATTTCAATAT 57.316 33.333 0.00 0.00 42.57 1.28
2005 2049 8.858003 ACGTCTAGTGTCATTTCAATATACAG 57.142 34.615 0.00 0.00 0.00 2.74
2006 2050 7.921214 ACGTCTAGTGTCATTTCAATATACAGG 59.079 37.037 0.00 0.00 0.00 4.00
2007 2051 7.096023 CGTCTAGTGTCATTTCAATATACAGGC 60.096 40.741 0.00 0.00 0.00 4.85
2008 2052 7.171678 GTCTAGTGTCATTTCAATATACAGGCC 59.828 40.741 0.00 0.00 0.00 5.19
2009 2053 5.133221 AGTGTCATTTCAATATACAGGCCC 58.867 41.667 0.00 0.00 0.00 5.80
2010 2054 4.024048 GTGTCATTTCAATATACAGGCCCG 60.024 45.833 0.00 0.00 0.00 6.13
2011 2055 3.502211 GTCATTTCAATATACAGGCCCGG 59.498 47.826 0.00 0.00 0.00 5.73
2012 2056 1.975660 TTTCAATATACAGGCCCGGC 58.024 50.000 0.00 0.00 0.00 6.13
2013 2057 0.840617 TTCAATATACAGGCCCGGCA 59.159 50.000 12.58 0.00 0.00 5.69
2014 2058 0.396435 TCAATATACAGGCCCGGCAG 59.604 55.000 12.58 5.60 0.00 4.85
2015 2059 0.606401 CAATATACAGGCCCGGCAGG 60.606 60.000 12.58 4.78 39.47 4.85
2025 2069 3.458163 CCGGCAGGGACGCTCTAA 61.458 66.667 0.00 0.00 38.47 2.10
2026 2070 2.105128 CGGCAGGGACGCTCTAAG 59.895 66.667 0.00 0.00 0.00 2.18
2027 2071 2.711922 CGGCAGGGACGCTCTAAGT 61.712 63.158 0.00 0.00 0.00 2.24
2028 2072 1.597461 GGCAGGGACGCTCTAAGTT 59.403 57.895 0.00 0.00 0.00 2.66
2029 2073 0.036294 GGCAGGGACGCTCTAAGTTT 60.036 55.000 0.00 0.00 0.00 2.66
2030 2074 1.360820 GCAGGGACGCTCTAAGTTTC 58.639 55.000 0.00 0.00 0.00 2.78
2031 2075 1.630148 CAGGGACGCTCTAAGTTTCG 58.370 55.000 0.00 0.00 0.00 3.46
2032 2076 0.108756 AGGGACGCTCTAAGTTTCGC 60.109 55.000 0.00 0.00 0.00 4.70
2033 2077 0.108756 GGGACGCTCTAAGTTTCGCT 60.109 55.000 0.00 0.00 0.00 4.93
2034 2078 1.672145 GGGACGCTCTAAGTTTCGCTT 60.672 52.381 0.00 0.00 41.05 4.68
2035 2079 1.654602 GGACGCTCTAAGTTTCGCTTC 59.345 52.381 0.00 0.00 38.57 3.86
2036 2080 1.654602 GACGCTCTAAGTTTCGCTTCC 59.345 52.381 0.00 0.00 38.57 3.46
2037 2081 1.272769 ACGCTCTAAGTTTCGCTTCCT 59.727 47.619 0.00 0.00 38.57 3.36
2038 2082 1.656095 CGCTCTAAGTTTCGCTTCCTG 59.344 52.381 0.00 0.00 38.57 3.86
2039 2083 2.671351 CGCTCTAAGTTTCGCTTCCTGA 60.671 50.000 0.00 0.00 38.57 3.86
2040 2084 2.668945 GCTCTAAGTTTCGCTTCCTGAC 59.331 50.000 0.00 0.00 38.57 3.51
2041 2085 3.861131 GCTCTAAGTTTCGCTTCCTGACA 60.861 47.826 0.00 0.00 38.57 3.58
2042 2086 3.650139 TCTAAGTTTCGCTTCCTGACAC 58.350 45.455 0.00 0.00 38.57 3.67
2043 2087 2.622064 AAGTTTCGCTTCCTGACACT 57.378 45.000 0.00 0.00 30.06 3.55
2044 2088 3.746045 AAGTTTCGCTTCCTGACACTA 57.254 42.857 0.00 0.00 30.06 2.74
2045 2089 3.963428 AGTTTCGCTTCCTGACACTAT 57.037 42.857 0.00 0.00 0.00 2.12
2046 2090 4.273148 AGTTTCGCTTCCTGACACTATT 57.727 40.909 0.00 0.00 0.00 1.73
2047 2091 4.642429 AGTTTCGCTTCCTGACACTATTT 58.358 39.130 0.00 0.00 0.00 1.40
2048 2092 5.063880 AGTTTCGCTTCCTGACACTATTTT 58.936 37.500 0.00 0.00 0.00 1.82
2049 2093 5.531287 AGTTTCGCTTCCTGACACTATTTTT 59.469 36.000 0.00 0.00 0.00 1.94
2057 2101 9.129209 GCTTCCTGACACTATTTTTAAAATGAC 57.871 33.333 12.62 0.00 0.00 3.06
2059 2103 8.610248 TCCTGACACTATTTTTAAAATGACGA 57.390 30.769 12.62 0.00 0.00 4.20
2060 2104 9.058174 TCCTGACACTATTTTTAAAATGACGAA 57.942 29.630 12.62 0.00 0.00 3.85
2061 2105 9.840427 CCTGACACTATTTTTAAAATGACGAAT 57.160 29.630 12.62 0.00 0.00 3.34
2089 2133 6.647067 GTCTAGTGTCATTCCAATATACAGGC 59.353 42.308 0.00 0.00 0.00 4.85
2094 2138 2.922740 TTCCAATATACAGGCCCGAC 57.077 50.000 0.00 0.00 0.00 4.79
2097 2141 1.691976 CCAATATACAGGCCCGACAGA 59.308 52.381 0.00 0.00 0.00 3.41
2108 2152 1.630148 CCCGACAGAAACGCTCTAAG 58.370 55.000 0.00 0.00 31.12 2.18
2111 2155 3.057734 CCGACAGAAACGCTCTAAGTTT 58.942 45.455 0.00 0.00 43.60 2.66
2117 2161 4.129878 GAAACGCTCTAAGTTTCGCTTT 57.870 40.909 6.14 0.00 44.99 3.51
2123 2168 3.741344 GCTCTAAGTTTCGCTTTCTGACA 59.259 43.478 0.00 0.00 38.57 3.58
2133 2178 4.174009 TCGCTTTCTGACACTATAGCAAC 58.826 43.478 0.00 0.00 0.00 4.17
2138 2183 6.360370 TTTCTGACACTATAGCAACCTCTT 57.640 37.500 0.00 0.00 0.00 2.85
2142 2187 8.941995 TCTGACACTATAGCAACCTCTTATAT 57.058 34.615 0.00 0.00 0.00 0.86
2148 2193 9.737427 CACTATAGCAACCTCTTATATAATCGG 57.263 37.037 0.00 2.58 0.00 4.18
2172 2738 8.244802 CGGTATTAATCTTGTAGACCTATGAGG 58.755 40.741 0.00 0.00 42.49 3.86
2202 2845 4.526970 TGCCAATGAATAACCTTCCTCTC 58.473 43.478 0.00 0.00 0.00 3.20
2216 2859 6.525629 ACCTTCCTCTCAATATTAATGGTCG 58.474 40.000 0.00 0.00 0.00 4.79
2226 2869 7.648142 TCAATATTAATGGTCGGCTGAAATTC 58.352 34.615 0.00 0.00 0.00 2.17
2229 2872 1.463674 ATGGTCGGCTGAAATTCCAC 58.536 50.000 4.81 0.00 0.00 4.02
2233 2876 0.984230 TCGGCTGAAATTCCACCTCT 59.016 50.000 0.00 0.00 0.00 3.69
2234 2877 1.089920 CGGCTGAAATTCCACCTCTG 58.910 55.000 0.00 0.00 0.00 3.35
2238 2881 3.347216 GCTGAAATTCCACCTCTGCTTA 58.653 45.455 0.00 0.00 32.93 3.09
2239 2882 3.376546 GCTGAAATTCCACCTCTGCTTAG 59.623 47.826 0.00 0.00 32.93 2.18
2240 2883 3.347216 TGAAATTCCACCTCTGCTTAGC 58.653 45.455 0.00 0.00 0.00 3.09
2242 2885 3.728385 AATTCCACCTCTGCTTAGCTT 57.272 42.857 5.60 0.00 0.00 3.74
2244 2887 4.844349 ATTCCACCTCTGCTTAGCTTTA 57.156 40.909 5.60 0.00 0.00 1.85
2245 2888 3.611766 TCCACCTCTGCTTAGCTTTAC 57.388 47.619 5.60 0.00 0.00 2.01
2248 2891 4.041691 TCCACCTCTGCTTAGCTTTACTTT 59.958 41.667 5.60 0.00 0.00 2.66
2249 2892 5.247564 TCCACCTCTGCTTAGCTTTACTTTA 59.752 40.000 5.60 0.00 0.00 1.85
2250 2893 5.351740 CCACCTCTGCTTAGCTTTACTTTAC 59.648 44.000 5.60 0.00 0.00 2.01
2251 2894 5.351740 CACCTCTGCTTAGCTTTACTTTACC 59.648 44.000 5.60 0.00 0.00 2.85
2252 2895 5.248705 ACCTCTGCTTAGCTTTACTTTACCT 59.751 40.000 5.60 0.00 0.00 3.08
2253 2896 6.174049 CCTCTGCTTAGCTTTACTTTACCTT 58.826 40.000 5.60 0.00 0.00 3.50
2254 2897 6.655425 CCTCTGCTTAGCTTTACTTTACCTTT 59.345 38.462 5.60 0.00 0.00 3.11
2255 2898 7.822822 CCTCTGCTTAGCTTTACTTTACCTTTA 59.177 37.037 5.60 0.00 0.00 1.85
2256 2899 9.384764 CTCTGCTTAGCTTTACTTTACCTTTAT 57.615 33.333 5.60 0.00 0.00 1.40
2257 2900 9.734984 TCTGCTTAGCTTTACTTTACCTTTATT 57.265 29.630 5.60 0.00 0.00 1.40
2258 2901 9.774742 CTGCTTAGCTTTACTTTACCTTTATTG 57.225 33.333 5.60 0.00 0.00 1.90
2259 2902 8.241367 TGCTTAGCTTTACTTTACCTTTATTGC 58.759 33.333 5.60 0.00 0.00 3.56
2260 2903 8.241367 GCTTAGCTTTACTTTACCTTTATTGCA 58.759 33.333 0.00 0.00 0.00 4.08
2261 2904 9.556030 CTTAGCTTTACTTTACCTTTATTGCAC 57.444 33.333 0.00 0.00 0.00 4.57
2262 2905 7.519032 AGCTTTACTTTACCTTTATTGCACA 57.481 32.000 0.00 0.00 0.00 4.57
2268 2911 7.759489 ACTTTACCTTTATTGCACATCTTCA 57.241 32.000 0.00 0.00 0.00 3.02
2270 2913 7.230510 ACTTTACCTTTATTGCACATCTTCACA 59.769 33.333 0.00 0.00 0.00 3.58
2302 2945 4.335874 AGCATGACAAGATGAGAAAGATGC 59.664 41.667 0.00 0.00 35.09 3.91
2303 2946 4.335874 GCATGACAAGATGAGAAAGATGCT 59.664 41.667 0.00 0.00 32.72 3.79
2310 2953 8.571461 ACAAGATGAGAAAGATGCTCAATAAA 57.429 30.769 0.00 0.00 44.71 1.40
2311 2954 8.675504 ACAAGATGAGAAAGATGCTCAATAAAG 58.324 33.333 0.00 0.00 44.71 1.85
2314 2957 9.240734 AGATGAGAAAGATGCTCAATAAAGTTT 57.759 29.630 0.00 0.00 44.71 2.66
2326 2969 7.094805 TGCTCAATAAAGTTTTACGAAGCTCAT 60.095 33.333 0.00 0.00 30.84 2.90
2334 2977 9.485206 AAAGTTTTACGAAGCTCATTAAGTCTA 57.515 29.630 0.00 0.00 0.00 2.59
2344 2987 8.900983 AAGCTCATTAAGTCTAAGATGGATTC 57.099 34.615 0.00 0.00 0.00 2.52
2345 2988 7.449247 AGCTCATTAAGTCTAAGATGGATTCC 58.551 38.462 0.00 0.00 0.00 3.01
2349 2992 8.265055 TCATTAAGTCTAAGATGGATTCCGTTT 58.735 33.333 0.00 0.00 0.00 3.60
2356 2999 4.152284 AGATGGATTCCGTTTCCTTACC 57.848 45.455 0.00 0.00 34.17 2.85
2367 3010 5.239963 TCCGTTTCCTTACCAAAGATCAAAC 59.760 40.000 0.00 0.00 34.37 2.93
2375 3018 7.176690 TCCTTACCAAAGATCAAACCATTTCTC 59.823 37.037 0.00 0.00 34.37 2.87
2380 3023 7.033791 CCAAAGATCAAACCATTTCTCAGATG 58.966 38.462 0.00 0.00 0.00 2.90
2381 3024 5.831702 AGATCAAACCATTTCTCAGATGC 57.168 39.130 0.00 0.00 0.00 3.91
2382 3025 5.507637 AGATCAAACCATTTCTCAGATGCT 58.492 37.500 0.00 0.00 0.00 3.79
2390 3033 6.479884 ACCATTTCTCAGATGCTAAACTCTT 58.520 36.000 0.00 0.00 0.00 2.85
2391 3034 6.597280 ACCATTTCTCAGATGCTAAACTCTTC 59.403 38.462 0.00 0.00 0.00 2.87
2392 3035 6.238049 CCATTTCTCAGATGCTAAACTCTTCG 60.238 42.308 0.00 0.00 0.00 3.79
2406 3049 7.905493 GCTAAACTCTTCGGAACATGAAAATAG 59.095 37.037 0.00 0.00 0.00 1.73
2410 3053 7.584987 ACTCTTCGGAACATGAAAATAGTTTG 58.415 34.615 0.00 0.00 0.00 2.93
2411 3054 6.378582 TCTTCGGAACATGAAAATAGTTTGC 58.621 36.000 0.00 0.00 0.00 3.68
2413 3056 5.938322 TCGGAACATGAAAATAGTTTGCTC 58.062 37.500 0.00 0.00 0.00 4.26
2414 3057 4.788100 CGGAACATGAAAATAGTTTGCTCG 59.212 41.667 0.00 0.00 0.00 5.03
2416 3059 5.569059 GGAACATGAAAATAGTTTGCTCGTG 59.431 40.000 0.00 0.00 0.00 4.35
2417 3060 4.475944 ACATGAAAATAGTTTGCTCGTGC 58.524 39.130 0.00 1.71 40.20 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.239217 TGTGGCTTCAATCATGTAGATACT 57.761 37.500 0.00 0.00 35.39 2.12
1 2 7.502120 AATGTGGCTTCAATCATGTAGATAC 57.498 36.000 0.00 0.00 35.39 2.24
3 4 9.445878 CTATAATGTGGCTTCAATCATGTAGAT 57.554 33.333 0.00 0.00 39.09 1.98
4 5 8.650490 TCTATAATGTGGCTTCAATCATGTAGA 58.350 33.333 0.00 0.00 0.00 2.59
5 6 8.837788 TCTATAATGTGGCTTCAATCATGTAG 57.162 34.615 0.00 0.00 0.00 2.74
7 8 9.970553 ATATCTATAATGTGGCTTCAATCATGT 57.029 29.630 0.00 0.00 0.00 3.21
14 15 9.929180 GAGTTGTATATCTATAATGTGGCTTCA 57.071 33.333 0.00 0.00 0.00 3.02
15 16 9.372369 GGAGTTGTATATCTATAATGTGGCTTC 57.628 37.037 0.00 0.00 0.00 3.86
16 17 8.880244 TGGAGTTGTATATCTATAATGTGGCTT 58.120 33.333 0.00 0.00 0.00 4.35
48 49 5.471116 TGGTGCTTCAATCATGTAGATATGC 59.529 40.000 0.00 0.00 35.39 3.14
190 193 2.806945 TGAAGGCCGAGATCCAAAAT 57.193 45.000 0.00 0.00 0.00 1.82
204 207 6.284891 TCAAAAATTTGGCCTCTATGAAGG 57.715 37.500 3.32 0.00 38.66 3.46
238 241 6.655003 CACCTCACATCCTTGTTTACTTGTAT 59.345 38.462 0.00 0.00 32.34 2.29
300 303 5.365403 TTGTCTTTTTATACAGGTTGCCG 57.635 39.130 0.00 0.00 0.00 5.69
304 307 9.927668 CCATGAATTTGTCTTTTTATACAGGTT 57.072 29.630 0.00 0.00 0.00 3.50
472 491 8.491605 AACGCAAAATGCAAAATTCATTAAAG 57.508 26.923 2.99 0.00 45.36 1.85
476 495 7.859598 TCTAAACGCAAAATGCAAAATTCATT 58.140 26.923 2.99 0.00 45.36 2.57
505 524 0.392998 GGAGGCCGAGCTTCATGAAA 60.393 55.000 9.88 0.00 36.34 2.69
507 526 1.552799 TTGGAGGCCGAGCTTCATGA 61.553 55.000 0.00 0.00 36.34 3.07
603 622 1.070758 CCCGATCCATCTTGGTACAGG 59.929 57.143 0.00 0.00 42.39 4.00
605 624 1.874129 ACCCGATCCATCTTGGTACA 58.126 50.000 0.00 0.00 39.03 2.90
606 625 3.203716 GAAACCCGATCCATCTTGGTAC 58.796 50.000 0.00 0.00 39.03 3.34
610 629 2.991250 AGTGAAACCCGATCCATCTTG 58.009 47.619 0.00 0.00 37.80 3.02
648 667 2.891936 TGCGCATGCCGTCATCTC 60.892 61.111 13.15 0.00 41.78 2.75
649 668 2.296814 TAGTGCGCATGCCGTCATCT 62.297 55.000 15.91 4.80 41.78 2.90
650 669 1.825285 CTAGTGCGCATGCCGTCATC 61.825 60.000 15.91 0.00 41.78 2.92
651 670 1.884464 CTAGTGCGCATGCCGTCAT 60.884 57.895 15.91 0.00 41.78 3.06
652 671 2.509111 CTAGTGCGCATGCCGTCA 60.509 61.111 15.91 4.92 41.78 4.35
653 672 2.509336 ACTAGTGCGCATGCCGTC 60.509 61.111 15.91 0.00 41.78 4.79
694 714 7.333528 TCAGCACTAGTTTGTGAAAGAAAAT 57.666 32.000 0.00 0.00 40.12 1.82
699 719 4.380531 TCCTCAGCACTAGTTTGTGAAAG 58.619 43.478 0.00 0.00 40.12 2.62
711 731 1.261480 AACACGATCTCCTCAGCACT 58.739 50.000 0.00 0.00 0.00 4.40
744 764 3.666797 CACGTAATTGCGCGTCAGATATA 59.333 43.478 16.17 0.00 39.48 0.86
753 774 2.384309 TGGGACACGTAATTGCGCG 61.384 57.895 16.17 9.21 34.88 6.86
828 850 1.134818 ACTCTGCTCACGTGTGTTCAA 60.135 47.619 16.51 0.00 0.00 2.69
886 908 2.500509 TGGTTGCAAAAAGTTAGCGG 57.499 45.000 0.00 0.00 0.00 5.52
1016 1038 2.622064 AATTGATGGTCCGCTACTCC 57.378 50.000 0.00 0.00 0.00 3.85
1017 1039 3.798202 AGAAATTGATGGTCCGCTACTC 58.202 45.455 0.00 0.00 0.00 2.59
1018 1040 3.914426 AGAAATTGATGGTCCGCTACT 57.086 42.857 0.00 0.00 0.00 2.57
1019 1041 3.495001 GCTAGAAATTGATGGTCCGCTAC 59.505 47.826 0.00 0.00 0.00 3.58
1020 1042 3.728845 GCTAGAAATTGATGGTCCGCTA 58.271 45.455 0.00 0.00 0.00 4.26
1021 1043 2.565841 GCTAGAAATTGATGGTCCGCT 58.434 47.619 0.00 0.00 0.00 5.52
1022 1044 1.261619 CGCTAGAAATTGATGGTCCGC 59.738 52.381 0.00 0.00 0.00 5.54
1023 1045 1.261619 GCGCTAGAAATTGATGGTCCG 59.738 52.381 0.00 0.00 0.00 4.79
1047 1073 4.635765 TGTTCGAAGTTTGATGGATGGATC 59.364 41.667 0.00 0.00 0.00 3.36
1068 1094 3.937706 GCTGTCAGATAGAATGCTTGTGT 59.062 43.478 3.32 0.00 0.00 3.72
1069 1095 4.190001 AGCTGTCAGATAGAATGCTTGTG 58.810 43.478 3.32 0.00 34.68 3.33
1070 1096 4.161942 AGAGCTGTCAGATAGAATGCTTGT 59.838 41.667 3.32 0.00 37.25 3.16
1091 1117 1.304962 TGAACCAGCCTCCGCTAGA 60.305 57.895 0.00 0.00 46.25 2.43
1097 1123 2.152016 GTTGTTACTGAACCAGCCTCC 58.848 52.381 0.00 0.00 34.37 4.30
1111 1137 1.334239 GCACGAACGCCATTGTTGTTA 60.334 47.619 0.00 0.00 30.75 2.41
1468 1494 3.636282 ATACTGCGACAACAAAAACCC 57.364 42.857 0.00 0.00 0.00 4.11
1517 1543 5.763444 ACTTCACATCGACGAACAAATAG 57.237 39.130 0.00 0.00 0.00 1.73
1535 1561 5.405873 GTGACCAAAACAGCTACTCTACTTC 59.594 44.000 0.00 0.00 0.00 3.01
1579 1605 6.531503 AAAGAGGAGTCAAGTTGATCGATA 57.468 37.500 9.18 0.00 0.00 2.92
1624 1650 1.133199 AGAGAAGATCGGAGGGAGCAT 60.133 52.381 0.00 0.00 32.03 3.79
1722 1759 7.372396 GCGGAGTTTGTAATAAATGATTGTACG 59.628 37.037 0.00 0.00 0.00 3.67
1734 1772 3.331150 CTGTGTGGCGGAGTTTGTAATA 58.669 45.455 0.00 0.00 0.00 0.98
1748 1786 2.669569 CTGTTCCGCCCTGTGTGG 60.670 66.667 0.00 0.00 46.66 4.17
1752 1790 0.400213 TTCATTCTGTTCCGCCCTGT 59.600 50.000 0.00 0.00 0.00 4.00
1755 1793 2.556622 TCTTTTTCATTCTGTTCCGCCC 59.443 45.455 0.00 0.00 0.00 6.13
1757 1795 6.420604 TGATTTTCTTTTTCATTCTGTTCCGC 59.579 34.615 0.00 0.00 0.00 5.54
1809 1847 0.625849 AATTTGGTGGCTCCCGAGAT 59.374 50.000 2.66 0.00 34.77 2.75
1810 1848 0.404040 AAATTTGGTGGCTCCCGAGA 59.596 50.000 2.66 0.00 34.77 4.04
1812 1850 1.531739 GCAAATTTGGTGGCTCCCGA 61.532 55.000 19.47 0.00 34.77 5.14
1813 1851 1.079888 GCAAATTTGGTGGCTCCCG 60.080 57.895 19.47 0.00 34.77 5.14
1814 1852 1.296392 GGCAAATTTGGTGGCTCCC 59.704 57.895 19.47 6.65 38.46 4.30
1815 1853 1.194121 AGGGCAAATTTGGTGGCTCC 61.194 55.000 19.47 10.46 41.14 4.70
1816 1854 0.037046 CAGGGCAAATTTGGTGGCTC 60.037 55.000 19.47 5.18 41.14 4.70
1817 1855 0.763986 ACAGGGCAAATTTGGTGGCT 60.764 50.000 19.47 0.00 41.14 4.75
1821 1862 3.242011 AGATCAACAGGGCAAATTTGGT 58.758 40.909 19.47 6.18 0.00 3.67
1823 1864 5.299148 TCAAAGATCAACAGGGCAAATTTG 58.701 37.500 14.03 14.03 0.00 2.32
1853 1897 9.582431 AATATCTCAAAGATGCTGTTGAATTTG 57.418 29.630 0.00 0.00 35.37 2.32
1861 1905 8.565896 TGTTGTAAATATCTCAAAGATGCTGT 57.434 30.769 0.00 0.00 35.37 4.40
1883 1927 6.211384 CCCTTGTTGATTTAAAGGAGGATGTT 59.789 38.462 2.25 0.00 42.65 2.71
1886 1930 6.152638 TCCCTTGTTGATTTAAAGGAGGAT 57.847 37.500 2.25 0.00 42.65 3.24
1887 1931 5.592587 TCCCTTGTTGATTTAAAGGAGGA 57.407 39.130 2.25 0.00 42.65 3.71
1891 1935 6.588719 TGTCATCCCTTGTTGATTTAAAGG 57.411 37.500 0.00 0.00 40.21 3.11
1910 1954 7.757941 TGGAAGAAATTGTATGAACATGTCA 57.242 32.000 0.00 0.00 41.67 3.58
1914 1958 7.092716 GTGCTTGGAAGAAATTGTATGAACAT 58.907 34.615 0.00 0.00 34.97 2.71
1918 1962 6.647334 TTGTGCTTGGAAGAAATTGTATGA 57.353 33.333 0.00 0.00 0.00 2.15
1927 1971 1.039856 GCCCTTTGTGCTTGGAAGAA 58.960 50.000 0.00 0.00 0.00 2.52
1937 1981 1.654220 CTCCGTTGTGCCCTTTGTG 59.346 57.895 0.00 0.00 0.00 3.33
1941 1985 1.228552 ATTGCTCCGTTGTGCCCTT 60.229 52.632 0.00 0.00 0.00 3.95
1945 1989 2.352503 AATTGATTGCTCCGTTGTGC 57.647 45.000 0.00 0.00 0.00 4.57
1946 1990 6.761731 TTAAAAATTGATTGCTCCGTTGTG 57.238 33.333 0.00 0.00 0.00 3.33
1947 1991 7.778470 TTTTAAAAATTGATTGCTCCGTTGT 57.222 28.000 0.00 0.00 0.00 3.32
1951 1995 9.956797 CTGTTATTTTAAAAATTGATTGCTCCG 57.043 29.630 4.44 0.00 0.00 4.63
1968 2012 9.871238 AATGACACTAGACGTATCTGTTATTTT 57.129 29.630 0.00 0.00 36.29 1.82
1969 2013 9.871238 AAATGACACTAGACGTATCTGTTATTT 57.129 29.630 13.48 13.48 36.29 1.40
1970 2014 9.517609 GAAATGACACTAGACGTATCTGTTATT 57.482 33.333 0.00 0.00 36.29 1.40
1971 2015 8.683615 TGAAATGACACTAGACGTATCTGTTAT 58.316 33.333 0.00 0.00 36.29 1.89
1972 2016 8.047413 TGAAATGACACTAGACGTATCTGTTA 57.953 34.615 0.00 0.00 36.29 2.41
1973 2017 6.920817 TGAAATGACACTAGACGTATCTGTT 58.079 36.000 0.00 0.00 36.29 3.16
1974 2018 6.510879 TGAAATGACACTAGACGTATCTGT 57.489 37.500 0.00 0.00 36.29 3.41
1975 2019 7.993821 ATTGAAATGACACTAGACGTATCTG 57.006 36.000 0.00 0.00 36.29 2.90
1979 2023 9.946165 CTGTATATTGAAATGACACTAGACGTA 57.054 33.333 0.00 0.00 0.00 3.57
1980 2024 7.921214 CCTGTATATTGAAATGACACTAGACGT 59.079 37.037 0.00 0.00 0.00 4.34
1981 2025 7.096023 GCCTGTATATTGAAATGACACTAGACG 60.096 40.741 0.00 0.00 0.00 4.18
1982 2026 7.171678 GGCCTGTATATTGAAATGACACTAGAC 59.828 40.741 0.00 0.00 0.00 2.59
1983 2027 7.217200 GGCCTGTATATTGAAATGACACTAGA 58.783 38.462 0.00 0.00 0.00 2.43
1984 2028 6.428159 GGGCCTGTATATTGAAATGACACTAG 59.572 42.308 0.84 0.00 0.00 2.57
1985 2029 6.296026 GGGCCTGTATATTGAAATGACACTA 58.704 40.000 0.84 0.00 0.00 2.74
1986 2030 5.133221 GGGCCTGTATATTGAAATGACACT 58.867 41.667 0.84 0.00 0.00 3.55
1987 2031 4.024048 CGGGCCTGTATATTGAAATGACAC 60.024 45.833 2.29 0.00 0.00 3.67
1988 2032 4.133820 CGGGCCTGTATATTGAAATGACA 58.866 43.478 2.29 0.00 0.00 3.58
1989 2033 3.502211 CCGGGCCTGTATATTGAAATGAC 59.498 47.826 11.58 0.00 0.00 3.06
1990 2034 3.750371 CCGGGCCTGTATATTGAAATGA 58.250 45.455 11.58 0.00 0.00 2.57
1991 2035 2.228822 GCCGGGCCTGTATATTGAAATG 59.771 50.000 11.58 0.00 0.00 2.32
1992 2036 2.158534 TGCCGGGCCTGTATATTGAAAT 60.159 45.455 17.97 0.00 0.00 2.17
1993 2037 1.213182 TGCCGGGCCTGTATATTGAAA 59.787 47.619 17.97 0.00 0.00 2.69
1994 2038 0.840617 TGCCGGGCCTGTATATTGAA 59.159 50.000 17.97 0.00 0.00 2.69
1995 2039 0.396435 CTGCCGGGCCTGTATATTGA 59.604 55.000 17.97 0.00 0.00 2.57
1996 2040 0.606401 CCTGCCGGGCCTGTATATTG 60.606 60.000 17.97 0.00 0.00 1.90
1997 2041 1.761174 CCTGCCGGGCCTGTATATT 59.239 57.895 17.97 0.00 0.00 1.28
1998 2042 2.224159 CCCTGCCGGGCCTGTATAT 61.224 63.158 17.97 0.00 45.33 0.86
1999 2043 2.847234 CCCTGCCGGGCCTGTATA 60.847 66.667 17.97 0.00 45.33 1.47
2008 2052 3.432051 CTTAGAGCGTCCCTGCCGG 62.432 68.421 0.00 0.00 34.65 6.13
2009 2053 2.105128 CTTAGAGCGTCCCTGCCG 59.895 66.667 0.00 0.00 34.65 5.69
2010 2054 0.036294 AAACTTAGAGCGTCCCTGCC 60.036 55.000 0.00 0.00 34.65 4.85
2011 2055 1.360820 GAAACTTAGAGCGTCCCTGC 58.639 55.000 0.00 0.00 0.00 4.85
2012 2056 1.630148 CGAAACTTAGAGCGTCCCTG 58.370 55.000 0.00 0.00 0.00 4.45
2013 2057 0.108756 GCGAAACTTAGAGCGTCCCT 60.109 55.000 0.00 0.00 0.00 4.20
2014 2058 0.108756 AGCGAAACTTAGAGCGTCCC 60.109 55.000 0.00 0.00 34.34 4.46
2015 2059 1.654602 GAAGCGAAACTTAGAGCGTCC 59.345 52.381 0.00 0.00 39.29 4.79
2016 2060 1.654602 GGAAGCGAAACTTAGAGCGTC 59.345 52.381 0.00 0.00 39.29 5.19
2017 2061 1.272769 AGGAAGCGAAACTTAGAGCGT 59.727 47.619 0.00 0.00 39.29 5.07
2018 2062 1.656095 CAGGAAGCGAAACTTAGAGCG 59.344 52.381 0.00 0.00 39.29 5.03
2019 2063 2.668945 GTCAGGAAGCGAAACTTAGAGC 59.331 50.000 0.00 0.00 39.29 4.09
2020 2064 3.675698 GTGTCAGGAAGCGAAACTTAGAG 59.324 47.826 0.00 0.00 39.29 2.43
2021 2065 3.321111 AGTGTCAGGAAGCGAAACTTAGA 59.679 43.478 0.00 0.00 39.29 2.10
2022 2066 3.654414 AGTGTCAGGAAGCGAAACTTAG 58.346 45.455 0.00 0.00 39.29 2.18
2023 2067 3.746045 AGTGTCAGGAAGCGAAACTTA 57.254 42.857 0.00 0.00 39.29 2.24
2024 2068 2.622064 AGTGTCAGGAAGCGAAACTT 57.378 45.000 0.00 0.00 42.98 2.66
2025 2069 3.963428 ATAGTGTCAGGAAGCGAAACT 57.037 42.857 0.00 0.00 35.15 2.66
2026 2070 5.358298 AAAATAGTGTCAGGAAGCGAAAC 57.642 39.130 0.00 0.00 0.00 2.78
2027 2071 7.499321 TTAAAAATAGTGTCAGGAAGCGAAA 57.501 32.000 0.00 0.00 0.00 3.46
2028 2072 7.499321 TTTAAAAATAGTGTCAGGAAGCGAA 57.501 32.000 0.00 0.00 0.00 4.70
2029 2073 7.499321 TTTTAAAAATAGTGTCAGGAAGCGA 57.501 32.000 0.00 0.00 0.00 4.93
2030 2074 8.020819 TCATTTTAAAAATAGTGTCAGGAAGCG 58.979 33.333 4.44 0.00 0.00 4.68
2031 2075 9.129209 GTCATTTTAAAAATAGTGTCAGGAAGC 57.871 33.333 4.44 0.00 0.00 3.86
2032 2076 9.329913 CGTCATTTTAAAAATAGTGTCAGGAAG 57.670 33.333 4.44 0.00 0.00 3.46
2033 2077 9.058174 TCGTCATTTTAAAAATAGTGTCAGGAA 57.942 29.630 4.44 0.00 0.00 3.36
2034 2078 8.610248 TCGTCATTTTAAAAATAGTGTCAGGA 57.390 30.769 4.44 0.00 0.00 3.86
2035 2079 9.840427 ATTCGTCATTTTAAAAATAGTGTCAGG 57.160 29.630 4.44 0.00 0.00 3.86
2057 2101 4.916870 TGGAATGACACTAGACGTATTCG 58.083 43.478 0.00 0.00 43.34 3.34
2059 2103 9.909644 GTATATTGGAATGACACTAGACGTATT 57.090 33.333 0.00 0.00 0.00 1.89
2060 2104 9.074576 TGTATATTGGAATGACACTAGACGTAT 57.925 33.333 0.00 0.00 0.00 3.06
2061 2105 8.454570 TGTATATTGGAATGACACTAGACGTA 57.545 34.615 0.00 0.00 0.00 3.57
2063 2107 6.863645 CCTGTATATTGGAATGACACTAGACG 59.136 42.308 0.00 0.00 0.00 4.18
2073 2117 3.074412 GTCGGGCCTGTATATTGGAATG 58.926 50.000 12.43 0.00 0.00 2.67
2074 2118 2.708861 TGTCGGGCCTGTATATTGGAAT 59.291 45.455 12.43 0.00 0.00 3.01
2076 2120 1.691976 CTGTCGGGCCTGTATATTGGA 59.308 52.381 12.43 0.00 0.00 3.53
2078 2122 3.469008 TTCTGTCGGGCCTGTATATTG 57.531 47.619 12.43 0.00 0.00 1.90
2089 2133 1.067776 ACTTAGAGCGTTTCTGTCGGG 60.068 52.381 2.37 0.00 36.61 5.14
2094 2138 2.731976 AGCGAAACTTAGAGCGTTTCTG 59.268 45.455 12.15 7.97 44.88 3.02
2097 2141 3.808174 AGAAAGCGAAACTTAGAGCGTTT 59.192 39.130 0.00 0.00 37.75 3.60
2108 2152 4.625742 TGCTATAGTGTCAGAAAGCGAAAC 59.374 41.667 0.84 0.00 32.67 2.78
2111 2155 4.174009 GTTGCTATAGTGTCAGAAAGCGA 58.826 43.478 0.84 0.00 32.67 4.93
2117 2161 8.941995 ATATAAGAGGTTGCTATAGTGTCAGA 57.058 34.615 0.84 0.00 0.00 3.27
2123 2168 9.476928 ACCGATTATATAAGAGGTTGCTATAGT 57.523 33.333 15.18 0.00 0.00 2.12
2172 2738 0.396974 TATTCATTGGCAGCCCCCAC 60.397 55.000 9.64 0.00 33.82 4.61
2202 2845 6.863126 GGAATTTCAGCCGACCATTAATATTG 59.137 38.462 0.00 0.00 0.00 1.90
2213 2856 1.087501 GAGGTGGAATTTCAGCCGAC 58.912 55.000 12.38 1.45 35.93 4.79
2215 2858 1.089920 CAGAGGTGGAATTTCAGCCG 58.910 55.000 12.38 0.00 35.93 5.52
2216 2859 0.813821 GCAGAGGTGGAATTTCAGCC 59.186 55.000 12.38 4.92 35.93 4.85
2226 2869 3.618690 AGTAAAGCTAAGCAGAGGTGG 57.381 47.619 0.00 0.00 0.00 4.61
2229 2872 5.735766 AGGTAAAGTAAAGCTAAGCAGAGG 58.264 41.667 0.00 0.00 0.00 3.69
2233 2876 8.241367 GCAATAAAGGTAAAGTAAAGCTAAGCA 58.759 33.333 0.00 0.00 0.00 3.91
2234 2877 8.241367 TGCAATAAAGGTAAAGTAAAGCTAAGC 58.759 33.333 0.00 0.00 0.00 3.09
2238 2881 7.519032 TGTGCAATAAAGGTAAAGTAAAGCT 57.481 32.000 0.00 0.00 0.00 3.74
2239 2882 8.244113 AGATGTGCAATAAAGGTAAAGTAAAGC 58.756 33.333 0.00 0.00 0.00 3.51
2242 2885 9.290988 TGAAGATGTGCAATAAAGGTAAAGTAA 57.709 29.630 0.00 0.00 0.00 2.24
2244 2887 7.230510 TGTGAAGATGTGCAATAAAGGTAAAGT 59.769 33.333 0.00 0.00 0.00 2.66
2245 2888 7.592938 TGTGAAGATGTGCAATAAAGGTAAAG 58.407 34.615 0.00 0.00 0.00 1.85
2248 2891 6.404623 GCATGTGAAGATGTGCAATAAAGGTA 60.405 38.462 0.00 0.00 37.52 3.08
2249 2892 5.622914 GCATGTGAAGATGTGCAATAAAGGT 60.623 40.000 0.00 0.00 37.52 3.50
2250 2893 4.802039 GCATGTGAAGATGTGCAATAAAGG 59.198 41.667 0.00 0.00 37.52 3.11
2251 2894 5.404096 TGCATGTGAAGATGTGCAATAAAG 58.596 37.500 0.00 0.00 43.83 1.85
2252 2895 5.388408 TGCATGTGAAGATGTGCAATAAA 57.612 34.783 0.00 0.00 43.83 1.40
2257 2900 3.945981 AATTGCATGTGAAGATGTGCA 57.054 38.095 0.00 0.00 44.97 4.57
2258 2901 4.266976 GCTAAATTGCATGTGAAGATGTGC 59.733 41.667 0.00 0.00 38.05 4.57
2259 2902 5.404096 TGCTAAATTGCATGTGAAGATGTG 58.596 37.500 0.00 0.00 38.12 3.21
2260 2903 5.648178 TGCTAAATTGCATGTGAAGATGT 57.352 34.783 0.00 0.00 38.12 3.06
2286 2929 8.675504 ACTTTATTGAGCATCTTTCTCATCTTG 58.324 33.333 0.00 0.00 39.96 3.02
2310 2953 9.141400 CTTAGACTTAATGAGCTTCGTAAAACT 57.859 33.333 0.00 0.00 0.00 2.66
2311 2954 9.136952 TCTTAGACTTAATGAGCTTCGTAAAAC 57.863 33.333 0.00 0.00 0.00 2.43
2314 2957 7.921214 CCATCTTAGACTTAATGAGCTTCGTAA 59.079 37.037 0.00 0.00 0.00 3.18
2326 2969 7.046033 GGAAACGGAATCCATCTTAGACTTAA 58.954 38.462 0.00 0.00 36.92 1.85
2328 2971 5.189934 AGGAAACGGAATCCATCTTAGACTT 59.810 40.000 0.00 0.00 39.55 3.01
2331 2974 5.693769 AAGGAAACGGAATCCATCTTAGA 57.306 39.130 0.00 0.00 39.55 2.10
2334 2977 4.018779 TGGTAAGGAAACGGAATCCATCTT 60.019 41.667 0.00 0.00 39.55 2.40
2344 2987 5.458015 GTTTGATCTTTGGTAAGGAAACGG 58.542 41.667 0.00 0.00 32.02 4.44
2345 2988 5.009210 TGGTTTGATCTTTGGTAAGGAAACG 59.991 40.000 0.00 0.00 32.30 3.60
2349 2992 7.010160 AGAAATGGTTTGATCTTTGGTAAGGA 58.990 34.615 0.00 0.00 32.02 3.36
2356 2999 6.530534 GCATCTGAGAAATGGTTTGATCTTTG 59.469 38.462 0.00 0.00 0.00 2.77
2367 3010 6.238049 CGAAGAGTTTAGCATCTGAGAAATGG 60.238 42.308 0.00 0.00 0.00 3.16
2375 3018 4.245660 TGTTCCGAAGAGTTTAGCATCTG 58.754 43.478 0.00 0.00 0.00 2.90
2380 3023 5.607119 TTTCATGTTCCGAAGAGTTTAGC 57.393 39.130 0.00 0.00 0.00 3.09
2381 3024 8.936864 ACTATTTTCATGTTCCGAAGAGTTTAG 58.063 33.333 0.00 0.00 0.00 1.85
2382 3025 8.842358 ACTATTTTCATGTTCCGAAGAGTTTA 57.158 30.769 0.00 0.00 0.00 2.01
2390 3033 5.390461 CGAGCAAACTATTTTCATGTTCCGA 60.390 40.000 0.00 0.00 0.00 4.55
2391 3034 4.788100 CGAGCAAACTATTTTCATGTTCCG 59.212 41.667 0.00 0.00 0.00 4.30
2392 3035 5.569059 CACGAGCAAACTATTTTCATGTTCC 59.431 40.000 0.00 0.00 0.00 3.62
2413 3056 8.150279 ATTGGATCAATTAAATTCGTCTGCACG 61.150 37.037 0.00 0.00 37.86 5.34
2414 3057 5.879237 TGGATCAATTAAATTCGTCTGCAC 58.121 37.500 0.00 0.00 0.00 4.57
2416 3059 9.515020 TTTATTGGATCAATTAAATTCGTCTGC 57.485 29.630 0.00 0.00 35.54 4.26


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

AutoCloner maintained by Alex Coulton.