Origin IGS: aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attcgaagttttacaattttccccatattctttctcaattttacttggtattttaaattttttgatgtataatggaagagcagttatatttaggattcggcctttattataggaggtttttt Mask Tandem Repeat Region ================================================ aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Find is-nt database================================================ Query_seq: TDE2104:TDE2105|TDE2104:TDE2105:hypothetical protein:hypothetical protein:<-<-:2131174..2131295 122 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2104:TDE2105|TDE2104:TDE2105:hypothetical protein:hypothetical protein:<-<-:2131174..2131295 122 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2104:TDE2105|TDE2104:TDE2105:hypothetical protein:hypothetical protein:<-<-:2131174..2131295 122 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 27 End: 122 .......................... M L N I T A L P L Y I K K F K I P S K I E K E Y G E N C K T S N aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat 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: 87 Start: 50 End: 79 .................................................CTTGGTATTTTAAATTTTTTGATGTATAAT........................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 33 End: 62 ................................TTTGATGTATAATGGAAGAGCAGTTATATT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2104:TDE2105|TDE2104:TDE2105:hypothetical protein:hypothetical protein:<-<-:2131174..2131295 122 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE2104_TDE2105|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2131174,2131295]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat aaaaaacctcctataataaaggccgaatcctaaatataactgctcttccattatacatcaaaaaatttaaaataccaagtaaaattgagaaagaatatggggaaaattgtaaaacttcgaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACCUCCUAUAAUAAAGGCCGAAUCCUAAAUAUAACUGCUCUUCCAUUAUACAUCAAAAAAUUUAAAAUACCAAGUAAAAUUGAGAAAGAAUAUGGGGAAAAUUGUAAAACUUCGAAU ........(((((((....(((......)))........((..((((..(((.(((......................))).))).)))).))..))))))).................... ( -9.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCGAAGUUUUACAAUUUUCCCCAUAUUCUUUCUCAAUUUUACUUGGUAUUUUAAAUUUUUUGAUGUAUAAUGGAAGAGCAGUUAUAUUUAGGAUUCGGCCUUUAUUAUAGGAGGUUUUUU ((((.((((...((..((((((..((((......((((......((((....)))).....)))).))))...))))))...))...)))).))))..(((((((......))))))).... (-12.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 815 50 1 141 92 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 346 43 2 133 92 NC_002967:TDE2242|5end_antigen,_putative_2282034..2282264_NEGATIVE 247 31 5 208 180 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 247 31 5 98 70 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 242 44 6 116 68 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 235 60 19 109 70 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 231 49 4 139 94 NC_002967:TDE1663|5end_OmpA_family_protein_1717319..1717549_POSITIVE 228 50 3 128 72 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 227 42 4 58 14 NC_002967:TDE1528|5end_hypothetical_protein_1571725..1571955_POSITIVE 226 118 75 55 16 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 220 49 7 61 9 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 220 49 7 132 98 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 214 61 28 185 153 NC_002967:TDE1415|5end_nucleotidyl_transferase/aminotransferase,_class_V_1457941..1458171_POSITIVE 211 48 8 141 104 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 210 47 11 218 171 NC_002967:TDE1140|5end_hypothetical_protein_1169845..1170075_NEGATIVE 208 69 21 181 134 NC_002967:TDE0815|5end_hypothetical_protein_837365..837595_NEGATIVE 207 43 10 70 45 NC_002967:TDE1658|5end_basic_membrane_protein,_putative_1708731..1708961_NEGATIVE 207 50 7 199 164 NC_002967:TDE1506|5end_L-serine_dehydratase,_iron-sulfur-dependent,_alpha_subunit_1555042..1555272_NEGATIVE 207 50 15 66 29 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 207 50 6 57 11 NC_002967:TDE0313|5end_TrkA_domain_protein_345374..345604_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 481 90 44 88 40 NC_002967:TDE2243|3end_CutC_family_protein_2282214..2282364_NEGATIVE 242 44 6 101 53 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 239 58 18 58 10 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 235 60 19 109 70 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 231 49 4 55 10 NC_002967:TDE1662|3end_replicative_DNA_helicase_1717315..1717465_POSITIVE 228 50 3 117 61 NC_002967:TDE2058|3end_hypothetical_protein_2085354..2085504_NEGATIVE 227 42 4 48 4 NC_002967:TDE1527|3end_hypothetical_protein_1571795..1571945_POSITIVE 226 118 75 58 19 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 211 48 8 144 107 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 207 50 15 73 36 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 205 31 1 104 63 NC_002967:TDE2187|3end_ParB-like_nuclease_domain_protein_2221147..2221297_NEGATIVE 202 49 20 133 97 NC_002967:TDE2474|3end_acetyltransferase,_GNAT_family_2496602..2496752_NEGATIVE 201 50 6 149 100 NC_002967:TDE0053|3end_flagellar_biosynthetic_protein_FliR_62467..62617_POSITIVE 199 42 8 58 26 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 199 44 8 108 75 NC_002967:TDE0516|3end_hypothetical_protein_563808..563958_NEGATIVE 197 43 7 37 1 NC_002967:TDE0922|3end_ABC_transporter,_ATP-binding/permease_protein_941847..941997_NEGATIVE 196 57 13 114 60 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 195 46 1 99 47 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 195 43 7 128 87 NC_002967:TDE0381|3end_hypothetical_protein_434461..434611_POSITIVE 194 48 10 55 22 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE