Origin IGS: tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaggaatgcaggagttatgtctgtgttaatatcggaataatttactattttttttaaatattttctataaatataatgaggagggagaatataaaaaatttaggagaaaaaaa Mask Tandem Repeat Region ================================================ tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Find is-nt database================================================ Query_seq: TDE1991:TDE1992|TDE1991:TDE1992:hypothetical protein:OmpA family protein:<-->:2009489..2009603 115 tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1991:TDE1992|TDE1991:TDE1992:hypothetical protein:OmpA family protein:<-->:2009489..2009603 115 tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1991:TDE1992|TDE1991:TDE1992:hypothetical protein:OmpA family protein:<-->:2009489..2009603 115 tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 15 End: 113 .............. M F Y I L P P H Y I Y R K Y L K K I V N Y S D I N T D I T P A F L .. tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1991:TDE1992|TDE1991:TDE1992:hypothetical protein:OmpA family protein:<-->:2009489..2009603 115 tttttttctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Intra-Species Hit: Count: 1 Min: 8 Max: 115 Len: 108 Subject: NC_002967_TDE1991_TDE1992|hypothetical protein:OmpA family protein|NEGATIVE:POSITIVE|[2009489,2009603]|115 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 108 Query Start:8 Query End:115 Subject Strand: POSITIVE Subject Start: 8 Subject End: 115 .......ctcctaaattttttatattctccctcctcattatatttatagaaaatatttnnnnnnnntagtaaattattccgatattaacacagacataactcctgcattccttaa .......ctcctaaattttttatattctccctcctcattatatttatagaaaatatttaaaaaaaatagtaaattattccgatattaacacagacataactcctgcattccttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUAAAUUUUUUAUAUUCUCCCUCCUCAUUAUAUUUAUAGAAAAUAUUUAAAAAAAAUAGUAAAUUAUUCCGAUAUUAACACAGACAUAACUCCUGCAUUCCUUAA .......((((((((((....................))))))))))....................................(((.........))).......... ( -3.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGGAAUGCAGGAGUUAUGUCUGUGUUAAUAUCGGAAUAAUUUACUAUUUUUUUUAAAUAUUUUCUAUAAAUAUAAUGAGGAGGGAGAAUAUAAAAAAUUUAGGAG ......((((((((.......)))))))).................(((..(((((((..((((((((.................)))))))))))))))..)))... (-15.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 718 100 51 198 149 NC_002967:TDE1991|5end_hypothetical_protein_2009398..2009628_NEGATIVE 626 50 1 148 99 NC_002967:TDE2135|5end_hypothetical_protein_2164586..2164816_POSITIVE 543 50 1 147 98 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 490 42 1 200 158 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 488 69 23 54 8 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 449 65 21 163 118 NC_002967:TDE2689|5end_hypothetical_protein_2728376..2728606_POSITIVE 446 65 23 44 2 NC_002967:TDE2688|5end_hypothetical_protein_2728257..2728487_POSITIVE 414 42 1 139 99 NC_002967:TDE2196|5end_hypothetical_protein_2232647..2232877_NEGATIVE 403 70 21 151 101 NC_002967:TDE1891|5end_hypothetical_protein_1911206..1911436_POSITIVE 387 42 1 139 99 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 367 67 21 52 6 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 335 33 1 231 199 NC_002967:TDE2312|5end_hypothetical_protein_2348451..2348681_POSITIVE 248 70 37 34 1 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 240 99 66 178 141 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 226 46 8 129 83 NC_002967:TDE2560|5end_hypothetical_protein_2587311..2587541_POSITIVE 205 29 7 59 37 NC_002967:TDE1008|5end_flagellar_protein,_putative_1032106..1032336_POSITIVE 204 31 2 217 187 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 200 48 12 137 96 NC_002967:TDE0077|5end_glycine_reductase_complex_proprotein_GrdE1_88732..88962_NEGATIVE 198 35 21 154 140 NC_002967:TDE1118|5end_tyrosine_phenol-lyase_1151261..1151491_NEGATIVE 197 45 3 159 120 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 626 50 1 104 55 NC_002967:TDE2134|3end_hypothetical_protein_2164622..2164772_POSITIVE 406 47 1 151 104 NC_002967:TDE2688|3end_hypothetical_protein_2728462..2728612_POSITIVE 403 70 21 94 44 NC_002967:TDE1890|3end_hypothetical_protein_1911229..1911379_POSITIVE 401 42 1 146 105 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 369 42 3 39 1 NC_002967:TDE2197|3end_hypothetical_protein_2232747..2232897_NEGATIVE 248 70 37 141 108 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 235 67 24 89 47 NC_002967:TDE0979|3end_penicillin_binding_protein_1002510..1002660_NEGATIVE 200 48 12 124 83 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 196 100 72 121 99 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 193 29 5 105 79 NC_002967:TDE0836|3end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_855527..855677_NEGATIVE 190 38 2 68 31 NC_002967:TDE0552|3end_ankyrin_repeat_protein_588329..588479_NEGATIVE 190 41 7 105 72 NC_002967:TDE0036|3end_hypothetical_protein_42135..42285_NEGATIVE 189 52 15 93 59 NC_002967:TDE1418|3end_hypothetical_protein_1463380..1463530_POSITIVE 188 97 61 45 20 NC_002967:TDE0601|3end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_638834..638984_NEGATIVE 187 27 8 74 55 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 181 100 55 130 76 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 176 25 1 126 102 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 174 27 3 31 11 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE 173 50 22 44 11 NC_002967:TDE0662|3end_hypothetical_protein_697572..697722_NEGATIVE 172 42 3 74 36 NC_002967:TDE2122|3end_DHH_superfamily_protein_2154726..2154876_NEGATIVE