Origin IGS: gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta .........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 tagtgcttcgtactcatctgcgtgtctcattgccaatgatatcggttatgagttctgctctgaaacagaatcagggcaggtaatccccctttaccccctctttttgtatgccttccctcatccgtaaaaacacgtcactctccaatccggcaaagccgtgaaaatatccttttctttgtttttctcggaatcgacctgaaatgaaaaatcatatatttatatgattttatatgtaaaaaaatatttcatgtttagatcaaaagcacttgtttttctcctgtttttttagaaatattttgcaatatattaatttaaagcattatatagatttgaaacgggttatttttttgtgatatgttttgttttttttacagcatagaaatcatatatttatatgattgacac Mask Tandem Repeat Region ================================================ gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Find is-nt database================================================ Query_seq: TF1593:TF1594|TF1593:TF1594:hypothetical protein:hypothetical protein:->->:1709638..1710042 405 gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1593:TF1594|TF1593:TF1594:hypothetical protein:hypothetical protein:->->:1709638..1710042 405 gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1593:TF1594|TF1593:TF1594:hypothetical protein:hypothetical protein:->->:1709638..1710042 405 gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 164 End: 268 ................................................................................................................................................................... M F L H I K S Y K Y M I F H F R S I P R K T K K R I F S R L C R I G E ......................................................................................................................................... Protein_Len: 32 Strand: + Start: 190 End: 285 ............................................................................................................................................................................................. M Y D F S F Q V D S E K N K E K D I F T A L P D W R V T C F Y G ........................................................................................................................ Protein_Len: 43 Strand: + Start: 204 End: 332 ........................................................................................................................................................................................................... M S G R F R E K Q R K G Y F H G F A G L E S D V F L R M R E G I Q K E G V K G D Y L P ......................................................................... Protein_Len: 32 Strand: - Start: 282 End: 377 ......................................................................................................................................................................................................................................................................................... P H P F A Y L F L P Y L P I V Q G S E T E S C F E Y G I D N A M ............................ Protein_Len: 44 Strand: - Start: 205 End: 336 ............................................................................................................................................................................................................ K L D I G L F V F F L I N E R S Q R I P S H R T K V S S P L C V F L P P L P P N G A R M ..................................................................... Protein_Len: 36 Strand: - Start: 56 End: 163 ....................................................... L F I V R K L D I Y H K L N I Y Q L I N R F F C S F F L H K Q D L C S M .................................................................................................................................................................................................................................................. gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta 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: 81 Start: 341 End: 370 ....................................................................................................................................................................................................................................................................................................................................................TTTCAGAGCAGAACTCATAACCGATATCAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -4.8 Tail_Score: -4.99134 Start: 182 End: 197 Full_Region: TTTTTACATATAAAA TCATAT AAAT ATATGA TTTTTCATTTCAGGT .....................................................................................................................................................................................TCATATAAATATATGA................................................................................................................................................................................................................ TransTerm Strand: - Conf: 67 HP_score: -2.9 Tail_Score: -4.96501 Start: 232 End: 246 Full_Region: atccggcaaagccgt gaaaa tatcc ttttc tttgtttttctcgga .......................................................................................................................................................................................................................................gaaaatatccttttc............................................................................................................................................................... Find igs database================================================ Query_seq: TF1593:TF1594|TF1593:TF1594:hypothetical protein:hypothetical protein:->->:1709638..1710042 405 gtgtcaatcatataaatatatgatttctatgctgtaaaaaaaacaaaacatatcacaaaaaaataacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta Intra-Species Hit: Count: 1 Min: 1 Max: 405 Len: 405 Subject: tfor_TF1593_TF1594|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1709638,1710042]|405 HSP 1 e-value: 1.0E-169 bit: 595.0 Len: 342 Query Start:64 Query End:405 Subject Strand: POSITIVE Subject Start: 64 Subject End: 405 ...............................................................taacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctnnnnnnncaggagaaaaacaagtgcttttgatctaaacatgaaatannnnnnnacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta ...............................................................taacccgtttcaaatctatataatgctttaaattaatatattgcaaaatatttctaaaaaaacaggagaaaaacaagtgcttttgatctaaacatgaaatatttttttacatataaaatcatataaatatatgatttttcatttcaggtcgattccgagaaaaacaaagaaaaggatattttcacggctttgccggattggagagtgacgtgtttttacggatgagggaaggcatacaaaaagagggggtaaagggggattacctgccctgattctgtttcagagcagaactcataaccgatatcattggcaatgagacacgcagatgagtacgaagcacta HSP 2 e-value: 7.0E-11 bit: 69.9 Len: 35 Query Start:1 Query End:35 Subject Strand: POSITIVE Subject Start: 1 Subject End: 35 gtgtcaatcatataaatatatgatttctatgctgt.................................................................................................................................................................................................................................................................................................................................................................................. gtgtcaatcatataaatatatgatttctatgctgt.................................................................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCAAUCAUAUAAAUAUAUGAUUUCUAUGCUGUAAAAAAAACAAAACAUAUCACAAAAAAAUAACCCGUUUCAAAUCUAUAUAAUGCUUUAAAUUAAUAUAUUGCAAAAUAUUUCUAAAAAAACAGGAGAAAAACAAGUGCUUUUGAUCUAAACAUGAAAUAUUUUUUUACAUAUAAAAUCAUAUAAAUAUAUGAUUUUUCAUUUCAGGUCGAUUCCGAGAAAAACAAAGAAAAGGAUAUUUUCACGGCUUUGCCGGAUUGGAGAGUGACGUGUUUUUACGGAUGAGGGAAGGCAUACAAAAAGAGGGGGUAAAGGGGGAUUACCUGCCCUGAUUCUGUUUCAGAGCAGAACUCAUAACCGAUAUCAUUGGCAAUGAGACACGCAGAUGAGUACGAAGCACUA ((((.(((((((((..((((((((((.((((.((((((((((........................((.((((.......((((..(((..((........))..)))..))))........)))).)).......((((....))))................))))))))))))))))))))))))..))))))))).(((((((...((((.((((((..........(((((.....))))).((((...))))..))))))..))))(((((((..(.(((((.....((.............(((((...(((......))))))))(((((((((....))))))).))....))....))))).)....)))))))..)))))))......)))).. (-85.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGCUUCGUACUCAUCUGCGUGUCUCAUUGCCAAUGAUAUCGGUUAUGAGUUCUGCUCUGAAACAGAAUCAGGGCAGGUAAUCCCCCUUUACCCCCUCUUUUUGUAUGCCUUCCCUCAUCCGUAAAAACACGUCACUCUCCAAUCCGGCAAAGCCGUGAAAAUAUCCUUUUCUUUGUUUUUCUCGGAAUCGACCUGAAAUGAAAAAUCAUAUAUUUAUAUGAUUUUAUAUGUAAAAAAAUAUUUCAUGUUUAGAUCAAAAGCACUUGUUUUUCUCCUGUUUUUUUAGAAAUAUUUUGCAAUAUAUUAAUUUAAAGCAUUAUAUAGAUUUGAAACGGGUUAUUUUUUUGUGAUAUGUUUUGUUUUUUUUACAGCAUAGAAAUCAUAUAUUUAUAUGAUUGACAC ..(((.(((((..(((...(((...(((((.(((.........))).)))))...)))..))).((((((..((((..(((((.......)))))))))..)))))).............((((.(((((((...............((((...)))).(((((.....)))))..)))))))..))))...........))))).(((((((((..(((((((((((.((((((((((((((...((((((((((..((((((....))))))..((((((((.......((((..(((..((........))..)))..))))......)))))))).......)))).))))))...)))))))))....))))))))))))))))..)))))))))..))) (-90.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 320 272 163 127 tfor:TF1528|5end_malate_dehydrogenase_1633287..1633517_POSITIVE 358 290 248 50 4 tfor:TF0946|5end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_989482..989712_POSITIVE 356 329 281 157 100 tfor:TF2066|5end_nucleotidyltransferase_family_protein_2231835..2232065_POSITIVE 345 296 256 74 22 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 344 330 284 66 13 tfor:TF2914|5end_hypothetical_protein_3109345..3109575_POSITIVE 344 327 284 88 49 tfor:TF1650|5end_integrase_1760039..1760269_POSITIVE 340 296 257 229 181 tfor:TF0141|5end_exodeoxyribonuclease_VII,_large_subunit_148422..148652_POSITIVE 339 348 304 231 180 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 335 290 241 208 144 tfor:TF2238|5end_conserved_hypothetical_protein_2414098..2414328_POSITIVE 333 290 244 51 8 tfor:TF2917|5end_conserved_hypothetical_protein_3112255..3112485_POSITIVE 333 297 255 73 27 tfor:TF0512|5end_2-oxoglutarate_oxidoreductase,_alpha_subunit_537111..537341_POSITIVE 331 340 294 210 158 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 331 296 257 203 143 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 329 289 246 83 28 tfor:TF1776|5end_urocanate_hydratase_1914660..1914890_POSITIVE 329 330 282 50 2 tfor:TF1603|5end_RNA_polymerase_ECF-type_sigma_factor_1717176..1717406_POSITIVE 325 321 282 41 4 tfor:TF1478|5end_membrane_fusion_efflux_protein_1571101..1571331_POSITIVE 325 289 241 78 31 tfor:TF0467|5end_acetyltransferase-related_protein_485936..486166_POSITIVE 322 295 255 199 154 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 322 289 241 179 128 tfor:TF1003|5end_conserved_hypothetical_protein;_possible_secreted_glycosylhydrolase_1058177..1058407_POSITIVE 321 290 245 201 156 tfor:TF2440|5end_conserved_hypothetical_protein;_possible_DNA_mismatch_repair_protein_2616858..2617088_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 296 254 71 36 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 345 296 256 67 15 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 344 327 284 88 49 tfor:TF1649|3end_hypothetical_protein_1760119..1760269_POSITIVE 342 349 304 147 94 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 338 349 304 105 52 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 337 349 304 126 75 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 336 295 257 128 78 tfor:TF0069|3end_conserved_hypothetical_protein_76881..77031_POSITIVE 333 297 255 61 15 tfor:TF0511|3end_hypothetical_protein_537179..537329_POSITIVE 331 340 294 80 28 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 325 321 282 63 26 tfor:TF1476|3end_outer_membrane_protein_P49_1571203..1571353_POSITIVE 321 297 251 126 82 tfor:TF2078|3end_dehydrogenase_2245471..2245621_POSITIVE 318 358 311 92 49 tfor:TF0485|3end_transposase_fragment_507624..507774_POSITIVE 316 330 282 67 23 tfor:TF1684|3end_zinc_protease_1800331..1800481_POSITIVE 316 399 367 147 108 tfor:TF1152|3end_permease,_major_facilitator_superfamily_1234618..1234768_POSITIVE 314 349 305 81 41 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 313 298 254 146 106 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 313 340 305 114 70 tfor:TF0779|3end_possible_outer_membrane_protein_831874..832024_POSITIVE 313 288 249 126 85 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 306 297 251 83 35 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 305 356 317 93 50 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE