Origin IGS: gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat .........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 attccaagtgtatatggttataagggggagctattcatattttgtttcacaacatgtttttcccgactgattttctctgcgctaagcaccgtctcaaactcattcgatcctttgatcagaccgagagagattaagccaaaatgccaaacaataaaacctcaaaaaacatctgtcctatagaacaaacactgaagctcctgactatattatcttccgatctcttcttagacctcacgacttactttctaccctcaaaagaaagaggggaaagcgagtgaagagccggtcttttttctc Mask Tandem Repeat Region ================================================ gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Find is-nt database================================================ Query_seq: PG0179:PG0180|PG0179:PG0180:hypothetical protein:lipoprotein, putative:->->:202898..203194 297 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0179:PG0180|PG0179:PG0180:hypothetical protein:lipoprotein, putative:->->:202898..203194 297 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0179:PG0180|PG0179:PG0180:hypothetical protein:lipoprotein, putative:->->:202898..203194 297 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 63 End: 164 .............................................................. M R S K K R S E D N I V R S F S V C S I G Q M F F E V L L F G I L A ..................................................................................................................................... Protein_Len: 44 Strand: + Start: 146 End: 277 ................................................................................................................................................. M V W H F G L I S L G L I K G S N E F E T V L S A E K I S R E K H V V K Q N M N S S P L .................... Protein_Len: 33 Strand: - Start: 167 End: 265 ...................................................................................................................................................................... D R E T Q D F S R I L K L R H K A C L F D T P F F M N H F L I H M ................................ Protein_Len: 59 Strand: - Start: 121 End: 297 ........................................................................................................................ L V S T K Q P K I T Q C K P K I E R P R I L P D F S N S V T S L A S F I L R S F C T T F C F I F L E G K Y G Y V S P M Protein_Len: 45 Strand: - Start: 23 End: 157 ...................... E S E G R E K S P L F Y T T L D L F L D S S L I T L L K L T Q E I P C I N K S T K N N P M ............................................................................................................................................ Protein_Len: 42 Strand: - Start: 3 End: 128 .. F F S R S K V R K G R K R K L T S L L D H P R L L S R F I I Y D P A E T N T R Y S M ......................................................................................................................................................................... gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat 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================================================ gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0179:PG0180|PG0179:PG0180:hypothetical protein:lipoprotein, putative:->->:202898..203194 297 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Intra-Species Hit: Count: 1 Min: 1 Max: 297 Len: 297 Subject: NC_002950_PG0179_PG0180|hypothetical protein:lipoprotein, putative|POSITIVE:POSITIVE|[202898,203194]|297 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 297 Query Start:1 Query End:297 Subject Strand: POSITIVE Subject Start: 1 Subject End: 297 gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat gagaaaaaagaccggctcttcactcgctttcccctctttcttttgagggtagaaagtaagtcgtgaggtctaagaagagatcggaagataatatagtcaggagcttcagtgtttgttctataggacagatgttttttgaggttttattgtttggcattttggcttaatctctctcggtctgatcaaaggatcgaatgagtttgagacggtgcttagcgcagagaaaatcagtcgggaaaaacatgttgtgaaacaaaatatgaatagctcccccttataaccatatacacttggaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAAAAAGACCGGCUCUUCACUCGCUUUCCCCUCUUUCUUUUGAGGGUAGAAAGUAAGUCGUGAGGUCUAAGAAGAGAUCGGAAGAUAAUAUAGUCAGGAGCUUCAGUGUUUGUUCUAUAGGACAGAUGUUUUUUGAGGUUUUAUUGUUUGGCAUUUUGGCUUAAUCUCUCUCGGUCUGAUCAAAGGAUCGAAUGAGUUUGAGACGGUGCUUAGCGCAGAGAAAAUCAGUCGGGAAAAACAUGUUGUGAAACAAAAUAUGAAUAGCUCCCCCUUAUAACCAUAUACACUUGGAAU ...........((((((((((....(((((((((((........)))))..)))))).((((....)).))..)))))).)))).......(((((...(((((((((...((((((...((.((((....((((((((((((((..((((.((((((....(((((.(((..(((((((.......)))))))..))).)))))..)))))).)))).....))))))..))))))))....)))).)).))))))...)))..))))))...))))).(((........)))... (-87.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCAAGUGUAUAUGGUUAUAAGGGGGAGCUAUUCAUAUUUUGUUUCACAACAUGUUUUUCCCGACUGAUUUUCUCUGCGCUAAGCACCGUCUCAAACUCAUUCGAUCCUUUGAUCAGACCGAGAGAGAUUAAGCCAAAAUGCCAAACAAUAAAACCUCAAAAAACAUCUGUCCUAUAGAACAAACACUGAAGCUCCUGACUAUAUUAUCUUCCGAUCUCUUCUUAGACCUCACGACUUACUUUCUACCCUCAAAAGAAAGAGGGGAAAGCGAGUGAAGAGCCGGUCUUUUUUCUC .....(((...((((((((......(((((((..(((...(((((((.(((..((((((((................(((.....)))..(((((...(((..((((((....)))).))..))).)))))..............................)))))))).)))......)))))))...))))))))))))))))))...)))(((..((((((...(....)...(((..(((((..(((((........))))))))))..))))))))).)))........... (-62.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 50 12 227 192 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 355 236 191 134 91 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 339 70 24 105 54 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 339 70 24 105 54 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 337 47 1 188 140 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 337 210 161 61 10 NC_002950:PG0300|5end_TPR_domain_protein_336570..336800_POSITIVE 330 80 31 80 35 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 328 240 192 224 170 NC_002950:PG0130|5end_phosphoglyceromutase_152668..152898_NEGATIVE 326 189 142 159 101 NC_002950:PG1954|5end_NAD_dependent_epimerase/reductase-related_protein_2044513..2044743_POSITIVE 325 41 2 169 130 NC_002950:PG0336|5end_hypothetical_protein_371292..371522_NEGATIVE 324 220 173 188 149 NC_002950:PG0219|5end_hypothetical_protein_255558..255788_NEGATIVE 320 87 43 75 34 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 316 177 131 101 39 NC_002950:PG0759|5end_TPR_domain_protein_810785..811015_NEGATIVE 315 275 231 46 9 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 314 104 63 181 144 NC_002950:PG0016|5end_sigma-54_dependent_DNA-binding_response_regulator_16947..17177_POSITIVE 312 70 29 200 163 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 312 219 172 139 91 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 309 236 192 64 11 NC_002950:PG1731|5end_3-dehydroquinate_dehydratase_1820103..1820333_NEGATIVE 309 53 12 75 18 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 306 54 13 59 7 NC_002950:PG1115|5end_signal_recognition_particle_protein_1187470..1187700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 60 12 75 20 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 355 236 191 137 94 NC_002950:PG0214|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_251543..251693_POSITIVE 330 80 31 67 22 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 329 223 182 74 23 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 325 41 2 84 45 NC_002950:PG0337|3end_hypothetical_protein_371377..371527_NEGATIVE 324 220 173 133 94 NC_002950:PG0221|3end_hypothetical_protein_255613..255763_NEGATIVE 324 50 2 52 1 NC_002950:PG0090|3end_Dps_family_protein_106083..106233_POSITIVE 320 87 43 54 13 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 318 68 23 149 108 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 315 50 12 81 51 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 315 218 173 139 85 NC_002950:PG0158|3end_competence_protein_F-related_protein_180995..181145_POSITIVE 314 63 22 107 54 NC_002950:PG1196|3end_hypothetical_protein_1275359..1275509_POSITIVE 312 70 29 99 62 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 312 49 9 72 38 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 308 209 161 144 100 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 306 237 192 100 43 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 304 247 202 55 7 NC_002950:PG0631|3end_MotA/TolQ/ExbB_proton_channel_family_protein_684960..685110_POSITIVE 302 238 191 78 17 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 302 58 15 142 97 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE 301 70 21 130 80 NC_002950:PG0635|3end_ribosomal_protein_L11_methyltransferase_686838..686988_NEGATIVE