Origin IGS: tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat .........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 atccaacgacagcatagattagaacttttcatagacgcgagtagcaatagggcgagacattccatcagagagaatgtactcgcccttactacatttgagaaggaaaccggaggtcttatgcggcctccataaatgaattttgaaacagccccgcgatcaatcgtggatcctttcccccgactcaatttgtttgtatttcatctcggcataaaaatggaatttttaattgcatttataggtagggtgtgcaaatgcgcaatggtagtttttatgtttgggagaaagtcggaaaatagttacttttgtttttatgcataacgattgcttttgcccatttgatgggcgaaaacaaatatgatcacagtaaagaca Mask Tandem Repeat Region ================================================ tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Find is-nt database================================================ Query_seq: PG0418:PG0419|PG0418:PG0419:ATP-dependent Clp protease, proteolytic subunit:hypothetical protein:<-<-:459420..459791 372 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0418:PG0419|PG0418:PG0419:ATP-dependent Clp protease, proteolytic subunit:hypothetical protein:<-<-:459420..459791 372 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0418:PG0419|PG0418:PG0419:ATP-dependent Clp protease, proteolytic subunit:hypothetical protein:<-<-:459420..459791 372 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 19 End: 147 .................. M C F R P S N G Q K Q S L C I K T K V T I F R L S P K H K N Y H C A F A H P T Y K C N ................................................................................................................................................................................................................................. Protein_Len: 39 Strand: + Start: 235 End: 351 .......................................................................................................................................................................................................................................... M H L W R P H K T S G F L L K C S K G E Y I L S D G M S R P I A T R V Y E K F ..................... Protein_Len: 60 Strand: + Start: 188 End: 370 ........................................................................................................................................................................................... M S R G K G S T I D R G A V S K F I Y G G R I R P P V S F S N V V R A S T F S L M E C L A L L L L A S M K S S N L C C R .. Protein_Len: 43 Strand: - Start: 244 End: 372 ................................................................................................................................................................................................................................................... P P R M L G G T E K E F T T L A L V N E R I S H R A R N S S A D I F L E L R H Q R Q M Protein_Len: 60 Strand: - Start: 58 End: 240 ......................................................... Y F C F Y S N E S K R G F M F V V M A C K C V R G I F A I L F E M K I G L H F V F L N L R P F P D V I S R P A T E F N M .................................................................................................................................... tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat 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================================================ tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.2 Tail_Score: -3.35438 Start: 245 End: 271 Full_Region: TCAAAATTCATTTAT GGAGGCCGCA TAAGACC TCCGGTTTCC TTCTCAAATGTAGTA ....................................................................................................................................................................................................................................................GGAGGCCGCATAAGACCTCCGGTTTCC..................................................................................................... TransTerm Strand: + Conf: 73 HP_score: -9.4 Tail_Score: -3.21925 Start: 286 End: 325 Full_Region: CTTCTCAAATGTAGT AAGGGCGAGTACATTCTCT CTG ATGGAATGTCTCGCCCTA TTGCTACTCGCGTCT .............................................................................................................................................................................................................................................................................................AAGGGCGAGTACATTCTCTCTGATGGAATGTCTCGCCCTA............................................... TransTerm Strand: + Conf: 83 HP_score: -12.0 Tail_Score: -3.17229 Start: 288 End: 323 Full_Region: TCTCAAATGTAGTAA GGGCGAGTACATTCTCT CTG ATGGAATGTCTCGCCC TATTGCTACTCGCGT ...............................................................................................................................................................................................................................................................................................GGGCGAGTACATTCTCTCTGATGGAATGTCTCGCCC................................................. TransTerm Strand: - Conf: 73 HP_score: -9.9 Tail_Score: -3.25088 Start: 288 End: 323 Full_Region: acgcgagtagcaata gggcgagacattc catcagaga gaatgtactcgccc ttactacatttgaga ...............................................................................................................................................................................................................................................................................................gggcgagacattccatcagagagaatgtactcgccc................................................. Find igs database================================================ Query_seq: PG0418:PG0419|PG0418:PG0419:ATP-dependent Clp protease, proteolytic subunit:hypothetical protein:<-<-:459420..459791 372 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Intra-Species Hit: Count: 1 Min: 1 Max: 372 Len: 372 Subject: NC_002950_PG0418_PG0419|ATP-dependent Clp protease, proteolytic subunit:hypothetical protein|NEGATIVE:NEGATIVE|[459420,459791]|372 HSP 1 e-value: 0.0 bit: 737.0 Len: 372 Query Start:1 Query End:372 Subject Strand: POSITIVE Subject Start: 1 Subject End: 372 tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat tgtctttactgtgatcatatttgttttcgcccatcaaatgggcaaaagcaatcgttatgcataaaaacaaaagtaactattttccgactttctcccaaacataaaaactaccattgcgcatttgcacaccctacctataaatgcaattaaaaattccatttttatgccgagatgaaatacaaacaaattgagtcgggggaaaggatccacgattgatcgcggggctgtttcaaaattcatttatggaggccgcataagacctccggtttccttctcaaatgtagtaagggcgagtacattctctctgatggaatgtctcgccctattgctactcgcgtctatgaaaagttctaatctatgctgtcgttggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUUACUGUGAUCAUAUUUGUUUUCGCCCAUCAAAUGGGCAAAAGCAAUCGUUAUGCAUAAAAACAAAAGUAACUAUUUUCCGACUUUCUCCCAAACAUAAAAACUACCAUUGCGCAUUUGCACACCCUACCUAUAAAUGCAAUUAAAAAUUCCAUUUUUAUGCCGAGAUGAAAUACAAACAAAUUGAGUCGGGGGAAAGGAUCCACGAUUGAUCGCGGGGCUGUUUCAAAAUUCAUUUAUGGAGGCCGCAUAAGACCUCCGGUUUCCUUCUCAAAUGUAGUAAGGGCGAGUACAUUCUCUCUGAUGGAAUGUCUCGCCCUAUUGCUACUCGCGUCUAUGAAAAGUUCUAAUCUAUGCUGUCGUUGGAU (((.((((.(((.((.((..(((((((.((((((...)))))).)))))))..)).))))))))).))).......((.((..(((((((...........................(((((((.............)))))))............((((((......))))))...............)))))))..)).)).(((((((((.(((...((((((.(((((............((((((((...........)))))))).........((((((((((((((.(((((((.......)))))))))))))))..)))))).........))))))))))).)))......)))).))))) (-96.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCAACGACAGCAUAGAUUAGAACUUUUCAUAGACGCGAGUAGCAAUAGGGCGAGACAUUCCAUCAGAGAGAAUGUACUCGCCCUUACUACAUUUGAGAAGGAAACCGGAGGUCUUAUGCGGCCUCCAUAAAUGAAUUUUGAAACAGCCCCGCGAUCAAUCGUGGAUCCUUUCCCCCGACUCAAUUUGUUUGUAUUUCAUCUCGGCAUAAAAAUGGAAUUUUUAAUUGCAUUUAUAGGUAGGGUGUGCAAAUGCGCAAUGGUAGUUUUUAUGUUUGGGAGAAAGUCGGAAAAUAGUUACUUUUGUUUUUAUGCAUAACGAUUGCUUUUGCCCAUUUGAUGGGCGAAAACAAAUAUGAUCACAGUAAAGACA .......((..(((((((...((.....))...((((.(((((((...(((((((((((((((......).)))))).))))))))..........(..(((((....(((((((......)))))))......................((((((....)))))).)))))..).(((((.(((.....)))..((((.(((((((((((((((...........((((........))))..(((((....)))))......))))))))).)))))))))))))))......))))))).))))))))))).......(((.((((((((((...)))))))))).)))......))............ (-107.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 884 130 81 221 172 NC_002950:PG0418|5end_ATP-dependent_Clp_protease,_proteolytic_subunit_459329..459559_NEGATIVE 389 230 189 212 162 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 369 336 305 230 196 NC_002950:PG1810|5end_2-oxoglutarate_oxidoreductase,_beta_subunit_1906757..1906987_NEGATIVE 357 267 221 200 157 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 353 228 190 153 97 NC_002950:PG2200|5end_TPR_domain_protein_2308807..2309037_NEGATIVE 346 260 213 54 6 NC_002950:PG1771|5end_phenylalanyl-tRNA_synthetase_alpha_subunit_1858038..1858268_POSITIVE 345 340 295 48 2 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 339 230 189 67 22 NC_002950:PG1826|5end_hypothetical_protein_1920065..1920295_NEGATIVE 334 238 197 80 21 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 332 339 299 92 41 NC_002950:PG1994|5end_D-tyrosyl-tRNA_deacylase_2085127..2085357_POSITIVE 331 328 283 142 86 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 331 319 271 74 22 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 329 229 190 96 56 NC_002950:PG0013|5end_hypothetical_protein_15591..15821_POSITIVE 327 289 245 223 182 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 324 339 299 84 47 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 323 221 187 72 41 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 321 346 303 95 36 NC_002950:PG0135|5end_dimethyladenosine_transferase_157943..158173_NEGATIVE 320 224 187 152 108 NC_002950:PG1254|5end_acetyltransferase,_GNAT_family_1332121..1332351_NEGATIVE 317 231 192 172 119 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 314 225 192 70 24 NC_002950:PG0358|5end_aspartate_carbamoyltransferase_regulatory_subunit_392367..392597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 230 189 123 73 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 367 227 191 43 2 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 353 228 190 117 61 NC_002950:PG2201|3end_peptide_deformylase_2308843..2308993_NEGATIVE 337 339 292 85 28 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 332 339 299 85 34 NC_002950:PG1993|3end_excinuclease_ABC,_C_subunit_2085200..2085350_POSITIVE 329 229 190 86 46 NC_002950:PG0012|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_15661..15811_POSITIVE 328 322 284 151 119 NC_002950:PG0474|3end_low-specificity_L-threonine_aldolase_515011..515161_NEGATIVE 326 230 187 149 93 NC_002950:PG1732|3end_integrase/recombinase_XerD_1821177..1821327_POSITIVE 323 221 187 64 33 NC_002950:PG0142|3end_SpoOJ_regulator_protein_164755..164905_NEGATIVE 322 306 261 89 50 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 320 224 187 145 101 NC_002950:PG1255|3end_recombination_protein_RecR_1332128..1332278_NEGATIVE 314 225 192 57 11 NC_002950:PG0357|3end_aspartate_carbamoyltransferase_catalytic_subunit_392434..392584_POSITIVE 309 339 294 123 64 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 308 338 291 62 5 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 307 329 287 58 21 NC_002950:PG2074|3end_hypothetical_protein_2174503..2174653_NEGATIVE 307 329 287 58 21 NC_002950:PG1670|3end_hypothetical_protein_1755695..1755845_NEGATIVE 307 329 287 58 21 NC_002950:PG1265|3end_hypothetical_protein_1345024..1345174_NEGATIVE 307 329 287 58 21 NC_002950:PG0102|3end_hypothetical_protein_121241..121391_POSITIVE 306 370 326 81 33 NC_002950:PG1373|3end_hypothetical_protein_1455105..1455255_POSITIVE 305 325 290 150 111 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE