Origin IGS: ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta .........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 taagccgcaagaaaaggtagacggttttctggaaaaaggtctaccctttcttcaaaataggtctacctttttttcttcagcttagttctctgtgagaatgccacgaacgcagttagtcatagaatgcacggcattcgtttttaggctataaaacgttttaagcgtatataatttgttcggtagcattgcaagacgtcagtttgtacccacaaactgcgcccagctcccctcgttagattgtcggggagataagaccgtaatcactccgttctcatcggtcagtattcaagaattaagagacaatgaatcatctataatgattaactttcaaagaagcttatatgaacagatataataaaaagactgtcaaatggcagcaacagaataaggaagagcagaagatgaa Mask Tandem Repeat Region ================================================ ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaccgtctaccttttcttgcggctta Find is-nt database================================================ Query_seq: TF1631:TF1632|TF1631:TF1632:hypothetical protein:conserved hypothetical protein:->->:1743594..1743999 406 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1631:TF1632|TF1631:TF1632:hypothetical protein:conserved hypothetical protein:->->:1743594..1743999 406 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1631:TF1632|TF1631:TF1632:hypothetical protein:conserved hypothetical protein:->->:1743594..1743999 406 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 221 End: 322 ............................................................................................................................................................................................................................ M L P N K L Y T L K T F Y S L K T N A V H S M T N C V R G I L T E N .................................................................................... Protein_Len: 60 Strand: - Start: 55 End: 234 ...................................................... I Q E Y L S R Q F N I M I S S E N D R L E Q I S V S S F P T I V T K D G R C D L S P L Q A C N T P V F Q R R A I S G F M ............................................................................................................................................................................ ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta 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: 26 End: 55 .........................GTTGCTGCCATTTGACAGTCTTTTTATTAT............................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -2.9 Tail_Score: -3.42699 Start: 139 End: 165 Full_Region: ccctcgttagattgt cggggagataa gaccg taatcactccg ttctcatcggtcagt ..........................................................................................................................................cggggagataagaccgtaatcactccg................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 70 HP_score: -5.1 Tail_Score: -4.64766 Start: 270 End: 286 Full_Region: aacgcagttagtcat agaatgc acg gcattcg tttttaggctataaa .............................................................................................................................................................................................................................................................................agaatgcacggcattcg........................................................................................................................ TransTerm Strand: - Conf: 74 HP_score: -8.6 Tail_Score: -3.38378 Start: 271 End: 285 Full_Region: acgcagttagtcata gaatgc acg gcattc gtttttaggctataa ..............................................................................................................................................................................................................................................................................gaatgcacggcattc......................................................................................................................... Find igs database================================================ Query_seq: TF1631:TF1632|TF1631:TF1632:hypothetical protein:conserved hypothetical protein:->->:1743594..1743999 406 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Intra-Species Hit: Count: 1 Min: 1 Max: 406 Len: 406 Subject: tfor_TF1631_TF1632|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1743594,1743999]|406 HSP 1 e-value: 0.0 bit: 763.0 Len: 406 Query Start:1 Query End:406 Subject Strand: POSITIVE Subject Start: 1 Subject End: 406 ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagnnnnnnnggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta ttcatcttctgctcttccttattctgttgctgccatttgacagtctttttattatatctgttcatataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaagaaaaaaaggtagacctattttgaagaaagggtagacctttttccagaaaaccgtctaccttttcttgcggctta Inter-species Hit: Count: 2 Min: 66 Max: 332 Len: 267 Subject: pint_PI1543_PI1544|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1463342,1463646]|305 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 267 Query Start:66 Query End:332 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 .................................................................ataagcttctttgaaagttaatcattatagatgattcattgtctcttaattcttgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatatacgcttaaaacgttttatagcctaaaaacgaatgccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagctgaag.......................................................................... .................................................................ataagtttccttgaaagtttatcattgtagatgattcattgtttcttaattcctgaatactgaccgatgagaacggagtgattacggtcttatctccccgacaatcgaacgaggggagcaaga-gcagtttgtgggtacaaactgacgtcttgcaatgctaccgaacaaattatttacgcttaaaacgttttatagcctaaaaatgaattccgtgcattctatgactaactgcgttcgtggcattctcacagagaactaagccgaag.......................................................................... Subject: pint_PI0745_PI0746|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[675731,676110]|380 HSP 1 e-value: 2.0E-23 bit: 111.0 Len: 104 Query Start:125 Query End:228 Subject Strand: NEGATIVE Subject Start: 180 Subject End: 281 ............................................................................................................................ctgaccgatgagaacggagtgattacggtcttatctccccgacaatctaacgaggggagctgggcgcagtttgtgggtacaaactgacgtcttgcaatgctacc.................................................................................................................................................................................. ............................................................................................................................ctgaccgatgagaacggagtgattacggtctaacct-cccgataattaaacgaggagagc-aagcgcagtttgtgggtacaaactgacgtcttgcaatgctacc.................................................................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGCUUCUUUGAAAGUUAAUCAUUAUAGAUGAUUCAUUGUCUCUUAAUUCUUGAAUACUGACCGAUGAGAACGGAGUGAUUACGGUCUUAUCUCCCCGACAAUCUAACGAGGGGAGCUGGGCGCAGUUUGUGGGUACAAACUGACGUCUUGCAAUGCUACCGAACAAAUUAUAUACGCUUAAAACGUUUUAUAGCCUAAAAACGAAUGCCGUGCAUUCUAUGACUAACUGCGUUCGUGGCAUUCUCACAGAGAACUAAGCUGAAG .....((((...((.(((.(((((((...))))))).))).)).((((.(((((.......(((((.(((..((...))..)))))))).....(((((.....((....)))))))((.(((((((((((((....)))))))).))))).)).(((((((.((((...(((((.(((.......)))..))))).........((((((...)))))).............))))))))))).......))))).))))..)))) (-67.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCAGCUUAGUUCUCUGUGAGAAUGCCACGAACGCAGUUAGUCAUAGAAUGCACGGCAUUCGUUUUUAGGCUAUAAAACGUUUUAAGCGUAUAUAAUUUGUUCGGUAGCAUUGCAAGACGUCAGUUUGUACCCACAAACUGCGCCCAGCUCCCCUCGUUAGAUUGUCGGGGAGAUAAGACCGUAAUCACUCCGUUCUCAUCGGUCAGUAUUCAAGAAUUAAGAGACAAUGAAUCAUCUAUAAUGAUUAACUUUCAAAGAAGCUUAU ....(((((.((((((...)))))).....(((...((((((((((.((((((..(((...((((((((((((((..((((..(((........)))..))))..))))).))).)))))).((((((((....)))))))).)))...((((((.((......))..))))))....(((((..................))))).))))))........(((((.......)).)))...)))))))))))))....)))))... (-68.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 159 116 86 38 tfor:TF2243|5end_possible_mobilization_protein_2417384..2417614_POSITIVE 382 139 97 52 5 tfor:TF2916|5end_conserved_hypothetical_protein_3111559..3111789_POSITIVE 370 159 114 61 21 tfor:TF1657|5end_lauroyl/myristoyl_acyltransferase_1772425..1772655_POSITIVE 366 153 114 215 187 tfor:TF2468|5end_hypothetical_protein_2646287..2646517_POSITIVE 356 139 94 91 45 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 350 158 113 226 167 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 345 138 91 91 33 tfor:TF2094|5end_6-phosphofructokinase_2262437..2262667_POSITIVE 345 159 111 213 157 tfor:TF0712|5end_TPR-repeat-containing_protein_761348..761578_POSITIVE 344 137 97 80 40 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 344 152 111 66 26 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 337 146 101 63 20 tfor:TF2644|5end_possible_thiamine_pyrophosphokinase_2813058..2813288_POSITIVE 337 126 83 134 79 tfor:TF0684|5end_conserved_hypothetical_protein_728853..729083_POSITIVE 337 243 207 44 5 tfor:TF0428|5end_methylmalonyl-CoA_mutase,_beta_subunit_447809..448039_POSITIVE 335 248 205 217 171 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 333 146 102 68 22 tfor:TF1121|5end_ABC_transporter_ATP-binding/permease_component,_bacteriocin/lantibiotic_exporter_1195183..1195413_POSITIVE 330 238 196 66 15 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 330 238 196 176 125 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 327 148 109 53 15 tfor:TF0377|5end_FtsK/SpoIIIE_family_cell_division_protein_394944..395174_POSITIVE 326 127 82 219 180 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 326 121 85 71 43 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 160 113 71 18 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 370 159 114 61 21 tfor:TF1656|3end_possible_2-methylthioadenine_synthetase_1772505..1772655_POSITIVE 343 158 113 93 41 tfor:TF1750|3end_hypothetical_protein_1886566..1886716_POSITIVE 342 138 94 62 2 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 337 126 83 115 60 tfor:TF0683|3end_conserved_hypothetical_protein_728914..729064_POSITIVE 336 129 85 62 14 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 333 146 102 61 15 tfor:TF1120|3end_conserved_hypothetical_protein_1195256..1195406_POSITIVE 327 148 109 53 15 tfor:TF0376|3end_conserved_hypothetical_protein_395024..395174_POSITIVE 323 159 111 72 20 tfor:TF0961|3end_translation_initiation_inhibitor,_endoribonuclease_activity_1011673..1011823_POSITIVE 319 159 111 151 108 tfor:TF2328|3end_conserved_hypothetical_protein_2488349..2488499_POSITIVE 318 136 91 82 37 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 312 118 72 146 97 tfor:TF2572|3end_50S_ribosomal_protein_L30_2743334..2743484_POSITIVE 312 152 115 38 2 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 311 136 98 137 101 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 310 102 64 53 21 tfor:TF2235|3end_tetracycline_resistance_protein_related_to_CtnDOT_tetQ_2410260..2410410_POSITIVE 309 136 93 60 13 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 309 160 111 84 50 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 306 100 59 130 83 tfor:TF1282|3end_tRNA_delta-2_isopentenylpyrophosphate_transferase_1367431..1367581_POSITIVE 306 141 104 80 37 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 305 100 51 122 73 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE