Origin IGS: aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggagtgcttaaaatgaataaaacaatggcctgtgaagactgcgaagcaatagatgaagttttcggtaaaatgggcgaaatgcaaaaaaaaatcgcaataaaaaaaataaccgagatggaagaatctttggaaaaacttgaagatgaattgaccgatattattaacacccattcaaatatattgactgaaaattgatggagcttttt Mask Tandem Repeat Region ================================================ aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Find is-nt database================================================ Query_seq: TDE2434:TDE2435|TDE2434:TDE2435:polysaccharide deacetylase family protein:hypothetical protein:<-<-:2465748..2465955 208 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2434:TDE2435|TDE2434:TDE2435:polysaccharide deacetylase family protein:hypothetical protein:<-<-:2465748..2465955 208 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2434:TDE2435|TDE2434:TDE2435:polysaccharide deacetylase family protein:hypothetical protein:<-<-:2465748..2465955 208 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 59 End: 196 .......................................................... M H L Q V F P K I L P S R L F F L L R F F F A F R P F Y R K L H L L L R S L H R P L F Y S F ............ Protein_Len: 57 Strand: + Start: 36 End: 206 ................................... M G V N N I G Q F I F K F F Q R F F H L G Y F F Y C D F F L H F A H F T E N F I Y C F A V F T G H C F I H F K H S .. Protein_Len: 60 Strand: + Start: 28 End: 207 ........................... M F E W V L I I S V N S S S S F S K D S S I S V I F F I A I F F C I S P I L P K T S S I A S Q S S Q A I V L F I L S T P . Protein_Len: 60 Strand: - Start: 15 End: 203 .............. L I N S H T N I I D T L E D E L K E L S E E M E T I K K I A I K K Q M E G M K G F V E D I A E C D E C A M T K N M K L M ..... aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt 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================================================ aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2434:TDE2435|TDE2434:TDE2435:polysaccharide deacetylase family protein:hypothetical protein:<-<-:2465748..2465955 208 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggttattttttttattgcgatttttttttgcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: NC_002967_TDE2434_TDE2435|polysaccharide deacetylase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2465748,2465955]|208 HSP 1 e-value: 5.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggtta............................................................................................................ aaaaagctccatcaattttcagtcaatatatttgaatgggtgttaataatatcggtcaattcatcttcaagtttttccaaagattcttccatctcggtta............................................................................................................ HSP 2 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:125 Query End:208 Subject Strand: POSITIVE Subject Start: 125 Subject End: 208 ............................................................................................................................gcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt ............................................................................................................................gcatttcgcccattttaccgaaaacttcatctattgcttcgcagtcttcacaggccattgttttattcattttaagcactcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGCUCCAUCAAUUUUCAGUCAAUAUAUUUGAAUGGGUGUUAAUAAUAUCGGUCAAUUCAUCUUCAAGUUUUUCCAAAGAUUCUUCCAUCUCGGUUAUUUUUUUUAUUGCGAUUUUUUUUUGCAUUUCGCCCAUUUUACCGAAAACUUCAUCUAUUGCUUCGCAGUCUUCACAGGCCAUUGUUUUAUUCAUUUUAAGCACUCCUU .....(((..............((((.....)))).((((((..((((((...((((...........((((((......((((......))))((((............(((((.......))))).............)))).)))))).....(((((...))))).......)))))))))).)))))).....)))....... (-26.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAGUGCUUAAAAUGAAUAAAACAAUGGCCUGUGAAGACUGCGAAGCAAUAGAUGAAGUUUUCGGUAAAAUGGGCGAAAUGCAAAAAAAAAUCGCAAUAAAAAAAAUAACCGAGAUGGAAGAAUCUUUGGAAAAACUUGAAGAUGAAUUGACCGAUAUUAUUAACACCCAUUCAAAUAUAUUGACUGAAAAUUGAUGGAGCUUUUU .......((((...((.(((.........((((((....((((.(((((..........)))))))))...))))))...............((((((((...........((.....))....(((((..(......)..)))))..))))..))))............((.((((.....)))).))...))).)).))))..... (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 100 51 191 142 NC_002967:TDE2434|5end_polysaccharide_deacetylase_family_protein_2465657..2465887_NEGATIVE 293 138 92 142 95 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 293 185 141 192 150 NC_002967:TDE0026|5end_TraB_family_protein_33016..33246_NEGATIVE 285 145 110 203 168 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 279 168 125 79 39 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 275 180 134 173 139 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 274 134 102 151 119 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 270 180 142 78 37 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 267 107 61 84 36 NC_002967:TDE1955|5end_hypothetical_protein_1970900..1971130_NEGATIVE 267 180 135 88 44 NC_002967:TDE1643|5end_PASTA_domain_protein_1694551..1694781_NEGATIVE 267 189 142 66 16 NC_002967:TDE0516|5end_hypothetical_protein_564122..564352_NEGATIVE 263 193 153 142 86 NC_002967:TDE0113|5end_Tpl_protein_132615..132845_POSITIVE 261 99 52 112 60 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 261 183 141 150 95 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 260 178 131 150 87 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 260 180 131 61 13 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 259 99 61 63 24 NC_002967:TDE1460|5end_hypothetical_protein_1511091..1511321_NEGATIVE 258 179 142 190 142 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 258 126 81 79 28 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 257 180 131 177 129 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 110 61 102 49 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 293 138 92 142 95 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 275 180 134 151 117 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 274 134 102 150 118 NC_002967:TDE0284|3end_hypothetical_protein_312826..312976_NEGATIVE 270 180 142 85 44 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 267 180 135 61 17 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 264 179 132 135 76 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 263 193 153 131 75 NC_002967:TDE0112|3end_hypothetical_protein_132684..132834_POSITIVE 261 99 52 112 60 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 261 183 141 144 89 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 259 179 134 126 86 NC_002967:TDE1076|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1108056..1108206_POSITIVE 258 179 142 135 87 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 258 119 71 150 102 NC_002967:TDE0947|3end_translation_elongation_factor_G,_putative_968714..968864_NEGATIVE 254 184 157 39 6 NC_002967:TDE1970|3end_sensory_box_histidine_kinase_1984497..1984647_NEGATIVE 254 187 158 118 95 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 249 167 132 85 58 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 246 180 139 129 91 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 245 179 132 136 88 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 244 96 53 108 57 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 243 189 156 41 6 NC_002967:TDE0517|3end_hypothetical_protein_564147..564297_NEGATIVE