Origin IGS: taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatccgttttaagaaatatataaacaaccaacagaggctgtccttccgagtttatgactcttctgggcagccccaatattttcttgtacggaagaatctgtctattctttcttctcgcttactgcaactcagcagcctcctctcgccactta Mask Tandem Repeat Region ================================================ taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Find is-nt database================================================ Query_seq: TF2889:TF2891|TF2889:TF2891:50S ribosomal protein L27:lipoprotein:->->:3078749..3078901 153 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2889:TF2891|TF2889:TF2891:50S ribosomal protein L27:lipoprotein:->->:3078749..3078901 153 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2889:TF2891|TF2889:TF2891:50S ribosomal protein L27:lipoprotein:->->:3078749..3078901 153 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 56 End: 151 ....................................................... M L P Y K K I L G L P R R V I N S E G Q P L L V V Y I F L K T D .. Protein_Len: 50 Strand: - Start: 2 End: 151 . L P S L L S S L Q L L R S S L I S L N K R V L F Y Q P Q G S S D Y V R F S L R Q Q N N I Y K K F R M .. Protein_Len: 33 Strand: - Start: 1 End: 99 L H R S S A A S N C Y A L L F F L C I R G Y L F I N P S G L L T M ...................................................... taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca 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================================================ taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -3.8 Tail_Score: -3.43676 Start: 42 End: 63 Full_Region: aatattttcttgtac ggaagaat ctgtct attctttc ttctcgcttactgca .........................................ggaagaatctgtctattctttc.......................................................................................... TransTerm Strand: + Conf: 61 HP_score: -2.5 Tail_Score: -4.33576 Start: 113 End: 128 Full_Region: ATAAACTCGGAAGGA CAGCC TCTGTT GGTTG TTTATATATTTCTTA ................................................................................................................CAGCCTCTGTTGGTTG......................... Find igs database================================================ Query_seq: TF2889:TF2891|TF2889:TF2891:50S ribosomal protein L27:lipoprotein:->->:3078749..3078901 153 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: tfor_TF2889_TF2891|50S ribosomal protein L27:lipoprotein|POSITIVE:POSITIVE|[3078749,3078901]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca taagtggcgagaggaggctgctgagttgcagtaagcgagaagaaagaatagacagattcttccgtacaagaaaatattggggctgcccagaagagtcataaactcggaaggacagcctctgttggttgtttatatatttcttaaaacggatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUGGCGAGAGGAGGCUGCUGAGUUGCAGUAAGCGAGAAGAAAGAAUAGACAGAUUCUUCCGUACAAGAAAAUAUUGGGGCUGCCCAGAAGAGUCAUAAACUCGGAAGGACAGCCUCUGUUGGUUGUUUAUAUAUUUCUUAAAACGGAUCA ((((..((.((.(((((((((((((((.......(((.((((((............)))))))))....((.....(((((....))))).....))...))))))).....)))))))).)).))..))))..................... (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCCGUUUUAAGAAAUAUAUAAACAACCAACAGAGGCUGUCCUUCCGAGUUUAUGACUCUUCUGGGCAGCCCCAAUAUUUUCUUGUACGGAAGAAUCUGUCUAUUCUUUCUUCUCGCUUACUGCAACUCAGCAGCCUCCUCUCGCCACUUA ...(((((..(((((((.((((...(........).((((((((....(((((...)))))....))))))))...))))))))))).))))).((((......))))..............((((......))))................. (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 128 82 117 65 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 380 120 74 67 10 tfor:TF1907|5end_ADP-heptose:LPS_heptosyltransferase_II_2061579..2061809_POSITIVE 373 39 3 52 16 tfor:TF1168|5end_hypothetical_protein_1248755..1248985_POSITIVE 364 48 3 118 70 tfor:TF3046|5end_hypothetical_protein_3274948..3275178_POSITIVE 360 123 82 71 23 tfor:TF3154|5end_conserved_hypothetical_protein_3389219..3389449_POSITIVE 360 47 4 66 14 tfor:TF2244|5end_possible_mobilization_protein_2419425..2419655_POSITIVE 354 128 81 83 37 tfor:TF0278|5end_conserved_hypothetical_protein_305570..305800_POSITIVE 351 121 81 86 51 tfor:TF0194|5end_hypothetical_protein_215193..215423_POSITIVE 347 39 3 196 160 tfor:TF2666|5end_hypothetical_protein_2841818..2842048_POSITIVE 347 39 3 52 15 tfor:TF1588|5end_hypothetical_protein_1702268..1702498_POSITIVE 346 39 7 212 174 tfor:TF1894|5end_hypothetical_protein_2046739..2046969_POSITIVE 342 39 3 42 2 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 339 49 2 47 2 tfor:TF2369|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2534554..2534784_POSITIVE 336 39 5 211 169 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 335 113 76 196 149 tfor:TF1683|5end_conserved_hypothetical_protein_1795787..1796017_POSITIVE 334 53 12 64 18 tfor:TF0489|5end_D-xylose-proton_symporter_511493..511723_POSITIVE 327 119 74 186 140 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 325 120 79 176 141 tfor:TF2887|5end_phosphomannomutase/phosphoglucomutase_3076327..3076557_POSITIVE 319 45 2 63 21 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 318 120 77 157 112 tfor:TF3078|5end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3306609..3306839_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 39 3 149 113 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 360 123 82 96 48 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 354 128 81 80 34 tfor:TF0277|3end_outer_membrane_protein_305647..305797_POSITIVE 352 39 3 149 110 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 351 39 3 149 113 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 351 39 3 149 113 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 351 121 81 53 18 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 350 129 85 63 8 tfor:TF1906|3end_conserved_hypothetical_protein_2061646..2061796_POSITIVE 339 127 83 148 106 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 325 120 79 39 4 tfor:TF2886|3end_RNA_methylase_SpoU_family_3076270..3076420_POSITIVE 324 40 6 47 11 tfor:TF3113|3end_hypothetical_protein_3349706..3349856_POSITIVE 324 57 16 138 94 tfor:TF0563|3end_signal_recognition_particle-docking_protein_FtsY_596243..596393_POSITIVE 316 124 81 79 27 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 314 48 4 103 54 tfor:TF2081|3end_phosphopantetheine_adenylyltransferase_2249031..2249181_POSITIVE 313 39 3 149 113 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 309 47 4 79 18 tfor:TF0855|3end_membrane_protein,_possible_exporter_908199..908349_POSITIVE 305 32 2 149 119 tfor:TF1466|3end_DNA_gyrase_modulator_1557084..1557234_POSITIVE 304 120 77 138 91 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 296 85 42 77 33 tfor:TF2356|3end_PAP2_superfamily_protein_2522409..2522559_POSITIVE 294 39 3 143 114 tfor:TF2763|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2948594..2948744_POSITIVE