Origin IGS: aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct .........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 agctttgatgctttaatcatgatgttgttaattcggtcgctaattaacgactttttcaggaaacaatcatgataaaaaagaaaaaaacaagtctaaaatgcgctaaaacgactctttagtgtcctttttgtagagaaaaataaaagaaatcgagcaatttgtcatttttttagcatctattcttgttccaatcgtaaataagtctttatatttacgccctaattaaaatt Mask Tandem Repeat Region ================================================ aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Find is-nt database================================================ Query_seq: TF0202:TF0203|TF0202:TF0203:folylpolyglutamate synthase:PhoH-like protein:->->:229165..229394 230 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0202:TF0203|TF0202:TF0203:folylpolyglutamate synthase:PhoH-like protein:->->:229165..229394 230 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0202:TF0203|TF0202:TF0203:folylpolyglutamate synthase:PhoH-like protein:->->:229165..229394 230 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Predict ORF larger than 30AA ================================================ aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct 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: 84 Start: 133 End: 162 ....................................................................................................................................TTTTAGACTTGTTTTTTTCTTTTTTATCAT.................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 65 End: 94 ................................................................AATGACAAATTGCTCGATTTCTTTTATTTT........................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0202:TF0203|TF0202:TF0203:folylpolyglutamate synthase:PhoH-like protein:->->:229165..229394 230 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttgtttttttcttttttatcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: tfor_TF0202_TF0203|folylpolyglutamate synthase:PhoH-like protein|POSITIVE:POSITIVE|[229165,229394]|230 HSP 1 e-value: 4.0E-63 bit: 242.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctnnnnnnntgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttg....................................................................................... aattttaattagggcgtaaatataaagacttatttacgattggaacaagaatagatgctaaaaaaatgacaaattgctcgatttcttttatttttctctacaaaaaggacactaaagagtcgttttagcgcattttagacttg....................................................................................... HSP 2 e-value: 8.0E-34 bit: 145.0 Len: 73 Query Start:158 Query End:230 Subject Strand: POSITIVE Subject Start: 158 Subject End: 230 .............................................................................................................................................................atcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct .............................................................................................................................................................atcatgattgtttcctgaaaaagtcgttaattagcgaccgaattaacaacatcatgattaaagcatcaaagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAAUUAGGGCGUAAAUAUAAAGACUUAUUUACGAUUGGAACAAGAAUAGAUGCUAAAAAAAUGACAAAUUGCUCGAUUUCUUUUAUUUUUCUCUACAAAAAGGACACUAAAGAGUCGUUUUAGCGCAUUUUAGACUUGUUUUUUUCUUUUUUAUCAUGAUUGUUUCCUGAAAAAGUCGUUAAUUAGCGACCGAAUUAACAACAUCAUGAUUAAAGCAUCAAAGCU ..............((((((((........))))))))...((((((((...((((((...((((((((.(((((....)))))...)))))))).......((((.(((........))).))))...))))))....))))))))...((((...((((((((.(((..........((((((....)))))).........))))))))))).)))).......... (-42.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUUGAUGCUUUAAUCAUGAUGUUGUUAAUUCGGUCGCUAAUUAACGACUUUUUCAGGAAACAAUCAUGAUAAAAAAGAAAAAAACAAGUCUAAAAUGCGCUAAAACGACUCUUUAGUGUCCUUUUUGUAGAGAAAAAUAAAAGAAAUCGAGCAAUUUGUCAUUUUUUUAGCAUCUAUUCUUGUUCCAAUCGUAAAUAAGUCUUUAUAUUUACGCCCUAAUUAAAAUU ......(((((....((((((((((((((((((.(....).)))))))))).......(....).))))))))....(((((((..((((((.......((((((((.......))))))))..(((((((........)))))))..........))))))..))))))).)))))...............((((((((........)))))))).............. (-42.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 208 161 197 144 tfor:TF2978|5end_conserved_hypothetical_protein_3186076..3186306_POSITIVE 254 197 159 97 61 tfor:TF3061|5end_conserved_hypothetical_protein_3285022..3285252_POSITIVE 244 193 159 138 113 tfor:TF0309|5end_conserved_hypothetical_protein_334174..334404_POSITIVE 240 55 11 99 55 tfor:TF1230|5end_hypothetical_protein_1314905..1315135_POSITIVE 239 197 158 100 63 tfor:TF2317|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_II_2474418..2474648_POSITIVE 238 198 154 221 169 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 234 80 37 83 43 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 233 58 13 184 134 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 232 168 121 96 56 tfor:TF2736|5end_methylglyoxal_synthase_2917917..2918147_POSITIVE 230 211 171 90 50 tfor:TF2017|5end_conserved_hypothetical_protein_2173504..2173734_POSITIVE 230 216 171 201 155 tfor:TF1971|5end_biotin_carboxyl_carrier_protein_2117976..2118206_POSITIVE 228 193 151 107 71 tfor:TF1104|5end_hypothetical_protein_1171956..1172186_POSITIVE 226 197 152 170 121 tfor:TF3164|5end_hypothetical_protein_3403897..3404127_POSITIVE 226 180 135 166 116 tfor:TF3089|5end_ISPg2_(PGIS2)_transposase_3323803..3324033_POSITIVE 226 99 76 80 55 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 226 130 91 112 71 tfor:TF1773|5end_hypothetical_protein_1910939..1911169_POSITIVE 226 99 76 80 55 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 225 199 153 222 169 tfor:TF2053|5end_glycosyltransferase_2217102..2217332_POSITIVE 224 58 11 79 33 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 224 58 11 79 33 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 90 43 77 33 tfor:TF2484|3end_hypothetical_protein_2660306..2660456_POSITIVE 307 208 161 89 36 tfor:TF2977|3end_candidate_b-glycosyltransferase,_Glycosyltransferase_Family_2_protein_3186048..3186198_POSITIVE 256 229 191 109 64 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 255 143 106 44 4 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 254 197 159 125 89 tfor:TF3060|3end_conserved_hypothetical_protein_3285130..3285280_POSITIVE 247 57 11 138 96 tfor:TF1948|3end_conserved_hypothetical_protein_2096795..2096945_POSITIVE 239 197 158 100 63 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 236 160 128 53 19 tfor:TF0379|3end_conserved_hypothetical_protein,_nif3_family_400632..400782_POSITIVE 234 80 37 64 24 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 226 180 135 74 24 tfor:TF3088|3end_conserved_hypothetical_protein_3323791..3323941_POSITIVE 226 201 167 144 108 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 226 99 76 66 41 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 226 99 76 66 41 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 224 176 133 101 45 tfor:TF0719|3end_hypothetical_protein_770054..770204_POSITIVE 222 160 117 151 93 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 221 42 12 71 39 tfor:TF0901|3end_conserved_hypothetical_protein_947273..947423_POSITIVE 220 129 86 44 3 tfor:TF2963|3end_type_I_restriction_enzyme_3175070..3175220_POSITIVE 218 223 186 119 86 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 218 193 154 151 107 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 218 133 91 140 106 tfor:TF0100|3end_conserved_hypothetical_protein_111703..111853_POSITIVE