Origin IGS: aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagcaattattgtaaagttttaaatggcttttaaagtccattcagcttatattaaaatcccacaaagcataagccttgtgggattttttaatagcaaatattatggtttgatacttaaaaaacagtt Mask Tandem Repeat Region ================================================ aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Find is-nt database================================================ Query_seq: PI2115:PI2116|PI2115:PI2116:hypothetical protein:fumarate reductase/succinate dehydrogenase, iron-sulfur protein:->->:2065226..2065354 129 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2115:PI2116|PI2115:PI2116:hypothetical protein:fumarate reductase/succinate dehydrogenase, iron-sulfur protein:->->:2065226..2065354 129 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2115:PI2116|PI2115:PI2116:hypothetical protein:fumarate reductase/succinate dehydrogenase, iron-sulfur protein:->->:2065226..2065354 129 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 3 End: 104 .. Q K K L I L G Y Y K S N F F G V L S I S Q P I K I Y A S H V K F A M ......................... aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta 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: 84 Start: 70 End: 99 .....................................................................TTTTAAAGTCCATTCAGCTTATATTAAAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -4.35116 Start: 45 End: 70 Full_Region: TTTGCTATTAAAAAA TCCCACAAGGC TTAT GCTTTGTGGGA TTTTAATATAAGCTG ............................................TCCCACAAGGCTTATGCTTTGTGGGA........................................................... TransTerm Strand: - Conf: 100 HP_score: -11.9 Tail_Score: -5.14563 Start: 45 End: 70 Full_Region: cagcttatattaaaa tcccacaaagc ataa gccttgtggga ttttttaatagcaaa ............................................tcccacaaagcataagccttgtggga........................................................... Find igs database================================================ Query_seq: PI2115:PI2116|PI2115:PI2116:hypothetical protein:fumarate reductase/succinate dehydrogenase, iron-sulfur protein:->->:2065226..2065354 129 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: pint_PI2115_PI2116|hypothetical protein:fumarate reductase/succinate dehydrogenase, iron-sulfur protein|POSITIVE:POSITIVE|[2065226,2065354]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta aactgttttttaagtatcaaaccataatatttgctattaaaaaatcccacaaggcttatgctttgtgggattttaatataagctgaatggactttaaaagccatttaaaactttacaataattgcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGUUUUUUAAGUAUCAAACCAUAAUAUUUGCUAUUAAAAAAUCCCACAAGGCUUAUGCUUUGUGGGAUUUUAAUAUAAGCUGAAUGGACUUUAAAAGCCAUUUAAAACUUUACAAUAAUUGCUUUA .(((........))).................((.((((.(((((((((((((((....))))))))))))))).........(((((((.((.....)))))))))...........)))).)).... (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCAAUUAUUGUAAAGUUUUAAAUGGCUUUUAAAGUCCAUUCAGCUUAUAUUAAAAUCCCACAAAGCAUAAGCCUUGUGGGAUUUUUUAAUAGCAAAUAUUAUGGUUUGAUACUUAAAAAACAGUU ..........(((((.((((.((((((((((.....))))......(((......((((((((((((.((....)).)))))))))))).....)))..........)))))).)))).....))))). (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 88 41 216 149 pint:PI0062|5end_endopeptidase_60963..61193_POSITIVE 291 74 40 160 126 pint:PI0640|5end_conserved_hypothetical_protein_583289..583519_POSITIVE 247 72 36 225 183 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 240 100 51 149 104 pint:PI0922|5end_conserved_hypothetical_protein_852844..853074_POSITIVE 238 90 45 110 72 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 237 100 51 47 6 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 235 88 45 96 54 pint:PI2077|5end_hypothetical_protein_2035892..2036122_POSITIVE 228 67 21 78 38 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 226 94 51 197 154 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 218 89 41 67 25 pint:PI1399|5end_hypothetical_protein_1320573..1320803_POSITIVE 217 86 46 57 12 pint:PI2062|5end_type_I_restriction-modification_system_2021658..2021888_POSITIVE 217 90 45 60 15 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 217 107 61 33 1 pint:PI0368|5end_hypothetical_protein_339582..339812_POSITIVE 217 68 45 154 128 pint:PI0208|5end_possible_peptidase,_M23/M37_family_200676..200906_POSITIVE 214 90 46 231 194 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 214 90 46 143 106 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 209 99 51 122 78 pint:PI1953|5end_possible_ABC-type_permease_1907135..1907365_POSITIVE 209 91 52 55 5 pint:PI1939|5end_hypothetical_protein_1896428..1896658_POSITIVE 207 90 47 169 126 pint:PI2118|5end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_N-terminal_2066466..2066696_POSITIVE 207 84 50 201 168 pint:PI0541|5end_GTP-binding_protein,_GTP1/OBG_family_493760..493990_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 78 33 56 8 pint:PI2115|3end_hypothetical_protein_2065165..2065315_POSITIVE 243 89 52 92 55 pint:PI0326|3end_ISPg3-related_transposase_307768..307918_POSITIVE 240 100 51 144 99 pint:PI0921|3end_acyltransferase_852919..853069_POSITIVE 238 90 45 50 12 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 226 94 51 120 77 pint:PI0894|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_(2-oxoglutarate-ferredoxin_oxidoreductase)_826350..826500_POSITIVE 218 89 41 86 44 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 217 68 45 150 124 pint:PI0207|3end_conserved_hypothetical_protein_200752..200902_POSITIVE 215 68 44 52 18 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 212 100 51 107 58 pint:PI0924|3end_possible_glycosyl_hydrolase_855953..856103_POSITIVE 211 93 53 149 98 pint:PI1388|3end_transcriptional_regulator,_LuxR_family_1310024..1310174_POSITIVE 211 74 38 64 28 pint:PI0794|3end_long-chain-fatty-acid--CoA_ligase_732865..733015_POSITIVE 210 70 31 81 44 pint:PI1883|3end_conserved_hypothetical_protein;_possible_surface_protein_1826174..1826324_POSITIVE 210 98 51 106 43 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 209 68 38 49 18 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 207 73 39 70 33 pint:PI1503|3end_30S_ribosomal_protein_S15_1423780..1423930_POSITIVE 207 84 50 89 56 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 206 86 45 137 103 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 206 90 42 94 46 pint:PI1196|3end_hypothetical_protein_1113630..1113780_POSITIVE 203 89 46 133 76 pint:PI0243|3end_hypothetical_protein_240738..240888_POSITIVE 202 75 33 66 30 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE