Origin IGS: ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttattttctaagatggcaatttcttcttccagaccttctaagtcaaagagaccccctgaaagaagctaatttttcacgatttgcgtcaatcttttgacgaatttctgaaatgtccataaatacctcttttcacatatcgtttaattataacataaattaaacagtttgcctaatctcacattcagcagcttacattttatcggattttccctagctaggcaagacaagcgactccttgtcacctaattgttagaaaagtaatataatgacatggggttggaagaattatttcaagacttcctagacttcatccatgaataaacgaaacagataattgccataatttattaggtattcagataaaagggagactctccataggtgcttaagcatttccaagttttgaaaaatatgctagactaaaacc Mask Tandem Repeat Region ================================================ ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Find is-nt database================================================ Query_seq: SSA_0868:SSA_0869|SSA_0868:SSA_0869:hypothetical protein:Peptide chain release factor 2, putative:<-->:861626..862053 428 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0868:SSA_0869|SSA_0868:SSA_0869:hypothetical protein:Peptide chain release factor 2, putative:<-->:861626..862053 428 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0868:SSA_0869|SSA_0868:SSA_0869:hypothetical protein:Peptide chain release factor 2, putative:<-->:861626..862053 428 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 17 End: 124 ................ M F Q N L E M L K H L W R V S L L S E Y L I N Y G N Y L F R L F M D E V ................................................................................................................................................................................................................................................................................................................ Protein_Len: 33 Strand: + Start: 186 End: 284 ......................................................................................................................................................................................... M T R S R L S C L A R E N P I K C K L L N V R L G K L F N L C Y N ................................................................................................................................................ ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag 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: 87 Start: 255 End: 284 ..............................................................................................................................................................................................................................................................TTAGGCAAACTGTTTAATTTATGTTATAAT................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 205 End: 234 ............................................................................................................................................................................................................CTTGCCTAGCTAGGGAAAATCCGATAAAAT.................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 164 End: 193 ...................................................................................................................................................................CTTGTCACCTAATTGTTAGAAAAGTAATAT........................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -5.6 Tail_Score: -3.07816 Start: 188 End: 205 Full_Region: TTCTAACAATTAGGT GACAAG GAGTCG CTTGTC TTGCCTAGCTAGGGA ...........................................................................................................................................................................................GACAAGGAGTCGCTTGTC............................................................................................................................................................................................................................... TransTerm Strand: + Conf: 42 HP_score: -2.4 Tail_Score: -3.09878 Start: 190 End: 203 Full_Region: CTAACAATTAGGTGA CAAG GAGTCG CTTG TCTTGCCTAGCTAGG .............................................................................................................................................................................................CAAGGAGTCGCTTG................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0868:SSA_0869|SSA_0868:SSA_0869:hypothetical protein:Peptide chain release factor 2, putative:<-->:861626..862053 428 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Intra-Species Hit: Count: 1 Min: 1 Max: 428 Len: 428 Subject: NC_009009_SSA_0868_SSA_0869|hypothetical protein:Peptide chain release factor 2, putative|NEGATIVE:POSITIVE|[861626,862053]|428 HSP 1 e-value: 0.0 bit: 848.0 Len: 428 Query Start:1 Query End:428 Subject Strand: POSITIVE Subject Start: 1 Subject End: 428 ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag ggttttagtctagcatatttttcaaaacttggaaatgcttaagcacctatggagagtctcccttttatctgaatacctaataaattatggcaattatctgtttcgtttattcatggatgaagtctaggaagtcttgaaataattcttccaaccccatgtcattatattacttttctaacaattaggtgacaaggagtcgcttgtcttgcctagctagggaaaatccgataaaatgtaagctgctgaatgtgagattaggcaaactgtttaatttatgttataattaaacgatatgtgaaaagaggtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaataag Inter-species Hit: Count: 3 Min: 305 Max: 424 Len: 120 Subject: smit_SMT_494_SMT_495|K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2)|POSITIVE:POSITIVE|[428952,429177]|226 HSP 1 e-value: 4.0E-40 bit: 167.0 Len: 120 Query Start:305 Query End:424 Subject Strand: POSITIVE Subject Start: 103 Subject End: 222 ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaa.... ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaa.... Subject: NC_008533_SPD_0657_SPD_0658|acetoin utilization protein AcuB, putative:peptide chain release factor 2|POSITIVE:POSITIVE|[675788,676000]|213 HSP 1 e-value: 2.0E-35 bit: 151.0 Len: 112 Query Start:305 Query End:416 Subject Strand: POSITIVE Subject Start: 102 Subject End: 213 ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatc............ ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagtaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaagggctagaggaagagattgccatc............ Subject: NC_003098_spr0664_spr0665|hypothetical protein:peptide chain release factor 2|POSITIVE:POSITIVE|[668257,668469]|213 HSP 1 e-value: 2.0E-35 bit: 151.0 Len: 112 Query Start:305 Query End:416 Subject Strand: POSITIVE Subject Start: 102 Subject End: 213 ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatc............ ................................................................................................................................................................................................................................................................................................................gtatttatggacatttcagtaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaagggctagaggaagagattgccatc............ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUUAUGGACAUUUCAGAAAUUCGUCAAAAGAUUGACGCAAAUCGUGAAAAAUUAGCUUCUUUCAGGGGGUCUCUUUGACUUAGAAGGUCUGGAAGAAGAAAUUGCCAUCUUAGAAAA ......((((...(((((((....((((((....))))))....)).)))))......((((((((((((((((.....)))))......)))))))))))......))))......... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUAAGAUGGCAAUUUCUUCUUCCAGACCUUCUAAGUCAAAGAGACCCCCUGAAAGAAGCUAAUUUUUCACGAUUUGCGUCAAUCUUUUGACGAAUUUCUGAAAUGUCCAUAAAUAC .........((((((....((((((.(((...((((.......)))).....))).))))))......(((((.((....((((((....))))))....))))))))).))))...... (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 87 58 225 193 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 334 98 57 193 150 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 285 89 49 227 185 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 280 95 55 165 121 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 275 70 25 111 70 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 270 98 54 70 29 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 265 109 62 102 49 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 263 70 22 166 114 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 262 69 21 217 169 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 261 97 54 229 184 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 258 108 66 168 135 NC_009009:SSA_2084|5end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2089424..2089654_NEGATIVE 256 99 57 173 122 NC_009009:SSA_1031|5end_DNA_topology_modulation_protein_FlaR,_putative_1048255..1048485_NEGATIVE 253 97 61 229 187 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 253 96 56 134 91 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 252 94 58 94 58 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 252 97 55 171 120 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 251 109 61 184 126 NC_009009:SSA_2349|5end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2351708..2351938_NEGATIVE 251 97 51 72 30 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 250 109 61 130 75 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 250 94 66 197 164 NC_009009:SSA_0544|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_539819..540049_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 98 57 72 29 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 303 90 48 89 39 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 279 108 66 54 7 NC_009009:SSA_1995|3end_hypothetical_protein_1992672..1992822_NEGATIVE 275 70 25 98 57 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE 271 115 79 145 98 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 270 98 54 64 23 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 265 109 62 118 65 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 258 108 66 144 111 NC_009009:SSA_2085|3end_Glyoxylate_reductase,_NADH-dependent,_putative_2089448..2089598_NEGATIVE 256 99 57 115 64 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 253 96 56 108 65 NC_009009:SSA_0104|3end_Queuine_tRNA-ribosyltransferase,_putative_106815..106965_POSITIVE 252 94 58 97 61 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 251 97 51 75 33 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE 250 104 67 125 78 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 249 95 51 146 104 NC_009009:SSA_0483|3end_Siroheme_synthase,_putative_484556..484706_POSITIVE 247 119 74 151 110 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 244 78 32 73 13 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 244 96 51 133 82 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 244 88 48 60 19 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 239 84 61 139 115 NC_009009:SSA_1984|3end_Cell_surface_SD_repeat_antigen_precursor,_putative_1976048..1976198_NEGATIVE 237 98 55 120 75 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE