Origin IGS: aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttaataaagtcagttttccgctcaatttcatttttttaccatttatccgtattttaagctcgacttttgagcaaaagtgtagtatcctataagtacaatgaaattgtgtggaggaaatt Mask Tandem Repeat Region ================================================ aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Find is-nt database================================================ Query_seq: TDE1296:TDE1297|TDE1296:TDE1297:ribosomal subunit interface protein, putative:LysM domain/M23/M37 peptidase domain protein:<-<-:1333845..1333966 122 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1296:TDE1297|TDE1296:TDE1297:ribosomal subunit interface protein, putative:LysM domain/M23/M37 peptidase domain protein:<-<-:1333845..1333966 122 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1296:TDE1297|TDE1296:TDE1297:ribosomal subunit interface protein, putative:LysM domain/M23/M37 peptidase domain protein:<-<-:1333845..1333966 122 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 2 End: 121 . M S S T Q F H C T Y R I L H F C S K V E L K I R I N G K K M K L S G K L T L L K . aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa 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================================================ aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1296:TDE1297|TDE1296:TDE1297:ribosomal subunit interface protein, putative:LysM domain/M23/M37 peptidase domain protein:<-<-:1333845..1333966 122 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE1296_TDE1297|ribosomal subunit interface protein, putative:LysM domain/M23/M37 peptidase domain protein|NEGATIVE:NEGATIVE|[1333845,1333966]|122 HSP 1 e-value: 7.0E-51 bit: 200.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtnnnnnnntgaaattgagcggaaaactgactttattaaaaa aatttcctccacacaatttcattgtacttataggatactacacttttgctcaaaagtcgagcttaaaatacggataaatggtaaaaaaatgaaattgagcggaaaactgactttattaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCCUCCACACAAUUUCAUUGUACUUAUAGGAUACUACACUUUUGCUCAAAAGUCGAGCUUAAAAUACGGAUAAAUGGUAAAAAAAUGAAAUUGAGCGGAAAACUGACUUUAUUAAAAA .......(((.(.((((((((((.((((..(((....))).......((((.......)))).................))))....)))))))))).).)))................... (-22.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAUAAAGUCAGUUUUCCGCUCAAUUUCAUUUUUUUACCAUUUAUCCGUAUUUUAAGCUCGACUUUUGAGCAAAAGUGUAGUAUCCUAUAAGUACAAUGAAAUUGUGUGGAGGAAAUU ................((((((((.((((((((((.........................((((((...)))))).....(((((....))))).....)))))))))).)))))))).... (-28.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 807 80 31 171 122 NC_002967:TDE1296|5end_ribosomal_subunit_interface_protein,_putative_1333754..1333984_NEGATIVE 249 77 33 208 154 NC_002967:TDE2546|5end_hypothetical_protein_2572761..2572991_NEGATIVE 244 112 71 210 174 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 240 75 40 157 122 NC_002967:TDE2423|5end_ribosomal_protein_L10_2454034..2454264_NEGATIVE 221 84 43 69 23 NC_002967:TDE2170|5end_hypothetical_protein_2201749..2201979_NEGATIVE 220 85 44 180 128 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 217 81 48 82 44 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 215 73 31 129 81 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 213 81 47 33 5 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 205 63 36 121 83 NC_002967:TDE2483|5end_hypothetical_protein_2506659..2506889_NEGATIVE 205 97 56 44 8 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 203 49 4 137 95 NC_002967:TDE1480|5end_hypothetical_protein_1525581..1525811_NEGATIVE 203 70 22 118 64 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 202 103 68 198 164 NC_002967:TDE1574|5end_hypothetical_protein_1621800..1622030_POSITIVE 202 50 4 144 97 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 202 84 41 122 79 NC_002967:TDE0339|5end_transcriptional_regulator,_TetR_family_377871..378101_POSITIVE 201 63 21 176 114 NC_002967:TDE2308|5end_hypothetical_protein_2345604..2345834_POSITIVE 201 66 21 140 104 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 201 66 21 140 104 NC_002967:TDE1802|5end_hypothetical_protein_1838108..1838338_NEGATIVE 201 67 21 203 151 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 76 32 63 15 NC_002967:TDE1121|3end_hypothetical_protein_1152814..1152964_NEGATIVE 227 83 45 126 79 NC_002967:TDE0359|3end_ABC_transporter,_ATP-binding/permease_protein_402193..402343_NEGATIVE 217 81 48 72 34 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 215 73 31 125 77 NC_002967:TDE1381|3end_V-type_ATP_synthase_subunit_E_1421288..1421438_NEGATIVE 205 63 36 127 89 NC_002967:TDE2484|3end_hypothetical_protein_2506653..2506803_NEGATIVE 205 97 56 51 15 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 202 112 80 55 22 NC_002967:TDE0991|3end_ribosomal_protein_L28_1017874..1018024_NEGATIVE 202 50 4 132 85 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 201 67 21 90 38 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 200 69 32 97 61 NC_002967:TDE0450|3end_hypothetical_protein_507096..507246_NEGATIVE 200 111 71 41 3 NC_002967:TDE0062|3end_PTS_system,_IIA_component_69661..69811_POSITIVE 199 100 56 138 105 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 196 87 46 51 3 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 192 84 43 134 82 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 191 73 32 41 4 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 191 74 31 55 11 NC_002967:TDE0717|3end_hypothetical_protein_752380..752530_POSITIVE 190 81 51 50 22 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 189 60 27 56 23 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 188 100 59 89 42 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 188 75 38 120 91 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE