Multiple sequence alignment - TraesCS2B01G271200

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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 TraesCS2B01G271200 chr2B 100.000 5417 0 0 1 5417 371160561 371165977 0.000000e+00 10004.0
1 TraesCS2B01G271200 chr2B 96.947 131 4 0 2072 2202 150604821 150604691 2.540000e-53 220.0
2 TraesCS2B01G271200 chr2D 95.030 2173 76 15 3264 5417 299891556 299889397 0.000000e+00 3386.0
3 TraesCS2B01G271200 chr2D 94.541 1264 38 5 819 2074 299894007 299892767 0.000000e+00 1923.0
4 TraesCS2B01G271200 chr2D 94.752 1067 45 10 2202 3266 299892771 299891714 0.000000e+00 1650.0
5 TraesCS2B01G271200 chr2D 96.509 802 13 5 1 791 299894792 299893995 0.000000e+00 1312.0
6 TraesCS2B01G271200 chr2D 96.296 135 5 0 2070 2204 429922274 429922140 7.060000e-54 222.0
7 TraesCS2B01G271200 chr2D 91.209 91 7 1 3707 3796 449065582 449065492 7.370000e-24 122.0
8 TraesCS2B01G271200 chr2A 97.166 1694 38 4 2858 4548 376083366 376081680 0.000000e+00 2854.0
9 TraesCS2B01G271200 chr2A 95.041 847 31 6 928 1767 376086719 376085877 0.000000e+00 1321.0
10 TraesCS2B01G271200 chr2A 95.939 788 27 4 4 791 376101118 376100336 0.000000e+00 1273.0
11 TraesCS2B01G271200 chr2A 94.845 679 19 9 4627 5290 376080438 376079761 0.000000e+00 1046.0
12 TraesCS2B01G271200 chr2A 95.695 604 21 3 2202 2804 376083965 376083366 0.000000e+00 966.0
13 TraesCS2B01G271200 chr2A 91.250 320 12 1 1755 2074 376084264 376083961 6.490000e-114 422.0
14 TraesCS2B01G271200 chr2A 95.000 140 6 1 5277 5415 376078375 376078236 9.140000e-53 219.0
15 TraesCS2B01G271200 chr2A 94.505 91 4 1 3707 3796 593655910 593656000 7.320000e-29 139.0
16 TraesCS2B01G271200 chr2A 91.209 91 8 0 3699 3789 1378612 1378702 2.050000e-24 124.0
17 TraesCS2B01G271200 chr2A 100.000 31 0 0 889 919 376086744 376086714 2.110000e-04 58.4
18 TraesCS2B01G271200 chr1A 97.037 135 4 0 2073 2207 285990976 285990842 1.520000e-55 228.0
19 TraesCS2B01G271200 chr4B 95.556 135 4 1 2070 2204 120507178 120507310 1.180000e-51 215.0
20 TraesCS2B01G271200 chr4A 96.183 131 5 0 2072 2202 114583194 114583324 1.180000e-51 215.0
21 TraesCS2B01G271200 chr4A 87.097 93 10 2 3699 3791 296251357 296251447 2.670000e-18 104.0
22 TraesCS2B01G271200 chr1B 85.377 212 23 3 1 212 27302887 27303090 4.250000e-51 213.0
23 TraesCS2B01G271200 chr5D 94.853 136 5 1 2070 2205 23153989 23153856 1.530000e-50 211.0
24 TraesCS2B01G271200 chr6D 95.420 131 6 0 2072 2202 117041149 117041019 5.500000e-50 209.0
25 TraesCS2B01G271200 chr3D 94.203 138 6 2 2067 2202 402475906 402476043 5.500000e-50 209.0
26 TraesCS2B01G271200 chr1D 94.737 133 7 0 2072 2204 491989454 491989322 1.980000e-49 207.0
27 TraesCS2B01G271200 chr5A 94.186 86 4 1 3706 3791 383880466 383880550 4.400000e-26 130.0
28 TraesCS2B01G271200 chr3A 88.764 89 9 1 3707 3794 652027538 652027626 2.060000e-19 108.0
29 TraesCS2B01G271200 chr3A 87.778 90 11 0 3704 3793 646737256 646737345 7.420000e-19 106.0


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 TraesCS2B01G271200 chr2B 371160561 371165977 5416 False 10004.000000 10004 100.000 1 5417 1 chr2B.!!$F1 5416
1 TraesCS2B01G271200 chr2D 299889397 299894792 5395 True 2067.750000 3386 95.208 1 5417 4 chr2D.!!$R3 5416
2 TraesCS2B01G271200 chr2A 376100336 376101118 782 True 1273.000000 1273 95.939 4 791 1 chr2A.!!$R1 787
3 TraesCS2B01G271200 chr2A 376078236 376086744 8508 True 983.771429 2854 95.571 889 5415 7 chr2A.!!$R2 4526

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
465 474 0.185175 GACTCCTCCTCCTCCTCCTC 59.815 65.0 0.0 0.0 0.00 3.71 F
816 825 0.196118 TTTCTGAGGGGAGGGGAACT 59.804 55.0 0.0 0.0 0.00 3.01 F
817 826 0.196118 TTCTGAGGGGAGGGGAACTT 59.804 55.0 0.0 0.0 0.00 2.66 F
2170 3819 0.103208 CTCCGCAGCTCCTCGTATTT 59.897 55.0 0.0 0.0 0.00 1.40 F
2616 4265 0.109781 CAATCGCAAAGACAACCCGG 60.110 55.0 0.0 0.0 0.00 5.73 F
2984 4633 0.607217 GGTTTCCAGGTGGGGTTACG 60.607 60.0 0.0 0.0 37.22 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 3782 0.034670 AGCATCTGTTTCCCAGCTCC 60.035 55.000 0.00 0.0 41.25 4.70 R
2151 3800 0.103208 AAATACGAGGAGCTGCGGAG 59.897 55.000 0.00 0.0 0.00 4.63 R
2189 3838 0.107654 CTTCCTAAGGCCCTGTTCGG 60.108 60.000 0.00 0.0 0.00 4.30 R
2984 4633 1.740025 GCAGTACCAGTGAAGGAATGC 59.260 52.381 0.00 0.0 0.00 3.56 R
4316 6143 1.488393 GCCTGCAGGGTAGAAAGATCT 59.512 52.381 33.46 0.0 36.25 2.75 R
4815 7810 1.271325 TGGATCCAAAGTGCGTCATGT 60.271 47.619 13.46 0.0 0.00 3.21 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
53 54 7.117236 TGTGATTTTACACCGACAGTCTAATTC 59.883 37.037 0.00 0.00 39.69 2.17
57 58 3.986277 ACACCGACAGTCTAATTCGTTT 58.014 40.909 0.00 0.00 0.00 3.60
66 67 7.377766 ACAGTCTAATTCGTTTATTGTGCAT 57.622 32.000 0.00 0.00 0.00 3.96
415 424 3.993865 TACCTCAGCATCGGCCCCA 62.994 63.158 0.00 0.00 42.56 4.96
446 455 0.390860 CTCTTCCCACTCCGCCATAG 59.609 60.000 0.00 0.00 0.00 2.23
464 473 0.254107 AGACTCCTCCTCCTCCTCCT 60.254 60.000 0.00 0.00 0.00 3.69
465 474 0.185175 GACTCCTCCTCCTCCTCCTC 59.815 65.000 0.00 0.00 0.00 3.71
466 475 1.293683 ACTCCTCCTCCTCCTCCTCC 61.294 65.000 0.00 0.00 0.00 4.30
753 762 1.153745 GCTTCGTGGCGATGACTCT 60.154 57.895 8.29 0.00 35.23 3.24
782 791 2.039418 TCAGACCATCGGACTTATGGG 58.961 52.381 7.02 0.00 46.89 4.00
788 797 0.666913 ATCGGACTTATGGGTCGTCG 59.333 55.000 0.00 0.00 37.12 5.12
791 800 1.101331 GGACTTATGGGTCGTCGTCT 58.899 55.000 0.00 0.00 37.12 4.18
792 801 1.475682 GGACTTATGGGTCGTCGTCTT 59.524 52.381 0.00 0.00 37.12 3.01
793 802 2.094338 GGACTTATGGGTCGTCGTCTTT 60.094 50.000 0.00 0.00 37.12 2.52
794 803 3.582780 GACTTATGGGTCGTCGTCTTTT 58.417 45.455 0.00 0.00 0.00 2.27
795 804 3.992427 GACTTATGGGTCGTCGTCTTTTT 59.008 43.478 0.00 0.00 0.00 1.94
813 822 3.608912 TTTTTCTGAGGGGAGGGGA 57.391 52.632 0.00 0.00 0.00 4.81
814 823 1.841334 TTTTTCTGAGGGGAGGGGAA 58.159 50.000 0.00 0.00 0.00 3.97
815 824 1.073098 TTTTCTGAGGGGAGGGGAAC 58.927 55.000 0.00 0.00 0.00 3.62
816 825 0.196118 TTTCTGAGGGGAGGGGAACT 59.804 55.000 0.00 0.00 0.00 3.01
817 826 0.196118 TTCTGAGGGGAGGGGAACTT 59.804 55.000 0.00 0.00 0.00 2.66
832 841 0.883833 AACTTATGGGTCGTCGTCGT 59.116 50.000 1.33 0.00 38.33 4.34
842 851 2.012414 CGTCGTCGTTTCGGCTTCA 61.012 57.895 0.00 0.00 33.02 3.02
843 852 1.485943 GTCGTCGTTTCGGCTTCAC 59.514 57.895 0.00 0.00 32.43 3.18
844 853 0.938168 GTCGTCGTTTCGGCTTCACT 60.938 55.000 0.00 0.00 32.43 3.41
845 854 0.249155 TCGTCGTTTCGGCTTCACTT 60.249 50.000 0.00 0.00 0.00 3.16
919 936 2.461695 TCACTTCTCTCCTCCATCCAC 58.538 52.381 0.00 0.00 0.00 4.02
920 937 2.182827 CACTTCTCTCCTCCATCCACA 58.817 52.381 0.00 0.00 0.00 4.17
921 938 2.568956 CACTTCTCTCCTCCATCCACAA 59.431 50.000 0.00 0.00 0.00 3.33
922 939 3.199508 CACTTCTCTCCTCCATCCACAAT 59.800 47.826 0.00 0.00 0.00 2.71
923 940 3.848975 ACTTCTCTCCTCCATCCACAATT 59.151 43.478 0.00 0.00 0.00 2.32
924 941 3.920231 TCTCTCCTCCATCCACAATTG 57.080 47.619 3.24 3.24 0.00 2.32
925 942 2.092753 TCTCTCCTCCATCCACAATTGC 60.093 50.000 5.05 0.00 0.00 3.56
926 943 1.634973 TCTCCTCCATCCACAATTGCA 59.365 47.619 5.05 0.00 0.00 4.08
927 944 1.747355 CTCCTCCATCCACAATTGCAC 59.253 52.381 5.05 0.00 0.00 4.57
928 945 1.075212 TCCTCCATCCACAATTGCACA 59.925 47.619 5.05 0.00 0.00 4.57
929 946 2.104967 CCTCCATCCACAATTGCACAT 58.895 47.619 5.05 0.00 0.00 3.21
930 947 2.100252 CCTCCATCCACAATTGCACATC 59.900 50.000 5.05 0.00 0.00 3.06
931 948 2.756207 CTCCATCCACAATTGCACATCA 59.244 45.455 5.05 0.00 0.00 3.07
932 949 2.492881 TCCATCCACAATTGCACATCAC 59.507 45.455 5.05 0.00 0.00 3.06
933 950 2.231721 CCATCCACAATTGCACATCACA 59.768 45.455 5.05 0.00 0.00 3.58
1067 1088 5.872963 TCTCACCTTTACCCCTAAAAGAAC 58.127 41.667 0.00 0.00 36.27 3.01
1143 1167 2.427506 CTGCTCTTACCCAAACTGACC 58.572 52.381 0.00 0.00 0.00 4.02
1152 1176 1.966451 CAAACTGACCGCTCACCCC 60.966 63.158 0.00 0.00 0.00 4.95
1209 1233 2.146342 CCAGACATCGCAGTGAACTTT 58.854 47.619 0.00 0.00 0.00 2.66
1232 1256 0.756070 GGTAGGACCTTCTCCCTCCG 60.756 65.000 0.00 0.00 40.53 4.63
1275 1299 7.053316 TGACATCATTTTTGTTCTTGGTGAT 57.947 32.000 0.00 0.00 0.00 3.06
1278 1302 8.145316 ACATCATTTTTGTTCTTGGTGATTTG 57.855 30.769 0.00 0.00 0.00 2.32
1346 1370 1.305219 GCATCTACCACGGCAAGCAA 61.305 55.000 0.00 0.00 0.00 3.91
1432 1456 4.720649 TTGTATGACTACCTGTCTGCTC 57.279 45.455 0.00 0.00 45.54 4.26
1441 1465 0.685785 CCTGTCTGCTCTGCCTCCTA 60.686 60.000 0.00 0.00 0.00 2.94
1442 1466 0.459489 CTGTCTGCTCTGCCTCCTAC 59.541 60.000 0.00 0.00 0.00 3.18
1580 1604 1.739667 CCGAGACCGATGGTATGCA 59.260 57.895 0.00 0.00 35.25 3.96
1656 1680 1.909700 TGCGCCTGAGGAATTTCTTT 58.090 45.000 0.65 0.00 0.00 2.52
1688 1712 0.466739 TATGCAATGCAGGGAGGCTG 60.467 55.000 14.98 0.00 43.65 4.85
1691 1715 1.941999 GCAATGCAGGGAGGCTGTTC 61.942 60.000 0.00 0.00 34.04 3.18
1763 3412 1.134521 TCTTGCTTTGGTCGTGACTGT 60.135 47.619 0.00 0.00 0.00 3.55
1769 3418 3.426963 GCTTTGGTCGTGACTGTTTTTGA 60.427 43.478 0.00 0.00 0.00 2.69
1799 3448 2.278854 GTGCATTTGTGCTTTGGTTGT 58.721 42.857 0.00 0.00 35.49 3.32
1841 3490 4.518249 GATGGTTTAGGAGTTTGAGGAGG 58.482 47.826 0.00 0.00 0.00 4.30
1885 3534 2.694760 GGCTCTCTTGGCTTTGGCG 61.695 63.158 0.00 0.00 39.81 5.69
1960 3609 6.494842 TGTTTGAGAATTTACACAGTGCTTC 58.505 36.000 0.00 0.00 0.00 3.86
1970 3619 3.859650 CAGTGCTTCAACTGCAAGG 57.140 52.632 0.00 0.00 41.05 3.61
1977 3626 2.739609 GCTTCAACTGCAAGGCAAAAGT 60.740 45.455 0.00 0.00 38.41 2.66
2013 3662 6.625300 GCTCTAGTGATGGACTTTCTCGTAAA 60.625 42.308 0.00 0.00 35.96 2.01
2074 3723 4.578105 CCCTGAGAATCTTGTCAATTAGGC 59.422 45.833 0.00 0.00 34.92 3.93
2075 3724 4.578105 CCTGAGAATCTTGTCAATTAGGCC 59.422 45.833 0.00 0.00 34.92 5.19
2076 3725 4.526970 TGAGAATCTTGTCAATTAGGCCC 58.473 43.478 0.00 0.00 34.92 5.80
2077 3726 4.228210 TGAGAATCTTGTCAATTAGGCCCT 59.772 41.667 0.00 0.00 34.92 5.19
2078 3727 4.530875 AGAATCTTGTCAATTAGGCCCTG 58.469 43.478 0.00 0.00 0.00 4.45
2079 3728 4.018050 AGAATCTTGTCAATTAGGCCCTGT 60.018 41.667 0.00 0.00 0.00 4.00
2080 3729 3.806949 TCTTGTCAATTAGGCCCTGTT 57.193 42.857 0.00 0.00 0.00 3.16
2081 3730 3.686016 TCTTGTCAATTAGGCCCTGTTC 58.314 45.455 0.00 0.00 0.00 3.18
2082 3731 2.107950 TGTCAATTAGGCCCTGTTCG 57.892 50.000 0.00 0.00 0.00 3.95
2083 3732 1.339631 TGTCAATTAGGCCCTGTTCGG 60.340 52.381 0.00 0.00 0.00 4.30
2084 3733 1.065709 GTCAATTAGGCCCTGTTCGGA 60.066 52.381 0.00 0.00 33.16 4.55
2085 3734 1.209504 TCAATTAGGCCCTGTTCGGAG 59.790 52.381 0.00 0.00 33.16 4.63
2086 3735 1.209504 CAATTAGGCCCTGTTCGGAGA 59.790 52.381 0.00 0.00 33.16 3.71
2087 3736 0.831307 ATTAGGCCCTGTTCGGAGAC 59.169 55.000 0.00 0.00 34.32 3.36
2088 3737 1.262640 TTAGGCCCTGTTCGGAGACC 61.263 60.000 0.00 0.00 34.32 3.85
2089 3738 4.097361 GGCCCTGTTCGGAGACCC 62.097 72.222 0.00 0.00 34.32 4.46
2090 3739 3.319198 GCCCTGTTCGGAGACCCA 61.319 66.667 0.00 0.00 34.32 4.51
2091 3740 2.663196 CCCTGTTCGGAGACCCAC 59.337 66.667 0.00 0.00 34.32 4.61
2092 3741 2.663196 CCTGTTCGGAGACCCACC 59.337 66.667 0.00 0.00 34.32 4.61
2093 3742 2.214216 CCTGTTCGGAGACCCACCA 61.214 63.158 0.00 0.00 34.32 4.17
2094 3743 1.004918 CTGTTCGGAGACCCACCAC 60.005 63.158 0.00 0.00 34.32 4.16
2095 3744 1.458777 TGTTCGGAGACCCACCACT 60.459 57.895 0.00 0.00 34.32 4.00
2096 3745 1.292541 GTTCGGAGACCCACCACTC 59.707 63.158 0.00 0.00 34.32 3.51
2097 3746 1.911766 TTCGGAGACCCACCACTCC 60.912 63.158 0.00 0.00 46.31 3.85
2100 3749 3.069778 GAGACCCACCACTCCACC 58.930 66.667 0.00 0.00 0.00 4.61
2101 3750 1.841556 GAGACCCACCACTCCACCA 60.842 63.158 0.00 0.00 0.00 4.17
2102 3751 2.113243 GAGACCCACCACTCCACCAC 62.113 65.000 0.00 0.00 0.00 4.16
2103 3752 2.039831 ACCCACCACTCCACCACT 60.040 61.111 0.00 0.00 0.00 4.00
2104 3753 2.113243 GACCCACCACTCCACCACTC 62.113 65.000 0.00 0.00 0.00 3.51
2105 3754 2.750350 CCACCACTCCACCACTCC 59.250 66.667 0.00 0.00 0.00 3.85
2106 3755 2.343758 CACCACTCCACCACTCCG 59.656 66.667 0.00 0.00 0.00 4.63
2107 3756 3.626924 ACCACTCCACCACTCCGC 61.627 66.667 0.00 0.00 0.00 5.54
2108 3757 3.314331 CCACTCCACCACTCCGCT 61.314 66.667 0.00 0.00 0.00 5.52
2109 3758 2.262915 CACTCCACCACTCCGCTC 59.737 66.667 0.00 0.00 0.00 5.03
2110 3759 2.997897 ACTCCACCACTCCGCTCC 60.998 66.667 0.00 0.00 0.00 4.70
2111 3760 3.775654 CTCCACCACTCCGCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
2124 3773 4.356979 CTCCCGGAGCTGGAGTTA 57.643 61.111 0.73 0.00 43.68 2.24
2125 3774 2.591915 CTCCCGGAGCTGGAGTTAA 58.408 57.895 0.73 0.00 43.68 2.01
2126 3775 0.902531 CTCCCGGAGCTGGAGTTAAA 59.097 55.000 0.73 0.00 43.68 1.52
2127 3776 1.278127 CTCCCGGAGCTGGAGTTAAAA 59.722 52.381 0.73 0.00 43.68 1.52
2128 3777 1.700739 TCCCGGAGCTGGAGTTAAAAA 59.299 47.619 0.73 0.00 0.00 1.94
2129 3778 2.084546 CCCGGAGCTGGAGTTAAAAAG 58.915 52.381 0.73 0.00 0.00 2.27
2130 3779 1.468914 CCGGAGCTGGAGTTAAAAAGC 59.531 52.381 0.00 0.00 35.86 3.51
2131 3780 2.151202 CGGAGCTGGAGTTAAAAAGCA 58.849 47.619 0.00 0.00 38.14 3.91
2132 3781 2.095718 CGGAGCTGGAGTTAAAAAGCAC 60.096 50.000 0.00 0.00 38.14 4.40
2133 3782 2.095718 GGAGCTGGAGTTAAAAAGCACG 60.096 50.000 0.00 0.00 38.14 5.34
2134 3783 1.880027 AGCTGGAGTTAAAAAGCACGG 59.120 47.619 0.00 0.00 38.14 4.94
2135 3784 1.877443 GCTGGAGTTAAAAAGCACGGA 59.123 47.619 0.00 0.00 35.69 4.69
2136 3785 2.095718 GCTGGAGTTAAAAAGCACGGAG 60.096 50.000 0.00 0.00 35.69 4.63
2137 3786 1.877443 TGGAGTTAAAAAGCACGGAGC 59.123 47.619 0.00 0.00 46.19 4.70
2146 3795 2.281484 GCACGGAGCTGGGAAACA 60.281 61.111 0.00 0.00 41.15 2.83
2156 3805 1.377202 TGGGAAACAGATGCTCCGC 60.377 57.895 0.00 0.00 0.00 5.54
2157 3806 1.377202 GGGAAACAGATGCTCCGCA 60.377 57.895 0.00 0.00 44.86 5.69
2158 3807 1.372087 GGGAAACAGATGCTCCGCAG 61.372 60.000 0.00 0.00 43.65 5.18
2159 3808 1.427020 GAAACAGATGCTCCGCAGC 59.573 57.895 0.00 0.00 45.98 5.25
2167 3816 3.518998 GCTCCGCAGCTCCTCGTA 61.519 66.667 0.00 0.00 43.09 3.43
2168 3817 2.851071 GCTCCGCAGCTCCTCGTAT 61.851 63.158 0.00 0.00 43.09 3.06
2169 3818 1.736586 CTCCGCAGCTCCTCGTATT 59.263 57.895 0.00 0.00 0.00 1.89
2170 3819 0.103208 CTCCGCAGCTCCTCGTATTT 59.897 55.000 0.00 0.00 0.00 1.40
2171 3820 0.535335 TCCGCAGCTCCTCGTATTTT 59.465 50.000 0.00 0.00 0.00 1.82
2172 3821 1.066430 TCCGCAGCTCCTCGTATTTTT 60.066 47.619 0.00 0.00 0.00 1.94
2173 3822 2.166870 TCCGCAGCTCCTCGTATTTTTA 59.833 45.455 0.00 0.00 0.00 1.52
2174 3823 2.540101 CCGCAGCTCCTCGTATTTTTAG 59.460 50.000 0.00 0.00 0.00 1.85
2175 3824 2.540101 CGCAGCTCCTCGTATTTTTAGG 59.460 50.000 0.00 0.00 0.00 2.69
2176 3825 3.737047 CGCAGCTCCTCGTATTTTTAGGA 60.737 47.826 0.00 0.00 37.07 2.94
2181 3830 4.402056 TCCTCGTATTTTTAGGAGCTGG 57.598 45.455 0.00 0.00 34.46 4.85
2182 3831 4.028131 TCCTCGTATTTTTAGGAGCTGGA 58.972 43.478 0.00 0.00 34.46 3.86
2183 3832 4.099573 TCCTCGTATTTTTAGGAGCTGGAG 59.900 45.833 0.00 0.00 34.46 3.86
2184 3833 4.141914 CCTCGTATTTTTAGGAGCTGGAGT 60.142 45.833 0.00 0.00 32.37 3.85
2185 3834 4.755411 TCGTATTTTTAGGAGCTGGAGTG 58.245 43.478 0.00 0.00 0.00 3.51
2186 3835 4.464951 TCGTATTTTTAGGAGCTGGAGTGA 59.535 41.667 0.00 0.00 0.00 3.41
2187 3836 4.567159 CGTATTTTTAGGAGCTGGAGTGAC 59.433 45.833 0.00 0.00 0.00 3.67
2188 3837 4.917906 ATTTTTAGGAGCTGGAGTGACT 57.082 40.909 0.00 0.00 0.00 3.41
2189 3838 3.963428 TTTTAGGAGCTGGAGTGACTC 57.037 47.619 3.47 3.47 0.00 3.36
2198 3847 1.592223 GGAGTGACTCCGAACAGGG 59.408 63.158 16.95 0.00 41.08 4.45
2199 3848 1.079750 GAGTGACTCCGAACAGGGC 60.080 63.158 0.00 0.00 41.52 5.19
2200 3849 2.047179 GTGACTCCGAACAGGGCC 60.047 66.667 0.00 0.00 41.52 5.80
2201 3850 2.203788 TGACTCCGAACAGGGCCT 60.204 61.111 0.00 0.00 41.52 5.19
2202 3851 1.841556 TGACTCCGAACAGGGCCTT 60.842 57.895 1.32 0.00 41.52 4.35
2203 3852 0.543410 TGACTCCGAACAGGGCCTTA 60.543 55.000 1.32 0.00 41.52 2.69
2204 3853 0.175989 GACTCCGAACAGGGCCTTAG 59.824 60.000 1.32 0.00 41.52 2.18
2205 3854 1.265454 ACTCCGAACAGGGCCTTAGG 61.265 60.000 1.32 5.04 41.52 2.69
2234 3883 5.192927 CCCCAACTCATTCATTGCTTACTA 58.807 41.667 0.00 0.00 0.00 1.82
2402 4051 7.734924 AGATATGATCTTTTGCGCAATAAGA 57.265 32.000 31.12 31.12 35.76 2.10
2551 4200 4.335416 AGTGTGGTTTGGATTATGACAGG 58.665 43.478 0.00 0.00 0.00 4.00
2562 4211 5.425217 TGGATTATGACAGGCTTCAGTTCTA 59.575 40.000 5.78 0.03 0.00 2.10
2575 4224 7.292120 AGGCTTCAGTTCTATCCTTCAGATATT 59.708 37.037 0.00 0.00 36.84 1.28
2614 4263 1.930371 GCACAATCGCAAAGACAACCC 60.930 52.381 0.00 0.00 0.00 4.11
2616 4265 0.109781 CAATCGCAAAGACAACCCGG 60.110 55.000 0.00 0.00 0.00 5.73
2639 4288 5.160641 GCAATTACTCGGCATTTTCTGAAA 58.839 37.500 0.00 0.00 0.00 2.69
2640 4289 5.807011 GCAATTACTCGGCATTTTCTGAAAT 59.193 36.000 3.31 0.00 35.90 2.17
2804 4453 5.596836 AGACCACAATGACAAAACACAAT 57.403 34.783 0.00 0.00 0.00 2.71
2822 4471 9.775854 AAACACAATTGATGATCATGGTAAAAA 57.224 25.926 14.30 0.00 0.00 1.94
2984 4633 0.607217 GGTTTCCAGGTGGGGTTACG 60.607 60.000 0.00 0.00 37.22 3.18
3141 4790 5.343058 CACAAACATTCTTTCATTAGTGGCG 59.657 40.000 0.00 0.00 0.00 5.69
3369 5179 2.393646 GAGGTATTCCTGCAGAGAGGT 58.606 52.381 17.39 6.38 45.24 3.85
3582 5403 2.775911 TTGGACTGATCTCCAAGCTG 57.224 50.000 11.43 0.00 44.05 4.24
3607 5428 8.894731 TGCAACTTTGTATGTCAAGTTTACTTA 58.105 29.630 0.00 0.00 37.35 2.24
3843 5664 8.017946 GTCTTTATCAAATGAAGTTCTGACCAC 58.982 37.037 4.17 0.00 0.00 4.16
3844 5665 7.939039 TCTTTATCAAATGAAGTTCTGACCACT 59.061 33.333 4.17 0.00 0.00 4.00
3845 5666 9.219603 CTTTATCAAATGAAGTTCTGACCACTA 57.780 33.333 4.17 0.00 0.00 2.74
3846 5667 9.567776 TTTATCAAATGAAGTTCTGACCACTAA 57.432 29.630 4.17 0.00 0.00 2.24
3847 5668 6.861065 TCAAATGAAGTTCTGACCACTAAC 57.139 37.500 4.17 0.00 0.00 2.34
3848 5669 5.763204 TCAAATGAAGTTCTGACCACTAACC 59.237 40.000 4.17 0.00 0.00 2.85
3849 5670 4.974645 ATGAAGTTCTGACCACTAACCA 57.025 40.909 4.17 0.00 0.00 3.67
4037 5860 5.869753 TGACTTCTCTATTCTTTTGCTGC 57.130 39.130 0.00 0.00 0.00 5.25
4052 5875 3.713858 TGCTGCGCTAAATATTTGCAT 57.286 38.095 9.73 0.00 34.66 3.96
4065 5889 7.701539 AAATATTTGCATGTGACTCTTACCA 57.298 32.000 0.00 0.00 0.00 3.25
4228 6055 4.510167 AGGAAACATCATACCTTCCCTG 57.490 45.455 0.00 0.00 38.50 4.45
4538 6365 9.558396 AATTTGACAAGCTTCAATTTGGAAATA 57.442 25.926 0.00 0.00 35.42 1.40
4552 6379 5.651172 TTGGAAATAGCATCGTATGTTCG 57.349 39.130 0.00 0.00 0.00 3.95
4556 6383 4.948864 AATAGCATCGTATGTTCGTTCG 57.051 40.909 0.00 0.00 0.00 3.95
4562 6389 0.638746 CGTATGTTCGTTCGTGCCTC 59.361 55.000 0.00 0.00 0.00 4.70
4575 6402 3.849911 TCGTGCCTCAGAGATTAAAGTG 58.150 45.455 0.00 0.00 0.00 3.16
4815 7810 9.725019 ACATCTCTACTGAATTGAACATGTTTA 57.275 29.630 13.36 5.62 0.00 2.01
4854 7850 7.946219 TGGATCCAGATATTTCTGCAACATATT 59.054 33.333 11.44 0.00 46.76 1.28
5272 8277 7.232330 TCACCAGTGAATCCATGTCAAATTAAA 59.768 33.333 0.00 0.00 36.53 1.52
5364 9768 7.163001 TGATCTATCCATGCATAGAGTACAC 57.837 40.000 11.90 2.77 38.50 2.90
5368 9772 4.926140 TCCATGCATAGAGTACACAGAG 57.074 45.455 0.00 0.00 0.00 3.35
5377 9781 9.185680 TGCATAGAGTACACAGAGAAGTTATAA 57.814 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.483808 TTCTCACTGTAATGGTGCACA 57.516 42.857 20.43 5.24 34.97 4.57
415 424 2.432510 GTGGGAAGAGGATGAAGACGAT 59.567 50.000 0.00 0.00 0.00 3.73
446 455 0.185175 GAGGAGGAGGAGGAGGAGTC 59.815 65.000 0.00 0.00 0.00 3.36
749 758 0.765510 GGTCTGACCCAAACCAGAGT 59.234 55.000 16.14 0.00 39.77 3.24
753 762 0.036164 CGATGGTCTGACCCAAACCA 59.964 55.000 23.42 5.23 46.51 3.67
795 804 1.427753 GTTCCCCTCCCCTCAGAAAAA 59.572 52.381 0.00 0.00 0.00 1.94
796 805 1.073098 GTTCCCCTCCCCTCAGAAAA 58.927 55.000 0.00 0.00 0.00 2.29
797 806 0.196118 AGTTCCCCTCCCCTCAGAAA 59.804 55.000 0.00 0.00 0.00 2.52
798 807 0.196118 AAGTTCCCCTCCCCTCAGAA 59.804 55.000 0.00 0.00 0.00 3.02
799 808 1.098589 TAAGTTCCCCTCCCCTCAGA 58.901 55.000 0.00 0.00 0.00 3.27
800 809 1.771255 CATAAGTTCCCCTCCCCTCAG 59.229 57.143 0.00 0.00 0.00 3.35
801 810 1.628043 CCATAAGTTCCCCTCCCCTCA 60.628 57.143 0.00 0.00 0.00 3.86
802 811 1.141185 CCATAAGTTCCCCTCCCCTC 58.859 60.000 0.00 0.00 0.00 4.30
803 812 0.328548 CCCATAAGTTCCCCTCCCCT 60.329 60.000 0.00 0.00 0.00 4.79
804 813 0.626574 ACCCATAAGTTCCCCTCCCC 60.627 60.000 0.00 0.00 0.00 4.81
805 814 0.844660 GACCCATAAGTTCCCCTCCC 59.155 60.000 0.00 0.00 0.00 4.30
806 815 0.468648 CGACCCATAAGTTCCCCTCC 59.531 60.000 0.00 0.00 0.00 4.30
807 816 1.138464 GACGACCCATAAGTTCCCCTC 59.862 57.143 0.00 0.00 0.00 4.30
808 817 1.201424 GACGACCCATAAGTTCCCCT 58.799 55.000 0.00 0.00 0.00 4.79
809 818 0.179092 CGACGACCCATAAGTTCCCC 60.179 60.000 0.00 0.00 0.00 4.81
810 819 0.533951 ACGACGACCCATAAGTTCCC 59.466 55.000 0.00 0.00 0.00 3.97
811 820 1.796617 CGACGACGACCCATAAGTTCC 60.797 57.143 0.00 0.00 42.66 3.62
812 821 1.135575 ACGACGACGACCCATAAGTTC 60.136 52.381 15.32 0.00 42.66 3.01
813 822 0.883833 ACGACGACGACCCATAAGTT 59.116 50.000 15.32 0.00 42.66 2.66
814 823 0.883833 AACGACGACGACCCATAAGT 59.116 50.000 15.32 0.00 42.66 2.24
815 824 1.916000 GAAACGACGACGACCCATAAG 59.084 52.381 15.32 0.00 42.66 1.73
816 825 1.728825 CGAAACGACGACGACCCATAA 60.729 52.381 15.32 0.00 42.66 1.90
817 826 0.179192 CGAAACGACGACGACCCATA 60.179 55.000 15.32 0.00 42.66 2.74
832 841 4.698304 CCCAATAAGTAAGTGAAGCCGAAA 59.302 41.667 0.00 0.00 0.00 3.46
842 851 4.832823 AGTTGCAAAGCCCAATAAGTAAGT 59.167 37.500 0.00 0.00 0.00 2.24
843 852 5.163513 CAGTTGCAAAGCCCAATAAGTAAG 58.836 41.667 0.00 0.00 0.00 2.34
844 853 4.586841 ACAGTTGCAAAGCCCAATAAGTAA 59.413 37.500 0.00 0.00 0.00 2.24
845 854 4.148838 ACAGTTGCAAAGCCCAATAAGTA 58.851 39.130 0.00 0.00 0.00 2.24
919 936 6.965500 GTCTCTCTTTATGTGATGTGCAATTG 59.035 38.462 0.00 0.00 0.00 2.32
920 937 6.883217 AGTCTCTCTTTATGTGATGTGCAATT 59.117 34.615 0.00 0.00 0.00 2.32
921 938 6.413052 AGTCTCTCTTTATGTGATGTGCAAT 58.587 36.000 0.00 0.00 0.00 3.56
922 939 5.798132 AGTCTCTCTTTATGTGATGTGCAA 58.202 37.500 0.00 0.00 0.00 4.08
923 940 5.411831 AGTCTCTCTTTATGTGATGTGCA 57.588 39.130 0.00 0.00 0.00 4.57
924 941 5.871524 TGAAGTCTCTCTTTATGTGATGTGC 59.128 40.000 0.00 0.00 36.40 4.57
925 942 8.388853 CAATGAAGTCTCTCTTTATGTGATGTG 58.611 37.037 0.00 0.00 36.40 3.21
926 943 7.065563 GCAATGAAGTCTCTCTTTATGTGATGT 59.934 37.037 0.00 0.00 36.40 3.06
927 944 7.280428 AGCAATGAAGTCTCTCTTTATGTGATG 59.720 37.037 0.00 0.00 36.40 3.07
928 945 7.337167 AGCAATGAAGTCTCTCTTTATGTGAT 58.663 34.615 0.00 0.00 36.40 3.06
929 946 6.705302 AGCAATGAAGTCTCTCTTTATGTGA 58.295 36.000 0.00 0.00 36.40 3.58
930 947 6.036953 GGAGCAATGAAGTCTCTCTTTATGTG 59.963 42.308 0.00 0.00 36.40 3.21
931 948 6.112058 GGAGCAATGAAGTCTCTCTTTATGT 58.888 40.000 0.00 0.00 36.40 2.29
932 949 6.111382 TGGAGCAATGAAGTCTCTCTTTATG 58.889 40.000 0.00 0.00 36.40 1.90
933 950 6.305272 TGGAGCAATGAAGTCTCTCTTTAT 57.695 37.500 0.00 0.00 36.40 1.40
1067 1088 2.693074 AGCAAAGGGTGGTTTTAGTGTG 59.307 45.455 0.00 0.00 32.77 3.82
1143 1167 3.465403 CAGAGGAGGGGGTGAGCG 61.465 72.222 0.00 0.00 0.00 5.03
1152 1176 2.604139 GGGGTAGAAGATCAGAGGAGG 58.396 57.143 0.00 0.00 0.00 4.30
1209 1233 2.244252 GAGGGAGAAGGTCCTACCAGTA 59.756 54.545 10.53 0.00 46.06 2.74
1232 1256 1.467342 CAGCTTTAAGGTGTTACGGGC 59.533 52.381 15.15 0.00 38.80 6.13
1346 1370 3.005539 AGGTCGGCAGAGTGGCAT 61.006 61.111 0.00 0.00 43.94 4.40
1401 1425 3.494626 GGTAGTCATACAATGATGCGGTG 59.505 47.826 0.00 0.00 42.04 4.94
1432 1456 2.079925 GCAGAACAAAGTAGGAGGCAG 58.920 52.381 0.00 0.00 0.00 4.85
1441 1465 1.134220 TCAACCGGAGCAGAACAAAGT 60.134 47.619 9.46 0.00 0.00 2.66
1442 1466 1.593196 TCAACCGGAGCAGAACAAAG 58.407 50.000 9.46 0.00 0.00 2.77
1580 1604 1.119684 TACACCATCATAGCAGCCGT 58.880 50.000 0.00 0.00 0.00 5.68
1656 1680 3.563508 CATTGCATACACACGCAGAAAA 58.436 40.909 0.00 0.00 39.75 2.29
1660 1684 0.168568 TGCATTGCATACACACGCAG 59.831 50.000 7.38 0.00 39.75 5.18
1688 1712 1.668151 GACTCCCACGGTGCAGAAC 60.668 63.158 1.68 0.00 0.00 3.01
1691 1715 3.625897 TGGACTCCCACGGTGCAG 61.626 66.667 1.68 3.27 37.58 4.41
1712 1736 3.502211 CCAATATTACCCCGCATCTTGTC 59.498 47.826 0.00 0.00 0.00 3.18
1715 1739 4.447138 TTCCAATATTACCCCGCATCTT 57.553 40.909 0.00 0.00 0.00 2.40
1763 3412 7.546316 CACAAATGCACATATCCATCTCAAAAA 59.454 33.333 0.00 0.00 0.00 1.94
1799 3448 9.802039 AACCATCCAAAAAGTAGTAAATGTAGA 57.198 29.630 0.00 0.00 0.00 2.59
1841 3490 3.400054 CCCTTCCGGGTCTCCACC 61.400 72.222 0.00 0.00 46.12 4.61
1885 3534 0.105778 CCTTCTCGATGCCCTCCTTC 59.894 60.000 0.00 0.00 0.00 3.46
1960 3609 4.737054 CCTATACTTTTGCCTTGCAGTTG 58.263 43.478 0.00 0.00 40.61 3.16
1968 3617 4.990526 AGCATATGCCTATACTTTTGCCT 58.009 39.130 23.96 0.00 43.38 4.75
1969 3618 5.006386 AGAGCATATGCCTATACTTTTGCC 58.994 41.667 23.96 0.00 43.38 4.52
1970 3619 6.876257 ACTAGAGCATATGCCTATACTTTTGC 59.124 38.462 23.96 0.00 43.38 3.68
1977 3626 6.322456 GTCCATCACTAGAGCATATGCCTATA 59.678 42.308 23.96 12.97 43.38 1.31
2013 3662 6.079712 AGCAAAGATAAGGGTATCCAAAGT 57.920 37.500 0.00 0.00 37.43 2.66
2074 3723 2.663196 GTGGGTCTCCGAACAGGG 59.337 66.667 0.00 0.00 41.52 4.45
2075 3724 2.214216 TGGTGGGTCTCCGAACAGG 61.214 63.158 0.00 0.00 42.97 4.00
2076 3725 1.004918 GTGGTGGGTCTCCGAACAG 60.005 63.158 0.00 0.00 35.24 3.16
2077 3726 1.458777 AGTGGTGGGTCTCCGAACA 60.459 57.895 0.00 0.00 35.24 3.18
2078 3727 1.292541 GAGTGGTGGGTCTCCGAAC 59.707 63.158 0.00 0.00 35.24 3.95
2079 3728 1.911766 GGAGTGGTGGGTCTCCGAA 60.912 63.158 0.00 0.00 40.36 4.30
2080 3729 2.283676 GGAGTGGTGGGTCTCCGA 60.284 66.667 0.00 0.00 40.36 4.55
2083 3732 1.841556 TGGTGGAGTGGTGGGTCTC 60.842 63.158 0.00 0.00 0.00 3.36
2084 3733 2.147387 GTGGTGGAGTGGTGGGTCT 61.147 63.158 0.00 0.00 0.00 3.85
2085 3734 2.113243 GAGTGGTGGAGTGGTGGGTC 62.113 65.000 0.00 0.00 0.00 4.46
2086 3735 2.039831 AGTGGTGGAGTGGTGGGT 60.040 61.111 0.00 0.00 0.00 4.51
2087 3736 2.750350 GAGTGGTGGAGTGGTGGG 59.250 66.667 0.00 0.00 0.00 4.61
2088 3737 2.750350 GGAGTGGTGGAGTGGTGG 59.250 66.667 0.00 0.00 0.00 4.61
2089 3738 2.343758 CGGAGTGGTGGAGTGGTG 59.656 66.667 0.00 0.00 0.00 4.17
2090 3739 3.626924 GCGGAGTGGTGGAGTGGT 61.627 66.667 0.00 0.00 0.00 4.16
2091 3740 3.302347 GAGCGGAGTGGTGGAGTGG 62.302 68.421 0.00 0.00 0.00 4.00
2092 3741 2.262915 GAGCGGAGTGGTGGAGTG 59.737 66.667 0.00 0.00 0.00 3.51
2093 3742 2.997897 GGAGCGGAGTGGTGGAGT 60.998 66.667 0.00 0.00 0.00 3.85
2094 3743 3.775654 GGGAGCGGAGTGGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
2108 3757 1.354101 TTTTAACTCCAGCTCCGGGA 58.646 50.000 0.00 0.00 0.00 5.14
2109 3758 2.084546 CTTTTTAACTCCAGCTCCGGG 58.915 52.381 0.00 0.00 0.00 5.73
2110 3759 1.468914 GCTTTTTAACTCCAGCTCCGG 59.531 52.381 0.00 0.00 0.00 5.14
2111 3760 2.095718 GTGCTTTTTAACTCCAGCTCCG 60.096 50.000 0.00 0.00 33.15 4.63
2112 3761 2.095718 CGTGCTTTTTAACTCCAGCTCC 60.096 50.000 0.00 0.00 33.15 4.70
2113 3762 2.095718 CCGTGCTTTTTAACTCCAGCTC 60.096 50.000 0.00 0.00 33.15 4.09
2114 3763 1.880027 CCGTGCTTTTTAACTCCAGCT 59.120 47.619 0.00 0.00 33.15 4.24
2115 3764 1.877443 TCCGTGCTTTTTAACTCCAGC 59.123 47.619 0.00 0.00 0.00 4.85
2116 3765 2.095718 GCTCCGTGCTTTTTAACTCCAG 60.096 50.000 0.00 0.00 38.95 3.86
2117 3766 1.877443 GCTCCGTGCTTTTTAACTCCA 59.123 47.619 0.00 0.00 38.95 3.86
2118 3767 2.613730 GCTCCGTGCTTTTTAACTCC 57.386 50.000 0.00 0.00 38.95 3.85
2129 3778 2.281484 TGTTTCCCAGCTCCGTGC 60.281 61.111 0.00 0.00 43.29 5.34
2130 3779 0.036010 ATCTGTTTCCCAGCTCCGTG 60.036 55.000 0.00 0.00 41.25 4.94
2131 3780 0.036010 CATCTGTTTCCCAGCTCCGT 60.036 55.000 0.00 0.00 41.25 4.69
2132 3781 1.372087 GCATCTGTTTCCCAGCTCCG 61.372 60.000 0.00 0.00 41.25 4.63
2133 3782 0.034670 AGCATCTGTTTCCCAGCTCC 60.035 55.000 0.00 0.00 41.25 4.70
2134 3783 1.377536 GAGCATCTGTTTCCCAGCTC 58.622 55.000 0.00 0.00 41.25 4.09
2135 3784 0.034670 GGAGCATCTGTTTCCCAGCT 60.035 55.000 0.00 0.00 41.25 4.24
2136 3785 1.372087 CGGAGCATCTGTTTCCCAGC 61.372 60.000 0.00 0.00 41.25 4.85
2137 3786 2.772739 CGGAGCATCTGTTTCCCAG 58.227 57.895 0.00 0.00 42.97 4.45
2151 3800 0.103208 AAATACGAGGAGCTGCGGAG 59.897 55.000 0.00 0.00 0.00 4.63
2152 3801 0.535335 AAAATACGAGGAGCTGCGGA 59.465 50.000 0.00 0.00 0.00 5.54
2153 3802 1.369625 AAAAATACGAGGAGCTGCGG 58.630 50.000 0.00 0.00 0.00 5.69
2154 3803 2.540101 CCTAAAAATACGAGGAGCTGCG 59.460 50.000 0.00 0.00 31.45 5.18
2155 3804 3.793559 TCCTAAAAATACGAGGAGCTGC 58.206 45.455 0.00 0.00 34.36 5.25
2160 3809 4.028131 TCCAGCTCCTAAAAATACGAGGA 58.972 43.478 0.00 0.00 37.02 3.71
2161 3810 4.141914 ACTCCAGCTCCTAAAAATACGAGG 60.142 45.833 0.00 0.00 0.00 4.63
2162 3811 4.806247 CACTCCAGCTCCTAAAAATACGAG 59.194 45.833 0.00 0.00 0.00 4.18
2163 3812 4.464951 TCACTCCAGCTCCTAAAAATACGA 59.535 41.667 0.00 0.00 0.00 3.43
2164 3813 4.567159 GTCACTCCAGCTCCTAAAAATACG 59.433 45.833 0.00 0.00 0.00 3.06
2165 3814 5.735766 AGTCACTCCAGCTCCTAAAAATAC 58.264 41.667 0.00 0.00 0.00 1.89
2166 3815 5.978814 GAGTCACTCCAGCTCCTAAAAATA 58.021 41.667 0.00 0.00 0.00 1.40
2167 3816 4.837972 GAGTCACTCCAGCTCCTAAAAAT 58.162 43.478 0.00 0.00 0.00 1.82
2168 3817 4.273148 GAGTCACTCCAGCTCCTAAAAA 57.727 45.455 0.00 0.00 0.00 1.94
2169 3818 3.963428 GAGTCACTCCAGCTCCTAAAA 57.037 47.619 0.00 0.00 0.00 1.52
2180 3829 1.592223 CCCTGTTCGGAGTCACTCC 59.408 63.158 14.67 14.67 46.44 3.85
2181 3830 1.079750 GCCCTGTTCGGAGTCACTC 60.080 63.158 0.00 0.00 33.16 3.51
2182 3831 2.584391 GGCCCTGTTCGGAGTCACT 61.584 63.158 0.00 0.00 33.16 3.41
2183 3832 2.047179 GGCCCTGTTCGGAGTCAC 60.047 66.667 0.00 0.00 33.16 3.67
2184 3833 0.543410 TAAGGCCCTGTTCGGAGTCA 60.543 55.000 0.00 0.00 33.16 3.41
2185 3834 0.175989 CTAAGGCCCTGTTCGGAGTC 59.824 60.000 0.00 0.00 33.16 3.36
2186 3835 1.265454 CCTAAGGCCCTGTTCGGAGT 61.265 60.000 0.00 0.00 33.16 3.85
2187 3836 0.976073 TCCTAAGGCCCTGTTCGGAG 60.976 60.000 0.00 0.00 33.16 4.63
2188 3837 0.545787 TTCCTAAGGCCCTGTTCGGA 60.546 55.000 0.00 0.00 33.16 4.55
2189 3838 0.107654 CTTCCTAAGGCCCTGTTCGG 60.108 60.000 0.00 0.00 0.00 4.30
2190 3839 0.107654 CCTTCCTAAGGCCCTGTTCG 60.108 60.000 0.00 0.00 42.78 3.95
2191 3840 3.884226 CCTTCCTAAGGCCCTGTTC 57.116 57.895 0.00 0.00 42.78 3.18
2200 3849 2.266279 TGAGTTGGGGTCCTTCCTAAG 58.734 52.381 0.00 0.00 36.25 2.18
2201 3850 2.426431 TGAGTTGGGGTCCTTCCTAA 57.574 50.000 0.00 0.00 36.25 2.69
2202 3851 2.661176 ATGAGTTGGGGTCCTTCCTA 57.339 50.000 0.00 0.00 36.25 2.94
2203 3852 1.636003 GAATGAGTTGGGGTCCTTCCT 59.364 52.381 0.00 0.00 36.25 3.36
2204 3853 1.354368 TGAATGAGTTGGGGTCCTTCC 59.646 52.381 0.00 0.00 0.00 3.46
2205 3854 2.879103 TGAATGAGTTGGGGTCCTTC 57.121 50.000 0.00 0.00 0.00 3.46
2271 3920 1.271597 GGTTGCCACAGAAGGACATCT 60.272 52.381 0.00 0.00 0.00 2.90
2551 4200 8.147058 TGAATATCTGAAGGATAGAACTGAAGC 58.853 37.037 0.00 0.00 39.89 3.86
2575 4224 3.055819 GTGCAGGACCATACTTCTTCTGA 60.056 47.826 0.00 0.00 0.00 3.27
2614 4263 2.097466 AGAAAATGCCGAGTAATTGCCG 59.903 45.455 0.00 0.00 0.00 5.69
2616 4265 4.355543 TCAGAAAATGCCGAGTAATTGC 57.644 40.909 0.00 0.00 0.00 3.56
2822 4471 6.639632 ACAAAGATGTATGAAACAGTGCTT 57.360 33.333 0.00 0.00 42.70 3.91
2984 4633 1.740025 GCAGTACCAGTGAAGGAATGC 59.260 52.381 0.00 0.00 0.00 3.56
3141 4790 7.596621 GCCATTAAGCCAATCTAAATAGCTTTC 59.403 37.037 0.00 0.00 40.76 2.62
3582 5403 9.166126 GTAAGTAAACTTGACATACAAAGTTGC 57.834 33.333 5.62 0.00 38.08 4.17
3607 5428 6.610075 AAGCAAAATAATCATTCCAGGTGT 57.390 33.333 0.00 0.00 0.00 4.16
3843 5664 8.755018 CAGAAAACTTTAATTGCAAGTGGTTAG 58.245 33.333 10.14 4.02 34.59 2.34
3844 5665 7.223777 GCAGAAAACTTTAATTGCAAGTGGTTA 59.776 33.333 10.14 0.00 34.59 2.85
3845 5666 6.037062 GCAGAAAACTTTAATTGCAAGTGGTT 59.963 34.615 10.14 8.95 34.59 3.67
3846 5667 5.523552 GCAGAAAACTTTAATTGCAAGTGGT 59.476 36.000 10.14 3.06 34.59 4.16
3847 5668 5.050159 GGCAGAAAACTTTAATTGCAAGTGG 60.050 40.000 10.14 2.42 34.59 4.00
3848 5669 5.523188 TGGCAGAAAACTTTAATTGCAAGTG 59.477 36.000 10.14 0.00 34.59 3.16
3849 5670 5.669477 TGGCAGAAAACTTTAATTGCAAGT 58.331 33.333 4.94 4.58 35.94 3.16
3980 5802 6.857964 CCACAAACAGTTGATTACAGATTGTC 59.142 38.462 0.00 0.00 37.22 3.18
3983 5805 6.016276 GGTCCACAAACAGTTGATTACAGATT 60.016 38.462 0.00 0.00 38.20 2.40
4001 5823 2.105821 AGAAGTCAATTTCCGGTCCACA 59.894 45.455 0.00 0.00 0.00 4.17
4037 5860 6.052840 AGAGTCACATGCAAATATTTAGCG 57.947 37.500 0.00 0.00 0.00 4.26
4228 6055 7.527568 AACCTAGCCATATTAGAGTGTCTAC 57.472 40.000 0.00 0.00 0.00 2.59
4264 6091 3.576648 ACGTTAGTAGCAAAGCTCTGTC 58.423 45.455 0.00 0.00 40.44 3.51
4316 6143 1.488393 GCCTGCAGGGTAGAAAGATCT 59.512 52.381 33.46 0.00 36.25 2.75
4409 6236 6.259608 ACAATTCACTCTGCATTATCAGCTAC 59.740 38.462 0.00 0.00 34.19 3.58
4538 6365 1.917955 CACGAACGAACATACGATGCT 59.082 47.619 0.14 0.00 37.03 3.79
4552 6379 4.092091 CACTTTAATCTCTGAGGCACGAAC 59.908 45.833 4.59 0.00 0.00 3.95
4556 6383 3.338249 TGCACTTTAATCTCTGAGGCAC 58.662 45.455 4.59 0.00 0.00 5.01
4562 6389 8.896744 TGGAAATAATCTGCACTTTAATCTCTG 58.103 33.333 0.00 0.00 0.00 3.35
4661 7651 4.744795 TTAGGCTCTTAGCTCCTTTCTG 57.255 45.455 0.00 0.00 41.99 3.02
4740 7730 4.148079 TGGATTGACTAATTGGTTGTGCA 58.852 39.130 0.00 0.00 0.00 4.57
4815 7810 1.271325 TGGATCCAAAGTGCGTCATGT 60.271 47.619 13.46 0.00 0.00 3.21
4821 7816 4.818546 AGAAATATCTGGATCCAAAGTGCG 59.181 41.667 17.00 2.72 33.59 5.34
4876 7878 1.572415 AGTGGGATTTCAGCCATGGAT 59.428 47.619 18.40 6.18 0.00 3.41
4880 7882 2.731572 CAGAAGTGGGATTTCAGCCAT 58.268 47.619 0.00 0.00 0.00 4.40
5272 8277 3.846588 ACCCTAAGATCTCACCAACATGT 59.153 43.478 0.00 0.00 0.00 3.21
5339 9743 7.233348 TGTGTACTCTATGCATGGATAGATCAA 59.767 37.037 30.10 18.55 34.98 2.57


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

AutoCloner maintained by Alex Coulton.