Multiple sequence alignment - TraesCS3B01G351200

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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 TraesCS3B01G351200 chr3B 100.000 4725 0 0 1 4725 561232909 561228185 0.000000e+00 8726
1 TraesCS3B01G351200 chr3B 84.459 296 32 10 3525 3810 561229305 561229014 3.600000e-71 279
2 TraesCS3B01G351200 chr3B 84.459 296 32 10 3605 3896 561229385 561229100 3.600000e-71 279
3 TraesCS3B01G351200 chr3B 99.338 151 0 1 4576 4725 561105629 561105479 6.020000e-69 272
4 TraesCS3B01G351200 chr3A 91.834 2596 111 45 1755 4319 556553846 556556371 0.000000e+00 3526
5 TraesCS3B01G351200 chr3A 92.937 1784 73 24 847 2585 556552896 556554671 0.000000e+00 2547
6 TraesCS3B01G351200 chr3A 85.909 809 60 16 1 793 556552007 556552777 0.000000e+00 813
7 TraesCS3B01G351200 chr3A 87.778 360 16 10 4377 4725 556556380 556556722 3.430000e-106 396
8 TraesCS3B01G351200 chr3A 81.013 316 41 11 3510 3810 556555632 556555943 2.840000e-57 233
9 TraesCS3B01G351200 chr3A 94.558 147 8 0 4579 4725 556659171 556659317 1.320000e-55 228
10 TraesCS3B01G351200 chr3D 92.890 1744 65 17 884 2585 429302152 429300426 0.000000e+00 2479
11 TraesCS3B01G351200 chr3D 89.953 1264 69 21 2598 3842 429300443 429299219 0.000000e+00 1578
12 TraesCS3B01G351200 chr3D 88.742 1137 71 26 3619 4725 429299522 429298413 0.000000e+00 1338
13 TraesCS3B01G351200 chr3D 87.677 495 39 7 173 648 429304124 429303633 1.490000e-154 556
14 TraesCS3B01G351200 chr3D 88.742 151 10 3 4576 4725 429107335 429107191 1.350000e-40 178
15 TraesCS3B01G351200 chr6A 77.309 379 68 14 3338 3716 69364341 69364701 1.720000e-49 207
16 TraesCS3B01G351200 chr6A 94.521 73 4 0 4377 4449 69376752 69376824 3.860000e-21 113
17 TraesCS3B01G351200 chr6B 93.671 79 5 0 4380 4458 182827448 182827370 8.310000e-23 119
18 TraesCS3B01G351200 chr6D 94.286 70 4 0 4380 4449 98197344 98197413 1.800000e-19 108


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 TraesCS3B01G351200 chr3B 561228185 561232909 4724 True 3094.666667 8726 89.639333 1 4725 3 chr3B.!!$R2 4724
1 TraesCS3B01G351200 chr3A 556552007 556556722 4715 False 1503.000000 3526 87.894200 1 4725 5 chr3A.!!$F2 4724
2 TraesCS3B01G351200 chr3D 429298413 429304124 5711 True 1487.750000 2479 89.815500 173 4725 4 chr3D.!!$R2 4552

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
162 172 0.097674 GCTTGCGAGCGAATGTTGAT 59.902 50.0 10.93 0.0 39.48 2.57 F
1011 2490 0.975556 AACATCCCCCAAAATCCGCC 60.976 55.0 0.00 0.0 0.00 6.13 F
1678 3159 0.392998 GATTCGGTCCAGTGTGGCAT 60.393 55.0 0.00 0.0 37.47 4.40 F
3267 4779 0.389948 AATCCTCGTGGTCACTTCGC 60.390 55.0 2.99 0.0 34.23 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 3141 0.038166 AATGCCACACTGGACCGAAT 59.962 50.0 0.00 0.0 40.96 3.34 R
2103 3611 0.603569 CGTGCCCAGTTAGTCTCTGT 59.396 55.0 0.00 0.0 0.00 3.41 R
3676 5200 0.031721 AACTCAAGGGACGACGACAC 59.968 55.0 0.00 0.0 0.00 3.67 R
4482 6032 0.109226 GGAAACGTCTCCACTCTCCG 60.109 60.0 2.12 0.0 35.36 4.63 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
42 43 2.301296 TCAAGAGCTCTGAACTCCCTTG 59.699 50.000 19.06 8.49 34.56 3.61
43 44 0.612744 AGAGCTCTGAACTCCCTTGC 59.387 55.000 17.42 0.00 34.56 4.01
51 52 0.968405 GAACTCCCTTGCATGCCAAA 59.032 50.000 16.68 2.34 31.94 3.28
52 53 1.551883 GAACTCCCTTGCATGCCAAAT 59.448 47.619 16.68 0.00 31.94 2.32
53 54 0.899720 ACTCCCTTGCATGCCAAATG 59.100 50.000 16.68 3.75 31.94 2.32
54 55 0.461339 CTCCCTTGCATGCCAAATGC 60.461 55.000 16.68 3.37 44.76 3.56
66 67 1.798813 GCCAAATGCACGCACCTATTC 60.799 52.381 0.00 0.00 40.77 1.75
67 68 1.202290 CCAAATGCACGCACCTATTCC 60.202 52.381 0.00 0.00 0.00 3.01
70 71 2.817834 GCACGCACCTATTCCGCA 60.818 61.111 0.00 0.00 0.00 5.69
72 73 2.508439 ACGCACCTATTCCGCACG 60.508 61.111 0.00 0.00 0.00 5.34
75 76 2.180204 GCACCTATTCCGCACGCAT 61.180 57.895 0.00 0.00 0.00 4.73
88 89 4.025229 TCCGCACGCATATTTATTTCAGTC 60.025 41.667 0.00 0.00 0.00 3.51
98 99 2.010145 TATTTCAGTCGCTGCCTGAC 57.990 50.000 7.92 4.12 38.62 3.51
100 101 0.319900 TTTCAGTCGCTGCCTGACTC 60.320 55.000 7.92 0.00 44.60 3.36
101 102 1.181741 TTCAGTCGCTGCCTGACTCT 61.182 55.000 7.92 0.00 44.60 3.24
102 103 0.322546 TCAGTCGCTGCCTGACTCTA 60.323 55.000 7.15 0.00 44.60 2.43
115 125 6.913170 TGCCTGACTCTATTTCATTTGAAAC 58.087 36.000 7.83 0.00 45.55 2.78
117 127 7.231317 TGCCTGACTCTATTTCATTTGAAACTT 59.769 33.333 7.83 0.00 45.55 2.66
118 128 7.540055 GCCTGACTCTATTTCATTTGAAACTTG 59.460 37.037 7.83 2.63 45.55 3.16
129 139 7.639113 TCATTTGAAACTTGTACTTGGACTT 57.361 32.000 0.00 0.00 0.00 3.01
130 140 7.479980 TCATTTGAAACTTGTACTTGGACTTG 58.520 34.615 0.00 0.00 0.00 3.16
133 143 7.639113 TTGAAACTTGTACTTGGACTTGATT 57.361 32.000 0.00 0.00 0.00 2.57
151 161 0.874390 TTGCTAAGTTGGCTTGCGAG 59.126 50.000 12.78 0.00 36.22 5.03
160 170 4.047030 GCTTGCGAGCGAATGTTG 57.953 55.556 10.93 0.00 39.48 3.33
161 171 1.497278 GCTTGCGAGCGAATGTTGA 59.503 52.632 10.93 0.00 39.48 3.18
162 172 0.097674 GCTTGCGAGCGAATGTTGAT 59.902 50.000 10.93 0.00 39.48 2.57
163 173 1.853646 GCTTGCGAGCGAATGTTGATC 60.854 52.381 10.93 0.00 39.48 2.92
164 174 1.662629 CTTGCGAGCGAATGTTGATCT 59.337 47.619 0.00 0.00 0.00 2.75
165 175 1.725641 TGCGAGCGAATGTTGATCTT 58.274 45.000 0.00 0.00 0.00 2.40
166 176 2.887337 TGCGAGCGAATGTTGATCTTA 58.113 42.857 0.00 0.00 0.00 2.10
167 177 2.603110 TGCGAGCGAATGTTGATCTTAC 59.397 45.455 0.00 0.00 0.00 2.34
168 178 2.860735 GCGAGCGAATGTTGATCTTACT 59.139 45.455 0.00 0.00 0.00 2.24
169 179 3.060873 GCGAGCGAATGTTGATCTTACTC 60.061 47.826 0.00 0.00 0.00 2.59
170 180 3.487574 CGAGCGAATGTTGATCTTACTCC 59.512 47.826 0.00 0.00 0.00 3.85
171 181 4.688021 GAGCGAATGTTGATCTTACTCCT 58.312 43.478 0.00 0.00 0.00 3.69
177 187 6.591834 CGAATGTTGATCTTACTCCTCTGTTT 59.408 38.462 0.00 0.00 0.00 2.83
190 200 3.134623 TCCTCTGTTTCTTCACTGCAGAA 59.865 43.478 23.35 4.22 36.02 3.02
226 236 2.176273 CCAATCGGAGCGCAAGGAG 61.176 63.158 11.47 0.00 38.28 3.69
306 320 3.857854 CATCCACTGCACGAGCGC 61.858 66.667 0.00 0.00 46.23 5.92
406 420 5.557325 CGTCGTGTGATGTTTTATGTTGTCA 60.557 40.000 0.00 0.00 0.00 3.58
487 502 1.172180 TTTGCAAGTCCAGGCTTCCG 61.172 55.000 0.00 0.00 0.00 4.30
562 595 1.068741 GGGTAATGGACGCTGTCTAGG 59.931 57.143 8.26 0.00 37.99 3.02
632 665 3.889196 TCTTTGTGACATTTACCGCAC 57.111 42.857 0.00 0.00 0.00 5.34
634 667 1.867166 TTGTGACATTTACCGCACGA 58.133 45.000 0.00 0.00 34.12 4.35
655 1963 5.699001 ACGATACATGCTGTTAGTGTTTTCA 59.301 36.000 0.00 0.00 0.00 2.69
664 1972 6.529829 TGCTGTTAGTGTTTTCATTTTGACAC 59.470 34.615 0.00 0.00 41.94 3.67
675 1983 3.186409 TCATTTTGACACGCTAGAGCAAC 59.814 43.478 1.89 0.00 42.21 4.17
678 1986 2.232756 TGACACGCTAGAGCAACAAA 57.767 45.000 1.89 0.00 42.21 2.83
682 1990 2.224066 ACACGCTAGAGCAACAAAGAGT 60.224 45.455 1.89 0.00 42.21 3.24
685 1993 3.506455 ACGCTAGAGCAACAAAGAGTAGA 59.494 43.478 1.89 0.00 42.21 2.59
686 1994 4.158764 ACGCTAGAGCAACAAAGAGTAGAT 59.841 41.667 1.89 0.00 42.21 1.98
687 1995 5.357314 ACGCTAGAGCAACAAAGAGTAGATA 59.643 40.000 1.89 0.00 42.21 1.98
690 1998 7.535940 CGCTAGAGCAACAAAGAGTAGATATAC 59.464 40.741 1.89 0.00 42.21 1.47
695 2003 9.967346 GAGCAACAAAGAGTAGATATACATACA 57.033 33.333 0.00 0.00 0.00 2.29
697 2005 9.197694 GCAACAAAGAGTAGATATACATACAGG 57.802 37.037 0.00 0.00 0.00 4.00
710 2018 8.980481 ATATACATACAGGTGAAAAAGGAAGG 57.020 34.615 0.00 0.00 0.00 3.46
716 2024 3.823304 CAGGTGAAAAAGGAAGGGAGAAG 59.177 47.826 0.00 0.00 0.00 2.85
727 2035 5.565509 AGGAAGGGAGAAGATGAAAAAGAC 58.434 41.667 0.00 0.00 0.00 3.01
728 2036 4.393371 GGAAGGGAGAAGATGAAAAAGACG 59.607 45.833 0.00 0.00 0.00 4.18
730 2038 4.570930 AGGGAGAAGATGAAAAAGACGAC 58.429 43.478 0.00 0.00 0.00 4.34
827 2284 4.047822 GGTTTCGAAAATGTTGACATGCA 58.952 39.130 13.10 0.00 36.56 3.96
828 2285 4.148696 GGTTTCGAAAATGTTGACATGCAG 59.851 41.667 13.10 0.00 36.56 4.41
829 2286 4.566545 TTCGAAAATGTTGACATGCAGT 57.433 36.364 0.00 0.00 36.56 4.40
831 2288 4.536065 TCGAAAATGTTGACATGCAGTTC 58.464 39.130 0.00 0.00 36.56 3.01
832 2289 4.036144 TCGAAAATGTTGACATGCAGTTCA 59.964 37.500 0.00 0.00 36.56 3.18
833 2290 4.739228 CGAAAATGTTGACATGCAGTTCAA 59.261 37.500 8.36 8.36 36.56 2.69
834 2291 5.231779 CGAAAATGTTGACATGCAGTTCAAA 59.768 36.000 12.98 6.08 36.56 2.69
835 2292 6.237781 CGAAAATGTTGACATGCAGTTCAAAA 60.238 34.615 12.98 9.31 36.56 2.44
914 2375 4.214758 TGACATGCTTCTCTGTGACAATTG 59.785 41.667 3.24 3.24 0.00 2.32
915 2376 3.057736 ACATGCTTCTCTGTGACAATTGC 60.058 43.478 5.05 0.00 0.00 3.56
916 2377 1.881973 TGCTTCTCTGTGACAATTGCC 59.118 47.619 5.05 0.00 0.00 4.52
917 2378 1.881973 GCTTCTCTGTGACAATTGCCA 59.118 47.619 5.05 0.00 0.00 4.92
918 2379 2.351157 GCTTCTCTGTGACAATTGCCAC 60.351 50.000 17.04 17.04 0.00 5.01
960 2421 3.234041 CGCGCGTCTCGTCTCTTG 61.234 66.667 24.19 0.00 41.07 3.02
969 2431 1.671901 CTCGTCTCTTGCCTCCCCTC 61.672 65.000 0.00 0.00 0.00 4.30
989 2451 0.987294 CCCTCTTCCTCAGAAAGGCA 59.013 55.000 0.00 0.00 45.78 4.75
996 2458 4.895297 TCTTCCTCAGAAAGGCAAAAACAT 59.105 37.500 0.00 0.00 45.78 2.71
1008 2470 3.081061 GCAAAAACATCCCCCAAAATCC 58.919 45.455 0.00 0.00 0.00 3.01
1011 2490 0.975556 AACATCCCCCAAAATCCGCC 60.976 55.000 0.00 0.00 0.00 6.13
1283 2762 2.122729 CTCACCCTCACCTCCCCA 59.877 66.667 0.00 0.00 0.00 4.96
1385 2866 3.136345 CTCTCCTGATGCGCTCGCT 62.136 63.158 9.73 1.08 42.51 4.93
1386 2867 2.202851 CTCCTGATGCGCTCGCTT 60.203 61.111 9.73 9.07 42.51 4.68
1484 2965 4.767255 GACCTCGGGTGCAGGCTG 62.767 72.222 10.94 10.94 35.25 4.85
1660 3141 1.673923 CGCTCAGCAGGTCAGATTTGA 60.674 52.381 0.00 0.00 0.00 2.69
1670 3151 2.939103 GGTCAGATTTGATTCGGTCCAG 59.061 50.000 0.00 0.00 35.39 3.86
1675 3156 1.890876 TTTGATTCGGTCCAGTGTGG 58.109 50.000 0.00 0.00 39.43 4.17
1678 3159 0.392998 GATTCGGTCCAGTGTGGCAT 60.393 55.000 0.00 0.00 37.47 4.40
1701 3182 2.257286 CTGCCCTGTGTATGCAACGC 62.257 60.000 0.00 0.00 39.17 4.84
1739 3220 3.319405 CCGTAGTCCATGCTAGTCTGAAT 59.681 47.826 0.00 0.00 0.00 2.57
1913 3421 1.955778 CATCCTTTGGTGTCAGTTGCA 59.044 47.619 0.00 0.00 0.00 4.08
1980 3488 9.729023 TTATACATCAATACTTTTGGCATTTCG 57.271 29.630 0.00 0.00 0.00 3.46
2004 3512 5.049543 GCATGGAGCTCATAGAATTTCAGTC 60.050 44.000 17.19 0.00 41.15 3.51
2096 3604 9.823098 CATATTGTTTTCTATAGCTGCATCTTC 57.177 33.333 1.02 0.00 0.00 2.87
2103 3611 1.583556 TAGCTGCATCTTCAAGGGGA 58.416 50.000 1.02 0.00 0.00 4.81
2121 3629 1.066787 GGACAGAGACTAACTGGGCAC 60.067 57.143 0.00 0.00 39.38 5.01
2133 3641 0.893270 CTGGGCACGGATTTGGTTGA 60.893 55.000 0.00 0.00 0.00 3.18
2178 3686 2.508361 GCATTAGCTGCCCCACATT 58.492 52.632 0.00 0.00 45.66 2.71
2299 3807 3.682858 TGCCTACACATAAGTTTCTTCGC 59.317 43.478 0.00 0.00 0.00 4.70
2318 3826 7.639039 TCTTCGCATATGTGACCATTAAATTC 58.361 34.615 18.40 0.00 33.83 2.17
2319 3827 6.312399 TCGCATATGTGACCATTAAATTCC 57.688 37.500 14.94 0.00 32.29 3.01
2389 3897 6.711277 TGAGTGCAGATAGTTGACCTTATTT 58.289 36.000 0.00 0.00 0.00 1.40
2534 4042 9.388506 CTCAATGTTCTACTCCTGATATGTTTT 57.611 33.333 0.00 0.00 0.00 2.43
2535 4043 9.383519 TCAATGTTCTACTCCTGATATGTTTTC 57.616 33.333 0.00 0.00 0.00 2.29
2584 4093 9.630098 ATTCAACATAAACTTGCTTCAGTATTG 57.370 29.630 0.00 0.00 0.00 1.90
2585 4094 8.165239 TCAACATAAACTTGCTTCAGTATTGT 57.835 30.769 0.00 0.00 0.00 2.71
2586 4095 8.289618 TCAACATAAACTTGCTTCAGTATTGTC 58.710 33.333 0.00 0.00 0.00 3.18
2587 4096 7.145932 ACATAAACTTGCTTCAGTATTGTCC 57.854 36.000 0.00 0.00 0.00 4.02
2588 4097 6.151144 ACATAAACTTGCTTCAGTATTGTCCC 59.849 38.462 0.00 0.00 0.00 4.46
2589 4098 3.073274 ACTTGCTTCAGTATTGTCCCC 57.927 47.619 0.00 0.00 0.00 4.81
2590 4099 2.644798 ACTTGCTTCAGTATTGTCCCCT 59.355 45.455 0.00 0.00 0.00 4.79
2591 4100 3.844211 ACTTGCTTCAGTATTGTCCCCTA 59.156 43.478 0.00 0.00 0.00 3.53
2592 4101 4.288626 ACTTGCTTCAGTATTGTCCCCTAA 59.711 41.667 0.00 0.00 0.00 2.69
2593 4102 4.919774 TGCTTCAGTATTGTCCCCTAAA 57.080 40.909 0.00 0.00 0.00 1.85
2594 4103 4.843728 TGCTTCAGTATTGTCCCCTAAAG 58.156 43.478 0.00 0.00 0.00 1.85
2595 4104 4.534500 TGCTTCAGTATTGTCCCCTAAAGA 59.466 41.667 0.00 0.00 0.00 2.52
2596 4105 5.013704 TGCTTCAGTATTGTCCCCTAAAGAA 59.986 40.000 0.00 0.00 0.00 2.52
2597 4106 5.944007 GCTTCAGTATTGTCCCCTAAAGAAA 59.056 40.000 0.00 0.00 0.00 2.52
2598 4107 6.433093 GCTTCAGTATTGTCCCCTAAAGAAAA 59.567 38.462 0.00 0.00 0.00 2.29
2599 4108 7.039993 GCTTCAGTATTGTCCCCTAAAGAAAAA 60.040 37.037 0.00 0.00 0.00 1.94
2600 4109 7.754851 TCAGTATTGTCCCCTAAAGAAAAAC 57.245 36.000 0.00 0.00 0.00 2.43
2601 4110 6.428771 TCAGTATTGTCCCCTAAAGAAAAACG 59.571 38.462 0.00 0.00 0.00 3.60
2602 4111 6.206048 CAGTATTGTCCCCTAAAGAAAAACGT 59.794 38.462 0.00 0.00 0.00 3.99
2603 4112 4.904253 TTGTCCCCTAAAGAAAAACGTG 57.096 40.909 0.00 0.00 0.00 4.49
2604 4113 2.619646 TGTCCCCTAAAGAAAAACGTGC 59.380 45.455 0.00 0.00 0.00 5.34
2605 4114 2.882761 GTCCCCTAAAGAAAAACGTGCT 59.117 45.455 0.00 0.00 0.00 4.40
2646 4155 0.617413 CACCCCTGCTCAGTCATCTT 59.383 55.000 0.00 0.00 0.00 2.40
2647 4156 1.004044 CACCCCTGCTCAGTCATCTTT 59.996 52.381 0.00 0.00 0.00 2.52
2688 4197 3.120649 GCCGTCAGAACTTTGATACACAC 60.121 47.826 0.00 0.00 0.00 3.82
2689 4198 3.121279 CCGTCAGAACTTTGATACACACG 59.879 47.826 0.00 0.00 0.00 4.49
2690 4199 3.421826 CGTCAGAACTTTGATACACACGC 60.422 47.826 0.00 0.00 0.00 5.34
2691 4200 2.729360 TCAGAACTTTGATACACACGCG 59.271 45.455 3.53 3.53 0.00 6.01
2692 4201 2.475111 CAGAACTTTGATACACACGCGT 59.525 45.455 5.58 5.58 0.00 6.01
2693 4202 2.729882 AGAACTTTGATACACACGCGTC 59.270 45.455 9.86 0.00 0.00 5.19
2694 4203 2.143008 ACTTTGATACACACGCGTCA 57.857 45.000 9.86 0.00 0.00 4.35
2695 4204 2.058798 ACTTTGATACACACGCGTCAG 58.941 47.619 9.86 7.46 0.00 3.51
2696 4205 2.287970 ACTTTGATACACACGCGTCAGA 60.288 45.455 9.86 0.00 0.00 3.27
2697 4206 2.425578 TTGATACACACGCGTCAGAA 57.574 45.000 9.86 0.00 0.00 3.02
2698 4207 1.693467 TGATACACACGCGTCAGAAC 58.307 50.000 9.86 0.00 0.00 3.01
2699 4208 1.268625 TGATACACACGCGTCAGAACT 59.731 47.619 9.86 0.00 0.00 3.01
2700 4209 2.287970 TGATACACACGCGTCAGAACTT 60.288 45.455 9.86 0.00 0.00 2.66
2701 4210 2.212869 TACACACGCGTCAGAACTTT 57.787 45.000 9.86 0.00 0.00 2.66
2702 4211 0.650512 ACACACGCGTCAGAACTTTG 59.349 50.000 9.86 0.00 0.00 2.77
2703 4212 0.927537 CACACGCGTCAGAACTTTGA 59.072 50.000 9.86 0.00 0.00 2.69
2704 4213 1.526887 CACACGCGTCAGAACTTTGAT 59.473 47.619 9.86 0.00 0.00 2.57
2705 4214 2.729360 CACACGCGTCAGAACTTTGATA 59.271 45.455 9.86 0.00 0.00 2.15
2706 4215 2.729882 ACACGCGTCAGAACTTTGATAC 59.270 45.455 9.86 0.00 0.00 2.24
2707 4216 2.729360 CACGCGTCAGAACTTTGATACA 59.271 45.455 9.86 0.00 0.00 2.29
2708 4217 2.729882 ACGCGTCAGAACTTTGATACAC 59.270 45.455 5.58 0.00 0.00 2.90
2709 4218 2.729360 CGCGTCAGAACTTTGATACACA 59.271 45.455 0.00 0.00 0.00 3.72
2737 4246 8.682016 GCTGCTATTGTATTTGCTTTATAAACG 58.318 33.333 0.00 0.00 0.00 3.60
2790 4299 9.278734 GGCTAAAATATTCTTTTCTCACTTTCG 57.721 33.333 0.00 0.00 0.00 3.46
2908 4417 2.359975 GTCCGGGCTGTTCCAAGG 60.360 66.667 0.00 0.00 36.21 3.61
3002 4511 4.074970 CAACACTTGGCTATGGAGAAACT 58.925 43.478 0.00 0.00 0.00 2.66
3004 4513 3.073062 ACACTTGGCTATGGAGAAACTGT 59.927 43.478 0.00 0.00 0.00 3.55
3014 4523 2.106511 TGGAGAAACTGTGAGGGAAAGG 59.893 50.000 0.00 0.00 0.00 3.11
3015 4524 2.155279 GAGAAACTGTGAGGGAAAGGC 58.845 52.381 0.00 0.00 0.00 4.35
3016 4525 1.777272 AGAAACTGTGAGGGAAAGGCT 59.223 47.619 0.00 0.00 0.00 4.58
3028 4537 2.224793 GGGAAAGGCTAAGTTCAGTGGT 60.225 50.000 0.00 0.00 0.00 4.16
3033 4542 3.676093 AGGCTAAGTTCAGTGGTAAAGC 58.324 45.455 0.00 0.00 0.00 3.51
3035 4544 3.437049 GGCTAAGTTCAGTGGTAAAGCAG 59.563 47.826 0.00 0.00 0.00 4.24
3244 4756 6.933521 GGATTGTCAGCTCATCATACTGTTAT 59.066 38.462 0.00 0.00 33.12 1.89
3267 4779 0.389948 AATCCTCGTGGTCACTTCGC 60.390 55.000 2.99 0.00 34.23 4.70
3307 4819 1.005630 GTGCTCTGACAAGACGCCT 60.006 57.895 0.00 0.00 0.00 5.52
3325 4837 2.975799 GTGAAGAACGGCGGGCAA 60.976 61.111 13.24 0.00 0.00 4.52
3431 4943 2.697751 AGGAGAAGGATGGTCAAGATCG 59.302 50.000 0.00 0.00 0.00 3.69
3443 4955 1.081892 CAAGATCGCCAGTCCAACAG 58.918 55.000 0.00 0.00 0.00 3.16
3501 5013 2.655090 TCCTGTGGTGCAAAGATTGA 57.345 45.000 0.00 0.00 0.00 2.57
3534 5046 1.203364 ACCCATCCCTGTCTCTTGAGT 60.203 52.381 0.00 0.00 0.00 3.41
3535 5047 1.912043 CCCATCCCTGTCTCTTGAGTT 59.088 52.381 0.00 0.00 0.00 3.01
3536 5048 3.107601 CCCATCCCTGTCTCTTGAGTTA 58.892 50.000 0.00 0.00 0.00 2.24
3544 5063 4.021894 CCTGTCTCTTGAGTTATATCCCCG 60.022 50.000 0.00 0.00 0.00 5.73
3567 5086 5.739161 CGAGTAAATTTTATGTTGCTCCTGC 59.261 40.000 0.00 0.00 34.18 4.85
3593 5112 0.439985 CGACAACAGCTGGATGAACG 59.560 55.000 23.60 21.62 0.00 3.95
3622 5146 2.385803 TCGTCCCTTGAGTTATCTCCC 58.614 52.381 0.00 0.00 39.75 4.30
3631 5155 5.880887 CCTTGAGTTATCTCCCCAAGTAAAC 59.119 44.000 0.00 0.00 39.75 2.01
3655 5179 2.099141 TCTTGGTCCTGCAAAGATCG 57.901 50.000 0.00 0.00 32.40 3.69
3676 5200 0.725686 CAGCAGCTGGATGAAGAACG 59.274 55.000 17.12 0.00 33.82 3.95
3819 5343 6.861065 TTCTGCTCCTGTAAAGTTTAACAG 57.139 37.500 13.76 13.76 42.25 3.16
3820 5344 5.925509 TCTGCTCCTGTAAAGTTTAACAGT 58.074 37.500 16.88 0.00 41.25 3.55
3833 5357 8.990163 AAAGTTTAACAGTTGGATAGGAAGAA 57.010 30.769 0.00 0.00 0.00 2.52
3865 5389 5.501156 CAACCTAGCTCCCTTGAGTTATTT 58.499 41.667 0.00 0.00 40.95 1.40
3914 5438 5.354234 GTGTAACTAACAGATGGATGGTTGG 59.646 44.000 0.00 0.00 39.29 3.77
3948 5473 4.141287 TGGGAACTCTTGTGGTACAATTG 58.859 43.478 3.24 3.24 44.16 2.32
3955 5486 3.137544 TCTTGTGGTACAATTGACCCTGT 59.862 43.478 13.59 0.00 44.16 4.00
3982 5513 1.883084 CTACCGGCGCCATCTGTTC 60.883 63.158 28.98 0.00 0.00 3.18
4004 5538 2.814336 CCTTTAACCCTGTTCTGTCAGC 59.186 50.000 0.00 0.00 34.47 4.26
4046 5580 6.820656 AGTGTCTTCCTGATGCAGTTTATTAG 59.179 38.462 0.00 0.00 0.00 1.73
4049 5583 7.981789 TGTCTTCCTGATGCAGTTTATTAGTAG 59.018 37.037 0.00 0.00 0.00 2.57
4052 5586 9.250624 CTTCCTGATGCAGTTTATTAGTAGTAC 57.749 37.037 0.00 0.00 0.00 2.73
4053 5587 8.534954 TCCTGATGCAGTTTATTAGTAGTACT 57.465 34.615 8.14 8.14 0.00 2.73
4108 5647 0.592637 TTGAGCACTTGTTGGATGCG 59.407 50.000 0.00 0.00 44.25 4.73
4154 5693 1.417890 ACTTTCAGGCAGCACAGTAGT 59.582 47.619 0.00 0.00 0.00 2.73
4155 5694 2.632996 ACTTTCAGGCAGCACAGTAGTA 59.367 45.455 0.00 0.00 0.00 1.82
4156 5695 2.743636 TTCAGGCAGCACAGTAGTAC 57.256 50.000 0.00 0.00 0.00 2.73
4157 5696 1.924731 TCAGGCAGCACAGTAGTACT 58.075 50.000 0.00 0.00 0.00 2.73
4158 5697 3.081710 TCAGGCAGCACAGTAGTACTA 57.918 47.619 1.57 0.00 0.00 1.82
4159 5698 2.753452 TCAGGCAGCACAGTAGTACTAC 59.247 50.000 23.03 23.03 36.35 2.73
4164 5703 3.381908 GCAGCACAGTAGTACTACCATCT 59.618 47.826 25.97 16.11 36.75 2.90
4167 5706 4.641094 AGCACAGTAGTACTACCATCTGAC 59.359 45.833 25.97 15.60 36.75 3.51
4237 5776 3.599285 TAGTTGGGCTTGGGTCGCG 62.599 63.158 0.00 0.00 0.00 5.87
4307 5851 4.954970 CGTGGCTGCTGTTGGGGT 62.955 66.667 0.00 0.00 0.00 4.95
4308 5852 3.297620 GTGGCTGCTGTTGGGGTG 61.298 66.667 0.00 0.00 0.00 4.61
4472 6022 4.416738 GCCCAGGTCAGCAGGGAC 62.417 72.222 8.88 0.00 45.80 4.46
4482 6032 4.056125 GCAGGGACGCAAAAGGGC 62.056 66.667 0.00 0.00 0.00 5.19
4542 6092 1.225854 GTCTTGCTTGCGATGCGAC 60.226 57.895 0.00 0.00 0.00 5.19
4582 6132 2.707902 GGGATCAGAATTCCGTGGC 58.292 57.895 0.65 0.00 33.82 5.01
4583 6133 1.160329 GGGATCAGAATTCCGTGGCG 61.160 60.000 0.65 0.00 33.82 5.69
4628 6189 4.736896 GACGTCGAAAGCGCCCCT 62.737 66.667 2.29 0.00 37.46 4.79
4634 6195 2.761195 CGAAAGCGCCCCTAAAGCC 61.761 63.158 2.29 0.00 0.00 4.35
4653 6214 4.217159 GCCCCCGCGATTAGACGT 62.217 66.667 8.23 0.00 35.59 4.34
4654 6215 2.027169 CCCCCGCGATTAGACGTC 59.973 66.667 8.23 7.70 35.59 4.34
4655 6216 2.353145 CCCCGCGATTAGACGTCG 60.353 66.667 8.23 0.00 41.77 5.12
4656 6217 2.353145 CCCGCGATTAGACGTCGG 60.353 66.667 8.23 6.25 44.96 4.79
4691 6252 4.083862 GGCGCTCGGGTCCTTTCT 62.084 66.667 7.64 0.00 0.00 2.52
4692 6253 2.047179 GCGCTCGGGTCCTTTCTT 60.047 61.111 0.00 0.00 0.00 2.52
4693 6254 2.101233 GCGCTCGGGTCCTTTCTTC 61.101 63.158 0.00 0.00 0.00 2.87
4696 6263 1.192428 GCTCGGGTCCTTTCTTCCTA 58.808 55.000 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.180204 GCGGAATAGGTGCGTGCAT 61.180 57.895 0.00 0.00 44.08 3.96
52 53 2.817834 GCGGAATAGGTGCGTGCA 60.818 61.111 0.00 0.00 44.08 4.57
53 54 2.817834 TGCGGAATAGGTGCGTGC 60.818 61.111 0.00 0.00 44.08 5.34
54 55 2.798501 CGTGCGGAATAGGTGCGTG 61.799 63.158 0.00 0.00 44.08 5.34
55 56 2.508439 CGTGCGGAATAGGTGCGT 60.508 61.111 0.00 0.00 44.08 5.24
66 67 4.209452 ACTGAAATAAATATGCGTGCGG 57.791 40.909 0.00 0.00 0.00 5.69
67 68 3.894288 CGACTGAAATAAATATGCGTGCG 59.106 43.478 0.00 0.00 0.00 5.34
70 71 4.552767 GCAGCGACTGAAATAAATATGCGT 60.553 41.667 10.46 0.00 32.44 5.24
72 73 4.023707 AGGCAGCGACTGAAATAAATATGC 60.024 41.667 10.46 0.00 32.44 3.14
75 76 4.765273 TCAGGCAGCGACTGAAATAAATA 58.235 39.130 11.01 0.00 45.60 1.40
88 89 2.299993 TGAAATAGAGTCAGGCAGCG 57.700 50.000 0.00 0.00 0.00 5.18
101 102 9.959749 GTCCAAGTACAAGTTTCAAATGAAATA 57.040 29.630 11.40 0.00 44.69 1.40
102 103 8.695456 AGTCCAAGTACAAGTTTCAAATGAAAT 58.305 29.630 11.40 0.00 44.69 2.17
115 125 6.428159 ACTTAGCAATCAAGTCCAAGTACAAG 59.572 38.462 0.00 0.00 30.36 3.16
117 127 5.865085 ACTTAGCAATCAAGTCCAAGTACA 58.135 37.500 0.00 0.00 30.36 2.90
118 128 6.348540 CCAACTTAGCAATCAAGTCCAAGTAC 60.349 42.308 0.00 0.00 35.19 2.73
124 134 3.084786 AGCCAACTTAGCAATCAAGTCC 58.915 45.455 0.00 0.00 35.19 3.85
129 139 1.199789 CGCAAGCCAACTTAGCAATCA 59.800 47.619 0.00 0.00 33.74 2.57
130 140 1.468520 TCGCAAGCCAACTTAGCAATC 59.531 47.619 0.00 0.00 33.74 2.67
133 143 1.577328 GCTCGCAAGCCAACTTAGCA 61.577 55.000 0.00 0.00 43.10 3.49
151 161 4.505922 CAGAGGAGTAAGATCAACATTCGC 59.494 45.833 0.00 0.00 0.00 4.70
152 162 5.655488 ACAGAGGAGTAAGATCAACATTCG 58.345 41.667 0.00 0.00 0.00 3.34
153 163 7.821846 AGAAACAGAGGAGTAAGATCAACATTC 59.178 37.037 0.00 0.00 0.00 2.67
154 164 7.684529 AGAAACAGAGGAGTAAGATCAACATT 58.315 34.615 0.00 0.00 0.00 2.71
155 165 7.251321 AGAAACAGAGGAGTAAGATCAACAT 57.749 36.000 0.00 0.00 0.00 2.71
156 166 6.672266 AGAAACAGAGGAGTAAGATCAACA 57.328 37.500 0.00 0.00 0.00 3.33
157 167 7.117092 GTGAAGAAACAGAGGAGTAAGATCAAC 59.883 40.741 0.00 0.00 0.00 3.18
158 168 7.015682 AGTGAAGAAACAGAGGAGTAAGATCAA 59.984 37.037 0.00 0.00 0.00 2.57
159 169 6.495181 AGTGAAGAAACAGAGGAGTAAGATCA 59.505 38.462 0.00 0.00 0.00 2.92
160 170 6.811170 CAGTGAAGAAACAGAGGAGTAAGATC 59.189 42.308 0.00 0.00 0.00 2.75
161 171 6.696411 CAGTGAAGAAACAGAGGAGTAAGAT 58.304 40.000 0.00 0.00 0.00 2.40
162 172 5.509840 GCAGTGAAGAAACAGAGGAGTAAGA 60.510 44.000 0.00 0.00 0.00 2.10
163 173 4.688413 GCAGTGAAGAAACAGAGGAGTAAG 59.312 45.833 0.00 0.00 0.00 2.34
164 174 4.100963 TGCAGTGAAGAAACAGAGGAGTAA 59.899 41.667 0.00 0.00 0.00 2.24
165 175 3.641436 TGCAGTGAAGAAACAGAGGAGTA 59.359 43.478 0.00 0.00 0.00 2.59
166 176 2.435805 TGCAGTGAAGAAACAGAGGAGT 59.564 45.455 0.00 0.00 0.00 3.85
167 177 3.065655 CTGCAGTGAAGAAACAGAGGAG 58.934 50.000 5.25 0.00 0.00 3.69
168 178 2.700371 TCTGCAGTGAAGAAACAGAGGA 59.300 45.455 14.67 0.00 32.65 3.71
169 179 3.117491 TCTGCAGTGAAGAAACAGAGG 57.883 47.619 14.67 0.00 32.65 3.69
170 180 5.065731 AGTTTTCTGCAGTGAAGAAACAGAG 59.934 40.000 23.57 0.00 41.98 3.35
171 181 4.943705 AGTTTTCTGCAGTGAAGAAACAGA 59.056 37.500 23.57 8.83 41.98 3.41
177 187 3.470709 CCTCAGTTTTCTGCAGTGAAGA 58.529 45.455 14.67 0.00 46.59 2.87
190 200 1.188863 GGATGCCATTGCCTCAGTTT 58.811 50.000 0.00 0.00 34.19 2.66
212 222 3.760035 GGTCTCCTTGCGCTCCGA 61.760 66.667 9.73 0.00 0.00 4.55
226 236 1.279271 AGGTACACAAGCCTCATGGTC 59.721 52.381 0.00 0.00 35.27 4.02
306 320 1.191096 GCCAGTTTATGATTTGCGCG 58.809 50.000 0.00 0.00 0.00 6.86
406 420 5.409826 GCAATAGTTCAGTCTACTTGCAGTT 59.590 40.000 0.00 0.00 36.16 3.16
441 456 6.910536 AGAGAGGTTCATAAAAATACAGCG 57.089 37.500 0.00 0.00 0.00 5.18
512 527 4.142816 CCAATGCAGAAAACTACCGAAGAG 60.143 45.833 0.00 0.00 0.00 2.85
518 533 6.404734 CCAAGTATCCAATGCAGAAAACTACC 60.405 42.308 0.00 0.00 0.00 3.18
519 534 6.404734 CCCAAGTATCCAATGCAGAAAACTAC 60.405 42.308 0.00 0.00 0.00 2.73
562 595 7.075741 GGACACAAACATGTACATACAGAAAC 58.924 38.462 8.32 0.00 39.92 2.78
655 1963 3.138304 TGTTGCTCTAGCGTGTCAAAAT 58.862 40.909 0.00 0.00 45.83 1.82
664 1972 4.098055 TCTACTCTTTGTTGCTCTAGCG 57.902 45.455 0.00 0.00 45.83 4.26
685 1993 7.998964 CCCTTCCTTTTTCACCTGTATGTATAT 59.001 37.037 0.00 0.00 0.00 0.86
686 1994 7.183112 TCCCTTCCTTTTTCACCTGTATGTATA 59.817 37.037 0.00 0.00 0.00 1.47
687 1995 6.011981 TCCCTTCCTTTTTCACCTGTATGTAT 60.012 38.462 0.00 0.00 0.00 2.29
690 1998 4.662278 TCCCTTCCTTTTTCACCTGTATG 58.338 43.478 0.00 0.00 0.00 2.39
692 2000 3.977999 TCTCCCTTCCTTTTTCACCTGTA 59.022 43.478 0.00 0.00 0.00 2.74
695 2003 3.722101 TCTTCTCCCTTCCTTTTTCACCT 59.278 43.478 0.00 0.00 0.00 4.00
697 2005 5.316987 TCATCTTCTCCCTTCCTTTTTCAC 58.683 41.667 0.00 0.00 0.00 3.18
698 2006 5.582950 TCATCTTCTCCCTTCCTTTTTCA 57.417 39.130 0.00 0.00 0.00 2.69
710 2018 7.762159 AGATTAGTCGTCTTTTTCATCTTCTCC 59.238 37.037 0.00 0.00 0.00 3.71
835 2292 8.606602 GCATGTCAACATTTTCTTCTTCTTTTT 58.393 29.630 0.00 0.00 33.61 1.94
837 2294 6.703165 GGCATGTCAACATTTTCTTCTTCTTT 59.297 34.615 0.00 0.00 33.61 2.52
838 2295 6.041296 AGGCATGTCAACATTTTCTTCTTCTT 59.959 34.615 0.00 0.00 33.61 2.52
840 2297 5.776744 AGGCATGTCAACATTTTCTTCTTC 58.223 37.500 0.00 0.00 33.61 2.87
841 2298 5.537674 AGAGGCATGTCAACATTTTCTTCTT 59.462 36.000 0.00 0.00 33.61 2.52
843 2300 5.048504 TGAGAGGCATGTCAACATTTTCTTC 60.049 40.000 0.00 0.00 33.61 2.87
844 2301 4.828939 TGAGAGGCATGTCAACATTTTCTT 59.171 37.500 0.00 0.00 33.61 2.52
845 2302 4.401022 TGAGAGGCATGTCAACATTTTCT 58.599 39.130 0.00 0.00 33.61 2.52
883 2340 5.628193 CACAGAGAAGCATGTCAACATTTTC 59.372 40.000 0.00 1.76 33.61 2.29
914 2375 2.195123 AAACGCTAACCGCATGTGGC 62.195 55.000 25.33 10.06 41.76 5.01
915 2376 0.239879 AAAACGCTAACCGCATGTGG 59.760 50.000 23.88 23.88 41.76 4.17
916 2377 1.069568 TGAAAACGCTAACCGCATGTG 60.070 47.619 0.00 0.00 41.76 3.21
917 2378 1.231221 TGAAAACGCTAACCGCATGT 58.769 45.000 0.00 0.00 41.76 3.21
918 2379 2.542766 ATGAAAACGCTAACCGCATG 57.457 45.000 0.00 0.00 41.76 4.06
959 2420 3.626596 AAGAGGGGAGGGGAGGCA 61.627 66.667 0.00 0.00 0.00 4.75
960 2421 2.770475 GAAGAGGGGAGGGGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
989 2451 2.290008 GCGGATTTTGGGGGATGTTTTT 60.290 45.455 0.00 0.00 0.00 1.94
1020 2499 3.659092 CGCTGAACTTGCCGCCAA 61.659 61.111 0.00 0.00 0.00 4.52
1484 2965 4.526770 CGGAAATCCCCGGTGTAC 57.473 61.111 0.00 0.00 45.43 2.90
1660 3141 0.038166 AATGCCACACTGGACCGAAT 59.962 50.000 0.00 0.00 40.96 3.34
1678 3159 2.284754 TGCATACACAGGGCAGAAAA 57.715 45.000 0.00 0.00 32.95 2.29
1688 3169 0.865111 GTGACAGCGTTGCATACACA 59.135 50.000 0.00 0.00 31.62 3.72
1701 3182 2.031516 CGGCTGGCTGAAGTGACAG 61.032 63.158 0.00 0.00 40.43 3.51
1716 3197 1.033574 AGACTAGCATGGACTACGGC 58.966 55.000 0.00 0.00 0.00 5.68
1913 3421 6.229936 TGAACTAGGTTGTAACTGACAGTT 57.770 37.500 23.61 23.61 41.97 3.16
1980 3488 4.820716 ACTGAAATTCTATGAGCTCCATGC 59.179 41.667 12.15 0.00 43.29 4.06
2004 3512 6.757897 TCAACAGGCTATACCAAATTTCTG 57.242 37.500 0.00 0.00 43.14 3.02
2096 3604 2.234908 CCAGTTAGTCTCTGTCCCCTTG 59.765 54.545 0.00 0.00 0.00 3.61
2103 3611 0.603569 CGTGCCCAGTTAGTCTCTGT 59.396 55.000 0.00 0.00 0.00 3.41
2121 3629 1.608590 ACAGCTGTTCAACCAAATCCG 59.391 47.619 15.25 0.00 0.00 4.18
2133 3641 3.838244 TGAGGAAGTACAACAGCTGTT 57.162 42.857 26.36 26.36 39.64 3.16
2178 3686 6.102615 AGCATCCACCCCATTAGTAAAATAGA 59.897 38.462 0.00 0.00 0.00 1.98
2299 3807 6.975196 TGGGGAATTTAATGGTCACATATG 57.025 37.500 0.00 0.00 35.94 1.78
2367 3875 6.372659 CACAAATAAGGTCAACTATCTGCACT 59.627 38.462 0.00 0.00 0.00 4.40
2571 4080 4.919774 TTAGGGGACAATACTGAAGCAA 57.080 40.909 0.00 0.00 0.00 3.91
2576 4085 6.428771 CGTTTTTCTTTAGGGGACAATACTGA 59.571 38.462 0.00 0.00 0.00 3.41
2577 4086 6.206048 ACGTTTTTCTTTAGGGGACAATACTG 59.794 38.462 0.00 0.00 0.00 2.74
2578 4087 6.206048 CACGTTTTTCTTTAGGGGACAATACT 59.794 38.462 0.00 0.00 0.00 2.12
2579 4088 6.376177 CACGTTTTTCTTTAGGGGACAATAC 58.624 40.000 0.00 0.00 0.00 1.89
2580 4089 5.048573 GCACGTTTTTCTTTAGGGGACAATA 60.049 40.000 0.00 0.00 0.00 1.90
2581 4090 4.261867 GCACGTTTTTCTTTAGGGGACAAT 60.262 41.667 0.00 0.00 0.00 2.71
2582 4091 3.067040 GCACGTTTTTCTTTAGGGGACAA 59.933 43.478 0.00 0.00 0.00 3.18
2583 4092 2.619646 GCACGTTTTTCTTTAGGGGACA 59.380 45.455 0.00 0.00 0.00 4.02
2584 4093 2.882761 AGCACGTTTTTCTTTAGGGGAC 59.117 45.455 0.00 0.00 0.00 4.46
2585 4094 3.217681 AGCACGTTTTTCTTTAGGGGA 57.782 42.857 0.00 0.00 0.00 4.81
2586 4095 3.316868 TGAAGCACGTTTTTCTTTAGGGG 59.683 43.478 9.47 0.00 0.00 4.79
2587 4096 4.036380 ACTGAAGCACGTTTTTCTTTAGGG 59.964 41.667 9.47 0.00 30.57 3.53
2588 4097 5.169836 ACTGAAGCACGTTTTTCTTTAGG 57.830 39.130 9.47 0.53 30.57 2.69
2589 4098 7.323656 CCAATACTGAAGCACGTTTTTCTTTAG 59.676 37.037 9.47 8.02 32.01 1.85
2590 4099 7.136119 CCAATACTGAAGCACGTTTTTCTTTA 58.864 34.615 9.47 2.91 0.00 1.85
2591 4100 5.977129 CCAATACTGAAGCACGTTTTTCTTT 59.023 36.000 9.47 1.19 0.00 2.52
2592 4101 5.067283 ACCAATACTGAAGCACGTTTTTCTT 59.933 36.000 9.47 0.75 0.00 2.52
2593 4102 4.578928 ACCAATACTGAAGCACGTTTTTCT 59.421 37.500 9.47 0.00 0.00 2.52
2594 4103 4.675114 CACCAATACTGAAGCACGTTTTTC 59.325 41.667 0.00 0.00 0.00 2.29
2595 4104 4.097286 ACACCAATACTGAAGCACGTTTTT 59.903 37.500 0.00 0.00 0.00 1.94
2596 4105 3.630312 ACACCAATACTGAAGCACGTTTT 59.370 39.130 0.00 0.00 0.00 2.43
2597 4106 3.211045 ACACCAATACTGAAGCACGTTT 58.789 40.909 0.00 0.00 0.00 3.60
2598 4107 2.846193 ACACCAATACTGAAGCACGTT 58.154 42.857 0.00 0.00 0.00 3.99
2599 4108 2.543777 ACACCAATACTGAAGCACGT 57.456 45.000 0.00 0.00 0.00 4.49
2600 4109 4.451096 ACTTAACACCAATACTGAAGCACG 59.549 41.667 0.00 0.00 0.00 5.34
2601 4110 5.941948 ACTTAACACCAATACTGAAGCAC 57.058 39.130 0.00 0.00 0.00 4.40
2602 4111 6.296026 AGAACTTAACACCAATACTGAAGCA 58.704 36.000 0.00 0.00 0.00 3.91
2603 4112 6.426937 TGAGAACTTAACACCAATACTGAAGC 59.573 38.462 0.00 0.00 0.00 3.86
2604 4113 7.797819 GTGAGAACTTAACACCAATACTGAAG 58.202 38.462 0.00 0.00 0.00 3.02
2605 4114 7.724305 GTGAGAACTTAACACCAATACTGAA 57.276 36.000 0.00 0.00 0.00 3.02
2646 4155 6.694447 ACGGCTACACAGAATTTTAGACTAA 58.306 36.000 0.00 0.00 0.00 2.24
2647 4156 6.071784 TGACGGCTACACAGAATTTTAGACTA 60.072 38.462 0.00 0.00 0.00 2.59
2688 4197 2.729360 TGTGTATCAAAGTTCTGACGCG 59.271 45.455 3.53 3.53 0.00 6.01
2689 4198 3.421826 CGTGTGTATCAAAGTTCTGACGC 60.422 47.826 0.00 0.00 0.00 5.19
2690 4199 3.421826 GCGTGTGTATCAAAGTTCTGACG 60.422 47.826 0.00 0.00 0.00 4.35
2691 4200 3.741344 AGCGTGTGTATCAAAGTTCTGAC 59.259 43.478 0.00 0.00 0.00 3.51
2692 4201 3.740832 CAGCGTGTGTATCAAAGTTCTGA 59.259 43.478 0.00 0.00 0.00 3.27
2693 4202 3.665323 GCAGCGTGTGTATCAAAGTTCTG 60.665 47.826 0.00 0.00 0.00 3.02
2694 4203 2.480419 GCAGCGTGTGTATCAAAGTTCT 59.520 45.455 0.00 0.00 0.00 3.01
2695 4204 2.480419 AGCAGCGTGTGTATCAAAGTTC 59.520 45.455 0.00 0.00 0.00 3.01
2696 4205 2.494059 AGCAGCGTGTGTATCAAAGTT 58.506 42.857 0.00 0.00 0.00 2.66
2697 4206 2.169832 AGCAGCGTGTGTATCAAAGT 57.830 45.000 0.00 0.00 0.00 2.66
2698 4207 4.093408 ACAATAGCAGCGTGTGTATCAAAG 59.907 41.667 0.00 0.00 0.00 2.77
2699 4208 4.000325 ACAATAGCAGCGTGTGTATCAAA 59.000 39.130 0.00 0.00 0.00 2.69
2700 4209 3.595173 ACAATAGCAGCGTGTGTATCAA 58.405 40.909 0.00 0.00 0.00 2.57
2701 4210 3.245518 ACAATAGCAGCGTGTGTATCA 57.754 42.857 0.00 0.00 0.00 2.15
2702 4211 5.907197 AATACAATAGCAGCGTGTGTATC 57.093 39.130 14.55 0.00 35.00 2.24
2703 4212 5.504010 GCAAATACAATAGCAGCGTGTGTAT 60.504 40.000 10.46 10.46 37.06 2.29
2704 4213 4.201773 GCAAATACAATAGCAGCGTGTGTA 60.202 41.667 9.06 8.18 0.00 2.90
2705 4214 3.426159 GCAAATACAATAGCAGCGTGTGT 60.426 43.478 9.06 6.44 0.00 3.72
2706 4215 3.100817 GCAAATACAATAGCAGCGTGTG 58.899 45.455 9.06 1.07 0.00 3.82
2707 4216 3.009723 AGCAAATACAATAGCAGCGTGT 58.990 40.909 5.01 5.01 0.00 4.49
2708 4217 3.680642 AGCAAATACAATAGCAGCGTG 57.319 42.857 0.00 0.00 0.00 5.34
2709 4218 4.701956 AAAGCAAATACAATAGCAGCGT 57.298 36.364 0.00 0.00 0.00 5.07
2737 4246 6.815641 TCAGAAGAAGAAGATCAATGTGTAGC 59.184 38.462 0.00 0.00 0.00 3.58
2908 4417 1.299468 CTCGATGCTCAGGCCGTAC 60.299 63.158 0.00 0.00 37.74 3.67
3002 4511 2.708861 TGAACTTAGCCTTTCCCTCACA 59.291 45.455 0.00 0.00 0.00 3.58
3004 4513 2.979678 ACTGAACTTAGCCTTTCCCTCA 59.020 45.455 0.00 0.00 0.00 3.86
3014 4523 3.120165 GCTGCTTTACCACTGAACTTAGC 60.120 47.826 0.00 0.00 0.00 3.09
3015 4524 4.065088 TGCTGCTTTACCACTGAACTTAG 58.935 43.478 0.00 0.00 0.00 2.18
3016 4525 4.065088 CTGCTGCTTTACCACTGAACTTA 58.935 43.478 0.00 0.00 0.00 2.24
3028 4537 3.074412 GGTAGACTTTGCTGCTGCTTTA 58.926 45.455 17.00 0.00 40.48 1.85
3033 4542 2.462456 TCTGGTAGACTTTGCTGCTG 57.538 50.000 0.00 0.00 0.00 4.41
3035 4544 1.399791 GCATCTGGTAGACTTTGCTGC 59.600 52.381 0.00 0.00 0.00 5.25
3244 4756 1.338107 AGTGACCACGAGGATTCACA 58.662 50.000 19.74 4.97 41.19 3.58
3307 4819 3.758973 TTGCCCGCCGTTCTTCACA 62.759 57.895 0.00 0.00 0.00 3.58
3325 4837 2.048127 GGCGTCGAGTTTCCAGCT 60.048 61.111 0.00 0.00 0.00 4.24
3431 4943 1.070134 TCTGTACACTGTTGGACTGGC 59.930 52.381 0.00 0.00 37.48 4.85
3443 4955 6.507900 TCATTATAGCTCTGCTTCTGTACAC 58.492 40.000 0.00 0.00 40.44 2.90
3501 5013 1.004394 GGATGGGTTCTTCGGGTTCTT 59.996 52.381 0.00 0.00 0.00 2.52
3535 5047 9.005777 GCAACATAAAATTTACTCGGGGATATA 57.994 33.333 0.00 0.00 0.00 0.86
3536 5048 7.724061 AGCAACATAAAATTTACTCGGGGATAT 59.276 33.333 0.00 0.00 0.00 1.63
3567 5086 2.416747 TCCAGCTGTTGTCGATCTTTG 58.583 47.619 13.81 0.00 0.00 2.77
3568 5087 2.839486 TCCAGCTGTTGTCGATCTTT 57.161 45.000 13.81 0.00 0.00 2.52
3575 5094 1.461127 GTCGTTCATCCAGCTGTTGTC 59.539 52.381 13.81 7.21 0.00 3.18
3593 5112 2.959707 ACTCAAGGGACGATGATAGGTC 59.040 50.000 0.00 0.00 0.00 3.85
3631 5155 5.220739 CGATCTTTGCAGGACCAAGATAAAG 60.221 44.000 9.93 6.38 0.00 1.85
3655 5179 1.736681 GTTCTTCATCCAGCTGCTGTC 59.263 52.381 26.41 3.78 0.00 3.51
3676 5200 0.031721 AACTCAAGGGACGACGACAC 59.968 55.000 0.00 0.00 0.00 3.67
3721 5245 1.065926 TGCTGTCGATCTTTGCAGGAT 60.066 47.619 4.29 4.29 0.00 3.24
3819 5343 3.610911 CCACAGGTTCTTCCTATCCAAC 58.389 50.000 0.00 0.00 46.24 3.77
3820 5344 2.576191 CCCACAGGTTCTTCCTATCCAA 59.424 50.000 0.00 0.00 46.24 3.53
3833 5357 1.842381 GAGCTAGGTTGCCCACAGGT 61.842 60.000 0.00 0.00 34.57 4.00
3840 5364 0.107459 CTCAAGGGAGCTAGGTTGCC 60.107 60.000 0.00 0.00 33.67 4.52
3843 5367 5.780958 AAATAACTCAAGGGAGCTAGGTT 57.219 39.130 0.00 0.00 45.42 3.50
3955 5486 4.077184 CGCCGGTAGCACCCAGAA 62.077 66.667 1.90 0.00 44.04 3.02
3982 5513 3.412386 CTGACAGAACAGGGTTAAAGGG 58.588 50.000 0.00 0.00 34.64 3.95
3984 5515 3.476552 TGCTGACAGAACAGGGTTAAAG 58.523 45.455 6.65 0.00 38.22 1.85
4004 5538 6.492007 AGACACTAACTGAAATGCATCTTG 57.508 37.500 0.00 0.00 0.00 3.02
4019 5553 4.623932 AACTGCATCAGGAAGACACTAA 57.376 40.909 0.00 0.00 35.51 2.24
4022 5556 5.886960 AATAAACTGCATCAGGAAGACAC 57.113 39.130 0.00 0.00 35.51 3.67
4052 5586 7.237173 GCTTTCTATGTTGCAAAGTACTACAG 58.763 38.462 0.00 0.00 30.99 2.74
4053 5587 6.148811 GGCTTTCTATGTTGCAAAGTACTACA 59.851 38.462 0.00 0.00 30.99 2.74
4108 5647 7.916552 TGCTTTACTGTCTAGAAACTTTTGTC 58.083 34.615 0.00 0.00 0.00 3.18
4154 5693 6.192234 GAGTTTTCTCGTCAGATGGTAGTA 57.808 41.667 0.00 0.00 37.19 1.82
4155 5694 5.061920 GAGTTTTCTCGTCAGATGGTAGT 57.938 43.478 0.00 0.00 37.19 2.73
4237 5776 1.298859 ATTTTCTCCTGCGCACGGAC 61.299 55.000 20.28 0.00 0.00 4.79
4332 5882 2.495409 ATCGCCGTATCGCCTTCCA 61.495 57.895 0.00 0.00 0.00 3.53
4381 5931 2.662596 TCGGTGCCGAAAGCTCAT 59.337 55.556 11.22 0.00 46.01 2.90
4482 6032 0.109226 GGAAACGTCTCCACTCTCCG 60.109 60.000 2.12 0.00 35.36 4.63
4483 6033 3.816580 GGAAACGTCTCCACTCTCC 57.183 57.895 2.12 0.00 35.36 3.71
4506 6056 4.570874 GGGATTCCCTGCCCGCTC 62.571 72.222 14.98 0.00 41.34 5.03
4559 6109 0.468226 CGGAATTCTGATCCCGGGAA 59.532 55.000 30.84 11.59 38.42 3.97
4583 6133 2.819595 ATCGGCGCATCACACCAC 60.820 61.111 10.83 0.00 0.00 4.16
4606 6167 2.126965 CGCTTTCGACGTCGGACT 60.127 61.111 35.05 0.00 40.29 3.85
4634 6195 2.280186 GTCTAATCGCGGGGGCAG 60.280 66.667 6.13 0.00 0.00 4.85
4638 6199 2.353145 CGACGTCTAATCGCGGGG 60.353 66.667 14.70 0.00 31.96 5.73
4643 6204 0.315706 GACCGACCGACGTCTAATCG 60.316 60.000 19.83 19.83 40.78 3.34
4656 6217 4.808238 GACGAGCGACCGACCGAC 62.808 72.222 9.87 2.12 0.00 4.79
4691 6252 1.798735 CGACGCTTCGGTCTAGGAA 59.201 57.895 4.41 0.00 41.89 3.36
4692 6253 3.494378 CGACGCTTCGGTCTAGGA 58.506 61.111 4.41 0.00 41.89 2.94


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

AutoCloner maintained by Alex Coulton.