Origin IGS: aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggctcctatcgtataataaaaagtcttacctatggtaaactgaatgacaaaaatgccgaaaataattagtatatacgatatagttaatgcaatcatcctacttgatttgtgtttcataatgttatagtttatataaactaaggaataattgcaatacttataaggagttatt Mask Tandem Repeat Region ================================================ aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Find is-nt database================================================ Query_seq: TDE0993:TDE0994|TDE0993:TDE0994:lipoprotein, putative:hypothetical protein:<-->:1020506..1020677 172 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0993:TDE0994|TDE0993:TDE0994:lipoprotein, putative:hypothetical protein:<-->:1020506..1020677 172 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0993:TDE0994|TDE0993:TDE0994:lipoprotein, putative:hypothetical protein:<-->:1020506..1020677 172 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 2 End: 172 . M T P Y K Y C N Y S L V Y I N Y N I M K H K S S R M I A L T I S Y I L I I F G I F V I Q F T I G K T F Y Y T I G A aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc 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================================================ aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -3.5 Tail_Score: -5.19328 Start: 133 End: 150 Full_Region: CATTTTTGTCATTCA GTTTACC ATA GGTAAGAC TTTTTATTATACGAT ....................................................................................................................................GTTTACCATAGGTAAGAC...................... Find igs database================================================ Query_seq: TDE0993:TDE0994|TDE0993:TDE0994:lipoprotein, putative:hypothetical protein:<-->:1020506..1020677 172 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_002967_TDE0993_TDE0994|lipoprotein, putative:hypothetical protein|NEGATIVE:POSITIVE|[1020506,1020677]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc aataactccttataagtattgcaattattccttagtttatataaactataacattatgaaacacaaatcaagtaggatgattgcattaactatatcgtatatactaattattttcggcatttttgtcattcagtttaccataggtaagactttttattatacgataggagcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACUCCUUAUAAGUAUUGCAAUUAUUCCUUAGUUUAUAUAAACUAUAACAUUAUGAAACACAAAUCAAGUAGGAUGAUUGCAUUAACUAUAUCGUAUAUACUAAUUAUUUUCGGCAUUUUUGUCAUUCAGUUUACCAUAGGUAAGACUUUUUAUUAUACGAUAGGAGCC .....((((.....(((..(((((((((((..((((((....))))))........(((........)))....)))))))))))...))).(((((((((..............((((....))))....((((((((...))).)))))......))))))))))))).. (-37.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUCCUAUCGUAUAAUAAAAAGUCUUACCUAUGGUAAACUGAAUGACAAAAAUGCCGAAAAUAAUUAGUAUAUACGAUAUAGUUAAUGCAAUCAUCCUACUUGAUUUGUGUUUCAUAAUGUUAUAGUUUAUAUAAACUAAGGAAUAAUUGCAAUACUUAUAAGGAGUUAUU (((((((((((((((......(((.(((((...))))))))............(((..(......)..)))))))))))..(((...((((((..((((...(((........)))........((((((....))))))))))...))))))..)))....)))))))... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 120 71 211 162 NC_002967:TDE0993|5end_lipoprotein,_putative_1020415..1020645_NEGATIVE 277 144 110 103 68 NC_002967:TDE0846|5end_hypothetical_protein_868623..868853_POSITIVE 256 40 4 129 96 NC_002967:TDE0379|5end_hypothetical_protein_432458..432688_POSITIVE 246 140 101 41 3 NC_002967:TDE2176|5end_site-specific_recombinase,_putative_2206239..2206469_NEGATIVE 246 150 113 137 94 NC_002967:TDE0264|5end_ribbon-helix-helix_protein,_CopG_family_297287..297517_NEGATIVE 233 156 111 66 18 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 233 170 136 105 66 NC_002967:TDE0936|5end_hypothetical_protein_959979..960209_NEGATIVE 232 153 115 102 58 NC_002967:TDE1218|5end_flagellum-specific_ATP_synthase_FliI_1250447..1250677_POSITIVE 227 135 95 203 167 NC_002967:TDE0735|5end_hypothetical_protein_775003..775233_NEGATIVE 224 149 107 213 179 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 216 127 89 99 59 NC_002967:TDE1432|5end_hypothetical_protein_1475878..1476108_POSITIVE 214 42 4 134 97 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 213 158 111 77 33 NC_002967:TDE2504|5end_O-sialoglycoprotein_endopeptidase_2529001..2529231_POSITIVE 213 160 115 109 52 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 212 149 108 148 100 NC_002967:TDE0727|5end_iron-sulfur_cluster-binding_protein_766721..766951_POSITIVE 210 148 110 215 181 NC_002967:TDE0192|5end_hypothetical_protein_228581..228811_NEGATIVE 208 99 52 135 89 NC_002967:TDE1940|5end_hypothetical_protein_1956508..1956738_NEGATIVE 208 144 109 178 143 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 207 148 115 166 128 NC_002967:TDE2230|5end_hypothetical_protein_2269011..2269241_POSITIVE 207 145 102 195 151 NC_002967:TDE1724|5end_hypothetical_protein_1777761..1777991_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 40 4 107 74 NC_002967:TDE0378|3end_hypothetical_protein_432516..432666_POSITIVE 232 153 115 92 48 NC_002967:TDE1217|3end_flagellar_assembly_protein_1250517..1250667_POSITIVE 216 127 89 111 71 NC_002967:TDE1431|3end_glycosyl_transferase,_group_1_family_protein_1475970..1476120_POSITIVE 214 42 4 141 104 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 213 158 111 75 31 NC_002967:TDE2503|3end_hypothetical_protein_2529079..2529229_POSITIVE 213 160 115 119 62 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 208 99 52 138 92 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 207 145 102 133 89 NC_002967:TDE1723|3end_hypothetical_protein_1777779..1777929_POSITIVE 206 119 71 87 42 NC_002967:TDE0124|3end_rhomboid_family_protein_142244..142394_NEGATIVE 205 148 107 109 62 NC_002967:TDE0368|3end_type_I_restriction-modification_system,_S_subunit,_putative_416557..416707_NEGATIVE 202 46 6 51 7 NC_002967:TDE1181|3end_methyltransferase_domain_protein_1210538..1210688_POSITIVE 200 159 114 122 70 NC_002967:TDE0174|3end_nicotinate_phosphoribosyltransferase_208050..208200_POSITIVE 199 147 101 140 95 NC_002967:TDE0372|3end_ABC_transporter,_ATP-binding/permease_protein_424632..424782_NEGATIVE 199 166 121 115 75 NC_002967:TDE0256|3end_hypothetical_protein_290742..290892_NEGATIVE 196 165 129 90 49 NC_002967:TDE2705|3end_ISTde3,_transposase_2751127..2751277_NEGATIVE 193 157 113 137 94 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 189 140 96 53 13 NC_002967:TDE1678|3end_ribosomal_protein_S6_1730202..1730352_NEGATIVE 189 44 14 65 40 NC_002967:TDE1501|3end_pyruvate_phosphate_dikinase_1550922..1551072_POSITIVE 189 158 113 95 50 NC_002967:TDE0867|3end_hypothetical_protein_890400..890550_POSITIVE 188 155 113 57 22 NC_002967:TDE2318|3end_LysM_domain/M23/M37_peptidase_domain_protein_2355868..2356018_POSITIVE