Origin IGS: ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actccatactccttcatttcgaaatagtttacactctctcatctaagttgcttattccgcactccatagatttcaagagagtatcagagaaataggctcgtaaaataggagaaaattcctagctccaaagcatggattgcaagcggtattctctcctctgatattat Mask Tandem Repeat Region ================================================ ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Find is-nt database================================================ Query_seq: SSA_0539:SSA_0540|SSA_0539:SSA_0540:PduO protein, putative:Glycerol uptake facilitator protein, putative:->->:534928..535094 167 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0539:SSA_0540|SSA_0539:SSA_0540:PduO protein, putative:Glycerol uptake facilitator protein, putative:->->:534928..535094 167 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0539:SSA_0540|SSA_0539:SSA_0540:PduO protein, putative:Glycerol uptake facilitator protein, putative:->->:534928..535094 167 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Predict ORF larger than 30AA ================================================ ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt 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================================================ ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -3.3 Tail_Score: -4.09511 Start: 47 End: 62 Full_Region: TCCATGCTTTGGAGC TAGGA ATTTTC TCCTA TTTTACGAGCCTATT ..............................................TAGGAATTTTCTCCTA......................................................................................................... Find igs database================================================ Query_seq: SSA_0539:SSA_0540|SSA_0539:SSA_0540:PduO protein, putative:Glycerol uptake facilitator protein, putative:->->:534928..535094 167 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_009009_SSA_0539_SSA_0540|PduO protein, putative:Glycerol uptake facilitator protein, putative|POSITIVE:POSITIVE|[534928,535094]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt ataatatcagaggagagaataccgcttgcaatccatgctttggagctaggaattttctcctattttacgagcctatttctctgatactctcttgaaatctatggagtgcggaataagcaacttagatgagagagtgtaaactatttcgaaatgaaggagtatggagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAUCAGAGGAGAGAAUACCGCUUGCAAUCCAUGCUUUGGAGCUAGGAAUUUUCUCCUAUUUUACGAGCCUAUUUCUCUGAUACUCUCUUGAAAUCUAUGGAGUGCGGAAUAAGCAACUUAGAUGAGAGAGUGUAAACUAUUUCGAAAUGAAGGAGUAUGGAGU ..........((((((((((.((....((..((((.....))))))..)).)))))))))).................((((.((((((((((...(((((.(...(((.......))).).)))))))))))))))....((((((........)))))).)))). (-46.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCCAUACUCCUUCAUUUCGAAAUAGUUUACACUCUCUCAUCUAAGUUGCUUAUUCCGCACUCCAUAGAUUUCAAGAGAGUAUCAGAGAAAUAGGCUCGUAAAAUAGGAGAAAAUUCCUAGCUCCAAAGCAUGGAUUGCAAGCGGUAUUCUCUCCUCUGAUAUUAU .......(((..(((.....)))..)))....(((((((.((((((((.((.......)))))...)))))....)))))))(((((((......((.(((....((((((....))))))((((((.....))))..))..)))))........)))))))..... (-33.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 57 11 81 33 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 325 48 4 223 166 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 307 60 14 195 142 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 306 49 10 218 178 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 303 43 7 207 175 NC_009009:SSA_0850|5end_Ubiquitin_C-terminal_hydrolase,_putative_836818..837048_POSITIVE 301 83 41 231 191 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 294 64 21 222 181 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 293 50 8 173 131 NC_009009:SSA_0872|5end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_865305..865535_NEGATIVE 290 59 18 121 80 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 290 50 4 160 109 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 289 66 23 224 177 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 289 50 7 70 28 NC_009009:SSA_1043|5end_Homoserine_dehydrogenase,_putative_1058565..1058795_POSITIVE 282 53 15 174 118 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 280 70 26 63 10 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 280 80 36 99 47 NC_009009:SSA_0133|5end_50S_ribosomal_protein_L17,_putative_122096..122326_POSITIVE 279 50 7 198 160 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 279 130 82 172 113 NC_009009:SSA_0730|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_714818..715048_POSITIVE 277 49 9 189 154 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 272 47 5 71 7 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 271 61 21 56 15 NC_009009:SSA_0856|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_843210..843440_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 57 11 81 33 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 326 60 11 79 30 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 303 43 7 73 41 NC_009009:SSA_0849|3end_Signal_peptidase_I,_putative_836764..836914_POSITIVE 299 85 41 90 44 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 290 79 49 71 40 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 281 60 13 151 99 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 280 70 26 59 6 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 280 90 43 109 53 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 280 80 36 87 35 NC_009009:SSA_0132|3end_DNA-directed_RNA_polymerase,_alpha_chain,_putative_122164..122314_POSITIVE 271 42 3 139 100 NC_009009:SSA_2208|3end_Preprotein_translocase_secE_component,_putative_2207734..2207884_NEGATIVE 271 90 45 56 1 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 270 86 48 107 70 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 270 94 58 126 85 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 265 112 71 80 27 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 261 60 12 59 17 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 260 132 92 62 13 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 260 128 81 68 33 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 260 50 19 135 98 NC_009009:SSA_0226|3end_60_kDa_chaperonin_220649..220799_POSITIVE 258 70 24 67 13 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 256 85 41 67 4 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE