Multiple sequence alignment - TraesCS2D01G526000

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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 TraesCS2D01G526000 chr2D 100.000 3513 0 0 1 3513 614650505 614646993 0.000000e+00 6488.0
1 TraesCS2D01G526000 chr2B 90.041 2450 200 21 1 2436 749033261 749030842 0.000000e+00 3133.0
2 TraesCS2D01G526000 chr2B 80.155 776 76 36 2437 3184 749030809 749030084 3.130000e-140 508.0
3 TraesCS2D01G526000 chr2B 90.688 247 13 4 3207 3449 749030093 749029853 1.570000e-83 320.0
4 TraesCS2D01G526000 chr2B 87.879 66 7 1 3449 3513 749029828 749029763 3.760000e-10 76.8
5 TraesCS2D01G526000 chr2A 89.837 2450 210 21 1 2436 745044815 745042391 0.000000e+00 3109.0
6 TraesCS2D01G526000 chr2A 91.538 520 30 10 2984 3492 745041759 745041243 0.000000e+00 704.0
7 TraesCS2D01G526000 chr2A 85.687 517 55 12 2439 2946 745042356 745041850 8.640000e-146 527.0


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 TraesCS2D01G526000 chr2D 614646993 614650505 3512 True 6488.000000 6488 100.000000 1 3513 1 chr2D.!!$R1 3512
1 TraesCS2D01G526000 chr2B 749029763 749033261 3498 True 1009.450000 3133 87.190750 1 3513 4 chr2B.!!$R1 3512
2 TraesCS2D01G526000 chr2A 745041243 745044815 3572 True 1446.666667 3109 89.020667 1 3492 3 chr2A.!!$R1 3491

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
36 39 1.270550 CAACTTTCTGGACCATGGTGC 59.729 52.381 28.15 28.15 36.97 5.01 F
231 234 1.539827 CCACTGGGTCGTTTGATTTCC 59.460 52.381 0.00 0.00 0.00 3.13 F
1175 1188 0.036306 ATCCGTTTGGGTGTCTGTCC 59.964 55.000 0.00 0.00 37.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1159 0.179000 CCAAACGGATCTCCCTCCTG 59.821 60.0 0.0 0.0 32.77 3.86 R
1932 1945 0.179020 TGTGGACAAAGTGCTGGAGG 60.179 55.0 0.0 0.0 0.00 4.30 R
2986 3122 0.245539 TCAGTTCGATCCAACCGTCC 59.754 55.0 0.0 0.0 0.00 4.79 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
36 39 1.270550 CAACTTTCTGGACCATGGTGC 59.729 52.381 28.15 28.15 36.97 5.01
52 55 1.997311 TGCAGTGGCTCCTATGGCT 60.997 57.895 0.00 0.00 41.91 4.75
72 75 5.123227 GGCTAGTACCAGCATGTCATTTTA 58.877 41.667 15.30 0.00 43.67 1.52
73 76 5.007724 GGCTAGTACCAGCATGTCATTTTAC 59.992 44.000 15.30 0.00 43.67 2.01
78 81 7.165485 AGTACCAGCATGTCATTTTACTGTTA 58.835 34.615 0.00 0.00 0.00 2.41
99 102 1.645710 GATGGGGATATGGGTCTCGT 58.354 55.000 0.00 0.00 0.00 4.18
122 125 2.564947 AGGAGAGGATCGATGGCATTAC 59.435 50.000 0.54 0.00 42.67 1.89
208 211 5.772393 ATAGTATGTGGAGTTTGTCCCAA 57.228 39.130 0.00 0.00 46.31 4.12
211 214 5.010282 AGTATGTGGAGTTTGTCCCAATTC 58.990 41.667 0.00 0.00 46.31 2.17
231 234 1.539827 CCACTGGGTCGTTTGATTTCC 59.460 52.381 0.00 0.00 0.00 3.13
258 261 2.134933 CGCCCTCTCTTAGACCCCC 61.135 68.421 0.00 0.00 0.00 5.40
261 264 1.977202 GCCCTCTCTTAGACCCCCATT 60.977 57.143 0.00 0.00 0.00 3.16
263 266 2.629639 CCCTCTCTTAGACCCCCATTGA 60.630 54.545 0.00 0.00 0.00 2.57
279 282 6.099557 CCCCCATTGAATTTAGAAGCCATTAA 59.900 38.462 0.00 0.00 0.00 1.40
321 324 7.551617 ACAAAATATACTCTTAAGGTTGTCGGG 59.448 37.037 1.85 0.00 0.00 5.14
336 339 3.595173 TGTCGGGACACACATAAGATTG 58.405 45.455 0.00 0.00 36.21 2.67
366 369 9.887629 TTTTACCAAATATCATGCAATTGACAT 57.112 25.926 10.34 9.43 0.00 3.06
491 497 8.668510 ATGCATACTAAAAAGACATGTCCTAG 57.331 34.615 22.21 17.92 0.00 3.02
538 544 5.525378 GTGAGACTAAATGTATTCCTGCCTG 59.475 44.000 0.00 0.00 0.00 4.85
545 551 8.275040 ACTAAATGTATTCCTGCCTGTTAAGAT 58.725 33.333 0.00 0.00 0.00 2.40
635 641 5.018809 ACCAAATCCCTAACTCGTACTGTA 58.981 41.667 0.00 0.00 0.00 2.74
642 648 6.051717 TCCCTAACTCGTACTGTAGATGTAC 58.948 44.000 0.00 0.00 37.50 2.90
649 655 8.327941 ACTCGTACTGTAGATGTACTTGTAAA 57.672 34.615 1.30 0.00 38.39 2.01
693 699 7.850982 GGATAAACACTATGACGTGCATTTAAG 59.149 37.037 0.00 0.00 38.45 1.85
702 708 6.804534 TGACGTGCATTTAAGAAAAGTTTG 57.195 33.333 0.00 0.00 0.00 2.93
711 717 9.255304 GCATTTAAGAAAAGTTTGTTGGATGTA 57.745 29.630 0.00 0.00 0.00 2.29
1032 1045 3.500289 GGAGCTCATCCTCACCTATCTCT 60.500 52.174 17.19 0.00 45.64 3.10
1110 1123 2.012673 CCTTGTAGCTTGCCATCTGTC 58.987 52.381 0.00 0.00 0.00 3.51
1120 1133 5.047847 GCTTGCCATCTGTCGTAATAAGTA 58.952 41.667 0.00 0.00 0.00 2.24
1132 1145 6.207221 TGTCGTAATAAGTACTCCAGTTGTCA 59.793 38.462 0.00 0.00 0.00 3.58
1146 1159 4.380867 CCAGTTGTCATTTTGAGTATGCCC 60.381 45.833 0.00 0.00 0.00 5.36
1175 1188 0.036306 ATCCGTTTGGGTGTCTGTCC 59.964 55.000 0.00 0.00 37.00 4.02
1182 1195 1.517832 GGGTGTCTGTCCCATCGAG 59.482 63.158 0.00 0.00 44.05 4.04
1200 1213 2.244651 GGACGACAAACAGCGCAGT 61.245 57.895 11.47 4.25 0.00 4.40
1239 1252 3.183754 ACGTGCTGGTTTGTTTAAAAGC 58.816 40.909 0.00 1.20 32.69 3.51
1277 1290 1.524961 TCACTGGCGTGAAGGTTGT 59.475 52.632 9.19 0.00 46.61 3.32
1287 1300 3.199677 CGTGAAGGTTGTTGTTGTCCTA 58.800 45.455 0.00 0.00 0.00 2.94
1335 1348 2.818274 GGGACGCCATCGGTGAAC 60.818 66.667 0.00 0.00 40.69 3.18
1362 1375 8.133627 CCTATTATTGATGCTTTCTTGTCAAGG 58.866 37.037 12.66 0.00 34.45 3.61
1374 1387 5.779241 TCTTGTCAAGGGATCCACTTATT 57.221 39.130 15.23 0.00 0.00 1.40
1453 1466 3.391296 GGCTAGGTTGGACATGGAGAATA 59.609 47.826 0.00 0.00 0.00 1.75
1456 1469 4.494091 AGGTTGGACATGGAGAATACAG 57.506 45.455 0.00 0.00 0.00 2.74
1526 1539 0.251787 GCTGAAAACCCAGGGATGGT 60.252 55.000 14.54 0.00 37.85 3.55
1542 1555 6.268387 CAGGGATGGTGGCAAATAATATCTTT 59.732 38.462 0.00 0.00 0.00 2.52
1545 1558 6.863126 GGATGGTGGCAAATAATATCTTTTCG 59.137 38.462 0.00 0.00 0.00 3.46
1566 1579 4.528596 TCGAGGGAAAAAGATCTCAGTCTT 59.471 41.667 0.00 0.00 40.05 3.01
1568 1581 4.916183 AGGGAAAAAGATCTCAGTCTTGG 58.084 43.478 0.00 0.00 38.41 3.61
1581 1594 4.411013 TCAGTCTTGGAGATCTCAACAGA 58.589 43.478 23.85 17.05 0.00 3.41
1603 1616 3.244215 ACTCTTCAATGACCTCTTGCGAA 60.244 43.478 0.00 0.00 0.00 4.70
1626 1639 3.704566 TCAAGGAGCATATTAGACACCGT 59.295 43.478 0.00 0.00 0.00 4.83
1633 1646 3.679980 GCATATTAGACACCGTATGCCTG 59.320 47.826 5.19 0.00 42.06 4.85
1670 1683 4.567537 CCATGAAATAAGGACTGGTGGTCA 60.568 45.833 0.00 0.00 46.16 4.02
1674 1687 5.300792 TGAAATAAGGACTGGTGGTCAAAAC 59.699 40.000 0.00 0.00 46.16 2.43
1685 1698 2.926838 GTGGTCAAAACGTGCAACAAAT 59.073 40.909 0.00 0.00 35.74 2.32
1713 1726 0.770499 TGCCAAGAGGTCCATCACAA 59.230 50.000 0.00 0.00 37.19 3.33
1733 1746 4.460731 ACAAGATCACTCGAAGACTCATCA 59.539 41.667 0.00 0.00 0.00 3.07
1734 1747 5.047731 ACAAGATCACTCGAAGACTCATCAA 60.048 40.000 0.00 0.00 0.00 2.57
1737 1750 1.916651 CACTCGAAGACTCATCAAGCG 59.083 52.381 0.00 0.00 0.00 4.68
1741 1754 2.164422 TCGAAGACTCATCAAGCGTCAT 59.836 45.455 0.00 0.00 34.40 3.06
1743 1756 3.241900 CGAAGACTCATCAAGCGTCATTG 60.242 47.826 0.00 0.00 34.40 2.82
1747 1760 2.095567 ACTCATCAAGCGTCATTGCAAC 60.096 45.455 0.00 0.00 37.31 4.17
1750 1763 1.246649 TCAAGCGTCATTGCAACCAT 58.753 45.000 0.00 0.00 37.31 3.55
1752 1765 1.068402 CAAGCGTCATTGCAACCATCA 60.068 47.619 0.00 0.00 37.31 3.07
1760 1773 3.562557 TCATTGCAACCATCATCATCTCG 59.437 43.478 0.00 0.00 0.00 4.04
1763 1776 0.863799 CAACCATCATCATCTCGCCG 59.136 55.000 0.00 0.00 0.00 6.46
1765 1778 0.465705 ACCATCATCATCTCGCCGTT 59.534 50.000 0.00 0.00 0.00 4.44
1768 1781 2.355756 CCATCATCATCTCGCCGTTTTT 59.644 45.455 0.00 0.00 0.00 1.94
1817 1830 1.110442 CCACCAACACCACAACACAT 58.890 50.000 0.00 0.00 0.00 3.21
1823 1836 3.305950 CCAACACCACAACACATTATGGG 60.306 47.826 0.00 0.00 36.47 4.00
1826 1839 2.161410 CACCACAACACATTATGGGACG 59.839 50.000 0.00 0.00 36.47 4.79
1861 1874 2.567169 CAGGTACCACAGATGTTCCAGA 59.433 50.000 15.94 0.00 0.00 3.86
1865 1878 0.692476 CCACAGATGTTCCAGACCCA 59.308 55.000 0.00 0.00 0.00 4.51
1881 1894 1.586028 CCAACCATCACCTTTGGCG 59.414 57.895 0.00 0.00 37.81 5.69
1883 1896 2.275380 AACCATCACCTTTGGCGCC 61.275 57.895 22.73 22.73 37.81 6.53
1903 1916 0.463833 CCGGTTGAGGTCCCTTATGC 60.464 60.000 0.00 0.00 0.00 3.14
1932 1945 9.007901 CCAATTCCTCATCAGGTATAAGATTTC 57.992 37.037 0.00 0.00 41.28 2.17
1938 1951 7.308450 TCATCAGGTATAAGATTTCCTCCAG 57.692 40.000 0.00 0.00 0.00 3.86
1951 1964 0.179020 CCTCCAGCACTTTGTCCACA 60.179 55.000 0.00 0.00 0.00 4.17
1961 1974 4.497507 GCACTTTGTCCACACCTTTAGAAC 60.498 45.833 0.00 0.00 0.00 3.01
1971 1984 5.106555 CCACACCTTTAGAACTATGCAAGTG 60.107 44.000 0.00 0.00 38.88 3.16
1974 1987 5.874810 CACCTTTAGAACTATGCAAGTGCTA 59.125 40.000 10.84 10.84 42.92 3.49
2016 2030 3.343941 TTCCTATGCAGGTACCACAAC 57.656 47.619 15.94 0.34 43.18 3.32
2018 2032 3.715287 TCCTATGCAGGTACCACAACTA 58.285 45.455 15.94 1.77 43.18 2.24
2038 2052 0.106918 TTTCAGTCCACACCACCACC 60.107 55.000 0.00 0.00 0.00 4.61
2039 2053 0.986019 TTCAGTCCACACCACCACCT 60.986 55.000 0.00 0.00 0.00 4.00
2040 2054 1.071471 CAGTCCACACCACCACCTC 59.929 63.158 0.00 0.00 0.00 3.85
2041 2055 2.147387 AGTCCACACCACCACCTCC 61.147 63.158 0.00 0.00 0.00 4.30
2042 2056 2.040359 TCCACACCACCACCTCCA 60.040 61.111 0.00 0.00 0.00 3.86
2043 2057 2.113139 CCACACCACCACCTCCAC 59.887 66.667 0.00 0.00 0.00 4.02
2046 2060 2.147387 ACACCACCACCTCCACCTC 61.147 63.158 0.00 0.00 0.00 3.85
2056 2070 3.273654 TCCACCTCCGACTCCCCT 61.274 66.667 0.00 0.00 0.00 4.79
2057 2071 3.077556 CCACCTCCGACTCCCCTG 61.078 72.222 0.00 0.00 0.00 4.45
2069 2083 1.856873 TCCCCTGTTGGCATCCCTT 60.857 57.895 0.00 0.00 0.00 3.95
2077 2091 2.375174 TGTTGGCATCCCTTCTACAACT 59.625 45.455 0.00 0.00 39.03 3.16
2110 2124 2.574824 AGGTACATGGTTTACCTCCACC 59.425 50.000 7.53 3.12 45.30 4.61
2121 2135 2.528818 CCTCCACCACCTCAGCCAA 61.529 63.158 0.00 0.00 0.00 4.52
2127 2141 1.338020 CACCACCTCAGCCAAAACTTC 59.662 52.381 0.00 0.00 0.00 3.01
2153 2167 6.711277 AGAATATGCAAGTCCTTACAAGACA 58.289 36.000 0.00 0.00 36.68 3.41
2155 2169 7.665559 AGAATATGCAAGTCCTTACAAGACAAA 59.334 33.333 0.00 0.00 36.68 2.83
2156 2170 5.695851 ATGCAAGTCCTTACAAGACAAAG 57.304 39.130 0.00 0.00 36.68 2.77
2189 2203 5.071788 ACAGAACAAGACAATCCCTAACTCA 59.928 40.000 0.00 0.00 0.00 3.41
2190 2204 5.997746 CAGAACAAGACAATCCCTAACTCAA 59.002 40.000 0.00 0.00 0.00 3.02
2191 2205 6.656693 CAGAACAAGACAATCCCTAACTCAAT 59.343 38.462 0.00 0.00 0.00 2.57
2192 2206 6.881602 AGAACAAGACAATCCCTAACTCAATC 59.118 38.462 0.00 0.00 0.00 2.67
2194 2208 5.178797 CAAGACAATCCCTAACTCAATCGT 58.821 41.667 0.00 0.00 0.00 3.73
2195 2209 5.422214 AGACAATCCCTAACTCAATCGTT 57.578 39.130 0.00 0.00 0.00 3.85
2196 2210 5.178797 AGACAATCCCTAACTCAATCGTTG 58.821 41.667 0.00 0.00 0.00 4.10
2209 2223 4.311606 TCAATCGTTGAGAACATTTCGGA 58.688 39.130 0.00 0.00 34.08 4.55
2210 2224 4.388773 TCAATCGTTGAGAACATTTCGGAG 59.611 41.667 0.00 0.00 34.08 4.63
2211 2225 2.683968 TCGTTGAGAACATTTCGGAGG 58.316 47.619 0.00 0.00 34.02 4.30
2212 2226 1.128692 CGTTGAGAACATTTCGGAGGC 59.871 52.381 0.00 0.00 34.02 4.70
2213 2227 2.151202 GTTGAGAACATTTCGGAGGCA 58.849 47.619 0.00 0.00 34.02 4.75
2214 2228 2.749621 GTTGAGAACATTTCGGAGGCAT 59.250 45.455 0.00 0.00 34.02 4.40
2216 2230 1.943340 GAGAACATTTCGGAGGCATCC 59.057 52.381 7.52 7.52 42.81 3.51
2217 2231 1.025041 GAACATTTCGGAGGCATCCC 58.975 55.000 12.67 0.00 43.39 3.85
2221 2235 2.608970 ATTTCGGAGGCATCCCCACG 62.609 60.000 12.67 0.00 43.39 4.94
2224 2238 3.728373 GGAGGCATCCCCACGGTT 61.728 66.667 5.99 0.00 40.03 4.44
2225 2239 2.124695 GAGGCATCCCCACGGTTC 60.125 66.667 0.00 0.00 35.39 3.62
2226 2240 2.610859 AGGCATCCCCACGGTTCT 60.611 61.111 0.00 0.00 35.39 3.01
2227 2241 2.198304 GAGGCATCCCCACGGTTCTT 62.198 60.000 0.00 0.00 35.39 2.52
2228 2242 1.304134 GGCATCCCCACGGTTCTTT 60.304 57.895 0.00 0.00 0.00 2.52
2229 2243 0.898326 GGCATCCCCACGGTTCTTTT 60.898 55.000 0.00 0.00 0.00 2.27
2230 2244 0.526211 GCATCCCCACGGTTCTTTTC 59.474 55.000 0.00 0.00 0.00 2.29
2231 2245 1.904287 CATCCCCACGGTTCTTTTCA 58.096 50.000 0.00 0.00 0.00 2.69
2232 2246 2.446435 CATCCCCACGGTTCTTTTCAT 58.554 47.619 0.00 0.00 0.00 2.57
2233 2247 2.194201 TCCCCACGGTTCTTTTCATC 57.806 50.000 0.00 0.00 0.00 2.92
2234 2248 1.173913 CCCCACGGTTCTTTTCATCC 58.826 55.000 0.00 0.00 0.00 3.51
2235 2249 0.802494 CCCACGGTTCTTTTCATCCG 59.198 55.000 0.00 0.00 46.98 4.18
2236 2250 0.802494 CCACGGTTCTTTTCATCCGG 59.198 55.000 0.00 0.00 46.06 5.14
2241 2255 1.243902 GTTCTTTTCATCCGGTGGCA 58.756 50.000 0.00 0.00 0.00 4.92
2248 2262 3.507162 TTCATCCGGTGGCAATGATAT 57.493 42.857 0.00 0.00 30.03 1.63
2252 2266 2.329267 TCCGGTGGCAATGATATCTCT 58.671 47.619 0.00 0.00 0.00 3.10
2278 2292 3.249189 TCCTTTGGACCAGGCGCT 61.249 61.111 7.64 0.00 0.00 5.92
2293 2307 2.092968 AGGCGCTCTACAATGAAATCCA 60.093 45.455 7.64 0.00 0.00 3.41
2317 2331 3.555966 GGATGGATTCTTACTTGGGGTG 58.444 50.000 0.00 0.00 0.00 4.61
2318 2332 2.507407 TGGATTCTTACTTGGGGTGC 57.493 50.000 0.00 0.00 0.00 5.01
2322 2336 4.017958 TGGATTCTTACTTGGGGTGCAATA 60.018 41.667 0.00 0.00 0.00 1.90
2357 2371 3.880490 GCCAATATAACATGGGACGTGAA 59.120 43.478 0.00 0.00 37.19 3.18
2388 2402 0.681733 TGCACCACCAGAGTCTTCTC 59.318 55.000 0.00 0.00 40.70 2.87
2390 2404 0.389166 CACCACCAGAGTCTTCTCGC 60.389 60.000 0.00 0.00 44.65 5.03
2401 2415 1.111277 TCTTCTCGCGGGAATGATGA 58.889 50.000 23.81 13.25 0.00 2.92
2441 2487 3.447586 TCGGAGGACATCTTTAGTCAAGG 59.552 47.826 0.00 0.00 37.74 3.61
2481 2527 2.549754 CCATTAGGTGCCATTGTCGATC 59.450 50.000 0.00 0.00 0.00 3.69
2487 2533 2.223641 GGTGCCATTGTCGATCGTACTA 60.224 50.000 15.94 9.31 0.00 1.82
2511 2558 3.120321 TGTTAAGCTTCTTCGAGGCAA 57.880 42.857 0.00 0.00 37.11 4.52
2528 2576 6.806249 TCGAGGCAAAATAAACATTTCATGTC 59.194 34.615 0.00 0.00 44.07 3.06
2529 2577 6.808212 CGAGGCAAAATAAACATTTCATGTCT 59.192 34.615 0.00 0.00 44.07 3.41
2571 2619 9.827411 GAACTTTGTTTCTGTATGACTAATTCC 57.173 33.333 0.00 0.00 0.00 3.01
2572 2620 8.918202 ACTTTGTTTCTGTATGACTAATTCCA 57.082 30.769 0.00 0.00 0.00 3.53
2585 2633 6.186957 TGACTAATTCCATGTAATGCTTGGT 58.813 36.000 3.45 0.00 44.97 3.67
2594 2642 6.072175 TCCATGTAATGCTTGGTGTTCTTTAC 60.072 38.462 3.45 0.00 44.97 2.01
2596 2644 6.312399 TGTAATGCTTGGTGTTCTTTACTG 57.688 37.500 0.00 0.00 0.00 2.74
2603 2651 6.995686 TGCTTGGTGTTCTTTACTGAGATTAA 59.004 34.615 0.00 0.00 0.00 1.40
2604 2652 7.173218 TGCTTGGTGTTCTTTACTGAGATTAAG 59.827 37.037 0.00 0.00 0.00 1.85
2605 2653 7.173390 GCTTGGTGTTCTTTACTGAGATTAAGT 59.827 37.037 0.00 0.00 0.00 2.24
2670 2720 4.436242 TTGCTTTCTCTATCGACGAACT 57.564 40.909 0.00 0.00 0.00 3.01
2683 2733 3.252701 TCGACGAACTAGAGGAATATGCC 59.747 47.826 0.00 0.00 0.00 4.40
2720 2773 9.946165 AGTTATTTTAAACTTCAGTAGCACAAC 57.054 29.630 0.00 0.00 36.26 3.32
2734 2787 7.027161 CAGTAGCACAACCCAAACATTATTAC 58.973 38.462 0.00 0.00 0.00 1.89
2735 2788 5.054390 AGCACAACCCAAACATTATTACG 57.946 39.130 0.00 0.00 0.00 3.18
2737 2790 5.706369 AGCACAACCCAAACATTATTACGTA 59.294 36.000 0.00 0.00 0.00 3.57
2739 2792 7.030768 GCACAACCCAAACATTATTACGTAAT 58.969 34.615 23.36 23.36 33.23 1.89
2740 2793 7.542824 GCACAACCCAAACATTATTACGTAATT 59.457 33.333 24.81 6.40 30.53 1.40
2741 2794 9.068008 CACAACCCAAACATTATTACGTAATTC 57.932 33.333 24.81 0.00 30.53 2.17
2742 2795 7.964011 ACAACCCAAACATTATTACGTAATTCG 59.036 33.333 24.81 15.62 46.00 3.34
2743 2796 7.018635 ACCCAAACATTATTACGTAATTCGG 57.981 36.000 24.81 16.08 44.69 4.30
2744 2797 6.822676 ACCCAAACATTATTACGTAATTCGGA 59.177 34.615 24.81 5.29 44.69 4.55
2745 2798 7.499895 ACCCAAACATTATTACGTAATTCGGAT 59.500 33.333 24.81 11.82 44.69 4.18
2746 2799 8.991026 CCCAAACATTATTACGTAATTCGGATA 58.009 33.333 24.81 4.17 44.69 2.59
2750 2803 9.985730 AACATTATTACGTAATTCGGATAAGGA 57.014 29.630 24.81 1.24 44.69 3.36
2751 2804 9.415544 ACATTATTACGTAATTCGGATAAGGAC 57.584 33.333 24.81 0.00 44.69 3.85
2752 2805 9.414295 CATTATTACGTAATTCGGATAAGGACA 57.586 33.333 24.81 0.52 44.69 4.02
2754 2807 7.884816 ATTACGTAATTCGGATAAGGACATG 57.115 36.000 15.07 0.00 44.69 3.21
2755 2808 5.524971 ACGTAATTCGGATAAGGACATGA 57.475 39.130 0.00 0.00 44.69 3.07
2756 2809 5.529791 ACGTAATTCGGATAAGGACATGAG 58.470 41.667 0.00 0.00 44.69 2.90
2757 2810 5.301045 ACGTAATTCGGATAAGGACATGAGA 59.699 40.000 0.00 0.00 44.69 3.27
2758 2811 6.015350 ACGTAATTCGGATAAGGACATGAGAT 60.015 38.462 0.00 0.00 44.69 2.75
2759 2812 7.176165 ACGTAATTCGGATAAGGACATGAGATA 59.824 37.037 0.00 0.00 44.69 1.98
2760 2813 8.027189 CGTAATTCGGATAAGGACATGAGATAA 58.973 37.037 0.00 0.00 35.71 1.75
2761 2814 9.360093 GTAATTCGGATAAGGACATGAGATAAG 57.640 37.037 0.00 0.00 0.00 1.73
2762 2815 6.978674 TTCGGATAAGGACATGAGATAAGT 57.021 37.500 0.00 0.00 0.00 2.24
2781 2851 0.325296 TACTAGGCACACCCCTCCTG 60.325 60.000 0.00 0.00 36.41 3.86
2801 2872 2.299013 TGACTGACCAAGCACGAATAGT 59.701 45.455 0.00 0.00 0.00 2.12
2807 2878 4.945543 TGACCAAGCACGAATAGTACTAGA 59.054 41.667 8.85 0.00 0.00 2.43
2811 2882 5.392703 CCAAGCACGAATAGTACTAGACACA 60.393 44.000 8.85 0.00 0.00 3.72
2815 2886 7.416022 AGCACGAATAGTACTAGACACATAAC 58.584 38.462 8.85 0.00 0.00 1.89
2816 2887 6.356452 GCACGAATAGTACTAGACACATAACG 59.644 42.308 8.85 4.42 0.00 3.18
2852 2923 2.919971 AGCTCGTTTGCTCTGTTCC 58.080 52.632 0.00 0.00 39.34 3.62
2879 2950 1.002366 CTTGCACGCTGTAAGGCTAG 58.998 55.000 0.00 0.00 36.60 3.42
2880 2951 0.606096 TTGCACGCTGTAAGGCTAGA 59.394 50.000 0.00 0.00 0.00 2.43
2916 2988 3.367395 CGATGACCTTGTTCTGCTGAGTA 60.367 47.826 0.00 0.00 0.00 2.59
2938 3016 2.487762 TGTTTTCCAATCATCGTCTGCC 59.512 45.455 0.00 0.00 0.00 4.85
2946 3024 0.251916 TCATCGTCTGCCCCGAAATT 59.748 50.000 0.00 0.00 37.93 1.82
2949 3027 1.611519 TCGTCTGCCCCGAAATTTTT 58.388 45.000 0.00 0.00 0.00 1.94
2967 3057 4.886247 TTTTTCTATCCAATTACGCGGG 57.114 40.909 12.47 0.43 0.00 6.13
2969 3059 0.034337 TCTATCCAATTACGCGGGCC 59.966 55.000 12.47 0.00 0.00 5.80
2986 3122 1.416049 CCGTGAAGCGACGTGAATG 59.584 57.895 0.00 0.00 44.77 2.67
3002 3138 1.664151 GAATGGACGGTTGGATCGAAC 59.336 52.381 11.81 11.81 0.00 3.95
3043 3179 8.187480 GCTGTGATCAGATCATACGTAAGATAT 58.813 37.037 16.37 7.65 43.76 1.63
3056 3192 6.179504 ACGTAAGATATATACAGCGACAGG 57.820 41.667 0.00 0.00 43.62 4.00
3183 3327 3.608662 ACCCGTCGACCTCGCAAA 61.609 61.111 10.58 0.00 39.60 3.68
3194 3338 2.135933 ACCTCGCAAAAACTTCTCGAG 58.864 47.619 5.93 5.93 44.21 4.04
3262 3406 1.317613 TTTCGCAGGTTGCTGACAAT 58.682 45.000 0.00 0.00 42.25 2.71
3272 3416 1.980772 GCTGACAATGCTTGCCCCT 60.981 57.895 0.00 0.00 0.00 4.79
3304 3448 1.522668 TGAAACGCAACATCAGAGGG 58.477 50.000 0.00 0.00 0.00 4.30
3422 3569 7.931578 TTTTTACCGATTACCATTCACAGAT 57.068 32.000 0.00 0.00 0.00 2.90
3428 3575 6.036735 ACCGATTACCATTCACAGATAAAACG 59.963 38.462 0.00 0.00 0.00 3.60
3429 3576 6.256975 CCGATTACCATTCACAGATAAAACGA 59.743 38.462 0.00 0.00 0.00 3.85
3489 3662 7.882179 TCTAAACAGCATATATAAGCACTCGA 58.118 34.615 12.18 0.00 0.00 4.04
3504 3677 4.511457 CACTCGATGTGTGATCAATGAC 57.489 45.455 0.00 0.00 41.53 3.06
3505 3678 3.928375 CACTCGATGTGTGATCAATGACA 59.072 43.478 0.00 1.11 41.53 3.58
3506 3679 3.928992 ACTCGATGTGTGATCAATGACAC 59.071 43.478 0.00 5.87 43.75 3.67
3507 3680 2.923020 TCGATGTGTGATCAATGACACG 59.077 45.455 0.00 7.88 45.92 4.49
3509 3682 2.542020 TGTGTGATCAATGACACGGT 57.458 45.000 0.00 0.00 45.92 4.83
3510 3683 2.142319 TGTGTGATCAATGACACGGTG 58.858 47.619 6.58 6.58 45.92 4.94
3511 3684 2.224161 TGTGTGATCAATGACACGGTGA 60.224 45.455 16.29 0.00 45.92 4.02
3512 3685 3.002791 GTGTGATCAATGACACGGTGAT 58.997 45.455 16.29 0.00 35.36 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 39 1.418334 ACTAGCCATAGGAGCCACTG 58.582 55.000 0.00 0.00 32.90 3.66
52 55 6.707290 ACAGTAAAATGACATGCTGGTACTA 58.293 36.000 0.00 0.00 0.00 1.82
72 75 2.637872 CCCATATCCCCATCGTAACAGT 59.362 50.000 0.00 0.00 0.00 3.55
73 76 2.637872 ACCCATATCCCCATCGTAACAG 59.362 50.000 0.00 0.00 0.00 3.16
78 81 1.645710 GAGACCCATATCCCCATCGT 58.354 55.000 0.00 0.00 0.00 3.73
99 102 2.381752 TGCCATCGATCCTCTCCTAA 57.618 50.000 0.00 0.00 0.00 2.69
208 211 2.879103 ATCAAACGACCCAGTGGAAT 57.121 45.000 11.95 0.00 34.81 3.01
211 214 1.539827 GGAAATCAAACGACCCAGTGG 59.460 52.381 0.63 0.63 37.80 4.00
231 234 2.859273 AAGAGAGGGCGTGCATTCCG 62.859 60.000 0.00 0.00 0.00 4.30
258 261 9.643693 ACAAGTTAATGGCTTCTAAATTCAATG 57.356 29.630 0.00 0.00 0.00 2.82
299 302 6.381994 TGTCCCGACAACCTTAAGAGTATATT 59.618 38.462 3.36 0.00 38.56 1.28
319 322 5.705609 AACAACAATCTTATGTGTGTCCC 57.294 39.130 0.00 0.00 32.81 4.46
321 324 8.132362 TGGTAAAACAACAATCTTATGTGTGTC 58.868 33.333 0.00 0.00 32.81 3.67
336 339 9.757859 CAATTGCATGATATTTGGTAAAACAAC 57.242 29.630 0.00 0.00 0.00 3.32
417 420 1.269051 GGAGGCGGTCTTGTTTGTTTG 60.269 52.381 0.00 0.00 0.00 2.93
419 422 0.822121 GGGAGGCGGTCTTGTTTGTT 60.822 55.000 0.00 0.00 0.00 2.83
476 482 5.499004 TTACTGGCTAGGACATGTCTTTT 57.501 39.130 24.50 13.25 0.00 2.27
502 508 7.978982 ACATTTAGTCTCACAAACATATCAGC 58.021 34.615 0.00 0.00 0.00 4.26
553 559 9.708222 CGGTTTGAGAATTGAGTTAATATCTTG 57.292 33.333 0.00 0.00 0.00 3.02
601 607 4.946160 AGGGATTTGGTGTAGGAAATCA 57.054 40.909 0.00 0.00 39.40 2.57
606 612 3.449737 CGAGTTAGGGATTTGGTGTAGGA 59.550 47.826 0.00 0.00 0.00 2.94
693 699 8.352942 AGTTCATCTACATCCAACAAACTTTTC 58.647 33.333 0.00 0.00 0.00 2.29
702 708 7.549134 TGTTATGTGAGTTCATCTACATCCAAC 59.451 37.037 0.00 0.00 34.03 3.77
781 787 3.987220 ACGCCATTAATTGTTGCTCAAAC 59.013 39.130 0.00 0.00 39.62 2.93
878 884 8.606830 ACTAGGATCCAAAGTTACATCTCTTTT 58.393 33.333 15.82 0.00 32.52 2.27
968 981 4.918037 CTTGCAAGCATAAACCTCATCTC 58.082 43.478 14.65 0.00 0.00 2.75
1032 1045 6.177310 TGTTGGCTAACTTTAGGTTACTGA 57.823 37.500 14.47 0.00 39.17 3.41
1073 1086 8.207545 AGCTACAAGGATCTAACAAAAGATAGG 58.792 37.037 0.00 0.00 36.33 2.57
1110 1123 8.475331 AAATGACAACTGGAGTACTTATTACG 57.525 34.615 0.00 0.00 35.61 3.18
1120 1133 5.182001 GCATACTCAAAATGACAACTGGAGT 59.818 40.000 0.00 0.00 37.79 3.85
1132 1145 3.303351 CCTCCTGGGCATACTCAAAAT 57.697 47.619 0.00 0.00 0.00 1.82
1146 1159 0.179000 CCAAACGGATCTCCCTCCTG 59.821 60.000 0.00 0.00 32.77 3.86
1182 1195 2.244651 ACTGCGCTGTTTGTCGTCC 61.245 57.895 14.78 0.00 0.00 4.79
1200 1213 1.537348 CGTCGTTTGGAGAAGGTGACA 60.537 52.381 0.00 0.00 0.00 3.58
1239 1252 2.202756 GCGGAGAGGTTACTGGCG 60.203 66.667 0.00 0.00 0.00 5.69
1277 1290 5.047021 CCTGATTCACTCTCTAGGACAACAA 60.047 44.000 0.00 0.00 0.00 2.83
1287 1300 4.224594 TGCATCTTTCCTGATTCACTCTCT 59.775 41.667 0.00 0.00 0.00 3.10
1335 1348 7.572523 TGACAAGAAAGCATCAATAATAGGG 57.427 36.000 0.00 0.00 0.00 3.53
1362 1375 3.471680 GAGTGGCTCAATAAGTGGATCC 58.528 50.000 4.20 4.20 0.00 3.36
1374 1387 3.573772 CTTGTCGGCGAGTGGCTCA 62.574 63.158 11.20 0.00 42.94 4.26
1422 1435 0.678048 CCAACCTAGCCACCTTGCTC 60.678 60.000 0.00 0.00 41.68 4.26
1453 1466 2.801483 TGCTCTCTTCTCTAGCACTGT 58.199 47.619 0.00 0.00 41.15 3.55
1456 1469 3.056179 AGGTTTGCTCTCTTCTCTAGCAC 60.056 47.826 0.00 0.00 45.41 4.40
1526 1539 6.361433 TCCCTCGAAAAGATATTATTTGCCA 58.639 36.000 0.00 0.00 0.00 4.92
1542 1555 4.528596 AGACTGAGATCTTTTTCCCTCGAA 59.471 41.667 0.00 0.00 0.00 3.71
1545 1558 4.940654 CCAAGACTGAGATCTTTTTCCCTC 59.059 45.833 0.00 0.00 36.78 4.30
1560 1573 4.220382 AGTCTGTTGAGATCTCCAAGACTG 59.780 45.833 31.34 22.13 39.25 3.51
1561 1574 4.415596 AGTCTGTTGAGATCTCCAAGACT 58.584 43.478 28.93 28.93 37.58 3.24
1566 1579 4.411013 TGAAGAGTCTGTTGAGATCTCCA 58.589 43.478 20.03 10.52 31.68 3.86
1568 1581 6.531240 GTCATTGAAGAGTCTGTTGAGATCTC 59.469 42.308 16.21 16.21 31.57 2.75
1581 1594 2.300152 TCGCAAGAGGTCATTGAAGAGT 59.700 45.455 0.00 0.00 45.01 3.24
1603 1616 4.345257 ACGGTGTCTAATATGCTCCTTGAT 59.655 41.667 0.00 0.00 0.00 2.57
1608 1621 3.927142 GCATACGGTGTCTAATATGCTCC 59.073 47.826 7.63 0.00 44.21 4.70
1626 1639 2.811504 GCCATGATGTAGTGCAGGCATA 60.812 50.000 4.62 0.00 40.29 3.14
1633 1646 1.971481 TCATGGCCATGATGTAGTGC 58.029 50.000 38.91 0.00 42.42 4.40
1652 1665 4.277423 CGTTTTGACCACCAGTCCTTATTT 59.723 41.667 0.00 0.00 45.68 1.40
1654 1667 3.181448 ACGTTTTGACCACCAGTCCTTAT 60.181 43.478 0.00 0.00 45.68 1.73
1655 1668 2.171027 ACGTTTTGACCACCAGTCCTTA 59.829 45.455 0.00 0.00 45.68 2.69
1670 1683 3.518634 ACTGGATTTGTTGCACGTTTT 57.481 38.095 0.00 0.00 0.00 2.43
1685 1698 1.073722 CCTCTTGGCAGCAACTGGA 59.926 57.895 0.00 0.00 31.21 3.86
1693 1706 0.325933 TGTGATGGACCTCTTGGCAG 59.674 55.000 0.00 0.00 36.63 4.85
1713 1726 4.439974 GCTTGATGAGTCTTCGAGTGATCT 60.440 45.833 19.46 0.00 29.32 2.75
1733 1746 1.246649 TGATGGTTGCAATGACGCTT 58.753 45.000 0.59 0.00 0.00 4.68
1734 1747 1.402968 GATGATGGTTGCAATGACGCT 59.597 47.619 0.59 0.00 0.00 5.07
1737 1750 4.554134 CGAGATGATGATGGTTGCAATGAC 60.554 45.833 0.59 0.00 0.00 3.06
1741 1754 1.672363 GCGAGATGATGATGGTTGCAA 59.328 47.619 0.00 0.00 0.00 4.08
1743 1756 0.590195 GGCGAGATGATGATGGTTGC 59.410 55.000 0.00 0.00 0.00 4.17
1747 1760 1.586422 AAACGGCGAGATGATGATGG 58.414 50.000 16.62 0.00 0.00 3.51
1750 1763 2.415168 GTGAAAAACGGCGAGATGATGA 59.585 45.455 16.62 0.00 0.00 2.92
1752 1765 1.737793 GGTGAAAAACGGCGAGATGAT 59.262 47.619 16.62 0.00 0.00 2.45
1817 1830 6.295249 TGCATATGAAAAGATCGTCCCATAA 58.705 36.000 6.97 0.00 0.00 1.90
1823 1836 5.177696 GGTACCTGCATATGAAAAGATCGTC 59.822 44.000 6.97 0.00 0.00 4.20
1826 1839 5.822519 TGTGGTACCTGCATATGAAAAGATC 59.177 40.000 14.36 0.00 0.00 2.75
1861 1874 0.831711 GCCAAAGGTGATGGTTGGGT 60.832 55.000 3.99 0.00 41.80 4.51
1865 1878 2.275380 GGCGCCAAAGGTGATGGTT 61.275 57.895 24.80 0.00 40.23 3.67
1883 1896 0.180406 CATAAGGGACCTCAACCGGG 59.820 60.000 6.32 0.00 0.00 5.73
1886 1899 2.092323 GTTGCATAAGGGACCTCAACC 58.908 52.381 8.64 0.00 0.00 3.77
1903 1916 7.282585 TCTTATACCTGATGAGGAATTGGTTG 58.717 38.462 4.75 0.00 42.93 3.77
1932 1945 0.179020 TGTGGACAAAGTGCTGGAGG 60.179 55.000 0.00 0.00 0.00 4.30
1938 1951 3.211045 TCTAAAGGTGTGGACAAAGTGC 58.789 45.455 0.00 0.00 0.00 4.40
1951 1964 4.911390 AGCACTTGCATAGTTCTAAAGGT 58.089 39.130 3.62 0.00 45.16 3.50
1961 1974 4.764679 TTTGTGGTTAGCACTTGCATAG 57.235 40.909 15.65 0.00 45.16 2.23
2016 2030 3.074412 GTGGTGGTGTGGACTGAAATAG 58.926 50.000 0.00 0.00 0.00 1.73
2018 2032 1.478654 GGTGGTGGTGTGGACTGAAAT 60.479 52.381 0.00 0.00 0.00 2.17
2038 2052 2.760385 GGGGAGTCGGAGGTGGAG 60.760 72.222 0.00 0.00 0.00 3.86
2039 2053 3.273654 AGGGGAGTCGGAGGTGGA 61.274 66.667 0.00 0.00 0.00 4.02
2040 2054 3.077556 CAGGGGAGTCGGAGGTGG 61.078 72.222 0.00 0.00 0.00 4.61
2041 2055 1.913762 AACAGGGGAGTCGGAGGTG 60.914 63.158 0.00 0.00 0.00 4.00
2042 2056 1.913762 CAACAGGGGAGTCGGAGGT 60.914 63.158 0.00 0.00 0.00 3.85
2043 2057 2.660064 CCAACAGGGGAGTCGGAGG 61.660 68.421 0.00 0.00 0.00 4.30
2046 2060 2.876368 GATGCCAACAGGGGAGTCGG 62.876 65.000 0.00 0.00 42.01 4.79
2056 2070 2.375174 AGTTGTAGAAGGGATGCCAACA 59.625 45.455 5.86 1.19 35.75 3.33
2057 2071 2.749621 CAGTTGTAGAAGGGATGCCAAC 59.250 50.000 5.86 0.00 34.01 3.77
2069 2083 4.808414 CTGGTCAAGATCCAGTTGTAGA 57.192 45.455 4.06 0.00 45.09 2.59
2077 2091 2.505407 CCATGTACCTGGTCAAGATCCA 59.495 50.000 0.63 0.00 0.00 3.41
2110 2124 2.951642 TCTTGAAGTTTTGGCTGAGGTG 59.048 45.455 0.00 0.00 0.00 4.00
2121 2135 7.530426 AAGGACTTGCATATTCTTGAAGTTT 57.470 32.000 0.00 0.00 0.00 2.66
2127 2141 7.119699 TGTCTTGTAAGGACTTGCATATTCTTG 59.880 37.037 3.74 0.00 35.24 3.02
2153 2167 2.957402 TGTTCTGTGATGGCTCCTTT 57.043 45.000 0.00 0.00 0.00 3.11
2155 2169 1.980765 TCTTGTTCTGTGATGGCTCCT 59.019 47.619 0.00 0.00 0.00 3.69
2156 2170 2.079925 GTCTTGTTCTGTGATGGCTCC 58.920 52.381 0.00 0.00 0.00 4.70
2189 2203 3.684788 CCTCCGAAATGTTCTCAACGATT 59.315 43.478 0.00 0.00 0.00 3.34
2190 2204 3.262420 CCTCCGAAATGTTCTCAACGAT 58.738 45.455 0.00 0.00 0.00 3.73
2191 2205 2.683968 CCTCCGAAATGTTCTCAACGA 58.316 47.619 0.00 0.00 0.00 3.85
2192 2206 1.128692 GCCTCCGAAATGTTCTCAACG 59.871 52.381 0.00 0.00 0.00 4.10
2194 2208 2.559698 TGCCTCCGAAATGTTCTCAA 57.440 45.000 0.00 0.00 0.00 3.02
2195 2209 2.632377 GATGCCTCCGAAATGTTCTCA 58.368 47.619 0.00 0.00 0.00 3.27
2196 2210 1.943340 GGATGCCTCCGAAATGTTCTC 59.057 52.381 0.00 0.00 0.00 2.87
2198 2212 1.025041 GGGATGCCTCCGAAATGTTC 58.975 55.000 1.58 0.00 43.11 3.18
2199 2213 0.395724 GGGGATGCCTCCGAAATGTT 60.396 55.000 2.19 0.00 43.11 2.71
2201 2215 1.103398 GTGGGGATGCCTCCGAAATG 61.103 60.000 2.19 0.00 43.11 2.32
2204 2218 3.781307 CGTGGGGATGCCTCCGAA 61.781 66.667 2.19 0.00 43.11 4.30
2207 2221 3.699134 GAACCGTGGGGATGCCTCC 62.699 68.421 2.19 0.00 41.26 4.30
2209 2223 1.789576 AAAGAACCGTGGGGATGCCT 61.790 55.000 2.19 0.00 36.97 4.75
2210 2224 0.898326 AAAAGAACCGTGGGGATGCC 60.898 55.000 0.00 0.00 36.97 4.40
2211 2225 0.526211 GAAAAGAACCGTGGGGATGC 59.474 55.000 0.00 0.00 36.97 3.91
2212 2226 1.904287 TGAAAAGAACCGTGGGGATG 58.096 50.000 0.00 0.00 36.97 3.51
2213 2227 2.620627 GGATGAAAAGAACCGTGGGGAT 60.621 50.000 0.00 0.00 36.97 3.85
2214 2228 1.271707 GGATGAAAAGAACCGTGGGGA 60.272 52.381 0.00 0.00 36.97 4.81
2216 2230 0.802494 CGGATGAAAAGAACCGTGGG 59.198 55.000 0.00 0.00 40.42 4.61
2217 2231 0.802494 CCGGATGAAAAGAACCGTGG 59.198 55.000 0.00 0.00 43.22 4.94
2221 2235 0.526211 GCCACCGGATGAAAAGAACC 59.474 55.000 9.46 0.00 0.00 3.62
2222 2236 1.243902 TGCCACCGGATGAAAAGAAC 58.756 50.000 9.46 0.00 0.00 3.01
2223 2237 1.988293 TTGCCACCGGATGAAAAGAA 58.012 45.000 9.46 0.00 0.00 2.52
2224 2238 1.818060 CATTGCCACCGGATGAAAAGA 59.182 47.619 9.46 0.00 0.00 2.52
2225 2239 1.818060 TCATTGCCACCGGATGAAAAG 59.182 47.619 9.46 0.00 0.00 2.27
2226 2240 1.916506 TCATTGCCACCGGATGAAAA 58.083 45.000 9.46 1.37 0.00 2.29
2227 2241 2.142356 ATCATTGCCACCGGATGAAA 57.858 45.000 9.46 0.00 33.89 2.69
2228 2242 3.072915 AGATATCATTGCCACCGGATGAA 59.927 43.478 9.46 0.00 33.89 2.57
2229 2243 2.639347 AGATATCATTGCCACCGGATGA 59.361 45.455 9.46 6.88 34.61 2.92
2230 2244 3.005554 GAGATATCATTGCCACCGGATG 58.994 50.000 9.46 0.00 0.00 3.51
2231 2245 2.909006 AGAGATATCATTGCCACCGGAT 59.091 45.455 9.46 0.00 0.00 4.18
2232 2246 2.300152 GAGAGATATCATTGCCACCGGA 59.700 50.000 9.46 0.00 0.00 5.14
2233 2247 2.613977 GGAGAGATATCATTGCCACCGG 60.614 54.545 0.00 0.00 0.00 5.28
2234 2248 2.301296 AGGAGAGATATCATTGCCACCG 59.699 50.000 5.32 0.00 0.00 4.94
2235 2249 4.363991 AAGGAGAGATATCATTGCCACC 57.636 45.455 5.32 0.00 0.00 4.61
2236 2250 5.353678 GCATAAGGAGAGATATCATTGCCAC 59.646 44.000 5.32 0.00 0.00 5.01
2241 2255 7.811482 AAGGAGCATAAGGAGAGATATCATT 57.189 36.000 5.32 0.00 0.00 2.57
2248 2262 3.452627 GTCCAAAGGAGCATAAGGAGAGA 59.547 47.826 0.00 0.00 29.39 3.10
2293 2307 3.205282 CCCCAAGTAAGAATCCATCCCTT 59.795 47.826 0.00 0.00 0.00 3.95
2310 2324 4.865905 ACATCATTACTATTGCACCCCAA 58.134 39.130 0.00 0.00 37.94 4.12
2317 2331 6.824305 ATTGGCCTACATCATTACTATTGC 57.176 37.500 3.32 0.00 0.00 3.56
2322 2336 9.453572 CATGTTATATTGGCCTACATCATTACT 57.546 33.333 3.32 0.00 0.00 2.24
2357 2371 0.250901 GTGGTGCATTGACCCACTCT 60.251 55.000 14.49 0.00 44.21 3.24
2388 2402 3.934579 TCAATATCATCATCATTCCCGCG 59.065 43.478 0.00 0.00 0.00 6.46
2390 2404 5.355910 TGCATCAATATCATCATCATTCCCG 59.644 40.000 0.00 0.00 0.00 5.14
2401 2415 5.589050 CCTCCGAATCATGCATCAATATCAT 59.411 40.000 0.00 0.00 0.00 2.45
2420 2434 3.430929 CCCTTGACTAAAGATGTCCTCCG 60.431 52.174 0.00 0.00 38.24 4.63
2441 2487 9.442047 CCTAATGGACACAGAATATCTTATTCC 57.558 37.037 4.12 0.00 34.57 3.01
2456 2502 2.423538 GACAATGGCACCTAATGGACAC 59.576 50.000 0.00 0.00 37.04 3.67
2458 2504 1.670811 CGACAATGGCACCTAATGGAC 59.329 52.381 0.00 0.00 37.04 4.02
2481 2527 7.946043 TCGAAGAAGCTTAACAAAATAGTACG 58.054 34.615 0.00 0.00 0.00 3.67
2487 2533 4.518970 TGCCTCGAAGAAGCTTAACAAAAT 59.481 37.500 0.00 0.00 45.63 1.82
2538 2586 8.292448 GTCATACAGAAACAAAGTTCATGACAT 58.708 33.333 0.00 0.00 37.84 3.06
2548 2596 9.778993 CATGGAATTAGTCATACAGAAACAAAG 57.221 33.333 0.00 0.00 0.00 2.77
2560 2608 6.835488 ACCAAGCATTACATGGAATTAGTCAT 59.165 34.615 0.00 0.00 39.64 3.06
2568 2616 4.406456 AGAACACCAAGCATTACATGGAA 58.594 39.130 0.00 0.00 39.64 3.53
2571 2619 6.803320 CAGTAAAGAACACCAAGCATTACATG 59.197 38.462 0.00 0.00 0.00 3.21
2572 2620 6.714810 TCAGTAAAGAACACCAAGCATTACAT 59.285 34.615 0.00 0.00 0.00 2.29
2662 2712 3.253677 AGGCATATTCCTCTAGTTCGTCG 59.746 47.826 0.00 0.00 0.00 5.12
2665 2715 4.855715 TCAGGCATATTCCTCTAGTTCG 57.144 45.455 0.00 0.00 33.25 3.95
2670 2720 8.494433 ACTGTAAAATTCAGGCATATTCCTCTA 58.506 33.333 0.00 0.00 37.25 2.43
2700 2750 5.194432 TGGGTTGTGCTACTGAAGTTTAAA 58.806 37.500 0.00 0.00 0.00 1.52
2709 2759 5.643379 ATAATGTTTGGGTTGTGCTACTG 57.357 39.130 0.00 0.00 0.00 2.74
2720 2773 7.249186 TCCGAATTACGTAATAATGTTTGGG 57.751 36.000 20.62 14.65 40.78 4.12
2734 2787 5.769367 TCTCATGTCCTTATCCGAATTACG 58.231 41.667 0.00 0.00 42.18 3.18
2735 2788 9.360093 CTTATCTCATGTCCTTATCCGAATTAC 57.640 37.037 0.00 0.00 0.00 1.89
2737 2790 7.967908 ACTTATCTCATGTCCTTATCCGAATT 58.032 34.615 0.00 0.00 0.00 2.17
2739 2792 6.978674 ACTTATCTCATGTCCTTATCCGAA 57.021 37.500 0.00 0.00 0.00 4.30
2740 2793 7.232188 AGTACTTATCTCATGTCCTTATCCGA 58.768 38.462 0.00 0.00 0.00 4.55
2741 2794 7.455641 AGTACTTATCTCATGTCCTTATCCG 57.544 40.000 0.00 0.00 0.00 4.18
2742 2795 8.962679 CCTAGTACTTATCTCATGTCCTTATCC 58.037 40.741 0.00 0.00 0.00 2.59
2743 2796 8.463607 GCCTAGTACTTATCTCATGTCCTTATC 58.536 40.741 0.00 0.00 0.00 1.75
2744 2797 7.950684 TGCCTAGTACTTATCTCATGTCCTTAT 59.049 37.037 0.00 0.00 0.00 1.73
2745 2798 7.230913 GTGCCTAGTACTTATCTCATGTCCTTA 59.769 40.741 0.00 0.00 0.00 2.69
2746 2799 6.041069 GTGCCTAGTACTTATCTCATGTCCTT 59.959 42.308 0.00 0.00 0.00 3.36
2747 2800 5.536916 GTGCCTAGTACTTATCTCATGTCCT 59.463 44.000 0.00 0.00 0.00 3.85
2748 2801 5.302059 TGTGCCTAGTACTTATCTCATGTCC 59.698 44.000 0.00 0.00 0.00 4.02
2749 2802 6.210078 GTGTGCCTAGTACTTATCTCATGTC 58.790 44.000 0.00 0.00 0.00 3.06
2750 2803 5.069251 GGTGTGCCTAGTACTTATCTCATGT 59.931 44.000 0.00 0.00 0.00 3.21
2751 2804 5.509840 GGGTGTGCCTAGTACTTATCTCATG 60.510 48.000 0.00 0.00 34.45 3.07
2752 2805 4.589374 GGGTGTGCCTAGTACTTATCTCAT 59.411 45.833 0.00 0.00 34.45 2.90
2753 2806 3.958798 GGGTGTGCCTAGTACTTATCTCA 59.041 47.826 0.00 0.00 34.45 3.27
2754 2807 3.321396 GGGGTGTGCCTAGTACTTATCTC 59.679 52.174 0.00 0.00 34.45 2.75
2755 2808 3.052033 AGGGGTGTGCCTAGTACTTATCT 60.052 47.826 0.00 0.00 34.45 1.98
2756 2809 3.306613 AGGGGTGTGCCTAGTACTTATC 58.693 50.000 0.00 0.00 34.45 1.75
2757 2810 3.306613 GAGGGGTGTGCCTAGTACTTAT 58.693 50.000 0.00 0.00 34.45 1.73
2758 2811 2.625087 GGAGGGGTGTGCCTAGTACTTA 60.625 54.545 0.00 0.00 34.45 2.24
2759 2812 1.569653 GAGGGGTGTGCCTAGTACTT 58.430 55.000 0.00 0.00 34.45 2.24
2760 2813 0.325390 GGAGGGGTGTGCCTAGTACT 60.325 60.000 0.00 0.00 34.45 2.73
2761 2814 0.325390 AGGAGGGGTGTGCCTAGTAC 60.325 60.000 0.00 0.00 34.45 2.73
2762 2815 0.325296 CAGGAGGGGTGTGCCTAGTA 60.325 60.000 0.00 0.00 34.45 1.82
2781 2851 2.960819 ACTATTCGTGCTTGGTCAGTC 58.039 47.619 0.00 0.00 0.00 3.51
2811 2882 9.477484 AGCTCGATCAGAAATTAATAACGTTAT 57.523 29.630 15.07 15.07 0.00 1.89
2815 2886 6.142480 ACGAGCTCGATCAGAAATTAATAACG 59.858 38.462 40.58 9.82 43.02 3.18
2816 2887 7.396190 ACGAGCTCGATCAGAAATTAATAAC 57.604 36.000 40.58 0.00 43.02 1.89
2852 2923 4.000557 AGCGTGCAAGCAACGACG 62.001 61.111 26.30 6.04 40.15 5.12
2879 2950 3.860536 GGTCATCGAGTTACTCTGCTTTC 59.139 47.826 10.83 0.00 0.00 2.62
2880 2951 3.511934 AGGTCATCGAGTTACTCTGCTTT 59.488 43.478 10.83 0.00 0.00 3.51
2894 2966 1.998315 CTCAGCAGAACAAGGTCATCG 59.002 52.381 0.00 0.00 0.00 3.84
2916 2988 3.129287 GGCAGACGATGATTGGAAAACAT 59.871 43.478 0.00 0.00 42.38 2.71
2946 3024 3.065648 GCCCGCGTAATTGGATAGAAAAA 59.934 43.478 4.92 0.00 0.00 1.94
2949 3027 1.541670 GGCCCGCGTAATTGGATAGAA 60.542 52.381 4.92 0.00 0.00 2.10
2956 3046 2.304516 CTTCACGGCCCGCGTAATTG 62.305 60.000 1.23 0.00 0.00 2.32
2967 3057 2.380410 ATTCACGTCGCTTCACGGC 61.380 57.895 0.00 0.00 44.41 5.68
2969 3059 1.006825 TCCATTCACGTCGCTTCACG 61.007 55.000 0.00 0.00 45.65 4.35
2979 3069 1.006832 GATCCAACCGTCCATTCACG 58.993 55.000 0.00 0.00 39.61 4.35
2986 3122 0.245539 TCAGTTCGATCCAACCGTCC 59.754 55.000 0.00 0.00 0.00 4.79
3026 3162 9.543783 TCGCTGTATATATCTTACGTATGATCT 57.456 33.333 22.91 17.17 0.00 2.75
3056 3192 6.237201 CGAACAAAAGAACAAACAGTACAAGC 60.237 38.462 0.00 0.00 0.00 4.01
3165 3307 3.851845 TTTGCGAGGTCGACGGGTG 62.852 63.158 9.92 0.30 43.02 4.61
3166 3308 2.647680 TTTTTGCGAGGTCGACGGGT 62.648 55.000 9.92 0.00 43.02 5.28
3183 3327 5.866633 GTGATGTCTCATTCTCGAGAAGTTT 59.133 40.000 29.89 13.45 43.51 2.66
3194 3338 2.299993 TGCGAGGTGATGTCTCATTC 57.700 50.000 0.00 0.00 32.98 2.67
3272 3416 1.886253 CGTTTCATGGGCATGGGCAA 61.886 55.000 0.00 0.00 43.71 4.52
3304 3448 2.042639 ATCCCATGCCCTGGTTGC 60.043 61.111 2.10 0.00 44.30 4.17
3437 3584 5.772393 TGGTGTGTTCATAGTCCCTTTAT 57.228 39.130 0.00 0.00 0.00 1.40
3489 3662 2.743664 CACCGTGTCATTGATCACACAT 59.256 45.455 12.93 0.00 42.67 3.21


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

AutoCloner maintained by Alex Coulton.