Origin IGS: gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctgaccgacactcctatacgggaaaagaggctacgttccgaggattattccttggaacgcagcctctttcgttagaaaaggaacctaatcggagaggaaagagcataaggaggggttataaactcggc Mask Tandem Repeat Region ================================================ gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Find is-nt database================================================ Query_seq: PG0158:PG0159|PG0158:PG0159:competence protein F-related protein:endopeptidase PepO:-><-:181056..181184 129 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0158:PG0159|PG0158:PG0159:competence protein F-related protein:endopeptidase PepO:-><-:181056..181184 129 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0158:PG0159|PG0158:PG0159:competence protein F-related protein:endopeptidase PepO:-><-:181056..181184 129 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 23 End: 112 ...................... M L F P L R L G S F S N E R G C V P R N N P R N V A S F P V ................. gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc 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================================================ gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -21.6 Tail_Score: -4.16943 Start: 63 End: 102 Full_Region: CCTTTTCTAACGAAA GAGGCTGCGTTCCAAGGA ATAA TCCTCGGAACGTAGCCTC TTTTCCCGTATAGGA ..............................................................GAGGCTGCGTTCCAAGGAATAATCCTCGGAACGTAGCCTC........................... TransTerm Strand: - Conf: 100 HP_score: -21.6 Tail_Score: -3.90112 Start: 63 End: 102 Full_Region: tcctatacgggaaaa gaggctacgttccgagga ttat tccttggaacgcagcctc tttcgttagaaaagg ..............................................................gaggctacgttccgaggattattccttggaacgcagcctc........................... Find igs database================================================ Query_seq: PG0158:PG0159|PG0158:PG0159:competence protein F-related protein:endopeptidase PepO:-><-:181056..181184 129 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002950_PG0158_PG0159|competence protein F-related protein:endopeptidase PepO|POSITIVE:NEGATIVE|[181056,181184]|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 gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc gccgagtttataacccctccttatgctctttcctctccgattaggttccttttctaacgaaagaggctgcgttccaaggaataatcctcggaacgtagcctcttttcccgtataggagtgtcggtcagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGAGUUUAUAACCCCUCCUUAUGCUCUUUCCUCUCCGAUUAGGUUCCUUUUCUAACGAAAGAGGCUGCGUUCCAAGGAAUAAUCCUCGGAACGUAGCCUCUUUUCCCGUAUAGGAGUGUCGGUCAGC (((((.........(.(((((.((((............((..((....))..))....(((((((((((((((((.((((....)))).)))))))))))))))))...))))))))).)))))).... (-50.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGACCGACACUCCUAUACGGGAAAAGAGGCUACGUUCCGAGGAUUAUUCCUUGGAACGCAGCCUCUUUCGUUAGAAAAGGAACCUAAUCGGAGAGGAAAGAGCAUAAGGAGGGGUUAUAAACUCGGC (((((..(((.(((((..((((...((((((((.(((((((((((....))))))))))).))))))))))))...........(((........)))..........)))))..)))......))))) (-48.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 108 61 76 31 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 381 55 14 209 159 NC_002950:PG2035|5end_tRNA_(guanine-N(1)-)-methyltransferase_2135852..2136082_POSITIVE 357 100 53 154 102 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 356 104 61 176 134 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 352 100 56 213 168 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 352 68 24 107 51 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 337 110 63 68 14 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 327 109 64 216 166 NC_002950:PG1997|5end_hypothetical_protein_2086831..2087061_POSITIVE 323 49 1 160 116 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 318 102 61 174 128 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 313 110 66 55 1 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 312 80 31 203 155 NC_002950:PG1467|5end_methlytransferase,_UbiE/COQ5_family_1543210..1543440_POSITIVE 311 95 59 61 8 NC_002950:PG0745|5end_lactoylglutathione_lyase,_putative_792380..792610_NEGATIVE 310 49 1 51 6 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 310 49 1 209 164 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 309 70 23 213 157 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 309 99 51 167 127 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 308 100 59 97 63 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 307 80 35 215 161 NC_002950:PG1647|5end_cardiolipin_synthetase_1726273..1726503_POSITIVE 302 102 63 212 173 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 106 61 49 7 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 403 108 61 79 34 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 380 117 77 39 3 NC_002950:PG0158|3end_competence_protein_F-related_protein_180995..181145_POSITIVE 362 108 61 68 22 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 356 104 61 63 21 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 354 120 78 74 22 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE 352 100 56 76 25 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 352 100 56 66 21 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 352 68 24 77 21 NC_002950:PG1017|3end_pyruvate_phosphate_dikinase_1078944..1079094_POSITIVE 350 107 62 54 13 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 345 106 62 43 6 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 337 110 63 71 17 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 334 110 61 140 97 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 332 69 24 81 36 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 332 110 61 73 28 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 326 102 63 63 21 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 321 80 32 90 37 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 320 108 62 58 26 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 318 90 41 145 91 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 318 102 61 77 31 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE