Origin IGS: tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc .........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 gatgtgacaacgtgaaaatcagagggaaaataggcgataggaggatggagcgattctccgacgataatcgatctttttcccaaagattttagttggaactcgattcaataagatgtgataacgtgaaaatcgttagagcattttatatagaatatacatgggaatggggcttactcccattcccatatttaatagaaaaagaggaactca Mask Tandem Repeat Region ================================================ tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Find is-nt database================================================ Query_seq: SMT_1180:SMT_1181|SMT_1180:SMT_1181:putative tagatose-6-phosphate aldose/ketose isomerase:phosphotransferase system, mannose/fructose-specific component IIA:<-<-:1139293..1139502 210 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1180:SMT_1181|SMT_1180:SMT_1181:putative tagatose-6-phosphate aldose/ketose isomerase:phosphotransferase system, mannose/fructose-specific component IIA:<-<-:1139293..1139502 210 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1180:SMT_1181|SMT_1180:SMT_1181:putative tagatose-6-phosphate aldose/ketose isomerase:phosphotransferase system, mannose/fructose-specific component IIA:<-<-:1139293..1139502 210 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 97 End: 189 ................................................................................................ M L L N R V P T K I F G K K I D Y R R R I A P S S Y R L F S L ..................... Protein_Len: 34 Strand: + Start: 107 End: 208 .......................................................................................................... M E F Q L K S L G K R S I I V G E S L H P P I A Y F P S D F H V V T .. Protein_Len: 39 Strand: - Start: 2 End: 118 . L E E K E I L Y P F P L L G W E W T Y E I Y F A R V I K V N D C R I S D L E M ............................................................................................ tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc 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================================================ tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -5.1 Tail_Score: -2.9039 Start: 17 End: 61 Full_Region: GAGTTCCTCTTTTTC TATTAAATATGGGAATGGG AGTAAGC CCCATTCCCATGTATATTC TATATAAAATGCTCT ................TATTAAATATGGGAATGGGAGTAAGCCCCATTCCCATGTATATTC..................................................................................................................................................... TransTerm Strand: - Conf: 86 HP_score: -10.5 Tail_Score: -3.72576 Start: 24 End: 54 Full_Region: tttatatagaatata catgggaatgggg cttac tcccattcccata tttaatagaaaaaga .......................catgggaatggggcttactcccattcccata............................................................................................................................................................ TransTerm Strand: - Conf: 95 HP_score: -13.1 Tail_Score: -3.44848 Start: 26 End: 52 Full_Region: tatatagaatataca tgggaatgggg cttac tcccattccca tatttaatagaaaaa .........................tgggaatggggcttactcccattccca.............................................................................................................................................................. TransTerm Strand: - Conf: 71 HP_score: -4.7 Tail_Score: -4.57341 Start: 138 End: 163 Full_Region: ggcgataggaggatg gagcgattctc cgac gataatcgatc tttttcccaaagatt .........................................................................................................................................gagcgattctccgacgataatcgatc............................................... Find igs database================================================ Query_seq: SMT_1180:SMT_1181|SMT_1180:SMT_1181:putative tagatose-6-phosphate aldose/ketose isomerase:phosphotransferase system, mannose/fructose-specific component IIA:<-<-:1139293..1139502 210 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: smit_SMT_1180_SMT_1181|putative tagatose-6-phosphate aldose/ketose isomerase:phosphotransferase system, mannose/fructose-specific component IIA|NEGATIVE:NEGATIVE|[1139293,1139502]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatctttgggaaaaagatcgattatcgtcggagaatcgctccatcctcctatcgcctattttccctctgattttcacgttgtcacatc Inter-species Hit: Count: 3 Min: 1 Max: 127 Len: 127 Subject: NC_008533_SPD_0069_SPD_0070|PTS system, IIA component:sugar isomerase domain protein AgaS|POSITIVE:POSITIVE|[70252,70549]|298 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 173 Subject End: 298 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatct................................................................................... tgagttcctctttttctattaaatataggaatgggagtaagctccattcccatgtatattctatataaaatgctctaacgattttcacgttgtcacat-gaattgaatcgagttccaactaaaatct................................................................................... Subject: NC_003098_spr0063_spr0064|Phosphotransferase system sugar-specific EII component:Tagatose-6-phosphate ketose/aldose isomerase|POSITIVE:POSITIVE|[70252,70548]|297 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 172 Subject End: 297 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatct................................................................................... tgagttcctctttttctattaaatataggaatgggagtaagctccattcccatgtatattctatataaaatgctctaacgattttcacgttgtcacat-gaattgaatcgagttccaactaaaatct................................................................................... Subject: NC_003028_SP_0064_SP_0065|PTS system, IIA component:sugar isomerase domain protein AgaS|POSITIVE:POSITIVE|[69362,69659]|298 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 173 Subject End: 298 tgagttcctctttttctattaaatatgggaatgggagtaagccccattcccatgtatattctatataaaatgctctaacgattttcacgttatcacatcttattgaatcgagttccaactaaaatct................................................................................... tgagttcctctttttctattaaatatgggaatgggagtaagctacattcccatgtatattctatataaaatgctctaacgattttcacgttgtcacat-gaattgaatcgagttccaactaaaatct................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUUCCUCUUUUUCUAUUAAAUAUGGGAAUGGGAGUAAGCCCCAUUCCCAUGUAUAUUCUAUAUAAAAUGCUCUAACGAUUUUCACGUUAUCACAUCUUAUUGAAUCGAGUUCCAACUAAAAUCU ..((((.(((............(((((((((((((.(....))))))))))))))..((((...((((.(((...(((((.......)))))...))).)))).)))).)))....))))....... (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUUAGUUGGAACUCGAUUCAAUAAGAUGUGAUAACGUGAAAAUCGUUAGAGCAUUUUAUAUAGAAUAUACAUGGGAAUGGGGCUUACUCCCAUUCCCAUAUUUAAUAGAAAAAGAGGAACUCA .......((((....(((..(((.(((((((((..((((((....).)))))..)))))))))...........((((((((((((.....))))))))))))........)))...))).)))).. (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 50 1 141 92 smit:SMT_1180|5end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1139202..1139432_NEGATIVE 294 120 73 214 162 smit:SMT_1553|5end_K04074_cell_division_initiation_protein_1535913..1536143_POSITIVE 270 49 2 148 94 smit:SMT_1714|5end_hypothetical_membrane_spanning_protein_1701356..1701586_POSITIVE 269 52 26 213 183 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 262 56 27 136 107 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 255 50 1 142 91 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 249 50 2 70 11 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 247 60 31 118 90 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 247 115 74 167 118 smit:SMT_1573|5end_MutT/NUDIX_family_protein_1566413..1566643_POSITIVE 247 51 11 143 97 smit:SMT_1279|5end_translation_elongation_factor_Ts_1242331..1242561_POSITIVE 245 50 9 144 104 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 243 51 25 176 142 smit:SMT_2046|5end_choline_binding_protein_C_1957519..1957749_NEGATIVE 241 76 31 98 49 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 241 76 31 98 49 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 238 77 31 160 100 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 238 50 5 40 5 smit:SMT_1829|5end_hypothetical_protein_1798156..1798386_POSITIVE 231 49 5 146 99 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 227 42 5 208 175 smit:SMT_329|5end_hypothetical_protein_265240..265470_POSITIVE 226 46 5 142 98 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 221 35 1 85 54 smit:SMT_1410|5end_exonuclease_RexA_1392182..1392412_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 49 2 136 82 smit:SMT_1713|3end_K03284_metal_ion_transporter,_MIT_family_1701424..1701574_POSITIVE 255 50 1 81 30 smit:SMT_1783|3end_peptide_methionine_sulfoxide_reductase_1760774..1760924_POSITIVE 251 51 14 145 88 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 247 115 74 144 95 smit:SMT_1572|3end_excinuclease_ABC_subunit_B_1566470..1566620_POSITIVE 247 51 11 64 18 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 243 51 25 98 64 smit:SMT_2047|3end_choline_binding_protein_F_1957597..1957747_NEGATIVE 240 106 69 107 63 smit:SMT_284|3end_putative_capsular_polysaccharide_biosynthesis_protein,glycosyl_transferase_family_2,_YveT_227459..227609_POSITIVE 234 114 71 101 53 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 226 46 5 128 84 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 223 49 3 64 18 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 222 75 33 102 58 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 221 35 1 88 57 smit:SMT_1411|3end_ATP-dependent_nuclease_subunit_B_1392179..1392329_NEGATIVE 221 50 3 143 93 smit:SMT_522|3end_K02003_447500..447650_POSITIVE 217 65 23 59 9 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 217 117 71 145 85 smit:SMT_1366|3end_K02238_competence_protein_ComEC_1344648..1344798_NEGATIVE 215 46 1 55 15 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 212 44 5 66 29 smit:SMT_2160|3end_cell_division_protein_FtsA_2034926..2035076_POSITIVE 212 62 30 83 52 smit:SMT_898|3end_polyribonucleotide_nucleotidyltransferase_844648..844798_NEGATIVE 211 44 13 64 28 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 210 50 1 71 2 smit:SMT_489|3end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_424507..424657_POSITIVE