Origin IGS: agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacattttctttctacttgtcacaacagacggatgaggcttttgtttcaagggctttcatgatataattgtaaaaaaagacagaacctttgtcaatgtataactgacaaagatggagaatttct Mask Tandem Repeat Region ================================================ agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Find is-nt database================================================ Query_seq: SMT_486:SMT_487|SMT_486:SMT_487:hypothetical protein:transcriptional regulator, TetR family:<-->:422396..422519 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_486:SMT_487|SMT_486:SMT_487:hypothetical protein:transcriptional regulator, TetR family:<-->:422396..422519 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_486:SMT_487|SMT_486:SMT_487:hypothetical protein:transcriptional regulator, TetR family:<-->:422396..422519 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 5 End: 109 .... M L H L C Q L Y I D K G S V F F Y N Y I M K A L E T K A S S V C C D K ............... agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt 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: 89 Start: 29 End: 58 ............................ATTGACAAAGGTTCTGTCTTTTTTTACAAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_486:SMT_487|SMT_486:SMT_487:hypothetical protein:transcriptional regulator, TetR family:<-->:422396..422519 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: smit_SMT_486_SMT_487|hypothetical protein:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[422396,422519]|124 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtcnnnnnnnacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt Inter-species Hit: Count: 3 Min: 1 Max: 124 Len: 124 Subject: NC_008533_SPD_0646_SPD_0647|hypothetical protein:transcriptional regulator, TetR family protein|NEGATIVE:POSITIVE|[666908,667031]|124 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtcnnnnnnnacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaaacccttgaaacaaaagcatcatccgtctgttgtgacaagtagaaagaaaatgtt Subject: NC_003098_spr0652_spr0653|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[659377,659500]|124 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtcnnnnnnnacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaaacccttgaaacaaaagcatcatccgtctgttgtgacaagtagaaagaaaatgtt Subject: NC_003028_SP_0742_SP_0743|hypothetical protein:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[704823,704946]|124 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 agaaattctccatctttgtcagttatacattgacaaaggttctgtcnnnnnnnacaattatatcatgaaagcccttgaaacaaaagcctcatccgtctgttgtgacaagtagaaagaaaatgtt agaaattctccatctttgtcagttatacattgacaaaggttctgtctttttttacaattatatcatgaaaacccttgaaacaaaagcatcatccgtctgttgtgacaagtagaaagaaaatgtt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUUCUCCAUCUUUGUCAGUUAUACAUUGACAAAGGUUCUGUCUUUUUUUACAAUUAUAUCAUGAAAGCCCUUGAAACAAAAGCCUCAUCCGUCUGUUGUGACAAGUAGAAAGAAAAUGUU ...........((((((((((((.....))))))))))))(((.((((((.(((((((......((((..((..(((...)))..)).))))......))))))).))).))).)))....... (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUUUUCUUUCUACUUGUCACAACAGACGGAUGAGGCUUUUGUUUCAAGGGCUUUCAUGAUAUAAUUGUAAAAAAAGACAGAACCUUUGUCAAUGUAUAACUGACAAAGAUGGAGAAUUUCU ...(((((((.(((..((((((......((..((((((((((((...))))))).)))))..................((((((...))))))...)).....))))))))).))))))).... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 110 61 201 152 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 282 99 57 170 119 smit:SMT_271|5end_autoinducer-2_production_protein_211736..211966_NEGATIVE 281 117 84 166 128 smit:SMT_851|5end_conserved_hypothetical_protein,_translation_initiation_inhibitor_protein_797446..797676_NEGATIVE 279 98 65 44 11 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 277 112 84 226 198 smit:SMT_610|5end_hypothetical_protein_521659..521889_POSITIVE 252 88 41 142 94 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 252 88 41 142 94 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 252 88 41 142 94 smit:SMT_201|5end_phosphoglycerate_mutase_131329..131559_POSITIVE 249 98 71 161 134 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 248 105 63 69 27 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 245 98 67 103 59 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 241 49 5 135 97 smit:SMT_730|5end_hypothetical_protein_638387..638617_NEGATIVE 240 75 35 179 133 smit:SMT_329|5end_hypothetical_protein_265240..265470_POSITIVE 239 106 61 170 128 smit:SMT_1836|5end_cytidine/deoxycytidylate_deaminase_family_protein_1804498..1804728_NEGATIVE 239 106 61 170 128 smit:SMT_1674|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1660501..1660731_NEGATIVE 239 41 1 135 92 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 236 118 71 140 96 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 235 106 69 148 114 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 235 106 69 148 114 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 235 46 6 44 3 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 110 61 134 81 smit:SMT_832|3end_hypothetical_protein_774376..774526_NEGATIVE 282 99 57 75 24 smit:SMT_272|3end_hypothetical_protein_211831..211981_NEGATIVE 267 107 84 145 117 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 259 48 6 121 76 smit:SMT_857|3end_endo-beta-N-acetylglucosaminidase_800881..801031_NEGATIVE 252 104 69 59 23 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 247 108 72 79 34 smit:SMT_1592|3end_putative_hemolysin_1581066..1581216_POSITIVE 242 103 67 53 16 smit:SMT_1979|3end_possible_cell_surface_protein_1910282..1910432_NEGATIVE 241 49 5 135 97 smit:SMT_731|3end_hypothetical_protein_predicted_by_Glimmer/Critica_638387..638537_NEGATIVE 239 41 1 50 7 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 237 104 63 71 40 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 236 118 71 138 94 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 235 45 1 46 5 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE 234 116 71 71 34 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 233 75 38 113 64 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 233 75 38 113 64 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE 231 110 71 46 4 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 224 113 74 101 64 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 224 55 13 73 34 smit:SMT_1842|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1807784..1807934_NEGATIVE 223 102 70 144 93 smit:SMT_1352|3end_formamidopyrimidine-DNA_glycosylase_1329817..1329967_NEGATIVE 222 105 68 140 101 smit:SMT_1301|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1263836..1263986_POSITIVE