Origin IGS: aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcttttaccatccgcagcgtattgtaaattcttacataacaaacctgccttacattatattacttatttcaaattttttcacctgcgtcggcttttttaaattctcttaatcttttttttggaataccgataatctatcacgaggactatt Mask Tandem Repeat Region ================================================ aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Find is-nt database================================================ Query_seq: TDE1186:TDE1187|TDE1186:TDE1187:hypothetical protein:hypothetical protein:<-->:1213576..1213727 152 aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1186:TDE1187|TDE1186:TDE1187:hypothetical protein:hypothetical protein:<-->:1213576..1213727 152 aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1186:TDE1187|TDE1186:TDE1187:hypothetical protein:hypothetical protein:<-->:1213576..1213727 152 aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 45 End: 152 ............................................ S F K F F G V C T F F N S I L L I I Y P L N T I Y S N V I R Q P H Y F M aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat 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: 83 Start: 69 End: 98 ....................................................................GGTGAAAAAATTTGAAATAAGTAATATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1186:TDE1187|TDE1186:TDE1187:hypothetical protein:hypothetical protein:<-->:1213576..1213727 152 aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_002967_TDE1186_TDE1187|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1213576,1213727]|152 HSP 1 e-value: 7.0E-67 bit: 254.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 aatagtcctcgtgatagattatcggtattccnnnnnnnngattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat aatagtcctcgtgatagattatcggtattccaaaaaaaagattaagagaatttaaaaaagccgacgcaggtgaaaaaatttgaaataagtaatataatgtaaggcaggtttgttatgtaagaatttacaatacgctgcggatggtaaaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGUCCUCGUGAUAGAUUAUCGGUAUUCCAAAAAAAAGAUUAAGAGAAUUUAAAAAAGCCGACGCAGGUGAAAAAAUUUGAAAUAAGUAAUAUAAUGUAAGGCAGGUUUGUUAUGUAAGAAUUUACAAUACGCUGCGGAUGGUAAAAGAU .......(((.((((........((....)).........)))).)))...........((((.((((((((...((((((.......((((((...((.....))....))))))....))))))....))).)))))..))))....... (-22.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUUACCAUCCGCAGCGUAUUGUAAAUUCUUACAUAACAAACCUGCCUUACAUUAUAUUACUUAUUUCAAAUUUUUUCACCUGCGUCGGCUUUUUUAAAUUCUCUUAAUCUUUUUUUUGGAAUACCGAUAAUCUAUCACGAGGACUAUU ........((....((((.((..(((((....)))))......))))))......................................(((((...(((((((................)))))))..)))))............))...... (-16.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 140 91 231 182 NC_002967:TDE1186|5end_hypothetical_protein_1213485..1213715_NEGATIVE 277 139 102 195 158 NC_002967:TDE2570|5end_ribonuclease_HI_2597375..2597605_POSITIVE 261 144 103 186 138 NC_002967:TDE2225|5end_thioesterase_family_protein_2264868..2265098_POSITIVE 261 144 103 61 13 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 261 144 103 186 138 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 250 144 104 186 136 NC_002967:TDE1195|5end_prolyl_endopeptidase_1229691..1229921_NEGATIVE 249 148 102 84 27 NC_002967:TDE2280|5end_transglycosylase,_SLT_family_2317358..2317588_NEGATIVE 245 89 43 115 73 NC_002967:TDE2440|5end_ABC_transporter,_ATP-binding/permease_protein,_putative_2472043..2472273_NEGATIVE 242 118 77 110 63 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 237 82 41 228 182 NC_002967:TDE0663|5end_hypothetical_protein_698097..698327_NEGATIVE 230 150 102 79 31 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 227 50 6 57 15 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 227 144 104 188 138 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 224 31 1 46 11 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 223 148 102 221 167 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 223 129 84 132 83 NC_002967:TDE0342|5end_integral_membrane_protein_MviN_383741..383971_NEGATIVE 222 145 124 37 18 NC_002967:TDE1075|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1105962..1106192_POSITIVE 220 149 106 151 113 NC_002967:TDE2761|5end_hypothetical_protein_2816537..2816767_NEGATIVE 219 138 92 225 190 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 219 70 35 222 183 NC_002967:TDE0490|5end_hypothetical_protein_546793..547023_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 146 103 151 106 NC_002967:TDE2228|3end_aminoacyl-histidine_dipeptidase,_putative_2267287..2267437_NEGATIVE 261 144 103 64 16 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 259 50 4 51 5 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 250 144 104 86 36 NC_002967:TDE1196|3end_hypothetical_protein_1229791..1229941_NEGATIVE 243 144 102 60 11 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 230 150 102 86 38 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE 227 144 104 86 36 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 224 30 8 47 22 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 223 148 102 147 93 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 222 89 48 78 32 NC_002967:TDE1614|3end_hypothetical_protein_1662295..1662445_NEGATIVE 222 145 124 24 5 NC_002967:TDE1074|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1106029..1106179_POSITIVE 220 149 106 125 87 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE 220 118 79 46 1 NC_002967:TDE0690|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_728078..728228_POSITIVE 219 139 103 51 18 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 219 150 103 43 6 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 218 64 21 47 9 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 217 99 55 79 20 NC_002967:TDE0812|3end_ABC_transporter,_ATP-binding/permease_protein_834137..834287_POSITIVE 215 110 62 61 4 NC_002967:TDE1883|3end_hypothetical_protein_1904910..1905060_NEGATIVE 213 93 58 66 29 NC_002967:TDE2567|3end_hypothetical_protein_2594198..2594348_NEGATIVE 212 75 51 81 59 NC_002967:TDE2263|3end_acetyl_hydrolase,_putative_2299277..2299427_NEGATIVE