Origin IGS: tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca .........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 tgaaagtgcttttcattaacttttcgaggtgttgatcgggggcaatagtatgccagctttgccatgataccgctacgaatgaaagacgtatcacgtatgtttgactcattatgaaatgtacttttcattcctcagagagatatatgactgctgagcggaaaatgcttaaatcatcgatca Mask Tandem Repeat Region ================================================ tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Find is-nt database================================================ Query_seq: TF1412:TF1413|TF1412:TF1413:conserved hypothetical protein:possible transmembrane protein:->->:1493317..1493496 180 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1412:TF1413|TF1412:TF1413:conserved hypothetical protein:possible transmembrane protein:->->:1493317..1493496 180 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1412:TF1413|TF1412:TF1413:conserved hypothetical protein:possible transmembrane protein:->->:1493317..1493496 180 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 53 End: 178 .................................................... M K S T F H N E S N I R D T S F I R S G I M A K L A Y Y C P R S T P R K V N E K H F .. Protein_Len: 37 Strand: + Start: 69 End: 179 .................................................................... M M S Q T Y V I R L S F V A V S W Q S W H T I A P D Q H L E K L M K S T F . tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca 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================================================ tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1412:TF1413|TF1412:TF1413:conserved hypothetical protein:possible transmembrane protein:->->:1493317..1493496 180 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: tfor_TF1412_TF1413|conserved hypothetical protein:possible transmembrane protein|POSITIVE:POSITIVE|[1493317,1493496]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca tgatcgatgatttaagcattttccgctcagcagtcatatatctctctgaggaatgaaaagtacatttcataatgagtcaaacatacgtgatacgtctttcattcgtagcggtatcatggcaaagctggcatactattgcccccgatcaacacctcgaaaagttaatgaaaagcactttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCGAUGAUUUAAGCAUUUUCCGCUCAGCAGUCAUAUAUCUCUCUGAGGAAUGAAAAGUACAUUUCAUAAUGAGUCAAACAUACGUGAUACGUCUUUCAUUCGUAGCGGUAUCAUGGCAAAGCUGGCAUACUAUUGCCCCCGAUCAACACCUCGAAAAGUUAAUGAAAAGCACUUUCA ((((((.(((((((...........(((((.((..........)))))))..((((((......))))))..)))))))......((((((((..((.........))..))))))))........((((......))))..)))))).......((((.((...(....)..)))))). (-36.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGUGCUUUUCAUUAACUUUUCGAGGUGUUGAUCGGGGGCAAUAGUAUGCCAGCUUUGCCAUGAUACCGCUACGAAUGAAAGACGUAUCACGUAUGUUUGACUCAUUAUGAAAUGUACUUUUCAUUCCUCAGAGAGAUAUAUGACUGCUGAGCGGAAAAUGCUUAAAUCAUCGAUCA .((((((((.((((((......((((.((((...((((..(((((.(((......)))))))).))))..)))).)))).((.((((((((...))))))))...))...)))))).)))))))).............(((..((((....((((((.....))))))..))))..))). (-44.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 150 102 67 20 tfor:TF1023|5end_ABC_transporter,_permease_component_1079197..1079427_POSITIVE 343 147 104 197 149 tfor:TF2770|5end_conserved_hypothetical_protein_2956308..2956538_POSITIVE 343 145 101 45 5 tfor:TF1957|5end_penicillin_tolerance_protein;_possible_isoprene_biosynthesis_related_protein_2107789..2108019_POSITIVE 341 129 86 178 126 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 325 144 103 149 106 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 324 130 86 56 17 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 323 149 104 226 181 tfor:TF2620|5end_conserved_hypothetical_protein_2796121..2796351_POSITIVE 323 129 86 226 182 tfor:TF0504|5end_Fe-S_oxidoreductase,_family_2_528433..528663_POSITIVE 323 130 85 52 7 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 321 126 85 227 186 tfor:TF0398|5end_Fe-S_oxidoreductase_418984..419214_POSITIVE 319 127 83 53 8 tfor:TF1952|5end_immunoreactive_84kD_antigen_PG93_2101443..2101673_POSITIVE 318 125 85 76 32 tfor:TF1900|5end_conserved_hypothetical_protein_2053867..2054097_POSITIVE 317 130 85 91 57 tfor:TF2275|5end_conserved_hypothetical_protein_2436934..2437164_POSITIVE 317 127 93 217 185 tfor:TF2270|5end_conserved_hypothetical_protein_2435463..2435693_POSITIVE 316 149 101 52 16 tfor:TF2773|5end_S-adenosylmethionine_tRNA_ribosyltransferase_2958117..2958347_POSITIVE 315 144 103 43 1 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 313 140 93 167 127 tfor:TF1333|5end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1413397..1413627_POSITIVE 313 130 82 217 166 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 311 132 93 74 22 tfor:TF2882|5end_conserved_hypothetical_protein_3073419..3073649_POSITIVE 309 129 86 198 150 tfor:TF2571|5end_30S_ribosomal_protein_S5_2742548..2742778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 150 102 49 2 tfor:TF1022|3end_chromosomal_replication_initiator_ATPase,_DnaA_1079259..1079409_POSITIVE 343 145 101 49 9 tfor:TF1956|3end_hypothetical_protein_2107873..2108023_POSITIVE 324 130 86 56 17 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 323 149 104 138 93 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 323 130 85 47 2 tfor:TF0243|3end_conserved_hypothetical_protein_274758..274908_POSITIVE 321 141 102 139 101 tfor:TF2281|3end_hypothetical_protein_2439995..2440145_POSITIVE 317 130 85 63 29 tfor:TF2274|3end_conserved_hypothetical_protein_2436986..2437136_POSITIVE 317 127 93 147 115 tfor:TF2267|3end_lysozyme-related_protein_2435473..2435623_POSITIVE 304 140 93 143 86 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 300 53 16 63 29 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 296 128 81 138 80 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 294 140 91 130 77 tfor:TF1814|3end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1956670..1956820_POSITIVE 293 145 108 49 15 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 292 129 82 148 89 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 290 157 111 48 1 tfor:TF0762|3end_chromate_transport_protein_809755..809905_POSITIVE 289 139 93 53 1 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 285 139 92 120 60 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 283 140 91 125 73 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 280 164 124 121 93 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 280 142 108 78 41 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE