Origin IGS: gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgctcgagaaattataaatagtttaacaatctaaacgctaagccctgtccgggctttttatatgcactctcctgtcatcaattgatatgttttttaatgggcgtgtaatctggtcttgatgagctgtaataataaacatgctataatgtctgc Mask Tandem Repeat Region ================================================ gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Find is-nt database================================================ Query_seq: SSA_2211:SSA_2212|SSA_2211:SSA_2212:Transmembrane protein, putative:Possible polysaccharide transport protein, putative:<-<-:2212564..2212716 153 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2211:SSA_2212|SSA_2211:SSA_2212:Transmembrane protein, putative:Possible polysaccharide transport protein, putative:<-<-:2212564..2212716 153 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2211:SSA_2212|SSA_2211:SSA_2212:Transmembrane protein, putative:Possible polysaccharide transport protein, putative:<-<-:2212564..2212716 153 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 15 End: 113 .............. M F I I T A H Q D Q I T R P L K N I S I D D R R V H I K S P D R A ........................................ gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca 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================================================ gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2211:SSA_2212|SSA_2211:SSA_2212:Transmembrane protein, putative:Possible polysaccharide transport protein, putative:<-<-:2212564..2212716 153 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_009009_SSA_2211_SSA_2212|Transmembrane protein, putative:Possible polysaccharide transport protein, putative|NEGATIVE:NEGATIVE|[2212564,2212716]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca gcagacattatagcatgtttattattacagctcatcaagaccagattacacgcccattaaaaaacatatcaattgatgacaggagagtgcatataaaaagcccggacagggcttagcgtttagattgttaaactatttataatttctcgagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGACAUUAUAGCAUGUUUAUUAUUACAGCUCAUCAAGACCAGAUUACACGCCCAUUAAAAAACAUAUCAAUUGAUGACAGGAGAGUGCAUAUAAAAAGCCCGGACAGGGCUUAGCGUUUAGAUUGUUAAACUAUUUAUAAUUUCUCGAGCA ..((((((......)))))).........((((...............(((.((((((((............))))))...))...)))..((((((((((((.....))))))...((((((....))))))..)))))).......)))). (-27.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUCGAGAAAUUAUAAAUAGUUUAACAAUCUAAACGCUAAGCCCUGUCCGGGCUUUUUAUAUGCACUCUCCUGUCAUCAAUUGAUAUGUUUUUUAAUGGGCGUGUAAUCUGGUCUUGAUGAGCUGUAAUAAUAAACAUGCUAUAAUGUCUGC ......(((.((((((.((.(((((..............((((((.....))))))......(((((((..(....((((....((((((((......))))))))....))))...)..))).))))....)))))))..)))))).))).. (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 956 120 71 211 162 NC_009009:SSA_2211|5end_Transmembrane_protein,_putative_2212473..2212703_NEGATIVE 344 125 82 194 153 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 323 134 96 151 116 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 314 117 71 200 148 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 310 129 96 48 8 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 302 127 81 188 135 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 296 118 74 216 180 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 294 123 85 170 126 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 289 148 101 99 41 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 288 55 11 219 170 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 287 124 81 222 174 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 284 112 73 43 2 NC_009009:SSA_0803|5end_hypothetical_protein_785145..785375_POSITIVE 275 119 77 57 5 NC_009009:SSA_1635|5end_hypothetical_protein_1639221..1639451_NEGATIVE 270 124 81 207 169 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 270 150 108 150 106 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 269 120 74 161 113 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 266 129 81 86 44 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 261 117 78 201 164 NC_009009:SSA_0208|5end_Conserved_uncharacterized_protein_206452..206682_NEGATIVE 260 117 82 222 184 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 259 117 74 227 181 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 134 96 141 106 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 302 127 81 109 56 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 302 45 3 111 56 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 293 114 89 76 47 NC_009009:SSA_0192|3end_Acetate_kinase,_putative_194182..194332_POSITIVE 289 148 101 76 18 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 285 138 100 84 43 NC_009009:SSA_0384|3end_hypothetical_protein_378449..378599_POSITIVE 284 112 73 46 5 NC_009009:SSA_0802|3end_hypothetical_protein_785228..785378_POSITIVE 279 117 73 95 58 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 270 150 108 139 95 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 265 119 88 128 104 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 261 117 78 81 44 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 260 117 82 150 112 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 260 127 81 105 59 NC_009009:SSA_0851|3end_Cation_efflux_family_protein,_putative_837644..837794_NEGATIVE 260 130 81 83 24 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 254 113 73 59 24 NC_009009:SSA_1705|3end_hypothetical_protein_1696398..1696548_NEGATIVE 248 129 100 66 31 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 248 135 99 55 10 NC_009009:SSA_1122|3end_Thioredoxin_family_protein,_putative_1148526..1148676_POSITIVE 245 128 81 94 43 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 245 125 82 59 16 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 244 118 75 96 32 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE