Multiple sequence alignment - TraesCS6A01G150200

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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 TraesCS6A01G150200 chr6A 100.000 3045 0 0 1 3045 133827020 133823976 0.000000e+00 5624.0
1 TraesCS6A01G150200 chr6D 88.557 2246 135 45 1 2181 108815974 108813786 0.000000e+00 2612.0
2 TraesCS6A01G150200 chr6D 85.679 817 81 20 2181 2990 108812100 108811313 0.000000e+00 828.0
3 TraesCS6A01G150200 chr6D 86.047 86 11 1 2373 2458 85212622 85212538 1.160000e-14 91.6
4 TraesCS6A01G150200 chr6B 88.686 1971 113 45 8 1943 198205691 198203796 0.000000e+00 2303.0
5 TraesCS6A01G150200 chr3A 85.185 81 11 1 2378 2458 8231993 8231914 7.000000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G150200 chr6A 133823976 133827020 3044 True 5624 5624 100.000 1 3045 1 chr6A.!!$R1 3044
1 TraesCS6A01G150200 chr6D 108811313 108815974 4661 True 1720 2612 87.118 1 2990 2 chr6D.!!$R2 2989
2 TraesCS6A01G150200 chr6B 198203796 198205691 1895 True 2303 2303 88.686 8 1943 1 chr6B.!!$R1 1935

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
736 764 0.170784 ATGCGCGCATGTTCAATTGA 59.829 45.000 42.86 14.22 35.03 2.57 F
1054 1095 0.179043 TCGACATCGAGGAGGAGGAG 60.179 60.000 3.06 0.00 44.22 3.69 F
1731 1798 1.000607 TGAAAACAGAGACGACCGGAG 60.001 52.381 9.46 3.87 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1872 0.034186 AGATCTTGGCCATTCCGCAA 60.034 50.0 6.09 0.0 37.80 4.85 R
1864 1945 0.043334 ACACCTGCCTCCTACCTCAT 59.957 55.0 0.00 0.0 0.00 2.90 R
2627 4398 0.108329 CAGGGTGGTACGCGATTCTT 60.108 55.0 15.93 0.0 41.51 2.52 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
94 98 1.353694 GGATGCTCCCTATGCCAAGAT 59.646 52.381 0.00 0.00 0.00 2.40
96 100 1.510492 TGCTCCCTATGCCAAGATGA 58.490 50.000 0.00 0.00 0.00 2.92
117 121 8.091449 AGATGAGAGAATTACATTTACCCGATC 58.909 37.037 0.00 0.00 0.00 3.69
119 123 5.539048 AGAGAATTACATTTACCCGATCGG 58.461 41.667 27.65 27.65 37.81 4.18
121 125 5.677567 AGAATTACATTTACCCGATCGGTT 58.322 37.500 31.22 21.72 45.36 4.44
122 126 5.756833 AGAATTACATTTACCCGATCGGTTC 59.243 40.000 31.22 22.19 45.36 3.62
139 143 3.630101 GGTTCTCACCGAGATATCGTTC 58.370 50.000 9.16 0.00 38.56 3.95
225 231 0.884514 CCATCTGCGCTAGCTAGCTA 59.115 55.000 36.02 25.55 46.85 3.32
226 232 1.135431 CCATCTGCGCTAGCTAGCTAG 60.135 57.143 37.09 37.09 46.85 3.42
493 505 2.839632 TCCGCAGCCTCCGATGAT 60.840 61.111 0.00 0.00 0.00 2.45
495 507 2.418777 CGCAGCCTCCGATGATCA 59.581 61.111 0.00 0.00 0.00 2.92
496 508 1.953138 CGCAGCCTCCGATGATCAC 60.953 63.158 0.00 0.00 0.00 3.06
497 509 1.596477 GCAGCCTCCGATGATCACC 60.596 63.158 0.00 0.00 0.00 4.02
499 511 1.455773 AGCCTCCGATGATCACCGA 60.456 57.895 12.18 0.00 0.00 4.69
500 512 0.829602 AGCCTCCGATGATCACCGAT 60.830 55.000 12.18 0.00 0.00 4.18
501 513 0.668706 GCCTCCGATGATCACCGATG 60.669 60.000 12.18 2.72 0.00 3.84
502 514 0.961753 CCTCCGATGATCACCGATGA 59.038 55.000 12.18 0.00 39.83 2.92
525 537 1.274167 ACGGTTTAAGAGCACGGATCA 59.726 47.619 0.00 0.00 0.00 2.92
550 577 3.979789 CACCCGCATTGTGCTACA 58.020 55.556 0.10 0.00 42.25 2.74
551 578 1.501741 CACCCGCATTGTGCTACAC 59.498 57.895 0.10 0.00 42.25 2.90
552 579 1.072332 ACCCGCATTGTGCTACACA 59.928 52.632 0.00 0.00 42.25 3.72
553 580 0.322456 ACCCGCATTGTGCTACACAT 60.322 50.000 0.57 0.00 44.16 3.21
554 581 0.810648 CCCGCATTGTGCTACACATT 59.189 50.000 0.57 0.00 44.16 2.71
555 582 1.202177 CCCGCATTGTGCTACACATTC 60.202 52.381 0.57 0.00 44.16 2.67
556 583 1.529622 CCGCATTGTGCTACACATTCG 60.530 52.381 0.57 5.71 44.16 3.34
557 584 1.128507 CGCATTGTGCTACACATTCGT 59.871 47.619 0.57 0.00 44.16 3.85
558 585 2.347150 CGCATTGTGCTACACATTCGTA 59.653 45.455 0.57 0.00 44.16 3.43
574 601 7.325338 ACACATTCGTACGTACATAATATGCTC 59.675 37.037 24.50 0.00 0.00 4.26
635 663 2.110578 TCTCGAAAGGATCATGGCAGA 58.889 47.619 0.00 0.00 0.00 4.26
658 686 3.368843 GTGGCAATAACAAAATGCAGAGC 59.631 43.478 0.00 0.00 41.80 4.09
675 703 2.301296 AGAGCAATCAGATACGGGGATG 59.699 50.000 0.00 0.00 0.00 3.51
676 704 1.160137 GCAATCAGATACGGGGATGC 58.840 55.000 0.00 0.00 0.00 3.91
677 705 1.271054 GCAATCAGATACGGGGATGCT 60.271 52.381 0.00 0.00 0.00 3.79
678 706 2.693069 CAATCAGATACGGGGATGCTC 58.307 52.381 0.00 0.00 0.00 4.26
704 732 2.112279 ACCTTGTACTCCCCAACTCA 57.888 50.000 0.00 0.00 0.00 3.41
735 763 2.656137 ATGCGCGCATGTTCAATTG 58.344 47.368 42.86 0.00 35.03 2.32
736 764 0.170784 ATGCGCGCATGTTCAATTGA 59.829 45.000 42.86 14.22 35.03 2.57
740 768 2.718490 GCGCGCATGTTCAATTGAAAAC 60.718 45.455 29.10 12.43 35.58 2.43
757 786 4.083324 TGAAAACAATCCGAGCTGTTCATC 60.083 41.667 0.00 0.00 34.71 2.92
763 792 1.012086 CCGAGCTGTTCATCCATGTG 58.988 55.000 0.00 0.00 0.00 3.21
764 793 1.676916 CCGAGCTGTTCATCCATGTGT 60.677 52.381 0.00 0.00 0.00 3.72
1007 1046 2.804527 CACACACAATGTCAGAGTCAGG 59.195 50.000 0.00 0.00 40.64 3.86
1052 1093 4.561452 TCGACATCGAGGAGGAGG 57.439 61.111 3.06 0.00 44.22 4.30
1053 1094 1.912971 TCGACATCGAGGAGGAGGA 59.087 57.895 3.06 0.00 44.22 3.71
1054 1095 0.179043 TCGACATCGAGGAGGAGGAG 60.179 60.000 3.06 0.00 44.22 3.69
1069 1110 1.880340 GGAGTCCATTGCTCGAGCG 60.880 63.158 30.75 17.44 45.83 5.03
1162 1203 1.067749 CTGAGCCTGAGATCCTGCG 59.932 63.158 0.00 0.00 0.00 5.18
1188 1229 2.681064 GCCATGGGCCTGCAAGAA 60.681 61.111 15.13 0.00 44.06 2.52
1359 1400 1.514443 GACGACGAGGCGGAAGAAG 60.514 63.158 0.00 0.00 35.12 2.85
1360 1401 2.202623 CGACGAGGCGGAAGAAGG 60.203 66.667 0.00 0.00 0.00 3.46
1372 1413 1.536662 AAGAAGGTGGCGAGGAGGT 60.537 57.895 0.00 0.00 0.00 3.85
1396 1437 3.141488 CCCAGAGGAGGACGACGG 61.141 72.222 0.00 0.00 33.47 4.79
1594 1635 4.368543 GACCGTCGTCCCACCACC 62.369 72.222 0.00 0.00 32.40 4.61
1596 1637 4.675029 CCGTCGTCCCACCACCAC 62.675 72.222 0.00 0.00 0.00 4.16
1607 1648 2.759114 CCACCACATGGCAGGTCT 59.241 61.111 0.00 0.00 43.24 3.85
1635 1693 1.080093 CTGTGCCCTGCATGCAAAG 60.080 57.895 22.88 16.46 41.91 2.77
1731 1798 1.000607 TGAAAACAGAGACGACCGGAG 60.001 52.381 9.46 3.87 0.00 4.63
1768 1835 2.985896 TGGAAACCAAGAATAGCGAGG 58.014 47.619 0.00 0.00 0.00 4.63
1769 1836 1.671328 GGAAACCAAGAATAGCGAGGC 59.329 52.381 0.00 0.00 0.00 4.70
1822 1899 2.614057 CGGAATGGCCAAGATCTTGTAC 59.386 50.000 29.03 22.01 38.85 2.90
1858 1939 3.153919 AGATCTAGGATCTCGGAACTGC 58.846 50.000 0.00 0.00 0.00 4.40
1863 1944 1.590259 GATCTCGGAACTGCGAGGC 60.590 63.158 18.70 9.11 33.50 4.70
1864 1945 2.284798 GATCTCGGAACTGCGAGGCA 62.285 60.000 18.70 2.99 36.92 4.75
1865 1946 1.680522 ATCTCGGAACTGCGAGGCAT 61.681 55.000 18.70 5.12 38.13 4.40
1867 1948 2.125552 CGGAACTGCGAGGCATGA 60.126 61.111 0.00 0.00 38.13 3.07
1868 1949 2.169789 CGGAACTGCGAGGCATGAG 61.170 63.158 0.00 0.00 38.13 2.90
1869 1950 1.817099 GGAACTGCGAGGCATGAGG 60.817 63.158 0.00 0.00 38.13 3.86
1870 1951 1.078848 GAACTGCGAGGCATGAGGT 60.079 57.895 0.00 0.00 38.13 3.85
1871 1952 0.175760 GAACTGCGAGGCATGAGGTA 59.824 55.000 0.00 0.00 38.13 3.08
1872 1953 0.176680 AACTGCGAGGCATGAGGTAG 59.823 55.000 0.00 0.00 38.13 3.18
1873 1954 1.068753 CTGCGAGGCATGAGGTAGG 59.931 63.158 0.00 0.00 38.13 3.18
1874 1955 1.381191 TGCGAGGCATGAGGTAGGA 60.381 57.895 0.00 0.00 31.71 2.94
1875 1956 1.365633 GCGAGGCATGAGGTAGGAG 59.634 63.158 0.00 0.00 0.00 3.69
1876 1957 2.045280 CGAGGCATGAGGTAGGAGG 58.955 63.158 0.00 0.00 0.00 4.30
1879 1960 1.053264 AGGCATGAGGTAGGAGGCAG 61.053 60.000 0.00 0.00 0.00 4.85
1894 1975 3.127533 CAGGTGTTAGCAGCGGCC 61.128 66.667 4.82 0.00 46.77 6.13
1962 2043 2.348998 CCAGCCGGGGAGATATGC 59.651 66.667 2.18 0.00 0.00 3.14
1968 2049 1.302033 CGGGGAGATATGCAGGTGC 60.302 63.158 0.00 0.00 42.50 5.01
1977 2058 1.766494 TATGCAGGTGCTGGGAATTG 58.234 50.000 3.18 0.00 42.66 2.32
1988 2069 0.464373 TGGGAATTGCCAGCTCGATC 60.464 55.000 15.64 0.00 38.95 3.69
1989 2070 0.464373 GGGAATTGCCAGCTCGATCA 60.464 55.000 11.71 0.00 38.95 2.92
2000 2081 3.374988 CCAGCTCGATCATGCTTGTAAAA 59.625 43.478 6.70 0.00 37.44 1.52
2016 2097 6.928492 GCTTGTAAAAATGGACTTGGAATTCA 59.072 34.615 7.93 0.00 0.00 2.57
2028 2109 2.571212 TGGAATTCAGTTGTGTTCGCT 58.429 42.857 7.93 0.00 0.00 4.93
2031 2112 3.003275 GGAATTCAGTTGTGTTCGCTTCA 59.997 43.478 7.93 0.00 0.00 3.02
2032 2113 3.885484 ATTCAGTTGTGTTCGCTTCAG 57.115 42.857 0.00 0.00 0.00 3.02
2034 2115 2.627945 TCAGTTGTGTTCGCTTCAGTT 58.372 42.857 0.00 0.00 0.00 3.16
2045 2126 3.076621 TCGCTTCAGTTCATGCTGATTT 58.923 40.909 4.16 0.00 43.99 2.17
2055 2136 5.459762 AGTTCATGCTGATTTGTTTGTTTCG 59.540 36.000 0.00 0.00 0.00 3.46
2064 2145 7.323049 TGATTTGTTTGTTTCGTCTTCCTTA 57.677 32.000 0.00 0.00 0.00 2.69
2067 2148 7.979115 TTTGTTTGTTTCGTCTTCCTTATTG 57.021 32.000 0.00 0.00 0.00 1.90
2079 2160 7.558807 TCGTCTTCCTTATTGTCCTCTGTAATA 59.441 37.037 0.00 0.00 0.00 0.98
2131 2214 6.359617 CGAAAAATTTATGTCGTCTGCTTGTT 59.640 34.615 9.50 0.00 0.00 2.83
2135 2218 1.229428 ATGTCGTCTGCTTGTTGGTG 58.771 50.000 0.00 0.00 0.00 4.17
2141 2224 1.065551 GTCTGCTTGTTGGTGTTGTCC 59.934 52.381 0.00 0.00 0.00 4.02
2143 2226 2.171659 TCTGCTTGTTGGTGTTGTCCTA 59.828 45.455 0.00 0.00 0.00 2.94
2144 2227 2.948979 CTGCTTGTTGGTGTTGTCCTAA 59.051 45.455 0.00 0.00 0.00 2.69
2148 2231 4.202111 GCTTGTTGGTGTTGTCCTAATGTT 60.202 41.667 0.00 0.00 0.00 2.71
2160 2243 7.602644 TGTTGTCCTAATGTTGATGTTCTAGTC 59.397 37.037 0.00 0.00 0.00 2.59
2169 2252 6.533730 TGTTGATGTTCTAGTCTTCATTGGT 58.466 36.000 0.00 0.00 0.00 3.67
2177 2260 1.165270 GTCTTCATTGGTTGGACCGG 58.835 55.000 0.00 0.00 42.58 5.28
2184 3953 3.053991 TCATTGGTTGGACCGGTATTCAT 60.054 43.478 7.34 0.00 42.58 2.57
2209 3978 2.256117 AAATCCTTATCCCGCCTTCG 57.744 50.000 0.00 0.00 0.00 3.79
2220 3989 2.359975 GCCTTCGGGTGGGTCTTG 60.360 66.667 0.00 0.00 37.45 3.02
2222 3991 1.991230 CCTTCGGGTGGGTCTTGAT 59.009 57.895 0.00 0.00 0.00 2.57
2225 3994 1.210478 CTTCGGGTGGGTCTTGATGAT 59.790 52.381 0.00 0.00 0.00 2.45
2227 3996 0.541392 CGGGTGGGTCTTGATGATGA 59.459 55.000 0.00 0.00 0.00 2.92
2236 4005 4.701651 GGGTCTTGATGATGATGACACAAA 59.298 41.667 0.96 0.00 31.98 2.83
2258 4027 1.263217 GTGTACTGCCTTTTGACGGTG 59.737 52.381 0.00 0.00 0.00 4.94
2259 4028 0.237498 GTACTGCCTTTTGACGGTGC 59.763 55.000 0.00 0.00 0.00 5.01
2266 4035 0.109597 CTTTTGACGGTGCTGATGCC 60.110 55.000 0.00 0.00 38.71 4.40
2285 4054 2.929592 GCCGAAGAATGGTCACGTAGTT 60.930 50.000 0.00 0.00 41.61 2.24
2300 4069 6.793680 GTCACGTAGTTGTAGGTAATTTTTGC 59.206 38.462 0.00 0.00 41.61 3.68
2321 4090 3.119849 GCCGCTTCTTGTAATGTGTTGAT 60.120 43.478 0.00 0.00 0.00 2.57
2326 4095 6.303970 CGCTTCTTGTAATGTGTTGATCTTTG 59.696 38.462 0.00 0.00 0.00 2.77
2332 4101 0.961019 TGTGTTGATCTTTGCTGGCC 59.039 50.000 0.00 0.00 0.00 5.36
2334 4103 1.068055 GTGTTGATCTTTGCTGGCCTG 60.068 52.381 3.32 4.26 0.00 4.85
2345 4114 1.296727 GCTGGCCTGTTTCGTATACC 58.703 55.000 11.69 0.00 0.00 2.73
2361 4130 4.454504 CGTATACCTTGTTGCAAGAGGTTT 59.545 41.667 29.41 24.86 40.83 3.27
2367 4136 5.362430 ACCTTGTTGCAAGAGGTTTTATCAA 59.638 36.000 22.65 9.36 40.83 2.57
2405 4174 4.461431 GGGGGTTTCGTTCTTATGTCATTT 59.539 41.667 0.00 0.00 0.00 2.32
2407 4176 5.182380 GGGGTTTCGTTCTTATGTCATTTCA 59.818 40.000 0.00 0.00 0.00 2.69
2411 4180 9.026074 GGTTTCGTTCTTATGTCATTTCAAAAA 57.974 29.630 0.00 0.00 0.00 1.94
2442 4211 3.780804 TGGGACTTTTCGAAGATTGGA 57.219 42.857 0.00 0.00 35.04 3.53
2452 4221 8.095169 ACTTTTCGAAGATTGGATGTAGTTAGT 58.905 33.333 0.00 0.00 35.04 2.24
2474 4243 9.613428 TTAGTCAATTTACTAATGGGTGATCTG 57.387 33.333 7.93 0.00 37.10 2.90
2476 4245 6.828785 GTCAATTTACTAATGGGTGATCTGGT 59.171 38.462 0.00 0.00 0.00 4.00
2477 4246 7.990886 GTCAATTTACTAATGGGTGATCTGGTA 59.009 37.037 0.00 0.00 0.00 3.25
2494 4263 4.518970 TCTGGTATGTGCAAAAGGAAACTC 59.481 41.667 0.00 0.00 42.68 3.01
2496 4265 3.365969 GGTATGTGCAAAAGGAAACTCCG 60.366 47.826 0.00 0.00 42.75 4.63
2498 4267 1.673920 TGTGCAAAAGGAAACTCCGTC 59.326 47.619 0.00 0.00 42.75 4.79
2502 4271 1.798813 CAAAAGGAAACTCCGTCCTCG 59.201 52.381 0.00 0.00 45.12 4.63
2507 4276 1.477295 GGAAACTCCGTCCTCGATTCT 59.523 52.381 0.00 0.00 39.71 2.40
2508 4277 2.531206 GAAACTCCGTCCTCGATTCTG 58.469 52.381 0.00 0.00 39.71 3.02
2539 4308 7.993821 TTTTTATGAAATCTTTTCGTGTGCA 57.006 28.000 5.23 0.00 0.00 4.57
2540 4309 8.586570 TTTTTATGAAATCTTTTCGTGTGCAT 57.413 26.923 0.00 0.00 0.00 3.96
2541 4310 7.795431 TTTATGAAATCTTTTCGTGTGCATC 57.205 32.000 0.00 0.00 0.00 3.91
2542 4311 5.633830 ATGAAATCTTTTCGTGTGCATCT 57.366 34.783 0.00 0.00 0.00 2.90
2546 4315 7.421599 TGAAATCTTTTCGTGTGCATCTTTTA 58.578 30.769 0.00 0.00 0.00 1.52
2560 4329 4.218417 GCATCTTTTAGGTGGAAGCTTTGA 59.782 41.667 0.00 0.00 46.63 2.69
2563 4332 6.976934 TCTTTTAGGTGGAAGCTTTGATTT 57.023 33.333 0.00 0.00 46.63 2.17
2565 4334 6.777580 TCTTTTAGGTGGAAGCTTTGATTTCT 59.222 34.615 0.00 0.00 46.63 2.52
2619 4390 6.485830 TTTCTAATGATCGATCCAACCTCT 57.514 37.500 22.31 2.21 0.00 3.69
2620 4391 6.485830 TTCTAATGATCGATCCAACCTCTT 57.514 37.500 22.31 7.24 0.00 2.85
2621 4392 6.485830 TCTAATGATCGATCCAACCTCTTT 57.514 37.500 22.31 4.84 0.00 2.52
2622 4393 7.597288 TCTAATGATCGATCCAACCTCTTTA 57.403 36.000 22.31 5.70 0.00 1.85
2623 4394 8.018537 TCTAATGATCGATCCAACCTCTTTAA 57.981 34.615 22.31 0.00 0.00 1.52
2624 4395 8.482943 TCTAATGATCGATCCAACCTCTTTAAA 58.517 33.333 22.31 0.00 0.00 1.52
2625 4396 7.938140 AATGATCGATCCAACCTCTTTAAAA 57.062 32.000 22.31 0.00 0.00 1.52
2626 4397 7.938140 ATGATCGATCCAACCTCTTTAAAAA 57.062 32.000 22.31 0.00 0.00 1.94
2644 4415 1.445871 AAAAGAATCGCGTACCACCC 58.554 50.000 5.77 0.00 0.00 4.61
2647 4418 1.217244 GAATCGCGTACCACCCTGT 59.783 57.895 5.77 0.00 0.00 4.00
2653 4424 0.949105 GCGTACCACCCTGTTCACTG 60.949 60.000 0.00 0.00 0.00 3.66
2654 4425 0.677288 CGTACCACCCTGTTCACTGA 59.323 55.000 0.00 0.00 0.00 3.41
2670 4441 1.141657 ACTGATTGCACACACCTCTGT 59.858 47.619 0.00 0.00 0.00 3.41
2673 4444 1.802960 GATTGCACACACCTCTGTCAG 59.197 52.381 0.00 0.00 0.00 3.51
2723 4495 7.888424 TGGACATCATATGGCTTTATTGATTG 58.112 34.615 2.13 0.00 38.72 2.67
2725 4497 8.579006 GGACATCATATGGCTTTATTGATTGAA 58.421 33.333 2.13 0.00 38.72 2.69
2726 4498 9.403110 GACATCATATGGCTTTATTGATTGAAC 57.597 33.333 2.13 0.00 34.69 3.18
2762 4534 9.868277 ATAGTTGAGAAAACAAAATCAAACACA 57.132 25.926 0.00 0.00 33.74 3.72
2795 4570 9.680315 ACACAAATTTTGAAATTAATGCCAATG 57.320 25.926 15.81 1.40 37.62 2.82
2804 4579 9.941325 TTGAAATTAATGCCAATGTAATGAAGT 57.059 25.926 0.00 0.00 0.00 3.01
2816 4591 8.278408 CCAATGTAATGAAGTCGTCATCTTATG 58.722 37.037 1.52 0.00 46.80 1.90
2817 4592 8.820933 CAATGTAATGAAGTCGTCATCTTATGT 58.179 33.333 1.52 0.00 46.80 2.29
2879 4654 8.070769 GCAAATCTATAAAAGCCAAGCTAGTAC 58.929 37.037 0.00 0.00 38.25 2.73
2899 4674 6.868622 AGTACAAGATGGACTGACATAGAAC 58.131 40.000 0.00 0.00 40.76 3.01
2905 4680 7.348080 AGATGGACTGACATAGAACGATTTA 57.652 36.000 0.00 0.00 0.00 1.40
2921 4696 1.519408 TTTAAAGAGCCACACGAGCC 58.481 50.000 0.00 0.00 0.00 4.70
2925 4700 4.008933 GAGCCACACGAGCCACCT 62.009 66.667 0.00 0.00 0.00 4.00
2926 4701 2.603473 AGCCACACGAGCCACCTA 60.603 61.111 0.00 0.00 0.00 3.08
2927 4702 1.961180 GAGCCACACGAGCCACCTAT 61.961 60.000 0.00 0.00 0.00 2.57
2938 4713 5.864474 CACGAGCCACCTATTATCATAAGAC 59.136 44.000 0.00 0.00 0.00 3.01
2959 4734 7.913674 AGACTTGAGAACCTAAAATTGCTAG 57.086 36.000 0.00 0.00 0.00 3.42
2965 4740 7.050377 TGAGAACCTAAAATTGCTAGATGAGG 58.950 38.462 0.00 0.00 0.00 3.86
2995 4770 7.704578 TTAAGGATATTAGCGCTAGAGATGT 57.295 36.000 17.98 6.89 0.00 3.06
2996 4771 8.803397 TTAAGGATATTAGCGCTAGAGATGTA 57.197 34.615 17.98 0.63 0.00 2.29
2997 4772 7.704578 AAGGATATTAGCGCTAGAGATGTAA 57.295 36.000 17.98 1.92 0.00 2.41
2998 4773 7.328277 AGGATATTAGCGCTAGAGATGTAAG 57.672 40.000 17.98 0.00 0.00 2.34
2999 4774 7.113437 AGGATATTAGCGCTAGAGATGTAAGA 58.887 38.462 17.98 0.00 0.00 2.10
3000 4775 7.612244 AGGATATTAGCGCTAGAGATGTAAGAA 59.388 37.037 17.98 0.00 0.00 2.52
3001 4776 8.410141 GGATATTAGCGCTAGAGATGTAAGAAT 58.590 37.037 17.98 7.97 0.00 2.40
3002 4777 9.796120 GATATTAGCGCTAGAGATGTAAGAATT 57.204 33.333 17.98 0.00 0.00 2.17
3005 4780 9.632807 ATTAGCGCTAGAGATGTAAGAATTTAG 57.367 33.333 17.98 0.00 0.00 1.85
3006 4781 7.045126 AGCGCTAGAGATGTAAGAATTTAGT 57.955 36.000 8.99 0.00 0.00 2.24
3007 4782 7.493367 AGCGCTAGAGATGTAAGAATTTAGTT 58.507 34.615 8.99 0.00 0.00 2.24
3008 4783 7.982354 AGCGCTAGAGATGTAAGAATTTAGTTT 59.018 33.333 8.99 0.00 0.00 2.66
3009 4784 8.604890 GCGCTAGAGATGTAAGAATTTAGTTTT 58.395 33.333 0.00 0.00 0.00 2.43
3031 4806 9.177304 GTTTTAAGGTTCTAAAACACACATAGC 57.823 33.333 12.00 0.00 45.18 2.97
3032 4807 5.959618 AAGGTTCTAAAACACACATAGCC 57.040 39.130 0.00 0.00 37.10 3.93
3033 4808 4.000988 AGGTTCTAAAACACACATAGCCG 58.999 43.478 0.00 0.00 37.10 5.52
3034 4809 3.998341 GGTTCTAAAACACACATAGCCGA 59.002 43.478 0.00 0.00 37.10 5.54
3035 4810 4.634443 GGTTCTAAAACACACATAGCCGAT 59.366 41.667 0.00 0.00 37.10 4.18
3036 4811 5.220605 GGTTCTAAAACACACATAGCCGATC 60.221 44.000 0.00 0.00 37.10 3.69
3037 4812 4.439057 TCTAAAACACACATAGCCGATCC 58.561 43.478 0.00 0.00 0.00 3.36
3038 4813 2.038387 AAACACACATAGCCGATCCC 57.962 50.000 0.00 0.00 0.00 3.85
3039 4814 1.204146 AACACACATAGCCGATCCCT 58.796 50.000 0.00 0.00 0.00 4.20
3040 4815 1.204146 ACACACATAGCCGATCCCTT 58.796 50.000 0.00 0.00 0.00 3.95
3041 4816 1.134401 ACACACATAGCCGATCCCTTG 60.134 52.381 0.00 0.00 0.00 3.61
3042 4817 1.138859 CACACATAGCCGATCCCTTGA 59.861 52.381 0.00 0.00 0.00 3.02
3043 4818 1.837439 ACACATAGCCGATCCCTTGAA 59.163 47.619 0.00 0.00 0.00 2.69
3044 4819 2.158900 ACACATAGCCGATCCCTTGAAG 60.159 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 98 6.213677 CGATCGGGTAAATGTAATTCTCTCA 58.786 40.000 7.38 0.00 33.67 3.27
96 100 5.539048 CCGATCGGGTAAATGTAATTCTCT 58.461 41.667 26.95 0.00 33.67 3.10
148 152 3.303990 CGATGGTAGAAAATTGGCCGATG 60.304 47.826 6.14 0.00 0.00 3.84
149 153 2.878406 CGATGGTAGAAAATTGGCCGAT 59.122 45.455 0.00 0.00 0.00 4.18
150 154 2.093394 TCGATGGTAGAAAATTGGCCGA 60.093 45.455 0.00 0.00 0.00 5.54
151 155 2.031683 GTCGATGGTAGAAAATTGGCCG 59.968 50.000 0.00 0.00 0.00 6.13
152 156 2.031683 CGTCGATGGTAGAAAATTGGCC 59.968 50.000 0.00 0.00 0.00 5.36
153 157 2.933906 TCGTCGATGGTAGAAAATTGGC 59.066 45.455 4.48 0.00 0.00 4.52
156 162 5.968387 GACATCGTCGATGGTAGAAAATT 57.032 39.130 32.48 13.30 43.60 1.82
225 231 0.895559 GTAGGCAGGCACCAAAAGCT 60.896 55.000 0.00 0.00 0.00 3.74
226 232 1.178534 TGTAGGCAGGCACCAAAAGC 61.179 55.000 0.00 0.00 0.00 3.51
227 233 0.598065 GTGTAGGCAGGCACCAAAAG 59.402 55.000 0.00 0.00 0.00 2.27
228 234 0.106469 TGTGTAGGCAGGCACCAAAA 60.106 50.000 0.00 0.00 34.94 2.44
431 437 1.228675 AAGAGGGGCAGGCAAACAG 60.229 57.895 0.00 0.00 0.00 3.16
497 509 4.148891 GTGCTCTTAAACCGTTTTCATCG 58.851 43.478 0.96 0.00 0.00 3.84
499 511 3.058501 CCGTGCTCTTAAACCGTTTTCAT 60.059 43.478 0.96 0.00 0.00 2.57
500 512 2.288458 CCGTGCTCTTAAACCGTTTTCA 59.712 45.455 0.96 0.00 0.00 2.69
501 513 2.545106 TCCGTGCTCTTAAACCGTTTTC 59.455 45.455 0.96 0.00 0.00 2.29
502 514 2.563702 TCCGTGCTCTTAAACCGTTTT 58.436 42.857 0.96 0.00 0.00 2.43
525 537 0.895100 ACAATGCGGGTGCTGAATGT 60.895 50.000 0.00 0.00 43.34 2.71
547 574 8.291740 AGCATATTATGTACGTACGAATGTGTA 58.708 33.333 29.42 16.65 31.75 2.90
548 575 7.143340 AGCATATTATGTACGTACGAATGTGT 58.857 34.615 29.42 21.13 31.75 3.72
549 576 7.537649 AGAGCATATTATGTACGTACGAATGTG 59.462 37.037 27.44 27.44 32.01 3.21
550 577 7.591165 AGAGCATATTATGTACGTACGAATGT 58.409 34.615 24.41 19.30 0.00 2.71
551 578 8.996933 GTAGAGCATATTATGTACGTACGAATG 58.003 37.037 24.41 20.09 0.00 2.67
552 579 8.944029 AGTAGAGCATATTATGTACGTACGAAT 58.056 33.333 24.41 21.29 0.00 3.34
553 580 8.315391 AGTAGAGCATATTATGTACGTACGAA 57.685 34.615 24.41 16.47 0.00 3.85
554 581 7.895975 AGTAGAGCATATTATGTACGTACGA 57.104 36.000 24.41 8.53 0.00 3.43
555 582 8.945758 AAAGTAGAGCATATTATGTACGTACG 57.054 34.615 20.18 15.01 0.00 3.67
574 601 4.475944 GTGCAACATGGCTTGTAAAGTAG 58.524 43.478 6.44 0.00 41.57 2.57
635 663 4.813027 CTCTGCATTTTGTTATTGCCACT 58.187 39.130 0.00 0.00 35.51 4.00
642 670 6.519679 TCTGATTGCTCTGCATTTTGTTAT 57.480 33.333 0.00 0.00 38.76 1.89
646 674 4.968181 CGTATCTGATTGCTCTGCATTTTG 59.032 41.667 0.00 0.00 38.76 2.44
658 686 2.037641 TGAGCATCCCCGTATCTGATTG 59.962 50.000 0.00 0.00 0.00 2.67
675 703 2.427812 GGAGTACAAGGTAGGAGTGAGC 59.572 54.545 0.00 0.00 0.00 4.26
676 704 3.025262 GGGAGTACAAGGTAGGAGTGAG 58.975 54.545 0.00 0.00 0.00 3.51
677 705 2.292061 GGGGAGTACAAGGTAGGAGTGA 60.292 54.545 0.00 0.00 0.00 3.41
678 706 2.108970 GGGGAGTACAAGGTAGGAGTG 58.891 57.143 0.00 0.00 0.00 3.51
704 732 3.425713 CGCATGTGGCTGACGCTT 61.426 61.111 0.00 0.00 41.67 4.68
735 763 3.896648 TGAACAGCTCGGATTGTTTTC 57.103 42.857 8.75 0.71 37.63 2.29
736 764 3.191371 GGATGAACAGCTCGGATTGTTTT 59.809 43.478 8.75 2.37 37.63 2.43
740 768 2.028420 TGGATGAACAGCTCGGATTG 57.972 50.000 0.00 0.00 0.00 2.67
757 786 1.619827 AGGGATTTGCACAACACATGG 59.380 47.619 0.00 0.00 0.00 3.66
763 792 6.058183 AGATAGTATCAGGGATTTGCACAAC 58.942 40.000 12.66 0.00 0.00 3.32
764 793 6.252599 AGATAGTATCAGGGATTTGCACAA 57.747 37.500 12.66 0.00 0.00 3.33
864 903 3.706373 CCGTGGTCCTGGGAGTGG 61.706 72.222 0.00 0.00 0.00 4.00
897 936 1.448365 TGGTGTGAGCTAGCATGCG 60.448 57.895 18.83 0.00 38.13 4.73
942 981 3.488090 GGACGAAAAGAGCGGGCG 61.488 66.667 0.00 0.00 0.00 6.13
943 982 3.125573 GGGACGAAAAGAGCGGGC 61.126 66.667 0.00 0.00 0.00 6.13
944 983 2.436115 GGGGACGAAAAGAGCGGG 60.436 66.667 0.00 0.00 0.00 6.13
1007 1046 2.676076 CCTAGCCAAATTGTTGTGTGC 58.324 47.619 0.00 0.00 32.40 4.57
1052 1093 1.880340 CCGCTCGAGCAATGGACTC 60.880 63.158 34.69 4.54 42.21 3.36
1053 1094 2.185350 CCGCTCGAGCAATGGACT 59.815 61.111 34.69 0.00 42.21 3.85
1054 1095 1.880340 CTCCGCTCGAGCAATGGAC 60.880 63.158 34.69 6.06 42.21 4.02
1269 1310 0.749049 ATGACGATGCTGCTGCTAGA 59.251 50.000 17.00 0.00 40.48 2.43
1359 1400 4.767255 CAGCACCTCCTCGCCACC 62.767 72.222 0.00 0.00 0.00 4.61
1360 1401 3.941657 GACAGCACCTCCTCGCCAC 62.942 68.421 0.00 0.00 0.00 5.01
1607 1648 2.226315 AGGGCACAGACATGGAGCA 61.226 57.895 0.00 0.00 34.39 4.26
1609 1650 1.748122 GCAGGGCACAGACATGGAG 60.748 63.158 0.00 0.00 0.00 3.86
1635 1693 4.082625 TCAAAGTGAATCACATGGTCATGC 60.083 41.667 16.38 0.00 42.39 4.06
1639 1704 5.695851 AAGTCAAAGTGAATCACATGGTC 57.304 39.130 16.38 10.38 36.74 4.02
1699 1766 0.100325 TGTTTTCAACTGCACTGGCG 59.900 50.000 0.00 0.00 45.35 5.69
1700 1767 1.405105 TCTGTTTTCAACTGCACTGGC 59.595 47.619 0.00 0.00 41.68 4.85
1768 1835 2.476320 GGCTCCTGATTTCTGCGGC 61.476 63.158 0.00 0.00 0.00 6.53
1769 1836 0.813210 GAGGCTCCTGATTTCTGCGG 60.813 60.000 2.15 0.00 0.00 5.69
1774 1847 4.865865 CCGGAGGCTCCTGATTTC 57.134 61.111 29.81 3.28 46.14 2.17
1797 1871 0.383231 GATCTTGGCCATTCCGCAAG 59.617 55.000 6.09 0.00 37.80 4.01
1798 1872 0.034186 AGATCTTGGCCATTCCGCAA 60.034 50.000 6.09 0.00 37.80 4.85
1802 1876 3.629398 CAGTACAAGATCTTGGCCATTCC 59.371 47.826 33.11 15.49 44.45 3.01
1822 1899 3.823281 AGATCTCATGCCTCTGAACAG 57.177 47.619 0.00 0.00 0.00 3.16
1858 1939 2.045280 CCTCCTACCTCATGCCTCG 58.955 63.158 0.00 0.00 0.00 4.63
1863 1944 0.467384 CACCTGCCTCCTACCTCATG 59.533 60.000 0.00 0.00 0.00 3.07
1864 1945 0.043334 ACACCTGCCTCCTACCTCAT 59.957 55.000 0.00 0.00 0.00 2.90
1865 1946 0.178903 AACACCTGCCTCCTACCTCA 60.179 55.000 0.00 0.00 0.00 3.86
1867 1948 1.867363 CTAACACCTGCCTCCTACCT 58.133 55.000 0.00 0.00 0.00 3.08
1868 1949 0.178301 GCTAACACCTGCCTCCTACC 59.822 60.000 0.00 0.00 0.00 3.18
1869 1950 0.902531 TGCTAACACCTGCCTCCTAC 59.097 55.000 0.00 0.00 0.00 3.18
1870 1951 1.195115 CTGCTAACACCTGCCTCCTA 58.805 55.000 0.00 0.00 0.00 2.94
1871 1952 1.986413 CTGCTAACACCTGCCTCCT 59.014 57.895 0.00 0.00 0.00 3.69
1872 1953 1.746991 GCTGCTAACACCTGCCTCC 60.747 63.158 0.00 0.00 0.00 4.30
1873 1954 2.103042 CGCTGCTAACACCTGCCTC 61.103 63.158 0.00 0.00 0.00 4.70
1874 1955 2.046892 CGCTGCTAACACCTGCCT 60.047 61.111 0.00 0.00 0.00 4.75
1875 1956 3.127533 CCGCTGCTAACACCTGCC 61.128 66.667 0.00 0.00 0.00 4.85
1876 1957 3.804193 GCCGCTGCTAACACCTGC 61.804 66.667 0.00 0.00 33.53 4.85
1879 1960 3.127533 CTGGCCGCTGCTAACACC 61.128 66.667 0.00 0.00 37.74 4.16
1894 1975 1.702886 CCTCGCTGACACTACAACTG 58.297 55.000 0.00 0.00 0.00 3.16
1962 2043 1.601419 CTGGCAATTCCCAGCACCTG 61.601 60.000 1.51 0.00 45.28 4.00
1977 2058 1.094073 ACAAGCATGATCGAGCTGGC 61.094 55.000 11.86 5.58 41.70 4.85
1984 2065 5.883661 AGTCCATTTTTACAAGCATGATCG 58.116 37.500 0.00 0.00 0.00 3.69
1988 2069 5.782047 TCCAAGTCCATTTTTACAAGCATG 58.218 37.500 0.00 0.00 0.00 4.06
1989 2070 6.418057 TTCCAAGTCCATTTTTACAAGCAT 57.582 33.333 0.00 0.00 0.00 3.79
2000 2081 4.895297 ACACAACTGAATTCCAAGTCCATT 59.105 37.500 2.27 0.00 0.00 3.16
2016 2097 2.627945 TGAACTGAAGCGAACACAACT 58.372 42.857 0.00 0.00 0.00 3.16
2045 2126 6.238538 GGACAATAAGGAAGACGAAACAAACA 60.239 38.462 0.00 0.00 0.00 2.83
2055 2136 9.482627 CATATTACAGAGGACAATAAGGAAGAC 57.517 37.037 0.00 0.00 0.00 3.01
2064 2145 8.378565 CCTTGGTATCATATTACAGAGGACAAT 58.621 37.037 0.00 0.00 32.01 2.71
2067 2148 7.233757 AGACCTTGGTATCATATTACAGAGGAC 59.766 40.741 10.26 6.32 33.41 3.85
2079 2160 3.133003 CGAGGACAAGACCTTGGTATCAT 59.867 47.826 13.58 1.07 44.45 2.45
2112 2195 4.072131 ACCAACAAGCAGACGACATAAAT 58.928 39.130 0.00 0.00 0.00 1.40
2116 2199 1.229428 CACCAACAAGCAGACGACAT 58.771 50.000 0.00 0.00 0.00 3.06
2119 2202 1.013596 CAACACCAACAAGCAGACGA 58.986 50.000 0.00 0.00 0.00 4.20
2121 2204 1.065551 GGACAACACCAACAAGCAGAC 59.934 52.381 0.00 0.00 0.00 3.51
2125 2208 3.317993 ACATTAGGACAACACCAACAAGC 59.682 43.478 0.00 0.00 0.00 4.01
2131 2214 4.724399 ACATCAACATTAGGACAACACCA 58.276 39.130 0.00 0.00 0.00 4.17
2135 2218 7.819900 AGACTAGAACATCAACATTAGGACAAC 59.180 37.037 0.00 0.00 0.00 3.32
2143 2226 7.667219 ACCAATGAAGACTAGAACATCAACATT 59.333 33.333 0.00 0.00 0.00 2.71
2144 2227 7.170965 ACCAATGAAGACTAGAACATCAACAT 58.829 34.615 0.00 0.00 0.00 2.71
2148 2231 5.939883 CCAACCAATGAAGACTAGAACATCA 59.060 40.000 0.00 0.00 0.00 3.07
2160 2243 2.483014 TACCGGTCCAACCAATGAAG 57.517 50.000 12.40 0.00 38.47 3.02
2169 2252 4.495690 TTCATCATGAATACCGGTCCAA 57.504 40.909 12.40 0.00 30.26 3.53
2177 2260 8.454106 CGGGATAAGGATTTTCATCATGAATAC 58.546 37.037 0.00 0.00 36.11 1.89
2184 3953 3.138283 AGGCGGGATAAGGATTTTCATCA 59.862 43.478 0.00 0.00 0.00 3.07
2209 3978 2.173356 TCATCATCATCAAGACCCACCC 59.827 50.000 0.00 0.00 0.00 4.61
2212 3981 3.263937 TGTGTCATCATCATCAAGACCCA 59.736 43.478 0.00 0.00 0.00 4.51
2213 3982 3.877559 TGTGTCATCATCATCAAGACCC 58.122 45.455 0.00 0.00 0.00 4.46
2236 4005 1.542547 CCGTCAAAAGGCAGTACACCT 60.543 52.381 1.73 1.73 40.02 4.00
2245 4014 0.109597 CATCAGCACCGTCAAAAGGC 60.110 55.000 0.00 0.00 0.00 4.35
2258 4027 0.659957 GACCATTCTTCGGCATCAGC 59.340 55.000 0.00 0.00 41.10 4.26
2259 4028 1.667724 GTGACCATTCTTCGGCATCAG 59.332 52.381 0.00 0.00 0.00 2.90
2266 4035 3.314553 ACAACTACGTGACCATTCTTCG 58.685 45.455 0.00 0.00 0.00 3.79
2285 4054 4.076394 AGAAGCGGCAAAAATTACCTACA 58.924 39.130 1.45 0.00 0.00 2.74
2300 4069 4.393062 AGATCAACACATTACAAGAAGCGG 59.607 41.667 0.00 0.00 0.00 5.52
2321 4090 0.465460 ACGAAACAGGCCAGCAAAGA 60.465 50.000 5.01 0.00 0.00 2.52
2326 4095 1.134491 AGGTATACGAAACAGGCCAGC 60.134 52.381 5.01 0.00 0.00 4.85
2332 4101 5.178623 TCTTGCAACAAGGTATACGAAACAG 59.821 40.000 7.44 0.00 0.00 3.16
2334 4103 5.390567 CCTCTTGCAACAAGGTATACGAAAC 60.391 44.000 12.99 0.00 0.00 2.78
2345 4114 7.951530 ATTTGATAAAACCTCTTGCAACAAG 57.048 32.000 0.00 0.81 0.00 3.16
2367 4136 7.010160 ACGAAACCCCCATGAATATGAATATT 58.990 34.615 0.00 0.00 36.36 1.28
2405 4174 8.572855 AAAGTCCCAATTGTTTCAATTTTTGA 57.427 26.923 4.43 1.24 38.04 2.69
2407 4176 8.180920 CGAAAAGTCCCAATTGTTTCAATTTTT 58.819 29.630 14.96 8.26 0.00 1.94
2411 4180 6.155475 TCGAAAAGTCCCAATTGTTTCAAT 57.845 33.333 14.96 0.00 0.00 2.57
2422 4191 3.780804 TCCAATCTTCGAAAAGTCCCA 57.219 42.857 0.00 0.00 33.95 4.37
2452 4221 6.969043 ACCAGATCACCCATTAGTAAATTGA 58.031 36.000 0.00 0.00 0.00 2.57
2464 4233 1.284313 TGCACATACCAGATCACCCA 58.716 50.000 0.00 0.00 0.00 4.51
2465 4234 2.418368 TTGCACATACCAGATCACCC 57.582 50.000 0.00 0.00 0.00 4.61
2467 4236 4.009675 TCCTTTTGCACATACCAGATCAC 58.990 43.478 0.00 0.00 0.00 3.06
2474 4243 3.365969 CGGAGTTTCCTTTTGCACATACC 60.366 47.826 0.00 0.00 33.30 2.73
2476 4245 3.482436 ACGGAGTTTCCTTTTGCACATA 58.518 40.909 0.00 0.00 37.78 2.29
2477 4246 2.306847 ACGGAGTTTCCTTTTGCACAT 58.693 42.857 0.00 0.00 37.78 3.21
2494 4263 2.798689 TCGCAGAATCGAGGACGG 59.201 61.111 0.00 0.00 40.21 4.79
2515 4284 7.993821 TGCACACGAAAAGATTTCATAAAAA 57.006 28.000 0.00 0.00 0.00 1.94
2528 4297 4.261405 CCACCTAAAAGATGCACACGAAAA 60.261 41.667 0.00 0.00 0.00 2.29
2531 4300 2.037902 TCCACCTAAAAGATGCACACGA 59.962 45.455 0.00 0.00 0.00 4.35
2532 4301 2.422597 TCCACCTAAAAGATGCACACG 58.577 47.619 0.00 0.00 0.00 4.49
2533 4302 3.366374 GCTTCCACCTAAAAGATGCACAC 60.366 47.826 0.00 0.00 0.00 3.82
2535 4304 3.084786 AGCTTCCACCTAAAAGATGCAC 58.915 45.455 0.00 0.00 0.00 4.57
2536 4305 3.439857 AGCTTCCACCTAAAAGATGCA 57.560 42.857 0.00 0.00 0.00 3.96
2537 4306 4.218417 TCAAAGCTTCCACCTAAAAGATGC 59.782 41.667 0.00 0.00 0.00 3.91
2538 4307 5.964958 TCAAAGCTTCCACCTAAAAGATG 57.035 39.130 0.00 0.00 0.00 2.90
2539 4308 7.452813 AGAAATCAAAGCTTCCACCTAAAAGAT 59.547 33.333 0.00 0.00 0.00 2.40
2540 4309 6.777580 AGAAATCAAAGCTTCCACCTAAAAGA 59.222 34.615 0.00 0.00 0.00 2.52
2541 4310 6.986250 AGAAATCAAAGCTTCCACCTAAAAG 58.014 36.000 0.00 0.00 0.00 2.27
2542 4311 6.549364 TGAGAAATCAAAGCTTCCACCTAAAA 59.451 34.615 0.00 0.00 0.00 1.52
2546 4315 3.823304 GTGAGAAATCAAAGCTTCCACCT 59.177 43.478 0.00 0.00 0.00 4.00
2596 4367 6.485830 AGAGGTTGGATCGATCATTAGAAA 57.514 37.500 25.93 7.99 0.00 2.52
2624 4395 1.808343 GGGTGGTACGCGATTCTTTTT 59.192 47.619 15.93 0.00 41.51 1.94
2625 4396 1.002773 AGGGTGGTACGCGATTCTTTT 59.997 47.619 15.93 0.00 41.51 2.27
2626 4397 0.611714 AGGGTGGTACGCGATTCTTT 59.388 50.000 15.93 0.00 41.51 2.52
2627 4398 0.108329 CAGGGTGGTACGCGATTCTT 60.108 55.000 15.93 0.00 41.51 2.52
2628 4399 1.255667 ACAGGGTGGTACGCGATTCT 61.256 55.000 15.93 0.00 41.51 2.40
2629 4400 0.390735 AACAGGGTGGTACGCGATTC 60.391 55.000 15.93 1.78 41.51 2.52
2630 4401 0.390735 GAACAGGGTGGTACGCGATT 60.391 55.000 15.93 0.00 41.51 3.34
2631 4402 1.217244 GAACAGGGTGGTACGCGAT 59.783 57.895 15.93 0.00 41.51 4.58
2632 4403 2.201708 TGAACAGGGTGGTACGCGA 61.202 57.895 15.93 0.00 41.51 5.87
2633 4404 2.025418 GTGAACAGGGTGGTACGCG 61.025 63.158 3.53 3.53 41.51 6.01
2634 4405 0.949105 CAGTGAACAGGGTGGTACGC 60.949 60.000 0.00 0.00 38.67 4.42
2635 4406 0.677288 TCAGTGAACAGGGTGGTACG 59.323 55.000 0.00 0.00 0.00 3.67
2636 4407 3.074412 CAATCAGTGAACAGGGTGGTAC 58.926 50.000 0.00 0.00 0.00 3.34
2647 4418 2.158769 AGAGGTGTGTGCAATCAGTGAA 60.159 45.455 0.00 0.00 0.00 3.18
2653 4424 1.802960 CTGACAGAGGTGTGTGCAATC 59.197 52.381 0.00 0.00 36.88 2.67
2654 4425 1.417517 TCTGACAGAGGTGTGTGCAAT 59.582 47.619 0.00 0.00 36.88 3.56
2691 4463 4.404640 AGCCATATGATGTCCATTTCCTG 58.595 43.478 3.65 0.00 36.71 3.86
2693 4465 5.796424 AAAGCCATATGATGTCCATTTCC 57.204 39.130 3.65 0.00 36.71 3.13
2694 4466 8.579006 TCAATAAAGCCATATGATGTCCATTTC 58.421 33.333 3.65 0.00 36.71 2.17
2695 4467 8.481492 TCAATAAAGCCATATGATGTCCATTT 57.519 30.769 3.65 0.00 36.71 2.32
2696 4468 8.660295 ATCAATAAAGCCATATGATGTCCATT 57.340 30.769 3.65 0.00 36.71 3.16
2697 4469 8.528643 CAATCAATAAAGCCATATGATGTCCAT 58.471 33.333 3.65 0.00 39.25 3.41
2698 4470 7.724951 TCAATCAATAAAGCCATATGATGTCCA 59.275 33.333 3.65 0.00 0.00 4.02
2699 4471 8.114331 TCAATCAATAAAGCCATATGATGTCC 57.886 34.615 3.65 0.00 0.00 4.02
2700 4472 9.403110 GTTCAATCAATAAAGCCATATGATGTC 57.597 33.333 3.65 0.00 0.00 3.06
2701 4473 8.916062 TGTTCAATCAATAAAGCCATATGATGT 58.084 29.630 3.65 0.00 0.00 3.06
2702 4474 9.752961 TTGTTCAATCAATAAAGCCATATGATG 57.247 29.630 3.65 0.00 0.00 3.07
2706 4478 9.941325 TTGTTTGTTCAATCAATAAAGCCATAT 57.059 25.926 5.33 0.00 0.00 1.78
2739 4511 8.162245 GTCTGTGTTTGATTTTGTTTTCTCAAC 58.838 33.333 0.00 0.00 0.00 3.18
2740 4512 7.061673 CGTCTGTGTTTGATTTTGTTTTCTCAA 59.938 33.333 0.00 0.00 0.00 3.02
2754 4526 6.612247 AATTTGTGTATCGTCTGTGTTTGA 57.388 33.333 0.00 0.00 0.00 2.69
2786 4561 4.699735 TGACGACTTCATTACATTGGCATT 59.300 37.500 0.00 0.00 0.00 3.56
2795 4570 8.635877 AGAACATAAGATGACGACTTCATTAC 57.364 34.615 0.00 0.00 45.67 1.89
2804 4579 4.104696 TGCGAAGAACATAAGATGACGA 57.895 40.909 0.00 0.00 0.00 4.20
2816 4591 1.222115 AACACCGAGCTGCGAAGAAC 61.222 55.000 0.00 0.00 44.57 3.01
2817 4592 0.531974 AAACACCGAGCTGCGAAGAA 60.532 50.000 0.00 0.00 44.57 2.52
2879 4654 4.998788 TCGTTCTATGTCAGTCCATCTTG 58.001 43.478 0.00 0.00 0.00 3.02
2899 4674 2.222819 GCTCGTGTGGCTCTTTAAATCG 60.223 50.000 0.00 0.00 0.00 3.34
2905 4680 1.598130 GTGGCTCGTGTGGCTCTTT 60.598 57.895 0.00 0.00 0.00 2.52
2921 4696 9.482627 GGTTCTCAAGTCTTATGATAATAGGTG 57.517 37.037 0.00 0.00 0.00 4.00
2938 4713 8.498054 TCATCTAGCAATTTTAGGTTCTCAAG 57.502 34.615 0.00 0.00 0.00 3.02
2983 4758 7.701809 AACTAAATTCTTACATCTCTAGCGC 57.298 36.000 0.00 0.00 0.00 5.92
3005 4780 9.177304 GCTATGTGTGTTTTAGAACCTTAAAAC 57.823 33.333 12.18 12.18 46.36 2.43
3006 4781 8.354426 GGCTATGTGTGTTTTAGAACCTTAAAA 58.646 33.333 0.00 0.00 34.80 1.52
3007 4782 7.308109 CGGCTATGTGTGTTTTAGAACCTTAAA 60.308 37.037 0.00 0.00 34.80 1.52
3008 4783 6.148150 CGGCTATGTGTGTTTTAGAACCTTAA 59.852 38.462 0.00 0.00 34.80 1.85
3009 4784 5.640357 CGGCTATGTGTGTTTTAGAACCTTA 59.360 40.000 0.00 0.00 34.80 2.69
3010 4785 4.454504 CGGCTATGTGTGTTTTAGAACCTT 59.545 41.667 0.00 0.00 34.80 3.50
3011 4786 4.000988 CGGCTATGTGTGTTTTAGAACCT 58.999 43.478 0.00 0.00 34.80 3.50
3012 4787 3.998341 TCGGCTATGTGTGTTTTAGAACC 59.002 43.478 0.00 0.00 34.80 3.62
3013 4788 5.220605 GGATCGGCTATGTGTGTTTTAGAAC 60.221 44.000 0.00 0.00 36.29 3.01
3014 4789 4.873827 GGATCGGCTATGTGTGTTTTAGAA 59.126 41.667 0.00 0.00 0.00 2.10
3015 4790 4.439057 GGATCGGCTATGTGTGTTTTAGA 58.561 43.478 0.00 0.00 0.00 2.10
3016 4791 3.560068 GGGATCGGCTATGTGTGTTTTAG 59.440 47.826 0.00 0.00 0.00 1.85
3017 4792 3.199071 AGGGATCGGCTATGTGTGTTTTA 59.801 43.478 0.00 0.00 0.00 1.52
3018 4793 2.026262 AGGGATCGGCTATGTGTGTTTT 60.026 45.455 0.00 0.00 0.00 2.43
3019 4794 1.559682 AGGGATCGGCTATGTGTGTTT 59.440 47.619 0.00 0.00 0.00 2.83
3020 4795 1.204146 AGGGATCGGCTATGTGTGTT 58.796 50.000 0.00 0.00 0.00 3.32
3021 4796 1.134401 CAAGGGATCGGCTATGTGTGT 60.134 52.381 0.00 0.00 0.00 3.72
3022 4797 1.138859 TCAAGGGATCGGCTATGTGTG 59.861 52.381 0.00 0.00 0.00 3.82
3023 4798 1.496060 TCAAGGGATCGGCTATGTGT 58.504 50.000 0.00 0.00 0.00 3.72
3024 4799 2.487934 CTTCAAGGGATCGGCTATGTG 58.512 52.381 0.00 0.00 0.00 3.21
3025 4800 2.918712 CTTCAAGGGATCGGCTATGT 57.081 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.