Origin IGS: taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataagccgatcttttaaagactcaaacaaaaaaaccaccgattagccaacaagactaatcggtggggtaacattctgctgttccttcagaaaaggcgccaaaatactgtaaacaaatagaacatattttaaatgaatattattaaacaccggttta Mask Tandem Repeat Region ================================================ taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Find is-nt database================================================ Query_seq: TDE0249:TDE0250|TDE0249:TDE0250:flavoredoxin, putative:sodium-dependent transporter, putative:-><-:283243..283399 157 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0249:TDE0250|TDE0249:TDE0250:flavoredoxin, putative:sodium-dependent transporter, putative:-><-:283243..283399 157 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0249:TDE0250|TDE0249:TDE0250:flavoredoxin, putative:sodium-dependent transporter, putative:-><-:283243..283399 157 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 8 End: 112 ....... M F N N I H L K Y V L F V Y S I L A P F L K E Q Q N V T P P I S L V G ............................................. taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt 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================================================ taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.3 Tail_Score: -5.96894 Start: 92 End: 122 Full_Region: CAGCAGAATGTTACC CCACCGATTAGTC TTGTT GGCTAATCGGTGG TTTTTTTGTTTGAGT ...........................................................................................CCACCGATTAGTCTTGTTGGCTAATCGGTGG................................... Find igs database================================================ Query_seq: TDE0249:TDE0250|TDE0249:TDE0250:flavoredoxin, putative:sodium-dependent transporter, putative:-><-:283243..283399 157 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002967_TDE0249_TDE0250|flavoredoxin, putative:sodium-dependent transporter, putative|POSITIVE:NEGATIVE|[283243,283399]|157 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggnnnnnnngtttgagtctttaaaagatcggcttatt taaaccggtgtttaataatattcatttaaaatatgttctatttgtttacagtattttggcgccttttctgaaggaacagcagaatgttaccccaccgattagtcttgttggctaatcggtggtttttttgtttgagtctttaaaagatcggcttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCGGUGUUUAAUAAUAUUCAUUUAAAAUAUGUUCUAUUUGUUUACAGUAUUUUGGCGCCUUUUCUGAAGGAACAGCAGAAUGUUACCCCACCGAUUAGUCUUGUUGGCUAAUCGGUGGUUUUUUUGUUUGAGUCUUUAAAAGAUCGGCUUAUU (((.(((((.(((...((.(((((..(((((.(((((((..((((((.(((......(....)....)))...)))))).)))))))....(((((((((((((.....)))))))))))))...)))))..))))).))..))).))))).))).. (-43.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAGCCGAUCUUUUAAAGACUCAAACAAAAAAACCACCGAUUAGCCAACAAGACUAAUCGGUGGGGUAACAUUCUGCUGUUCCUUCAGAAAAGGCGCCAAAAUACUGUAAACAAAUAGAACAUAUUUUAAAUGAAUAUUAUUAAACACCGGUUUA ..(((((((..........................(((((((((((.(.....).))))))))))).((((.((((....((.((((.....)))).)).......((((......))))..............)))).)))).......))))))) (-32.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 109 62 218 165 NC_002967:TDE2398|5end_conserved_hypothetical_protein_TIGR00278_2425807..2426037_NEGATIVE 316 120 71 160 108 NC_002967:TDE1603|5end_ABC_transporter,_ATP-binding_protein_1654856..1655086_NEGATIVE 306 90 41 163 102 NC_002967:TDE2148|5end_OmpA_family_protein_2185946..2186176_NEGATIVE 306 109 61 55 9 NC_002967:TDE1062|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1088430..1088660_POSITIVE 279 138 93 71 22 NC_002967:TDE2474|5end_acetyltransferase,_GNAT_family_2497096..2497326_NEGATIVE 279 130 90 133 96 NC_002967:TDE1468|5end_glycoprotease_family_protein_1517336..1517566_NEGATIVE 276 119 71 62 11 NC_002967:TDE1866|5end_hypothetical_protein_1892354..1892584_NEGATIVE 276 119 71 222 171 NC_002967:TDE1865|5end_peptidase,_M16_family_1892194..1892424_NEGATIVE 275 125 89 159 116 NC_002967:TDE2423|5end_ribosomal_protein_L10_2454034..2454264_NEGATIVE 272 110 61 174 122 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 270 138 95 87 34 NC_002967:TDE0947|5end_translation_elongation_factor_G,_putative_970792..971022_NEGATIVE 266 150 103 193 139 NC_002967:TDE2275|5end_tRNA_pseudouridine_synthase_A_2311076..2311306_POSITIVE 265 118 79 53 6 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 263 97 54 218 178 NC_002967:TDE2595|5end_hypothetical_protein_2631080..2631310_NEGATIVE 262 113 81 76 42 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 261 119 77 55 10 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 258 150 105 72 21 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 257 96 53 167 110 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 256 108 68 217 184 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 256 140 92 210 159 NC_002967:TDE1164|5end_hypothetical_protein_1198166..1198396_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 90 41 144 83 NC_002967:TDE2149|3end_transglycosylase,_SLT_family_2185965..2186115_NEGATIVE 306 109 61 55 9 NC_002967:TDE1061|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1088510..1088660_POSITIVE 292 137 93 99 55 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 279 130 90 136 99 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 276 119 71 65 14 NC_002967:TDE1867|3end_hypothetical_protein_1892351..1892501_NEGATIVE 274 104 69 68 23 NC_002967:TDE0463|3end_purine_nucleoside_phosphorylase_517964..518114_POSITIVE 269 139 97 148 97 NC_002967:TDE0704|3end_SPFH_domain/Band_7_family_protein_738429..738579_NEGATIVE 265 126 85 121 84 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 262 113 81 65 31 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 261 139 94 143 104 NC_002967:TDE2148|3end_OmpA_family_protein_2184597..2184747_NEGATIVE 261 119 77 88 43 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 258 150 105 66 15 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 256 120 89 148 113 NC_002967:TDE2424|3end_50S_ribosomal_protein_L1_2454037..2454187_NEGATIVE 256 139 94 151 100 NC_002967:TDE0228|3end_hypothetical_protein_259611..259761_NEGATIVE 255 98 57 64 14 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 254 137 100 73 20 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 254 129 84 120 66 NC_002967:TDE0789|3end_30S_ribosomal_protein_S13_817007..817157_POSITIVE 252 125 95 144 112 NC_002967:TDE2641|3end_Fic_family_protein_2682068..2682218_POSITIVE 252 140 104 41 1 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 252 150 101 112 64 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE