Origin IGS: taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctccagtacgtcagatttctcttttctgtattttcgtagtataatagggatacgtttagtttcatataatgagatatatatttttaacgaatattaaggagaacatta Mask Tandem Repeat Region ================================================ taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Find is-nt database================================================ Query_seq: SMT_1436:SMT_1437|SMT_1436:SMT_1437:conserved hypothetical protein TIGR00147:ADP-ribosylglycohydrolase:<-<-:1421346..1421454 109 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1436:SMT_1437|SMT_1436:SMT_1437:conserved hypothetical protein TIGR00147:ADP-ribosylglycohydrolase:<-<-:1421346..1421454 109 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1436:SMT_1437|SMT_1436:SMT_1437:conserved hypothetical protein TIGR00147:ADP-ribosylglycohydrolase:<-<-:1421346..1421454 109 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Predict ORF larger than 30AA ================================================ taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga 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: 64 End: 93 ...............................................................TTTCTCTTTTCTGTATTTTCGTAGTATAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1436:SMT_1437|SMT_1436:SMT_1437:conserved hypothetical protein TIGR00147:ADP-ribosylglycohydrolase:<-<-:1421346..1421454 109 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: smit_SMT_1436_SMT_1437|conserved hypothetical protein TIGR00147:ADP- ribosylglycohydrolase|NEGATIVE:NEGATIVE|[1421346, 1421454]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga taatgttctccttaatattcgttaaaaatatatatctcattatatgaaactaaacgtatccctattatactacgaaaatacagaaaagagaaatctgacgtactggaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGUUCUCCUUAAUAUUCGUUAAAAAUAUAUAUCUCAUUAUAUGAAACUAAACGUAUCCCUAUUAUACUACGAAAAUACAGAAAAGAGAAAUCUGACGUACUGGAGA ......(((((......(((((......((((((......)))))).........((((.......)))).)))))..(((.....(((....)))...)))..))))) (-15.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCAGUACGUCAGAUUUCUCUUUUCUGUAUUUUCGUAGUAUAAUAGGGAUACGUUUAGUUUCAUAUAAUGAGAUAUAUAUUUUUAACGAAUAUUAAGGAGAACAUUA (((((.......((((.........))))....(((((.((((.......)))).....(((((((...)))))))...........)))))......)))))...... (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 783 100 51 191 142 smit:SMT_1436|5end_conserved_hypothetical_protein_TIGR00147_1421255..1421485_NEGATIVE 267 77 32 135 94 smit:SMT_1215|5end_aromatic_amino_acid_aminotransferase_1174588..1174818_NEGATIVE 228 82 45 224 190 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 217 95 53 134 87 smit:SMT_551|5end_K07170_GAF_domain-containing_protein_468948..469178_POSITIVE 214 76 37 127 88 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 213 96 55 59 14 smit:SMT_1903|5end_hypothetical_protein_1852411..1852641_POSITIVE 204 100 54 179 131 smit:SMT_958|5end_hypothetical_protein_predicted_by_Glimmer/Critica_905052..905282_POSITIVE 193 99 58 217 166 smit:SMT_727|5end_phage_transcriptional_repressor_632513..632743_NEGATIVE 182 59 19 50 9 smit:SMT_907|5end_hypothetical_protein_856054..856284_NEGATIVE 181 100 54 87 45 smit:SMT_2116|5end_extramembranal_protein_2003251..2003481_POSITIVE 181 83 45 122 79 smit:SMT_1275|5end_rod_shape-determining_protein_MreC_1238594..1238824_POSITIVE 179 100 67 140 97 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 177 63 33 231 201 smit:SMT_210|5end_acetyltransferase,_GNAT_family_143380..143610_POSITIVE 176 98 55 159 110 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 173 75 32 167 109 smit:SMT_1421|5end_K02003_1407342..1407572_NEGATIVE 173 38 3 135 90 smit:SMT_1376|5end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1355553..1355783_NEGATIVE 172 86 54 153 116 smit:SMT_122|5end_hypothetical_protein_74456..74686_POSITIVE 170 82 45 158 121 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 167 69 21 76 30 smit:SMT_1513|5end_hypothetical_protein_1495582..1495812_NEGATIVE 166 78 33 110 65 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 95 53 48 1 smit:SMT_550|3end_K02945_small_subunit_ribosomal_protein_S1_468942..469092_POSITIVE 188 71 34 33 1 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 181 83 45 63 20 smit:SMT_1274|3end_K02008_cobalt_transport_system_permease_protein_1238615..1238765_POSITIVE 173 38 3 132 87 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 171 74 32 147 94 smit:SMT_1422|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1407357..1407507_NEGATIVE 167 86 56 31 1 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 156 91 55 62 30 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 154 100 55 118 67 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 150 100 61 63 25 smit:SMT_823|3end_putative_mucus_binding_protein_740995..741145_NEGATIVE 149 98 81 73 51 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 149 100 63 66 21 smit:SMT_335|3end_glutamine_synthetase_275179..275329_POSITIVE 147 100 62 84 40 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 147 100 62 84 40 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 147 100 62 84 40 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 147 100 62 84 40 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 146 75 36 48 14 smit:SMT_580|3end_K04094_glucose_inhibited_division_protein_Gid_498034..498184_POSITIVE 142 95 59 70 29 smit:SMT_1556|3end_phosphoglycerate_mutase_1541966..1542116_POSITIVE 141 97 54 64 19 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 139 99 56 75 25 smit:SMT_1851|3end_ABC_transporter,_permease_protein,_putative_1815578..1815728_NEGATIVE 139 93 58 69 28 smit:SMT_598|3end_K07273_lysozyme_514012..514162_NEGATIVE