Origin IGS: taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatatttttaataatgttcgtggctaagatgccacaaatgcgtaagaaaagtgtcgaaagatacaaaaaggttaggactcacctacttggtaaatcctaaccatatttttataaaatgtgattttatgctattataaaagcatcaaccactttagaagagtctta Mask Tandem Repeat Region ================================================ taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Find is-nt database================================================ Query_seq: PI0444:PI0446|PI0444:PI0446:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:413451..413617 167 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0444:PI0446|PI0444:PI0446:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:413451..413617 167 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0444:PI0446|PI0444:PI0446:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:413451..413617 167 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 69 End: 164 .................................................................... S K G L L H T R V K K Y R E V S K K R M Q P M K A V F M I L F M ... taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt 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================================================ taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 65 HP_score: -3.1 Tail_Score: -4.8667 Start: 61 End: 99 Full_Region: tgtcgaaagatacaa aaaggttaggactcacc tactt ggtaaatcctaaccata tttttataaaatgtg ............................................................aaaggttaggactcacctacttggtaaatcctaaccata.................................................................... TransTerm Strand: - Conf: 67 HP_score: -5.7 Tail_Score: -4.05067 Start: 63 End: 97 Full_Region: tcgaaagatacaaaa aggttaggactcacc tactt ggtaaatcctaacca tatttttataaaatg ..............................................................aggttaggactcacctacttggtaaatcctaacca...................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -5.14985 Start: 64 End: 96 Full_Region: ATTTTATAAAAATAT GGTTAGGATTTACC AAGTA GGTGAGTCCTAACC TTTTTGTATCTTTCG ...............................................................GGTTAGGATTTACCAAGTAGGTGAGTCCTAACC....................................................................... TransTerm Strand: - Conf: 74 HP_score: -9.2 Tail_Score: -3.02317 Start: 64 End: 96 Full_Region: cgaaagatacaaaaa ggttaggactcacc tactt ggtaaatcctaacc atatttttataaaat ...............................................................ggttaggactcacctacttggtaaatcctaacc....................................................................... Find igs database================================================ Query_seq: PI0444:PI0446|PI0444:PI0446:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:413451..413617 167 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: pint_PI0444_PI0446|50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit|POSITIVE:POSITIVE|[413451,413617]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt taagactcttctaaagtggttgatgcttttataatagcataaaatcacattttataaaaatatggttaggatttaccaagtaggtgagtcctaacctttttgtatctttcgacacttttcttacgcatttgtggcatcttagccacgaacattattaaaaatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACUCUUCUAAAGUGGUUGAUGCUUUUAUAAUAGCAUAAAAUCACAUUUUAUAAAAAUAUGGUUAGGAUUUACCAAGUAGGUGAGUCCUAACCUUUUUGUAUCUUUCGACACUUUUCUUACGCAUUUGUGGCAUCUUAGCCACGAACAUUAUUAAAAAUAUUUU (((((..........((((((.(((((........)))))..))))))....((((((((...((((((((((((((.....))))))))))))))))))))))..............)))))....((((((((......)))))))).................. (-49.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUUUUUAAUAAUGUUCGUGGCUAAGAUGCCACAAAUGCGUAAGAAAAGUGUCGAAAGAUACAAAAAGGUUAGGACUCACCUACUUGGUAAAUCCUAACCAUAUUUUUAUAAAAUGUGAUUUUAUGCUAUUAUAAAAGCAUCAACCACUUUAGAAGAGUCUUA ......(((((((....(((.(((((......)))))....((((((((...(((((....))))).....((((((((.(.(((.....))).).))))))))...................))))))))...............)))....)))))))....... (-43.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 120 71 80 29 pint:PI0745|5end_conserved_hypothetical_protein_675174..675404_POSITIVE 291 146 103 166 125 pint:PI1343|5end_conserved_hypothetical_protein_1257782..1258012_POSITIVE 286 134 98 74 37 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 282 148 104 225 184 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 266 144 104 58 24 pint:PI1676|5end_phosphatidate_cytidylyltransferase_1590896..1591126_POSITIVE 263 144 105 225 193 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 259 127 83 230 193 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 252 154 117 217 179 pint:PI2083|5end_hypothetical_protein_2040324..2040554_POSITIVE 252 134 106 29 3 pint:PI1065|5end_hypothetical_protein_983382..983612_POSITIVE 250 156 114 55 6 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 249 116 75 104 58 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 247 137 94 78 32 pint:PI1691|5end_hypothetical_protein_1605504..1605734_POSITIVE 243 126 83 94 34 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 242 144 101 73 25 pint:PI1935|5end_possible__internalin-related_protein_1883324..1883554_POSITIVE 242 147 101 175 123 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 239 146 117 91 58 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 238 105 61 226 180 pint:PI0289|5end_hypothetical_protein_272424..272654_POSITIVE 238 105 61 74 28 pint:PI0288|5end_hypothetical_protein_(possible_ISPg3-related_transposase)_272272..272502_POSITIVE 237 41 7 203 177 pint:PI1155|5end_hypothetical_protein_1080084..1080314_POSITIVE 237 147 101 198 162 pint:PI0429|5end_hypothetical_protein_396418..396648_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 146 103 103 62 pint:PI1342|3end_conserved_hypothetical_protein_1257799..1257949_POSITIVE 290 120 79 146 102 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 287 104 70 38 1 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 254 108 65 100 55 pint:PI0512|3end_conserved_hypothetical_protein_471440..471590_POSITIVE 252 154 117 76 38 pint:PI2082|3end_hypothetical_protein_2040263..2040413_POSITIVE 252 120 75 135 78 pint:PI0949|3end_endonuclease_883279..883429_POSITIVE 247 137 94 121 75 pint:PI1690|3end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1605627..1605777_POSITIVE 245 144 103 129 89 pint:PI0708|3end_conserved_hypothetical_protein_646234..646384_POSITIVE 243 126 83 94 34 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 238 105 61 74 28 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 237 41 7 123 97 pint:PI1154|3end_conserved_hypothetical_protein;_possible_periplasmic_solute-binding_protein_1080084..1080234_POSITIVE 229 55 13 71 29 pint:PI0145|3end_secDF_export_membrane_protein_139724..139874_POSITIVE 228 144 102 93 50 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 222 102 70 112 85 pint:PI2062|3end_type_I_restriction-modification_system_2024008..2024158_POSITIVE 222 145 124 145 123 pint:PI1537|3end_predicted_TPR-repeat-containing_protein_1459392..1459542_POSITIVE 220 126 88 58 13 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 220 146 110 82 50 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 218 148 107 127 82 pint:PI1704|3end_50S_ribosomal_protein_L32_1621680..1621830_POSITIVE 215 145 118 150 119 pint:PI2064|3end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2026991..2027141_POSITIVE 215 145 106 102 66 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE