Origin IGS: ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg .........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 cataccttagtttcacctgacaaagatacaagttttcaatgaaataatagaaaaaaagcaggaaataatcctataaaaccgctctaactgctttatatactatcgtttgacatacatcaagaatttgcggttttgcaaaaaacgaaccttgaaatatttgcaagtattccaaatactatctacctttgcatcgtcaaaaggttaatagattgtttaggttagtagtaatagatttaggtttttagttattttttaaaggtaaaagtttaacagattgtgtaataaggaaaacaaggagaccgtgaggcttcctctattcataagacaaaagacaattaaggttaaacaaaataa Mask Tandem Repeat Region ================================================ ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Find is-nt database================================================ Query_seq: PI1870:PI1871|PI1870:PI1871:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1815574..1815927 354 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1870:PI1871|PI1870:PI1871:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1815574..1815927 354 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1870:PI1871|PI1870:PI1871:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1815574..1815927 354 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 183 End: 281 ...................................................................................................................................................................................... M E Y L Q I F Q G S F F A K P Q I L D V C Q T I V Y K A V R A V L ......................................................................... Protein_Len: 36 Strand: - Start: 153 End: 260 ........................................................................................................................................................ G K S S A F T S L I Q F V Q L Y K L T R K K C F R L N K I Y T L R Y Y M .............................................................................................. Protein_Len: 44 Strand: - Start: 136 End: 267 ....................................................................................................................................... G L C D I L R K V I C L Y I T N P I S A F I E L N T K Q L V A F E Q H I D F S L I Y L M ....................................................................................... ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg 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: 82 Start: 178 End: 207 .................................................................................................................................................................................CTTGAAATATTTGCAAGTATTCCAAATACT................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -2.1 Tail_Score: -4.08219 Start: 282 End: 296 Full_Region: GTTAGAGCGGTTTTA TAGGA TTATT TCCTG CTTTTTTTCTATTAT .........................................................................................................................................................................................................................................................................................TAGGATTATTTCCTG.......................................................... Find igs database================================================ Query_seq: PI1870:PI1871|PI1870:PI1871:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1815574..1815927 354 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctgttaaacttttacctttaaaaaataactaaaaacctaaatctattactactaacctaaacaatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg Intra-Species Hit: Count: 1 Min: 1 Max: 354 Len: 354 Subject: pint_PI1870_PI1871|hypothetical protein:glycosyl transferase, group 1 family protein|POSITIVE:POSITIVE|[1815574,1815927]|354 HSP 1 e-value: 1.0E-103 bit: 377.0 Len: 211 Query Start:144 Query End:354 Subject Strand: POSITIVE Subject Start: 144 Subject End: 354 ...............................................................................................................................................aatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgcnnnnnnnctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg ...............................................................................................................................................aatctattaaccttttgacgatgcaaaggtagatagtatttggaatacttgcaaatatttcaaggttcgttttttgcaaaaccgcaaattcttgatgtatgtcaaacgatagtatataaagcagttagagcggttttataggattatttcctgctttttttctattatttcattgaaaacttgtatctttgtcaggtgaaactaaggtatg HSP 2 e-value: 3.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctg.............................................................................................................................................................................................................................................................................. ttattttgtttaaccttaattgtcttttgtcttatgaatagaggaagcctcacggtctccttgttttccttattacacaatctg.............................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUUGUUUAACCUUAAUUGUCUUUUGUCUUAUGAAUAGAGGAAGCCUCACGGUCUCCUUGUUUUCCUUAUUACACAAUCUGUUAAACUUUUACCUUUAAAAAAUAACUAAAAACCUAAAUCUAUUACUACUAACCUAAACAAUCUAUUAACCUUUUGACGAUGCAAAGGUAGAUAGUAUUUGGAAUACUUGCAAAUAUUUCAAGGUUCGUUUUUUGCAAAACCGCAAAUUCUUGAUGUAUGUCAAACGAUAGUAUAUAAAGCAGUUAGAGCGGUUUUAUAGGAUUAUUUCCUGCUUUUUUUCUAUUAUUUCAUUGAAAACUUGUAUCUUUGUCAGGUGAAACUAAGGUAUG .......(((((((....(((((.....((..((.(((..(((((..((....))..)))))...)))..))..)))))))..)))))))...((((((......................................(((((....(((((.((((((.(......))))))).)))))..)))))..((((((((((.((..((((.((((........((((((((.(((((((.(((((((((....)))).))))).))).))))...)))))))).(((((.....)))))....................))))..)))).)).)))).)))))).....)))))).. (-68.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUACCUUAGUUUCACCUGACAAAGAUACAAGUUUUCAAUGAAAUAAUAGAAAAAAAGCAGGAAAUAAUCCUAUAAAACCGCUCUAACUGCUUUAUAUACUAUCGUUUGACAUACAUCAAGAAUUUGCGGUUUUGCAAAAAACGAACCUUGAAAUAUUUGCAAGUAUUCCAAAUACUAUCUACCUUUGCAUCGUCAAAAGGUUAAUAGAUUGUUUAGGUUAGUAGUAAUAGAUUUAGGUUUUUAGUUAUUUUUUAAAGGUAAAAGUUUAACAGAUUGUGUAAUAAGGAAAACAAGGAGACCGUGAGGCUUCCUCUAUUCAUAAGACAAAAGACAAUUAAGGUUAAACAAAAUAA ..((((((.((((((..(((...((((....))))))).))))))....((((((.(((.(((.....)))...((((((..((((((((((...((.((....(((((..((((..((((.((((..(((((..........)))))...)))).))))...))))..))))).((((..((((((.........))))))..))))...)).))....))))))..))))....))))))..))).)))))).))))))...(((((((.((((((((......(((....((((..((....))..))))...))).....)).....))))))...)))))))....... (-67.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 195 157 231 195 pint:PI1369|5end_alkyl_hydroperoxide_reductase,_subunit__C_1289780..1290010_POSITIVE 297 288 242 143 94 pint:PI2032|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_1986544..1986774_POSITIVE 279 243 204 192 151 pint:PI1777|5end_conserved_hypothetical_protein_1709402..1709632_POSITIVE 273 60 14 89 28 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 271 247 204 84 39 pint:PI1002|5end_metal_dependent_hydrolase_923842..924072_POSITIVE 270 240 201 230 197 pint:PI0549|5end_hypothetical_protein_500504..500734_POSITIVE 269 329 283 102 51 pint:PI1701|5end_sensor_histidine_kinase_1619312..1619542_POSITIVE 269 73 36 188 139 pint:PI0569|5end_phosphoglycerate_kinase_513297..513527_POSITIVE 265 220 171 185 133 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 265 60 21 175 137 pint:PI1227|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148448..1148678_POSITIVE 265 59 13 194 138 pint:PI0449|5end_hypothetical_protein_422952..423182_POSITIVE 263 310 267 223 189 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 262 314 271 130 75 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 261 71 35 133 94 pint:PI0364|5end_hypothetical_protein_334002..334232_POSITIVE 259 68 25 171 125 pint:PI2091|5end_DNA_processing_protein_2048019..2048249_POSITIVE 258 297 254 143 100 pint:PI1442|5end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1363949..1364179_POSITIVE 257 258 211 70 27 pint:PI0517|5end_apparent_PorT_homolog_476261..476491_POSITIVE 255 210 163 169 129 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 252 77 43 77 30 pint:PI1830|5end_conserved_hypothetical_protein_1769439..1769669_POSITIVE 252 57 11 57 4 pint:PI0976|5end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_902297..902527_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 288 242 140 91 pint:PI2031|3end_hypothetical_protein_1986621..1986771_POSITIVE 287 68 21 126 76 pint:PI1688|3end_possible_GTPase_1603903..1604053_POSITIVE 279 243 204 135 94 pint:PI1776|3end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1709425..1709575_POSITIVE 271 247 204 84 39 pint:PI1001|3end_hypothetical_protein_923922..924072_POSITIVE 259 68 25 138 92 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 249 66 21 150 95 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 249 327 281 48 1 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 248 70 22 146 99 pint:PI2022|3end_hypothetical_protein_1978959..1979109_POSITIVE 247 339 295 47 14 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 246 230 184 139 92 pint:PI1156|3end_possible_glycerate_kinase_family_protein_1081781..1081931_POSITIVE 245 246 203 58 17 pint:PI1048|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_967193..967343_POSITIVE 244 57 23 128 92 pint:PI0705|3end_conserved_hypothetical_protein;_possible_lipoprotein_642271..642421_POSITIVE 241 209 162 92 41 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 240 349 306 101 53 pint:PI1568|3end_OmpA_family_protein_1491043..1491193_POSITIVE 238 227 181 70 26 pint:PI1366|3end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286647..1286797_POSITIVE 232 255 211 77 32 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 232 300 252 145 98 pint:PI0283|3end_Zn-dependent_peptidase_268881..269031_POSITIVE 230 55 13 106 65 pint:PI1695|3end_hypothetical_protein_1610310..1610460_POSITIVE 229 226 185 108 67 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 229 223 181 61 16 pint:PI0646|3end_hypothetical_protein_587205..587355_POSITIVE