Origin IGS: aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccgtaaatactacccctttcaaaaaaaaatgtaaataagataacggaaaaaaaagtaagatttttaagtaaattgacaaggacttaaaaagagtgtaaactcctcct Mask Tandem Repeat Region ================================================ aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Find is-nt database================================================ Query_seq: TDE1411:TDE1412|TDE1411:TDE1412:hypothetical protein:sodium/hydrogen exchanger family protein:<-->:1453493..1453601 109 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1411:TDE1412|TDE1411:TDE1412:hypothetical protein:sodium/hydrogen exchanger family protein:<-->:1453493..1453601 109 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1411:TDE1412|TDE1411:TDE1412:hypothetical protein:sodium/hydrogen exchanger family protein:<-->:1453493..1453601 109 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Predict ORF larger than 30AA ================================================ aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 72 End: 101 .......................................................................ATTTACATTTTTTTTTGAAAGGGGTAGTAT........ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 7 End: 36 ......ATTGACAAGGACTTAAAAAGAGTGTAAACT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1411:TDE1412|TDE1411:TDE1412:hypothetical protein:sodium/hydrogen exchanger family protein:<-->:1453493..1453601 109 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE1411_TDE1412|hypothetical protein:sodium/hydrogen exchanger family protein|NEGATIVE:POSITIVE|[1453493,1453601]|109 HSP 1 e-value: 3.0E-25 bit: 115.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacnnnnnnnnccgttatcttatttacannnnnnnnngaaaggggtagtatttacggat aggaggagtttacactctttttaagtccttgtcaatttacttaaaaatcttacttttttttccgttatcttatttacatttttttttgaaaggggtagtatttacggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAGGAGUUUACACUCUUUUUAAGUCCUUGUCAAUUUACUUAAAAAUCUUACUUUUUUUUCCGUUAUCUUAUUUACAUUUUUUUUUGAAAGGGGUAGUAUUUACGGAU (((((((((....)))))))))......................................(((((........((((.(((((....)))))..)))).....))))). (-14.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCGUAAAUACUACCCCUUUCAAAAAAAAAUGUAAAUAAGAUAACGGAAAAAAAAGUAAGAUUUUUAAGUAAAUUGACAAGGACUUAAAAAGAGUGUAAACUCCUCCU .(((((......................................))))).............(((((((((...((....)).)))))))))((((....))))..... (-11.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 755 50 1 141 92 NC_002967:TDE1411|5end_hypothetical_protein_1453402..1453632_NEGATIVE 238 34 2 226 198 NC_002967:TDE2597|5end_ribulose-phosphate_3-epimerase_2632665..2632895_NEGATIVE 231 66 23 104 57 NC_002967:TDE0311|5end_thymidylate_synthase_342816..343046_POSITIVE 227 35 1 173 131 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 225 86 48 124 86 NC_002967:TDE2365|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399949..2400179_NEGATIVE 223 64 23 213 160 NC_002967:TDE0067|5end_cyclic_nucleotide-binding_protein_75188..75418_NEGATIVE 219 99 54 137 97 NC_002967:TDE1860|5end_hypothetical_protein_1886152..1886382_POSITIVE 217 49 1 160 113 NC_002967:TDE1944|5end_hypothetical_protein_1960434..1960664_POSITIVE 216 50 6 121 78 NC_002967:TDE0621|5end_MATE_efflux_family_protein_653314..653544_POSITIVE 212 100 60 124 74 NC_002967:TDE0496|5end_DNA-binding_protein,_putative_551189..551419_NEGATIVE 211 29 1 155 124 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 210 99 53 144 94 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 206 70 21 206 160 NC_002967:TDE2539|5end_hypothetical_protein_2565158..2565388_NEGATIVE 205 89 48 179 134 NC_002967:TDE0534|5end_hypothetical_protein_576513..576743_POSITIVE 203 50 9 130 93 NC_002967:TDE0535|5end_ABC_transporter,_ATP-binding_protein_577323..577553_POSITIVE 201 67 23 118 72 NC_002967:TDE2420|5end_DNA-directed_RNA_polymerase_beta'_subunit_2449234..2449464_NEGATIVE 200 95 60 171 123 NC_002967:TDE1056|5end_hypothetical_protein_1085210..1085440_POSITIVE 200 99 54 228 183 NC_002967:TDE0225|5end_prevent-host-death_family_protein_256377..256607_NEGATIVE 194 97 54 123 80 NC_002967:TDE2472|5end_ISTde1,_transposase_2494962..2495192_POSITIVE 194 97 54 123 80 NC_002967:TDE2033|5end_ISTde1,_transposase_2061476..2061706_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 68 21 111 58 NC_002967:TDE2555|3end_precorrin-8X_methylmutase_2582316..2582466_POSITIVE 227 35 1 113 71 NC_002967:TDE1596|3end_hypothetical_protein_1646099..1646249_NEGATIVE 225 86 48 114 76 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE 223 69 25 150 107 NC_002967:TDE1078|3end_metallo-beta-lactamase_family_protein_1111045..1111195_POSITIVE 219 99 54 135 95 NC_002967:TDE1859|3end_hypothetical_protein_1886230..1886380_POSITIVE 219 98 53 134 96 NC_002967:TDE0060|3end_hypothetical_protein_67527..67677_NEGATIVE 216 50 6 100 57 NC_002967:TDE0620|3end_hypothetical_protein_653373..653523_POSITIVE 210 99 53 122 72 NC_002967:TDE0137|3end_carbohydrate_kinase,_FGGY_family_158279..158429_POSITIVE 203 50 9 111 74 NC_002967:TDE0534|3end_hypothetical_protein_577384..577534_POSITIVE 201 67 23 93 47 NC_002967:TDE2421|3end_DNA-directed_RNA_polymerase_beta_subunit_2449259..2449409_NEGATIVE 199 97 64 119 90 NC_002967:TDE0451|3end_arginine_deiminase_509965..510115_POSITIVE 192 96 76 76 54 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 190 69 21 150 98 NC_002967:TDE0041|3end_birA_bifunctional_protein_48635..48785_POSITIVE 188 47 1 81 30 NC_002967:TDE1147|3end_hypothetical_protein_1185529..1185679_NEGATIVE 187 98 67 34 5 NC_002967:TDE1032|3end_hypothetical_protein_1061097..1061247_POSITIVE 185 100 59 56 9 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 183 50 7 104 62 NC_002967:TDE1312|3end_hypothetical_protein_1350715..1350865_POSITIVE 181 34 1 80 50 NC_002967:TDE1040|3end_ribosomal_protein_S15_1068288..1068438_POSITIVE 180 42 1 65 10 NC_002967:TDE0163|3end_flavodoxin_192946..193096_NEGATIVE 179 100 54 148 95 NC_002967:TDE1550|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1594509..1594659_POSITIVE