Origin IGS: aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctacttgcattacttaaaatgttataagatttaaatctaaaaatcattattactcatataacaaaaaacgaacaggctctttttctgtcattcagaagagaacttgttcgtttttatcttgctttt Mask Tandem Repeat Region ================================================ aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Find is-nt database================================================ Query_seq: SMT_1431:SMT_1432|SMT_1431:SMT_1432:K08986 putative membrane protein:hypothetical protein:-><-:1416715..1416841 127 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1431:SMT_1432|SMT_1431:SMT_1432:K08986 putative membrane protein:hypothetical protein:-><-:1416715..1416841 127 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1431:SMT_1432|SMT_1431:SMT_1432:K08986 putative membrane protein:hypothetical protein:-><-:1416715..1416841 127 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 2 End: 103 . F C S L F S C T R K Q I V S F S G T R K K N Y S Y Y H N K S K F R M ........................ aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc 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================================================ aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -8.2 Tail_Score: -5.16206 Start: 17 End: 58 Full_Region: tcatataacaaaaaa cgaacaggctctttttctg tcatt cagaagagaacttgttcg tttttatcttgcttt ................cgaacaggctctttttctgtcattcagaagagaacttgttcg..................................................................... Find igs database================================================ Query_seq: SMT_1431:SMT_1432|SMT_1431:SMT_1432:K08986 putative membrane protein:hypothetical protein:-><-:1416715..1416841 127 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_1431_SMT_1432|K08986 putative membrane protein:hypothetical protein|POSITIVE:NEGATIVE|[1416715,1416841]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgttttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc Inter-species Hit: Count: 2 Min: 1 Max: 127 Len: 127 Subject: NC_008533_SPD_0796_SPD_0797|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[813623,813751]|129 HSP 1 e-value: 2.0E-26 bit: 119.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 128 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgtt-ttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc aaaatcaagataaaaacgaacaagttctcttctgaataacagaaaaagagcctgttcgtttttttgttatatgaaaattagtgacttgtagattttcatcttataccatttccagcaatacaagtagc Subject: NC_003098_spr0803_spr0804|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[806092,806220]|129 HSP 1 e-value: 2.0E-26 bit: 119.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 128 aaaagcaagataaaaacgaacaagttctcttctgaatgacagaaaaagagcctgttcgtt-ttttgttatatgagtaataatgatttttagatttaaatcttataacattttaagtaatgcaagtagc aaaatcaagataaaaacgaacaagttctcttctgaataacagaaaaagagcctgttcgtttttttgttatatgaaaattagtgacttgtagattttcatcttataccatttccagcaatacaagtagc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGCAAGAUAAAAACGAACAAGUUCUCUUCUGAAUGACAGAAAAAGAGCCUGUUCGUUUUUUGUUAUAUGAGUAAUAAUGAUUUUUAGAUUUAAAUCUUAUAACAUUUUAAGUAAUGCAAGUAGC ....(((.((((((((((((((.(((((.(((((.....)))))..))))).)))))).))))))))......((.((((.(((((........))))))))).))...........)))....... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUACUUGCAUUACUUAAAAUGUUAUAAGAUUUAAAUCUAAAAAUCAUUAUUACUCAUAUAACAAAAAACGAACAGGCUCUUUUUCUGUCAUUCAGAAGAGAACUUGUUCGUUUUUAUCUUGCUUUU .......(((...........((.(((((((((........))))).)))).))..........(((((((((((((.((((((.(((.....))))))))).)))))))))))))....))).... (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 53 17 183 148 smit:SMT_269|5end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_207725..207955_POSITIVE 240 63 25 226 184 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 228 64 23 45 14 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 226 57 17 221 179 smit:SMT_988|5end_N-acetylneuraminate_lyase_932889..933119_NEGATIVE 222 65 23 78 12 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 219 57 14 200 147 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 219 59 18 70 22 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 216 67 25 143 100 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 216 61 23 139 93 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 216 67 25 143 100 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 212 58 17 174 129 smit:SMT_1698|5end_CMP-binding_factor_1680092..1680322_POSITIVE 210 65 29 159 115 smit:SMT_498|5end_hypothetical_protein_431751..431981_POSITIVE 209 74 36 229 187 smit:SMT_1137|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1079267..1079497_NEGATIVE 208 54 16 190 144 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 207 59 26 180 144 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 207 71 41 35 6 smit:SMT_344|5end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283974..284204_NEGATIVE 206 68 25 75 36 smit:SMT_974|5end_DNA-binding_response_regulator_922847..923077_NEGATIVE 203 69 22 206 153 smit:SMT_444|5end_thiamine-phosphate_pyrophosphorylase_383339..383569_POSITIVE 200 64 21 100 61 smit:SMT_1010|5end_hypothetical_protein_948292..948522_POSITIVE 198 74 34 214 175 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 60 12 76 28 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 259 67 32 72 35 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 225 90 41 106 45 smit:SMT_728|3end_hypothetical_protein_633203..633353_NEGATIVE 222 67 22 142 103 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 219 57 14 85 32 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 216 67 25 143 100 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 216 61 23 139 93 smit:SMT_1352|3end_formamidopyrimidine-DNA_glycosylase_1329817..1329967_NEGATIVE 216 67 25 143 100 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 210 65 29 138 94 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 207 56 27 28 1 smit:SMT_1221|3end_choline_binding_protein_A_1183986..1184136_NEGATIVE 205 69 37 44 12 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 204 73 35 82 37 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 202 67 21 95 50 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 202 67 41 90 62 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 201 60 17 48 3 smit:SMT_1264|3end_oligoendopeptidase_F_1230734..1230884_POSITIVE 200 64 21 88 49 smit:SMT_1009|3end_hypothetical_protein_predicted_by_Glimmer/Critica_948360..948510_POSITIVE 199 45 1 90 48 smit:SMT_1360|3end_lactoylglutathione_lyase_1338252..1338402_NEGATIVE 198 70 23 137 81 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 196 66 22 94 48 smit:SMT_1130|3end_MATE_efflux_family_protein_1063930..1064080_NEGATIVE 193 66 25 143 97 smit:SMT_365|3end_hypothetical_protein_301747..301897_POSITIVE