Origin IGS: taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca .........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 tgattatccgcacttatacctaatcattttaacttttatgattatgcgcgtttgattttatttgtaagtgtttgatctgtaaacttgtattctgatgcgtgatgtctgtgtcttgttctttttctttttctgccggggtatttgctgttttatgtaaattatgttttttaatgtgtttctttagattggtatccaatctttttgaggggatttctgtccgatgccgacaggaagtacggttatcgctccattctctgctta Mask Tandem Repeat Region ================================================ taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Find is-nt database================================================ Query_seq: TF1815:TF1817|TF1815:TF1817:conserved hypothetical protein:hypothetical protein:->->:1957503..1957763 261 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1815:TF1817|TF1815:TF1817:conserved hypothetical protein:hypothetical protein:->->:1957503..1957763 261 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1815:TF1817|TF1815:TF1817:conserved hypothetical protein:hypothetical protein:->->:1957503..1957763 261 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 100 End: 201 ................................................................................................... M I Y I K Q Q I P R Q K K K K N K T Q T S R I R I Q V Y R S N T Y K ............................................................ Protein_Len: 60 Strand: + Start: 51 End: 230 .................................................. M P S K R L D T N L K K H I K K H N L H K T A N T P A E K E K E Q D T D I T H Q N T S L Q I K H L Q I K S N A H N H K S ............................... Protein_Len: 54 Strand: - Start: 2 End: 163 . L L S H L S L R V E Q R C R V S I G E F L N S V L R F F C M L F C L K C L V A F V G A S F S F S C S V S M M .................................................................................................. taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca 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: 85 Start: 178 End: 207 .................................................................................................................................................................................GTTTACAGATCAAACACTTACAAATAAAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -8.6 Tail_Score: -4.58685 Start: 64 End: 78 Full_Region: taatgtgtttcttta gattgg tat ccaatc tttttgaggggattt ...............................................................gattggtatccaatc....................................................................................................................................................................................... Find igs database================================================ Query_seq: TF1815:TF1817|TF1815:TF1817:conserved hypothetical protein:hypothetical protein:->->:1957503..1957763 261 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatctaaagaaacacattaaaaaacataatttacataaaacagcaaataccccggcagaaaaagaaaaagaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca Intra-Species Hit: Count: 1 Min: 1 Max: 261 Len: 261 Subject: tfor_TF1815_TF1817|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1957503,1957763]|261 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 118 Query Start:144 Query End:261 Subject Strand: POSITIVE Subject Start: 144 Subject End: 261 ...............................................................................................................................................gaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca ...............................................................................................................................................gaacaagacacagacatcacgcatcagaatacaagtttacagatcaaacacttacaaataaaatcaaacgcgcataatcataaaagttaaaatgattaggtataagtgcggataatca HSP 2 e-value: 9.0E-37 bit: 155.0 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatc....................................................................................................................................................................................... taagcagagaatggagcgataaccgtacttcctgtcggcatcggacagaaatcccctcaaaaagattggataccaatc....................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAGAGAAUGGAGCGAUAACCGUACUUCCUGUCGGCAUCGGACAGAAAUCCCCUCAAAAAGAUUGGAUACCAAUCUAAAGAAACACAUUAAAAAACAUAAUUUACAUAAAACAGCAAAUACCCCGGCAGAAAAAGAAAAAGAACAAGACACAGACAUCACGCAUCAGAAUACAAGUUUACAGAUCAAACACUUACAAAUAAAAUCAAACGCGCAUAAUCAUAAAAGUUAAAAUGAUUAGGUAUAAGUGCGGAUAAUCA ......(((.((((........)))).))).(((((((....(((......)))........(((((((...)))))))..............................................)))))))..........................(((.(((((....((((..((((.......)))).........................(((((((..........))))))).))))..))))))))..... (-37.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAUCCGCACUUAUACCUAAUCAUUUUAACUUUUAUGAUUAUGCGCGUUUGAUUUUAUUUGUAAGUGUUUGAUCUGUAAACUUGUAUUCUGAUGCGUGAUGUCUGUGUCUUGUUCUUUUUCUUUUUCUGCCGGGGUAUUUGCUGUUUUAUGUAAAUUAUGUUUUUUAAUGUGUUUCUUUAGAUUGGUAUCCAAUCUUUUUGAGGGGAUUUCUGUCCGAUGCCGACAGGAAGUACGGUUAUCGCUCCAUUCUCUGCUUA .(((((...(((((((((..(((((((..........)))))))..((....))........))))))))).))))).........(((....((((.((((((.(((((...............(((((((.(((.((.(((((........)))))....................(((.(((((((...)))))))....))).((((....)))).)).))).)))))))))))).))))))..))))...)))... (-49.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 59 14 90 38 tfor:TF2512|5end_possible_abortive_infection_protein_2690247..2690477_POSITIVE 383 260 227 96 58 tfor:TF0269|5end_possible_transposase_element_297060..297290_POSITIVE 357 260 213 96 54 tfor:TF3047|5end_transposase_3275285..3275515_POSITIVE 357 260 213 96 54 tfor:TF2303|5end_conserved_hypothetical_protein_2458252..2458482_POSITIVE 357 260 213 96 54 tfor:TF2138|5end_conserved_hypothetical_protein_2314353..2314583_POSITIVE 357 260 213 96 54 tfor:TF1390|5end_possible_transposase_1462894..1463124_POSITIVE 357 260 213 96 54 tfor:TF0940|5end_transposase_981262..981492_POSITIVE 345 44 3 169 121 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 345 260 213 96 54 tfor:TF0198|5end_transposase_related_sequence_221054..221284_POSITIVE 344 48 12 103 60 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 337 58 13 189 149 tfor:TF0103|5end_rubredoxin_111850..112080_POSITIVE 335 58 16 76 31 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 332 39 4 186 146 tfor:TF1860|5end_aspartate_carbamoyltransferase,_catalytic_subunit_2016191..2016421_POSITIVE 331 47 3 210 145 tfor:TF3154|5end_conserved_hypothetical_protein_3389219..3389449_POSITIVE 331 58 11 188 140 tfor:TF0133|5end_transposase_element_145174..145404_POSITIVE 328 49 4 55 12 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 328 48 4 62 5 tfor:TF2446|5end_riboflavin-specific_deaminase_2622370..2622600_POSITIVE 326 48 1 189 131 tfor:TF0282|5end_probable_tonB-linked_outer_membrane_receptor_309101..309331_POSITIVE 325 57 17 64 31 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 323 58 16 219 160 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 50 6 132 96 tfor:TF2914|3end_hypothetical_protein_3109643..3109793_POSITIVE 357 260 213 123 81 tfor:TF2137|3end_hypothetical_protein_2314460..2314610_POSITIVE 357 260 213 89 47 tfor:TF1389|3end_hypothetical_protein_1462967..1463117_POSITIVE 344 48 12 55 12 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 328 49 4 52 9 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 323 56 12 50 9 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 323 45 4 46 7 tfor:TF0229|3end_beta-galactosidase_257003..257153_POSITIVE 320 52 11 82 40 tfor:TF1491|3end_mannosyltransferase_1592087..1592237_POSITIVE 319 50 6 147 99 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 316 60 13 82 33 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 312 55 11 150 90 tfor:TF2532|3end_ferric-uptake_regulator_2715708..2715858_POSITIVE 312 43 1 131 83 tfor:TF0581|3end_single_stranded_DNA-binding_protein_611932..612082_POSITIVE 310 49 2 108 70 tfor:TF2109|3end_possible_metallo-beta-lactamase_family_protein_2278960..2279110_POSITIVE 307 50 4 81 11 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 306 47 7 37 5 tfor:TF2475|3end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2654221..2654371_POSITIVE 301 44 4 57 2 tfor:TF1422|3end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1505823..1505973_POSITIVE 297 48 11 36 4 tfor:TF1804|3end_hypothetical_protein_1947957..1948107_POSITIVE 293 49 8 132 90 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 291 159 111 133 68 tfor:TF0244|3end_DNA_recombination_protein_275776..275926_POSITIVE 290 43 4 133 93 tfor:TF2345|3end_dGTP_triphosphohydrolase_2509774..2509924_POSITIVE