Origin IGS: tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcagtaacacgggaaggggctctgcaaggagttcctttcttacaatggccgtacggacgacacaaaaggaaagaactgctttcgagtacagcaagtacaatacgaccattatccattcataaaccataacaattaaaaacaaca Mask Tandem Repeat Region ================================================ tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Find is-nt database================================================ Query_seq: PI0163:PI0164|PI0163:PI0164:conserved hypothetical protein:conserved hypothetical protein:->->:158471..158617 147 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0163:PI0164|PI0163:PI0164:conserved hypothetical protein:conserved hypothetical protein:->->:158471..158617 147 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0163:PI0164|PI0163:PI0164:conserved hypothetical protein:conserved hypothetical protein:->->:158471..158617 147 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 29 End: 145 ............................ M D N G R I V L A V L E S S S F L L C R P Y G H C K K G T P C R A P S R V T D .. Protein_Len: 48 Strand: + Start: 3 End: 146 .. M F L I V M V Y E W I M V V L Y L L Y S K A V L S F C V V R T A I V R K E L L A E P L P V L L I . Protein_Len: 40 Strand: - Start: 26 End: 145 ......................... S H I I T T N Y K S Y E F A T R E K Q T T R V A M T L F S S R A S G R G T N S M .. Protein_Len: 35 Strand: - Start: 19 End: 123 .................. P K H I S L P R I T S A T S S L L E K R K H R G Y P W Q L F P V G Q M ........................ tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta 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================================================ tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -4.3 Tail_Score: -3.3393 Start: 62 End: 76 Full_Region: GTACTTGCTGTACTC GAAAG CAGTT CTTTC CTTTTGTGTCGTCCG .............................................................GAAAGCAGTTCTTTC....................................................................... Find igs database================================================ Query_seq: PI0163:PI0164|PI0163:PI0164:conserved hypothetical protein:conserved hypothetical protein:->->:158471..158617 147 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: pint_PI0163_PI0164|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[158471,158617]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta tgttgtttttaattgttatggtttatgaatggataatggtcgtattgtacttgctgtactcgaaagcagttctttccttttgtgtcgtccgtacggccattgtaagaaaggaactccttgcagagccccttcccgtgttactgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUGUUUUUAAUUGUUAUGGUUUAUGAAUGGAUAAUGGUCGUAUUGUACUUGCUGUACUCGAAAGCAGUUCUUUCCUUUUGUGUCGUCCGUACGGCCAUUGUAAGAAAGGAACUCCUUGCAGAGCCCCUUCCCGUGUUACUGAUUA ................(((((...........(((((((((((((.((((.....))))..(((((.....)))))..............)))))))))))))....((((..(((......)))..)))).))))).......... (-31.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAGUAACACGGGAAGGGGCUCUGCAAGGAGUUCCUUUCUUACAAUGGCCGUACGGACGACACAAAAGGAAAGAACUGCUUUCGAGUACAGCAAGUACAAUACGACCAUUAUCCAUUCAUAAACCAUAACAAUUAAAAACAACA .............(((((((((((((....)))))))))))))...(((((.((((...............(((((.....)))))..((((.....))))..)))).))))).................................. (-33.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 126 85 228 181 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 351 99 52 172 128 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 320 106 66 224 186 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 312 128 81 72 17 pint:PI0680|5end_hypothetical_protein_616958..617188_POSITIVE 308 140 93 158 108 pint:PI2033|5end_hypothetical_protein_1987068..1987298_POSITIVE 308 130 83 184 143 pint:PI0449|5end_hypothetical_protein_422952..423182_POSITIVE 307 98 51 169 128 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 301 103 61 133 100 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 297 130 81 42 1 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 297 128 83 117 70 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 296 126 82 90 49 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 295 98 51 52 6 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 294 128 84 154 100 pint:PI1010|5end_conserved_hypothetical_protein_930922..931152_POSITIVE 294 98 53 141 95 pint:PI0129|5end_hypothetical_protein_121709..121939_POSITIVE 293 129 86 136 97 pint:PI1241|5end_probable_phosphoesterase_1166365..1166595_POSITIVE 291 96 51 51 9 pint:PI1771|5end_alpha-glucosidase_1699996..1700226_POSITIVE 290 120 77 217 163 pint:PI1828|5end_peptidase,_M23/M37_family,_C-terminal_1768419..1768649_POSITIVE 289 103 66 170 117 pint:PI1503|5end_30S_ribosomal_protein_S15_1423428..1423658_POSITIVE 288 96 53 204 156 pint:PI0135|5end_internalin-related_protein_125849..126079_POSITIVE 287 138 96 157 121 pint:PI1509|5end_conserved_hypothetical_protein_1428103..1428333_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 128 82 128 51 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 320 120 71 73 14 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 315 126 81 115 75 pint:PI0537|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_492412..492562_POSITIVE 308 140 93 131 81 pint:PI2032|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_1987121..1987271_POSITIVE 297 130 81 46 5 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 297 128 83 106 59 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 289 103 66 146 93 pint:PI1502|3end_hypothetical_protein_1423484..1423634_POSITIVE 288 138 94 44 5 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 284 130 81 131 81 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 282 130 85 125 60 pint:PI0154|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_148311..148461_POSITIVE 282 129 89 146 113 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 276 128 82 142 98 pint:PI1955|3end_N_utilization_substance_protein_A_1913058..1913208_POSITIVE 276 97 51 136 91 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 273 89 46 69 17 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 272 135 94 78 41 pint:PI0890|3end_ribose_5-phosphate_isomerase_B_820931..821081_POSITIVE 271 96 51 109 53 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 271 124 83 51 14 pint:PI0399|3end_conserved_hypothetical_protein_364090..364240_POSITIVE 267 129 86 99 59 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 267 100 52 85 24 pint:PI0801|3end_hypothetical_protein_739687..739837_POSITIVE 266 78 36 45 3 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE