Multiple sequence alignment - TraesCS3A01G055600

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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 TraesCS3A01G055600 chr3A 100.000 3779 0 0 1 3779 32152837 32149059 0.000000e+00 6979.0
1 TraesCS3A01G055600 chr3A 86.620 284 31 3 1 283 32252900 32252623 1.320000e-79 307.0
2 TraesCS3A01G055600 chr3A 85.911 291 27 7 1 283 731227029 731226745 7.940000e-77 298.0
3 TraesCS3A01G055600 chr3A 89.474 57 2 1 3206 3262 637465431 637465379 6.770000e-08 69.4
4 TraesCS3A01G055600 chr3B 91.393 2068 120 28 1 2032 40246650 40244605 0.000000e+00 2780.0
5 TraesCS3A01G055600 chr3B 93.814 582 31 5 2246 2823 40244489 40243909 0.000000e+00 870.0
6 TraesCS3A01G055600 chr3B 91.434 502 33 5 3279 3779 40239314 40238822 0.000000e+00 680.0
7 TraesCS3A01G055600 chr3B 92.437 238 17 1 47 283 40866662 40866425 4.680000e-89 339.0
8 TraesCS3A01G055600 chr3B 83.881 335 41 9 2931 3262 40239722 40239398 1.320000e-79 307.0
9 TraesCS3A01G055600 chr3D 94.892 1253 60 3 783 2032 23063817 23062566 0.000000e+00 1956.0
10 TraesCS3A01G055600 chr3D 95.023 663 29 4 2246 2904 23062450 23061788 0.000000e+00 1038.0
11 TraesCS3A01G055600 chr3D 90.352 767 44 12 1 739 23064578 23063814 0.000000e+00 979.0
12 TraesCS3A01G055600 chr3D 91.089 505 31 6 3279 3779 23061327 23060833 0.000000e+00 671.0
13 TraesCS3A01G055600 chr3D 88.028 284 27 3 1 283 23174445 23174168 2.810000e-86 329.0
14 TraesCS3A01G055600 chr3D 80.851 94 14 2 3174 3267 23061495 23061406 1.880000e-08 71.3
15 TraesCS3A01G055600 chr1D 89.958 717 45 10 1 690 225396823 225397539 0.000000e+00 900.0
16 TraesCS3A01G055600 chr2D 80.619 872 122 33 1038 1885 419040492 419041340 6.890000e-177 630.0
17 TraesCS3A01G055600 chr2A 84.184 588 72 14 1038 1618 570785191 570784618 5.520000e-153 551.0
18 TraesCS3A01G055600 chr2A 88.028 142 17 0 1744 1885 570784484 570784343 6.490000e-38 169.0
19 TraesCS3A01G055600 chr2B 83.844 588 73 14 1038 1618 491181324 491181896 1.190000e-149 540.0
20 TraesCS3A01G055600 chr2B 86.620 142 19 0 1744 1885 491182031 491182172 1.410000e-34 158.0
21 TraesCS3A01G055600 chr4A 84.264 394 60 2 1065 1457 580908038 580907646 2.130000e-102 383.0
22 TraesCS3A01G055600 chr4A 100.000 29 0 0 2032 2060 387082704 387082732 2.000000e-03 54.7
23 TraesCS3A01G055600 chr6B 91.525 59 4 1 3199 3257 585569649 585569706 3.130000e-11 80.5
24 TraesCS3A01G055600 chr5D 88.710 62 3 3 3206 3267 211983833 211983776 5.240000e-09 73.1
25 TraesCS3A01G055600 chr1A 84.286 70 7 3 3206 3275 513727193 513727258 8.760000e-07 65.8
26 TraesCS3A01G055600 chr5B 89.796 49 4 1 3227 3274 490561478 490561526 1.130000e-05 62.1


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 TraesCS3A01G055600 chr3A 32149059 32152837 3778 True 6979.00 6979 100.0000 1 3779 1 chr3A.!!$R1 3778
1 TraesCS3A01G055600 chr3B 40243909 40246650 2741 True 1825.00 2780 92.6035 1 2823 2 chr3B.!!$R3 2822
2 TraesCS3A01G055600 chr3B 40238822 40239722 900 True 493.50 680 87.6575 2931 3779 2 chr3B.!!$R2 848
3 TraesCS3A01G055600 chr3D 23060833 23064578 3745 True 943.06 1956 90.4414 1 3779 5 chr3D.!!$R2 3778
4 TraesCS3A01G055600 chr1D 225396823 225397539 716 False 900.00 900 89.9580 1 690 1 chr1D.!!$F1 689
5 TraesCS3A01G055600 chr2D 419040492 419041340 848 False 630.00 630 80.6190 1038 1885 1 chr2D.!!$F1 847
6 TraesCS3A01G055600 chr2A 570784343 570785191 848 True 360.00 551 86.1060 1038 1885 2 chr2A.!!$R1 847
7 TraesCS3A01G055600 chr2B 491181324 491182172 848 False 349.00 540 85.2320 1038 1885 2 chr2B.!!$F1 847

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
338 345 1.078143 CTCAGGAAAGGGGAAGGCG 60.078 63.158 0.0 0.0 0.0 5.52 F
1818 1876 0.250467 GGCTGGCACTCAACTTCTCA 60.250 55.000 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2052 0.597637 AGTCGCGATTATCAAGCCCG 60.598 55.0 14.06 0.0 0.0 6.13 R
3062 3242 0.234106 CTCATGATGTTCGCCGCATC 59.766 55.0 0.00 0.0 42.1 3.91 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
338 345 1.078143 CTCAGGAAAGGGGAAGGCG 60.078 63.158 0.00 0.00 0.00 5.52
341 348 4.360405 GGAAAGGGGAAGGCGGCA 62.360 66.667 13.08 0.00 0.00 5.69
342 349 2.751837 GAAAGGGGAAGGCGGCAG 60.752 66.667 13.08 0.00 0.00 4.85
429 436 4.194640 TCTTTCAGAGCATGCCTAATCAC 58.805 43.478 15.66 0.00 0.00 3.06
464 471 2.309755 AGAAAGATGAGGGTGATGGCAA 59.690 45.455 0.00 0.00 0.00 4.52
540 547 1.892474 AGTCTGGACAAGAGAGAGCAC 59.108 52.381 3.51 0.00 34.84 4.40
544 551 1.345741 TGGACAAGAGAGAGCACAAGG 59.654 52.381 0.00 0.00 0.00 3.61
549 556 3.898123 ACAAGAGAGAGCACAAGGAGTTA 59.102 43.478 0.00 0.00 0.00 2.24
550 557 4.530161 ACAAGAGAGAGCACAAGGAGTTAT 59.470 41.667 0.00 0.00 0.00 1.89
552 559 4.348486 AGAGAGAGCACAAGGAGTTATGA 58.652 43.478 0.00 0.00 0.00 2.15
553 560 4.159506 AGAGAGAGCACAAGGAGTTATGAC 59.840 45.833 0.00 0.00 0.00 3.06
554 561 3.834813 AGAGAGCACAAGGAGTTATGACA 59.165 43.478 0.00 0.00 0.00 3.58
555 562 4.081752 AGAGAGCACAAGGAGTTATGACAG 60.082 45.833 0.00 0.00 0.00 3.51
556 563 3.834813 AGAGCACAAGGAGTTATGACAGA 59.165 43.478 0.00 0.00 0.00 3.41
557 564 4.081752 AGAGCACAAGGAGTTATGACAGAG 60.082 45.833 0.00 0.00 0.00 3.35
558 565 3.834813 AGCACAAGGAGTTATGACAGAGA 59.165 43.478 0.00 0.00 0.00 3.10
559 566 3.929610 GCACAAGGAGTTATGACAGAGAC 59.070 47.826 0.00 0.00 0.00 3.36
565 593 3.764434 GGAGTTATGACAGAGACAGTGGA 59.236 47.826 0.00 0.00 0.00 4.02
579 607 2.807247 GTGGAACTGCAAGGTGGTT 58.193 52.632 0.00 0.00 39.30 3.67
603 631 9.236006 GTTGGATTATGCTGTTCTAATATGGAT 57.764 33.333 0.00 0.00 0.00 3.41
613 641 8.531982 GCTGTTCTAATATGGATAGGTGTATGA 58.468 37.037 0.00 0.00 0.00 2.15
631 659 9.847706 GGTGTATGAGTACTGATATGTCATAAG 57.152 37.037 0.00 0.00 33.13 1.73
632 660 9.847706 GTGTATGAGTACTGATATGTCATAAGG 57.152 37.037 0.00 0.00 33.13 2.69
665 696 3.996957 TGTGGATAGGTGTATGGGTACA 58.003 45.455 0.00 0.00 38.46 2.90
669 700 5.307196 GTGGATAGGTGTATGGGTACAGATT 59.693 44.000 0.00 0.00 41.29 2.40
690 724 5.761165 TTGGTTGGTAGTTTAGTTGAAGC 57.239 39.130 0.00 0.00 0.00 3.86
735 769 5.525012 CCATACCATATAGCACATGGAATCG 59.475 44.000 15.73 4.08 44.95 3.34
762 796 1.758862 GGAGAAATGGCCCCAAATCTG 59.241 52.381 0.00 0.00 0.00 2.90
765 799 1.901833 GAAATGGCCCCAAATCTGTGT 59.098 47.619 0.00 0.00 0.00 3.72
776 810 3.119602 CCAAATCTGTGTGCTCTGGATTG 60.120 47.826 0.00 0.00 0.00 2.67
789 823 2.821378 TCTGGATTGTGGTTGCTTGATG 59.179 45.455 0.00 0.00 0.00 3.07
791 825 2.557924 TGGATTGTGGTTGCTTGATGTC 59.442 45.455 0.00 0.00 0.00 3.06
797 831 2.349886 GTGGTTGCTTGATGTCGATCTC 59.650 50.000 0.00 0.00 0.00 2.75
947 983 5.521906 TTTAAGCTTGCATGTGGTTGTTA 57.478 34.783 9.86 0.00 0.00 2.41
1007 1043 8.206867 TGAAATTTCTCGATACTCCAGATTGAT 58.793 33.333 18.64 0.00 0.00 2.57
1176 1212 0.539669 TTGACTCCGAGGAGCTCACA 60.540 55.000 17.19 10.87 45.54 3.58
1398 1434 0.916358 CCCACCTTGTCCCCTCATCT 60.916 60.000 0.00 0.00 0.00 2.90
1597 1639 1.446907 CTGCTGAGAACACCATGGTC 58.553 55.000 16.53 3.82 33.32 4.02
1618 1660 2.632377 GCATACAAAGCTGCTCAGGTA 58.368 47.619 1.00 6.55 38.35 3.08
1628 1670 2.771089 CTGCTCAGGTAGTTTGCTTGA 58.229 47.619 0.00 0.00 0.00 3.02
1647 1689 2.025981 TGACCTGGATTTCATGGTCCTG 60.026 50.000 0.00 11.22 45.98 3.86
1659 1701 4.326826 TCATGGTCCTGACATTGAACTTC 58.673 43.478 0.00 0.00 0.00 3.01
1668 1710 3.243035 TGACATTGAACTTCGTTGGCAAG 60.243 43.478 0.00 0.00 0.00 4.01
1674 1717 2.568623 ACTTCGTTGGCAAGGAATCT 57.431 45.000 29.01 17.58 35.07 2.40
1691 1743 4.560035 GGAATCTGTTTCATGCGTGATTTG 59.440 41.667 9.96 1.26 35.94 2.32
1718 1770 8.875168 TCCTGTTTAATTATTTGGTGGTGAATT 58.125 29.630 0.00 0.00 0.00 2.17
1736 1794 5.911838 GTGAATTTCTTGCTCAGTTGAGTTC 59.088 40.000 10.57 5.52 43.85 3.01
1764 1822 5.319453 TGAATCTTTCAGGAGATTGCACTT 58.681 37.500 4.97 0.00 44.27 3.16
1818 1876 0.250467 GGCTGGCACTCAACTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
1866 1924 2.665185 GACCGTGCTTGCGACCTT 60.665 61.111 0.00 0.00 0.00 3.50
1898 1956 7.683463 GCAGGTTTGTTTTCTACAATAACCAGT 60.683 37.037 11.82 0.00 44.68 4.00
1901 1959 7.977293 GGTTTGTTTTCTACAATAACCAGTTGT 59.023 33.333 0.00 0.00 45.72 3.32
1905 1963 5.940192 TTCTACAATAACCAGTTGTGCTG 57.060 39.130 2.04 0.00 44.63 4.41
1947 2005 7.323420 CAGTACATCTGAACTGAATAGAACCA 58.677 38.462 2.51 0.00 44.79 3.67
1975 2033 7.282675 GTGGATCTGAGATGATTCAAAGTCAAT 59.717 37.037 0.00 0.00 34.11 2.57
2009 2067 4.946784 AATATTCGGGCTTGATAATCGC 57.053 40.909 0.00 0.00 0.00 4.58
2032 2093 9.518906 TCGCGACTAATAATTGAATAACAAGTA 57.481 29.630 3.71 0.00 41.94 2.24
2033 2094 9.564041 CGCGACTAATAATTGAATAACAAGTAC 57.436 33.333 0.00 0.00 40.85 2.73
2034 2095 9.564041 GCGACTAATAATTGAATAACAAGTACG 57.436 33.333 0.00 0.00 40.85 3.67
2039 2100 8.889849 AATAATTGAATAACAAGTACGTGCAC 57.110 30.769 6.82 6.82 40.85 4.57
2040 2101 4.735662 TTGAATAACAAGTACGTGCACC 57.264 40.909 12.15 0.00 34.20 5.01
2041 2102 2.732500 TGAATAACAAGTACGTGCACCG 59.267 45.455 12.15 9.19 44.03 4.94
2042 2103 1.717194 ATAACAAGTACGTGCACCGG 58.283 50.000 12.15 0.00 42.24 5.28
2043 2104 0.319727 TAACAAGTACGTGCACCGGG 60.320 55.000 12.15 0.00 42.24 5.73
2044 2105 3.419759 CAAGTACGTGCACCGGGC 61.420 66.667 12.15 7.25 42.24 6.13
2045 2106 3.622826 AAGTACGTGCACCGGGCT 61.623 61.111 12.15 6.39 45.15 5.19
2046 2107 3.876589 AAGTACGTGCACCGGGCTG 62.877 63.158 12.15 6.32 45.15 4.85
2054 2115 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
2081 2142 7.925043 TTTGAGTAACAACTGTTAACAAGGA 57.075 32.000 10.03 7.02 41.58 3.36
2083 2144 8.514330 TTGAGTAACAACTGTTAACAAGGAAT 57.486 30.769 10.03 0.00 41.58 3.01
2094 2155 7.936847 ACTGTTAACAAGGAATCAGTGTTATGA 59.063 33.333 10.03 0.00 37.52 2.15
2096 2157 5.886960 AACAAGGAATCAGTGTTATGAGC 57.113 39.130 0.00 0.00 33.80 4.26
2106 2169 4.283467 TCAGTGTTATGAGCTACAGTTGGT 59.717 41.667 0.00 0.00 0.00 3.67
2115 2178 3.412386 AGCTACAGTTGGTTAGGCAAAG 58.588 45.455 0.00 0.00 0.00 2.77
2118 2181 4.083271 GCTACAGTTGGTTAGGCAAAGAAG 60.083 45.833 0.00 0.00 0.00 2.85
2121 2184 2.177016 AGTTGGTTAGGCAAAGAAGGGT 59.823 45.455 0.00 0.00 0.00 4.34
2130 2193 2.549926 GCAAAGAAGGGTTGTTGTTGG 58.450 47.619 0.00 0.00 0.00 3.77
2141 2204 3.636764 GGTTGTTGTTGGACCTGAAAGAT 59.363 43.478 0.00 0.00 34.07 2.40
2142 2205 4.261614 GGTTGTTGTTGGACCTGAAAGATC 60.262 45.833 0.00 0.00 34.07 2.75
2168 2233 8.664798 CGATAAAGAAATAATGACTGTTCCACA 58.335 33.333 0.00 0.00 0.00 4.17
2175 2240 9.722056 GAAATAATGACTGTTCCACATAATGTC 57.278 33.333 0.00 0.00 0.00 3.06
2176 2241 7.807977 ATAATGACTGTTCCACATAATGTCC 57.192 36.000 0.00 0.00 0.00 4.02
2178 2243 3.587061 TGACTGTTCCACATAATGTCCCT 59.413 43.478 0.00 0.00 0.00 4.20
2179 2244 3.941483 GACTGTTCCACATAATGTCCCTG 59.059 47.826 0.00 0.00 0.00 4.45
2180 2245 3.282021 CTGTTCCACATAATGTCCCTGG 58.718 50.000 0.00 0.00 0.00 4.45
2181 2246 2.647299 TGTTCCACATAATGTCCCTGGT 59.353 45.455 0.00 0.00 0.00 4.00
2182 2247 3.279434 GTTCCACATAATGTCCCTGGTC 58.721 50.000 0.00 0.00 0.00 4.02
2183 2248 2.556766 TCCACATAATGTCCCTGGTCA 58.443 47.619 0.00 0.00 0.00 4.02
2184 2249 3.122480 TCCACATAATGTCCCTGGTCAT 58.878 45.455 0.00 0.00 0.00 3.06
2185 2250 4.302930 TCCACATAATGTCCCTGGTCATA 58.697 43.478 0.00 0.00 0.00 2.15
2186 2251 4.347876 TCCACATAATGTCCCTGGTCATAG 59.652 45.833 0.00 0.00 0.00 2.23
2187 2252 4.505566 CCACATAATGTCCCTGGTCATAGG 60.506 50.000 0.00 0.00 37.59 2.57
2188 2253 4.347876 CACATAATGTCCCTGGTCATAGGA 59.652 45.833 0.00 0.00 40.42 2.94
2189 2254 5.013495 CACATAATGTCCCTGGTCATAGGAT 59.987 44.000 0.00 0.00 40.42 3.24
2190 2255 5.013495 ACATAATGTCCCTGGTCATAGGATG 59.987 44.000 0.00 4.57 40.42 3.51
2191 2256 2.866923 TGTCCCTGGTCATAGGATGA 57.133 50.000 0.00 0.00 40.42 2.92
2192 2257 3.350992 TGTCCCTGGTCATAGGATGAT 57.649 47.619 0.00 0.00 42.04 2.45
2193 2258 3.242867 TGTCCCTGGTCATAGGATGATC 58.757 50.000 0.00 0.00 42.04 2.92
2202 2267 7.959658 TGGTCATAGGATGATCAACAAAAAT 57.040 32.000 0.00 0.00 46.70 1.82
2203 2268 8.365060 TGGTCATAGGATGATCAACAAAAATT 57.635 30.769 0.00 0.00 46.70 1.82
2204 2269 9.473007 TGGTCATAGGATGATCAACAAAAATTA 57.527 29.630 0.00 0.00 46.70 1.40
2211 2276 8.596293 AGGATGATCAACAAAAATTATGGTTGT 58.404 29.630 0.00 4.27 40.96 3.32
2212 2277 9.868277 GGATGATCAACAAAAATTATGGTTGTA 57.132 29.630 0.00 4.48 40.96 2.41
2218 2283 8.301002 TCAACAAAAATTATGGTTGTAGTAGGC 58.699 33.333 12.77 0.00 40.96 3.93
2219 2284 8.303876 CAACAAAAATTATGGTTGTAGTAGGCT 58.696 33.333 0.00 0.00 36.70 4.58
2220 2285 8.417273 ACAAAAATTATGGTTGTAGTAGGCTT 57.583 30.769 0.00 0.00 33.80 4.35
2221 2286 8.866093 ACAAAAATTATGGTTGTAGTAGGCTTT 58.134 29.630 0.00 0.00 33.80 3.51
2222 2287 9.705290 CAAAAATTATGGTTGTAGTAGGCTTTT 57.295 29.630 0.00 0.00 0.00 2.27
2223 2288 9.923143 AAAAATTATGGTTGTAGTAGGCTTTTC 57.077 29.630 0.00 0.00 0.00 2.29
2224 2289 8.644374 AAATTATGGTTGTAGTAGGCTTTTCA 57.356 30.769 0.00 0.00 0.00 2.69
2225 2290 8.644374 AATTATGGTTGTAGTAGGCTTTTCAA 57.356 30.769 0.00 0.00 0.00 2.69
2226 2291 8.644374 ATTATGGTTGTAGTAGGCTTTTCAAA 57.356 30.769 0.00 0.00 0.00 2.69
2227 2292 6.575162 ATGGTTGTAGTAGGCTTTTCAAAG 57.425 37.500 0.00 0.00 39.03 2.77
2290 2356 7.608761 AGAGTATATACTGTAGCCTTACTCTGC 59.391 40.741 20.13 0.12 41.53 4.26
2452 2519 0.757188 CTCCCGAGCATACCCTCACT 60.757 60.000 0.00 0.00 0.00 3.41
2471 2538 4.081420 TCACTTGCTTCCTATCTTCTCACC 60.081 45.833 0.00 0.00 0.00 4.02
2492 2560 8.827177 TCACCGAATCAATCCTAAATATGTAC 57.173 34.615 0.00 0.00 0.00 2.90
2710 2778 1.962822 CTGCCTTGCTTGCTCGACA 60.963 57.895 0.00 0.00 0.00 4.35
2777 2846 7.097834 CCTTTGTGTTACTTTGGTGGTTTTAA 58.902 34.615 0.00 0.00 0.00 1.52
2780 2849 9.503399 TTTGTGTTACTTTGGTGGTTTTAAAAT 57.497 25.926 3.52 0.00 0.00 1.82
2803 2872 1.311859 TCTGCTGCTCTTGTTTGTGG 58.688 50.000 0.00 0.00 0.00 4.17
2825 2894 3.432326 GCCCCTTGTCTTCGTATTCATCT 60.432 47.826 0.00 0.00 0.00 2.90
2827 2896 4.383118 CCCCTTGTCTTCGTATTCATCTGT 60.383 45.833 0.00 0.00 0.00 3.41
2828 2897 4.568359 CCCTTGTCTTCGTATTCATCTGTG 59.432 45.833 0.00 0.00 0.00 3.66
2853 2922 1.080025 CTTTCCGGACGGGTGTCTC 60.080 63.158 1.83 0.00 44.83 3.36
2854 2923 1.532316 TTTCCGGACGGGTGTCTCT 60.532 57.895 1.83 0.00 44.83 3.10
2855 2924 1.812686 TTTCCGGACGGGTGTCTCTG 61.813 60.000 1.83 0.00 44.83 3.35
2856 2925 2.675423 CCGGACGGGTGTCTCTGA 60.675 66.667 0.00 0.00 44.83 3.27
2858 2927 1.080705 CGGACGGGTGTCTCTGAAC 60.081 63.158 0.00 0.00 44.83 3.18
2877 2948 0.961753 CCCTTCCACTTTGCCAAGTC 59.038 55.000 0.00 0.00 41.69 3.01
2878 2949 1.479389 CCCTTCCACTTTGCCAAGTCT 60.479 52.381 0.00 0.00 41.69 3.24
2880 2951 3.486383 CCTTCCACTTTGCCAAGTCTTA 58.514 45.455 0.00 0.00 41.69 2.10
2905 2976 3.605634 CCATGTTATGGGAGTTTCGACA 58.394 45.455 0.00 0.00 46.86 4.35
2906 2977 4.199310 CCATGTTATGGGAGTTTCGACAT 58.801 43.478 0.00 0.00 46.86 3.06
2907 2978 4.640201 CCATGTTATGGGAGTTTCGACATT 59.360 41.667 0.00 0.00 46.86 2.71
2918 3001 0.669318 TTCGACATTCACGGTGCTCC 60.669 55.000 2.51 0.00 0.00 4.70
2923 3006 2.673368 GACATTCACGGTGCTCCTAAAG 59.327 50.000 2.51 0.00 0.00 1.85
2965 3117 2.698797 ACCTGGTTATATGACTGGACCG 59.301 50.000 13.85 0.00 33.07 4.79
2967 3119 3.386726 CCTGGTTATATGACTGGACCGAA 59.613 47.826 0.00 0.00 33.07 4.30
3012 3164 4.764940 GCAACAAATTTGCAACTAGCTTG 58.235 39.130 18.12 12.58 45.94 4.01
3027 3179 5.183228 ACTAGCTTGCGTTATGTTAACCAT 58.817 37.500 2.48 0.00 37.58 3.55
3031 3211 5.008613 AGCTTGCGTTATGTTAACCATATGG 59.991 40.000 20.68 20.68 35.96 2.74
3032 3212 5.757886 CTTGCGTTATGTTAACCATATGGG 58.242 41.667 25.55 8.07 44.81 4.00
3045 3225 3.820557 CCATATGGGTTTCTACAGGTGG 58.179 50.000 14.52 0.00 0.00 4.61
3046 3226 3.202151 CCATATGGGTTTCTACAGGTGGT 59.798 47.826 14.52 0.00 0.00 4.16
3047 3227 4.410883 CCATATGGGTTTCTACAGGTGGTA 59.589 45.833 14.52 0.00 0.00 3.25
3048 3228 5.073144 CCATATGGGTTTCTACAGGTGGTAT 59.927 44.000 14.52 0.00 0.00 2.73
3049 3229 3.992943 TGGGTTTCTACAGGTGGTATG 57.007 47.619 0.00 0.00 0.00 2.39
3050 3230 2.026636 TGGGTTTCTACAGGTGGTATGC 60.027 50.000 0.00 0.00 0.00 3.14
3051 3231 2.026636 GGGTTTCTACAGGTGGTATGCA 60.027 50.000 0.00 0.00 0.00 3.96
3052 3232 3.270877 GGTTTCTACAGGTGGTATGCAG 58.729 50.000 0.00 0.00 0.00 4.41
3053 3233 3.055385 GGTTTCTACAGGTGGTATGCAGA 60.055 47.826 0.00 0.00 0.00 4.26
3054 3234 4.564821 GGTTTCTACAGGTGGTATGCAGAA 60.565 45.833 0.00 0.00 30.05 3.02
3055 3235 4.901197 TTCTACAGGTGGTATGCAGAAA 57.099 40.909 0.00 0.00 29.22 2.52
3056 3236 5.435686 TTCTACAGGTGGTATGCAGAAAT 57.564 39.130 0.00 0.00 29.22 2.17
3057 3237 5.023533 TCTACAGGTGGTATGCAGAAATC 57.976 43.478 0.00 0.00 0.00 2.17
3058 3238 4.716784 TCTACAGGTGGTATGCAGAAATCT 59.283 41.667 0.00 0.00 0.00 2.40
3059 3239 4.307032 ACAGGTGGTATGCAGAAATCTT 57.693 40.909 0.00 0.00 0.00 2.40
3060 3240 5.435686 ACAGGTGGTATGCAGAAATCTTA 57.564 39.130 0.00 0.00 0.00 2.10
3061 3241 6.006275 ACAGGTGGTATGCAGAAATCTTAT 57.994 37.500 0.00 0.00 0.00 1.73
3062 3242 5.824624 ACAGGTGGTATGCAGAAATCTTATG 59.175 40.000 0.00 0.00 0.00 1.90
3068 3248 4.761235 ATGCAGAAATCTTATGATGCGG 57.239 40.909 0.00 0.00 32.44 5.69
3069 3249 2.291465 TGCAGAAATCTTATGATGCGGC 59.709 45.455 0.00 0.00 33.31 6.53
3093 3273 5.569059 CGAACATCATGAGTTGTAAAAAGGC 59.431 40.000 13.14 0.00 0.00 4.35
3113 3293 0.457853 TTCCATAGCGACGACAGTGC 60.458 55.000 0.00 0.00 0.00 4.40
3114 3294 1.878522 CCATAGCGACGACAGTGCC 60.879 63.158 0.00 0.00 0.00 5.01
3115 3295 2.102357 ATAGCGACGACAGTGCCG 59.898 61.111 0.00 0.00 0.00 5.69
3119 3299 3.103911 CGACGACAGTGCCGGTTC 61.104 66.667 1.90 0.00 0.00 3.62
3120 3300 2.028484 GACGACAGTGCCGGTTCA 59.972 61.111 1.90 0.00 0.00 3.18
3121 3301 2.279918 ACGACAGTGCCGGTTCAC 60.280 61.111 1.90 3.26 37.24 3.18
3122 3302 2.279851 CGACAGTGCCGGTTCACA 60.280 61.111 13.75 0.00 39.35 3.58
3124 3304 1.831389 CGACAGTGCCGGTTCACAAG 61.831 60.000 13.75 8.53 39.35 3.16
3135 3317 3.502211 CCGGTTCACAAGTATTTCTGCTT 59.498 43.478 0.00 0.00 0.00 3.91
3136 3318 4.466828 CGGTTCACAAGTATTTCTGCTTG 58.533 43.478 0.00 0.00 46.81 4.01
3144 3326 6.785488 CAAGTATTTCTGCTTGTACTCACA 57.215 37.500 0.00 0.00 39.45 3.58
3145 3327 7.369803 CAAGTATTTCTGCTTGTACTCACAT 57.630 36.000 0.00 0.00 39.45 3.21
3146 3328 6.974932 AGTATTTCTGCTTGTACTCACATG 57.025 37.500 0.00 0.00 33.76 3.21
3150 3332 6.726258 TTTCTGCTTGTACTCACATGTATG 57.274 37.500 0.00 0.00 33.76 2.39
3151 3333 4.183865 TCTGCTTGTACTCACATGTATGC 58.816 43.478 0.00 0.00 33.76 3.14
3154 3336 3.242543 GCTTGTACTCACATGTATGCTGC 60.243 47.826 0.00 0.00 33.76 5.25
3160 3342 3.822735 ACTCACATGTATGCTGCTGTTTT 59.177 39.130 0.00 0.00 0.00 2.43
3171 3353 2.982470 GCTGCTGTTTTCTCATTTTCCG 59.018 45.455 0.00 0.00 0.00 4.30
3172 3354 2.982470 CTGCTGTTTTCTCATTTTCCGC 59.018 45.455 0.00 0.00 0.00 5.54
3212 3394 1.981495 AGCTTACAACTTGCTCCCTCT 59.019 47.619 0.00 0.00 30.41 3.69
3216 3398 2.262423 ACAACTTGCTCCCTCTGTTC 57.738 50.000 0.00 0.00 0.00 3.18
3222 3404 2.957402 TGCTCCCTCTGTTCACAAAT 57.043 45.000 0.00 0.00 0.00 2.32
3223 3405 4.202461 ACTTGCTCCCTCTGTTCACAAATA 60.202 41.667 0.00 0.00 0.00 1.40
3224 3406 3.674997 TGCTCCCTCTGTTCACAAATAC 58.325 45.455 0.00 0.00 0.00 1.89
3225 3407 3.327757 TGCTCCCTCTGTTCACAAATACT 59.672 43.478 0.00 0.00 0.00 2.12
3231 3413 9.319143 CTCCCTCTGTTCACAAATACTTATAAG 57.681 37.037 11.05 11.05 0.00 1.73
3267 3449 4.307443 TCAATACGGACTACATGCAGAG 57.693 45.455 0.00 0.00 0.00 3.35
3269 3451 3.992260 ATACGGACTACATGCAGAGTC 57.008 47.619 14.75 14.75 41.19 3.36
3270 3452 1.840737 ACGGACTACATGCAGAGTCT 58.159 50.000 19.78 0.00 41.56 3.24
3272 3454 3.556999 ACGGACTACATGCAGAGTCTAT 58.443 45.455 19.78 9.91 41.56 1.98
3273 3455 4.715713 ACGGACTACATGCAGAGTCTATA 58.284 43.478 19.78 0.00 41.56 1.31
3274 3456 5.317808 ACGGACTACATGCAGAGTCTATAT 58.682 41.667 19.78 6.33 41.56 0.86
3275 3457 5.182190 ACGGACTACATGCAGAGTCTATATG 59.818 44.000 19.78 12.06 41.56 1.78
3276 3458 5.406649 GGACTACATGCAGAGTCTATATGC 58.593 45.833 19.78 5.63 46.62 3.14
3284 3533 3.122613 GCAGAGTCTATATGCATGAACGC 59.877 47.826 10.16 4.04 45.71 4.84
3340 3589 2.097825 GGATTCTGCTTGCTTCCACAT 58.902 47.619 0.00 0.00 0.00 3.21
3341 3590 2.159282 GGATTCTGCTTGCTTCCACATG 60.159 50.000 0.00 0.00 0.00 3.21
3398 3647 9.466497 AAGTTCATCACATTTCCACTATTACAT 57.534 29.630 0.00 0.00 0.00 2.29
3407 3658 9.474313 ACATTTCCACTATTACATTACAACCAT 57.526 29.630 0.00 0.00 0.00 3.55
3424 3675 5.418840 ACAACCATTCACAGTATCCCAATTC 59.581 40.000 0.00 0.00 0.00 2.17
3429 3680 4.649267 TCACAGTATCCCAATTCCACAA 57.351 40.909 0.00 0.00 0.00 3.33
3433 3684 5.476599 CACAGTATCCCAATTCCACAAAGAA 59.523 40.000 0.00 0.00 0.00 2.52
3436 3687 7.092716 CAGTATCCCAATTCCACAAAGAAAAG 58.907 38.462 0.00 0.00 0.00 2.27
3438 3689 5.789643 TCCCAATTCCACAAAGAAAAGAG 57.210 39.130 0.00 0.00 0.00 2.85
3450 3702 7.040823 CCACAAAGAAAAGAGCAGAAACTATCT 60.041 37.037 0.00 0.00 39.68 1.98
3461 3714 8.001875 AGAGCAGAAACTATCTTCTCACCTATA 58.998 37.037 7.64 0.00 46.98 1.31
3469 3722 7.807198 ACTATCTTCTCACCTATAGACACTGA 58.193 38.462 0.00 0.00 0.00 3.41
3475 3728 8.824756 TTCTCACCTATAGACACTGAACTATT 57.175 34.615 0.00 0.00 32.57 1.73
3476 3729 8.226819 TCTCACCTATAGACACTGAACTATTG 57.773 38.462 0.00 0.00 32.57 1.90
3477 3730 7.834681 TCTCACCTATAGACACTGAACTATTGT 59.165 37.037 0.00 0.00 32.57 2.71
3498 3751 7.979444 TTGTAGACCAAGAATTTACAAGGAG 57.021 36.000 0.00 0.00 32.32 3.69
3507 3760 4.946157 AGAATTTACAAGGAGTGCATGGAG 59.054 41.667 0.00 0.00 0.00 3.86
3617 3870 1.212490 CGCCGGCATGAACATTTGT 59.788 52.632 28.98 0.00 0.00 2.83
3641 3894 3.818787 CATTGCAGCGGCTGGACC 61.819 66.667 29.44 14.71 41.91 4.46
3737 3990 2.304180 CCTCCAGTCACACTTCTCCATT 59.696 50.000 0.00 0.00 0.00 3.16
3761 4014 3.411517 CTGGCGGTCCTCCCCATT 61.412 66.667 0.00 0.00 34.94 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.286121 ACATCACCCCCATCCGGT 60.286 61.111 0.00 0.00 0.00 5.28
42 46 1.695114 CCCCCAGATACGGCACATCA 61.695 60.000 0.00 0.00 0.00 3.07
184 188 2.284995 GAGGTCAGCCCACTCCCT 60.285 66.667 0.00 0.00 34.66 4.20
186 190 3.775654 CCGAGGTCAGCCCACTCC 61.776 72.222 0.00 0.00 34.66 3.85
464 471 0.981277 CCCACCTCCACCCTTATCGT 60.981 60.000 0.00 0.00 0.00 3.73
540 547 5.167121 CACTGTCTCTGTCATAACTCCTTG 58.833 45.833 0.00 0.00 0.00 3.61
544 551 5.047660 AGTTCCACTGTCTCTGTCATAACTC 60.048 44.000 0.00 0.00 0.00 3.01
549 556 3.674528 CAGTTCCACTGTCTCTGTCAT 57.325 47.619 0.00 0.00 41.19 3.06
565 593 2.086610 AATCCAACCACCTTGCAGTT 57.913 45.000 0.00 0.00 0.00 3.16
613 641 7.014711 CAGGTGACCTTATGACATATCAGTACT 59.985 40.741 0.00 0.00 38.57 2.73
616 644 5.070981 CCAGGTGACCTTATGACATATCAGT 59.929 44.000 0.00 0.00 38.57 3.41
623 651 4.042809 ACATTTCCAGGTGACCTTATGACA 59.957 41.667 0.00 0.00 0.00 3.58
631 659 2.514458 ATCCACATTTCCAGGTGACC 57.486 50.000 0.00 0.00 37.18 4.02
632 660 3.054361 ACCTATCCACATTTCCAGGTGAC 60.054 47.826 0.00 0.00 37.18 3.67
665 696 6.206829 GCTTCAACTAAACTACCAACCAATCT 59.793 38.462 0.00 0.00 0.00 2.40
669 700 3.810941 CGCTTCAACTAAACTACCAACCA 59.189 43.478 0.00 0.00 0.00 3.67
690 724 2.184322 CCCATCTGTCCCGTGACG 59.816 66.667 0.00 0.00 44.86 4.35
718 752 4.456911 CCAAAGCGATTCCATGTGCTATAT 59.543 41.667 0.00 0.00 36.49 0.86
719 753 3.814842 CCAAAGCGATTCCATGTGCTATA 59.185 43.478 0.00 0.00 36.49 1.31
720 754 2.620115 CCAAAGCGATTCCATGTGCTAT 59.380 45.455 0.00 0.00 36.49 2.97
721 755 2.016318 CCAAAGCGATTCCATGTGCTA 58.984 47.619 0.00 0.00 36.49 3.49
722 756 0.813184 CCAAAGCGATTCCATGTGCT 59.187 50.000 0.00 0.00 39.89 4.40
735 769 1.617018 GGGCCATTTCTCCCCAAAGC 61.617 60.000 4.39 0.00 38.70 3.51
762 796 1.267806 CAACCACAATCCAGAGCACAC 59.732 52.381 0.00 0.00 0.00 3.82
765 799 0.111061 AGCAACCACAATCCAGAGCA 59.889 50.000 0.00 0.00 0.00 4.26
776 810 2.349886 GAGATCGACATCAAGCAACCAC 59.650 50.000 0.00 0.00 0.00 4.16
789 823 9.762062 CAACATACTATATACTGTGAGATCGAC 57.238 37.037 0.00 0.00 0.00 4.20
791 825 8.454894 AGCAACATACTATATACTGTGAGATCG 58.545 37.037 0.00 0.00 0.00 3.69
964 1000 8.239998 AGAAATTTCAGTTAGCTAAATGTCAGC 58.760 33.333 27.65 15.84 39.41 4.26
1007 1043 3.135712 TGGCTTCTAACAGTCACCAAAGA 59.864 43.478 0.00 0.00 0.00 2.52
1176 1212 2.493907 GAAGGTTGCGCTCCTCGACT 62.494 60.000 21.00 8.92 41.67 4.18
1398 1434 1.203187 ACCTTGGACTCTGGAGCAGTA 60.203 52.381 0.00 0.00 32.61 2.74
1618 1660 3.565307 TGAAATCCAGGTCAAGCAAACT 58.435 40.909 0.00 0.00 0.00 2.66
1628 1670 2.025887 GTCAGGACCATGAAATCCAGGT 60.026 50.000 11.72 0.00 37.47 4.00
1659 1701 2.293122 TGAAACAGATTCCTTGCCAACG 59.707 45.455 0.00 0.00 37.22 4.10
1668 1710 4.361451 AATCACGCATGAAACAGATTCC 57.639 40.909 0.00 0.00 38.69 3.01
1674 1717 2.884012 AGGACAAATCACGCATGAAACA 59.116 40.909 0.00 0.00 38.69 2.83
1691 1743 7.222000 TCACCACCAAATAATTAAACAGGAC 57.778 36.000 0.00 0.00 0.00 3.85
1718 1770 4.454678 ACATGAACTCAACTGAGCAAGAA 58.545 39.130 6.63 0.00 45.79 2.52
1736 1794 6.034591 GCAATCTCCTGAAAGATTCAACATG 58.965 40.000 0.00 0.00 42.68 3.21
1818 1876 8.546083 AGTTGAGGATCTCATAATAGAACACT 57.454 34.615 0.00 0.00 40.39 3.55
1866 1924 1.830477 AGAAAACAAACCTGCTTGGCA 59.170 42.857 0.00 0.00 40.22 4.92
1898 1956 9.276590 CTGATAAATCATAATAGACCAGCACAA 57.723 33.333 0.00 0.00 36.02 3.33
1901 1959 9.929180 GTACTGATAAATCATAATAGACCAGCA 57.071 33.333 0.00 0.00 36.02 4.41
1933 1991 6.070021 TCAGATCCACATGGTTCTATTCAGTT 60.070 38.462 10.51 0.00 41.12 3.16
1947 2005 6.660800 ACTTTGAATCATCTCAGATCCACAT 58.339 36.000 0.00 0.00 0.00 3.21
1975 2033 9.268268 CAAGCCCGAATATTAGATAAAACTGTA 57.732 33.333 0.00 0.00 0.00 2.74
1988 2046 3.370978 CGCGATTATCAAGCCCGAATATT 59.629 43.478 0.00 0.00 0.00 1.28
1994 2052 0.597637 AGTCGCGATTATCAAGCCCG 60.598 55.000 14.06 0.00 0.00 6.13
1996 2054 6.648725 ATTATTAGTCGCGATTATCAAGCC 57.351 37.500 14.06 0.00 0.00 4.35
2007 2065 9.564041 GTACTTGTTATTCAATTATTAGTCGCG 57.436 33.333 0.00 0.00 35.35 5.87
2055 2116 9.616156 TCCTTGTTAACAGTTGTTACTCAAATA 57.384 29.630 8.56 9.04 39.92 1.40
2056 2117 8.514330 TCCTTGTTAACAGTTGTTACTCAAAT 57.486 30.769 8.56 0.00 39.92 2.32
2057 2118 7.925043 TCCTTGTTAACAGTTGTTACTCAAA 57.075 32.000 8.56 6.46 39.92 2.69
2058 2119 7.925043 TTCCTTGTTAACAGTTGTTACTCAA 57.075 32.000 8.56 11.05 39.92 3.02
2059 2120 7.771361 TGATTCCTTGTTAACAGTTGTTACTCA 59.229 33.333 8.56 5.03 39.92 3.41
2060 2121 8.149973 TGATTCCTTGTTAACAGTTGTTACTC 57.850 34.615 8.56 2.82 39.92 2.59
2061 2122 7.773690 ACTGATTCCTTGTTAACAGTTGTTACT 59.226 33.333 8.56 0.00 39.92 2.24
2062 2123 7.855904 CACTGATTCCTTGTTAACAGTTGTTAC 59.144 37.037 8.56 0.94 39.92 2.50
2063 2124 7.554835 ACACTGATTCCTTGTTAACAGTTGTTA 59.445 33.333 8.56 0.73 39.31 2.41
2064 2125 6.377146 ACACTGATTCCTTGTTAACAGTTGTT 59.623 34.615 8.56 2.75 41.73 2.83
2065 2126 5.885912 ACACTGATTCCTTGTTAACAGTTGT 59.114 36.000 8.56 0.94 36.64 3.32
2066 2127 6.377327 ACACTGATTCCTTGTTAACAGTTG 57.623 37.500 8.56 3.69 36.64 3.16
2067 2128 8.567948 CATAACACTGATTCCTTGTTAACAGTT 58.432 33.333 8.56 7.87 38.77 3.16
2068 2129 7.936847 TCATAACACTGATTCCTTGTTAACAGT 59.063 33.333 8.56 0.00 38.77 3.55
2069 2130 8.322906 TCATAACACTGATTCCTTGTTAACAG 57.677 34.615 8.56 3.50 38.77 3.16
2070 2131 7.094805 GCTCATAACACTGATTCCTTGTTAACA 60.095 37.037 3.59 3.59 38.77 2.41
2071 2132 7.119846 AGCTCATAACACTGATTCCTTGTTAAC 59.880 37.037 0.00 0.00 38.77 2.01
2072 2133 7.168219 AGCTCATAACACTGATTCCTTGTTAA 58.832 34.615 9.86 0.00 38.77 2.01
2081 2142 5.877012 CCAACTGTAGCTCATAACACTGATT 59.123 40.000 0.00 0.00 0.00 2.57
2083 2144 4.283467 ACCAACTGTAGCTCATAACACTGA 59.717 41.667 0.00 0.00 0.00 3.41
2094 2155 3.072476 TCTTTGCCTAACCAACTGTAGCT 59.928 43.478 0.00 0.00 0.00 3.32
2096 2157 4.455877 CCTTCTTTGCCTAACCAACTGTAG 59.544 45.833 0.00 0.00 0.00 2.74
2106 2169 3.637769 ACAACAACCCTTCTTTGCCTAA 58.362 40.909 0.00 0.00 0.00 2.69
2115 2178 1.681264 CAGGTCCAACAACAACCCTTC 59.319 52.381 0.00 0.00 33.33 3.46
2118 2181 1.770294 TTCAGGTCCAACAACAACCC 58.230 50.000 0.00 0.00 33.33 4.11
2121 2184 3.563808 CGATCTTTCAGGTCCAACAACAA 59.436 43.478 0.00 0.00 0.00 2.83
2141 2204 8.879759 GTGGAACAGTCATTATTTCTTTATCGA 58.120 33.333 0.00 0.00 41.80 3.59
2142 2205 8.664798 TGTGGAACAGTCATTATTTCTTTATCG 58.335 33.333 0.00 0.00 45.67 2.92
2159 2224 9.480766 TATGACCAGGGACATTATGTGGAACAG 62.481 44.444 1.24 0.00 39.72 3.16
2160 2225 7.776624 TATGACCAGGGACATTATGTGGAACA 61.777 42.308 1.24 4.97 40.19 3.18
2161 2226 3.279434 GACCAGGGACATTATGTGGAAC 58.721 50.000 1.24 0.00 37.35 3.62
2162 2227 2.916269 TGACCAGGGACATTATGTGGAA 59.084 45.455 1.24 0.00 32.26 3.53
2163 2228 2.556766 TGACCAGGGACATTATGTGGA 58.443 47.619 1.24 0.00 32.26 4.02
2164 2229 3.582998 ATGACCAGGGACATTATGTGG 57.417 47.619 1.24 0.00 0.00 4.17
2165 2230 4.347876 TCCTATGACCAGGGACATTATGTG 59.652 45.833 1.24 0.00 36.26 3.21
2168 2233 5.415065 TCATCCTATGACCAGGGACATTAT 58.585 41.667 8.49 0.00 36.26 1.28
2169 2234 4.826616 TCATCCTATGACCAGGGACATTA 58.173 43.478 8.49 0.00 36.26 1.90
2170 2235 3.668821 TCATCCTATGACCAGGGACATT 58.331 45.455 8.49 0.00 36.26 2.71
2171 2236 3.350992 TCATCCTATGACCAGGGACAT 57.649 47.619 8.28 8.28 36.26 3.06
2172 2237 2.866923 TCATCCTATGACCAGGGACA 57.133 50.000 0.00 0.00 36.26 4.02
2173 2238 3.242867 TGATCATCCTATGACCAGGGAC 58.757 50.000 0.00 0.00 43.01 4.46
2175 2240 3.392285 TGTTGATCATCCTATGACCAGGG 59.608 47.826 0.00 0.00 43.01 4.45
2176 2241 4.694760 TGTTGATCATCCTATGACCAGG 57.305 45.455 0.00 0.00 43.01 4.45
2178 2243 7.959658 ATTTTTGTTGATCATCCTATGACCA 57.040 32.000 0.00 0.00 43.01 4.02
2185 2250 8.596293 ACAACCATAATTTTTGTTGATCATCCT 58.404 29.630 16.25 0.00 40.30 3.24
2186 2251 8.776376 ACAACCATAATTTTTGTTGATCATCC 57.224 30.769 16.25 0.00 40.30 3.51
2192 2257 8.301002 GCCTACTACAACCATAATTTTTGTTGA 58.699 33.333 16.25 3.68 40.30 3.18
2193 2258 8.303876 AGCCTACTACAACCATAATTTTTGTTG 58.696 33.333 10.11 10.11 42.80 3.33
2194 2259 8.417273 AGCCTACTACAACCATAATTTTTGTT 57.583 30.769 0.00 0.00 35.18 2.83
2195 2260 8.417273 AAGCCTACTACAACCATAATTTTTGT 57.583 30.769 0.00 0.00 37.27 2.83
2196 2261 9.705290 AAAAGCCTACTACAACCATAATTTTTG 57.295 29.630 0.00 0.00 0.00 2.44
2197 2262 9.923143 GAAAAGCCTACTACAACCATAATTTTT 57.077 29.630 0.00 0.00 0.00 1.94
2198 2263 9.084533 TGAAAAGCCTACTACAACCATAATTTT 57.915 29.630 0.00 0.00 0.00 1.82
2199 2264 8.644374 TGAAAAGCCTACTACAACCATAATTT 57.356 30.769 0.00 0.00 0.00 1.82
2200 2265 8.644374 TTGAAAAGCCTACTACAACCATAATT 57.356 30.769 0.00 0.00 0.00 1.40
2201 2266 8.644374 TTTGAAAAGCCTACTACAACCATAAT 57.356 30.769 0.00 0.00 0.00 1.28
2202 2267 8.106247 CTTTGAAAAGCCTACTACAACCATAA 57.894 34.615 0.00 0.00 0.00 1.90
2203 2268 7.681939 CTTTGAAAAGCCTACTACAACCATA 57.318 36.000 0.00 0.00 0.00 2.74
2204 2269 6.575162 CTTTGAAAAGCCTACTACAACCAT 57.425 37.500 0.00 0.00 0.00 3.55
2255 2320 9.616156 GGCTACAGTATATACTCTGCTATCTTA 57.384 37.037 12.62 0.00 33.46 2.10
2274 2340 2.263077 CAACGCAGAGTAAGGCTACAG 58.737 52.381 0.00 0.00 0.00 2.74
2289 2355 1.580845 AAGCCTGACATGAGCAACGC 61.581 55.000 0.00 2.20 0.00 4.84
2290 2356 0.877071 AAAGCCTGACATGAGCAACG 59.123 50.000 0.00 0.00 0.00 4.10
2452 2519 3.096852 TCGGTGAGAAGATAGGAAGCAA 58.903 45.455 0.00 0.00 0.00 3.91
2492 2560 0.734942 CAGCCAAGCAAAGCGGAATG 60.735 55.000 0.00 0.00 0.00 2.67
2523 2591 2.681848 AGCATCCTTCATTTCTTCAGCG 59.318 45.455 0.00 0.00 0.00 5.18
2589 2657 4.442706 AGCGAGAAAGACAAGTTTCTGAA 58.557 39.130 3.64 0.00 45.00 3.02
2590 2658 4.060038 AGCGAGAAAGACAAGTTTCTGA 57.940 40.909 3.64 0.00 45.00 3.27
2777 2846 5.876460 ACAAACAAGAGCAGCAGAAAAATTT 59.124 32.000 0.00 0.00 0.00 1.82
2780 2849 4.175516 CACAAACAAGAGCAGCAGAAAAA 58.824 39.130 0.00 0.00 0.00 1.94
2803 2872 2.396590 TGAATACGAAGACAAGGGGC 57.603 50.000 0.00 0.00 0.00 5.80
2825 2894 2.206750 CGTCCGGAAAGAAGAAACACA 58.793 47.619 5.23 0.00 0.00 3.72
2827 2896 1.541670 CCCGTCCGGAAAGAAGAAACA 60.542 52.381 5.23 0.00 37.50 2.83
2828 2897 1.154197 CCCGTCCGGAAAGAAGAAAC 58.846 55.000 5.23 0.00 37.50 2.78
2853 2922 0.961753 GGCAAAGTGGAAGGGTTCAG 59.038 55.000 0.00 0.00 0.00 3.02
2854 2923 0.260230 TGGCAAAGTGGAAGGGTTCA 59.740 50.000 0.00 0.00 0.00 3.18
2855 2924 1.341209 CTTGGCAAAGTGGAAGGGTTC 59.659 52.381 0.00 0.00 0.00 3.62
2856 2925 1.342975 ACTTGGCAAAGTGGAAGGGTT 60.343 47.619 5.44 0.00 45.12 4.11
2858 2927 0.961753 GACTTGGCAAAGTGGAAGGG 59.038 55.000 12.33 0.00 46.84 3.95
2923 3006 7.425606 CAGGTAAATAATACTCCCAAATGTGC 58.574 38.462 0.00 0.00 0.00 4.57
2945 3097 2.963101 TCGGTCCAGTCATATAACCAGG 59.037 50.000 0.00 0.00 0.00 4.45
2965 3117 2.545532 CGTCTCCATCTCAGATGCCTTC 60.546 54.545 9.41 0.00 0.00 3.46
2967 3119 1.039068 CGTCTCCATCTCAGATGCCT 58.961 55.000 9.41 0.00 0.00 4.75
2973 3125 2.662006 TGCTTTCGTCTCCATCTCAG 57.338 50.000 0.00 0.00 0.00 3.35
2977 3129 3.896648 TTTGTTGCTTTCGTCTCCATC 57.103 42.857 0.00 0.00 0.00 3.51
3027 3179 4.141574 GCATACCACCTGTAGAAACCCATA 60.142 45.833 0.00 0.00 31.61 2.74
3031 3211 3.055385 TCTGCATACCACCTGTAGAAACC 60.055 47.826 0.00 0.00 33.26 3.27
3032 3212 4.202245 TCTGCATACCACCTGTAGAAAC 57.798 45.455 0.00 0.00 33.26 2.78
3033 3213 4.901197 TTCTGCATACCACCTGTAGAAA 57.099 40.909 2.06 0.00 40.74 2.52
3034 3214 4.901197 TTTCTGCATACCACCTGTAGAA 57.099 40.909 0.00 0.59 41.56 2.10
3035 3215 4.716784 AGATTTCTGCATACCACCTGTAGA 59.283 41.667 0.00 0.00 34.18 2.59
3036 3216 5.028549 AGATTTCTGCATACCACCTGTAG 57.971 43.478 0.00 0.00 31.61 2.74
3037 3217 5.435686 AAGATTTCTGCATACCACCTGTA 57.564 39.130 0.00 0.00 0.00 2.74
3038 3218 4.307032 AAGATTTCTGCATACCACCTGT 57.693 40.909 0.00 0.00 0.00 4.00
3039 3219 6.057533 TCATAAGATTTCTGCATACCACCTG 58.942 40.000 0.00 0.00 0.00 4.00
3040 3220 6.252599 TCATAAGATTTCTGCATACCACCT 57.747 37.500 0.00 0.00 0.00 4.00
3041 3221 6.569226 GCATCATAAGATTTCTGCATACCACC 60.569 42.308 0.00 0.00 30.20 4.61
3042 3222 6.376978 GCATCATAAGATTTCTGCATACCAC 58.623 40.000 0.00 0.00 30.20 4.16
3043 3223 5.179929 CGCATCATAAGATTTCTGCATACCA 59.820 40.000 0.00 0.00 30.20 3.25
3044 3224 5.391310 CCGCATCATAAGATTTCTGCATACC 60.391 44.000 0.00 0.00 30.20 2.73
3045 3225 5.625251 CCGCATCATAAGATTTCTGCATAC 58.375 41.667 0.00 0.00 30.20 2.39
3046 3226 4.154737 GCCGCATCATAAGATTTCTGCATA 59.845 41.667 0.00 0.00 30.20 3.14
3047 3227 3.057736 GCCGCATCATAAGATTTCTGCAT 60.058 43.478 0.00 0.00 30.20 3.96
3048 3228 2.291465 GCCGCATCATAAGATTTCTGCA 59.709 45.455 0.00 0.00 30.20 4.41
3049 3229 2.663879 CGCCGCATCATAAGATTTCTGC 60.664 50.000 0.00 0.00 30.20 4.26
3050 3230 2.802247 TCGCCGCATCATAAGATTTCTG 59.198 45.455 0.00 0.00 30.20 3.02
3051 3231 3.111853 TCGCCGCATCATAAGATTTCT 57.888 42.857 0.00 0.00 30.20 2.52
3052 3232 3.002246 TGTTCGCCGCATCATAAGATTTC 59.998 43.478 0.00 0.00 30.20 2.17
3053 3233 2.942376 TGTTCGCCGCATCATAAGATTT 59.058 40.909 0.00 0.00 30.20 2.17
3054 3234 2.560504 TGTTCGCCGCATCATAAGATT 58.439 42.857 0.00 0.00 30.20 2.40
3055 3235 2.238942 TGTTCGCCGCATCATAAGAT 57.761 45.000 0.00 0.00 33.87 2.40
3056 3236 2.135139 GATGTTCGCCGCATCATAAGA 58.865 47.619 0.64 0.00 41.56 2.10
3057 3237 1.866601 TGATGTTCGCCGCATCATAAG 59.133 47.619 3.70 0.00 45.18 1.73
3058 3238 1.946745 TGATGTTCGCCGCATCATAA 58.053 45.000 3.70 0.00 45.18 1.90
3059 3239 3.677002 TGATGTTCGCCGCATCATA 57.323 47.368 3.70 0.00 45.18 2.15
3060 3240 4.538233 TGATGTTCGCCGCATCAT 57.462 50.000 3.70 0.00 45.18 2.45
3062 3242 0.234106 CTCATGATGTTCGCCGCATC 59.766 55.000 0.00 0.00 42.10 3.91
3068 3248 5.569059 CCTTTTTACAACTCATGATGTTCGC 59.431 40.000 7.24 0.00 31.59 4.70
3069 3249 5.569059 GCCTTTTTACAACTCATGATGTTCG 59.431 40.000 7.24 6.60 31.59 3.95
3077 3257 6.127619 GCTATGGAAGCCTTTTTACAACTCAT 60.128 38.462 0.00 0.00 46.25 2.90
3093 3273 1.550065 CACTGTCGTCGCTATGGAAG 58.450 55.000 0.00 0.00 0.00 3.46
3113 3293 3.074412 AGCAGAAATACTTGTGAACCGG 58.926 45.455 0.00 0.00 0.00 5.28
3114 3294 4.466828 CAAGCAGAAATACTTGTGAACCG 58.533 43.478 0.00 0.00 38.75 4.44
3121 3301 6.785488 TGTGAGTACAAGCAGAAATACTTG 57.215 37.500 0.00 0.00 46.91 3.16
3122 3302 6.936900 ACATGTGAGTACAAGCAGAAATACTT 59.063 34.615 0.00 0.00 40.84 2.24
3124 3304 6.727824 ACATGTGAGTACAAGCAGAAATAC 57.272 37.500 0.00 0.00 40.84 1.89
3135 3317 3.055891 ACAGCAGCATACATGTGAGTACA 60.056 43.478 9.11 0.00 41.89 2.90
3136 3318 3.525537 ACAGCAGCATACATGTGAGTAC 58.474 45.455 9.11 0.00 0.00 2.73
3138 3320 2.775911 ACAGCAGCATACATGTGAGT 57.224 45.000 9.11 0.00 0.00 3.41
3139 3321 4.155462 AGAAAACAGCAGCATACATGTGAG 59.845 41.667 9.11 1.45 0.00 3.51
3140 3322 4.074259 AGAAAACAGCAGCATACATGTGA 58.926 39.130 9.11 0.00 0.00 3.58
3141 3323 4.083164 TGAGAAAACAGCAGCATACATGTG 60.083 41.667 9.11 0.00 0.00 3.21
3142 3324 4.074259 TGAGAAAACAGCAGCATACATGT 58.926 39.130 2.69 2.69 0.00 3.21
3143 3325 4.690184 TGAGAAAACAGCAGCATACATG 57.310 40.909 0.00 0.00 0.00 3.21
3144 3326 5.909621 AATGAGAAAACAGCAGCATACAT 57.090 34.783 0.00 0.00 0.00 2.29
3145 3327 5.710513 AAATGAGAAAACAGCAGCATACA 57.289 34.783 0.00 0.00 0.00 2.29
3146 3328 5.574443 GGAAAATGAGAAAACAGCAGCATAC 59.426 40.000 0.00 0.00 0.00 2.39
3150 3332 2.982470 CGGAAAATGAGAAAACAGCAGC 59.018 45.455 0.00 0.00 0.00 5.25
3151 3333 2.982470 GCGGAAAATGAGAAAACAGCAG 59.018 45.455 0.00 0.00 0.00 4.24
3154 3336 3.503748 AGGAGCGGAAAATGAGAAAACAG 59.496 43.478 0.00 0.00 0.00 3.16
3160 3342 2.618045 GGGAAAGGAGCGGAAAATGAGA 60.618 50.000 0.00 0.00 0.00 3.27
3171 3353 0.899717 TGTTGCATGGGGAAAGGAGC 60.900 55.000 0.00 0.00 0.00 4.70
3172 3354 1.631405 TTGTTGCATGGGGAAAGGAG 58.369 50.000 0.00 0.00 0.00 3.69
3239 3421 7.441836 TGCATGTAGTCCGTATTGAAATATCT 58.558 34.615 0.00 0.00 0.00 1.98
3253 3435 5.047731 TGCATATAGACTCTGCATGTAGTCC 60.048 44.000 10.80 1.82 42.56 3.85
3262 3444 3.122613 GCGTTCATGCATATAGACTCTGC 59.877 47.826 0.00 0.00 36.45 4.26
3267 3449 2.738846 CCCTGCGTTCATGCATATAGAC 59.261 50.000 0.00 0.00 45.26 2.59
3269 3451 2.998670 CTCCCTGCGTTCATGCATATAG 59.001 50.000 0.00 0.00 45.26 1.31
3270 3452 2.368548 ACTCCCTGCGTTCATGCATATA 59.631 45.455 0.00 0.00 45.26 0.86
3272 3454 0.541392 ACTCCCTGCGTTCATGCATA 59.459 50.000 0.00 0.00 45.26 3.14
3273 3455 0.541392 TACTCCCTGCGTTCATGCAT 59.459 50.000 0.00 0.00 45.26 3.96
3274 3456 0.391130 GTACTCCCTGCGTTCATGCA 60.391 55.000 0.00 0.00 43.95 3.96
3275 3457 0.391130 TGTACTCCCTGCGTTCATGC 60.391 55.000 0.00 0.00 0.00 4.06
3276 3458 2.315925 ATGTACTCCCTGCGTTCATG 57.684 50.000 0.00 0.00 0.00 3.07
3277 3459 3.388024 ACATATGTACTCCCTGCGTTCAT 59.612 43.478 6.56 0.00 0.00 2.57
3282 3531 1.270305 CCCACATATGTACTCCCTGCG 60.270 57.143 8.32 0.00 0.00 5.18
3284 3533 1.768275 TGCCCACATATGTACTCCCTG 59.232 52.381 8.32 0.00 0.00 4.45
3318 3567 2.097825 GTGGAAGCAAGCAGAATCCAT 58.902 47.619 10.54 0.00 41.83 3.41
3340 3589 2.158667 AGCATGATCCATCAGTGCATCA 60.159 45.455 18.22 0.00 40.50 3.07
3341 3590 2.484651 GAGCATGATCCATCAGTGCATC 59.515 50.000 18.22 12.29 40.50 3.91
3398 3647 5.506730 TGGGATACTGTGAATGGTTGTAA 57.493 39.130 0.00 0.00 0.00 2.41
3407 3658 4.649267 TGTGGAATTGGGATACTGTGAA 57.351 40.909 0.00 0.00 0.00 3.18
3424 3675 5.254339 AGTTTCTGCTCTTTTCTTTGTGG 57.746 39.130 0.00 0.00 0.00 4.17
3438 3689 8.079809 GTCTATAGGTGAGAAGATAGTTTCTGC 58.920 40.741 0.00 0.00 37.53 4.26
3450 3702 8.687242 CAATAGTTCAGTGTCTATAGGTGAGAA 58.313 37.037 0.00 0.00 0.00 2.87
3461 3714 6.493802 TCTTGGTCTACAATAGTTCAGTGTCT 59.506 38.462 0.00 0.00 38.65 3.41
3475 3728 6.934645 CACTCCTTGTAAATTCTTGGTCTACA 59.065 38.462 0.00 0.00 0.00 2.74
3476 3729 6.128254 GCACTCCTTGTAAATTCTTGGTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
3477 3730 5.938125 GCACTCCTTGTAAATTCTTGGTCTA 59.062 40.000 0.00 0.00 0.00 2.59
3507 3760 1.726853 CTGGAAGACGGATGGACAAC 58.273 55.000 0.00 0.00 34.07 3.32
3638 3891 1.522580 GAAGCAGGCGGAGATGGTC 60.523 63.158 0.00 0.00 0.00 4.02
3641 3894 0.813210 GGAAGAAGCAGGCGGAGATG 60.813 60.000 0.00 0.00 0.00 2.90
3761 4014 2.654877 GACGAGTTCAGGGGCGAA 59.345 61.111 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.